From a3b63bb1ff1af0091d8a53f899ffe9d562092340 Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Tue, 23 Jan 2024 08:18:59 +0000
Subject: [PATCH 01/89] add: new structure template (comment)

---
 docs/10_domains/20_physical_chemistry.mdx | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index e91b4222..cdf25c4e 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -14,6 +14,16 @@ import {LbeChip} from '@site/src/components/lbe/LbeElements.js';
 Physical chemistry is an interdisciplinary science at the frontier between chemistry and physics, whose topics go beyond the classical areas of the respective individual sciences. While preparative chemistry focuses on questions of the methodology of chemical synthesis of known and new substances, physical chemistry attempts to describe the properties of substances and their transformation by applying concepts of physics to objects of chemistry by means of theoretical and experimental methods. Along with organic and inorganic chemistry, physical chemistry therefore represents one of the three key disciplines of "classical" chemistry, since it provides the theoretical basis for technical chemistry and process engineering. Its knowledge is also an integral part of many other disciplines and is used, for example, for description and understanding in biology and medicine, meteorology as well as the earth sciences. Due to this great interdisciplinarity and the use of numerous physicochemical methods in almost all areas of chemistry, a complete description of physical chemistry as profile is hardly possible, which is why this article explicitly makes no claim to do so.
 :::
 
+<!--new structure: 
+
+Introduction (Daten-bezogen) (Introduction)
+Welche Art von Daten? (Data Types)
+Welche ELNs / Tools bieten sich an? (ELNs and Other Tools) 
+Wie / Wo können Daten publiziert werden? (Repos nennen) (Repositories)
+Herausforderungen (Challenges)
+
+ -->
+
 # Methods Profiles
 
 ## EPR spectroscopy

From 9000de466e53d1063e74fd33b2827650c6940918 Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Tue, 23 Jan 2024 10:06:20 +0000
Subject: [PATCH 02/89] add: outlined new article in meetng

---
 docs/10_domains/20_physical_chemistry.mdx | 36 ++++++++++++++++++++++-
 1 file changed, 35 insertions(+), 1 deletion(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index cdf25c4e..7bb59404 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -17,13 +17,47 @@ Physical chemistry is an interdisciplinary science at the frontier between chemi
 <!--new structure: 
 
 Introduction (Daten-bezogen) (Introduction)
+- diverse methodology can be used to analyze a broad range of subjects -> results in diverse types of data formats 
+- large datasets 
+- rather data-literate 
+
 Welche Art von Daten? (Data Types)
+- eigene Skripte (python, jupyter, matlab)
+
+
 Welche ELNs / Tools bieten sich an? (ELNs and Other Tools) 
+- elabftw
+- (openBIS)
+- Omero (Tool, UDE nutzt OME+eLabFTW)
+- NOMAD
+- iochem-bd
+- git (Versionierung Skripte)
+- Datalad ('git für Forschungsdaten/Metadaten') 
+
 Wie / Wo können Daten publiziert werden? (Repos nennen) (Repositories)
-Herausforderungen (Challenges)
+- RADAR4Chem -> alles
+- iochem-bd (comp. chemistry)
+- NOMAD (simulations)
+- Image Data Resource (https://idr.openmicroscopy.org/) 
+
 
+Herausforderungen (Challenges)
+- non-bio imaging data missing repo/long-term archive
+- large datasets can be difficult to manage and publish
+- diverse methodology can be used to analyze a broad range of subjects
+- no unified tool to manage everything (such as chemotion)
  -->
 
+<!-- images? -->
+
+
+<!-- Nikki's suggestions: 
+- Extend table to see what data types are supported by which tools (this could also assist infrstructure providers in gap analysis)
+- Can include methods and data types from SFB 985/RWTH
+-->
+
+
+
 # Methods Profiles
 
 ## EPR spectroscopy

From e222b81c25b927f76d29781424f2dd96b6f267b7 Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Tue, 23 Jan 2024 10:07:22 +0000
Subject: [PATCH 03/89] add: link to methods table in gdrive

---
 docs/10_domains/20_physical_chemistry.mdx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index 7bb59404..ebebd1b3 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -53,7 +53,7 @@ Herausforderungen (Challenges)
 
 <!-- Nikki's suggestions: 
 - Extend table to see what data types are supported by which tools (this could also assist infrstructure providers in gap analysis)
-- Can include methods and data types from SFB 985/RWTH
+- Can include methods and data types from SFB 985/RWTH (https://docs.google.com/spreadsheets/d/1gdi5gUH3cy4I2sy055IPqOKvfBDzRouW/edit?usp=drive_link&ouid=109474882186950125832&rtpof=true&sd=true)
 -->
 
 

From 80d1a33b64045f42be212321bfa1c4329ab697c9 Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Fri, 26 Jan 2024 10:48:07 +0000
Subject: [PATCH 04/89] add: first draft of introduction

---
 docs/10_domains/20_physical_chemistry.mdx | 22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index ebebd1b3..cadff2e2 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -56,8 +56,23 @@ Herausforderungen (Challenges)
 - Can include methods and data types from SFB 985/RWTH (https://docs.google.com/spreadsheets/d/1gdi5gUH3cy4I2sy055IPqOKvfBDzRouW/edit?usp=drive_link&ouid=109474882186950125832&rtpof=true&sd=true)
 -->
 
+# Introduction 
 
+Physical Chemistry encompasses a variety of sub-dicsiplines, covering vast methodology, which, in turn produce heterogenous data. 
+From spectroscopic measurement data, imaging, to simulation input files and in-house data analysis code, many physical chemists are experienced in handling digital data. 
+They are often well-versed in developing software solutions to support their work. While some work with large data volumes on a regular basis, other methodologies result in small, text-based files. This discipline includes many data-literate members, the expertise of which may be harnessed to implement tools and solutions to manage their research group's data in a unified and streamlined manner. 
 
+# Data Types 
+
+## Methods Data Format Overview
+
+<Methods defaultProfile={"physical"} />
+
+:::note *This table will be continuously updated with new recommendations on interoperable open file formats.
+:::
+
+
+<!-- old content
 # Methods Profiles
 
 ## EPR spectroscopy
@@ -142,10 +157,5 @@ Herausforderungen (Challenges)
 - trajectory files are typically too large to store in commonly used repository environments, even when using compressed file formats. To make this data FAIR, standards for handling large amounts of data must be developed or solutions from other fields applied
 - reproducibility of long time-scale molecular dynamics is unattainable (numerical noise will eventually affect the resulting trajectories, especially in a multicore environment). Depending on the numerical accuracy and the specific implementation, deviations can be observed as soon as in the picosecond range. However, thermodynamic averages or other probabilistic measurements should be achieved within a suitable margin of error. This margin would have to be estimated and provided by the authors of a publication
 
+--> 
 
-# Methods Data Format Overview
-
-<Methods defaultProfile={"physical"} />
-
-:::note *This table will be continuously updated with new recommendations on interoperable open file formats.
-:::

From 508043606e5ff5463676a207114c1c5ad43e71d5 Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Fri, 26 Jan 2024 12:03:12 +0000
Subject: [PATCH 05/89] add: (attempt) first draft on data types

---
 docs/10_domains/20_physical_chemistry.mdx | 36 +++++++++++++++--------
 1 file changed, 23 insertions(+), 13 deletions(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index cadff2e2..5d6ad94c 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -17,13 +17,16 @@ Physical chemistry is an interdisciplinary science at the frontier between chemi
 <!--new structure: 
 
 Introduction (Daten-bezogen) (Introduction)
-- diverse methodology can be used to analyze a broad range of subjects -> results in diverse types of data formats 
-- large datasets 
-- rather data-literate 
+- [x] diverse methodology can be used to analyze a broad range of subjects -> results in diverse types of data formats 
+- [x] large datasets (nikki: könnte ich noch besser beschreiben, aber ich denke das kann man in Challenges nochmal angehen)
+- [x] rather data-literate 
 
 Welche Art von Daten? (Data Types)
-- eigene Skripte (python, jupyter, matlab)
-
+- text-basierte Dateien (z.B. Oberflächenanalyse)
+- Datanbanken (zetasizer: sqlite)
+- imaging (inkl. image stacks)
+- Code (from small scripts to software; python, jupyter, matlab)
+- Simulations (input files, output)
 
 Welche ELNs / Tools bieten sich an? (ELNs and Other Tools) 
 - elabftw
@@ -56,20 +59,27 @@ Herausforderungen (Challenges)
 - Can include methods and data types from SFB 985/RWTH (https://docs.google.com/spreadsheets/d/1gdi5gUH3cy4I2sy055IPqOKvfBDzRouW/edit?usp=drive_link&ouid=109474882186950125832&rtpof=true&sd=true)
 -->
 
-# Introduction 
+## Introduction 
+
+Physical Chemistry encompasses a variety of sub-disciplines, covering vast methodology, which, in turn produce heterogenous data. 
+From spectroscopic measurement data, imaging, to simulation input files and in-house data analysis code, many physical chemists are experienced in handling digital data. They are often well-versed in developing software solutions to support their work. While some work with large data volumes on a regular basis, other methodologies result in small, text-based files. This discipline includes many data-literate members, the expertise of which may be harnessed to implement tools and solutions to manage their research group's data in a unified and streamlined manner. 
 
-Physical Chemistry encompasses a variety of sub-dicsiplines, covering vast methodology, which, in turn produce heterogenous data. 
-From spectroscopic measurement data, imaging, to simulation input files and in-house data analysis code, many physical chemists are experienced in handling digital data. 
-They are often well-versed in developing software solutions to support their work. While some work with large data volumes on a regular basis, other methodologies result in small, text-based files. This discipline includes many data-literate members, the expertise of which may be harnessed to implement tools and solutions to manage their research group's data in a unified and streamlined manner. 
+## Data Types 
 
-# Data Types 
+As mentioned, the data produced in physical chemistry and its diverse sub-disciples are varied. One research group may work intensively with imaging data such as superresolution microscopy, while the other may work on method development, and again others may analyze spectroscopic data or conduct numeric simulations—or even any combination of these. The table below provides and overview of typical methods employed along with their data types and recommended formats.
 
-## Methods Data Format Overview
+### Methods Data Format Overview
+
+<!--need to update-->
 
 <Methods defaultProfile={"physical"} />
 
-:::note *This table will be continuously updated with new recommendations on interoperable open file formats.
-:::
+:::note *This table will be continuously updated with new recommendations on interoperable open file formats.:::
+
+## ELNs and Other Tools
+
+
+
 
 
 <!-- old content

From 3795ad3ca80acb8c8f2f63084d68808d64bf2c8a Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Fri, 26 Jan 2024 14:12:40 +0000
Subject: [PATCH 06/89] add: first draft elns and other tools

---
 docs/10_domains/20_physical_chemistry.mdx | 22 ++++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index 5d6ad94c..5673a79e 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -67,10 +67,10 @@ From spectroscopic measurement data, imaging, to simulation input files and in-h
 ## Data Types 
 
 As mentioned, the data produced in physical chemistry and its diverse sub-disciples are varied. One research group may work intensively with imaging data such as superresolution microscopy, while the other may work on method development, and again others may analyze spectroscopic data or conduct numeric simulations—or even any combination of these. The table below provides and overview of typical methods employed along with their data types and recommended formats.
+<!-- should the above be more specific? --->
 
 ### Methods Data Format Overview
-
-<!--need to update-->
+<!--need to update table-->
 
 <Methods defaultProfile={"physical"} />
 
@@ -78,8 +78,26 @@ As mentioned, the data produced in physical chemistry and its diverse sub-discip
 
 ## ELNs and Other Tools
 
+For effective data management, software tools should be selected in a uniform manner within a project or research group with the aim to organize and streamline workflows. This involves establishing clear usage guidelines, including metadata templates drawn from minimum information standards for a given method, where available. These should be outlined in a [data management plan (DMP)](docs/dmp) for each project. Many universities supply tools and templates for DMPs (see the [respective article](doc/dmp) for more information).
+
+An [electronic lab notebooks (ELNs)](docs/eln) helps in the day-to-day planning and structured documentation of experiments, while some also assist in data workflow management. For disciplines with diverse research, ELNs must be flexible and customizable. Examples here are LabIMotion, eLabFTW, and openBIS. Certain universities may have a central option, while each research group may chose what best fits their needs and resources. The [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) lists many options and the article on [choosing an ELN](docs/chose_eln) provides further assistance.
+
+In addition to ELNs, tools such as [Omero](https://www.openmicroscopy.org/omero/) and [NOMAD Oasis] are local repositories that enable researcher to make manage their data and make them [publication](docs/data_publication) ready. [NOMAD](https://nomad-lab.eu/nomad-lab/index.html) also offers other tools to assist in workflow management.
 
+For those writing scripts and developing research software solutions, git is a highly recommended versioning tool. May universities also have their own instances of [GitLab](https://about.gitlab.com/) to assist in better managing software projects.
+
+Specifically for research data, [DataLad](https://www.datalad.org/), which is built on top of git, can greatly assist in tracking the metadata while processing and analyzing data. While it works for steps carried out with GUI applications, its true power comes in handy for those using script-based analysis and processing steps.
+<!--shoudl extend the table to show which tools (and repos) support which file types-->
+
+- elabftw
+- (openBIS)
+- Omero (Tool, UDE nutzt OME+eLabFTW)
+- NOMAD
+- iochem-bd
+- git (Versionierung Skripte)
+- Datalad ('git für Forschungsdaten/Metadaten') 
 
+## Repositories
 
 
 <!-- old content

From 245928b0a3cd2b7bbad917aff77b5d7a13be9347 Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Fri, 26 Jan 2024 15:15:20 +0000
Subject: [PATCH 07/89] add: first draft publishing data, challenges

---
 docs/10_domains/20_physical_chemistry.mdx | 29 ++++++++++++-----------
 1 file changed, 15 insertions(+), 14 deletions(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index 5673a79e..e3069443 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -41,15 +41,14 @@ Wie / Wo können Daten publiziert werden? (Repos nennen) (Repositories)
 - RADAR4Chem -> alles
 - iochem-bd (comp. chemistry)
 - NOMAD (simulations)
-- Image Data Resource (https://idr.openmicroscopy.org/) 
-
+- Image Data Resource (https://idr.openmicroscopy.org/)  
+<Nikki: wo ist der Unterschied zw. Simulations u. Comp. Chemistry? Bei uns steht auch dass NOMAD für simulations ist, aber es ist ja eigentlich alle Materials Science Daten, oder?>
 
 Herausforderungen (Challenges)
 - non-bio imaging data missing repo/long-term archive
 - large datasets can be difficult to manage and publish
 - diverse methodology can be used to analyze a broad range of subjects
 - no unified tool to manage everything (such as chemotion)
- -->
 
 <!-- images? -->
 
@@ -78,27 +77,29 @@ As mentioned, the data produced in physical chemistry and its diverse sub-discip
 
 ## ELNs and Other Tools
 
-For effective data management, software tools should be selected in a uniform manner within a project or research group with the aim to organize and streamline workflows. This involves establishing clear usage guidelines, including metadata templates drawn from minimum information standards for a given method, where available. These should be outlined in a [data management plan (DMP)](docs/dmp) for each project. Many universities supply tools and templates for DMPs (see the [respective article](doc/dmp) for more information).
+For effective data management, software tools should be selected in a uniform manner within a project or research group with the aim to [organize](docs/data_organisation) and streamline workflows. This involves establishing clear usage guidelines, including metadata templates drawn from minimum information standards for a given method, where available. These should be outlined in a [data management plan (DMP)](docs/dmp) for each project. Many universities supply tools and templates for DMPs (see the [respective article](doc/dmp) for more information).
 
 An [electronic lab notebooks (ELNs)](docs/eln) helps in the day-to-day planning and structured documentation of experiments, while some also assist in data workflow management. For disciplines with diverse research, ELNs must be flexible and customizable. Examples here are LabIMotion, eLabFTW, and openBIS. Certain universities may have a central option, while each research group may chose what best fits their needs and resources. The [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) lists many options and the article on [choosing an ELN](docs/chose_eln) provides further assistance.
 
-In addition to ELNs, tools such as [Omero](https://www.openmicroscopy.org/omero/) and [NOMAD Oasis] are local repositories that enable researcher to make manage their data and make them [publication](docs/data_publication) ready. [NOMAD](https://nomad-lab.eu/nomad-lab/index.html) also offers other tools to assist in workflow management.
+In addition to ELNs, tools such as [Omero](https://www.openmicroscopy.org/omero/) and [NOMAD Oasis] are local repositories that enable researcher to make manage their data and make them [publication](docs/data_publication) ready. [NOMAD](https://nomad-lab.eu/nomad-lab/index.html) also offers other tools to assist in workflow management in materials-science-related fields. 
 
 For those writing scripts and developing research software solutions, git is a highly recommended versioning tool. May universities also have their own instances of [GitLab](https://about.gitlab.com/) to assist in better managing software projects.
 
 Specifically for research data, [DataLad](https://www.datalad.org/), which is built on top of git, can greatly assist in tracking the metadata while processing and analyzing data. While it works for steps carried out with GUI applications, its true power comes in handy for those using script-based analysis and processing steps.
-<!--shoudl extend the table to show which tools (and repos) support which file types-->
+<!--should extend the table to show which tools (and repos) support which file types-->
 
-- elabftw
-- (openBIS)
-- Omero (Tool, UDE nutzt OME+eLabFTW)
-- NOMAD
-- iochem-bd
-- git (Versionierung Skripte)
-- Datalad ('git für Forschungsdaten/Metadaten') 
+## Publishing Data
+
+[Publishing research data](docs/data_publication), especially that underlying a published article, is an important aspect that allows others in the research community to replicate and build upon a researchers work. [Research data repositories](docs/repositories) serve as platforms for data publication and can greatly assist in [FAIR](docs/fair) data publication. Such repositories range from subject-specific to general and institutional. For many in physical chemistry and its varied data, general repositories such as [RADAR4Chem](https://radar.products.fiz-karlsruhe.de/de/radarabout/radar4chem) presents an option for publishing data for which now (sub-)discipline-specific repository has been established. [ioChem-BD](https://www.iochem-bd.org/) serves as a computational chemistry repository and includes a conversion service for many common data types to ensure interoperability. The [Image Data Resource (IDR)](https://idr.openmicroscopy.org/) makes biological imaging data available to the community, while self-hosted Omero repositoy can assist those working with other types of imaging data (a public non-biology version of the IDR is not yet available). <!--Nikki: as far as I know--> For more information on choices, head [here](docs/choose_repository).
+
+For work that includes developing in-house research software solutions: **software is data and an integral part of research and should be published as such**. While only GitHub currently offers an automatic workflow for publishing software releases to [zenodo](https://zenodo.org/), there are methods to assign the [software a DOI, therefore making it citable](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/gitlab/repo-doi/).
+
+
+## Challenges
 
-## Repositories
+Common challenges in physical chemistry and FAIR data often go hand-in-hand with the large variety of sub-disciplines, methodology, and thus diverse data types. Many working in physical chemistry labs may have established their own personal workflows. Working within a group streamline and unify common steps and to establish reusable templates for metadata, be it in ELNs or in the local file system, can provide structured information not just for fellow researchers, but also for those working on FAIR data infrastructure, such as ELNs and research data repositories.
 
+Especially in imaging, large data volume can strain the local [storage](docs/data_storage) resources. Central storage solution can provide assistance and should be used in combination with best research data management practices to ensure the data's re-usability and avoid unorganized and inefficient use of large storage systems.
 
 <!-- old content
 # Methods Profiles

From 0d4150f6dcd61ab89a4f8d8b194ca5d10b248ba9 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Wed, 3 Apr 2024 17:00:59 +0200
Subject: [PATCH 08/89] refactor: article structure

---
 docs/10_domains/10_analytical_chemistry.mdx | 83 ++-------------------
 1 file changed, 8 insertions(+), 75 deletions(-)

diff --git a/docs/10_domains/10_analytical_chemistry.mdx b/docs/10_domains/10_analytical_chemistry.mdx
index 533dfa22..1393aa86 100644
--- a/docs/10_domains/10_analytical_chemistry.mdx
+++ b/docs/10_domains/10_analytical_chemistry.mdx
@@ -4,84 +4,17 @@ nfdi4chem-id: dac
 slug: "/analytical_chemistry"
 ---
 
-import Methods from '@site/src/components/Methods.js';
-import {LbeChip} from '@site/src/components/lbe/LbeElements.js';
+import { LbeChip } from "@site/src/components/lbe/LbeElements.js";
 
-<LbeChip title="analytical chemistry" /><LbeChip title="chemometric" />
+<LbeChip title="analytical chemistry" />
+<LbeChip title="chemometric" />
 
+## Introduction
 
-:::info Summary:
+## Data Types
 
-Analytical chemistry is one of the oldest scientific disciplines and an interdisciplinary science, combining methods of physical, inorganic and organic chemistry. Analytical chemistry aims to acquire, process, and evaluate signals to qualify and quantify the composition and to unravel the structure of matter. The analytical chemist applies classical (wet) chemistry and instrumental methods for separation, identification (qualification) and quantification. The discipline is related to many research fields in life, environmental, earth, and engineering sciences, such as metabolomics, medicine, and geochemistry. <br/>
-A typical workflow begins with the conceptualisation of the research question, and the planning of experiments, methods, and surveys to evaluate the hypotheses. Surveys are utilised in life, environmental, and earth sciences to perform experiments and/or to obtain samples required to support the research (e.g., laboratory and field campaigns, cohort studies). Experiments are conducted and samples are processed applying existing or newly established methods along with recording of accompanying metadata. Analytical chemistry applies already in the experimental or sampling stage as conditions need to be controlled or metadata has to be acquired (e.g., pH, temperature, colour). Once the product of the experiment or sample processing is obtained, it is analysed with suitable direct or combined methods for identification and quantification. Processing and interpretation of the acquired research data and [metadata](/docs/metadata) support the answering of the research question and decisions for further experiments, research, and measures.
-:::
+## ELNs and Other Tools
 
-## Type of experiments for chemical analysis
+## Publishing Data
 
-### Sampling
-
-- Collecting of materials for analysis
-- Transport and storage without alteration of samples
-- Small-scale experiments to develop / optimise approaches and equipment
-- Upscaling of methods to obtain sufficient material for a comprehensive analysis
-
-### Sample processing
-
-- Preparation of the sample for analysis:
-    - Direct methods: no further treatment (e.g., pH, RFA, MALDI, direct infusion)
-    - Single methods:
-        - Dissolving
-        - Extraction
-        - Pulverising 
-    - Combined methods:
-        - Extraction and enrichment (e.g., solid-phase extraction, aqua regia digestion, volatilisation of solvents)
-        - Separation of interfering compounds (e.g., chromatography, precipitation)
-        - Chemical transforming in measurable form (e.g., complexing, derivatisation)
-- Small-scale experiments for screening / optimization of separation conditions and upscaling
-
-### Determination and evaluation
-- Product characterisation with feasible methods (e.g., NMR spectroscopy, mass spectrometry, IR spectroscopy, UV/vis spectroscopy, elemental analysis)
-    - to identify analytes (targeted and non-targeted)
-    - to assess the constitution of mixtures
-    - to quantify analytes
-
-## Planning of experiments
-
-- New and reused analytical methods and research ideas are derived from previous work of the own research group, scientific literature, datasets published in [repositories](/docs/repositories), and requirements of public calls for research, development and demonstration projects.
-- Experimental design follows a logical order to achieve a specific goal, such as analytical selectivity and sensitivity, or in the case of a non-targeted analysis (e.g., in metabolomics), a coverage of a broad physical-chemical domain of analytes.
-- Planning is concluded by adding the experimental details. All [metadata](/docs/metadata) is [documented](/docs/data_documentation) in an [ELN](/docs/eln) (e.g., [Chemotion ELN](https://www.chemotion.net/chemotionsaurus/index.html)) including references.
-
-## Documentation of experiments
-
-- Documentation of research data and metadata is carried out digitally using an ELN.
-- Experimental conditions (e.g., solvents, temperature, duration, pressure) are noted in the ELN and if available a laboratory information system.
-- Observations and results of analytical methods with no digital output (i.e. no data files) are added manually to the ELN entry of the experiment, which may include temperatures, or the pH (with metadata where applicable).
-- Obtained data from analytical instruments (e.g., NMR, MS, or IR data) are uploaded to the Chemotion ELN in open file formats and directly attached to the respective ELN experiment entry including instrumental setup metadata.
-- In case instrumental metadata is not convertible to open format without information loss, conditions need to be documented in the ELN.
-- Metadata related to the obtained data, such as mass, volumes, or solvent of measurement, have to be provided according to [metadata standards](/docs/format_standards).
-
-## Data producing methods
-
-- Data can be collected during the experiment or after the experiment by analysing the obtained product.
-- Manually determined data: Experimental observations, mass, volumes, pH, etc.
-- Digital data are obtained with analytical instruments. An overview of file extensions, file sizes, and converters for several analytical methods is given in the table below.
-- Raw data files in proprietary file formats should be saved alongside interoperable open file formats by using converters or the analytical device software. If no specific open format is currently available, export as .txt or .csv is recommended. Please be aware that metadata included in the header of .txt or .csv files may not follow a defined (open) format and metadata should be additionally also added into the ELN.
-
-<Methods defaultProfile={"synthetic"} />
-
-:::note *This table will be continuously updated with new recommendations on interoperable open file formats.
-:::
-
-## Data analysis
-
-- Research data can be processed, analysed and compared (also to data of other experiments) within the [Chemotion ELN](https://www.chemotion.net/chemotionsaurus/index.html).
-- Optionally, preprocessing of digital data with software of analytical device before data are transferred to the Chemotion ELN (cf. data producing methods).
-- A detailed view, evaluation and interpretation of results is carried out with the Chemotion ELN features.
-
-
-## Publishing research data
-
-- In addition to a research article in a scientific journal, the underlying research data are [published](/docs/data_publishing) in a [repository](/docs/repositories) and linked to the article to realise research data management according to the [FAIR data principles](/docs/fair) ([Best practice examples](/docs/best_practice)).
-- Data publications in repositories include raw and processed data for reuse.
-- The use of the [Chemotion ELN](https://www.chemotion.net/chemotionsaurus/index.html) enables a direct transfer of research data and the respective metadata to the [Chemotion Repository](https://www.chemotion-repository.net/welcome). Subsequently, these data are automatically shared with other repositories, e.g. [PubChem](https://pubchem.ncbi.nlm.nih.gov/). For the publication of research data in other discipline-specific repositories, such as the [MassBank](https://massbank.eu/MassBank/) for reference mass spectra, data have to be exported from the Chemotion ELN and submitted to the respective database.
-- A [persistent identifier](/docs/pid) (e.g., DOI) is generated for a dataset by a repository (e.g., [DataCite](https://datacite.org/) for the Chemotion Repository), which is given in the journal article or corresponding supporting information to link the data publication with the manuscript.
+## Challenges

From fbcf8344a3e8fb3b967813456f6c07151085a667 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Wed, 3 Apr 2024 17:50:24 +0200
Subject: [PATCH 09/89] feat: text draft

---
 docs/10_domains/10_analytical_chemistry.mdx | 31 +++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/docs/10_domains/10_analytical_chemistry.mdx b/docs/10_domains/10_analytical_chemistry.mdx
index 1393aa86..597ed816 100644
--- a/docs/10_domains/10_analytical_chemistry.mdx
+++ b/docs/10_domains/10_analytical_chemistry.mdx
@@ -11,10 +11,41 @@ import { LbeChip } from "@site/src/components/lbe/LbeElements.js";
 
 ## Introduction
 
+Although analytical chemistry is one of the oldest branches of chemistry, it continues to evolve. New methods and technologies are constantly being developed. Providing the tools and techniques needed to identify and quantify the chemical constituents of a sample, analytical chemistry is a cornerstone of both academia and industry. It is essential for a wide range of applications, from environmental monitoring to drug discovery.
+
+Despite the diversity of analytical methods, a common denominator is the large amount of data generated by instrumental methods. This data must be processed and interpreted to extract meaningful information. This makes analytical chemistry a challenging field for research data management.
+
 ## Data Types
 
+Unlike some other areas of chemistry, most research data in analytical chemistry are generated by instrumental methods. In addition, the size and complexity of the data can vary greatly depending on the method used.
+
+Techniques like mass spectrometry, chromatography, and spectroscopy generate complex data consisting of raw data files, metadata, and processed data. Raw data files are often proprietary and require specialised software to open and interpret. Metadata is crucial for understanding experimental conditions and parameters. Processed data can range from simple peak lists to complex multivariate models.
+
+Some open data formats are available for specific data types, such as mass spectrometry data in the [mzML format](https://www.psidev.info/mzML). The [JCAMP-DX format](https://iupac.org/what-we-do/digital-standards/jcamp-dx/) is used for optical spectroscopy data. This format is also suitable for NMR spectroscopy data, but with some major limitations. For chromatography or combined chromatography-mass spectrometry data the situation is more complex as many vendors have their own proprietary formats.
+
 ## ELNs and Other Tools
 
+General chemistry ELNs can typically be used for analytical chemistry data and may be well suited to your research topic. However, there are also specialised tools that are tailored to the needs of analytical chemists. These tools often include features for managing instrument data, processing raw data files and visualising results. They may also include tools for chemometric analysis.
+
 ## Publishing Data
 
+Data from analytical chemistry can be published on several platforms, depending on the research subject and data type.
+
+If the analytical data have a more supporting role in a larger study it may be appropriate to publish the data in a general data repository. If the research focuses more on the analytical method itself, it may be more appropriate to publish the data in a specialised repository.
+
+General data repositories include [Zenodo](https://zenodo.org/) or [RADAR4Chem](https://radar.products.fiz-karlsruhe.de/de/radarabout/radar4chem). For analytical data in context with synthetic chemistry data, [Chemotion Repository](https://chemotion-repository.de/) might also be a suitable option.
+
+For method-specific data, several specialised repositories are available. A few examples include:
+
+-   [MassBank EU](https://massbank.eu/)  
+    A field-specific ecosystem of databases and tools for mass spectrometry reference spectra.
+-   [MetaboLights](https://www.ebi.ac.uk/metabolights/)  
+    A repository for metabolomic studies.
+-   [nmrXiv](https://nmrxiv.org/)  
+    A repository for NMR data.
+
+This list is not exhaustive, and there may be other repositories that are more suitable for your data.
+
 ## Challenges
+
+The biggest challenge in managing analytical chemistry data is the diversity of the field. Different methods generate different types of data, and the data can vary greatly in size and complexity. As mentioned above, the large number of different vendors and proprietary data formats is a major barrier to data sharing and reuse.

From a6d8a50c53a694b7a5dea9cc1208dad938ca7c94 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Fri, 19 Apr 2024 19:03:09 +0200
Subject: [PATCH 10/89] chore: update packages

---
 package.json | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/package.json b/package.json
index 610f8c83..22108dbd 100644
--- a/package.json
+++ b/package.json
@@ -15,11 +15,11 @@
         "crowdin": "crowdin"
     },
     "dependencies": {
-        "@crowdin/cli": "^3.18.0",
-        "@docusaurus/core": "^3.1.1",
-        "@docusaurus/preset-classic": "^3.1.1",
+        "@crowdin/cli": "^3.19.2",
+        "@docusaurus/core": "^3.2.1",
+        "@docusaurus/preset-classic": "^3.2.1",
         "@easyops-cn/docusaurus-search-local": "^0.40.1",
-        "@fontsource/ibm-plex-sans": "^5.0.18",
+        "@fontsource/ibm-plex-sans": "^5.0.19",
         "@mdx-js/react": "^3.0.1",
         "clsx": "^2.1.0",
         "docusaurus-plugin-matomo": "^0.0.8",
@@ -30,8 +30,8 @@
         "react-tagcloud": "^2.3.3"
     },
     "devDependencies": {
-        "@docusaurus/module-type-aliases": "^3.1.1",
-        "@docusaurus/types": "3.1.1"
+        "@docusaurus/module-type-aliases": "^3.2.1",
+        "@docusaurus/types": "3.2.1"
     },
     "browserslist": {
         "production": [

From 5ec762026b198f7280daf40ed0837456a0546668 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Fri, 19 Apr 2024 19:03:38 +0200
Subject: [PATCH 11/89] feat: getEln script for ELN Finder

---
 .gitignore         | 2 ++
 scripts/getElns.sh | 9 +++++++++
 2 files changed, 11 insertions(+)
 create mode 100644 scripts/getElns.sh

diff --git a/.gitignore b/.gitignore
index c711a218..e2a08f1f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,8 @@
 fonts
 # Localisation files
 /i18n
+# API data
+elnData.json
 # Generated files
 .docusaurus
 .cache-loader
diff --git a/scripts/getElns.sh b/scripts/getElns.sh
new file mode 100644
index 00000000..16cffe18
--- /dev/null
+++ b/scripts/getElns.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+# get the data from the eln-finder
+
+curl -o eln-finder.json "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?sort=dc.title,ASC&f.K03=Chemistry,equals"
+
+# add current date and time to the json
+
+jq ". + {date: \"$(date -u)\" }" eln-finder.json > eln-finder-dated.json

From b9878f2695b831372626d5b7c9da21b5447e9bdf Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Fri, 19 Apr 2024 19:03:53 +0200
Subject: [PATCH 12/89] feat: show ELNs from ELN Finder

---
 docs/10_domains/10_analytical_chemistry.mdx |   3 +
 package.json                                |   1 +
 src/components/eln/ElnFinder.js             | 100 ++++++++++++++++++++
 src/components/eln/ShortenDesc.js           |  43 +++++++++
 4 files changed, 147 insertions(+)
 create mode 100644 src/components/eln/ElnFinder.js
 create mode 100644 src/components/eln/ShortenDesc.js

diff --git a/docs/10_domains/10_analytical_chemistry.mdx b/docs/10_domains/10_analytical_chemistry.mdx
index 597ed816..ec969a2b 100644
--- a/docs/10_domains/10_analytical_chemistry.mdx
+++ b/docs/10_domains/10_analytical_chemistry.mdx
@@ -5,6 +5,7 @@ slug: "/analytical_chemistry"
 ---
 
 import { LbeChip } from "@site/src/components/lbe/LbeElements.js";
+import ElnFinder from "@site/src/components/eln/ElnFinder.js";
 
 <LbeChip title="analytical chemistry" />
 <LbeChip title="chemometric" />
@@ -27,6 +28,8 @@ Some open data formats are available for specific data types, such as mass spect
 
 General chemistry ELNs can typically be used for analytical chemistry data and may be well suited to your research topic. However, there are also specialised tools that are tailored to the needs of analytical chemists. These tools often include features for managing instrument data, processing raw data files and visualising results. They may also include tools for chemometric analysis.
 
+<ElnFinder />
+
 ## Publishing Data
 
 Data from analytical chemistry can be published on several platforms, depending on the research subject and data type.
diff --git a/package.json b/package.json
index 22108dbd..1bc76e49 100644
--- a/package.json
+++ b/package.json
@@ -24,6 +24,7 @@
         "clsx": "^2.1.0",
         "docusaurus-plugin-matomo": "^0.0.8",
         "i": "^0.3.7",
+        "moment": "^2.30.1",
         "prism-react-renderer": "^2.3.1",
         "react": "^18.2.0",
         "react-dom": "^18.2.0",
diff --git a/src/components/eln/ElnFinder.js b/src/components/eln/ElnFinder.js
new file mode 100644
index 00000000..bdac32a0
--- /dev/null
+++ b/src/components/eln/ElnFinder.js
@@ -0,0 +1,100 @@
+import React, { useState, useEffect } from "react";
+import Link from "@docusaurus/Link";
+import moment from "moment";
+
+import ShortenDesc from "./ShortenDesc";
+
+// const elnData = require("@site/static/assets/eln_test.json");
+
+function ElnFinder() {
+    const [elnData, setElnData] = useState(null);
+    const [error, setError] = useState(null);
+
+    useEffect(() => {
+        fetch("../../assets/elnData.json")
+            .then((response) => response.json())
+            .then((data) => {
+                setElnData(data);
+                console.log(data);
+            })
+            .catch((error) => {
+                setError(error);
+                console.error(error);
+            });
+    }, []);
+
+    if (!elnData) {
+        return <em>Loading...</em>;
+    }
+
+    let elnTable = [];
+
+    const dateDownloaded = moment(elnData.date);
+    const relativeDate = moment(dateDownloaded).fromNow();
+
+    console.log(relativeDate);
+
+    try {
+        const chemElns = elnData["_embedded"].searchResult["_embedded"].objects;
+
+        chemElns.map((eln) => {
+            elnTable.push({
+                name: eln["_embedded"].indexableObject.name,
+                url: eln["_embedded"].indexableObject.metadata[
+                    "dc.identifier.uri"
+                ][0].value,
+                license:
+                    eln["_embedded"].indexableObject.metadata[
+                        "K.lizenzmodell"
+                    ][0].value,
+                desc: eln["_embedded"].indexableObject.metadata[
+                    "dc.description.abstract"
+                ][0].value,
+            });
+        });
+    } catch (error) {
+        return <em>Failed to process ELN data</em>;
+    }
+
+    return (
+        <React.Fragment>
+            <p>
+                <em>
+                    Data kindly provided by{" "}
+                    <Link to="https://eln-finder.ulb.tu-darmstadt.de/">
+                        ELN Finder
+                    </Link>{" "}
+                    (
+                    {relativeDate !== "Invalid date"
+                        ? "last updated " + relativeDate
+                        : "last update unknown"}
+                    ).
+                </em>
+            </p>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Name</th>
+                        <th>License</th>
+                        <th>Description</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    {elnTable.map((eln) => (
+                        <tr>
+                            <td>
+                                <Link to={eln.url}>{eln.name}</Link>
+                            </td>
+                            <td>{eln.license}</td>
+                            <td>
+                                <ShortenDesc desc={eln.desc} length={200} />
+                            </td>
+                        </tr>
+                    ))}
+                </tbody>
+            </table>
+        </React.Fragment>
+    );
+}
+
+export default ElnFinder;
diff --git a/src/components/eln/ShortenDesc.js b/src/components/eln/ShortenDesc.js
new file mode 100644
index 00000000..1d0ac69f
--- /dev/null
+++ b/src/components/eln/ShortenDesc.js
@@ -0,0 +1,43 @@
+import React, { useState } from "react";
+
+// shorten the description of the experiment up to the next blank, comma or period after 100 characters
+
+function ShortenDesc({ desc, length }) {
+    const [collapsed, setCollapsed] = useState(true);
+
+    if (desc.length <= length) {
+        return <React.Fragment>{desc}</React.Fragment>;
+    }
+
+    return (
+        <React.Fragment>
+            {collapsed ? (
+                <span
+                    title={desc}
+                    onClick={() => setCollapsed(!collapsed)}
+                    style={{ cursor: "pointer" }}
+                >
+                    {desc.slice(0, length) +
+                        desc.slice(length).split(/[\s,\.]/)[0] +
+                        " ..."}
+
+                    <button className="lbe__block__author-trigger">
+                        expand &#9660;
+                    </button>
+                </span>
+            ) : (
+                <span
+                    onClick={() => setCollapsed(!collapsed)}
+                    style={{ cursor: "pointer" }}
+                >
+                    {desc}
+                    <button className="lbe__block__author-trigger">
+                        collapse &#9650;
+                    </button>
+                </span>
+            )}
+        </React.Fragment>
+    );
+}
+
+export default ShortenDesc;

From 70240b329798479a401cf95ab1096548aa018f07 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 22 Apr 2024 13:03:12 +0200
Subject: [PATCH 13/89] chore: target dir for eln script

---
 scripts/getElns.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/scripts/getElns.sh b/scripts/getElns.sh
index 16cffe18..41f576b0 100644
--- a/scripts/getElns.sh
+++ b/scripts/getElns.sh
@@ -1,9 +1,11 @@
 #!/bin/bash
 
+targetDir="/git/n4c-kb_jl/build/assets"
+
 # get the data from the eln-finder
 
 curl -o eln-finder.json "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?sort=dc.title,ASC&f.K03=Chemistry,equals"
 
 # add current date and time to the json
 
-jq ". + {date: \"$(date -u)\" }" eln-finder.json > eln-finder-dated.json
+jq ". + {date: \"$(date -u)\" }" eln-finder.json > $targetDir/eln-finder-dated.json

From bab437cd351a27f8327b9f667e2373e0b48eb73e Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 22 Apr 2024 13:04:11 +0200
Subject: [PATCH 14/89] fix: chmod +x

---
 scripts/getElns.sh     | 0
 scripts/slugginator.sh | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 scripts/getElns.sh
 mode change 100644 => 100755 scripts/slugginator.sh

diff --git a/scripts/getElns.sh b/scripts/getElns.sh
old mode 100644
new mode 100755
diff --git a/scripts/slugginator.sh b/scripts/slugginator.sh
old mode 100644
new mode 100755

From f38dae72317b2a9927c7a78240176de71ff4e243 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 22 Apr 2024 13:06:19 +0200
Subject: [PATCH 15/89] fix: filename

---
 scripts/getElns.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/getElns.sh b/scripts/getElns.sh
index 41f576b0..49ad3a3d 100755
--- a/scripts/getElns.sh
+++ b/scripts/getElns.sh
@@ -8,4 +8,4 @@ curl -o eln-finder.json "https://eln-finder.ulb.tu-darmstadt.de/server/api/disco
 
 # add current date and time to the json
 
-jq ". + {date: \"$(date -u)\" }" eln-finder.json > $targetDir/eln-finder-dated.json
+jq ". + {date: \"$(date -u)\" }" eln-finder.json > $targetDir/elnData.json

From 8d8075eef3c4c1525576cc0f3e16a7249591d5aa Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 22 Apr 2024 13:07:25 +0200
Subject: [PATCH 16/89] fix: better target dir

---
 scripts/getElns.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/getElns.sh b/scripts/getElns.sh
index 49ad3a3d..d7778b40 100755
--- a/scripts/getElns.sh
+++ b/scripts/getElns.sh
@@ -1,6 +1,7 @@
 #!/bin/bash
 
-targetDir="/git/n4c-kb_jl/build/assets"
+targetDir="/var/www/html/staging/knowledge_base/assets"
+# targetDir="/var/www/html/knowledge_base/assets"
 
 # get the data from the eln-finder
 

From 19d9bd8884eba16fb96cff5a85d26b2d85091127 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 22 Apr 2024 14:26:04 +0200
Subject: [PATCH 17/89] chore: make Open source bold

---
 src/components/eln/ElnFinder.js | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/components/eln/ElnFinder.js b/src/components/eln/ElnFinder.js
index bdac32a0..5120f210 100644
--- a/src/components/eln/ElnFinder.js
+++ b/src/components/eln/ElnFinder.js
@@ -85,7 +85,13 @@ function ElnFinder() {
                             <td>
                                 <Link to={eln.url}>{eln.name}</Link>
                             </td>
-                            <td>{eln.license}</td>
+                            <td>
+                                {eln.license === "Open Source" ? (
+                                    <strong>{eln.license}</strong>
+                                ) : (
+                                    eln.license
+                                )}
+                            </td>
                             <td>
                                 <ShortenDesc desc={eln.desc} length={200} />
                             </td>

From b30cd07eeb1345eb7fae8301d9f9afc4953a2016 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 22 Apr 2024 15:51:45 +0200
Subject: [PATCH 18/89] chore: remove unnec. console output

---
 src/components/eln/ElnFinder.js | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/components/eln/ElnFinder.js b/src/components/eln/ElnFinder.js
index 5120f210..6f826abf 100644
--- a/src/components/eln/ElnFinder.js
+++ b/src/components/eln/ElnFinder.js
@@ -32,8 +32,6 @@ function ElnFinder() {
     const dateDownloaded = moment(elnData.date);
     const relativeDate = moment(dateDownloaded).fromNow();
 
-    console.log(relativeDate);
-
     try {
         const chemElns = elnData["_embedded"].searchResult["_embedded"].objects;
 

From b9adfcdf68bf5201f13dffaf9c091634ce9a5ee6 Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Mon, 6 May 2024 11:18:32 +0000
Subject: [PATCH 19/89] updated titles to fit other articles

---
 docs/10_domains/20_physical_chemistry.mdx | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index e3069443..6527eed3 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -60,22 +60,25 @@ Herausforderungen (Challenges)
 
 ## Introduction 
 
-Physical Chemistry encompasses a variety of sub-disciplines, covering vast methodology, which, in turn produce heterogenous data. 
+Physical Chemistry encompasses a variety of sub-disciplines, covering vast methodology, which, in turn, produce heterogenous data. 
 From spectroscopic measurement data, imaging, to simulation input files and in-house data analysis code, many physical chemists are experienced in handling digital data. They are often well-versed in developing software solutions to support their work. While some work with large data volumes on a regular basis, other methodologies result in small, text-based files. This discipline includes many data-literate members, the expertise of which may be harnessed to implement tools and solutions to manage their research group's data in a unified and streamlined manner. 
 
-## Data Types 
+## What Type of Data?
+
+As mentioned, the data produced in physical chemistry and its diverse sub-disciples are varied. One research group may work intensively with imaging data such as superresolution microscopy, while the other may work on method development, and again others may analyze spectroscopic data or conduct numeric simulations—or even any combination of these. The table below provides an overview of typical methods employed along with their data types and recommended formats.
+
+
 
-As mentioned, the data produced in physical chemistry and its diverse sub-disciples are varied. One research group may work intensively with imaging data such as superresolution microscopy, while the other may work on method development, and again others may analyze spectroscopic data or conduct numeric simulations—or even any combination of these. The table below provides and overview of typical methods employed along with their data types and recommended formats.
 <!-- should the above be more specific? --->
 
 ### Methods Data Format Overview
-<!--need to update table-->
+<!--are we still doing this table at all?-->
 
 <Methods defaultProfile={"physical"} />
 
 :::note *This table will be continuously updated with new recommendations on interoperable open file formats.:::
 
-## ELNs and Other Tools
+## What ELNs/Tools?
 
 For effective data management, software tools should be selected in a uniform manner within a project or research group with the aim to [organize](docs/data_organisation) and streamline workflows. This involves establishing clear usage guidelines, including metadata templates drawn from minimum information standards for a given method, where available. These should be outlined in a [data management plan (DMP)](docs/dmp) for each project. Many universities supply tools and templates for DMPs (see the [respective article](doc/dmp) for more information).
 
@@ -88,7 +91,7 @@ For those writing scripts and developing research software solutions, git is a h
 Specifically for research data, [DataLad](https://www.datalad.org/), which is built on top of git, can greatly assist in tracking the metadata while processing and analyzing data. While it works for steps carried out with GUI applications, its true power comes in handy for those using script-based analysis and processing steps.
 <!--should extend the table to show which tools (and repos) support which file types-->
 
-## Publishing Data
+## How and where can data be published?
 
 [Publishing research data](docs/data_publication), especially that underlying a published article, is an important aspect that allows others in the research community to replicate and build upon a researchers work. [Research data repositories](docs/repositories) serve as platforms for data publication and can greatly assist in [FAIR](docs/fair) data publication. Such repositories range from subject-specific to general and institutional. For many in physical chemistry and its varied data, general repositories such as [RADAR4Chem](https://radar.products.fiz-karlsruhe.de/de/radarabout/radar4chem) presents an option for publishing data for which now (sub-)discipline-specific repository has been established. [ioChem-BD](https://www.iochem-bd.org/) serves as a computational chemistry repository and includes a conversion service for many common data types to ensure interoperability. The [Image Data Resource (IDR)](https://idr.openmicroscopy.org/) makes biological imaging data available to the community, while self-hosted Omero repositoy can assist those working with other types of imaging data (a public non-biology version of the IDR is not yet available). <!--Nikki: as far as I know--> For more information on choices, head [here](docs/choose_repository).
 

From 94f9c00196926b152468d63fb6843e19ef07b6cf Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Mon, 6 May 2024 11:39:59 +0000
Subject: [PATCH 20/89] updated data types and tools sections

---
 docs/10_domains/20_physical_chemistry.mdx | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index 6527eed3..292dfab2 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -65,8 +65,7 @@ From spectroscopic measurement data, imaging, to simulation input files and in-h
 
 ## What Type of Data?
 
-As mentioned, the data produced in physical chemistry and its diverse sub-disciples are varied. One research group may work intensively with imaging data such as superresolution microscopy, while the other may work on method development, and again others may analyze spectroscopic data or conduct numeric simulations—or even any combination of these. The table below provides an overview of typical methods employed along with their data types and recommended formats.
-
+As mentioned, the data produced in physical chemistry and its diverse sub-disciples are varied. One research group may work intensively with imaging data such as superresolution microscopy, while the other may work on method development, and again others may analyze spectroscopic data or conduct numeric simulations—or even any combination of these. The [table](#methods-data-format-overview) below provides an overview of typical methods employed along with their data types and recommended open formats.
 
 
 <!-- should the above be more specific? --->
@@ -82,14 +81,15 @@ As mentioned, the data produced in physical chemistry and its diverse sub-discip
 
 For effective data management, software tools should be selected in a uniform manner within a project or research group with the aim to [organize](docs/data_organisation) and streamline workflows. This involves establishing clear usage guidelines, including metadata templates drawn from minimum information standards for a given method, where available. These should be outlined in a [data management plan (DMP)](docs/dmp) for each project. Many universities supply tools and templates for DMPs (see the [respective article](doc/dmp) for more information).
 
-An [electronic lab notebooks (ELNs)](docs/eln) helps in the day-to-day planning and structured documentation of experiments, while some also assist in data workflow management. For disciplines with diverse research, ELNs must be flexible and customizable. Examples here are LabIMotion, eLabFTW, and openBIS. Certain universities may have a central option, while each research group may chose what best fits their needs and resources. The [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) lists many options and the article on [choosing an ELN](docs/chose_eln) provides further assistance.
+An [electronic lab notebooks (ELNs)](docs/eln) helps in the day-to-day planning and structured documentation of experiments, while some also assist in data workflow management. For disciplines with diverse research, ELNs must be flexible and customizable. Certain universities may have a central option, while each research group may chose what best fits their needs and resources if they are able to host or procure their own solution. The [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) lists many options and the article on [choosing an ELN](docs/chose_eln) provides further assistance.
 
-In addition to ELNs, tools such as [Omero](https://www.openmicroscopy.org/omero/) and [NOMAD Oasis] are local repositories that enable researcher to make manage their data and make them [publication](docs/data_publication) ready. [NOMAD](https://nomad-lab.eu/nomad-lab/index.html) also offers other tools to assist in workflow management in materials-science-related fields. 
+In addition to ELNs, tools such as local repository and research dat management tools can assist in making data publication ready.
 
-For those writing scripts and developing research software solutions, git is a highly recommended versioning tool. May universities also have their own instances of [GitLab](https://about.gitlab.com/) to assist in better managing software projects.
+For those writing scripts and developing research software solutions, git is a highly recommended versioning tool. May universities also have their own instances of [GitLab](https://about.gitlab.com/) to assist in managing software projects. 
 
 Specifically for research data, [DataLad](https://www.datalad.org/), which is built on top of git, can greatly assist in tracking the metadata while processing and analyzing data. While it works for steps carried out with GUI applications, its true power comes in handy for those using script-based analysis and processing steps.
-<!--should extend the table to show which tools (and repos) support which file types-->
+
+As many physical chemists may establish their own workflows or develop their own tools to acquire and work with their data, it is highly recommended to adhere to community-specific standards for file formats and metadata, where available. A bare mininum is to establish documentation and format standards within a research group, ensuring an efficient knowledge transfer from one generation of researchers to the next. An ELN can greatly assist in providing templates for documentation, while a DMP should be used to record the format standards. Employing automated workflows, e.g., from device to ELN and data storage systems, can greatly reduce manual steps in day-to-day work and can automatically ensure data and documentation is complete and formatted correctly. Some tools provide out-of-the-box solutions, such as device integration, while others provide options such as REST APIs to build custom methods.
 
 ## How and where can data be published?
 

From 75eabceb8178bb17f595a3400b8702123bccc2fc Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Mon, 6 May 2024 11:44:45 +0000
Subject: [PATCH 21/89] small updates to tools

---
 docs/10_domains/20_physical_chemistry.mdx | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index 292dfab2..affc9631 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -89,15 +89,14 @@ For those writing scripts and developing research software solutions, git is a h
 
 Specifically for research data, [DataLad](https://www.datalad.org/), which is built on top of git, can greatly assist in tracking the metadata while processing and analyzing data. While it works for steps carried out with GUI applications, its true power comes in handy for those using script-based analysis and processing steps.
 
-As many physical chemists may establish their own workflows or develop their own tools to acquire and work with their data, it is highly recommended to adhere to community-specific standards for file formats and metadata, where available. A bare mininum is to establish documentation and format standards within a research group, ensuring an efficient knowledge transfer from one generation of researchers to the next. An ELN can greatly assist in providing templates for documentation, while a DMP should be used to record the format standards. Employing automated workflows, e.g., from device to ELN and data storage systems, can greatly reduce manual steps in day-to-day work and can automatically ensure data and documentation is complete and formatted correctly. Some tools provide out-of-the-box solutions, such as device integration, while others provide options such as REST APIs to build custom methods.
+As many physical chemists may establish their own workflows or develop their own tools to acquire, process, and analyze their data, it is highly recommended to adhere to community-specific standards for file formats and metadata, where available. A bare mininum is to establish documentation and format standards within a research group, ensuring an efficient knowledge transfer from one generation of researchers to the next. An ELN can greatly assist in providing templates for documentation, while a DMP should be used to record the format standards. Employing automated workflows, e.g., from device to ELN and data storage systems, can greatly reduce manual steps in day-to-day work and can automatically ensure data and documentation are complete and formatted correctly. Some tools provide out-of-the-box solutions, such as device integration, while others provide options such as REST APIs to build custom methods.
 
 ## How and where can data be published?
 
-[Publishing research data](docs/data_publication), especially that underlying a published article, is an important aspect that allows others in the research community to replicate and build upon a researchers work. [Research data repositories](docs/repositories) serve as platforms for data publication and can greatly assist in [FAIR](docs/fair) data publication. Such repositories range from subject-specific to general and institutional. For many in physical chemistry and its varied data, general repositories such as [RADAR4Chem](https://radar.products.fiz-karlsruhe.de/de/radarabout/radar4chem) presents an option for publishing data for which now (sub-)discipline-specific repository has been established. [ioChem-BD](https://www.iochem-bd.org/) serves as a computational chemistry repository and includes a conversion service for many common data types to ensure interoperability. The [Image Data Resource (IDR)](https://idr.openmicroscopy.org/) makes biological imaging data available to the community, while self-hosted Omero repositoy can assist those working with other types of imaging data (a public non-biology version of the IDR is not yet available). <!--Nikki: as far as I know--> For more information on choices, head [here](docs/choose_repository).
+[Publishing research data](docs/data_publication), especially that underlying a published article, is an important aspect that allows others in the research community to replicate and build upon a researchers work. [Research data repositories](docs/repositories) serve as platforms for data publication and can greatly assist in [FAIR](docs/fair) data publication. Such repositories range from subject-specific to general and institutional. For many in physical chemistry and its varied data, general repositories such as [RADAR4Chem](https://radar.products.fiz-karlsruhe.de/de/radarabout/radar4chem) presents an option for publishing data for which now (sub-)discipline-specific repository has been established. [ioChem-BD](https://www.iochem-bd.org/) serves as a computational chemistry repository and includes a conversion service for many common data types to ensure interoperability. The [Image Data Resource (IDR)](https://idr.openmicroscopy.org/) makes biological imaging data available to the community, while self-hosted Omero repositoy can assist those working with other types of imaging data. <!--Nikki: as far as I know--> For more information on choices, head [here](docs/choose_repository).
 
 For work that includes developing in-house research software solutions: **software is data and an integral part of research and should be published as such**. While only GitHub currently offers an automatic workflow for publishing software releases to [zenodo](https://zenodo.org/), there are methods to assign the [software a DOI, therefore making it citable](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/gitlab/repo-doi/).
 
-
 ## Challenges
 
 Common challenges in physical chemistry and FAIR data often go hand-in-hand with the large variety of sub-disciplines, methodology, and thus diverse data types. Many working in physical chemistry labs may have established their own personal workflows. Working within a group streamline and unify common steps and to establish reusable templates for metadata, be it in ELNs or in the local file system, can provide structured information not just for fellow researchers, but also for those working on FAIR data infrastructure, such as ELNs and research data repositories.

From e32c5cfabc2aa2408ab3002a5de36898311ea270 Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Mon, 6 May 2024 11:45:07 +0000
Subject: [PATCH 22/89] removed notes and old content comments

---
 docs/10_domains/20_physical_chemistry.mdx | 130 ----------------------
 1 file changed, 130 deletions(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index affc9631..79a602b9 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -14,49 +14,6 @@ import {LbeChip} from '@site/src/components/lbe/LbeElements.js';
 Physical chemistry is an interdisciplinary science at the frontier between chemistry and physics, whose topics go beyond the classical areas of the respective individual sciences. While preparative chemistry focuses on questions of the methodology of chemical synthesis of known and new substances, physical chemistry attempts to describe the properties of substances and their transformation by applying concepts of physics to objects of chemistry by means of theoretical and experimental methods. Along with organic and inorganic chemistry, physical chemistry therefore represents one of the three key disciplines of "classical" chemistry, since it provides the theoretical basis for technical chemistry and process engineering. Its knowledge is also an integral part of many other disciplines and is used, for example, for description and understanding in biology and medicine, meteorology as well as the earth sciences. Due to this great interdisciplinarity and the use of numerous physicochemical methods in almost all areas of chemistry, a complete description of physical chemistry as profile is hardly possible, which is why this article explicitly makes no claim to do so.
 :::
 
-<!--new structure: 
-
-Introduction (Daten-bezogen) (Introduction)
-- [x] diverse methodology can be used to analyze a broad range of subjects -> results in diverse types of data formats 
-- [x] large datasets (nikki: könnte ich noch besser beschreiben, aber ich denke das kann man in Challenges nochmal angehen)
-- [x] rather data-literate 
-
-Welche Art von Daten? (Data Types)
-- text-basierte Dateien (z.B. Oberflächenanalyse)
-- Datanbanken (zetasizer: sqlite)
-- imaging (inkl. image stacks)
-- Code (from small scripts to software; python, jupyter, matlab)
-- Simulations (input files, output)
-
-Welche ELNs / Tools bieten sich an? (ELNs and Other Tools) 
-- elabftw
-- (openBIS)
-- Omero (Tool, UDE nutzt OME+eLabFTW)
-- NOMAD
-- iochem-bd
-- git (Versionierung Skripte)
-- Datalad ('git für Forschungsdaten/Metadaten') 
-
-Wie / Wo können Daten publiziert werden? (Repos nennen) (Repositories)
-- RADAR4Chem -> alles
-- iochem-bd (comp. chemistry)
-- NOMAD (simulations)
-- Image Data Resource (https://idr.openmicroscopy.org/)  
-<Nikki: wo ist der Unterschied zw. Simulations u. Comp. Chemistry? Bei uns steht auch dass NOMAD für simulations ist, aber es ist ja eigentlich alle Materials Science Daten, oder?>
-
-Herausforderungen (Challenges)
-- non-bio imaging data missing repo/long-term archive
-- large datasets can be difficult to manage and publish
-- diverse methodology can be used to analyze a broad range of subjects
-- no unified tool to manage everything (such as chemotion)
-
-<!-- images? -->
-
-
-<!-- Nikki's suggestions: 
-- Extend table to see what data types are supported by which tools (this could also assist infrstructure providers in gap analysis)
-- Can include methods and data types from SFB 985/RWTH (https://docs.google.com/spreadsheets/d/1gdi5gUH3cy4I2sy055IPqOKvfBDzRouW/edit?usp=drive_link&ouid=109474882186950125832&rtpof=true&sd=true)
--->
 
 ## Introduction 
 
@@ -103,90 +60,3 @@ Common challenges in physical chemistry and FAIR data often go hand-in-hand with
 
 Especially in imaging, large data volume can strain the local [storage](docs/data_storage) resources. Central storage solution can provide assistance and should be used in combination with best research data management practices to ensure the data's re-usability and avoid unorganized and inefficient use of large storage systems.
 
-<!-- old content
-# Methods Profiles
-
-## EPR spectroscopy
-
-### What is it?
-- **E**lectron **P**aramagnetic **R**esonance spectroscopy belongs together with NMR (**N**uclear **M**agnetic **R**esonance) spectroscopy to the group of magnetic resonance methods
-- measures the resonant microwave absorption of a paramagnetic sample in an external magnetic field (i.e measurement needs unpaired electrons)
-
-### For what?
-- provides information about the electronic/atomic structure and the chemical environment (e.g. local environmental polarity) of the sample
-- for the characterisation of molecular dynamics on the time scale of approx. 10 ps-1 μs (allows e.g. conclusions to be drawn about local nanoviscosity)
-- for distance measurements in the range of about 1-8 nm
-
-### What kind of data is generated?
-- almost exclusively [proprietary file formats](/docs/format_standards) (e.g. .spe or .DTA/.DSC) of the "Bruker Corporation" company
-- transfer into [open file formats](/docs/format_standards) (e.g. .txt or .csv) either via Bruker software on the measuring device itself or via tools like [SpinToolbox](https://www.spintoolbox.com/en/)
-- analysis of data using Bruker software or e.g. [EasySpin](https://www.easyspin.org/) as open-source toolbox for MATLAB
-
-### How to do it [FAIR](/docs/fair)?
-- [documentation of all research data](/docs/data_documentation) and [metadata](/docs/metadata) is carried out digitally using an suitable [ELN](/docs/eln) (possibly in addition to a manual laboratory notebook in paper form)
-- experimental conditions (e.g. sample concentration, solvent etc.) and measurement parameters (e.g. frequency, temperature) are noted in the [ELN](/docs/eln)
-- observations, deviations from planned measurement protocol or other peculiarities during measurement with no digital output (i.e. no data files) are added manually to the [ELN](/docs/eln) entry of the experiment
-- obtained unprocessed raw files from measurements are uploaded to [ELN](/docs/eln) in open file formats and attached directly to the respective [ELN](/docs/eln) experiment entry, including metadata with data on the instrument (e.g. manufacturer, type, etc.), measurement conditions & parameters
-- [metadata](/docs/metadata) related to the obtained data, such as temperature or solvent of measurement, follow common [metadata standards](/docs/metadata)
-- research data are processed, analysed and compared with open non-proprietary software tools
-- simultaneously with [publication](/docs/data_publication) as a research article in a scientific journal, the underlying research data is published in an open data [repository](/docs/repositories) and linked to the article (incl. semantically richly annotated raw and processed data in open data formats for reuse)
-- an unique [persistent identifier](/docs/pid) (e.g. DOI) is generated for each dataset as well as for the journal publication
-
-## Quantum Mechanical (QM) calculations
-
-### What is it?
-- **Q**uantum **M**echanical calculations are one of the major computational tools to elucidate molecular properties on a first-principles basis
-- solving the Schrödinger equation provides the electronic energy of a molecule/molecular system, from which properties can be derived as higher-order derivatives. Descriptors can also be computed from orbital/density data which is equally available
-
-### For what?
-- calculated molecular properties include e.g. molecular structures (usually local minima and transition states), energies, spectroscopic parameters/properties, dipole moments, polarizabilities and non-observables such as atomic charges and topological analysis
-- properties can be calculated prior to conducting experimental measurements to guide synthesis (computational screening) or a posteriori to help interpret experimental results atomistically
-- the application range depends on the level of theory used. Correlated wave function methods are commonly applied to systems with less than 100 atoms, density functional theory (DFT) up to 500 atoms, semiempirical methods can be routinely applied in the range of thousands
-
-### What kind of data is generated?
-- data formats depend strongly on the program that is used for the QM calculations, e.g. Gaussian, ORCA, Molpro, TURBOMOLE or Jaguar, but generally formatted text files are used as input and log files. Compressed data formats are used to store wavefunction, density information and operators. Molecular structures are provided in human-readable format
-- data analysis is carried out using custom scripts. A few programs provide their own scripts for common tasks (such as plotting of molecular orbitals) and dedicated GUIs
-
-### How to do it [FAIR](/docs/fair)?
-- [documentation of all research data](/docs/data_documentation) and [metadata](/docs/metadata) is carried out digitally using a suitable repository (e.g. NOMAD, ioChem-BD or a general-purpose repository) to store the input files, main log and structures files (if not included in the log)
-- reproducibility of calculations to within numerical accuracy can be ensured by storing the input files and adding the program and its version (ideally even the compiler version and any compiler flags) as metadata. Numerical thresholds are well defined but reproducibility of calculations across different programs and versions is not guaranteed. This warrants the safekeeping of version specific source files for the same time period as the stored data
-- data analysis scripts should be uploaded to the repository in open file formats, attached directly to the corresponding data entry and accompanied with appropriate documentation
-- if possible, analysis and evaluation of calculations should be conducted with open, non-proprietary software tools
-- simultaneously with [publication](/docs/data_publication) as a research article in a scientific journal, the data in the [repository](/docs/repositories) is linked to the article (incl. semantically richly annotated raw and processed data, if possible in open data formats for reuse)
-- a unique [persistent identifier](/docs/pid) (e.g. DOI) is generated for the dataset as well as for the journal publication
-- XML and CML (Chemical Markup Language) is used by a few software packages but this is not common practice
-
-### Challenges to make data FAIR
-- no standardised transfer into [open file formats](/docs/format_standards). All repositories of quantum chemical calculations to date make use of in-house parsers to extract the calculation data from uploaded logs. This trend hinders the improvement of FAIR practices since new developers are not provided with a template for log files. Any new software can only be featured in repositories after a unique parser is developed
-- lack of open meta-input and output file formats that are necessary to enable full interoperability of different programs and tools used for QM calculations. Particularly concerning is the lack of standards for: z-matrix and xyz file formats, trajectory files in molecular dynamics or structure optimisations, definition of isotopes, potential energy surfaces as well as equations used in the derivation of properties including thermodynamic quantities
-
-## Molecular Mechanical (MM) simulations
-
-### What is it?
-- **M**olecular **M**echanical simulations approximate intra- and intermolecular interactions using simple Newtonian mechanics and neglect quantum effects
-- the system is parametrised with a suitable force field and propagated in time by solving the system’s Newtonian equations of motion. Potentials or modifications of the force field parameters can be applied to extract thermodynamic/kinetic data
-
-### For what?
-- systems can be as large as millions of atoms, allowing for the investigation of protein dynamics and protein-ligand interactions on a microsecond timescale. More complex systems such as protein-protein interactions or proteins embedded in a biomembrane can also be simulated
-- simulations of pure liquids, mixtures or interfaces between liquids and solids or gases enable the investigation of such systems
-- explaining and interpreting the behaviour of macroscopic systems by investigating them at a microscopic level
-
-### What kind of data is generated?
-- data formats depend strongly on the program that is used for the MM calculations, e.g. AMBER, CHARMM, GROMACS, LAMMPS or NAMD but in general specifically formatted text files are used as input and log files, and a binary representation for checkpoint and trajectory files
-- analysis of data using tools provided by the software’s manufacturer or custom scripts
-
-### How to do it [FAIR](/docs/fair)?
-- [documentation of all research data](/docs/data_documentation) and [metadata](/docs/metadata) is carried out digitally using a suitable repository to store the data
-- reproducibility of calculations can be ensured by storing the input file and adding the program and its version (ideally including the compiler and any compiler flags) as metadata
-- if possible, analysis and evaluation of calculations should be conducted with open non-proprietary software tools
-- simultaneously with [publication](/docs/data_publication) as a research article in a scientific journal, the data in the [repository](/docs/repositories) is linked to the article (incl. semantically richly annotated raw and processed data, if possible in open data formats for reuse)
-- a unique [persistent identifier](/docs/pid) (e.g. DOI) is generated for each dataset as well as for the journal publication
-
-### Challenges to make data FAIR
-- no standardised transfer into [open file formats](/docs/format_standards) for different simulation packages
-- development of open meta-input and output file formats is required to handle the multitude of different programs and tools used in MM calculations in accordance with the FAIR principles. Tools such as PLUMED can help users with this problem
-- trajectory files are typically too large to store in commonly used repository environments, even when using compressed file formats. To make this data FAIR, standards for handling large amounts of data must be developed or solutions from other fields applied
-- reproducibility of long time-scale molecular dynamics is unattainable (numerical noise will eventually affect the resulting trajectories, especially in a multicore environment). Depending on the numerical accuracy and the specific implementation, deviations can be observed as soon as in the picosecond range. However, thermodynamic averages or other probabilistic measurements should be achieved within a suitable margin of error. This margin would have to be estimated and provided by the authors of a publication
-
---> 
-

From f9c85658050db58709e0f8f4bbd241bc40e45f2c Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Tue, 9 Jul 2024 17:49:10 +0200
Subject: [PATCH 23/89] test: eln-finder staging

---
 docusaurus.config.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docusaurus.config.js b/docusaurus.config.js
index d088c2d5..c55bba2f 100644
--- a/docusaurus.config.js
+++ b/docusaurus.config.js
@@ -11,14 +11,14 @@ const title = "NFDI4Chem Knowledge Base";
 const description =
     "Supporting scientists to digitalise all steps of chemical research: to collect, store, process, analyse, publish, and reuse research data";
 const url = "https://knowledgebase.nfdi4chem.de/";
-const baseUrl = "/knowledge_base/";
+// const baseUrl = "/knowledge_base/";
 
 const navbar = require("./navbar.json");
 const footerLinks = require("./footer.json");
 
 // Use for stagging:
 // const baseUrl = '/staging/knowledge_base_matomo/';
-// const baseUrl = '/staging/knowledge_base/';
+const baseUrl = "/staging_eln/knowledge_base/";
 
 const config = {
     title: title,

From b2bfb6d3b21bff99f9448464b68e7d94e69b5845 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Tue, 9 Jul 2024 19:39:00 +0200
Subject: [PATCH 24/89] test: eln-finder staging

---
 scripts/getElns.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/getElns.sh b/scripts/getElns.sh
index d7778b40..47a73e52 100755
--- a/scripts/getElns.sh
+++ b/scripts/getElns.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-targetDir="/var/www/html/staging/knowledge_base/assets"
+targetDir="/var/www/html/staging_eln/knowledge_base/assets"
 # targetDir="/var/www/html/knowledge_base/assets"
 
 # get the data from the eln-finder

From fadab2654bbb4a2e7f20203aa534fabddacc2fe3 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Tue, 9 Jul 2024 19:39:48 +0200
Subject: [PATCH 25/89] feat: display ELNs as cards

---
 src/components/eln/Eln.module.css | 60 +++++++++++++++++++++++++++++++
 src/components/eln/ElnCard.js     | 33 +++++++++++++++++
 src/components/eln/ElnStack.js    | 45 +++++++++++++++++++++++
 src/components/eln/LicenseChip.js | 14 ++++++++
 src/components/eln/SubdiscChip.js |  8 +++++
 src/css/custom.css                |  2 +-
 6 files changed, 161 insertions(+), 1 deletion(-)
 create mode 100644 src/components/eln/Eln.module.css
 create mode 100644 src/components/eln/ElnCard.js
 create mode 100644 src/components/eln/ElnStack.js
 create mode 100644 src/components/eln/LicenseChip.js
 create mode 100644 src/components/eln/SubdiscChip.js

diff --git a/src/components/eln/Eln.module.css b/src/components/eln/Eln.module.css
new file mode 100644
index 00000000..073d8bfc
--- /dev/null
+++ b/src/components/eln/Eln.module.css
@@ -0,0 +1,60 @@
+/********** ELN-Finder ************/
+
+.eln {
+    display: flex;
+    flex-direction: row;
+    flex-wrap: wrap;
+    justify-content: space-evenly;
+}
+
+/* Search / Filter section */
+
+.eln__searchfilter {
+    padding: 0;
+    width: 100%;
+}
+
+.eln__card {
+    width: 48%;
+    margin: 0.1rem;
+    padding: 0.75rem;
+    border: 1px dashed var(--ifm-color-primary);
+    margin-bottom: 0.75rem;
+    transition: all var(--n4c-transform-time) ease-in-out;
+}
+
+.eln__card__header {
+    display: flex;
+    justify-content: space-between;
+    align-items: center;
+}
+
+.eln__card__desc {
+    padding: 0.5rem;
+}
+
+@media screen and (max-width: 1200px) {
+    .eln {
+        display: flex;
+        flex-direction: column;
+    }
+
+    .eln__card {
+        width: 100%;
+        padding: 0.75rem;
+        border: 1px dashed var(--ifm-color-primary);
+        margin-bottom: 0.75rem;
+        transition: all var(--n4c-transform-time) ease-in-out;
+    }
+}
+
+.eln__card__link {
+    display: flex;
+    padding: 0.5rem;
+}
+
+.eln__licenseChip--opensource {
+    background-color: var(--ifm-color-primary);
+    color: white;
+    font-weight: bold;
+}
diff --git a/src/components/eln/ElnCard.js b/src/components/eln/ElnCard.js
new file mode 100644
index 00000000..46d0279d
--- /dev/null
+++ b/src/components/eln/ElnCard.js
@@ -0,0 +1,33 @@
+import RepoButton from "@site/src/components/repos/RepoButton";
+
+import LicenseChip from "./LicenseChip.js";
+import ShortenDesc from "./ShortenDesc.js";
+import SubdiscChip from "./SubdiscChip.js";
+
+import styles from "./Eln.module.css";
+
+function ElnCard({ eln }) {
+    console.log(eln);
+
+    return (
+        <div className={styles.eln__card}>
+            <div className={styles.eln__card__header}>
+                <h3>{eln.name}</h3>
+                <LicenseChip license={eln.license} />
+            </div>
+            <RepoButton url={eln.url} name="Profile Page" />
+            <div className={styles.eln__card__desc}>
+                <ShortenDesc desc={eln.desc} length={200} />
+            </div>
+            <div className={styles.eln__card__desc}>
+                {eln.subDisc.length > 0
+                    ? eln.subDisc.map((subdisc, idx) => (
+                          <SubdiscChip subdisc={subdisc} key={idx} />
+                      ))
+                    : null}
+            </div>
+        </div>
+    );
+}
+
+export default ElnCard;
diff --git a/src/components/eln/ElnStack.js b/src/components/eln/ElnStack.js
new file mode 100644
index 00000000..a9592a83
--- /dev/null
+++ b/src/components/eln/ElnStack.js
@@ -0,0 +1,45 @@
+import Link from "@docusaurus/Link";
+import ShortenDesc from "./ShortenDesc";
+import ElnCard from "./ElnCard";
+import styles from "./Eln.module.css";
+
+function ElnStack({ elnTable }) {
+    return (
+        <div className={styles.eln}>
+            {elnTable.map((eln, idx) => (
+                <ElnCard {...{ eln }} key={idx} />
+            ))}
+        </div>
+    );
+}
+
+export default ElnStack;
+
+// <table>
+//     <thead>
+//         <tr>
+//             <th>Name</th>
+//             <th>License</th>
+//             <th>Description</th>
+//         </tr>
+//     </thead>
+//     <tbody>
+//         {elnTable.map((eln) => (
+//             <tr>
+//                 <td>
+//                     <Link to={eln.url}>{eln.name}</Link>
+//                 </td>
+//                 <td>
+//                     {eln.license === "Open Source" ? (
+//                         <strong>{eln.license}</strong>
+//                     ) : (
+//                         eln.license
+//                     )}
+//                 </td>
+//                 <td>
+//                     <ShortenDesc desc={eln.desc} length={200} />
+//                 </td>
+//             </tr>
+//         ))}
+//     </tbody>
+// </table>
diff --git a/src/components/eln/LicenseChip.js b/src/components/eln/LicenseChip.js
new file mode 100644
index 00000000..63207a91
--- /dev/null
+++ b/src/components/eln/LicenseChip.js
@@ -0,0 +1,14 @@
+import styles from "./Eln.module.css";
+import clsx from "clsx";
+
+function LicenseChip({ license }) {
+    let style = "lbe__filterbutton lbe__chip";
+
+    if (license === "Open Source") {
+        style = clsx(styles["eln__licenseChip--opensource"], style);
+    }
+
+    return <button className={style}>{license}</button>;
+}
+
+export default LicenseChip;
diff --git a/src/components/eln/SubdiscChip.js b/src/components/eln/SubdiscChip.js
new file mode 100644
index 00000000..914ee25a
--- /dev/null
+++ b/src/components/eln/SubdiscChip.js
@@ -0,0 +1,8 @@
+import styles from "./Eln.module.css";
+import clsx from "clsx";
+
+function SubdiscChip({ subdisc }) {
+    return <button className={"lbe__filterbutton "}>{subdisc}</button>;
+}
+
+export default SubdiscChip;
diff --git a/src/css/custom.css b/src/css/custom.css
index e75fe2c5..11e3b570 100644
--- a/src/css/custom.css
+++ b/src/css/custom.css
@@ -649,7 +649,7 @@ table thead tr {
     color: var(--ifm-color-primary);
 }
 
-.lbe__filterbutton.lbe__chip {
+.lbe__chip {
     background: var(--ifm-breadcrumb-item-background-active);
     color: var(--ifm-color-primary);
     font-size: calc(0.8rem * var(--ifm-breadcrumb-size-multiplier));

From ce10fb2fba83294a1de9b45c50b97c885c05cfee Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Tue, 9 Jul 2024 19:40:05 +0200
Subject: [PATCH 26/89] feat: abstraction of ElnFinder component

---
 src/components/eln/ElnFinder.js | 65 +++++++++++----------------------
 src/components/eln/ElnStatus.js | 21 +++++++++++
 2 files changed, 42 insertions(+), 44 deletions(-)
 create mode 100644 src/components/eln/ElnStatus.js

diff --git a/src/components/eln/ElnFinder.js b/src/components/eln/ElnFinder.js
index 6f826abf..d9b1752f 100644
--- a/src/components/eln/ElnFinder.js
+++ b/src/components/eln/ElnFinder.js
@@ -1,8 +1,8 @@
 import React, { useState, useEffect } from "react";
-import Link from "@docusaurus/Link";
 import moment from "moment";
 
-import ShortenDesc from "./ShortenDesc";
+import ElnStack from "./ElnStack";
+import ElnStatus from "./ElnStatus";
 
 // const elnData = require("@site/static/assets/eln_test.json");
 
@@ -28,6 +28,7 @@ function ElnFinder() {
     }
 
     let elnTable = [];
+    let allSubDisc = [];
 
     const dateDownloaded = moment(elnData.date);
     const relativeDate = moment(dateDownloaded).fromNow();
@@ -36,6 +37,14 @@ function ElnFinder() {
         const chemElns = elnData["_embedded"].searchResult["_embedded"].objects;
 
         chemElns.map((eln) => {
+            let subDisc = [];
+            eln["_embedded"].indexableObject.metadata["dc.subject"].map(
+                (discipline) =>
+                    discipline.value.startsWith("Chemistry:")
+                        ? subDisc.push(discipline.value.split(":")[1])
+                        : null
+            );
+
             elnTable.push({
                 name: eln["_embedded"].indexableObject.name,
                 url: eln["_embedded"].indexableObject.metadata[
@@ -48,55 +57,23 @@ function ElnFinder() {
                 desc: eln["_embedded"].indexableObject.metadata[
                     "dc.description.abstract"
                 ][0].value,
+                subDisc: subDisc,
             });
+            allSubDisc.push(subDisc);
+            console.log(elnTable);
         });
+
+        allSubDisc = [...new Set(allSubDisc.flat())];
+        console.log(allSubDisc);
     } catch (error) {
-        return <em>Failed to process ELN data</em>;
+        console.error(error);
+        return <em>Failed to process ELN data.</em>;
     }
 
     return (
         <React.Fragment>
-            <p>
-                <em>
-                    Data kindly provided by{" "}
-                    <Link to="https://eln-finder.ulb.tu-darmstadt.de/">
-                        ELN Finder
-                    </Link>{" "}
-                    (
-                    {relativeDate !== "Invalid date"
-                        ? "last updated " + relativeDate
-                        : "last update unknown"}
-                    ).
-                </em>
-            </p>
-            <table>
-                <thead>
-                    <tr>
-                        <th>Name</th>
-                        <th>License</th>
-                        <th>Description</th>
-                    </tr>
-                </thead>
-                <tbody>
-                    {elnTable.map((eln) => (
-                        <tr>
-                            <td>
-                                <Link to={eln.url}>{eln.name}</Link>
-                            </td>
-                            <td>
-                                {eln.license === "Open Source" ? (
-                                    <strong>{eln.license}</strong>
-                                ) : (
-                                    eln.license
-                                )}
-                            </td>
-                            <td>
-                                <ShortenDesc desc={eln.desc} length={200} />
-                            </td>
-                        </tr>
-                    ))}
-                </tbody>
-            </table>
+            <ElnStatus {...{ relativeDate }} />
+            <ElnStack {...{ elnTable }} />
         </React.Fragment>
     );
 }
diff --git a/src/components/eln/ElnStatus.js b/src/components/eln/ElnStatus.js
new file mode 100644
index 00000000..108f58e2
--- /dev/null
+++ b/src/components/eln/ElnStatus.js
@@ -0,0 +1,21 @@
+import Link from "@docusaurus/Link";
+
+function ElnStatus({ relativeDate }) {
+    return (
+        <p>
+            <em>
+                Data kindly provided by{" "}
+                <Link to="https://eln-finder.ulb.tu-darmstadt.de/">
+                    ELN Finder
+                </Link>{" "}
+                (
+                {relativeDate !== "Invalid date"
+                    ? "last updated " + relativeDate
+                    : "last update unknown"}
+                ).
+            </em>
+        </p>
+    );
+}
+
+export default ElnStatus;

From e84a44aa0d17c4f6317d7f44ba24a3aa61d701cc Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Wed, 10 Jul 2024 14:16:34 +0200
Subject: [PATCH 27/89] chore: remove unnec. code

---
 src/components/eln/ElnStack.js | 31 -------------------------------
 1 file changed, 31 deletions(-)

diff --git a/src/components/eln/ElnStack.js b/src/components/eln/ElnStack.js
index a9592a83..037dc73f 100644
--- a/src/components/eln/ElnStack.js
+++ b/src/components/eln/ElnStack.js
@@ -1,5 +1,3 @@
-import Link from "@docusaurus/Link";
-import ShortenDesc from "./ShortenDesc";
 import ElnCard from "./ElnCard";
 import styles from "./Eln.module.css";
 
@@ -14,32 +12,3 @@ function ElnStack({ elnTable }) {
 }
 
 export default ElnStack;
-
-// <table>
-//     <thead>
-//         <tr>
-//             <th>Name</th>
-//             <th>License</th>
-//             <th>Description</th>
-//         </tr>
-//     </thead>
-//     <tbody>
-//         {elnTable.map((eln) => (
-//             <tr>
-//                 <td>
-//                     <Link to={eln.url}>{eln.name}</Link>
-//                 </td>
-//                 <td>
-//                     {eln.license === "Open Source" ? (
-//                         <strong>{eln.license}</strong>
-//                     ) : (
-//                         eln.license
-//                     )}
-//                 </td>
-//                 <td>
-//                     <ShortenDesc desc={eln.desc} length={200} />
-//                 </td>
-//             </tr>
-//         ))}
-//     </tbody>
-// </table>

From 821571ce973f4c9f4c26c34f1e7f2d6690aedeaa Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Wed, 10 Jul 2024 14:16:58 +0200
Subject: [PATCH 28/89] chore: remove unnec. code

---
 src/components/eln/SubdiscChip.js | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/components/eln/SubdiscChip.js b/src/components/eln/SubdiscChip.js
index 914ee25a..9c446cc6 100644
--- a/src/components/eln/SubdiscChip.js
+++ b/src/components/eln/SubdiscChip.js
@@ -1,6 +1,3 @@
-import styles from "./Eln.module.css";
-import clsx from "clsx";
-
 function SubdiscChip({ subdisc }) {
     return <button className={"lbe__filterbutton "}>{subdisc}</button>;
 }

From 447289e232b87da80f35b8fe218c9ffa622cf44e Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Wed, 10 Jul 2024 15:48:21 +0200
Subject: [PATCH 29/89] refactor: reorganize chips

---
 package.json                      |  1 +
 src/components/eln/ElnChips.js    | 28 ++++++++++++++++++++++++++++
 src/components/eln/LicenseChip.js | 14 --------------
 src/components/eln/SubdiscChip.js |  5 -----
 4 files changed, 29 insertions(+), 19 deletions(-)
 create mode 100644 src/components/eln/ElnChips.js
 delete mode 100644 src/components/eln/LicenseChip.js
 delete mode 100644 src/components/eln/SubdiscChip.js

diff --git a/package.json b/package.json
index f7ba2f0a..c6a8b7ff 100644
--- a/package.json
+++ b/package.json
@@ -29,6 +29,7 @@
         "react": "^18.3.1",
         "react-dom": "^18.3.1",
         "react-tagcloud": "^2.3.3",
+        "use-immer": "^0.10.0",
         "video-privacy": "^1.0.2"
     },
     "devDependencies": {
diff --git a/src/components/eln/ElnChips.js b/src/components/eln/ElnChips.js
new file mode 100644
index 00000000..7c611dd8
--- /dev/null
+++ b/src/components/eln/ElnChips.js
@@ -0,0 +1,28 @@
+import styles from "./Eln.module.css";
+import clsx from "clsx";
+
+function LicenseChip({ license }) {
+    let style = "lbe__filterbutton lbe__chip";
+
+    if (license === "Open Source") {
+        style = clsx(styles["eln__licenseChip--opensource"], style);
+    }
+
+    return <button className={style}>{license}</button>;
+}
+
+function SubdiscChip({ subdisc, active }) {
+    return (
+        <button
+            className={
+                active
+                    ? "lbe__filterbutton lbe__filterbutton--active"
+                    : "lbe__filterbutton"
+            }
+        >
+            {subdisc}
+        </button>
+    );
+}
+
+export { SubdiscChip, LicenseChip };
diff --git a/src/components/eln/LicenseChip.js b/src/components/eln/LicenseChip.js
deleted file mode 100644
index 63207a91..00000000
--- a/src/components/eln/LicenseChip.js
+++ /dev/null
@@ -1,14 +0,0 @@
-import styles from "./Eln.module.css";
-import clsx from "clsx";
-
-function LicenseChip({ license }) {
-    let style = "lbe__filterbutton lbe__chip";
-
-    if (license === "Open Source") {
-        style = clsx(styles["eln__licenseChip--opensource"], style);
-    }
-
-    return <button className={style}>{license}</button>;
-}
-
-export default LicenseChip;
diff --git a/src/components/eln/SubdiscChip.js b/src/components/eln/SubdiscChip.js
deleted file mode 100644
index 9c446cc6..00000000
--- a/src/components/eln/SubdiscChip.js
+++ /dev/null
@@ -1,5 +0,0 @@
-function SubdiscChip({ subdisc }) {
-    return <button className={"lbe__filterbutton "}>{subdisc}</button>;
-}
-
-export default SubdiscChip;

From d00b1e304349c8aeb36d0abb14770fbac234b2bb Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Wed, 10 Jul 2024 15:48:49 +0200
Subject: [PATCH 30/89] feat: text search component

---
 src/components/eln/elnFilter/TextSearch.js | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 src/components/eln/elnFilter/TextSearch.js

diff --git a/src/components/eln/elnFilter/TextSearch.js b/src/components/eln/elnFilter/TextSearch.js
new file mode 100644
index 00000000..c7359d5e
--- /dev/null
+++ b/src/components/eln/elnFilter/TextSearch.js
@@ -0,0 +1,22 @@
+function TextSearch({ resultOutput, filter, setFilter }) {
+    const handleChange = (e) =>
+        setFilter((draft) => {
+            draft.text = e.target.value;
+        });
+
+    return (
+        <div className="lbe__searchfilter__search">
+            <input
+                type="search"
+                className="navbar__search-input"
+                placeholder="Type to search"
+                value={filter.text}
+                onChange={handleChange}
+            />
+            &ensp;
+            <em>{resultOutput}</em>
+        </div>
+    );
+}
+
+export default TextSearch;

From aabd5bc27451fdd68e9855c1ab9878106e001e72 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Wed, 10 Jul 2024 15:49:22 +0200
Subject: [PATCH 31/89] refactor: reorganize chips

---
 src/components/eln/ElnCard.js | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/components/eln/ElnCard.js b/src/components/eln/ElnCard.js
index 46d0279d..591f1f6e 100644
--- a/src/components/eln/ElnCard.js
+++ b/src/components/eln/ElnCard.js
@@ -1,14 +1,11 @@
 import RepoButton from "@site/src/components/repos/RepoButton";
 
-import LicenseChip from "./LicenseChip.js";
+import { LicenseChip, SubdiscChip } from "./ElnChips.js";
 import ShortenDesc from "./ShortenDesc.js";
-import SubdiscChip from "./SubdiscChip.js";
 
 import styles from "./Eln.module.css";
 
 function ElnCard({ eln }) {
-    console.log(eln);
-
     return (
         <div className={styles.eln__card}>
             <div className={styles.eln__card__header}>

From f6e449e33f3353c4de046a8ee31aa149e287bf01 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Wed, 10 Jul 2024 15:49:40 +0200
Subject: [PATCH 32/89] feat: first draft for filtering

---
 src/components/eln/Eln.module.css            | 14 ++++-
 src/components/eln/ElnFilter.js              | 65 ++++++++++++++++++++
 src/components/eln/ElnFinder.js              | 63 ++++++++++++++++++-
 src/components/eln/ElnStack.js               | 11 ++--
 src/components/eln/elnFilter/FilterButton.js |  7 +++
 5 files changed, 151 insertions(+), 9 deletions(-)
 create mode 100644 src/components/eln/ElnFilter.js
 create mode 100644 src/components/eln/elnFilter/FilterButton.js

diff --git a/src/components/eln/Eln.module.css b/src/components/eln/Eln.module.css
index 073d8bfc..6ece488f 100644
--- a/src/components/eln/Eln.module.css
+++ b/src/components/eln/Eln.module.css
@@ -10,8 +10,11 @@
 /* Search / Filter section */
 
 .eln__searchfilter {
-    padding: 0;
-    width: 100%;
+    width: calc(96% + 0.75rem);
+    margin: 0.1rem;
+    padding: 0.75rem;
+    border: 1px dashed var(--ifm-color-primary);
+    margin-bottom: 0.75rem;
 }
 
 .eln__card {
@@ -39,6 +42,13 @@
         flex-direction: column;
     }
 
+    .eln__searchfilter {
+        width: 100%;
+        padding: 0.75rem;
+        border: 1px dashed var(--ifm-color-primary);
+        margin-bottom: 0.75rem;
+    }
+
     .eln__card {
         width: 100%;
         padding: 0.75rem;
diff --git a/src/components/eln/ElnFilter.js b/src/components/eln/ElnFilter.js
new file mode 100644
index 00000000..7a971014
--- /dev/null
+++ b/src/components/eln/ElnFilter.js
@@ -0,0 +1,65 @@
+import React from "react";
+
+import TextSearch from "./elnFilter/TextSearch";
+import FilterButton from "./elnFilter/FilterButton";
+
+import styles from "./Eln.module.css";
+
+// Assemble buttons for filtering section
+
+function ButtonFilters({ allSubDisc, allLicenses, filter, setFilter }) {
+    let subDiscButtons = ["All", ...allSubDisc];
+    let licenseButtons = ["All", ...allLicenses];
+
+    return (
+        <React.Fragment>
+            <div className="lbe__searchfilter__section">
+                <h4>Filter by subdisciplines</h4>
+                <p>
+                    {subDiscButtons.map((props, idx) => (
+                        <FilterButton
+                            key={idx}
+                            label={props}
+                            type="subDisc"
+                            numbered={true}
+                            {...{ filter, setFilter }}
+                        />
+                    ))}
+                </p>
+            </div>
+            <div className="lbe__searchfilter__section">
+                <h4>Filter by license</h4>
+                <p>
+                    {licenseButtons.map((props, idx) => (
+                        <FilterButton
+                            key={idx}
+                            label={props}
+                            type="license"
+                            numbered={true}
+                            {...{ filter, setFilter }}
+                        />
+                    ))}
+                </p>
+            </div>
+        </React.Fragment>
+    );
+}
+
+function ElnFilter({
+    allSubDisc,
+    allLicenses,
+    filter,
+    setFilter,
+    resultOutput,
+}) {
+    return (
+        <div className={styles.eln__searchfilter}>
+            <TextSearch {...{ resultOutput, filter, setFilter }} />
+            <ButtonFilters
+                {...{ allSubDisc, allLicenses, filter, setFilter }}
+            />
+        </div>
+    );
+}
+
+export default ElnFilter;
diff --git a/src/components/eln/ElnFinder.js b/src/components/eln/ElnFinder.js
index d9b1752f..a9e973eb 100644
--- a/src/components/eln/ElnFinder.js
+++ b/src/components/eln/ElnFinder.js
@@ -1,8 +1,12 @@
 import React, { useState, useEffect } from "react";
 import moment from "moment";
+import { useImmer } from "use-immer";
 
-import ElnStack from "./ElnStack";
 import ElnStatus from "./ElnStatus";
+import ElnFilter from "./ElnFilter";
+import ElnStack from "./ElnStack";
+
+import styles from "./Eln.module.css";
 
 // const elnData = require("@site/static/assets/eln_test.json");
 
@@ -10,6 +14,8 @@ function ElnFinder() {
     const [elnData, setElnData] = useState(null);
     const [error, setError] = useState(null);
 
+    const [filter, setFilter] = useImmer({});
+
     useEffect(() => {
         fetch("../../assets/elnData.json")
             .then((response) => response.json())
@@ -29,6 +35,7 @@ function ElnFinder() {
 
     let elnTable = [];
     let allSubDisc = [];
+    let allLicenses = [];
 
     const dateDownloaded = moment(elnData.date);
     const relativeDate = moment(dateDownloaded).fromNow();
@@ -60,20 +67,72 @@ function ElnFinder() {
                 subDisc: subDisc,
             });
             allSubDisc.push(subDisc);
+            allLicenses.push(
+                eln["_embedded"].indexableObject.metadata["K.lizenzmodell"][0]
+                    .value
+            );
             console.log(elnTable);
         });
 
         allSubDisc = [...new Set(allSubDisc.flat())];
+        allLicenses = [...new Set(allLicenses)];
         console.log(allSubDisc);
+        console.log(allLicenses);
     } catch (error) {
         console.error(error);
         return <em>Failed to process ELN data.</em>;
     }
 
+    const filteredTable = elnTable.filter((eln) => {
+        if (filter.text) {
+            return JSON.stringify(eln).toLowerCase().includes(filter.text);
+        }
+
+        if (filter.subDisc) {
+            return eln.subDisc.includes(filter.subDisc);
+        }
+
+        if (filter.license) {
+            return eln.license.includes(filter.license);
+        } else {
+            return true;
+        }
+    });
+
+    const numberOfResults = filteredTable.length;
+
+    let resultOutput = null;
+
+    switch (numberOfResults) {
+        case elnTable.length:
+            resultOutput = null;
+            break;
+        case 0:
+            resultOutput = "No results found.";
+            break;
+        case 1:
+            resultOutput = "1 result found.";
+            break;
+        default:
+            resultOutput = numberOfResults + " results found.";
+            break;
+    }
+
     return (
         <React.Fragment>
             <ElnStatus {...{ relativeDate }} />
-            <ElnStack {...{ elnTable }} />
+            <div className={styles.eln}>
+                <ElnFilter
+                    {...{
+                        allSubDisc,
+                        allLicenses,
+                        filter,
+                        setFilter,
+                        resultOutput,
+                    }}
+                />
+                <ElnStack {...{ filteredTable }} />
+            </div>
         </React.Fragment>
     );
 }
diff --git a/src/components/eln/ElnStack.js b/src/components/eln/ElnStack.js
index 037dc73f..16706aad 100644
--- a/src/components/eln/ElnStack.js
+++ b/src/components/eln/ElnStack.js
@@ -1,13 +1,14 @@
+import React from "react";
+
 import ElnCard from "./ElnCard";
-import styles from "./Eln.module.css";
 
-function ElnStack({ elnTable }) {
+function ElnStack({ filteredTable }) {
     return (
-        <div className={styles.eln}>
-            {elnTable.map((eln, idx) => (
+        <React.Fragment>
+            {filteredTable.map((eln, idx) => (
                 <ElnCard {...{ eln }} key={idx} />
             ))}
-        </div>
+        </React.Fragment>
     );
 }
 
diff --git a/src/components/eln/elnFilter/FilterButton.js b/src/components/eln/elnFilter/FilterButton.js
new file mode 100644
index 00000000..41251438
--- /dev/null
+++ b/src/components/eln/elnFilter/FilterButton.js
@@ -0,0 +1,7 @@
+function FilterButton({ label }) {
+    let buttonClass = "lbe__filterbutton";
+
+    return <button className={buttonClass}>{label}</button>;
+}
+
+export default FilterButton;

From f276007a36c3d5313c8b82bd32939bc84d66cc84 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Wed, 10 Jul 2024 17:30:03 +0200
Subject: [PATCH 33/89] feat: handling of button filtering

---
 .../eln/{ => elnFilter}/ElnFilter.js          | 49 ++++++++++++++-----
 src/components/eln/elnFilter/FilterButton.js  | 23 ++++++++-
 2 files changed, 59 insertions(+), 13 deletions(-)
 rename src/components/eln/{ => elnFilter}/ElnFilter.js (51%)

diff --git a/src/components/eln/ElnFilter.js b/src/components/eln/elnFilter/ElnFilter.js
similarity index 51%
rename from src/components/eln/ElnFilter.js
rename to src/components/eln/elnFilter/ElnFilter.js
index 7a971014..3d2b909e 100644
--- a/src/components/eln/ElnFilter.js
+++ b/src/components/eln/elnFilter/ElnFilter.js
@@ -1,9 +1,9 @@
 import React from "react";
 
-import TextSearch from "./elnFilter/TextSearch";
-import FilterButton from "./elnFilter/FilterButton";
+import TextSearch from "./TextSearch";
+import FilterButton from "./FilterButton";
 
-import styles from "./Eln.module.css";
+import styles from "../Eln.module.css";
 
 // Assemble buttons for filtering section
 
@@ -11,16 +11,38 @@ function ButtonFilters({ allSubDisc, allLicenses, filter, setFilter }) {
     let subDiscButtons = ["All", ...allSubDisc];
     let licenseButtons = ["All", ...allLicenses];
 
+    // Check if active prop should be handed to FilterButton
+
+    function isActive(type, label) {
+        // check if filter value is equal to label
+
+        if (filter[type] === label) {
+            return true;
+        }
+
+        // check if object is empty and label is "All"
+
+        if (
+            (label === "All" && Object.keys(filter).length === 0) ||
+            (label === "All" && !filter[type])
+        ) {
+            return true;
+        } else {
+            return false;
+        }
+    }
+
     return (
         <React.Fragment>
             <div className="lbe__searchfilter__section">
                 <h4>Filter by subdisciplines</h4>
                 <p>
-                    {subDiscButtons.map((props, idx) => (
+                    {subDiscButtons.map((subDisc, idx) => (
                         <FilterButton
                             key={idx}
-                            label={props}
+                            label={subDisc}
                             type="subDisc"
+                            active={isActive("subDisc", subDisc)}
                             numbered={true}
                             {...{ filter, setFilter }}
                         />
@@ -30,11 +52,12 @@ function ButtonFilters({ allSubDisc, allLicenses, filter, setFilter }) {
             <div className="lbe__searchfilter__section">
                 <h4>Filter by license</h4>
                 <p>
-                    {licenseButtons.map((props, idx) => (
+                    {licenseButtons.map((license, idx) => (
                         <FilterButton
                             key={idx}
-                            label={props}
+                            label={license}
                             type="license"
+                            active={isActive("license", license)}
                             numbered={true}
                             {...{ filter, setFilter }}
                         />
@@ -54,10 +77,14 @@ function ElnFilter({
 }) {
     return (
         <div className={styles.eln__searchfilter}>
-            <TextSearch {...{ resultOutput, filter, setFilter }} />
-            <ButtonFilters
-                {...{ allSubDisc, allLicenses, filter, setFilter }}
-            />
+            <div className={styles["eln__searchfilter__text"]}>
+                <TextSearch {...{ resultOutput, filter, setFilter }} />
+            </div>
+            <div className={styles["eln__searchfilter__buttons"]}>
+                <ButtonFilters
+                    {...{ allSubDisc, allLicenses, filter, setFilter }}
+                />
+            </div>
         </div>
     );
 }
diff --git a/src/components/eln/elnFilter/FilterButton.js b/src/components/eln/elnFilter/FilterButton.js
index 41251438..f733bb54 100644
--- a/src/components/eln/elnFilter/FilterButton.js
+++ b/src/components/eln/elnFilter/FilterButton.js
@@ -1,7 +1,26 @@
-function FilterButton({ label }) {
+function FilterButton(props) {
+    const handleClick = () => {
+        if (props.label === "All") {
+            props.setFilter((draft) => {
+                delete draft[props.type];
+            });
+        } else {
+            props.setFilter((draft) => {
+                draft[props.type] = props.label;
+            });
+        }
+    };
+
     let buttonClass = "lbe__filterbutton";
+    if (props.active) {
+        buttonClass += " lbe__filterbutton--active";
+    }
 
-    return <button className={buttonClass}>{label}</button>;
+    return (
+        <button className={buttonClass} onClick={handleClick}>
+            {props.label}
+        </button>
+    );
 }
 
 export default FilterButton;

From 8be570c8559387ee5486f43ffee4cdd0170eb9bb Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Wed, 10 Jul 2024 17:31:03 +0200
Subject: [PATCH 34/89] feat: improve behaviour and styling

---
 src/components/eln/Eln.module.css          | 39 +++++++++++++++++++++-
 src/components/eln/elnFilter/TextSearch.js | 24 ++++++++-----
 2 files changed, 53 insertions(+), 10 deletions(-)

diff --git a/src/components/eln/Eln.module.css b/src/components/eln/Eln.module.css
index 6ece488f..d2045f86 100644
--- a/src/components/eln/Eln.module.css
+++ b/src/components/eln/Eln.module.css
@@ -10,6 +10,9 @@
 /* Search / Filter section */
 
 .eln__searchfilter {
+    display: flex;
+    flex-direction: row;
+    align-items: center;
     width: calc(96% + 0.75rem);
     margin: 0.1rem;
     padding: 0.75rem;
@@ -17,6 +20,25 @@
     margin-bottom: 0.75rem;
 }
 
+.eln__searchfilter__text {
+    width: 30%;
+}
+
+.eln__searchfilter__buttons {
+    width: 70%;
+}
+
+.eln__searchfilter__search {
+    display: flex;
+    flex-direction: column;
+    justify-items: left;
+    padding: 0.5rem;
+}
+
+.eln__searchfilter__search > em {
+    color: var(--ifm-color-primary);
+}
+
 .eln__card {
     width: 48%;
     margin: 0.1rem;
@@ -36,19 +58,34 @@
     padding: 0.5rem;
 }
 
-@media screen and (max-width: 1200px) {
+@media screen and (max-width: 1400px) {
     .eln {
         display: flex;
         flex-direction: column;
     }
 
     .eln__searchfilter {
+        display: flex;
+        flex-direction: column;
+        align-items: center;
         width: 100%;
         padding: 0.75rem;
         border: 1px dashed var(--ifm-color-primary);
         margin-bottom: 0.75rem;
     }
 
+    .eln__searchfilter__text,
+    .eln__searchfilter__buttons {
+        width: 100%;
+    }
+
+    .eln__searchfilter__search {
+        display: flex;
+        flex-direction: row;
+        align-items: center;
+        padding: 0.5rem 0;
+    }
+
     .eln__card {
         width: 100%;
         padding: 0.75rem;
diff --git a/src/components/eln/elnFilter/TextSearch.js b/src/components/eln/elnFilter/TextSearch.js
index c7359d5e..7a03e2d0 100644
--- a/src/components/eln/elnFilter/TextSearch.js
+++ b/src/components/eln/elnFilter/TextSearch.js
@@ -1,19 +1,25 @@
+import styles from "../Eln.module.css";
+
 function TextSearch({ resultOutput, filter, setFilter }) {
     const handleChange = (e) =>
         setFilter((draft) => {
             draft.text = e.target.value;
         });
 
+    console.log(filter);
+
     return (
-        <div className="lbe__searchfilter__search">
-            <input
-                type="search"
-                className="navbar__search-input"
-                placeholder="Type to search"
-                value={filter.text}
-                onChange={handleChange}
-            />
-            &ensp;
+        <div className={styles.eln__searchfilter__search}>
+            <span>
+                <input
+                    type="search"
+                    className="navbar__search-input"
+                    placeholder="Type to search"
+                    value={filter.text ? filter.text : ""}
+                    onChange={handleChange}
+                />
+                &nbsp;
+            </span>
             <em>{resultOutput}</em>
         </div>
     );

From 5c5a8c8ce5e9e02b6df4c92b1837215100324fce Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Wed, 10 Jul 2024 17:31:25 +0200
Subject: [PATCH 35/89] feat: allow filtering through props

---
 src/components/eln/ElnFinder.js | 56 ++++++++++++++++++++++++---------
 1 file changed, 42 insertions(+), 14 deletions(-)

diff --git a/src/components/eln/ElnFinder.js b/src/components/eln/ElnFinder.js
index a9e973eb..2e0ecca5 100644
--- a/src/components/eln/ElnFinder.js
+++ b/src/components/eln/ElnFinder.js
@@ -3,18 +3,26 @@ import moment from "moment";
 import { useImmer } from "use-immer";
 
 import ElnStatus from "./ElnStatus";
-import ElnFilter from "./ElnFilter";
+import ElnFilter from "./elnFilter/ElnFilter";
 import ElnStack from "./ElnStack";
 
 import styles from "./Eln.module.css";
 
 // const elnData = require("@site/static/assets/eln_test.json");
 
-function ElnFinder() {
+function ElnFinder(props) {
+    // State for ELN data
+
     const [elnData, setElnData] = useState(null);
     const [error, setError] = useState(null);
 
-    const [filter, setFilter] = useImmer({});
+    // State for filtering
+
+    const [filter, setFilter] = useImmer(
+        props.subDisc ? { subDisc: props.subDisc } : {}
+    );
+
+    // Fetch ELN data
 
     useEffect(() => {
         fetch("../../assets/elnData.json")
@@ -29,17 +37,25 @@ function ElnFinder() {
             });
     }, []);
 
+    // Catch if fetch is still loading
+
     if (!elnData) {
         return <em>Loading...</em>;
     }
 
+    // Define working variables
+
     let elnTable = [];
     let allSubDisc = [];
     let allLicenses = [];
 
+    // Parse timestamp of ELN data
+
     const dateDownloaded = moment(elnData.date);
     const relativeDate = moment(dateDownloaded).fromNow();
 
+    // Assemble essential ELN data
+
     try {
         const chemElns = elnData["_embedded"].searchResult["_embedded"].objects;
 
@@ -71,34 +87,44 @@ function ElnFinder() {
                 eln["_embedded"].indexableObject.metadata["K.lizenzmodell"][0]
                     .value
             );
-            console.log(elnTable);
         });
 
         allSubDisc = [...new Set(allSubDisc.flat())];
         allLicenses = [...new Set(allLicenses)];
-        console.log(allSubDisc);
-        console.log(allLicenses);
     } catch (error) {
         console.error(error);
         return <em>Failed to process ELN data.</em>;
     }
 
+    // Filter ELN data based on filter state
+
     const filteredTable = elnTable.filter((eln) => {
-        if (filter.text) {
-            return JSON.stringify(eln).toLowerCase().includes(filter.text);
+        if (Object.keys(filter).length === 0) {
+            return true;
         }
 
-        if (filter.subDisc) {
-            return eln.subDisc.includes(filter.subDisc);
+        if (filter.subDisc && !eln.subDisc.includes(filter.subDisc)) {
+            return false;
         }
 
-        if (filter.license) {
-            return eln.license.includes(filter.license);
-        } else {
-            return true;
+        if (filter.license && eln.license !== filter.license) {
+            return false;
+        }
+
+        if (
+            filter.text &&
+            !JSON.stringify(eln)
+                .toLowerCase()
+                .includes(filter.text.toLowerCase())
+        ) {
+            return false;
         }
+
+        return true;
     });
 
+    // Determine number of results and generate output
+
     const numberOfResults = filteredTable.length;
 
     let resultOutput = null;
@@ -118,6 +144,8 @@ function ElnFinder() {
             break;
     }
 
+    // Render ELN Finder component
+
     return (
         <React.Fragment>
             <ElnStatus {...{ relativeDate }} />

From 992864e15855c12c8b4ebff6ba41eab8d488d168 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Wed, 10 Jul 2024 17:31:35 +0200
Subject: [PATCH 36/89] feat: eln-finder demo with props

---
 docs/10_domains/10_analytical_chemistry.mdx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/10_domains/10_analytical_chemistry.mdx b/docs/10_domains/10_analytical_chemistry.mdx
index ec969a2b..20293277 100644
--- a/docs/10_domains/10_analytical_chemistry.mdx
+++ b/docs/10_domains/10_analytical_chemistry.mdx
@@ -28,7 +28,7 @@ Some open data formats are available for specific data types, such as mass spect
 
 General chemistry ELNs can typically be used for analytical chemistry data and may be well suited to your research topic. However, there are also specialised tools that are tailored to the needs of analytical chemists. These tools often include features for managing instrument data, processing raw data files and visualising results. They may also include tools for chemometric analysis.
 
-<ElnFinder />
+<ElnFinder subDisc="Physical chemistry" />
 
 ## Publishing Data
 

From 4f616c3405afac10072e27f874d4695585964a8e Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Thu, 11 Jul 2024 16:50:58 +0200
Subject: [PATCH 37/89] chore: misc styling improvements

---
 src/components/eln/Eln.module.css          | 28 ++++++++++++----------
 src/components/eln/elnFilter/TextSearch.js | 10 +++++---
 2 files changed, 22 insertions(+), 16 deletions(-)

diff --git a/src/components/eln/Eln.module.css b/src/components/eln/Eln.module.css
index d2045f86..fe2ea79b 100644
--- a/src/components/eln/Eln.module.css
+++ b/src/components/eln/Eln.module.css
@@ -4,7 +4,7 @@
     display: flex;
     flex-direction: row;
     flex-wrap: wrap;
-    justify-content: space-evenly;
+    justify-content: space-between;
 }
 
 /* Search / Filter section */
@@ -12,39 +12,41 @@
 .eln__searchfilter {
     display: flex;
     flex-direction: row;
-    align-items: center;
-    width: calc(96% + 0.75rem);
-    margin: 0.1rem;
+    width: 100%;
     padding: 0.75rem;
     border: 1px dashed var(--ifm-color-primary);
-    margin-bottom: 0.75rem;
+    margin-bottom: 0.5rem;
 }
 
 .eln__searchfilter__text {
-    width: 30%;
+    translate: 0 20%;
+    min-width: 240px;
 }
 
 .eln__searchfilter__buttons {
-    width: 70%;
+    flex-grow: 1;
 }
 
 .eln__searchfilter__search {
     display: flex;
     flex-direction: column;
-    justify-items: left;
-    padding: 0.5rem;
+    padding: 0.5rem 0;
+}
+
+.eln__searchfilter__search > span {
+    text-align: center;
 }
 
 .eln__searchfilter__search > em {
     color: var(--ifm-color-primary);
+    text-align: center;
 }
 
 .eln__card {
-    width: 48%;
-    margin: 0.1rem;
+    width: 49.5%;
     padding: 0.75rem;
     border: 1px dashed var(--ifm-color-primary);
-    margin-bottom: 0.75rem;
+    margin-bottom: 0.5rem;
     transition: all var(--n4c-transform-time) ease-in-out;
 }
 
@@ -77,13 +79,13 @@
     .eln__searchfilter__text,
     .eln__searchfilter__buttons {
         width: 100%;
+        translate: 0;
     }
 
     .eln__searchfilter__search {
         display: flex;
         flex-direction: row;
         align-items: center;
-        padding: 0.5rem 0;
     }
 
     .eln__card {
diff --git a/src/components/eln/elnFilter/TextSearch.js b/src/components/eln/elnFilter/TextSearch.js
index 7a03e2d0..ad1a9ab5 100644
--- a/src/components/eln/elnFilter/TextSearch.js
+++ b/src/components/eln/elnFilter/TextSearch.js
@@ -1,3 +1,7 @@
+import React, { useState } from "react";
+
+import clsx from "clsx";
+
 import styles from "../Eln.module.css";
 
 function TextSearch({ resultOutput, filter, setFilter }) {
@@ -10,15 +14,15 @@ function TextSearch({ resultOutput, filter, setFilter }) {
 
     return (
         <div className={styles.eln__searchfilter__search}>
-            <span>
+            <span className="navbar__search">
                 <input
-                    type="search"
                     className="navbar__search-input"
+                    type="search"
                     placeholder="Type to search"
                     value={filter.text ? filter.text : ""}
                     onChange={handleChange}
                 />
-                &nbsp;
+                &ensp;
             </span>
             <em>{resultOutput}</em>
         </div>

From 99966d9bfa1c4d6f63d8919dbdbcd8f33d69d1a1 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Thu, 11 Jul 2024 16:51:15 +0200
Subject: [PATCH 38/89] chore: shorter desc.

---
 src/components/eln/ElnCard.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/eln/ElnCard.js b/src/components/eln/ElnCard.js
index 591f1f6e..e579eaeb 100644
--- a/src/components/eln/ElnCard.js
+++ b/src/components/eln/ElnCard.js
@@ -14,7 +14,7 @@ function ElnCard({ eln }) {
             </div>
             <RepoButton url={eln.url} name="Profile Page" />
             <div className={styles.eln__card__desc}>
-                <ShortenDesc desc={eln.desc} length={200} />
+                <ShortenDesc desc={eln.desc} length={100} />
             </div>
             <div className={styles.eln__card__desc}>
                 {eln.subDisc.length > 0

From 85525e6bf3396d65d6f929f889f7f79946b061a6 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Thu, 11 Jul 2024 17:28:04 +0200
Subject: [PATCH 39/89] chore: extend inherited class

---
 src/css/custom.css | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/css/custom.css b/src/css/custom.css
index 11e3b570..44f5f25b 100644
--- a/src/css/custom.css
+++ b/src/css/custom.css
@@ -585,7 +585,8 @@ table thead tr {
     margin: unset;
 }
 
-.lbe__searchfilter__section h4 {
+.lbe__searchfilter__section h4,
+h5 {
     margin: 0.5rem 0;
 }
 

From b37af83a8d7d5cf5e6e99d391ef0ee2d4ed1a388 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Thu, 11 Jul 2024 17:28:43 +0200
Subject: [PATCH 40/89] chore: improve styling

---
 src/components/eln/elnFilter/ElnFilter.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/components/eln/elnFilter/ElnFilter.js b/src/components/eln/elnFilter/ElnFilter.js
index 3d2b909e..89883b49 100644
--- a/src/components/eln/elnFilter/ElnFilter.js
+++ b/src/components/eln/elnFilter/ElnFilter.js
@@ -35,7 +35,7 @@ function ButtonFilters({ allSubDisc, allLicenses, filter, setFilter }) {
     return (
         <React.Fragment>
             <div className="lbe__searchfilter__section">
-                <h4>Filter by subdisciplines</h4>
+                <h5>Filter by subdisciplines</h5>
                 <p>
                     {subDiscButtons.map((subDisc, idx) => (
                         <FilterButton
@@ -50,7 +50,7 @@ function ButtonFilters({ allSubDisc, allLicenses, filter, setFilter }) {
                 </p>
             </div>
             <div className="lbe__searchfilter__section">
-                <h4>Filter by license</h4>
+                <h5>Filter by license</h5>
                 <p>
                     {licenseButtons.map((license, idx) => (
                         <FilterButton

From 39b31b26bc3e4a3ddf144e139d493dea057c7da1 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Thu, 11 Jul 2024 17:29:29 +0200
Subject: [PATCH 41/89] refactor: allow filtering from cards, remove chip
 components

---
 src/components/eln/Eln.module.css            |  6 ++++
 src/components/eln/ElnCard.js                | 29 +++++++++++++++-----
 src/components/eln/ElnChips.js               | 28 -------------------
 src/components/eln/ElnFinder.js              |  2 +-
 src/components/eln/ElnStack.js               |  4 +--
 src/components/eln/elnFilter/FilterButton.js | 14 +++++++---
 6 files changed, 41 insertions(+), 42 deletions(-)
 delete mode 100644 src/components/eln/ElnChips.js

diff --git a/src/components/eln/Eln.module.css b/src/components/eln/Eln.module.css
index fe2ea79b..3ecfac5c 100644
--- a/src/components/eln/Eln.module.css
+++ b/src/components/eln/Eln.module.css
@@ -107,3 +107,9 @@
     color: white;
     font-weight: bold;
 }
+
+.eln__filterbutton--secondary {
+    background-color: var(--ifm-breadcrumb-item-background-active);
+    color: var(--ifm-color-primary);
+    font-weight: unset;
+}
diff --git a/src/components/eln/ElnCard.js b/src/components/eln/ElnCard.js
index e579eaeb..8599b12a 100644
--- a/src/components/eln/ElnCard.js
+++ b/src/components/eln/ElnCard.js
@@ -1,16 +1,22 @@
 import RepoButton from "@site/src/components/repos/RepoButton";
 
-import { LicenseChip, SubdiscChip } from "./ElnChips.js";
+import FilterButton from "./elnFilter/FilterButton.js";
 import ShortenDesc from "./ShortenDesc.js";
 
 import styles from "./Eln.module.css";
 
-function ElnCard({ eln }) {
+function ElnCard({ eln, filter, setFilter }) {
     return (
         <div className={styles.eln__card}>
             <div className={styles.eln__card__header}>
-                <h3>{eln.name}</h3>
-                <LicenseChip license={eln.license} />
+                <h4>{eln.name}</h4>
+                <FilterButton
+                    secondary={eln.license !== "Open Source"}
+                    active={filter.license === eln.license}
+                    type="license"
+                    label={eln.license}
+                    {...{ filter, setFilter }}
+                />
             </div>
             <RepoButton url={eln.url} name="Profile Page" />
             <div className={styles.eln__card__desc}>
@@ -18,9 +24,18 @@ function ElnCard({ eln }) {
             </div>
             <div className={styles.eln__card__desc}>
                 {eln.subDisc.length > 0
-                    ? eln.subDisc.map((subdisc, idx) => (
-                          <SubdiscChip subdisc={subdisc} key={idx} />
-                      ))
+                    ? eln.subDisc.map((subdisc, idx) => {
+                          let isActive = filter.subDisc === subdisc;
+                          return (
+                              <FilterButton
+                                  active={isActive}
+                                  type="subDisc"
+                                  label={subdisc}
+                                  key={idx}
+                                  {...{ filter, setFilter }}
+                              />
+                          );
+                      })
                     : null}
             </div>
         </div>
diff --git a/src/components/eln/ElnChips.js b/src/components/eln/ElnChips.js
deleted file mode 100644
index 7c611dd8..00000000
--- a/src/components/eln/ElnChips.js
+++ /dev/null
@@ -1,28 +0,0 @@
-import styles from "./Eln.module.css";
-import clsx from "clsx";
-
-function LicenseChip({ license }) {
-    let style = "lbe__filterbutton lbe__chip";
-
-    if (license === "Open Source") {
-        style = clsx(styles["eln__licenseChip--opensource"], style);
-    }
-
-    return <button className={style}>{license}</button>;
-}
-
-function SubdiscChip({ subdisc, active }) {
-    return (
-        <button
-            className={
-                active
-                    ? "lbe__filterbutton lbe__filterbutton--active"
-                    : "lbe__filterbutton"
-            }
-        >
-            {subdisc}
-        </button>
-    );
-}
-
-export { SubdiscChip, LicenseChip };
diff --git a/src/components/eln/ElnFinder.js b/src/components/eln/ElnFinder.js
index 2e0ecca5..ae8d8d17 100644
--- a/src/components/eln/ElnFinder.js
+++ b/src/components/eln/ElnFinder.js
@@ -159,7 +159,7 @@ function ElnFinder(props) {
                         resultOutput,
                     }}
                 />
-                <ElnStack {...{ filteredTable }} />
+                <ElnStack {...{ filteredTable, filter, setFilter }} />
             </div>
         </React.Fragment>
     );
diff --git a/src/components/eln/ElnStack.js b/src/components/eln/ElnStack.js
index 16706aad..42b59029 100644
--- a/src/components/eln/ElnStack.js
+++ b/src/components/eln/ElnStack.js
@@ -2,11 +2,11 @@ import React from "react";
 
 import ElnCard from "./ElnCard";
 
-function ElnStack({ filteredTable }) {
+function ElnStack({ filteredTable, filter, setFilter }) {
     return (
         <React.Fragment>
             {filteredTable.map((eln, idx) => (
-                <ElnCard {...{ eln }} key={idx} />
+                <ElnCard {...{ eln, filter, setFilter }} key={idx} />
             ))}
         </React.Fragment>
     );
diff --git a/src/components/eln/elnFilter/FilterButton.js b/src/components/eln/elnFilter/FilterButton.js
index f733bb54..ee278ba4 100644
--- a/src/components/eln/elnFilter/FilterButton.js
+++ b/src/components/eln/elnFilter/FilterButton.js
@@ -1,3 +1,7 @@
+import clsx from "clsx";
+
+import styles from "../Eln.module.css";
+
 function FilterButton(props) {
     const handleClick = () => {
         if (props.label === "All") {
@@ -11,10 +15,12 @@ function FilterButton(props) {
         }
     };
 
-    let buttonClass = "lbe__filterbutton";
-    if (props.active) {
-        buttonClass += " lbe__filterbutton--active";
-    }
+    // Conditional styling for button
+
+    let buttonClass = clsx("lbe__filterbutton", {
+        [styles["eln__filterbutton--secondary"]]: props.secondary,
+        "lbe__filterbutton--active": props.active,
+    });
 
     return (
         <button className={buttonClass} onClick={handleClick}>

From 506c390ca739812864a1c42b492eabf3722f0003 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Thu, 11 Jul 2024 18:15:16 +0200
Subject: [PATCH 42/89] feat: reset button for input field

---
 src/components/eln/Eln.module.css          | 11 +++++++++++
 src/components/eln/elnFilter/TextSearch.js | 12 ++++++++++++
 2 files changed, 23 insertions(+)

diff --git a/src/components/eln/Eln.module.css b/src/components/eln/Eln.module.css
index 3ecfac5c..24a2f225 100644
--- a/src/components/eln/Eln.module.css
+++ b/src/components/eln/Eln.module.css
@@ -42,6 +42,17 @@
     text-align: center;
 }
 
+.eln__searchfilter__search__button {
+    position: absolute;
+    right: 1.5rem;
+    top: 50%;
+    transform: translate(0, -50%);
+    padding: 0;
+    background: none;
+    border: none;
+    line-height: 1rem;
+}
+
 .eln__card {
     width: 49.5%;
     padding: 0.75rem;
diff --git a/src/components/eln/elnFilter/TextSearch.js b/src/components/eln/elnFilter/TextSearch.js
index ad1a9ab5..56ab857a 100644
--- a/src/components/eln/elnFilter/TextSearch.js
+++ b/src/components/eln/elnFilter/TextSearch.js
@@ -22,6 +22,18 @@ function TextSearch({ resultOutput, filter, setFilter }) {
                     value={filter.text ? filter.text : ""}
                     onChange={handleChange}
                 />
+                {filter.text ? (
+                    <button
+                        className={styles.eln__searchfilter__search__button}
+                        onClick={() =>
+                            setFilter((draft) => {
+                                delete draft.text;
+                            })
+                        }
+                    >
+                        &#x2715;
+                    </button>
+                ) : null}
                 &ensp;
             </span>
             <em>{resultOutput}</em>

From 213ea2f1b648ff59412da06f834f0270e64d2fc7 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Thu, 11 Jul 2024 18:32:03 +0200
Subject: [PATCH 43/89] refactor: shorten code

---
 src/components/eln/elnFilter/TextSearch.js | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/components/eln/elnFilter/TextSearch.js b/src/components/eln/elnFilter/TextSearch.js
index 56ab857a..1559ea0d 100644
--- a/src/components/eln/elnFilter/TextSearch.js
+++ b/src/components/eln/elnFilter/TextSearch.js
@@ -10,8 +10,6 @@ function TextSearch({ resultOutput, filter, setFilter }) {
             draft.text = e.target.value;
         });
 
-    console.log(filter);
-
     return (
         <div className={styles.eln__searchfilter__search}>
             <span className="navbar__search">
@@ -22,7 +20,7 @@ function TextSearch({ resultOutput, filter, setFilter }) {
                     value={filter.text ? filter.text : ""}
                     onChange={handleChange}
                 />
-                {filter.text ? (
+                {filter.text && (
                     <button
                         className={styles.eln__searchfilter__search__button}
                         onClick={() =>
@@ -33,7 +31,7 @@ function TextSearch({ resultOutput, filter, setFilter }) {
                     >
                         &#x2715;
                     </button>
-                ) : null}
+                )}
                 &ensp;
             </span>
             <em>{resultOutput}</em>

From baa1775b15c096b475795ba73f563d57ea1a1cb9 Mon Sep 17 00:00:00 2001
From: BenjaminGolub <107389350+BenjaminGolub@users.noreply.github.com>
Date: Tue, 16 Jul 2024 16:06:17 +0200
Subject: [PATCH 44/89] Update 50_pharmaceutical_chemistry.mdx

Added the new pharmacy part (text from January 2024)
---
 .../50_pharmaceutical_chemistry.mdx           | 47 +++++--------------
 1 file changed, 13 insertions(+), 34 deletions(-)

diff --git a/docs/10_domains/50_pharmaceutical_chemistry.mdx b/docs/10_domains/50_pharmaceutical_chemistry.mdx
index b10ab140..77082ccf 100644
--- a/docs/10_domains/50_pharmaceutical_chemistry.mdx
+++ b/docs/10_domains/50_pharmaceutical_chemistry.mdx
@@ -8,48 +8,27 @@ import {LbeChip} from '@site/src/components/lbe/LbeElements.js';
 
 <LbeChip title="medicinal chemistry" /><LbeChip title="epidemiology" />
 
+## Welche Art von Daten?
 
-:::info Summary:
+Die häufigsten Arten von Daten in der pharmazeutischen/medizinischen Chemie lassen sich in drei Kategeorien einteilen: Synthese-Daten, analytische Daten und (Bio)Assay-Daten. Während die ersten beiden Typen von Daten (Synthese- und analytische Daten) in breiten Bereichen der Chemie eine Rolle spielen, sind (Bio)Assay-Daten, um etwa die biologische Aktivität einer Substanz zu untersuchen, eine Besonderheit der pharmazeutischen/medizinischen Chemie. 
 
-Medicinal chemistry is a chemistry-based, strongly interdisciplinary discipline. It deals with the discovery, development, identification, and synthesis of biologically active compounds, the interpretation of their mechanism of action at the molecular level, and the metabolism of the active compounds.
-The interactions of active compounds with their biological target(s) are analysed in silico (chemoinformatics), in vitro, and in vivo to determine selectivity and potential in terms of their therapeutic efficacy and safety.
-Medicinal chemists prepare and/or select suitable compounds for biological evaluation that, if found to be active, could serve as lead compounds. Chemical modifications to optimise these leads ideally result in promising candidates for preclinical studies in drug development, potentially followed by clinical studies.
+## Welche ELNs/Tools bieten sich an?
 
-:::
+Zur Planung des Forschungsdatenmanagements und der Erstellung von Datenmanagementplänen eignen sich Tools wie RDMO und DMP-Online. Viele Universitäten verfügen über eigene Instanzen von einer dieser Lösungen. 
 
-## Type of experiments
+Um die Ansprüche an ein FAIRes Datenmanagement umzusetzen, eignen sich im Besonderen elektronische Laborbücher, da diese den Forschenden viele Aufgaben der Dokumentation abnehmen können.  In der Community werden zum Beispiel die folgenden ELNs verwendet:
+Chemotion ELN, Sicformation, eLabFTW, eLabJournal, labfolder, Benchling. Der [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) hat noch weitere Optionen. Wie das richtige ELN für die Arbeitsgruppe ausgesucht werden kann, kann hier nachgelesen werden (Link zum Knowledge Base Artikel). 
 
-- Synthesis:
-  - Preparation of compounds including combinatorial approaches for biological evaluation in suitable test systems
-- Analysis:
-  - Characterisation of intermediate and final products
-  - Analysis of (quantitative) structure-activity relationships, molecular modelling studies
-  - Biological evaluation, activity assays
+## Wie und wo können Daten publiziert werden?
 
-## Planning of experiments
+Das Publizieren von Forschungsdaten ist wichtig, um anderen Forschenden die Möglichkeit zu geben, diese nachzunutzen. Um möglichst viele Forschende zu erreichen, kann die Auswahl des richtigen Repositoriums entscheidend sein (mehr dazu im Artikel zur Auswahl des richtigen Repositoriums). 
 
-Test systems are established, either target-oriented or phenotypic assays, to identify hit compounds. Alternatively, (potential) hit compounds can be selected from available data (e.g. publications) or by virtual screening.
-Starting from promising hit compounds, optimisation cycles are performed to improve the properties of the starting compounds. Suitable assay systems are required to obtain the necessary data to assess the compounds’ properties. These include potency efficacy, selectivity, potential bias, water solubility, lipophilicity, pharmacokinetic properties, e.g. bioavailability and metabolic stability, interaction with liver cytochrome P450 enzymes, hERG channel interaction, cell toxicity, potential genotoxicity, etc. The required properties depend e.g. on the indication and the application route of the drug.
+Für Synthese-Daten sowie analytische Daten empfehlen sich spezifische Repositorien wie z. B. Chemotion Repositorium (Synthese-Daten), MassBankEU (Massenspektren) oder nmrXiv (für NMR-Daten). Für die dritte Kategorie an Daten ((Bio)Assay-Daten) ist zurzeit kein optimales Repositorium bekannt, daher empfiehlt sich hier das generische Repositorium RADAR4Chem.
 
-## Documentation of experiments
+## Herausforderungen
 
-[Documentation](/docs/data_documentation) of research data and [metadata](/docs/metadata) is carried out, preferably digitally, using a suitable [ELN](/docs/eln) and/or a manual laboratory notebook in paper form.
+Im Vergleich zu vielen anderen Bereichen der Chemie, findet in der pharmazeutischen/medizinischen Chemie häufig eine sehr anwendungsbezogene Forschung statt, welche zu Patenten und Produktentwicklungen führen können. Daher sind besonders an die verwendeten elektronischen Laborbücher höhere Ansprüche im Bereich von Prüfprotokollen (audit trials) gestellt. Dies muss bei der Auswahl der verwendeten Tools von Anfang an berücksichtigt werden. Ebenso kann dies zu besonderen Auflagen bei der Veröffentlichung von Forschungsdaten führen.
 
-Using an ELN:
+Die Diversität der verwendeten Datenformate sowie der Analyseverfahren stellen zusätzlich eine Herausforderung für ein gutes FDM dar. Besonders wenn Labor/Analysegeräte verwendet werden, welche aufgrund ihrer Software nicht mehr oder nur über Umwege in ein Netzwerk integriert werden können. 
 
-- Experimental conditions and measurement parameters are noted in the ELN.
-- Observations, deviations from planned measurement protocols, or other peculiarities during measurement with no digital output (i.e. no data files) are added manually to the ELN experiment entry.
-- Obtained data from analytical instruments (e.g. NMR, MS, or IR data) are uploaded to the ELN in open file formats and directly attached to the respective experiment entry, including instrumental setup metadata.
-- Metadata related to the obtained data follow common metadata standards.
-
-## Data producing methods
-
-- Data can be collected during or after the experiment by analysing the obtained product.
-- Manually determined data: Experimental observations, appearance, yield, melting/boiling point, optical rotation, TLC Rf values, refraction index, etc.
-- Digital data are obtained with analytical devices. An overview on file extensions, file sizes and converters for several analytical methods is given in the table below.
-- Raw data files in proprietary file formats should be saved alongside interoperable [open file formats](/docs/format_standards) by using converters or the analytical device software. If no specific open format is currently available, an export as .txt or .csv is recommended. Please be aware that metadata included in the header of .txt or .csv files may not follow a defined (open) format and metadata should be additionally also added into the ELN.
-
-<Methods defaultProfile={"pharma"} />
-
-:::note *This table will be continuously updated with new recommendations on interoperable open file formats.
-:::
\ No newline at end of file
+Bei diesen Herausforderungen unterstützt NFDI4Chem gern, und Sie können uns jederzeit über den Helpdesk kontaktieren. 

From be39c097b09526dbe56992db9de54fc0c2504b8f Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Tue, 16 Jul 2024 18:13:57 +0200
Subject: [PATCH 45/89] chore: added link to Git

---
 docs/10_domains/20_physical_chemistry.mdx | 14 ++------------
 1 file changed, 2 insertions(+), 12 deletions(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index 8341ebaf..133f093b 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -21,17 +21,7 @@ From spectroscopic measurement data, imaging, to simulation input files and in-h
 
 ## What Type of Data?
 
-As mentioned, the data produced in physical chemistry and its diverse sub-disciples are varied. One research group may work intensively with imaging data such as superresolution microscopy, while the other may work on method development, and again others may analyze spectroscopic data or conduct numeric simulations—or even any combination of these. The [table](#methods-data-format-overview) below provides an overview of typical methods employed along with their data types and recommended open formats.
-
-<!-- should the above be more specific? --->
-
-### Methods Data Format Overview
-
-<!--are we still doing this table at all?-->
-
-<Methods defaultProfile={"physical"} />
-
-:::note \*This table will be continuously updated with new recommendations on interoperable open file formats.:::
+As mentioned, the data produced in physical chemistry and its diverse sub-disciples are varied. One research group may work intensively with imaging data such as superresolution microscopy, while the other may work on method development, and again others may analyze spectroscopic data or conduct numeric simulations—or even any combination of these.
 
 ## What ELNs/Tools?
 
@@ -41,7 +31,7 @@ An [electronic lab notebooks (ELNs)](docs/eln) helps in the day-to-day planning
 
 In addition to ELNs, tools such as local repository and research dat management tools can assist in making data publication ready.
 
-For those writing scripts and developing research software solutions, git is a highly recommended versioning tool. May universities also have their own instances of [GitLab](https://about.gitlab.com/) to assist in managing software projects.
+For those writing scripts and developing research software solutions, [Git](https://git-scm.com/) is a highly recommended versioning tool. May universities also have their own instances of [GitLab](https://about.gitlab.com/) to assist in managing software projects.
 
 Specifically for research data, [DataLad](https://www.datalad.org/), which is built on top of git, can greatly assist in tracking the metadata while processing and analyzing data. While it works for steps carried out with GUI applications, its true power comes in handy for those using script-based analysis and processing steps.
 

From e225cb9a0dc6075b440c86b55daef6ecb30e2f48 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Tue, 16 Jul 2024 18:16:30 +0200
Subject: [PATCH 46/89] chore: add ELN-finder

---
 docs/10_domains/20_physical_chemistry.mdx | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index 133f093b..d3e80eb8 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -27,7 +27,9 @@ As mentioned, the data produced in physical chemistry and its diverse sub-discip
 
 For effective data management, software tools should be selected in a uniform manner within a project or research group with the aim to [organize](docs/data_organisation) and streamline workflows. This involves establishing clear usage guidelines, including metadata templates drawn from minimum information standards for a given method, where available. These should be outlined in a [data management plan (DMP)](docs/dmp) for each project. Many universities supply tools and templates for DMPs (see the [respective article](doc/dmp) for more information).
 
-An [electronic lab notebooks (ELNs)](docs/eln) helps in the day-to-day planning and structured documentation of experiments, while some also assist in data workflow management. For disciplines with diverse research, ELNs must be flexible and customizable. Certain universities may have a central option, while each research group may chose what best fits their needs and resources if they are able to host or procure their own solution. The [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) lists many options and the article on [choosing an ELN](docs/chose_eln) provides further assistance.
+An [electronic lab notebooks (ELNs)](docs/eln) helps in the day-to-day planning and structured documentation of experiments, while some also assist in data workflow management. For disciplines with diverse research, ELNs must be flexible and customizable. Certain universities may have a central option, while each research group may chose what best fits their needs and resources if they are able to host or procure their own solution. The [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) lists many options and the article on [choosing an ELN](docs/chose_eln) provides further assistance:
+
+<ElnFinder subDisc="Physical chemistry" />
 
 In addition to ELNs, tools such as local repository and research dat management tools can assist in making data publication ready.
 

From d4be167366499c8ab09939d87ed4ede97f08abf9 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Tue, 16 Jul 2024 18:27:40 +0200
Subject: [PATCH 47/89] fix: eln-finder import

---
 docs/10_domains/20_physical_chemistry.mdx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index d3e80eb8..fe018316 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -3,8 +3,8 @@ title: "Physical and Computational Chemistry"
 slug: "/physical_chemistry"
 ---
 
-import Methods from "@site/src/components/Methods.js";
 import { LbeChip } from "@site/src/components/lbe/LbeElements.js";
+import ElnFinder from "@site/src/components/eln/ElnFinder.js";
 
 <LbeChip title="physical chemistry" />
 <LbeChip title="cheminformatics" />

From b7a0cac070766b71d3f6abab41271644708c146b Mon Sep 17 00:00:00 2001
From: BenjaminGolub <107389350+BenjaminGolub@users.noreply.github.com>
Date: Wed, 17 Jul 2024 07:32:25 +0200
Subject: [PATCH 48/89] Update 50_pharmaceutical_chemistry.mdx

Changed the language to English and used the right headlings
---
 .../50_pharmaceutical_chemistry.mdx           | 28 ++++++++++---------
 1 file changed, 15 insertions(+), 13 deletions(-)

diff --git a/docs/10_domains/50_pharmaceutical_chemistry.mdx b/docs/10_domains/50_pharmaceutical_chemistry.mdx
index 77082ccf..2369ac40 100644
--- a/docs/10_domains/50_pharmaceutical_chemistry.mdx
+++ b/docs/10_domains/50_pharmaceutical_chemistry.mdx
@@ -8,27 +8,29 @@ import {LbeChip} from '@site/src/components/lbe/LbeElements.js';
 
 <LbeChip title="medicinal chemistry" /><LbeChip title="epidemiology" />
 
-## Welche Art von Daten?
+## Introduction
 
-Die häufigsten Arten von Daten in der pharmazeutischen/medizinischen Chemie lassen sich in drei Kategeorien einteilen: Synthese-Daten, analytische Daten und (Bio)Assay-Daten. Während die ersten beiden Typen von Daten (Synthese- und analytische Daten) in breiten Bereichen der Chemie eine Rolle spielen, sind (Bio)Assay-Daten, um etwa die biologische Aktivität einer Substanz zu untersuchen, eine Besonderheit der pharmazeutischen/medizinischen Chemie. 
+Medicinal chemistry is a chemistry-based, strongly interdisciplinary discipline. It deals with the discovery, development, identification, and synthesis of biologically active compounds, the interpretation of their mechanism of action at the molecular level, and the metabolism of the active compounds. The interactions of active compounds with their biological target(s) are analysed in silico (chemoinformatics), in vitro, and in vivo to determine selectivity and potential in terms of their therapeutic efficacy and safety. Medicinal chemists prepare and/or select suitable compounds for biological evaluation that, if found to be active, could serve as lead compounds. Chemical modifications to optimise these leads ideally result in promising candidates for preclinical studies in drug development, potentially followed by clinical studies.
 
-## Welche ELNs/Tools bieten sich an?
 
-Zur Planung des Forschungsdatenmanagements und der Erstellung von Datenmanagementplänen eignen sich Tools wie RDMO und DMP-Online. Viele Universitäten verfügen über eigene Instanzen von einer dieser Lösungen. 
+## Data Types?
 
-Um die Ansprüche an ein FAIRes Datenmanagement umzusetzen, eignen sich im Besonderen elektronische Laborbücher, da diese den Forschenden viele Aufgaben der Dokumentation abnehmen können.  In der Community werden zum Beispiel die folgenden ELNs verwendet:
-Chemotion ELN, Sicformation, eLabFTW, eLabJournal, labfolder, Benchling. Der [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) hat noch weitere Optionen. Wie das richtige ELN für die Arbeitsgruppe ausgesucht werden kann, kann hier nachgelesen werden (Link zum Knowledge Base Artikel). 
+The most common types of data in pharmaceutical/medicinal chemistry can be divided into three categories: synthesis data, analytical data, and (bio)assay data. While the first two types of data (synthesis and analytical data) play a role in broad areas of chemistry, (bio)assay data, which is used to investigate the biological activity of a substance, is a particular feature of pharmaceutical/medicinal chemistry. 
 
-## Wie und wo können Daten publiziert werden?
+## ELNs and Other Tools?
 
-Das Publizieren von Forschungsdaten ist wichtig, um anderen Forschenden die Möglichkeit zu geben, diese nachzunutzen. Um möglichst viele Forschende zu erreichen, kann die Auswahl des richtigen Repositoriums entscheidend sein (mehr dazu im Artikel zur Auswahl des richtigen Repositoriums). 
+To meet the requirements for FAIR data management, electronic lab notebooks (ELNs) are particularly useful as they can take over many documentation tasks for researchers. The following ELNs are used in the community, for example: Chemotion ELN, Sicformation, eLabFTW, eLabJournal, labfolder, Benchling. The [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) offers additional options. How to choose the right ELN for the research group can be read [here](https://knowledgebase.nfdi4chem.de/knowledge_base/docs/choose_eln/). 
 
-Für Synthese-Daten sowie analytische Daten empfehlen sich spezifische Repositorien wie z. B. Chemotion Repositorium (Synthese-Daten), MassBankEU (Massenspektren) oder nmrXiv (für NMR-Daten). Für die dritte Kategorie an Daten ((Bio)Assay-Daten) ist zurzeit kein optimales Repositorium bekannt, daher empfiehlt sich hier das generische Repositorium RADAR4Chem.
+## Publishing Data
 
-## Herausforderungen
+Publishing research data is important to allow other researchers to reuse it. To reach as many researchers as possible, choosing the right repository can be crucial (check the [Choose a Repository](https://knowledgebase.nfdi4chem.de/knowledge_base/docs/choose_repository/) article for more information).
 
-Im Vergleich zu vielen anderen Bereichen der Chemie, findet in der pharmazeutischen/medizinischen Chemie häufig eine sehr anwendungsbezogene Forschung statt, welche zu Patenten und Produktentwicklungen führen können. Daher sind besonders an die verwendeten elektronischen Laborbücher höhere Ansprüche im Bereich von Prüfprotokollen (audit trials) gestellt. Dies muss bei der Auswahl der verwendeten Tools von Anfang an berücksichtigt werden. Ebenso kann dies zu besonderen Auflagen bei der Veröffentlichung von Forschungsdaten führen.
+For synthesis data and analytical data, specific repositories such as [Chemotion Repository](https://www.chemotion-repository.net/welcome) (synthesis data), [MassBankEU](https://massbank.eu/MassBank/) (mass spectra), or [nmrXiv](https://nmrxiv.org/) (for NMR data) are recommended. For the third category of data ((bio)assay data), no optimal repository is currently known, so the generic repository [RADAR4Chem](https://radar.products.fiz-karlsruhe.de/de/radarabout/radar4chem) is recommended.
 
-Die Diversität der verwendeten Datenformate sowie der Analyseverfahren stellen zusätzlich eine Herausforderung für ein gutes FDM dar. Besonders wenn Labor/Analysegeräte verwendet werden, welche aufgrund ihrer Software nicht mehr oder nur über Umwege in ein Netzwerk integriert werden können. 
+## Challenges
 
-Bei diesen Herausforderungen unterstützt NFDI4Chem gern, und Sie können uns jederzeit über den Helpdesk kontaktieren. 
+Compared to many other areas of chemistry, pharmaceutical/medicinal chemistry often involves highly application-oriented research that can lead to patents and product developments. Therefore, the electronic lab notebooks used must meet higher standards in the area of audit trails. This must be considered from the outset when selecting the tools to be used. Additionally, this can lead to special requirements for publishing research data.
+
+The diversity of data formats and analytical methods used also poses a challenge for good research data management (RDM). This is particularly true when laboratory/analytical instruments are used that can no longer be integrated into a network or can only be integrated via detours due to their software.
+
+NFDI4Chem is happy to assist with these challenges, and you can contact us anytime through the Helpdesk.

From e74002eb0b1de91a364eff3c9ae73c9f2d52f361 Mon Sep 17 00:00:00 2001
From: BenjaminGolub <107389350+BenjaminGolub@users.noreply.github.com>
Date: Wed, 17 Jul 2024 07:34:17 +0200
Subject: [PATCH 49/89] Update 50_pharmaceutical_chemistry.mdx

Removed question marks from the headings
---
 docs/10_domains/50_pharmaceutical_chemistry.mdx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/10_domains/50_pharmaceutical_chemistry.mdx b/docs/10_domains/50_pharmaceutical_chemistry.mdx
index 2369ac40..64c5f774 100644
--- a/docs/10_domains/50_pharmaceutical_chemistry.mdx
+++ b/docs/10_domains/50_pharmaceutical_chemistry.mdx
@@ -13,11 +13,11 @@ import {LbeChip} from '@site/src/components/lbe/LbeElements.js';
 Medicinal chemistry is a chemistry-based, strongly interdisciplinary discipline. It deals with the discovery, development, identification, and synthesis of biologically active compounds, the interpretation of their mechanism of action at the molecular level, and the metabolism of the active compounds. The interactions of active compounds with their biological target(s) are analysed in silico (chemoinformatics), in vitro, and in vivo to determine selectivity and potential in terms of their therapeutic efficacy and safety. Medicinal chemists prepare and/or select suitable compounds for biological evaluation that, if found to be active, could serve as lead compounds. Chemical modifications to optimise these leads ideally result in promising candidates for preclinical studies in drug development, potentially followed by clinical studies.
 
 
-## Data Types?
+## Data Types
 
 The most common types of data in pharmaceutical/medicinal chemistry can be divided into three categories: synthesis data, analytical data, and (bio)assay data. While the first two types of data (synthesis and analytical data) play a role in broad areas of chemistry, (bio)assay data, which is used to investigate the biological activity of a substance, is a particular feature of pharmaceutical/medicinal chemistry. 
 
-## ELNs and Other Tools?
+## ELNs and Other Tools
 
 To meet the requirements for FAIR data management, electronic lab notebooks (ELNs) are particularly useful as they can take over many documentation tasks for researchers. The following ELNs are used in the community, for example: Chemotion ELN, Sicformation, eLabFTW, eLabJournal, labfolder, Benchling. The [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) offers additional options. How to choose the right ELN for the research group can be read [here](https://knowledgebase.nfdi4chem.de/knowledge_base/docs/choose_eln/). 
 

From a611ad300fe14854a04205564930aea4671ed31e Mon Sep 17 00:00:00 2001
From: BenjaminGolub <107389350+BenjaminGolub@users.noreply.github.com>
Date: Wed, 17 Jul 2024 07:36:20 +0200
Subject: [PATCH 50/89] Update 50_pharmaceutical_chemistry.mdx

added a part about data management tools
---
 docs/10_domains/50_pharmaceutical_chemistry.mdx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/10_domains/50_pharmaceutical_chemistry.mdx b/docs/10_domains/50_pharmaceutical_chemistry.mdx
index 64c5f774..679bddd5 100644
--- a/docs/10_domains/50_pharmaceutical_chemistry.mdx
+++ b/docs/10_domains/50_pharmaceutical_chemistry.mdx
@@ -21,6 +21,8 @@ The most common types of data in pharmaceutical/medicinal chemistry can be divid
 
 To meet the requirements for FAIR data management, electronic lab notebooks (ELNs) are particularly useful as they can take over many documentation tasks for researchers. The following ELNs are used in the community, for example: Chemotion ELN, Sicformation, eLabFTW, eLabJournal, labfolder, Benchling. The [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) offers additional options. How to choose the right ELN for the research group can be read [here](https://knowledgebase.nfdi4chem.de/knowledge_base/docs/choose_eln/). 
 
+For the planning of research data management and the creation of data management plans, tools such as RDMO and DMP-Online are suitable. Many universities have their own instances of one of these solutions.
+
 ## Publishing Data
 
 Publishing research data is important to allow other researchers to reuse it. To reach as many researchers as possible, choosing the right repository can be crucial (check the [Choose a Repository](https://knowledgebase.nfdi4chem.de/knowledge_base/docs/choose_repository/) article for more information).

From 31d6f4519059bd51a1979cca456d3ed56d01086d Mon Sep 17 00:00:00 2001
From: Ted-Bender <122031815+Ted-Bender@users.noreply.github.com>
Date: Wed, 17 Jul 2024 09:44:06 +0200
Subject: [PATCH 51/89] Update 50_pharmaceutical_chemistry.mdx

I edited Benjamins Text in here
---
 .../50_pharmaceutical_chemistry.mdx           | 46 ++++++-------------
 1 file changed, 15 insertions(+), 31 deletions(-)

diff --git a/docs/10_domains/50_pharmaceutical_chemistry.mdx b/docs/10_domains/50_pharmaceutical_chemistry.mdx
index b10ab140..64fceff2 100644
--- a/docs/10_domains/50_pharmaceutical_chemistry.mdx
+++ b/docs/10_domains/50_pharmaceutical_chemistry.mdx
@@ -9,47 +9,31 @@ import {LbeChip} from '@site/src/components/lbe/LbeElements.js';
 <LbeChip title="medicinal chemistry" /><LbeChip title="epidemiology" />
 
 
-:::info Summary:
+## Introduction
+Medicinal chemistry is a chemistry-based, strongly interdisciplinary discipline. It deals with the discovery, development, identification, and synthesis of biologically active compounds, the interpretation of their mechanism of action at the molecular level, and the metabolism of the active compounds. The interactions of active compounds with their biological target(s) are analysed in silico (chemoinformatics), in vitro, and in vivo to determine selectivity and potential in terms of their therapeutic efficacy and safety. Medicinal chemists prepare and/or select suitable compounds for biological evaluation that, if found to be active, could serve as lead compounds. Chemical modifications to optimise these leads ideally result in promising candidates for preclinical studies in drug development, potentially followed by clinical studies.
 
-Medicinal chemistry is a chemistry-based, strongly interdisciplinary discipline. It deals with the discovery, development, identification, and synthesis of biologically active compounds, the interpretation of their mechanism of action at the molecular level, and the metabolism of the active compounds.
-The interactions of active compounds with their biological target(s) are analysed in silico (chemoinformatics), in vitro, and in vivo to determine selectivity and potential in terms of their therapeutic efficacy and safety.
-Medicinal chemists prepare and/or select suitable compounds for biological evaluation that, if found to be active, could serve as lead compounds. Chemical modifications to optimise these leads ideally result in promising candidates for preclinical studies in drug development, potentially followed by clinical studies.
 
-:::
+## Data Types
+The most common types of data in pharmaceutical/medical chemistry can be divided into three categories: Synthesis data, analytical data and (bio)assay data. While the first two types of data (synthesis and analytical data) play a role in broad areas of chemistry, (bio)assay data, for example to investigate the biological activity of a substance, are a specialty of pharmaceutical/medical chemistry.
 
-## Type of experiments
 
-- Synthesis:
-  - Preparation of compounds including combinatorial approaches for biological evaluation in suitable test systems
-- Analysis:
-  - Characterisation of intermediate and final products
-  - Analysis of (quantitative) structure-activity relationships, molecular modelling studies
-  - Biological evaluation, activity assays
+## ELNs and Other Tools
+Tools such as RDMO and DMP-Online are suitable for planning research data management and creating data management plans. Many universities have their own instances of one of these solutions. 
 
-## Planning of experiments
+Electronic lab notebooks are particularly suitable for implementing the requirements of FAIR data management, as they can relieve researchers of many documentation tasks.For example, the following ELNs are used in the community:
+Chemotion ELN, Sicformation, eLabFTW, eLabJournal, labfolder, Benchling. The ELN finder has even more options (https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1). How to select the right ELN for the workgroup can be read here (link to the Knowledge Base article).
 
-Test systems are established, either target-oriented or phenotypic assays, to identify hit compounds. Alternatively, (potential) hit compounds can be selected from available data (e.g. publications) or by virtual screening.
-Starting from promising hit compounds, optimisation cycles are performed to improve the properties of the starting compounds. Suitable assay systems are required to obtain the necessary data to assess the compounds’ properties. These include potency efficacy, selectivity, potential bias, water solubility, lipophilicity, pharmacokinetic properties, e.g. bioavailability and metabolic stability, interaction with liver cytochrome P450 enzymes, hERG channel interaction, cell toxicity, potential genotoxicity, etc. The required properties depend e.g. on the indication and the application route of the drug.
 
-## Documentation of experiments
+## Publishing Data
+Publishing research data is important in order to give other researchers the opportunity to reuse it. In order to reach as many researchers as possible, choosing the right repository can be crucial (more on this in the article on choosing the right repository).
 
-[Documentation](/docs/data_documentation) of research data and [metadata](/docs/metadata) is carried out, preferably digitally, using a suitable [ELN](/docs/eln) and/or a manual laboratory notebook in paper form.
+For synthesis data and analytical data, specific repositories such as [Chemotion Repository](https://www.chemotion-repository.net/welcome) (synthesis data), [MassBank EU](https://massbank.eu/) (mass spectra) or [nmrXiv](https://nmrxiv.org/) (for NMR data) are recommended. For the third category of data ((bio)assay data) no optimal repository is currently known, therefore the generic repository [RADAR4Chem](https://radar.products.fiz-karlsruhe.de/de/radarabout/radar4chem) is recommended.
 
-Using an ELN:
 
-- Experimental conditions and measurement parameters are noted in the ELN.
-- Observations, deviations from planned measurement protocols, or other peculiarities during measurement with no digital output (i.e. no data files) are added manually to the ELN experiment entry.
-- Obtained data from analytical instruments (e.g. NMR, MS, or IR data) are uploaded to the ELN in open file formats and directly attached to the respective experiment entry, including instrumental setup metadata.
-- Metadata related to the obtained data follow common metadata standards.
+## Challenges
+Compared to many other areas of chemistry, pharmaceutical/medical chemistry often involves very application-oriented research, which can lead to patents and product developments. For this reason, the electronic laboratory notebooks used are subject to particularly high demands in the area of audit trials. This must be taken into account from the outset when selecting the tools used. This can also lead to special requirements when publishing research data.
 
-## Data producing methods
+The diversity of the data formats used and the analysis methods also pose a challenge for good RDM. Especially when laboratory/analysis devices are used that can no longer be integrated into a network due to their software, or only via detours.
 
-- Data can be collected during or after the experiment by analysing the obtained product.
-- Manually determined data: Experimental observations, appearance, yield, melting/boiling point, optical rotation, TLC Rf values, refraction index, etc.
-- Digital data are obtained with analytical devices. An overview on file extensions, file sizes and converters for several analytical methods is given in the table below.
-- Raw data files in proprietary file formats should be saved alongside interoperable [open file formats](/docs/format_standards) by using converters or the analytical device software. If no specific open format is currently available, an export as .txt or .csv is recommended. Please be aware that metadata included in the header of .txt or .csv files may not follow a defined (open) format and metadata should be additionally also added into the ELN.
 
-<Methods defaultProfile={"pharma"} />
-
-:::note *This table will be continuously updated with new recommendations on interoperable open file formats.
-:::
\ No newline at end of file
+NFDI4Chem is happy to help with these challenges and you can contact us at any time via the helpdesk.

From d3ebaf8248319bfc5143b7cd497ca17ed0df7535 Mon Sep 17 00:00:00 2001
From: Ted-Bender <122031815+Ted-Bender@users.noreply.github.com>
Date: Wed, 17 Jul 2024 09:53:30 +0200
Subject: [PATCH 52/89] Update 50_pharmaceutical_chemistry.mdx

2 Link corrections
---
 docs/10_domains/50_pharmaceutical_chemistry.mdx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/10_domains/50_pharmaceutical_chemistry.mdx b/docs/10_domains/50_pharmaceutical_chemistry.mdx
index 64fceff2..c528b935 100644
--- a/docs/10_domains/50_pharmaceutical_chemistry.mdx
+++ b/docs/10_domains/50_pharmaceutical_chemistry.mdx
@@ -21,11 +21,11 @@ The most common types of data in pharmaceutical/medical chemistry can be divided
 Tools such as RDMO and DMP-Online are suitable for planning research data management and creating data management plans. Many universities have their own instances of one of these solutions. 
 
 Electronic lab notebooks are particularly suitable for implementing the requirements of FAIR data management, as they can relieve researchers of many documentation tasks.For example, the following ELNs are used in the community:
-Chemotion ELN, Sicformation, eLabFTW, eLabJournal, labfolder, Benchling. The ELN finder has even more options (https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1). How to select the right ELN for the workgroup can be read here (link to the Knowledge Base article).
+Chemotion ELN, Sicformation, eLabFTW, eLabJournal, labfolder, Benchling. The [ELN finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) has even more options. How to select the right ELN for the workgroup can be [read here](/docs/choose_eln).
 
 
 ## Publishing Data
-Publishing research data is important in order to give other researchers the opportunity to reuse it. In order to reach as many researchers as possible, choosing the right repository can be crucial (more on this in the article on choosing the right repository).
+Publishing research data is important in order to give other researchers the opportunity to reuse it. In order to reach as many researchers as possible, choosing the right repository can be crucial (more on this in the article on [choosing the right repository](/docs/choose_repository).
 
 For synthesis data and analytical data, specific repositories such as [Chemotion Repository](https://www.chemotion-repository.net/welcome) (synthesis data), [MassBank EU](https://massbank.eu/) (mass spectra) or [nmrXiv](https://nmrxiv.org/) (for NMR data) are recommended. For the third category of data ((bio)assay data) no optimal repository is currently known, therefore the generic repository [RADAR4Chem](https://radar.products.fiz-karlsruhe.de/de/radarabout/radar4chem) is recommended.
 

From 6689dced7db38d78a0e4f1b568c555f68b1fa4e1 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Tue, 20 Aug 2024 18:36:42 +0200
Subject: [PATCH 53/89] feat: ShortenDesc component

---
 src/components/commons/ShortenDesc.js | 43 +++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 src/components/commons/ShortenDesc.js

diff --git a/src/components/commons/ShortenDesc.js b/src/components/commons/ShortenDesc.js
new file mode 100644
index 00000000..1d0ac69f
--- /dev/null
+++ b/src/components/commons/ShortenDesc.js
@@ -0,0 +1,43 @@
+import React, { useState } from "react";
+
+// shorten the description of the experiment up to the next blank, comma or period after 100 characters
+
+function ShortenDesc({ desc, length }) {
+    const [collapsed, setCollapsed] = useState(true);
+
+    if (desc.length <= length) {
+        return <React.Fragment>{desc}</React.Fragment>;
+    }
+
+    return (
+        <React.Fragment>
+            {collapsed ? (
+                <span
+                    title={desc}
+                    onClick={() => setCollapsed(!collapsed)}
+                    style={{ cursor: "pointer" }}
+                >
+                    {desc.slice(0, length) +
+                        desc.slice(length).split(/[\s,\.]/)[0] +
+                        " ..."}
+
+                    <button className="lbe__block__author-trigger">
+                        expand &#9660;
+                    </button>
+                </span>
+            ) : (
+                <span
+                    onClick={() => setCollapsed(!collapsed)}
+                    style={{ cursor: "pointer" }}
+                >
+                    {desc}
+                    <button className="lbe__block__author-trigger">
+                        collapse &#9650;
+                    </button>
+                </span>
+            )}
+        </React.Fragment>
+    );
+}
+
+export default ShortenDesc;

From 0f053287c0b6f922b88bac74aab187cb78bfba94 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Tue, 20 Aug 2024 19:17:29 +0200
Subject: [PATCH 54/89] chore: consolidate ShortenDesc component

---
 src/components/eln/ElnCard.js     |  2 +-
 src/components/eln/ShortenDesc.js | 43 -------------------------------
 2 files changed, 1 insertion(+), 44 deletions(-)
 delete mode 100644 src/components/eln/ShortenDesc.js

diff --git a/src/components/eln/ElnCard.js b/src/components/eln/ElnCard.js
index 8599b12a..f45a45a4 100644
--- a/src/components/eln/ElnCard.js
+++ b/src/components/eln/ElnCard.js
@@ -1,7 +1,7 @@
 import RepoButton from "@site/src/components/repos/RepoButton";
 
 import FilterButton from "./elnFilter/FilterButton.js";
-import ShortenDesc from "./ShortenDesc.js";
+import ShortenDesc from "../commons/ShortenDesc.js";
 
 import styles from "./Eln.module.css";
 
diff --git a/src/components/eln/ShortenDesc.js b/src/components/eln/ShortenDesc.js
deleted file mode 100644
index 1d0ac69f..00000000
--- a/src/components/eln/ShortenDesc.js
+++ /dev/null
@@ -1,43 +0,0 @@
-import React, { useState } from "react";
-
-// shorten the description of the experiment up to the next blank, comma or period after 100 characters
-
-function ShortenDesc({ desc, length }) {
-    const [collapsed, setCollapsed] = useState(true);
-
-    if (desc.length <= length) {
-        return <React.Fragment>{desc}</React.Fragment>;
-    }
-
-    return (
-        <React.Fragment>
-            {collapsed ? (
-                <span
-                    title={desc}
-                    onClick={() => setCollapsed(!collapsed)}
-                    style={{ cursor: "pointer" }}
-                >
-                    {desc.slice(0, length) +
-                        desc.slice(length).split(/[\s,\.]/)[0] +
-                        " ..."}
-
-                    <button className="lbe__block__author-trigger">
-                        expand &#9660;
-                    </button>
-                </span>
-            ) : (
-                <span
-                    onClick={() => setCollapsed(!collapsed)}
-                    style={{ cursor: "pointer" }}
-                >
-                    {desc}
-                    <button className="lbe__block__author-trigger">
-                        collapse &#9650;
-                    </button>
-                </span>
-            )}
-        </React.Fragment>
-    );
-}
-
-export default ShortenDesc;

From e5e374691a822d016219197fde663fe138b101df Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Tue, 20 Aug 2024 19:18:07 +0200
Subject: [PATCH 55/89] fix: correct elnFinder subdisc

---
 docs/10_domains/10_analytical_chemistry.mdx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/10_domains/10_analytical_chemistry.mdx b/docs/10_domains/10_analytical_chemistry.mdx
index 20293277..3726256b 100644
--- a/docs/10_domains/10_analytical_chemistry.mdx
+++ b/docs/10_domains/10_analytical_chemistry.mdx
@@ -28,7 +28,7 @@ Some open data formats are available for specific data types, such as mass spect
 
 General chemistry ELNs can typically be used for analytical chemistry data and may be well suited to your research topic. However, there are also specialised tools that are tailored to the needs of analytical chemists. These tools often include features for managing instrument data, processing raw data files and visualising results. They may also include tools for chemometric analysis.
 
-<ElnFinder subDisc="Physical chemistry" />
+<ElnFinder subDisc="Analytical chemistry" />
 
 ## Publishing Data
 

From 84e4e11b73016834131b0381e3a65a1d185da4f2 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Sun, 8 Sep 2024 13:32:50 +0200
Subject: [PATCH 56/89] feat: pharmacy eln component

---
 src/components/eln/ElnFinderPharm.js | 151 +++++++++++++++++++++++++++
 1 file changed, 151 insertions(+)
 create mode 100644 src/components/eln/ElnFinderPharm.js

diff --git a/src/components/eln/ElnFinderPharm.js b/src/components/eln/ElnFinderPharm.js
new file mode 100644
index 00000000..9f828d11
--- /dev/null
+++ b/src/components/eln/ElnFinderPharm.js
@@ -0,0 +1,151 @@
+import React, { useState, useEffect } from "react";
+import moment from "moment";
+import { useImmer } from "use-immer";
+
+import ElnStatus from "./ElnStatus";
+import ElnFilter from "./elnFilter/ElnFilter";
+import ElnStack from "./ElnStack";
+
+import styles from "./Eln.module.css";
+
+// const elnData = require("@site/static/assets/eln_test.json");
+
+function ElnFinderPharm(props) {
+    // State for ELN data
+
+    const [elnData, setElnData] = useState(null);
+    const [error, setError] = useState(null);
+
+    // State for filtering
+
+    const [filter, setFilter] = useImmer(
+        props.subDisc ? { subDisc: props.subDisc } : {}
+    );
+
+    // Fetch ELN data
+
+    useEffect(() => {
+        fetch("../../assets/elnDataPharm.json")
+            .then((response) => response.json())
+            .then((data) => {
+                setElnData(data);
+                console.log(data);
+            })
+            .catch((error) => {
+                setError(error);
+                console.error(error);
+            });
+    }, []);
+
+    // Catch if fetch is still loading
+
+    if (!elnData) {
+        return <em>Loading...</em>;
+    }
+
+    // Define working variables
+
+    let elnTable = [];
+    let allLicenses = [];
+
+    // Parse timestamp of ELN data
+
+    const dateDownloaded = moment(elnData.date);
+    const relativeDate = moment(dateDownloaded).fromNow();
+
+    // Assemble essential ELN data
+
+    try {
+        const chemElns = elnData["_embedded"].searchResult["_embedded"].objects;
+
+        chemElns.map((eln) => {
+            elnTable.push({
+                name: eln["_embedded"].indexableObject.name,
+                url: eln["_embedded"].indexableObject.metadata[
+                    "dc.identifier.uri"
+                ][0].value,
+                license:
+                    eln["_embedded"].indexableObject.metadata[
+                        "K.lizenzmodell"
+                    ][0].value,
+                desc: eln["_embedded"].indexableObject.metadata[
+                    "dc.description.abstract"
+                ][0].value,
+            });
+            allLicenses.push(
+                eln["_embedded"].indexableObject.metadata["K.lizenzmodell"][0]
+                    .value
+            );
+        });
+
+        allLicenses = [...new Set(allLicenses)];
+    } catch (error) {
+        console.error(error);
+        return <em>Failed to process ELN data.</em>;
+    }
+
+    // Filter ELN data based on filter state
+
+    const filteredTable = elnTable.filter((eln) => {
+        if (Object.keys(filter).length === 0) {
+            return true;
+        }
+
+        if (filter.license && eln.license !== filter.license) {
+            return false;
+        }
+
+        if (
+            filter.text &&
+            !JSON.stringify(eln)
+                .toLowerCase()
+                .includes(filter.text.toLowerCase())
+        ) {
+            return false;
+        }
+
+        return true;
+    });
+
+    // Determine number of results and generate output
+
+    const numberOfResults = filteredTable.length;
+
+    let resultOutput = null;
+
+    switch (numberOfResults) {
+        case elnTable.length:
+            resultOutput = null;
+            break;
+        case 0:
+            resultOutput = "No results found.";
+            break;
+        case 1:
+            resultOutput = "1 result found.";
+            break;
+        default:
+            resultOutput = numberOfResults + " results found.";
+            break;
+    }
+
+    // Render ELN Finder component
+
+    return (
+        <React.Fragment>
+            <ElnStatus {...{ relativeDate }} />
+            <div className={styles.eln}>
+                <ElnFilter
+                    {...{
+                        allLicenses,
+                        filter,
+                        setFilter,
+                        resultOutput,
+                    }}
+                />
+                <ElnStack {...{ filteredTable, filter, setFilter }} />
+            </div>
+        </React.Fragment>
+    );
+}
+
+export default ElnFinderPharm;

From fd1e6aea32bcd2e4d79da870caaea2f686356a52 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Sun, 8 Sep 2024 13:33:08 +0200
Subject: [PATCH 57/89] refactor: adapt to work without subdisciplines

---
 src/components/eln/elnFilter/ElnFilter.js | 38 +++++++++++++----------
 1 file changed, 22 insertions(+), 16 deletions(-)

diff --git a/src/components/eln/elnFilter/ElnFilter.js b/src/components/eln/elnFilter/ElnFilter.js
index 89883b49..20f47689 100644
--- a/src/components/eln/elnFilter/ElnFilter.js
+++ b/src/components/eln/elnFilter/ElnFilter.js
@@ -8,7 +8,11 @@ import styles from "../Eln.module.css";
 // Assemble buttons for filtering section
 
 function ButtonFilters({ allSubDisc, allLicenses, filter, setFilter }) {
-    let subDiscButtons = ["All", ...allSubDisc];
+    let subDiscButtons = [];
+
+    if (allSubDisc) {
+        subDiscButtons = ["All", ...allSubDisc];
+    }
     let licenseButtons = ["All", ...allLicenses];
 
     // Check if active prop should be handed to FilterButton
@@ -34,21 +38,23 @@ function ButtonFilters({ allSubDisc, allLicenses, filter, setFilter }) {
 
     return (
         <React.Fragment>
-            <div className="lbe__searchfilter__section">
-                <h5>Filter by subdisciplines</h5>
-                <p>
-                    {subDiscButtons.map((subDisc, idx) => (
-                        <FilterButton
-                            key={idx}
-                            label={subDisc}
-                            type="subDisc"
-                            active={isActive("subDisc", subDisc)}
-                            numbered={true}
-                            {...{ filter, setFilter }}
-                        />
-                    ))}
-                </p>
-            </div>
+            {subDiscButtons.length > 0 && (
+                <div className="lbe__searchfilter__section">
+                    <h5>Filter by subdisciplines</h5>
+                    <p>
+                        {subDiscButtons.map((subDisc, idx) => (
+                            <FilterButton
+                                key={idx}
+                                label={subDisc}
+                                type="subDisc"
+                                active={isActive("subDisc", subDisc)}
+                                numbered={true}
+                                {...{ filter, setFilter }}
+                            />
+                        ))}
+                    </p>
+                </div>
+            )}
             <div className="lbe__searchfilter__section">
                 <h5>Filter by license</h5>
                 <p>

From 71f0d76b8b8997d8dcf678fdc478445e73c6034d Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Sun, 8 Sep 2024 13:33:27 +0200
Subject: [PATCH 58/89] feat: get pharmacy data

---
 scripts/getElns.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/scripts/getElns.sh b/scripts/getElns.sh
index 47a73e52..f22a4015 100755
--- a/scripts/getElns.sh
+++ b/scripts/getElns.sh
@@ -7,6 +7,9 @@ targetDir="/var/www/html/staging_eln/knowledge_base/assets"
 
 curl -o eln-finder.json "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?sort=dc.title,ASC&f.K03=Chemistry,equals"
 
+curl -o eln-finder-pharm.json "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?sort=dc.title,ASC&f.K03=Pharmacy,equals"
+
 # add current date and time to the json
 
 jq ". + {date: \"$(date -u)\" }" eln-finder.json > $targetDir/elnData.json
+jq ". + {date: \"$(date -u)\" }" eln-finder-pharm.json > $targetDir/elnDataPharm.json

From 17b077dc9bcf3c9cc06f397491fadbc51006291b Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Sun, 8 Sep 2024 13:45:07 +0200
Subject: [PATCH 59/89] fix: lf / add testing path

---
 scripts/getElns.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/getElns.sh b/scripts/getElns.sh
index f22a4015..aeff5da0 100755
--- a/scripts/getElns.sh
+++ b/scripts/getElns.sh
@@ -2,6 +2,7 @@
 
 targetDir="/var/www/html/staging_eln/knowledge_base/assets"
 # targetDir="/var/www/html/knowledge_base/assets"
+# targetDir="/git/n4c-kb_jl/static/assets"
 
 # get the data from the eln-finder
 

From 2b48212e4714334aa394f149f3cc6688f06ace67 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Sun, 8 Sep 2024 13:50:37 +0200
Subject: [PATCH 60/89] feat: add pharmacy ELNs component

---
 docs/10_domains/50_pharmaceutical_chemistry.mdx | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/docs/10_domains/50_pharmaceutical_chemistry.mdx b/docs/10_domains/50_pharmaceutical_chemistry.mdx
index 24025d84..ddf85136 100644
--- a/docs/10_domains/50_pharmaceutical_chemistry.mdx
+++ b/docs/10_domains/50_pharmaceutical_chemistry.mdx
@@ -3,10 +3,12 @@ title: "Medicinal / Pharmaceutical Chemistry"
 slug: "/pharmaceutical_chemistry"
 ---
 
-import Methods from '@site/src/components/Methods.js';
-import {LbeChip} from '@site/src/components/lbe/LbeElements.js';
+import Methods from "@site/src/components/Methods.js";
+import { LbeChip } from "@site/src/components/lbe/LbeElements.js";
+import ElnFinderPharm from "@site/src/components/eln/ElnFinderPharm.js";
 
-<LbeChip title="medicinal chemistry" /><LbeChip title="epidemiology" />
+<LbeChip title="medicinal chemistry" />
+<LbeChip title="epidemiology" />
 
 ## Introduction
 
@@ -14,11 +16,13 @@ Medicinal chemistry is a chemistry-based, strongly interdisciplinary discipline.
 
 ## Data Types
 
-The most common types of data in pharmaceutical/medicinal chemistry can be divided into three categories: synthesis data, analytical data, and (bio)assay data. While the first two types of data (synthesis and analytical data) play a role in broad areas of chemistry, (bio)assay data, which is used to investigate the biological activity of a substance, is a particular feature of pharmaceutical/medicinal chemistry. 
+The most common types of data in pharmaceutical/medicinal chemistry can be divided into three categories: synthesis data, analytical data, and (bio)assay data. While the first two types of data (synthesis and analytical data) play a role in broad areas of chemistry, (bio)assay data, which is used to investigate the biological activity of a substance, is a particular feature of pharmaceutical/medicinal chemistry.
 
 ## ELNs and Other Tools
 
-To meet the requirements for FAIR data management, electronic lab notebooks (ELNs) are particularly useful as they can take over many documentation tasks for researchers. The following ELNs are used in the community, for example: Chemotion ELN, Sicformation, eLabFTW, eLabJournal, labfolder, Benchling. The [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) offers additional options. How to choose the right ELN for the research group can be read [here](https://knowledgebase.nfdi4chem.de/knowledge_base/docs/choose_eln/). 
+To meet the requirements for FAIR data management, electronic lab notebooks (ELNs) are particularly useful as they can take over many documentation tasks for researchers. The [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) offers a selection of pharmacy-specific ELNs. How to choose the right ELN for the research group can be read [here](https://knowledgebase.nfdi4chem.de/knowledge_base/docs/choose_eln/).
+
+<ElnFinderPharm />
 
 For the planning of research data management and the creation of data management plans, tools such as RDMO and DMP-Online are suitable. Many universities have their own instances of one of these solutions.
 

From e9b978bb4a66527bc4613e44c8b28610a0cf073f Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Sun, 8 Sep 2024 13:50:54 +0200
Subject: [PATCH 61/89] fix: catch if no subdisciplines exist

---
 src/components/eln/ElnCard.js   |    32 +-
 static/assets/elnDataPharm.json | 14426 ++++++++++++++++++++++++++++++
 2 files changed, 14442 insertions(+), 16 deletions(-)
 create mode 100644 static/assets/elnDataPharm.json

diff --git a/src/components/eln/ElnCard.js b/src/components/eln/ElnCard.js
index f45a45a4..7da873ad 100644
--- a/src/components/eln/ElnCard.js
+++ b/src/components/eln/ElnCard.js
@@ -22,22 +22,22 @@ function ElnCard({ eln, filter, setFilter }) {
             <div className={styles.eln__card__desc}>
                 <ShortenDesc desc={eln.desc} length={100} />
             </div>
-            <div className={styles.eln__card__desc}>
-                {eln.subDisc.length > 0
-                    ? eln.subDisc.map((subdisc, idx) => {
-                          let isActive = filter.subDisc === subdisc;
-                          return (
-                              <FilterButton
-                                  active={isActive}
-                                  type="subDisc"
-                                  label={subdisc}
-                                  key={idx}
-                                  {...{ filter, setFilter }}
-                              />
-                          );
-                      })
-                    : null}
-            </div>
+            {eln.subDisc && eln.subDisc.length > 0 && (
+                <div className={styles.eln__card__desc}>
+                    {eln.subDisc.map((subdisc, idx) => {
+                        let isActive = filter.subDisc === subdisc;
+                        return (
+                            <FilterButton
+                                active={isActive}
+                                type="subDisc"
+                                label={subdisc}
+                                key={idx}
+                                {...{ filter, setFilter }}
+                            />
+                        );
+                    })}
+                </div>
+            )}
         </div>
     );
 }
diff --git a/static/assets/elnDataPharm.json b/static/assets/elnDataPharm.json
new file mode 100644
index 00000000..8e944769
--- /dev/null
+++ b/static/assets/elnDataPharm.json
@@ -0,0 +1,14426 @@
+{
+  "id": null,
+  "scope": null,
+  "query": null,
+  "appliedFilters": [
+    {
+      "filter": "K03",
+      "operator": "equals",
+      "value": "Pharmacy",
+      "label": "Pharmacy"
+    }
+  ],
+  "sort": {
+    "by": "dc.title",
+    "order": "ASC"
+  },
+  "configuration": null,
+  "type": "discover",
+  "_links": {
+    "self": {
+      "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals"
+    }
+  },
+  "_embedded": {
+    "searchResult": {
+      "_embedded": {
+        "objects": [
+          {
+            "hitHighlights": null,
+            "type": "discover",
+            "_links": {
+              "indexableObject": {
+                "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/core/items/2c960828-7c33-47b4-8c57-18cc1a9c01c1"
+              }
+            },
+            "_embedded": {
+              "indexableObject": {
+                "id": "2c960828-7c33-47b4-8c57-18cc1a9c01c1",
+                "uuid": "2c960828-7c33-47b4-8c57-18cc1a9c01c1",
+                "name": "Agilent SLIMS",
+                "handle": "eln/132",
+                "metadata": {
+                  "AK.K20": [
+                    {
+                      "value": "MassHunter, Mettler Balance, Biobank, iLab, SLIMS Cloud Label Printing & several enhanced functionalities of SLIMS",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Agilent OpenLAB CDS, Agilent SLIMS, Agilent OpenLAB ECM",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    }
+                  ],
+                  "AK.K33": [
+                    {
+                      "value": "GxP - FDA CFR 21 Part 11 / Annex 11; ISO 27001",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.anbieter.sitz": [
+                    {
+                      "value": "Belgium, Switzerland, China",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.automatisierung": [
+                    {
+                      "value": "Business Logics",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.daten.speicherort": [
+                    {
+                      "value": "Provider's Cloud: AWS",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.import.formate": [
+                    {
+                      "value": "import from connected devices possible",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.kollaboration": [
+                    {
+                      "value": "Group management",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.labormanagement.funktionen": [
+                    {
+                      "value": "Asset management, Instrument management",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.offline.function": [
+                    {
+                      "value": "no offline functionalities",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.sprachen": [
+                    {
+                      "value": "Dutch",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AT.aktiv": [
+                    {
+                      "value": "active",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AT.aktiv.info": [
+                    {
+                      "value": "Version 6.8",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AT.anbieter.sicherungsstrategie": [
+                    {
+                      "value": "see https://www.agilent.com/cs/library/quickreference/public/policy-slims68-security-and-architecture-5994-4614EN-agilent.pdf",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AT.community": [
+                    {
+                      "value": "Annual user meetings (presence or virtual)",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AT.exit.strategy": [
+                    {
+                      "value": "Migration possible",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AT.nutzer2": [
+                    {
+                      "value": "University of Bayreuth, UA/UZA, UZG, UZB",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AT.rezensionen": [
+                    {
+                      "value": "https://www.g2.com/products/agilent-slims/reviews",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.K08": [
+                    {
+                      "value": "K08_02",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.K31": [
+                    {
+                      "value": "Device connection",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.K33": [
+                    {
+                      "value": "HIPAA",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "ISO",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Good Laboratory Practice (GLP)",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    }
+                  ],
+                  "K.K41": [
+                    {
+                      "value": "Customizable user interface",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.anbieter.sitz": [
+                    {
+                      "value": "Germany",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Switzerland",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "USA",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    }
+                  ],
+                  "K.api": [
+                    {
+                      "value": "Java API",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "REST API",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Python library",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    }
+                  ],
+                  "K.automatisierung": [
+                    {
+                      "value": "Data analysis",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Device control",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Get data from instrument",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    }
+                  ],
+                  "K.betriebssystem": [
+                    {
+                      "value": "Android",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "iOS",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Linux",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    },
+                    {
+                      "value": "MacOS",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 3
+                    },
+                    {
+                      "value": "Windows",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 4
+                    }
+                  ],
+                  "K.beweis.sicherheit": [
+                    {
+                      "value": "Audit Trail",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Electronic signature",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "FDA CFR 21 Part 11",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    },
+                    {
+                      "value": "Versioning",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 3
+                    },
+                    {
+                      "value": "Timestamping",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 4
+                    }
+                  ],
+                  "K.daten.eingabe": [
+                    {
+                      "value": "Barcode Scanner",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Browser forms",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    }
+                  ],
+                  "K.daten.export": [
+                    {
+                      "value": "Formats suitable for long term archiving",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.daten.zugriff": [
+                    {
+                      "value": "Browser based",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Responsive Design",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    }
+                  ],
+                  "K.import.formate": [
+                    {
+                      "value": "MS Office formats",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Structured formats",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Table formats",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    }
+                  ],
+                  "K.import.methode": [
+                    {
+                      "value": "Drag & Drop / File Chooser",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.kollaboration": [
+                    {
+                      "value": "Rights management",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Role management",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    }
+                  ],
+                  "K.kontroll.vokabular": [
+                    {
+                      "value": "Not controlled",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Controlled Vocabulary",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    }
+                  ],
+                  "K.labormanagement.funktionen": [
+                    {
+                      "value": "Freezer Management",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Inventory (devices)",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "LIMS connectivity",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    },
+                    {
+                      "value": "Sample Tracking",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 3
+                    },
+                    {
+                      "value": "Materials database",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 4
+                    }
+                  ],
+                  "K.lizenzmodell": [
+                    {
+                      "value": "Closed Source",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.nutzungs.statistik": [
+                    {
+                      "value": "Usage statistics",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Configurable",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    }
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+                      "value": "Could easily connect via APIs to a lot of these but doesn't currently have inbuilt functionality. Working on slack and teams integration.",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.K31": [
+                    {
+                      "value": "Can retrieve from instruments, but not controlling instruments. All parsers are in Luma lab connect - parsers can be created to add to the openly available library.",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.K33": [
+                    {
+                      "value": "ISO9001, ISO27001, Working on GXP",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.K41": [
+                    {
+                      "value": "The software offers a range of customisation features, however the users also have the option to work with the provider to get them to implement more custom features",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.anbieter.sitz": [
+                    {
+                      "value": "Korea as well.",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.betriebssystem": [
+                    {
+                      "value": "Can be run on any OS via a web browser - need clarification on that question",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.daten.eingabe": [
+                    {
+                      "value": "HELM editor - pistoia alliance standard, APIs as well, JDBC Connection (connects between databases)",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.daten.export": [
+                    {
+                      "value": "PDF, some of it could be exported out in machine-readable format, need more details on the others (Will to advise)",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.daten.speicherort": [
+                    {
+                      "value": "Can be any of these depending on the users preference, can be run locally or on their cloud or on the Dotmatics AWS server.",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.daten.zugriff": [
+                    {
+                      "value": "Under modification for more responsive, some bits are currently.",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.fach": [
+                    {
+                      "value": "Do Chemicals and Materials count under Engineering? What does genetics mean? (Genius is linked in)",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.import.formate": [
+                    {
+                      "value": ".zip archives, txt, office files (xlxs, pptx, docx), pdf, images (not native tiff currently, but have jpg, png, bmp, gif), GENBank, PRISM, SnapGene, mol, rdx, SMILES, InChI, .csv, .tsv (will to update with more)",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.kollaboration": [
+                    {
+                      "value": "Comments are being worked on",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.kontroll.vokabular": [
+                    {
+                      "value": "Can adpat to companys specific requirements for controlled vocabularies",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.labormanagement.funktionen": [
+                    {
+                      "value": "Can integrate with multiple commercially available LIMS and are working on own LIMS system. Has own inventory system.",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.lizenzmodell": [
+                    {
+                      "value": "Commercial License with Annual Billing",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.nutzungs.statistik": [
+                    {
+                      "value": "Collects what users have installed to ensure that everything is working properly",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.nutzungsart": [
+                    {
+                      "value": "Either is available depending on customer preference.",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.offline.function": [
+                    {
+                      "value": "Onsite capabilities - where there is no internet connection. There are some Desktop tools that don't require internet connection (e.g. Vortex).",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.preismodell": [
+                    {
+                      "value": "Annual Billing - not a fixed cost, dependent on amount of users, customisation requirements etc",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.projektmanagement.tools": [
+                    {
+                      "value": "Cascade for task management.",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.sprachen": [
+                    {
+                      "value": "Hebru, Japanese",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.support": [
+                    {
+                      "value": "Both types of user training are available - can also support both at the user and at the admin level",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.templates": [
+                    {
+                      "value": "Can import export templates (depending on type) but not for the whole ELN, Microtitre plate templates via Excel",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.versionen": [
+                    {
+                      "value": "No demo versions available",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AK.workflows": [
+                    {
+                      "value": "Clarification on import/export workflows needed",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AT.aktiv": [
+                    {
+                      "value": "active",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AT.aktiv.info": [
+                    {
+                      "value": "Latest version release was 6.2.1 on the 19th December 2023",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AT.anbieter.sicherungsstrategie": [
+                    {
+                      "value": "Baked into the software.",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "AT.exit.strategy": [
+                    {
+                      "value": "Dotmatics would work with the customer on data export",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.K20": [
+                    {
+                      "value": "Marvin JS ChemAxon",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "MarvinSketch ChemAxon",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "ChemDraw",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    },
+                    {
+                      "value": "SnapGene",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 3
+                    }
+                  ],
+                  "K.K31": [
+                    {
+                      "value": "Device connection",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.K33": [
+                    {
+                      "value": "ISO",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.K41": [
+                    {
+                      "value": "Customizable user interface",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.anbieter.sitz": [
+                    {
+                      "value": "United Kingdom",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "USA",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    }
+                  ],
+                  "K.api": [
+                    {
+                      "value": "REST API",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.automatisierung": [
+                    {
+                      "value": "Get data from instrument",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Data analysis",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    }
+                  ],
+                  "K.betriebssystem": [
+                    {
+                      "value": "Linux",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "MacOS",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Windows",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    }
+                  ],
+                  "K.beweis.sicherheit": [
+                    {
+                      "value": "Versioning",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Timestamping",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Electronic signature",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    },
+                    {
+                      "value": "Audit Trail",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 3
+                    }
+                  ],
+                  "K.daten.eingabe": [
+                    {
+                      "value": "Barcode Scanner",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Browser forms",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Chemical editor",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    },
+                    {
+                      "value": "Microtitre plates",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 3
+                    },
+                    {
+                      "value": "Plain text editor",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 4
+                    },
+                    {
+                      "value": "Rich text editor",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 5
+                    },
+                    {
+                      "value": "Scientific calculator",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 6
+                    },
+                    {
+                      "value": "Table editor",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 7
+                    },
+                    {
+                      "value": "With external links",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 8
+                    },
+                    {
+                      "value": "With internal links",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 9
+                    }
+                  ],
+                  "K.daten.export": [
+                    {
+                      "value": "Complete content in document format",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.daten.zugriff": [
+                    {
+                      "value": "Browser based",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Responsive Design",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Local client",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    }
+                  ],
+                  "K.import.formate": [
+                    {
+                      "value": "Video formats",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Compressed formats",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Document formats",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    },
+                    {
+                      "value": "Image formats",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 3
+                    },
+                    {
+                      "value": "MS Office formats",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 4
+                    },
+                    {
+                      "value": "Scientific formats",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 5
+                    },
+                    {
+                      "value": "Structured formats",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 6
+                    },
+                    {
+                      "value": "Table formats",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 7
+                    }
+                  ],
+                  "K.import.methode": [
+                    {
+                      "value": "Drag & Drop / File Chooser",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.kollaboration": [
+                    {
+                      "value": "Rights management",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Role management",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    }
+                  ],
+                  "K.kontroll.vokabular": [
+                    {
+                      "value": "Controlled Vocabulary",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.labormanagement.funktionen": [
+                    {
+                      "value": "LIMS connectivity",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Materials database",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Inventory (devices)",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    },
+                    {
+                      "value": "Sample Tracking",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 3
+                    },
+                    {
+                      "value": "Freezer Management",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 4
+                    }
+                  ],
+                  "K.lizenzmodell": [
+                    {
+                      "value": "Closed Source",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.nutzungs.statistik": [
+                    {
+                      "value": "Usage statistics",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.nutzungsart": [
+                    {
+                      "value": "Software as a Service",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "On-premises",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    }
+                  ],
+                  "K.preismodell": [
+                    {
+                      "value": "Chargeable / Paid for / fee-based",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Industry",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Per person / Tiered Pricing",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    }
+                  ],
+                  "K.projektmanagement.tools": [
+                    {
+                      "value": "Task management",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    }
+                  ],
+                  "K.sprachen": [
+                    {
+                      "value": "English",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "French",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "German",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    },
+                    {
+                      "value": "Korean",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 3
+                    },
+                    {
+                      "value": "Mandarin Chinese",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 4
+                    },
+                    {
+                      "value": "Italian",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 5
+                    }
+                  ],
+                  "K.suchfunktion": [
+                    {
+                      "value": "Search by chemical structure",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Search for reactions",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Full text search",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    },
+                    {
+                      "value": "Database queries",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 3
+                    },
+                    {
+                      "value": "Conditional search",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 4
+                    },
+                    {
+                      "value": "BLAST search",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 5
+                    },
+                    {
+                      "value": "Advanced search",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 6
+                    }
+                  ],
+                  "K.support": [
+                    {
+                      "value": "Consulting",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Online documentation",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Support by provider",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    },
+                    {
+                      "value": "User training (online, on site)",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 3
+                    }
+                  ],
+                  "K.templates": [
+                    {
+                      "value": "Define own templates",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Import from internet sources",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Subject specific templates",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    },
+                    {
+                      "value": "Microtitre plate templates",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 3
+                    }
+                  ],
+                  "K.workflows": [
+                    {
+                      "value": "Project-related workflows",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 0
+                    },
+                    {
+                      "value": "Cross-project workflows",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 1
+                    },
+                    {
+                      "value": "Reports",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 2
+                    },
+                    {
+                      "value": "With workflows",
+                      "language": null,
+                      "authority": null,
+                      "confidence": -1,
+                      "place": 3
+                    }
+                  ],
+                  "S.K20": [
+                    {
+                      "value": "S03",
+                      "language": null,
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+              "label": "K04_10_02",
+              "count": 1,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K04_10=K04_10_02,equals"
+                }
+              }
+            },
+            {
+              "label": "K04_10_03",
+              "count": 1,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K04_10=K04_10_03,equals"
+                }
+              }
+            },
+            {
+              "label": "K04_10_05",
+              "count": 1,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K04_10=K04_10_05,equals"
+                }
+              }
+            },
+            {
+              "label": "K04_10_06",
+              "count": 1,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K04_10=K04_10_06,equals"
+                }
+              }
+            }
+          ]
+        }
+      },
+      {
+        "name": "K04_11",
+        "facetType": "text",
+        "facetLimit": 5,
+        "page": {
+          "number": 0,
+          "size": 5
+        },
+        "_links": {
+          "self": {
+            "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/facets/K04_11?f.K03=Pharmacy,equals&size=5"
+          }
+        },
+        "_embedded": {
+          "values": [
+            {
+              "label": "K04_11_01",
+              "count": 1,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K04_11=K04_11_01,equals"
+                }
+              }
+            },
+            {
+              "label": "K04_11_02",
+              "count": 1,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K04_11=K04_11_02,equals"
+                }
+              }
+            },
+            {
+              "label": "K04_11_04",
+              "count": 1,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K04_11=K04_11_04,equals"
+                }
+              }
+            }
+          ]
+        }
+      },
+      {
+        "name": "K05",
+        "facetType": "text",
+        "facetLimit": 5,
+        "page": {
+          "number": 0,
+          "size": 5
+        },
+        "_links": {
+          "self": {
+            "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/facets/K05?f.K03=Pharmacy,equals&size=5"
+          }
+        },
+        "_embedded": {
+          "values": [
+            {
+              "label": "Software as a Service",
+              "count": 8,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K05=Software%20as%20a%20Service,equals"
+                }
+              }
+            },
+            {
+              "label": "On-premises",
+              "count": 7,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K05=On-premises,equals"
+                }
+              }
+            }
+          ]
+        }
+      },
+      {
+        "name": "K42",
+        "facetType": "text",
+        "facetLimit": 5,
+        "page": {
+          "number": 0,
+          "size": 5
+        },
+        "_links": {
+          "self": {
+            "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/facets/K42?f.K03=Pharmacy,equals&size=5"
+          }
+        },
+        "_embedded": {
+          "values": [
+            {
+              "label": "Windows",
+              "count": 8,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K42=Windows,equals"
+                }
+              }
+            },
+            {
+              "label": "Linux",
+              "count": 6,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K42=Linux,equals"
+                }
+              }
+            },
+            {
+              "label": "MacOS",
+              "count": 5,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K42=MacOS,equals"
+                }
+              }
+            },
+            {
+              "label": "Android",
+              "count": 3,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K42=Android,equals"
+                }
+              }
+            },
+            {
+              "label": "iOS",
+              "count": 2,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K42=iOS,equals"
+                }
+              }
+            }
+          ]
+        }
+      },
+      {
+        "name": "K32",
+        "facetType": "text",
+        "facetLimit": 5,
+        "page": {
+          "number": 0,
+          "size": 5
+        },
+        "_links": {
+          "next": {
+            "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/facets/K32?f.K03=Pharmacy,equals&page=1&size=5"
+          },
+          "self": {
+            "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/facets/K32?f.K03=Pharmacy,equals&size=5"
+          }
+        },
+        "_embedded": {
+          "values": [
+            {
+              "label": "Electronic signature",
+              "count": 9,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K32=Electronic%20signature,equals"
+                }
+              }
+            },
+            {
+              "label": "Audit Trail",
+              "count": 8,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K32=Audit%20Trail,equals"
+                }
+              }
+            },
+            {
+              "label": "Timestamping",
+              "count": 8,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K32=Timestamping,equals"
+                }
+              }
+            },
+            {
+              "label": "Versioning",
+              "count": 8,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K32=Versioning,equals"
+                }
+              }
+            },
+            {
+              "label": "FDA CFR 21 Part 11",
+              "count": 6,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K32=FDA%20CFR%2021%20Part%2011,equals"
+                }
+              }
+            }
+          ]
+        }
+      },
+      {
+        "name": "K33",
+        "facetType": "text",
+        "facetLimit": 5,
+        "page": {
+          "number": 0,
+          "size": 5
+        },
+        "_links": {
+          "next": {
+            "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/facets/K33?f.K03=Pharmacy,equals&page=1&size=5"
+          },
+          "self": {
+            "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/facets/K33?f.K03=Pharmacy,equals&size=5"
+          }
+        },
+        "_embedded": {
+          "values": [
+            {
+              "label": "Good Laboratory Practice (GLP)",
+              "count": 6,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K33=Good%20Laboratory%20Practice%20(GLP),equals"
+                }
+              }
+            },
+            {
+              "label": "ISO",
+              "count": 6,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K33=ISO,equals"
+                }
+              }
+            },
+            {
+              "label": "Good Manufacturing Practice (GMP)",
+              "count": 4,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K33=Good%20Manufacturing%20Practice%20(GMP),equals"
+                }
+              }
+            },
+            {
+              "label": "HIPAA",
+              "count": 4,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K33=HIPAA,equals"
+                }
+              }
+            },
+            {
+              "label": "Good Clinical Practice (GCP)",
+              "count": 3,
+              "authorityKey": null,
+              "type": "discover",
+              "_links": {
+                "search": {
+                  "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals&f.K33=Good%20Clinical%20Practice%20(GCP),equals"
+                }
+              }
+            }
+          ]
+        }
+      }
+    ]
+  },
+  "date": "So 8. Sep 11:40:45 UTC 2024"
+}

From 1fc616e2f0515d5fac76f490d798db78e151e800 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Sun, 8 Sep 2024 13:52:15 +0200
Subject: [PATCH 62/89] chore: do not track data file

---
 .gitignore                      |     1 +
 static/assets/elnDataPharm.json | 14426 ------------------------------
 2 files changed, 1 insertion(+), 14426 deletions(-)
 delete mode 100644 static/assets/elnDataPharm.json

diff --git a/.gitignore b/.gitignore
index e2a08f1f..f3467e3c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,6 +7,7 @@ fonts
 /i18n
 # API data
 elnData.json
+elnDataPharm.json
 # Generated files
 .docusaurus
 .cache-loader
diff --git a/static/assets/elnDataPharm.json b/static/assets/elnDataPharm.json
deleted file mode 100644
index 8e944769..00000000
--- a/static/assets/elnDataPharm.json
+++ /dev/null
@@ -1,14426 +0,0 @@
-{
-  "id": null,
-  "scope": null,
-  "query": null,
-  "appliedFilters": [
-    {
-      "filter": "K03",
-      "operator": "equals",
-      "value": "Pharmacy",
-      "label": "Pharmacy"
-    }
-  ],
-  "sort": {
-    "by": "dc.title",
-    "order": "ASC"
-  },
-  "configuration": null,
-  "type": "discover",
-  "_links": {
-    "self": {
-      "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/discover/search/objects?f.K03=Pharmacy,equals"
-    }
-  },
-  "_embedded": {
-    "searchResult": {
-      "_embedded": {
-        "objects": [
-          {
-            "hitHighlights": null,
-            "type": "discover",
-            "_links": {
-              "indexableObject": {
-                "href": "https://eln-finder.ulb.tu-darmstadt.de/server/api/core/items/2c960828-7c33-47b4-8c57-18cc1a9c01c1"
-              }
-            },
-            "_embedded": {
-              "indexableObject": {
-                "id": "2c960828-7c33-47b4-8c57-18cc1a9c01c1",
-                "uuid": "2c960828-7c33-47b4-8c57-18cc1a9c01c1",
-                "name": "Agilent SLIMS",
-                "handle": "eln/132",
-                "metadata": {
-                  "AK.K20": [
-                    {
-                      "value": "MassHunter, Mettler Balance, Biobank, iLab, SLIMS Cloud Label Printing & several enhanced functionalities of SLIMS",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "Agilent OpenLAB CDS, Agilent SLIMS, Agilent OpenLAB ECM",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    }
-                  ],
-                  "AK.K33": [
-                    {
-                      "value": "GxP - FDA CFR 21 Part 11 / Annex 11; ISO 27001",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.anbieter.sitz": [
-                    {
-                      "value": "Belgium, Switzerland, China",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.automatisierung": [
-                    {
-                      "value": "Business Logics",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.daten.speicherort": [
-                    {
-                      "value": "Provider's Cloud: AWS",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.import.formate": [
-                    {
-                      "value": "import from connected devices possible",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.kollaboration": [
-                    {
-                      "value": "Group management",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.labormanagement.funktionen": [
-                    {
-                      "value": "Asset management, Instrument management",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.offline.function": [
-                    {
-                      "value": "no offline functionalities",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.sprachen": [
-                    {
-                      "value": "Dutch",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AT.aktiv": [
-                    {
-                      "value": "active",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AT.aktiv.info": [
-                    {
-                      "value": "Version 6.8",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AT.anbieter.sicherungsstrategie": [
-                    {
-                      "value": "see https://www.agilent.com/cs/library/quickreference/public/policy-slims68-security-and-architecture-5994-4614EN-agilent.pdf",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AT.community": [
-                    {
-                      "value": "Annual user meetings (presence or virtual)",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AT.exit.strategy": [
-                    {
-                      "value": "Migration possible",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AT.nutzer2": [
-                    {
-                      "value": "University of Bayreuth, UA/UZA, UZG, UZB",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AT.rezensionen": [
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-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
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-                    }
-                  ],
-                  "K.K08": [
-                    {
-                      "value": "K08_02",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "K.K31": [
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-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "K.K33": [
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-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
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-                      "value": "ISO",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
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-                    {
-                      "value": "Good Laboratory Practice (GLP)",
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-                      "authority": null,
-                      "confidence": -1,
-                      "place": 2
-                    }
-                  ],
-                  "K.K41": [
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-                      "value": "Customizable user interface",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "K.anbieter.sitz": [
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-                      "value": "Germany",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
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-                      "value": "Switzerland",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    },
-                    {
-                      "value": "USA",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 2
-                    }
-                  ],
-                  "K.api": [
-                    {
-                      "value": "Java API",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "REST API",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    },
-                    {
-                      "value": "Python library",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 2
-                    }
-                  ],
-                  "K.automatisierung": [
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-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "Device control",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    },
-                    {
-                      "value": "Get data from instrument",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 2
-                    }
-                  ],
-                  "K.betriebssystem": [
-                    {
-                      "value": "Android",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "iOS",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
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-                    },
-                    {
-                      "value": "Linux",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 2
-                    },
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-                    },
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-                    }
-                  ],
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-                  ],
-                  "AK.K31": [
-                    {
-                      "value": "via free add-ons: FLUICS PRINT, Eppendorf VisioNize® sense, Eppendorf RackScan, Eppendorf SafeCode Consumable, Elemental Machines, ZPL Label Printer, Implen NanoPhotometer",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.automatisierung": [
-                    {
-                      "value": "Data analysis: AI Processing via mpVision, image and video analysis via Pipsqueak Pro (add-ons required); from instrument: e. g. Eppendorf RackScan, Elemental Machines sensors (add-ons required, see \"Device connection\")",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.betriebssystem": [
-                    {
-                      "value": "application server: Microsoft Windows Server 2019, including the capacity for file storage; database server: Ubuntu Server 18.04 LTS (recommended: 20.04 LTS)",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.beweis.sicherheit": [
-                    {
-                      "value": "Functions for accreditation: The option to enable counter-signing is a group policy that can be activated by the group's administrator. In case of refusal, the witness can add a note about how to adjust the experiment before resubmitting it for signing.",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.daten.eingabe": [
-                    {
-                      "value": "Calendar function: With the Clustermarket add-on (third-party account required) booking and equipment details can be added to experiments.; Following barcode scanners have been validated to work: Motorola KE-5500, CHS 7Qi, CHS 7Xi, CHH 7xiRx, Datalogic Magellan 800i; Chemical editor requires ChemAxon MarvinJS add-on; dictation function via add-on \"Elementa\" (Beta)",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.daten.export": [
-                    {
-                      "value": "experiments, studies, projects: PDF with associated files, HTML, JSON, XML; inventory: PDF, CSV; batch export of all projects possible; For export of data in any custom format can be done using the API.",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.daten.speicherort": [
-                    {
-                      "value": "location of provider's cloud: Europe or US depending on clients country; cloud of own choice: Amazon Web Service",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.daten.zugriff": [
-                    {
-                      "value": "add-ons only available for Windows and Mac",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.import.formate": [
-                    {
-                      "value": "directly displayed in the ELN: PDFs, raster graphics (e. g. JPEG, PNG, TIF, BMP, GIF) and MS Office formats (docx, xlsx, pptx; Office Online Server add-on required)",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.import.methode": [
-                    {
-                      "value": "automatic import of data generated by devices (see \"Automation\")",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.kollaboration": [
-                    {
-                      "value": "Users from the own lab can be added to experiments as collaborators.; Project groups can be set up for collaboration with other labs.",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.nutzungs.statistik": [
-                    {
-                      "value": "The system administrator can check the latest login of each user and generate a license report, which provides and overview of the number of issued licenses by active users within the system.",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.nutzungsart": [
-                    {
-                      "value": "Installation and updates are always done by the manufacturer, even for a local on-premises installation.",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.preismodell": [
-                    {
-                      "value": "Academic: from €12.95 per user/month (cloud pricing; upgrade to private cloud or on-premises possible at any time); Industry: from €34.95 per user/month (cloud pricing; upgrade to private cloud or on-premises possible at any time)",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.projektmanagement.tools": [
-                    {
-                      "value": "Task management requires free add-on",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.sprachen": [
-                    {
-                      "value": "Google Translate add-on must be activated for French, German and Spanish",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.suchfunktion": [
-                    {
-                      "value": "Conditional search by filter functions; BLAST search requires CloneAssist add-on; search for reactions and chemical structure require ChemAssist and Marvin JS add-on",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.support": [
-                    {
-                      "value": "Support via helpdesk, phone, or live chat on the website",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.templates": [
-                    {
-                      "value": "Templates from internet sources, like protocols.io, can be imported the same way as own templates (by copy-paste actions); pre-configured protocols for molecular biology questions via add-on \"Enhanced LaB Execution\" (cloud only)",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AK.workflows": [
-                    {
-                      "value": "external links via Hyperlinks and external file storage (requires External File Link add-on and client app which is available for Windows and Mac; add-on breaks GLP compliance regarding file integrity ans versioning); internal links to other protocols and samples",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AT.aktiv": [
-                    {
-                      "value": "active",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AT.aktiv.info": [
-                    {
-                      "value": "latest release: 08 May 2023",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AT.anbieter.sicherungsstrategie": [
-                    {
-                      "value": "Cloud is hosted depending on the clients country from Europe (Netherlands and Irelands) or US (Ohio and North Virginia) data centers in High Availability installations. The hosting takes part in at least two geographically separated data centers. In this fully redundant infrastructure all data is replicated in real-time and archived on a third data base. Additionally, every 24 hours a full back-up of all data is stored in an encrypted vault in case of disaster recovery. eLabNext is ISO/IEC 27001:2013-certified and all servers are hosted from ISO 27001, SOCII, or ISEA 3201 compliant facilities. The system is protected by multiple firewalls, secure data transport using HTTPS encryption, regular security audits and preventive measures.",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AT.community": [
-                    {
-                      "value": "unknown",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AT.exit.strategy": [
-                    {
-                      "value": "see \"data export\"",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AT.nutzer": [
-                    {
-                      "value": "Faculty of Medicine and Faculty of Mathematics and Natural Sciences of the University of Cologne, contact: Stefan Schwenke, stefan.schwenke@uni-koeln.de, description: eLabJournal was launched in 2019 as a joint project between the two faculties. For data protection reasons, a cloud solution was rejected and the system was installed on premise on the local servers in the university's computer centre. As of December 2022, 691 researchers use the system. The users are distributed among 28 working groups of the Faculty of Mathematics and Natural Sciences in Biology and Biochemistry and 45 working groups of the Faculty of Medicine.",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "CECAD (cluster of excellence Cellular Stress Responses in Aging-Associated Diseases) at University of Cologne, Institute for Genetics, contact: Laurens Wachsmuth, l.wachsmuth@uni-koeln.de, description: eLabJournal is used as a replacement for the paper lab notebook. Most databases have been transferred to elabJournal and therefore it is used very much in the daily laboratory work.",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    },
-                    {
-                      "value": "Faculty of Medicine/University Medical Centre at RWTH Aachen, contact: Michael Kreisel (Research Data Management Advisor at the Faculty of Medicine), forschungsdekanat-elabjournal@ukaachen.de, description: As of December 2022, the instance includes about 200 users.",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 2
-                    }
-                  ],
-                  "AT.nutzer2": [
-                    {
-                      "value": "Wageningen University, Utrecht University, University Medical Center Groningen, Harvard Medical School, Bayer, Forschungszentrum Jülich, Cologne University and University Hospital Cologne, RWTH Aachen University",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "AT.rezensionen": [
-                    {
-                      "value": "https://www.elabnext.com/resources/case-studies/, https://www.capterra.com/p/180309/eLABJournal/reviews/",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "K.K08": [
-                    {
-                      "value": "K08_01",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "K08_02",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    }
-                  ],
-                  "K.K20": [
-                    {
-                      "value": "Create own plug-ins",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "Marvin JS ChemAxon",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    },
-                    {
-                      "value": "Dropbox",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 2
-                    },
-                    {
-                      "value": "Mendeley",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 3
-                    },
-                    {
-                      "value": "Google Drive",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 4
-                    },
-                    {
-                      "value": "Box",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 5
-                    }
-                  ],
-                  "K.K31": [
-                    {
-                      "value": "Device connection",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "K.K33": [
-                    {
-                      "value": "FERPA",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "FISMA",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    },
-                    {
-                      "value": "HIPAA",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 2
-                    },
-                    {
-                      "value": "ADA",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 3
-                    },
-                    {
-                      "value": "Good Laboratory Practice (GLP)",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 4
-                    },
-                    {
-                      "value": "ISO",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 5
-                    }
-                  ],
-                  "K.K41": [
-                    {
-                      "value": "Non-customizable user interface",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "K.anbieter.sitz": [
-                    {
-                      "value": "Netherlands",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "USA",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    }
-                  ],
-                  "K.api": [
-                    {
-                      "value": "REST API",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "SDK",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    }
-                  ],
-                  "K.automatisierung": [
-                    {
-                      "value": "Get data from instrument",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "Data analysis",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    }
-                  ],
-                  "K.betriebssystem": [
-                    {
-                      "value": "Windows",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "Linux",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    }
-                  ],
-                  "K.beweis.sicherheit": [
-                    {
-                      "value": "Audit Trail",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "FDA CFR 21 Part 11",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    },
-                    {
-                      "value": "Timestamping",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 2
-                    },
-                    {
-                      "value": "Versioning",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 3
-                    },
-                    {
-                      "value": "Electronic signature",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 4
-                    }
-                  ],
-                  "K.daten.eingabe": [
-                    {
-                      "value": "Barcode Scanner",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "Chemical editor",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    },
-                    {
-                      "value": "Table editor",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 2
-                    },
-                    {
-                      "value": "With external links",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 3
-                    },
-                    {
-                      "value": "Sketches",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 4
-                    },
-                    {
-                      "value": "With internal links",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 5
-                    },
-                    {
-                      "value": "Plain text editor",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 6
-                    },
-                    {
-                      "value": "Calendar function",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 7
-                    },
-                    {
-                      "value": "Mathematical formula editor",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 8
-                    },
-                    {
-                      "value": "Dictation function",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 9
-                    }
-                  ],
-                  "K.daten.export": [
-                    {
-                      "value": "Formats suitable for publication",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "Complete content in document format",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    },
-                    {
-                      "value": "Formats suitable for long term archiving",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 2
-                    }
-                  ],
-                  "K.daten.zugriff": [
-                    {
-                      "value": "Browser based",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "Mobile Application",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    }
-                  ],
-                  "K.import.formate": [
-                    {
-                      "value": "Document formats",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "Image formats",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    },
-                    {
-                      "value": "Compressed formats",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 2
-                    },
-                    {
-                      "value": "Audio formats",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 3
-                    },
-                    {
-                      "value": "Video formats",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 4
-                    },
-                    {
-                      "value": "Scientific formats",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 5
-                    },
-                    {
-                      "value": "MS Office formats",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 6
-                    },
-                    {
-                      "value": "Table formats",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 7
-                    },
-                    {
-                      "value": "Structured formats",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 8
-                    }
-                  ],
-                  "K.import.methode": [
-                    {
-                      "value": "Drag & Drop / File Chooser",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "Mobile phone photo (via app)",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    }
-                  ],
-                  "K.kollaboration": [
-                    {
-                      "value": "Role management",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "Rights management",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    },
-                    {
-                      "value": "Comments",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 2
-                    }
-                  ],
-                  "K.kontroll.vokabular": [
-                    {
-                      "value": "Not controlled",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "K.labormanagement.funktionen": [
-                    {
-                      "value": "Devices management",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "Materials database",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    },
-                    {
-                      "value": "Sample Tracking",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 2
-                    },
-                    {
-                      "value": "Ordering function",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 3
-                    },
-                    {
-                      "value": "Inventory (devices)",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 4
-                    },
-                    {
-                      "value": "Freezer Management",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 5
-                    }
-                  ],
-                  "K.lizenzmodell": [
-                    {
-                      "value": "Closed Source",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "K.nutzungs.statistik": [
-                    {
-                      "value": "No usage statistics",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    }
-                  ],
-                  "K.nutzungsart": [
-                    {
-                      "value": "Software as a Service",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "On-premises",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    }
-                  ],
-                  "K.preismodell": [
-                    {
-                      "value": "Chargeable / Paid for / fee-based",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 0
-                    },
-                    {
-                      "value": "Per person / Tiered Pricing",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 1
-                    },
-                    {
-                      "value": "Academic",
-                      "language": null,
-                      "authority": null,
-                      "confidence": -1,
-                      "place": 2
-                    },
-                    {
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-}

From 9d7bc6dd91735a2a560c326e8c6a5d0e2588124c Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Wed, 2 Oct 2024 11:06:23 +0200
Subject: [PATCH 63/89] feat: new synthetic chem text

---
 docs/10_domains/40_synthetic_chemistry.mdx | 81 ++++++++++------------
 1 file changed, 38 insertions(+), 43 deletions(-)

diff --git a/docs/10_domains/40_synthetic_chemistry.mdx b/docs/10_domains/40_synthetic_chemistry.mdx
index d9a2a64f..3bf8da5c 100644
--- a/docs/10_domains/40_synthetic_chemistry.mdx
+++ b/docs/10_domains/40_synthetic_chemistry.mdx
@@ -4,65 +4,60 @@ nfdi4chem-id: dsoic
 slug: "/synthetic_chemistry"
 ---
 
-import Methods from '@site/src/components/Methods.js';
-import {LbeChip} from '@site/src/components/lbe/LbeElements.js';
+import { LbeChip } from "@site/src/components/lbe/LbeElements.js";
+import ElnFinder from "@site/src/components/eln/ElnFinder.js";
 
-<LbeChip title="inorganic chemistry" /><LbeChip title="organic chemistry" />
+<LbeChip title="inorganic chemistry" />
+<LbeChip title="organic chemistry" />
 
-:::info Summary:
+# Introduction
 
-The main goal of a synthetic organic or inorganic chemist is to synthesise desired compounds. Established methods are applied, or new synthetic methods are developed. A typical workflow starts with the planning of the experiments and methods. These are then conducted and research data as well as accompanying metadata are collected along the way. Once the final product is obtained, it is analysed with suitable methods to identify properties of the synthesised material or to ascertain the efficacy of the selected synthetic method. Processing and interpretation of the obtained research data will lead to a proof of concept for a given reaction, optimised conditions for future experiments or upscaling.
-:::
+During the synthesis of a desired compound, all steps, such as planning, realisation and documentation of an experiment, or characterisation of the obtained product, provide research data. These data are synthetic procedures, experimental conditions, as well as manually and digital data collected with analytical devices. Processing and interpretation of the obtained research data will lead to a proof of concept for a given reaction, optimised conditions for future experiments or upscaling.
 
-## Type of experiments
+## Data Types
 
-- Synthesis: 
-    - Preparation of organic/inorganic substances.
-    - Small-scale experiments for screening/optimisation of reaction conditions.
-    - Upscaling of reactions to obtain sufficient product for comprehensive characterisation or as starting material for subsequent synthesis steps.
+In synthetic chemistry different types of research data can be obtained. In general, this data is not limited to characterisation of synthesised products. A typical experiment starts with its design and planning, followed by carrying out the procedure in a laboratory setting. During realisation of an experiment, observations, experimental conditions, and yields are documented. Ideally, this manually collected research data is recorded digitally in an [Electronic Lab Notebooks (ELN)](/docs/eln/).
 
+The synthesis of a specific product is followed by analysing its properties. Regarding data collection, both manually determined and digital data can be obtained. Observations and results of analytical methods with no digital output (i.e., no data files) can be added manually to the ELN entry of the experiment, which include for example melting/boiling point, optical rotation, TLC Rf values, or refraction index. Digital data are obtained from analytical instruments, e.g., NMR, IR, MS. These data can be uploaded seamlessly from the analytical devices to an ELN and analysed therein. An overview on file extensions, file sizes and converters for several analytical methods is given in the table below. It is recommended to save raw data files in [proprietary file formats](/docs/format_standards/) alongside interoperable [open file formats](/docs/format_standards/) by using converters or the software of the analytical device. If no specific open format is currently available, export as .txt or .csv is recommended.
 
-- Analysis:
-    - Product characterisation with feasible methods (e.g. NMR spectroscopy, mass spectrometry, IR spectroscopy, UV/vis spectroscopy, elemental analysis).
-    - to assess screening/optimisation conditions.
-    - to investigate desired product properties.
-    - to characterise materials’ properties comprehensively.
+Overall, [metadata](/docs/metadata/) should always be included when collecting and [storing](/docs/data_storage/) data to allow understanding of the research data in the long term.
 
-## Planning of experiments
+# What ELNs/Tools?
 
-- The implementation of newly inspired ideas is supported by previous work stored in the local instance of the electronic lab notebook (e.g. [Chemotion ELN](https://www.chemotion.net/chemotionsaurus/index.html)) of the own research group ([overview of ELNs for synthetic chemists](/docs/eln)), scientific literature or datasets published in [repositories](/docs/repositories) (discipline-specific repositories such as the [Chemotion repository](https://www.chemotion-repository.net/welcome)).
-- Experimental design follows a logical order to achieve a specific goal, such as increasing yield or purity.
-- Planning is concluded by adding the experimental details (e.g. quantities and scheduling procedures). All metadata is documented in an ELN (e.g. Chemotion ELN) including references.
+For planning research data management and creating data management plans, tools such as [RDMO](https://rdmorganiser.github.io/) and [DMP-Online](https://dmponline.dcc.ac.uk/) are suitable. Many universities have their own instances of these solutions.
 
-## Documentation of experiments
+If you want your data to comply with the [FAIR principles](/docs/fair/) it can be very tedious and extremely time consuming if you try to apply the FAIR principles to your data retrospectively if your existing workflows involve a large degree of analogue documentation (e.g. paper lab notebooks). The reality is that you need tools to take care of certain aspects of the FAIR principles automatically so you don’t have to apply them manually each time. [Electronic Lab Notebooks (ELNs)](/docs/eln/) are very powerful tools that can help you with this. Depending on what ELN you use, the [metadata](/docs/metadata/) can be automatically assigned in both human and [machine-readable formats](/docs/format_standards/). Furthermore, some ELNs can automatically generate interoperable [open file formats](/docs/format_standards/#format-standards-in-chemistry) for your analytical data. Choosing the right ELN can be challenging and this process should be thought about and carried out carefully. You can find out more on [how to choose the right ELN here](/docs/choose_eln/):
 
-- [Documentation of research data](/docs/data_documentation) and [metadata](/docs/metadata) is carried out digitally using an ELN.
-- Experimental conditions (e.g. solvents, temperature, duration, pressure) are noted in the ELN.
-- Observations and results of analytical methods with no digital output (i.e. no data files) are added manually to the ELN entry of the experiment, which may include appearance, yield, melting point, optical rotation or TLC Rf values (with metadata where applicable).
-- Obtained data from analytical instruments (e.g. NMR, MS or IR data) are uploaded to the Chemotion ELN in open file formats and directly attached to the respective ELN experiment entry including instrumental setup metadata.
-- Metadata related to the obtained data, such as temperature or solvent of measurement, have to be provided according to metadata standards, e.g. x.
+<ElnFinder subDisc="Synthetic chemistry" />
 
-## Data producing methods
+A tool to help you find the right ELN is the so-called [ELN finder](https://eln-finder.ulb.tu-darmstadt.de/home) which is a searchable online repository for many different ELNs. It is important to note that not one size fits all and that one ELN may be appropriate for one research group, another ELN may be more appropriate for a different research group. Within NFDI4Chem, Chemotion ELN is the reference instance (find out more here in our [knowledge base article overview of Chemotion](/docs/chemotion_eln/)). This means that our developments in automatically applying the FAIR data principles to research data are implemented in Chemotion first.
 
-- Data can be collected during the experiment or after the experiment by analysing the obtained product.
-- Manually determined data: Experimental observations, appearance, yield, melting/boiling point, optical rotation, TLC Rf values, refraction index, etc.
-- Digital data are obtained with analytical devices. An overview on file extensions, file sizes and converters for several analytical methods is given in the table below.
-- Raw data files in [proprietary file formats](/docs/format_standards) should be saved alongside interoperable [open file formats](/docs/format_standards) by using converters or the software of the analytical device. If no specific open format is currently available, export as .txt or .csv is recommended. Please be aware that metadata included in the header of .txt or .csv files may not follow a defined (open) format and metadata should be additionally also added into the ELN.
+Chemotion is especially suitable for synthetic chemistry as it originally started out as an ELN for synthetic chemistry but has now been extended to a wider array of scientific disciplines through its [LabIMotion extension](https://chemotion.net/docs/labimotion).
 
-<Methods defaultProfile={"synthetic"} />
+## Publishing Data
 
-:::note *This table will be continuously updated with new recommendations on interoperable open file formats.
-:::
+[Publishing research data](/docs/data_publication/) is important in order to allow for the reuse of data by other researchers or for machine learning. Especially for machine learning, it is crucial that the data is published in a structured and standardised way. Where can you publish your data? Open access [data repositories](/docs/repositories/) are a good solution to provide your data for reuse by others. Choosing the right repository is crucial and as a general rule of thumb it is better to deposit your data in data-specific or discipline-specific repositories as these enforce more standardisation in how the data are published thus allowing for better machine-readability.
 
-## Data analysis
+In order to reach as many researchers as possible, choosing the right repository can be crucial (more on this in the [article on choosing the right repository](/docs/choose_repository/)).
 
-- Research data are processed, analysed and compared (also to data of other experiments) within the Chemotion ELN.
-- Optionally, preprocessing of digital data with software of analytical device before data are transferred to the Chemotion ELN (cf. data producing methods).
-- A detailed view, evaluation and interpretation of results is carried out with the Chemotion ELN features.
+Above you can see a modified version of our decision tree from our guide how to choose the right repository. Here is a table giving an overview of what data fits into what repository:
 
-## Publishing research data
+| Data type                                                                                                 | Data format                                                                                                                                                                                                                                                                                                                                                | Suggested Repository                                                                     | Criteria for selection                                                                                                                 |
+| :-------------------------------------------------------------------------------------------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :--------------------------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------- |
+| Nuclear Magnetic Resonance                                                                                | Bruker XWIN-NMR format (zip), [JCAMP-DX](/docs/JCAMP-DX/)                                                                                                                                                                                                                                                                                                  | [**Chemotion**](https://www.chemotion-repository.net/welcome)                            | Passing basic checks, curation                                                                                                         |
+| Nuclear Magnetic Resonance                                                                                | Bruker XWIN-NMR format, JOEL format NMReData, nmrML, ISA JSON                                                                                                                                                                                                                                                                                              | [**nmrXiv**](https://docs.nmrxiv.org/)                                                   | Validations / Minimum information reporting standards                                                                                  |
+| Molecules and their properties, identification, reactions and experimental investigations                 | mass spectrometry: JCAMP-DX, [mzMl](/docs/mzML/), mzXML (open, visualisable and processable), RAW for selected mass data types (processed and converted in JCAMP-DX), IR and Raman: JCAMP-DX, XRD: JCAMP-DX, UV/VIS: JCAMP-DX, Cyclic voltammetry: JCAMP-DX. \*Chemotion repo offers the option to convert data from different file formats into JCAMP-DX. | [**Chemotion**](https://www.chemotion-repository.net/welcome)                            | Passing basic checks, curation                                                                                                         |
+| Inorganic crystal structures                                                                              | Crystallographic Information File (CIF)                                                                                                                                                                                                                                                                                                                    | [**ICSD**](https://icsd.fiz-karlsruhe.de/)                                               | Crystal structure data available                                                                                                       |
+| Organic and metal-organic crystal structures                                                              | Crystallographic Information File (CIF) but other supporting file formats accepted                                                                                                                                                                                                                                                                         | [**CSD**](https://www.ccdc.cam.ac.uk/structures/)                                        | Cell parameters (single crystal), full coordinates (powder), in CIF format                                                             |
+| Organic, inorganic and metal-organic crystal structure data                                               | primarily Crystallographic Information File (CIF) but other supporting file formats accepted                                                                                                                                                                                                                                                               | [**joint CCDC/FIZ Access Structures ServiceD**](https://www.ccdc.cam.ac.uk/structures//) | At least one CIF file must be included in the submission and structure factor data for all structures should be provided (if possible) |
+| Generic data from all disciplines of chemistry, all data that do not fit in the disciplinary repositories | format-independent                                                                                                                                                                                                                                                                                                                                         | [**RADAR4Chem**](https://www.radar-service.eu/de)                                        | Validation against metadata schema                                                                                                     |
 
-- In addition to a research article in a scientific journal, the underlying research data are published in a repository and linked to the article to realise research data management according to the [FAIR data principles](/docs/fair) ([Best practice examples](/docs/best_practice)).
-- Data publications in repositories include raw and processed data for reuse.
-- The use of the Chemotion ELN enables a direct transfer of research data and the respective metadata into the Chemotion Repository. Subsequently, these data are automatically shared with other repositories, e.g. [PubChem](https://pubchem.ncbi.nlm.nih.gov/). For the publication of research data in other discipline-specific repositories, such as the [CCDC](https://www.ccdc.cam.ac.uk/) for crystallographic data, data have to be exported from the Chemotion ELN and uploaded into the respective database.
-- A [persistent identifier](/docs/pid) (e.g. DOI) is generated for a dataset by a repository (via [DataCite](https://datacite.org/) for the Chemotion Repository), which is given in the journal article or corresponding supporting information to link the data publication with the manuscript.
+Your own institution may also have additional guidelines & resources for publishing data, therefore it is always worth consulting the research data management experts of your local institution.
+
+# Challenges
+
+While for some data types & workflows it may be obvious how to comply with the FAIR principles, for others it is not as no community standards have been set and/or no appropriate open data formats are available. This is especially true for more niche analytical methods. Remember though: FAIR is a spectrum not an absolute. Therefore even if one of your workflows may not be as FAIR as the other, if it is as FAIR as is currently possible then it is still worth doing.
+
+Many old devices do not put out open-data formats and some devices have no digital output at all which makes good RDM more challenging though not impossible given the right tools (e.g. Chemotion’s [ChemConverter](https://chemotion.net/docs/services/chemconverter) which automatically generates open file formats from analytical devices which are not capable of outputting them).
+
+One of the biggest challenges to RDM in Chemistry at the moment is the lack of inter-ELN interoperability. This means that it is very challenging if not impossible to transfer data between different ELNs. This makes it especially challenging for interdisciplinary collaborations where collaborating groups use different ELNs. There are, however, efforts underway to establish inter-ELN interoperability such as the [ELN consortium](https://github.com/TheELNConsortium/) of which Chemotion is a member.

From 3478405240883c4f0d7d9cb9b7814d623654d3aa Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 7 Oct 2024 16:58:00 +0200
Subject: [PATCH 64/89] chore: save table from prettier

---
 docs/10_domains/40_synthetic_chemistry.mdx | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/docs/10_domains/40_synthetic_chemistry.mdx b/docs/10_domains/40_synthetic_chemistry.mdx
index 3bf8da5c..0df9adf4 100644
--- a/docs/10_domains/40_synthetic_chemistry.mdx
+++ b/docs/10_domains/40_synthetic_chemistry.mdx
@@ -42,15 +42,17 @@ In order to reach as many researchers as possible, choosing the right repository
 
 Above you can see a modified version of our decision tree from our guide how to choose the right repository. Here is a table giving an overview of what data fits into what repository:
 
-| Data type                                                                                                 | Data format                                                                                                                                                                                                                                                                                                                                                | Suggested Repository                                                                     | Criteria for selection                                                                                                                 |
-| :-------------------------------------------------------------------------------------------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :--------------------------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------- |
-| Nuclear Magnetic Resonance                                                                                | Bruker XWIN-NMR format (zip), [JCAMP-DX](/docs/JCAMP-DX/)                                                                                                                                                                                                                                                                                                  | [**Chemotion**](https://www.chemotion-repository.net/welcome)                            | Passing basic checks, curation                                                                                                         |
-| Nuclear Magnetic Resonance                                                                                | Bruker XWIN-NMR format, JOEL format NMReData, nmrML, ISA JSON                                                                                                                                                                                                                                                                                              | [**nmrXiv**](https://docs.nmrxiv.org/)                                                   | Validations / Minimum information reporting standards                                                                                  |
-| Molecules and their properties, identification, reactions and experimental investigations                 | mass spectrometry: JCAMP-DX, [mzMl](/docs/mzML/), mzXML (open, visualisable and processable), RAW for selected mass data types (processed and converted in JCAMP-DX), IR and Raman: JCAMP-DX, XRD: JCAMP-DX, UV/VIS: JCAMP-DX, Cyclic voltammetry: JCAMP-DX. \*Chemotion repo offers the option to convert data from different file formats into JCAMP-DX. | [**Chemotion**](https://www.chemotion-repository.net/welcome)                            | Passing basic checks, curation                                                                                                         |
-| Inorganic crystal structures                                                                              | Crystallographic Information File (CIF)                                                                                                                                                                                                                                                                                                                    | [**ICSD**](https://icsd.fiz-karlsruhe.de/)                                               | Crystal structure data available                                                                                                       |
-| Organic and metal-organic crystal structures                                                              | Crystallographic Information File (CIF) but other supporting file formats accepted                                                                                                                                                                                                                                                                         | [**CSD**](https://www.ccdc.cam.ac.uk/structures/)                                        | Cell parameters (single crystal), full coordinates (powder), in CIF format                                                             |
-| Organic, inorganic and metal-organic crystal structure data                                               | primarily Crystallographic Information File (CIF) but other supporting file formats accepted                                                                                                                                                                                                                                                               | [**joint CCDC/FIZ Access Structures ServiceD**](https://www.ccdc.cam.ac.uk/structures//) | At least one CIF file must be included in the submission and structure factor data for all structures should be provided (if possible) |
-| Generic data from all disciplines of chemistry, all data that do not fit in the disciplinary repositories | format-independent                                                                                                                                                                                                                                                                                                                                         | [**RADAR4Chem**](https://www.radar-service.eu/de)                                        | Validation against metadata schema                                                                                                     |
+{/* prettier-ignore-start */}
+| Data type | Data format | Suggested Repository | Criteria for selection |
+| :---- | :---- | :---- | :---- |
+| Nuclear Magnetic Resonance | Bruker XWIN-NMR format (zip), [JCAMP-DX](https://knowledgebase.nfdi4chem.de/knowledge_base/docs/JCAMP-DX/) | [**Chemotion**](https://www.chemotion-repository.net/welcome) | Passing basic checks, curation |
+| Nuclear Magnetic Resonance | Bruker XWIN-NMR format, JOEL format NMReData, nmrML, ISA JSON | [**nmrXiv**](https://docs.nmrxiv.org/) | Validations / Minimum information reporting standards |
+| Molecules and their properties, identification, reactions and experimental investigations | mass spectrometry: JCAMP-DX, [mzMl](https://knowledgebase.nfdi4chem.de/knowledge_base/docs/mzML/), mzXML (open, visualisable and processable), RAW for selected mass data types (processed and converted in JCAMP-DX), IR and Raman: JCAMP-DX, XRD: JCAMP-DX, UV/VIS: JCAMP-DX, Cyclic voltammetry: JCAMP-DX. \*Chemotion repo offers the option to convert data from different file formats into JCAMP-DX. | [**Chemotion**](https://www.chemotion-repository.net/welcome) | Passing basic checks, curation |
+| Inorganic crystal structures | Crystallographic Information File (CIF) | [**ICSD**](https://icsd.fiz-karlsruhe.de/) | Crystal structure data available |
+| Organic and metal-organic crystal structures | Crystallographic Information File (CIF) but other supporting file formats accepted | [**CSD**](https://www.ccdc.cam.ac.uk/structures/) | Cell parameters (single crystal), full coordinates (powder), in CIF format |
+| Organic, inorganic and metal-organic crystal structure data | primarily Crystallographic Information File (CIF) but other supporting file formats accepted | [**joint CCDC/FIZ Access Structures ServiceD**](https://www.ccdc.cam.ac.uk/structures//) | At least one CIF file must be included in the submission and structure factor data for all structures should be provided (if possible) |
+| Generic data from all disciplines of chemistry, all data that do not fit in the disciplinary repositories | format-independent | [**RADAR4Chem**](https://www.radar-service.eu/de) | Validation against metadata schema |
+{/* prettier-ignore-end */}
 
 Your own institution may also have additional guidelines & resources for publishing data, therefore it is always worth consulting the research data management experts of your local institution.
 

From b0aba437b4e870c2c8c906cd45fe93bf63a0e6bc Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 7 Oct 2024 17:37:03 +0200
Subject: [PATCH 65/89] chore: harmonise headings

---
 docs/10_domains/20_physical_chemistry.mdx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index fe018316..54b2e655 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -19,11 +19,11 @@ Physical chemistry is an interdisciplinary science at the frontier between chemi
 Physical Chemistry encompasses a variety of sub-disciplines, covering vast methodology, which, in turn, produce heterogenous data.
 From spectroscopic measurement data, imaging, to simulation input files and in-house data analysis code, many physical chemists are experienced in handling digital data. They are often well-versed in developing software solutions to support their work. While some work with large data volumes on a regular basis, other methodologies result in small, text-based files. This discipline includes many data-literate members, the expertise of which may be harnessed to implement tools and solutions to manage their research group's data in a unified and streamlined manner.
 
-## What Type of Data?
+## Data Types
 
 As mentioned, the data produced in physical chemistry and its diverse sub-disciples are varied. One research group may work intensively with imaging data such as superresolution microscopy, while the other may work on method development, and again others may analyze spectroscopic data or conduct numeric simulations—or even any combination of these.
 
-## What ELNs/Tools?
+## ELNs and Other Tools
 
 For effective data management, software tools should be selected in a uniform manner within a project or research group with the aim to [organize](docs/data_organisation) and streamline workflows. This involves establishing clear usage guidelines, including metadata templates drawn from minimum information standards for a given method, where available. These should be outlined in a [data management plan (DMP)](docs/dmp) for each project. Many universities supply tools and templates for DMPs (see the [respective article](doc/dmp) for more information).
 
@@ -39,7 +39,7 @@ Specifically for research data, [DataLad](https://www.datalad.org/), which is bu
 
 As many physical chemists may establish their own workflows or develop their own tools to acquire, process, and analyze their data, it is highly recommended to adhere to community-specific standards for file formats and metadata, where available. A bare mininum is to establish documentation and format standards within a research group, ensuring an efficient knowledge transfer from one generation of researchers to the next. An ELN can greatly assist in providing templates for documentation, while a DMP should be used to record the format standards. Employing automated workflows, e.g., from device to ELN and data storage systems, can greatly reduce manual steps in day-to-day work and can automatically ensure data and documentation are complete and formatted correctly. Some tools provide out-of-the-box solutions, such as device integration, while others provide options such as REST APIs to build custom methods.
 
-## How and where can data be published?
+## Publishing Data
 
 [Publishing research data](docs/data_publication), especially that underlying a published article, is an important aspect that allows others in the research community to replicate and build upon a researchers work. [Research data repositories](docs/repositories) serve as platforms for data publication and can greatly assist in [FAIR](docs/fair) data publication. Such repositories range from subject-specific to general and institutional. For many in physical chemistry and its varied data, general repositories such as [RADAR4Chem](https://radar.products.fiz-karlsruhe.de/de/radarabout/radar4chem) presents an option for publishing data for which now (sub-)discipline-specific repository has been established. [ioChem-BD](https://www.iochem-bd.org/) serves as a computational chemistry repository and includes a conversion service for many common data types to ensure interoperability. The [Image Data Resource (IDR)](https://idr.openmicroscopy.org/) makes biological imaging data available to the community, while self-hosted Omero repositoy can assist those working with other types of imaging data. <!--Nikki: as far as I know--> For more information on choices, head [here](docs/choose_repository).
 

From b13982327d6e8dbce33eee0ec84c9d704328626b Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 7 Oct 2024 17:37:27 +0200
Subject: [PATCH 66/89] fix: mdx comment syntax

---
 docs/10_domains/20_physical_chemistry.mdx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index 54b2e655..00ac513e 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -41,7 +41,7 @@ As many physical chemists may establish their own workflows or develop their own
 
 ## Publishing Data
 
-[Publishing research data](docs/data_publication), especially that underlying a published article, is an important aspect that allows others in the research community to replicate and build upon a researchers work. [Research data repositories](docs/repositories) serve as platforms for data publication and can greatly assist in [FAIR](docs/fair) data publication. Such repositories range from subject-specific to general and institutional. For many in physical chemistry and its varied data, general repositories such as [RADAR4Chem](https://radar.products.fiz-karlsruhe.de/de/radarabout/radar4chem) presents an option for publishing data for which now (sub-)discipline-specific repository has been established. [ioChem-BD](https://www.iochem-bd.org/) serves as a computational chemistry repository and includes a conversion service for many common data types to ensure interoperability. The [Image Data Resource (IDR)](https://idr.openmicroscopy.org/) makes biological imaging data available to the community, while self-hosted Omero repositoy can assist those working with other types of imaging data. <!--Nikki: as far as I know--> For more information on choices, head [here](docs/choose_repository).
+[Publishing research data](docs/data_publication), especially that underlying a published article, is an important aspect that allows others in the research community to replicate and build upon a researchers work. [Research data repositories](docs/repositories) serve as platforms for data publication and can greatly assist in [FAIR](docs/fair) data publication. Such repositories range from subject-specific to general and institutional. For many in physical chemistry and its varied data, general repositories such as [RADAR4Chem](https://radar.products.fiz-karlsruhe.de/de/radarabout/radar4chem) presents an option for publishing data for which now (sub-)discipline-specific repository has been established. [ioChem-BD](https://www.iochem-bd.org/) serves as a computational chemistry repository and includes a conversion service for many common data types to ensure interoperability. The [Image Data Resource (IDR)](https://idr.openmicroscopy.org/) makes biological imaging data available to the community, while self-hosted Omero repositoy can assist those working with other types of imaging data. {/* <!--Nikki: as far as I know--> */} For more information on choices, head [here](docs/choose_repository).
 
 For work that includes developing in-house research software solutions: **software is data and an integral part of research and should be published as such**. While only GitHub currently offers an automatic workflow for publishing software releases to [zenodo](https://zenodo.org/), there are methods to assign the [software a DOI, therefore making it citable](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/gitlab/repo-doi/).
 

From a645213d9bd8e5c2b47477ef001b58994b5265ab Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 7 Oct 2024 17:37:59 +0200
Subject: [PATCH 67/89] chore: harmonise headings

---
 docs/10_domains/40_synthetic_chemistry.mdx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/10_domains/40_synthetic_chemistry.mdx b/docs/10_domains/40_synthetic_chemistry.mdx
index 0df9adf4..399ab995 100644
--- a/docs/10_domains/40_synthetic_chemistry.mdx
+++ b/docs/10_domains/40_synthetic_chemistry.mdx
@@ -22,7 +22,7 @@ The synthesis of a specific product is followed by analysing its properties. Reg
 
 Overall, [metadata](/docs/metadata/) should always be included when collecting and [storing](/docs/data_storage/) data to allow understanding of the research data in the long term.
 
-# What ELNs/Tools?
+# ELNs and Other Tools
 
 For planning research data management and creating data management plans, tools such as [RDMO](https://rdmorganiser.github.io/) and [DMP-Online](https://dmponline.dcc.ac.uk/) are suitable. Many universities have their own instances of these solutions.
 

From 0088a224e11f43d2ee2dfec1a1fe803bb5c90c80 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 7 Oct 2024 17:41:01 +0200
Subject: [PATCH 68/89] chore: remove polymer chem

---
 docs/10_domains/30_polymer_chemistry.mdx | 48 ------------------------
 1 file changed, 48 deletions(-)
 delete mode 100644 docs/10_domains/30_polymer_chemistry.mdx

diff --git a/docs/10_domains/30_polymer_chemistry.mdx b/docs/10_domains/30_polymer_chemistry.mdx
deleted file mode 100644
index 23af2c00..00000000
--- a/docs/10_domains/30_polymer_chemistry.mdx
+++ /dev/null
@@ -1,48 +0,0 @@
----
-title: "Polymer Chemistry"
-slug: "/polymer_chemistry"
----
-
-
-import Methods from '@site/src/components/Methods.js';
-
-:::info Summary:
-
-Polymer chemistry is focused on the synthesis and characterization of monomer units, macromolecules and resultant
-materials for applications in e.g. optics, electronics and energy, packaging and containers, coatings and adhesives,
-catalysis or medicine. Polymeric materials can be subdivided by their origin into synthetic, inorganic and
-biopolymers, where the latter is a significant subject of recent research as they can be derived from renewable
-resources and therefore are deemed to be part of the solution for a sustainable future. The toolbox for monomer synthesis and modification, their polymerization as well as post-functionalization are often translated form organic chemistry, yet for cutting-edge materials new experimental strategies have to be developed. Many characterization methods, especially for monomers or small polymers, can also be adapted from established organic chemistry. However, since macromolecules can feature highly complex structures, e.g. brushes, dendrimers, rings and star shapes, advanced methods such as (2D) SEC, LCCC, DOSY NMR, or electron microscopy need to be applied in order to obtain an exhaustive structure determination (for abbreviations see table below). For their subsequent application as high-tech material, their mechanical and physical properties play an important role as well, where cyclic voltammetry or rheological characterization are just a few examples for the vast array of techniques that are available. A standard approach for the development of new polymeric materials can be described as follows:
-
-- Preparation of organic/inorganic monomer units.
-- Small-scale experiments for screening/optimization of reaction conditions.
-- Upscaling of reactions to obtain sufficient product for subsequent polymerization steps.
-- (Co)polymerization of monomers in different ratios/chain lengths as well as optimization of reaction conditions.
-- Post-polymerization functionalization.
-- Synthesis of macroscopic materials through 3D printing, moulding etc.
-
-In order to collect comprehensive analytical data to characterize the synthesized materials the following steps can be taken:
-
-- Data can be collected during the experiment through online methods, drawing samples on a specific schedule, or after the experiment by analyzing the obtained product.
-- Manually determined data: Experimental observations such as colour change or precipitants, appearance, yield and consistency of the product, solubility etc.
-- Digital data are obtained with analytical devices. An overview on file extensions, file sizes and converters for several analytical methods is given in the table below.
-- When necessary, pre-processing of digital data with software of analytical device before data are transferred to the Chemotion-ELN.
-- Raw data files in proprietary file formats should be saved alongside interoperable open file formats by using converters or the software of the analytical device. If no specific open format is currently available, exporting as .txt or .csv is recommended. Please be aware that metadata included in the header of .txt or .csv files may not follow a defined (open) format and metadata should be additionally also added into the ELN.
-:::
-
-
-## Documentation and publication of research data
-
-The Chemotion-ELN was initially developed for organic chemistry and is now adapted for other disciplines in chemistry as well. The adaption for polymer chemistry and the integration of analytical methods are now ongoing, therefore the individual methods in the table below are marked respectively. Generally, the documentation of research data is conducted as follows:
-
-- Documentation of research data  is carried out digitally using an ELN.
-- Experimental conditions (e.g. solvents, temperature, duration, pressure) are noted in the ELN.
-- Observations and results of analytical methods with no digital output (i.e. no data files) are added manually to the ELN entry of the experiment, including colour change or precipitants, appearance, yield and consistency of the product, solubility etc.
-- Obtained data from analytical instruments (e.g. NMR, SEC, MS or IR data) are uploaded to the Chemotion-ELN in open file formats and directly attached to the respective ELN experiment entry including instrumental setup metadata.
-
-In an effort to realize research data management in line with the FAIR principles, the data can be published in a repository including raw and processed data for reuse, directly from the Chemotion-ELN. The use of the Chemotion-ELN enables a direct transfer of research data and the respective metadata into the Chemotion Repository. Subsequently, these data are automatically shared with other repositories, e.g. PubChem. For the publication of research data in other discipline-specific repositories, data have to be exported from the Chemotion-ELN and uploaded into the respective database.
-
-<Methods defaultProfile={"polymer"} />
-
-:::note *This table will be continuously updated with new recommendations on interoperable open file formats.
-:::

From b061f62f17ded115c86ab615445e161f4acd7a23 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 7 Oct 2024 17:43:11 +0200
Subject: [PATCH 69/89] chore: do not use summary for now

---
 docs/10_domains/20_physical_chemistry.mdx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index 00ac513e..7b75c797 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -9,10 +9,10 @@ import ElnFinder from "@site/src/components/eln/ElnFinder.js";
 <LbeChip title="physical chemistry" />
 <LbeChip title="cheminformatics" />
 
-:::info Summary:
-
+{/* prettier-ignore */}
+{/* :::info Summary:
 Physical chemistry is an interdisciplinary science at the frontier between chemistry and physics, whose topics go beyond the classical areas of the respective individual sciences. While preparative chemistry focuses on questions of the methodology of chemical synthesis of known and new substances, physical chemistry attempts to describe the properties of substances and their transformation by applying concepts of physics to objects of chemistry by means of theoretical and experimental methods. Along with organic and inorganic chemistry, physical chemistry therefore represents one of the three key disciplines of "classical" chemistry, since it provides the theoretical basis for technical chemistry and process engineering. Its knowledge is also an integral part of many other disciplines and is used, for example, for description and understanding in biology and medicine, meteorology as well as the earth sciences. Due to this great interdisciplinarity and the use of numerous physicochemical methods in almost all areas of chemistry, a complete description of physical chemistry as profile is hardly possible, which is why this article explicitly makes no claim to do so.
-:::
+::: \*/}
 
 ## Introduction
 

From e1fd7c6618ecb8825b4b9c80d3f97e8b03b99d95 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 7 Oct 2024 17:45:17 +0200
Subject: [PATCH 70/89] fix: heading depth

---
 docs/10_domains/40_synthetic_chemistry.mdx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/10_domains/40_synthetic_chemistry.mdx b/docs/10_domains/40_synthetic_chemistry.mdx
index 399ab995..1aee3983 100644
--- a/docs/10_domains/40_synthetic_chemistry.mdx
+++ b/docs/10_domains/40_synthetic_chemistry.mdx
@@ -10,7 +10,7 @@ import ElnFinder from "@site/src/components/eln/ElnFinder.js";
 <LbeChip title="inorganic chemistry" />
 <LbeChip title="organic chemistry" />
 
-# Introduction
+## Introduction
 
 During the synthesis of a desired compound, all steps, such as planning, realisation and documentation of an experiment, or characterisation of the obtained product, provide research data. These data are synthetic procedures, experimental conditions, as well as manually and digital data collected with analytical devices. Processing and interpretation of the obtained research data will lead to a proof of concept for a given reaction, optimised conditions for future experiments or upscaling.
 

From 4142627f5772a498a995b51d92f91e57037630f7 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Wed, 30 Oct 2024 17:36:27 +0100
Subject: [PATCH 71/89] chore: add link to contributing page

---
 footer.json | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/footer.json b/footer.json
index dfdeedb6..14bdc3c4 100644
--- a/footer.json
+++ b/footer.json
@@ -2,6 +2,10 @@
     {
         "title": "Contribute",
         "items": [
+            {
+                "label": "Getting Started",
+                "href": "/docs/contributing"
+            },
             {
                 "label": "Content (GitHub)",
                 "href": "https://github.com/NFDI4Chem/knowledge_base"

From 402cd55846129f07550758b17ca699a9be84c494 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Wed, 30 Oct 2024 17:37:07 +0100
Subject: [PATCH 72/89] fix: remove faq links

---
 footer.json | 4 ----
 navbar.json | 4 ----
 2 files changed, 8 deletions(-)

diff --git a/footer.json b/footer.json
index 14bdc3c4..b0f2400a 100644
--- a/footer.json
+++ b/footer.json
@@ -23,10 +23,6 @@
                 "label": "NFDI4Chem Website",
                 "href": "https://nfdi4chem.de"
             },
-            {
-                "label": "NFDI4Chem FAQ",
-                "href": "https://www.nfdi4chem.de/index.php/frequently-asked-questions/"
-            },
             {
                 "label": "NFDI4Chem Helpdesk",
                 "href": "https://nfdi4chem.de/index.php/helpdesk/"
diff --git a/navbar.json b/navbar.json
index 145bf9dd..22e47758 100644
--- a/navbar.json
+++ b/navbar.json
@@ -22,10 +22,6 @@
             "label": "Search Service",
             "href": "https://search.nfdi4chem.de/"
         },
-        {
-            "label": "FAQ",
-            "href": "https://www.nfdi4chem.de/index.php/frequently-asked-questions/"
-        },
         {
             "type": "localeDropdown",
             "position": "right",

From bf9d550d979b01a3f4d8cc52dacab714c7437ce1 Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Thu, 31 Oct 2024 09:20:41 +0000
Subject: [PATCH 73/89] fix typo, add comment

---
 .../10_publishing_standards_authors.mdx                       | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx
index b1103dd4..3714bde7 100644
--- a/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx
+++ b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx
@@ -5,6 +5,8 @@ slug: "/publishing_standards_authors"
 
 ### Use ORCID iD to identifiy authors and ROR to identifiy institutions
 
+<!--image "order of operations" needed (flowchart)-->
+
 :::tip Standard
 _Authors should provide their ORCID iD to identify the authors/creators and contributors, and their ROR identifier to identify the institution to which they are affiliated._
 :::
@@ -49,7 +51,7 @@ Research data repositories offer the option to add a related identifier to link
 _Researchers should link their datasets to be published to their corresponding articles using the relation type `IsSupplementTo`._
 :::
 
-According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. For published articles, [Crossref's documentation on relationships](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) recommends that `isSupplmenetTo` should be used to link datasets generated as part of research results. Please note that some repositories automatically detect whether the linked object is an article or some other dataset published in another repository, and therefore don't require authors to specify a relation(ship) type.
+According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. For published articles, [Crossref's documentation on relationships](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) recommends that `isSupplmentTo` should be used to link datasets generated as part of research results. Please note that some repositories automatically detect whether the linked object is an article or some other dataset published in another repository, and therefore don't require authors to specify a relation(ship) type.
 
 ### Usage of Collection DOIs
 

From e6e7a253b9766980a50b702c3b5e58ca0d635834 Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Thu, 31 Oct 2024 09:38:50 +0000
Subject: [PATCH 74/89] add more comment

---
 .../70_publishing_standards/10_publishing_standards_authors.mdx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx
index 3714bde7..1c82a5c6 100644
--- a/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx
+++ b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx
@@ -5,7 +5,7 @@ slug: "/publishing_standards_authors"
 
 ### Use ORCID iD to identifiy authors and ROR to identifiy institutions
 
-<!--image "order of operations" needed (flowchart)-->
+<!--image "order of operations" needed (flowchart). May need to highlight various types of workflows, e.g., at which stage of the manuscript publication process data should be published.-->
 
 :::tip Standard
 _Authors should provide their ORCID iD to identify the authors/creators and contributors, and their ROR identifier to identify the institution to which they are affiliated._

From b9ef569811fe197d5bef6ac96e236727049b005c Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Thu, 31 Oct 2024 09:52:36 +0000
Subject: [PATCH 75/89] add: emphasis on linking data via Crossref metadata;
 check: Crossref spelling

---
 .../20_publishing_standards_publishers.mdx                    | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx
index 2b13bd03..91807ada 100644
--- a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx
+++ b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx
@@ -33,7 +33,9 @@ To assist authors in selecting **well-established and community-specific [reposi
 *Journals should use the information available in data availability statements to enhance Crossref DOI metadata by linking articles to datasets.*
 :::
 
-With the DOI and repository name in hand, journals should enrich Crossref DOI metadata of articles published following the [FAIR](/docs/fair/) principles (e.g [F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below), [I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). This establishes a structured **link** between the DOI of the article and the  DOI of the dataset and ensures humans and machines alike can interpret the relationship between the published objects. For Crossref metadata, a `related_item` should be added to mention the name of the repository (equal to `publisher` in the corresponding dataset DataCite DOI metadata). 
+With the DOI and repository name in hand, journals should enrich Crossref DOI metadata of articles published following the [FAIR](/docs/fair/) principles (e.g [F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below), [I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). This establishes a structured **link** between the DOI of the article and the  DOI of the dataset and ensures humans and machines alike can interpret the relationship between the published objects. Without defining this relation, only humans can effectively interpret this connection through the data availability statement, effectively resulting in a missing link between the the reported results in the article and the underlying research data. For Crossref metadata, a `related_item` should be added to mention the name of the repository (equal to `publisher` in the corresponding dataset DataCite DOI metadata). 
+
+<!--image clarifiyng why this is important-->
 
 In agreement with [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/), the relationship type `isSupplementedBy` should be used.
 

From 2214efe69f57c4dcc77ea3a94934ea5e9a4f6575 Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Thu, 31 Oct 2024 09:58:04 +0000
Subject: [PATCH 76/89] fix: grammar

---
 .../20_publishing_standards_publishers.mdx                    | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx
index 91807ada..4314c8ab 100644
--- a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx
+++ b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx
@@ -73,13 +73,13 @@ A disadvantage of pre-submission is that researchers cannot link the dataset to
 
 Some repositories have an *under review* status alongside the *draft* and *published* statuses. A dataset *under review* is not editable and not yet published, i.e. it does not have a DOI registered. Therefore, the DOI cannot be validated. Nonetheless, the dataset has an internally reserved DOI and is accessible via a URL to provide access to editors and reviewers. This allows research data to be included in the review process. The URL to access the dataset should be requested by the submission system so that it can be forwarded to editors and reviewers.
 
-### Encourage authors to publish datasets *under review* prior the articles gets published
+### Encourage authors to publish datasets *under review* prior to article publication
 
 :::tip Standard
 *Journal author guidelines should require that datasets with status under review to be published prior to the publication of the associated article.*
 :::
 
-To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets *under review* should be published before the article gets published**. Once a manuscript has been accepted, the authors should be informed to publish their dataset *under review*. This ensures that the data has a registered DOI when the article gets published. Consequently, journals can run quality control checks on the provided DOI such as validation. This process must be explicitly communicated with authors through the author guidelines, yet, can also be included within other communication upon acceptance. Contemporaneous, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to the publication of the dataset. Finally, the article is published, and its DOI is registered.
+To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets *under review* should be published before the article is published**. Once a manuscript has been accepted, the authors should be informed to publish their dataset *under review*. This ensures that the data has a registered DOI when the article gets published. Consequently, journals can run quality control checks on the provided DOI such as validation. Publishers must explicitly communicate this process with authors through the author guidelines. In addition, other communication upon acceptance may also include this informaton. Contemporaneous, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to the publication of the dataset. Finally, the article is published, and its DOI is registered.
 
 ### Scholix.org
 

From 26fad7411b7281bdcea11db74a01d928c073747a Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Thu, 31 Oct 2024 13:34:00 +0000
Subject: [PATCH 77/89] add: note on third-party data ownership

---
 .../20_publishing_standards_publishers.mdx                      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx
index 4314c8ab..8ddbb898 100644
--- a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx
+++ b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx
@@ -25,7 +25,7 @@ To assist authors in selecting **well-established and community-specific [reposi
 *Journals should add a data availability statement to published articles and collect the necessary information through their submission systems.*
 :::
 
-[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or a similarly termed section should also be added to the manuscript submission system. Once a template has been selected by the submitter, the data availability statement should be editable to allow authors to add additional information, such as what data are included in the dataset, similar to what is currently often mentioned in the section on supporting information PDF files. The submission system should then require the submitter to provide the necessary information, such as the DOI (specified as [DOI name](https://www.doi.org/doi-handbook/HTML/doi-name-syntax2.html) e.g. `10.1000/182` or as a URL i.e. including a resolver e.g. `https://doi.org/10.1000/182` ), repository name, third party name and contact information, or reasons for restricted access and information on how to access a dataset, depending on the template used.
+[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or a similarly termed section should also be added to the manuscript submission system. Once a template has been selected by the submitter, the data availability statement should be editable to allow authors to add additional information, such as what data are included in the dataset, similar to what is currently often mentioned in the section on supporting information PDF files. The submission system should then require the submitter to provide the necessary information, such as the DOI (specified as [DOI name](https://www.doi.org/doi-handbook/HTML/doi-name-syntax2.html) e.g. `10.1000/182` or as a URL i.e. including a resolver e.g. `https://doi.org/10.1000/182` ), repository name, third party name and contact information (in case of third-party data ownership), or reasons for restricted access and information on how to access a dataset, depending on the template used.
 
 ### Link datasets to articles in Crossref DOI metadata
 

From 8b6a0c6e6e7c3b23de93e3e6d82bf70bd2597b0c Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Thu, 31 Oct 2024 13:40:16 +0000
Subject: [PATCH 78/89] fix comment on linking

---
 .../20_publishing_standards_publishers.mdx                      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx
index 8ddbb898..c34472d5 100644
--- a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx
+++ b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx
@@ -33,7 +33,7 @@ To assist authors in selecting **well-established and community-specific [reposi
 *Journals should use the information available in data availability statements to enhance Crossref DOI metadata by linking articles to datasets.*
 :::
 
-With the DOI and repository name in hand, journals should enrich Crossref DOI metadata of articles published following the [FAIR](/docs/fair/) principles (e.g [F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below), [I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). This establishes a structured **link** between the DOI of the article and the  DOI of the dataset and ensures humans and machines alike can interpret the relationship between the published objects. Without defining this relation, only humans can effectively interpret this connection through the data availability statement, effectively resulting in a missing link between the the reported results in the article and the underlying research data. For Crossref metadata, a `related_item` should be added to mention the name of the repository (equal to `publisher` in the corresponding dataset DataCite DOI metadata). 
+With the DOI and repository name in hand, journals should enrich Crossref DOI metadata of articles published following the [FAIR](/docs/fair/) principles (e.g [F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below), [I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). This establishes a structured **link** between the DOI of the article and the  DOI of the dataset and ensures humans and machines alike can interpret the relationship between the published objects. Without defining a relation in the Crossref metadata, only humans can effectively interpret this connection through the data availability statement, effectively resulting in a missing link between the the reported results in the article and the underlying research data. For Crossref metadata, a `related_item` should be added to mention the name of the repository (equal to `publisher` in the corresponding dataset DataCite DOI metadata). 
 
 <!--image clarifiyng why this is important-->
 

From 9f3f93768eed1d229eb846af163c7f7445fefada Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Thu, 31 Oct 2024 13:50:17 +0000
Subject: [PATCH 79/89] fix: generic sentence, improve text

---
 .../30_publishing_standards_infrastructure.mdx                  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx b/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx
index 5c2f184c..3cce7b07 100644
--- a/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx
+++ b/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx
@@ -9,7 +9,7 @@ slug: "/publishing_standards_infrastructure"
 *Research data repositories should include the metadata in datasets downloaded by researchers and exchanged with other resources.*
 :::
 
-While researchers upload their data, metadata is attached. For generic, multidisciplinary repositories, additional metadata is provided by researchers via a metadata editor. For field-specific repositories, the metadata is extracted from the analytical data files and provided by researchers along their lab workflows, as this is the case for Chemotion ELN. Once data is retrieved from a repository, this metadata should not be lost but should be included in the downloaded package. The minimum to include is the descriptive DataCite metadata. 
+Generic and technical metadata is attached to the dataset during the upload process. For generic, multidisciplinary repositories, researchers provide additional metadata via a metadata editor. For field-specific repositories, the metadata is extracted from the analytical data files and provided by researchers along their lab workflows, as this is the case for Chemotion ELN. Once data is retrieved from a repository, this metadata should not be lost but should be included in the downloaded package. The minimum to include is the descriptive DataCite metadata. 
 
 [BagIt](https://www.rfc-editor.org/rfc/rfc8493.html), a set of hierarchical file system conventions, is one solution to enable reliable file transfer and to include metadata in downloaded dataset, as this is already the case for RADAR. 
 

From e2a0ac12820fb9c35de60b14344876c262b9583f Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Thu, 31 Oct 2024 13:52:43 +0000
Subject: [PATCH 80/89] fix: grammar

---
 .../30_publishing_standards_infrastructure.mdx                | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx b/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx
index 3cce7b07..c6fac3d2 100644
--- a/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx
+++ b/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx
@@ -19,7 +19,7 @@ Generic and technical metadata is attached to the dataset during the upload proc
 *Research data repositories should include structured, domain-specific metadata in datasets downloaded by researchers and exchanged with other resources.*
 :::
 
-Beside of metadata following generic schemes such as DataCite's metadata scheme, domain-specific metadata should be part of each dataset. This metadata should also be provided in datasets downloaded by researchers for reuse or exchanged with other resources. 
+Besides metadata following generic schemes such as DataCite's metadata scheme, domain-specific metadata should be part of each dataset. This metadata should also be provided in datasets downloaded by researchers for reuse or exchanged with other resources. 
 
 One solution to this is to include Schema.org metadata making use of [RO-Crate](https://www.researchobject.org/) or by even [combining RO-Crate and BagIt](https://www.researchobject.org/ro-crate/specification/1.1/appendix/implementation-notes.html#adding-ro-crate-to-bagit). While BagIt focusses on reliable transfer, RO-Crate is about rich metadata. 
 
@@ -29,7 +29,7 @@ One solution to this is to include Schema.org metadata making use of [RO-Crate](
 *Research data repositories should provide a Collection DOI to wrap research data objects that are relevant to a single article that is to be published.*
 :::
 
-Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, each repository should allow authors to generate a **Collection DOI** that wraps relevant data that should be referenced in the data availability statement.
+Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, each repository should allow authors to generate a [**Collection DOI**](https://chemotion.net/docs/repo/doi) that wraps relevant data that should be referenced in the data availability statement.
 
 ### Embargo period and metadata accessibility
 

From 12cb7f35aecea727883887055b5630a1588d09a5 Mon Sep 17 00:00:00 2001
From: Nikki Parks <60778202+nap84@users.noreply.github.com>
Date: Thu, 31 Oct 2024 13:55:00 +0000
Subject: [PATCH 81/89] add links

---
 .../30_publishing_standards_infrastructure.mdx                  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx b/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx
index c6fac3d2..a5b4227c 100644
--- a/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx
+++ b/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx
@@ -19,7 +19,7 @@ Generic and technical metadata is attached to the dataset during the upload proc
 *Research data repositories should include structured, domain-specific metadata in datasets downloaded by researchers and exchanged with other resources.*
 :::
 
-Besides metadata following generic schemes such as DataCite's metadata scheme, domain-specific metadata should be part of each dataset. This metadata should also be provided in datasets downloaded by researchers for reuse or exchanged with other resources. 
+Besides metadata following generic schemes such as [DataCite's metadata scheme](https://schema.datacite.org/), domain-specific metadata should be part of each dataset. This metadata should also be provided in datasets downloaded by researchers for reuse or exchanged with other resources. 
 
 One solution to this is to include Schema.org metadata making use of [RO-Crate](https://www.researchobject.org/) or by even [combining RO-Crate and BagIt](https://www.researchobject.org/ro-crate/specification/1.1/appendix/implementation-notes.html#adding-ro-crate-to-bagit). While BagIt focusses on reliable transfer, RO-Crate is about rich metadata. 
 

From 3933e1290510db7bedb7bb288d984aaf25b9a1c5 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 4 Nov 2024 13:45:45 +0100
Subject: [PATCH 82/89] Update
 docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx

Co-authored-by: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com>
---
 .../70_publishing_standards/10_publishing_standards_authors.mdx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx
index 1c82a5c6..fcae5fcd 100644
--- a/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx
+++ b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx
@@ -51,7 +51,7 @@ Research data repositories offer the option to add a related identifier to link
 _Researchers should link their datasets to be published to their corresponding articles using the relation type `IsSupplementTo`._
 :::
 
-According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. For published articles, [Crossref's documentation on relationships](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) recommends that `isSupplmentTo` should be used to link datasets generated as part of research results. Please note that some repositories automatically detect whether the linked object is an article or some other dataset published in another repository, and therefore don't require authors to specify a relation(ship) type.
+According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. For published articles, [Crossref's documentation on relationships](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) recommends that `isSupplementTo` should be used to link datasets generated as part of research results. Please note that some repositories automatically detect whether the linked object is an article or some other dataset published in another repository, and therefore don't require authors to specify a relation(ship) type.
 
 ### Usage of Collection DOIs
 

From cf0cbb38599c74a1604d39c1101bbe84fda3ea21 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 4 Nov 2024 13:47:04 +0100
Subject: [PATCH 83/89] MDX style comments if absolutely necessary

---
 .../70_publishing_standards/10_publishing_standards_authors.mdx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx
index fcae5fcd..ff8ee603 100644
--- a/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx
+++ b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx
@@ -5,7 +5,7 @@ slug: "/publishing_standards_authors"
 
 ### Use ORCID iD to identifiy authors and ROR to identifiy institutions
 
-<!--image "order of operations" needed (flowchart). May need to highlight various types of workflows, e.g., at which stage of the manuscript publication process data should be published.-->
+{/* image "order of operations" needed (flowchart). May need to highlight various types of workflows, e.g., at which stage of the manuscript publication process data should be published. */}
 
 :::tip Standard
 _Authors should provide their ORCID iD to identify the authors/creators and contributors, and their ROR identifier to identify the institution to which they are affiliated._

From 4146d39f282bb4afdfb09bd8acc5a9a5614e2371 Mon Sep 17 00:00:00 2001
From: Ted-Bender <122031815+Ted-Bender@users.noreply.github.com>
Date: Tue, 5 Nov 2024 09:47:19 +0100
Subject: [PATCH 84/89] Update 10_dmp.mdx
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

RDMO ergänzt.
---
 docs/30_data/10_dmp.mdx | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/docs/30_data/10_dmp.mdx b/docs/30_data/10_dmp.mdx
index 4af450e6..157ef100 100644
--- a/docs/30_data/10_dmp.mdx
+++ b/docs/30_data/10_dmp.mdx
@@ -61,14 +61,16 @@ The DFG has been offering a [checklist](https://www.dfg.de/en/research_funding/p
 
 ## DMP Tools
 
-The creation of a DMP can be supported by various tools. Some of the most common tools are:
+The creation of a DMP can be supported by various tools. 
 
+NFDI4Chem is proud to present an RDMO template specifically tailored to the needs of chemists. At [https://rdmo.nfdi4chem.de/](https://rdmo.nfdi4chem.de/) you will find a questionnaire that will lead you to a detailed DMP for your project.
+The [Research Data Management Organiser (RDMO)](https://rdmo.aip.de/) is run at 45 research institutions in Germany and abroad (as of January 2022). It was developed in a DFG-funded project (2015–2020) and is now further maintained by the RDMO working group as an open source software. It offers several "question catalogs" for specific funding programs, disciplines, or research consortia. They enable researchers to organise their data management with the help of precisely formulated questions, help texts, multiple-choice answers. User-created catalogs may be reused and are available for download in a [central repository](https://github.com/rdmorganiser/rdmo-catalog).
+
+Further tools are:
 [DMPOnline](https://dmponline.dcc.ac.uk/) was developed by the UK Digital Curation Centre (DCC). It includes a template for Horizon Europe projects as well as from the main UK funders. It also provides short general explanations for every single question. DMPOnline and DMPTool are based on the software DMPRoadmap.
 
 [DMPTool](https://dmptool.org/) is run by the California Digital Library. Due to the different funding landscape in the US, the tool is only of limited use for German/European projects. One advantage is that DMPTool provides DMP examples on the website. It can be used without using the tool.
 
-[Research Data Management Organiser (RDMO)](https://rdmo.aip.de/) is run at 45 research institutions in Germany and abroad (as of January 2022). It was developed in a DFG-funded project (2015–2020) and is now further maintained by the RDMO working group as an open source software. It offers several "question catalogs" for specific funding programs, disciplines, or research consortia. They enable researchers to organise their data management with the help of precisely formulated questions, help texts, multiple-choice answers. User-created catalogs may be reused and are available for download in a [central repository](https://github.com/rdmorganiser/rdmo-catalog).
-
 To further support researchers in answering the questions, working groups have been formed, e.g. in Science Europe or the Research Data Alliance (RDA). The Science Europe Group is focusing on improving the general help texts, while the working group in the RDA focuses on [discipline-specific guidance](https://www.rd-alliance.org/groups/discipline-specific-guidance-data-management-plans-wg). Science Europe set up a new version of the [practical guide](https://www.scienceeurope.org/our-resources/practical-guide-to-the-international-alignment-of-research-data-management/) in January 2021.
 
 A comparison of commonly used DMP tools can be found in the [DMP-Toolguide](https://zenodo.org/record/4632308).

From 7b6423c853d151711b25fe95d15ed8c8f3e5a431 Mon Sep 17 00:00:00 2001
From: Ted-Bender <122031815+Ted-Bender@users.noreply.github.com>
Date: Mon, 11 Nov 2024 11:36:33 +0100
Subject: [PATCH 85/89] Update 15_choose_eln.mdx
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Defekten LabTrove-Link geändert.
---
 docs/40_smartlab/15_choose_eln.mdx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/40_smartlab/15_choose_eln.mdx b/docs/40_smartlab/15_choose_eln.mdx
index cc36060f..ed73d8a0 100644
--- a/docs/40_smartlab/15_choose_eln.mdx
+++ b/docs/40_smartlab/15_choose_eln.mdx
@@ -8,7 +8,7 @@ import useBaseUrl from '@docusaurus/useBaseUrl';
 
 # Choose the right ELN
 
-To date, there is not one ELN, that fits the requirements for all chemical disciplines. Furthermore, only a few ELNs meet the basic requirements for chemical sciences. This is most likely due to the challenges arising from drawing and processing chemical structures, a crucial and central step in being able to correlate research data to the corresponding chemical reaction or structure. The organisation of work with ELNs that support chemistry-specific functions can offer several benefits, such as the availability of [chemical structure identifiers](/docs/machine-readable_chemical_structures) and [standardised formats](/docs/format_standards) as well as the integration of manifold tools and workflows that facilitate scientific work. The direct integration of tools enables a direct support of the scientist without the need to search for additional services and software, thus bringing new developments and information directly to the scientists’ awareness. Some Open Source examples for systems in chemistry that offer the necessary support for chemical structures include [Indigo-ELN](https://lifescience.opensource.epam.com/indigo/eln/index.html), [LabTrove](http://labtrove.org/), [OpenEnventory](http://www.open-enventory.de/), and [Chemotion ELN](https://eln.chemotion.net/home).
+To date, there is not one ELN, that fits the requirements for all chemical disciplines. Furthermore, only a few ELNs meet the basic requirements for chemical sciences. This is most likely due to the challenges arising from drawing and processing chemical structures, a crucial and central step in being able to correlate research data to the corresponding chemical reaction or structure. The organisation of work with ELNs that support chemistry-specific functions can offer several benefits, such as the availability of [chemical structure identifiers](/docs/machine-readable_chemical_structures) and [standardised formats](/docs/format_standards) as well as the integration of manifold tools and workflows that facilitate scientific work. The direct integration of tools enables a direct support of the scientist without the need to search for additional services and software, thus bringing new developments and information directly to the scientists’ awareness. Some Open Source examples for systems in chemistry that offer the necessary support for chemical structures include [Indigo-ELN](https://lifescience.opensource.epam.com/indigo/eln/index.html), [LabTrove](https://sourceforge.net/projects/labtrove/), [OpenEnventory](http://www.open-enventory.de/), and [Chemotion ELN](https://eln.chemotion.net/home).
 
 Therefore, choosing the right ELN is crucial for a successful implementation of an ELN in a laboratory. Three steps should be taken to establish an ELN: 1) Needs assessment, 2) Testing and 3) Introducing the chosen ELN.
 

From 718ec96a1c4ec294eae47cab7981106e602c6a57 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 11 Nov 2024 16:33:01 +0100
Subject: [PATCH 86/89] fix: broken link

---
 .../62_data_formats/00_format_standards.mdx   | 42 +++++++------------
 1 file changed, 16 insertions(+), 26 deletions(-)

diff --git a/docs/60_topics/62_data_formats/00_format_standards.mdx b/docs/60_topics/62_data_formats/00_format_standards.mdx
index e9339c0e..ab4ebe48 100644
--- a/docs/60_topics/62_data_formats/00_format_standards.mdx
+++ b/docs/60_topics/62_data_formats/00_format_standards.mdx
@@ -14,7 +14,7 @@ A successful data format standard is defined by the data model and the data repr
 
 The **Data model** describes how data is organised, which information they contain, the data types (e.g. text, numbers, lists), the relationship between these components, and rules of component and data integrity. Conceptually, the model and its components can be organised in different ways, e.g. flat, multidimensional, as network or hierarchical. The meaning of the applied components has to be well described in an unambiguous way. [Ontologies](/docs/ontology) can be consulted to ensure a consistent usage of the components in the context of the model. As the data model is abstract, it is necessary to implement representations for it, such as a database or data file on a computer.
 
-Digital files containing data are only one way to represent a data model. Other **representations** would be response data from API requests or results from a database query. 
+Digital files containing data are only one way to represent a data model. Other **representations** would be response data from API requests or results from a database query.
 
 **File formats** as models can be categorised by different criteria: proprietorially vs. openly specified, binary vs. text, simple vs. complex or flat vs. n-dimensional. For long-term storage, a compact binary format may be the first choice, while for further processing with cheminformatics tools a format based on standards like Comma Separated Values (CSV), Extensible Markup Language (XML) or JavaScript Object Notation (JSON) may be more favourable due to support by most programming languages. When thinking about data strategies, open formats should be considered. Proprietary formats may prevent further reuse due to issues connected to licensing, poor documentation and support by the vendor. Complex data often need more complex formats to express the meaning and relation of data.
 
@@ -24,26 +24,23 @@ Any software importing or exporting a file format has to include readers and/or
 
 ## Generic format standards
 
-There are several generic formats to store data in a structured way. The format specifications do not define any domain specific elements, but some fields for document metadata, like a version, may be required to conform the specification. To create domain specific document formats, the elements including semantic descriptions have to be specified separately. 
+There are several generic formats to store data in a structured way. The format specifications do not define any domain specific elements, but some fields for document metadata, like a version, may be required to conform the specification. To create domain specific document formats, the elements including semantic descriptions have to be specified separately.
 Some of these formats have a corresponding schema format, which allows a formalised description of documents. Schemas describe the data types, relations and order of elements and attributes in the element. They also have fields for description of the data to add semantic meaning in the context of the format.
 
 [Comma separated values (CSV)](https://datatracker.ietf.org/doc/html/rfc4180) is a simple ASCII Text format for tabular data. The values are stored as a single table with the columns separated by commas. The first line of the table may be interpreted as table header. It does not define any metadata, but these are often added as comments to the header. Although the specification does not mention comments, it is common to interpret line starting with a hash sign ("#") (or sometimes another character) as comment lines. There are variants of the format which use tabulators, semicolons or other characters to separate the values. Many vendors use the CSV format or variants of it as export format, because it is readable for humans and can be easily converted to other table formats like Excel sheets. Due to the lack of defined metadata and column descriptions it may be challenging to compare data from CSV files of different vendors as column titles or the units for values can often only be understood in the context of instrument and software.
 
-[Extensible Markup Language (XML)](https://www.w3.org/XML/Core/#Publications) is a markup language to structure documents. The Document is organised by elements and their attributes and the scope of an element is marked by tags for the start and the end.  Elements can be nested and may include values. This allows for a representation of complex  data models, including multidimensional data and hierarchies. Because an XML file is a text file it is readable for humans, but the repeated tags distract from the information contained in values. Because of the verbosity XML files tend be grow fast and are often huge compared to other formats. Thus, XML allows for large datasets to store these as [BASE64](https://doi.org/10.17487%2FRFC3548) encoded binaries. XML allows straight forward definition of specific formats by schemas and [XML Schema Definition (XSD)](https://www.w3.org/TR/xmlschema11-1/) is the most common standard for these. Implementations for reading, writing and validating XML files exist in most programming languages. For these reasons, many file formats in chemistry are based on XML.
+[Extensible Markup Language (XML)](https://www.w3.org/XML/Core/#Publications) is a markup language to structure documents. The Document is organised by elements and their attributes and the scope of an element is marked by tags for the start and the end. Elements can be nested and may include values. This allows for a representation of complex data models, including multidimensional data and hierarchies. Because an XML file is a text file it is readable for humans, but the repeated tags distract from the information contained in values. Because of the verbosity XML files tend be grow fast and are often huge compared to other formats. Thus, XML allows for large datasets to store these as [BASE64](https://doi.org/10.17487%2FRFC3548) encoded binaries. XML allows straight forward definition of specific formats by schemas and [XML Schema Definition (XSD)](https://www.w3.org/TR/xmlschema11-1/) is the most common standard for these. Implementations for reading, writing and validating XML files exist in most programming languages. For these reasons, many file formats in chemistry are based on XML.
 
 As XML, the [Javascript Object Notation (JSON)](https://www.ecma-international.org/wp-content/uploads/ECMA-404_2nd_edition_december_2017.pdf) was created to exchange data in the World Wide Web. Where XML has element tags for structuring the document, JSON uses braces, brackets and commas. Because of less verbosity the format is better readable for humans and files may be smaller. With [JSON Schema](http://json-schema.org/specification.html) there is a draft for a schema format to describe JSON documents. Even if JSON is less common for file formats, it is often used if data are exchanged by Application Programming Languages (API).
 
 Single datasets may be bundled to be stored as one unit, or large datasets may be split up to smaller files for better handling. Container formats allow to retain the relationship between the datafiles. This can be achieved by interlinking metadata in the datafiles or metafiles, by grouping files in containers or archives like [zip](https://www.iso.org/standard/60101.html) or tar, or by structured container file formats. An example for the cont approach is [HDF5](https://www.hdfgroup.org/solutions/hdf5/), which allows to combine a file system like structure with metadata. There are many implementations and tools for HDF5 and some formats for chemical data are based on it.
 
-
-
 ## Format standards in chemistry
 
-Many  formats used in chemistry are based on one of the generic formats from the last section. The following table lists some common formats used by chemists.
-
+Many formats used in chemistry are based on one of the generic formats from the last section. The following table lists some common formats used by chemists.
 
 | Format              | Data type         | Maintainer            | Parent Format | Specification    |
-|---------------------|-------------------|-----------------------|---------------|------------------|
+| ------------------- | ----------------- | --------------------- | ------------- | ---------------- |
 | JCAMP-DX            | multiple          | IUPAC                 | ASCII, Text   | open             |
 | AnIML               | multiple          | ASTM                  | XML           | open             |
 | netCDF              | multiple          | UCAR                  | CDF           | open             |
@@ -62,33 +59,30 @@ Many  formats used in chemistry are based on one of the generic formats from the
 | Perkin Elmer        | spectroscopy      | Perkin Elmer          | ASCII, Text   | proprietary      |
 | ThermofFisher Grams | spectroscopy      | ThermoFisher          | binary        | proprietary      |
 
-The [JCAMP-DX format](http://www.jcamp-dx.org/protocols.html) can  be applied for a wide range of spectral and analytical data. It was developed by the Joint Committee on Atomic and Molecular Physical Data (JCAMP) as a format for [IR spectroscopy](http://www.jcamp-dx.org/protocols.html#ir4.24) data since 1988 and is now maintained under the auspices of IUPAC. A general standard is proposed which can be used for different spectroscopic and spectrometric methods. Additionally, defined special standards for electron magnetic resonance  spectroscopy and [nuclear magnetic resonance (NMR)](http://www.jcamp-dx.org/protocols.html#nmr), chromatography and mass spectrometry  were [published](https://doi.org/10.1366%2F0003702944027840). Because the standard does not provide native support for ontology or controlled vocabulary use, and each implementation may use its own extensions, files from different sources can be incompatible. There is a Java reference implementation for this format available and there are libraries for other programming languages applicable like Python, R JavaScript and MATLAB. As JCAMP-DX is accepted as the exchange format for many analytical methods, there is a wide support by software for spectral analytics.
+The [JCAMP-DX format](http://www.jcamp-dx.org/protocols.html) can be applied for a wide range of spectral and analytical data. It was developed by the Joint Committee on Atomic and Molecular Physical Data (JCAMP) as a format for [IR spectroscopy](http://www.jcamp-dx.org/protocols.html#ir4.24) data since 1988 and is now maintained under the auspices of IUPAC. A general standard is proposed which can be used for different spectroscopic and spectrometric methods. Additionally, defined special standards for electron magnetic resonance spectroscopy and [nuclear magnetic resonance (NMR)](http://www.jcamp-dx.org/protocols.html#nmr), chromatography and mass spectrometry were [published](https://doi.org/10.1366%2F0003702944027840). Because the standard does not provide native support for ontology or controlled vocabulary use, and each implementation may use its own extensions, files from different sources can be incompatible. There is a Java reference implementation for this format available and there are libraries for other programming languages applicable like Python, R JavaScript and MATLAB. As JCAMP-DX is accepted as the exchange format for many analytical methods, there is a wide support by software for spectral analytics.
 
 The XML-based Analytical Information Markup Language (AnIML) has been created to be an ASTM International standard and covers different analytical techniques. The standard comprises schema definitions for a generic core and technique-specific documents. Thus, it is possible to define technique documents for various analytical measurements. As AnIML is fully specified by its XML schemas, it can be effortlessly implemented in any language with XML support. No reference implementation is available, but among the (few) open-source implementations Jmol/JSmol (formerly JSpecView) can import and visualise AniML documents. For developers working with the python programming language, a library is under development to create, parse and validate AniML files. There is also support by BSSN Software (now Merck) that promotes the format, often in combination with the device interface SiLA (Standardisation in Lab Automation).
 
 [NetCDF](https://doi.org/10.1109/38.56302) is a binary file format and software interface, mainly defined by its implementations by the Unidata community. It is an abstract model, which can be extended by self-describing objects. Thus, this model can be flexibly adopted to specific use cases. A family of ANDI (ANalytical Data Interchange) formats is specified by the ASTM, which are based on netCDF (see also ANDI-MS below).
 
-The [ISA (Investigation-Study-Assay) framework](https://doi.org/10.5281/zenodo.163640
-), originated from the bioscience community, defines the hierarchical ISA data model to store metadata on project context and study details, and analytical measurement data. As the abstract ISA data model already encourages the user to annotate any parameter or value with ontology terms, it assures well described datasets. Implementations are available as tab separated value files (ISA-Tab) or as JSON (ISA-JSON). The ISA API is a Python library implementing the model for usage with the ISA formats. The model is also applied for repositories such as MetaboLights. Moreover, journals such as ScientificData or GigaScience use the ISA data model to describe complex experimental setups covered in the manuscripts.
+The [ISA (Investigation-Study-Assay) framework](https://doi.org/10.5281/zenodo.163640), originated from the bioscience community, defines the hierarchical ISA data model to store metadata on project context and study details, and analytical measurement data. As the abstract ISA data model already encourages the user to annotate any parameter or value with ontology terms, it assures well described datasets. Implementations are available as tab separated value files (ISA-Tab) or as JSON (ISA-JSON). The ISA API is a Python library implementing the model for usage with the ISA formats. The model is also applied for repositories such as MetaboLights. Moreover, journals such as ScientificData or GigaScience use the ISA data model to describe complex experimental setups covered in the manuscripts.
 
 ### Format standards for analytical Data
 
 Experimental data obtained with spectroscopic methods such as infrared-spectroscopy, Raman and UV/Vis-spectroscopy, are often comparatively small in size and straightforward in their structure. Vendors store the raw data in proprietary formats, either as binary data or in ASCII. These can be exported as (or converted to) Excel spreadsheets or plain text tables with x,y pairs (or similar format). A header section may include metadata.
 
-Users have to further process such data for their specific needs, and currently no overarching specifications exist. Repositories may convert these to a specified format, e.g. [Chemotion ELN](https://www.chemotion.net/docs)  will convert text and Excel files to JCAMP-DX.
+Users have to further process such data for their specific needs, and currently no overarching specifications exist. Repositories may convert these to a specified format, e.g. [Chemotion ELN](https://www.chemotion.net/docs) will convert text and Excel files to JCAMP-DX.
 
 There are a few vendor formats which are popular for data exchange: GRAMS SPC, Perkin Elmer SP and Bruker OPUS files are supported not only by the format creators, but also by other vendors and instrument-agnostic software tools for e.g. statistical analysis.
 
 There were efforts to create a special format for ultraviolet-visible spectroscopy data, which was called [SpectroML](https://doi.org/10.1016/S1535-5535-04-00168-6), which have now been superseded by the more general AnIML . Harmonisation between instrument vendors and adoption of an open standard still needs to be achieved.
 
-
 #### Data formats for nuclear magnetic resonance spectroscopy (NMR)
 
 NMR is an indispensable analytical technique providing rich information on bonding and structure as well as molecule interaction and abundance of molecules in samples. Until now, it was common practice to publish the spectra as images in supplementary materials, regularly published as PDF files. Additionally, a list of shifts is reported, sometimes referred to as NMR text.
 
 However, the raw data containing the Free Induction Decays (FIDs), initially processed spectra and the instrument metadata is usually not published, which might allow for reanalysis and reuse. The importance of providing both FID raw data and extracted NMR spectra were previously demonstrated extensively.
 
-
 All instrument vendors have developed their own (binary) raw data formats. Since this FID data itself is mainly time-response data with a straight-forward structure, most of the vendor formats are supported by the software used within the NMR community. Many vendors also agreed to import and export the JCAMP-DX format, which has a [specification for FID raw data](https://doi.org/10.1366%2F0003702934067874) and is [recommended by IUPAC](https://doi.org/10.1351/pac199971081549).
 
 The JCAMP-DX format can also be used for exchange, import and export of multidimensional spectra. Because of the open and extensible nature of JCAMP-DX on the one hand and the lack of a controlled vocabulary on the other, there are already different flavours of the NMR format implementation, hence, validation or import might be challenging.
@@ -102,13 +96,13 @@ Recently, there were several additional open standard formats developed by the N
 Derived from the self-defining STAR format are the also more protein specific [NMR-STAR](https://doi.org/10.1007/s10858-018-0220-3) which is used by the BioMagResBank (BMRB) data format and defines over 4600 data item tags describing data and metadata, which are organised in more than 300 categories and 80 category groups. The [NMR Exchange Format (NEF)](https://doi.org/10.1038/nsmb.3041) format was developed for storage of NMR data in wwPDB. It is more accessible for software developers by reducing the complexity. Additionally, it is extensible with application-specific tags. As NMR-STAR and NEF both are derived from the STAR format, they are convertible, and the only formats accepted by wwPDB and BMRB. The Collaborative Computing Project for NMR (CCPN) is developing NEF, based on the data model for usage within their protein NMR focused software tools.
 
 #### Data standards in Mass Spectrometry
+
 A distinction that is rather important in different disciplines of chemistry is whether a particular spectrum is the data of interest, or whether a set of spectra shall be represented. In the former case, text-based file formats like [JCAMP-DX](https://doi.org/10.1366%2F0003702944027840), Mascot Generic File (MGF) or National Institute for Standards and Technology Mass spectrometry (NIST MSP) may be sufficient. However, for entire runs using, e.g., LC-MS or GC-MS with hundreds of chromatography-resolved spectra, more efficient file formats have been developed. The netCDF (Network Common Data Form) based [Analytical Data Interchange Protocol for Mass Spectrometry (ANDI-MS)](https://doi.org/10.1021/ac002727b) is an ASTM International standard. It was developed initially as an Analytical Instrument Association (AIA) standard as a follow-up of the ANDI for Chromatographic Data specification. Technically, it builds upon [NetCDF](https://doi.org/10.1109/38.56302), a generic and highly efficient container format. The ANDI-MS specification defines which elements are needed to encode mass spectrometry data.
 
 More complex MS experiments require capturing a rich set of instrumental settings such as per-scan polarity, isolation windows and collision energies. Several formats (mzXML, mzData) had been developed in the early days of proteomics, which have been merged into mzML by the [Proteomics Standards Initiative (PSI)](https://www.psidev.info/). Despite the term Proteomics in its name, many of the PSI standards can also be used for respective analytical data from samples beyond Proteomics. The XML based mzML data format is a widely accepted standard for analytical mass spectrometry data, recommended by several societies and infrastructures for data exchange and archival. There is also a wide range of tools, including converters and spectra viewers, and software libraries to work with mzML files. The use of the PSI-MS ontology as controlled vocabulary, combined with data validators, provides excellent interoperability between consumers and producers of mzML, regardless of the instrument vendor or analysis software.
 
 The XML-based nature of these formats ensures that the data is readable by most, if not all, computer systems and programming languages long-term. To improve performance for fast random access and parallel processing of data, the same data model was used in several formats like [mz5](https://doi.org/10.1074/mcp.O111.011379), [Toffee](https://doi.org/10.1038/s41598-020-65015-y) and [mzMLb](https://doi.org/10.1021/acs.jproteome.0c00192) which are based on HDF5, which itself is a container format and can be considered the successor to netCDF.
 
-
 #### Data Standards in X-ray Crystallography
 
 Crystal structure analyses by X-ray diffraction are fundamental techniques in chemistry to determine the atomic and molecular structure of materials. These techniques measure the angles and intensities of a diffracted x-ray beam and calculate structural information from the data. In case of single-crystal measurements, the raw datasets can be very large, while other methods like powder x-ray diffraction produce only two-dimensional raw data. Therefore, data from the latter are exchanged in simple text files, exported from the instrument vendor software.
@@ -117,25 +111,21 @@ With the [Crystallographic Information File (CIF)](https://doi.org/10.1107/S0108
 
 Databases and repositories such as The [Cambridge Structural Database (CSD)](https://doi.org/10.1107/S2052520616003954) and [Crystallography Open Database (COD)](https://doi.org/10.1093/nar/gkr900) will only accept CIF as format to deposit crystallographic data.
 
-
 #### Data Standards in X-Ray Absorption and Fluorescence Spectroscopy
 
-X-Ray absorption (XAS) as well as x-ray fluorescence (XRF) generates simple spectra described by the monochromatic x-ray radiation on the abscissa and the absorption of the sample on the ordinate. The spectra can be exported to in formats based on CSV, with multiple columns, but the units (e.g. energy, wavelength), column format and the included metadata often depend on the software used for measurement on the beamline or instrument, which interferes with interoperability. To compare XAS and XRF data measured on different beamlines and devices, it is also important to include parameters of the instrument and calibration into the dataset. For larger sets of XAS data the HDF5 format is [considered as standard format](https://doi.org/10.1107/S0909049512036886
-), which is already used by some beamline software, such as BLISS on the ESRF.
+X-Ray absorption (XAS) as well as x-ray fluorescence (XRF) generates simple spectra described by the monochromatic x-ray radiation on the abscissa and the absorption of the sample on the ordinate. The spectra can be exported to in formats based on CSV, with multiple columns, but the units (e.g. energy, wavelength), column format and the included metadata often depend on the software used for measurement on the beamline or instrument, which interferes with interoperability. To compare XAS and XRF data measured on different beamlines and devices, it is also important to include parameters of the instrument and calibration into the dataset. For larger sets of XAS data the HDF5 format is [considered as standard format](https://doi.org/10.1107/S0909049512036886), which is already used by some beamline software, such as BLISS on the ESRF.
 
 For the interchange of single X-Ray absorption spectra, the [XAFS Data Interchange (XDI)](https://doi.org/10.1088/1742-6596/712/1/012148) format was proposed , which combines a dictionary of relevant metadata and the data table in a text file. Thus, it is readable for humans and computers and compatible with most of the existing software accepting x,y-tables. The authors of the format also provide an implementation in C and bindings for several other programming languages such as Fortran, Perl and Python. The format was already accepted for import to the reference sample database at [Diamond Light Source](https://doi.org/10.1016/j.radphyschem.2019.108479) and the [X-ray Absorption Data Library](https://xaslib.xrayabsorption.org/elem/) of the International X-ray Absorption Society.
 
 There is no existing standard for XRF files, so most of the software tools provide some kind of import dialog to select matching columns and units from text files exported by the vendor software or can read data contained in HDF5 files.
 
-
 ### Format standards for structural Data
 
-To describe chemical structures as a simple ASCII string there is the SMILES format, which is an open standard as OpenSMILES since 2007. For more information about SMILES and its variants read the [simplified molecular-input line-entry system  (SMILES)](/docs/smiles) article in this knowledge base.
-
-Another one line encoding of structures, mainly intended for searching information about compounds,  is the [International Chemical Identifier (InChi)](/docs/inchi), which has also an open specification and is described [separately](/docs/inchi).
+To describe chemical structures as a simple ASCII string there is the SMILES format, which is an open standard as OpenSMILES since 2007. For more information about SMILES and its variants read the [simplified molecular-input line-entry system (SMILES)](/docs/smiles) article in this knowledge base.
 
-A simple Text format for chemical structures is the [XYZ format](http://openbabel.org/wiki/XYZ_(format)), which only contains the coordinates for the atoms of a molecule. As the format lacks a formal specification the implementations for XYZ may differ and result in incompatible files.
+Another one line encoding of structures, mainly intended for searching information about compounds, is the [International Chemical Identifier (InChi)](/docs/inchi), which has also an open specification and is described [separately](/docs/inchi).
 
+A simple Text format for chemical structures is the [XYZ format](https://openbabel.org/docs/FileFormats/XYZ_cartesian_coordinates_format.html), which only contains the coordinates for the atoms of a molecule. As the format lacks a formal specification the implementations for XYZ may differ and result in incompatible files.
 
 The [Chemical Table File](https://discover.3ds.com/sites/default/files/2020-08/biovia_ctfileformats_2020.pdf) was originally created by MDL Information Systems, now BIOVIA. It is now an open standard, but download of the specification requires registration. The files are text based consisting of a header and several data blocks with the structural information for the molecules.
 
@@ -145,6 +135,6 @@ The structure data file (SDF) is a derivative of the chemical data file and can
 
 ## Sources and further information
 
-- [The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research](https://doi.org/10.1039/C7NP00064B)
-- [Dissemination of original NMR data enhances reproducibility and integrity in chemical research](https://doi.org/10.1039/C6NP00022C)
-- [NMReDATA: Tools and applications](https://doi.org/10.1002/mrc.5146)
+-   [The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research](https://doi.org/10.1039/C7NP00064B)
+-   [Dissemination of original NMR data enhances reproducibility and integrity in chemical research](https://doi.org/10.1039/C6NP00022C)
+-   [NMReDATA: Tools and applications](https://doi.org/10.1002/mrc.5146)

From de18a23c8356c7c4f6a124fc51f97cc01e7a62fe Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 11 Nov 2024 16:35:40 +0100
Subject: [PATCH 87/89] fix: broken link

---
 docs/00_intro/10_fair.mdx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/00_intro/10_fair.mdx b/docs/00_intro/10_fair.mdx
index 2542a204..d774508a 100644
--- a/docs/00_intro/10_fair.mdx
+++ b/docs/00_intro/10_fair.mdx
@@ -92,7 +92,7 @@ Especially when looking at metadata, effective and efficient machine readability
 
 ### I2. (meta)data use vocabularies that follow FAIR principles
 
-The applied vocabularies or ontologies should be well-documented and resolvable using a PID. For instance, CHMO mentioned [above](#i1-metadata-use-a-formal-accessible-shared-and-broadly-applicable-language-for-knowledge-representation) uses a [persistent URL (PURL)](http://www.purlz.org/home), resolvable using a standard web browser through `http`, while the [documentation](https://github.com/rsc-ontologies/rsc-cmo) is publicly available on Github.
+The applied vocabularies or ontologies should be well-documented and resolvable using a PID. For instance, CHMO mentioned [above](#i1-metadata-use-a-formal-accessible-shared-and-broadly-applicable-language-for-knowledge-representation) uses a [persistent URL (PURL)](https://en.wikipedia.org/wiki/Persistent_uniform_resource_locator), resolvable using a standard web browser through `http`, while the [documentation](https://github.com/rsc-ontologies/rsc-cmo) is publicly available on Github.
 
 ### I3. (meta)data include qualified references to other (meta)data
 

From 17b6e75f33b88881cae18dedac33e88ba8793f02 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 11 Nov 2024 16:43:48 +0100
Subject: [PATCH 88/89] fix: broken links

---
 docs/20_role/20_research_group_member.mdx | 37 ++++++++++++++---------
 1 file changed, 22 insertions(+), 15 deletions(-)

diff --git a/docs/20_role/20_research_group_member.mdx b/docs/20_role/20_research_group_member.mdx
index 160705b0..46d77b4e 100644
--- a/docs/20_role/20_research_group_member.mdx
+++ b/docs/20_role/20_research_group_member.mdx
@@ -5,7 +5,7 @@ slug: "/research_group_member"
 
 # Research Group Member
 
-import useBaseUrl from '@docusaurus/useBaseUrl';
+import useBaseUrl from "@docusaurus/useBaseUrl";
 
 :::info Applies to:
 This article applies to research group members (PhD students, Postdocs and other scientists), who are generating scientific data.
@@ -17,28 +17,35 @@ As a research group member, you are the one who is doing the actual research. Th
 
 ## Data handling
 
-<img alt="Data LifeCycle" src={useBaseUrl('/img/Intro/DataLifeCycle_KB.svg')} width="500" align="right" vspace="10" hspace="10"/>
+<img
+    alt="Data LifeCycle"
+    src={useBaseUrl("/img/Intro/DataLifeCycle_KB.svg")}
+    width="500"
+    align="right"
+    vspace="10"
+    hspace="10"
+/>
 
 In recent years, many new digital tools have been developed to support researchers with their RDM needs. The technical possibilities are briefly explained below. For more details, please refer to the linked related chapters. If you want to learn more about domain-specific data production methods, have a look at the [domain-specific profiles](/docs/role_guide).
 
-The most efficient way to properly handle your research data and corresponding [metadata](/docs/metadata) starts when planning the experiment according to the [data life cycle](/docs/data_life_cycle) (see figure on the right). In order to have all data directly available in a digital format, the use of [electronic lab notebooks (ELNs)](/docs/eln) is strongly recommended. ELNs can support you in your daily work, from planning experiments to data processing and analysis. For example, after peak assignment in an obtained spectroscopic dataset—which can be performed entirely in one digital environment—peak lists can automatically be generated by ELNs such as the [Chemotion ELN](https://eln.chemotion.net/home) for theses or publications. Furthermore, ELNs are very powerful in preparing your data for [data publishing](/docs/data_publishing) in suitable [repositories](/docs/repositories) as well as for [data storage and archiving](/docs/data_storage). You are therefore facilitating future research in your working group by assembling an internal database in an invaluable manner. In addition to the group you are working in, publishing [well-organised](/docs/data_organisation) and [documented](/docs/data_documentation) research data can help other researchers significantly in terms of searching and re-using your data. [Best practice examples](/docs/best_practice) can guide you to better understand how efficient data handling works.
+The most efficient way to properly handle your research data and corresponding [metadata](/docs/metadata) starts when planning the experiment according to the [data life cycle](/docs/data_life_cycle) (see figure on the right). In order to have all data directly available in a digital format, the use of [electronic lab notebooks (ELNs)](/docs/eln) is strongly recommended. ELNs can support you in your daily work, from planning experiments to data processing and analysis. For example, after peak assignment in an obtained spectroscopic dataset—which can be performed entirely in one digital environment—peak lists can automatically be generated by ELNs such as the [Chemotion ELN](https://www.chemotion.net/) for theses or publications. Furthermore, ELNs are very powerful in preparing your data for [data publishing](/docs/data_publishing) in suitable [repositories](/docs/repositories) as well as for [data storage and archiving](/docs/data_storage). You are therefore facilitating future research in your working group by assembling an internal database in an invaluable manner. In addition to the group you are working in, publishing [well-organised](/docs/data_organisation) and [documented](/docs/data_documentation) research data can help other researchers significantly in terms of searching and re-using your data. [Best practice examples](/docs/best_practice) can guide you to better understand how efficient data handling works.
 
 ## Recommendations – how to start
 
-The use of an ELN for data handling has clear advantages (see [above](#data-handling)). Generally, selecting an [ELN](/docs/eln) and a [repository](/docs/repositories) for data deposition depends on the [chemical sub-domain](/docs/domain_guide). Since 60 % of the chemists work synthetically, the electronic lab notebook [Chemotion ELN](https://www.chemotion.net/chemotionsaurus/) in combination with the repository [Chemotion Repository](https://www.chemotion-repository.net/welcome) may be the right choice for you. 
+The use of an ELN for data handling has clear advantages (see [above](#data-handling)). Generally, selecting an [ELN](/docs/eln) and a [repository](/docs/repositories) for data deposition depends on the [chemical sub-domain](/docs/domain_guide). Since 60 % of the chemists work synthetically, the electronic lab notebook [Chemotion ELN](https://www.chemotion.net/) in combination with the repository [Chemotion Repository](https://www.chemotion-repository.net/) may be the right choice for you.
 
 :::tip Advantages of Chemotion
 
-- [Data life cycle](/docs/data_life_cycle) fully covered—from experiment planning to publication
-- Drawing chemical structures—automatic calculation of quantities and yields
-- Many spectra can be directly analysed in the Chemotion environment using ChemSpectra
-- Experimental information for the experimental section of theses or publications can be generated and exported by the software—no manual peak listing required
-- A plausibility check is available for NMR spectra
-- SciFinder search is directly integrated
-- Building an internal database—advancing collaboration and data exchange in the group.
-- Seamless export from ELN to repository as a FAIR data deposit with a [persistent identifier (DOI)](/docs/pid) for each molecule
-- User management—access rights, sharing, and syncing.
-- Academic version is free of charge
+-   [Data life cycle](/docs/data_life_cycle) fully covered—from experiment planning to publication
+-   Drawing chemical structures—automatic calculation of quantities and yields
+-   Many spectra can be directly analysed in the Chemotion environment using ChemSpectra
+-   Experimental information for the experimental section of theses or publications can be generated and exported by the software—no manual peak listing required
+-   A plausibility check is available for NMR spectra
+-   SciFinder search is directly integrated
+-   Building an internal database—advancing collaboration and data exchange in the group.
+-   Seamless export from ELN to repository as a FAIR data deposit with a [persistent identifier (DOI)](/docs/pid) for each molecule
+-   User management—access rights, sharing, and syncing.
+-   Academic version is free of charge
 
 **When running your own Chemotion instance, you keep control of your data.**
 
@@ -46,7 +53,7 @@ The use of an ELN for data handling has clear advantages (see [above](#data-hand
 
 :::info Info:
 
-For more information on Chemotion, the [Chemotion introductory video](https://www.youtube.com/watch?v=tZHaP6DW-Dw) (in German) provides a good overview of Chemotion as a tool in research data management. 
+For more information on Chemotion, the [Chemotion introductory video](https://www.youtube.com/watch?v=tZHaP6DW-Dw) (in German) provides a good overview of Chemotion as a tool in research data management.
 
 :::
 

From ba15ce063bc32146ed4c00451e0f5e705d3c8390 Mon Sep 17 00:00:00 2001
From: Johannes Liermann <liermann@uni-mainz.de>
Date: Mon, 11 Nov 2024 17:04:22 +0100
Subject: [PATCH 89/89] fix: remove button for polymer chem.

---
 src/components/N4CFeatures.js | 286 +++++++++++++++++-----------------
 1 file changed, 145 insertions(+), 141 deletions(-)

diff --git a/src/components/N4CFeatures.js b/src/components/N4CFeatures.js
index 7fdcadab..3f8953ff 100644
--- a/src/components/N4CFeatures.js
+++ b/src/components/N4CFeatures.js
@@ -1,150 +1,154 @@
-import React from 'react';
-import Link from '@docusaurus/Link';
-import useBaseUrl from '@docusaurus/useBaseUrl';
-import Translate from '@docusaurus/Translate';
+import React from "react";
+import Link from "@docusaurus/Link";
+import useBaseUrl from "@docusaurus/useBaseUrl";
+import Translate from "@docusaurus/Translate";
 
 const features = {
-  entry: [
-    {
-      "title": <Translate>Domains</Translate>,
-      "svg": "/img/nfdi4chem_Domains_white.svg",
-      "link": "/docs/domain_guide"
-    },
-    {
-      "title": <Translate>Roles</Translate>,
-      "svg": "/img/nfdi4chem_Roles_white.svg",
-      "link": "/docs/role_guide"
-    },
-    {
-      "title": <Translate>Handling Data</Translate>,
-      "svg": "/img/nfdi4chem_Handling_Data_white.svg",
-      "link": "/docs/data_guide"
-    },
-    {
-      "title": <Translate>Electronic Lab Notebooks</Translate>,
-      "svg": "/img/nfdi4chem_SmartLab_white.svg",
-      "link": "/docs/smartlab"
-    },
-    {
-      "title": <Translate>Data Publishing</Translate>,
-      "svg": "/img/nfdi4chem_Data_Publication_white.svg",
-      "link": "/docs/data_publishing"
-    }
-  ],
-  domains: [
-    {
-      "title": <Translate>Synthetic Chemistry</Translate>,
-      "svg": "/img/nfdi4chem_Synthetic_Chemistry.svg",
-      "link":  "/docs/synthetic_chemistry"
-    },
-    {
-      "title": <Translate>Analytical Chemistry</Translate>,
-      "svg": "/img/nfdi4chem_Analytical_Chemistry.svg",
-      "link":  "/docs/analytical_chemistry"
-    },
-    {
-      "title": <Translate>Physical Chemistry</Translate>,
-      "svg": "/img/nfdi4chem_Physial_Chemistry.svg",
-      "link":  "/docs/physical_chemistry"
-    },
-    {
-      "title": <Translate>Polymer Chemistry</Translate>,
-      "svg": "/img/nfdi4chem_Polymer_Chemistry.svg",
-      "link":  "/docs/polymer_chemistry"
-    },
-    {
-      "title": <Translate>Pharmaceutical Chemistry</Translate>,
-      "svg": "/img/nfdi4chem_Medicinal-Pharmaceutical_Chemistry.svg",
-      "link":  "/docs/pharmaceutical_chemistry"
-    }
-  ],
-  roles: [
-    {
-      "title": <Translate>Research Group Leader</Translate>,
-      "svg": "/img/nfdi4chem_Research_Group_Leader.svg",
-      "link": "/docs/research_group_leader"
-    },
-    {
-      "title": <Translate>Research Group Member</Translate>,
-      "svg": "/img/nfdi4chem_Research_Group_Member.svg",
-      "link": "/docs/research_group_member"
-    },
-    {
-      "title": <Translate>Student</Translate>,
-      "svg": "/img/nfdi4chem_Student.svg",
-      "link": "/docs/student"
-    },
-    {
-      "title": <Translate>Data Steward</Translate>,
-      "svg": "/img/nfdi4chem_Data_Steward.svg",
-      "link": "/docs/data_steward"
-    },
-    {
-      "title": <Translate>Core Facility Manager</Translate>,
-      "svg": "/img/nfdi4chem_Core_Facility_Manager.svg",
-      "link": "/docs/core_facility_manager"
-    }
-  ],
-  stakeholders_data_publishing: [
-    {
-      "title": <Translate>Authors</Translate>,
-      "svg": "/img/nfdi4chem_Research_Group_Member.svg",
-      "link": "/docs/publishing_standards_authors"
-    },
-    {
-      "title": <Translate>Academic Publishers</Translate>,
-      "svg": "/img/nfdi4chem_Data_Publication.svg",
-      "link": "/docs/publishing_standards_publishers"
-    },
-    {
-      "title": <Translate>Infrastructure Providers</Translate>,
-      "svg": "/img/nfdi4chem_Core_Facility_Manager.svg",
-      "link": "/docs/publishing_standards_infrastructure"
-    }
-  ]
+    entry: [
+        {
+            title: <Translate>Domains</Translate>,
+            svg: "/img/nfdi4chem_Domains_white.svg",
+            link: "/docs/domain_guide",
+        },
+        {
+            title: <Translate>Roles</Translate>,
+            svg: "/img/nfdi4chem_Roles_white.svg",
+            link: "/docs/role_guide",
+        },
+        {
+            title: <Translate>Handling Data</Translate>,
+            svg: "/img/nfdi4chem_Handling_Data_white.svg",
+            link: "/docs/data_guide",
+        },
+        {
+            title: <Translate>Electronic Lab Notebooks</Translate>,
+            svg: "/img/nfdi4chem_SmartLab_white.svg",
+            link: "/docs/smartlab",
+        },
+        {
+            title: <Translate>Data Publishing</Translate>,
+            svg: "/img/nfdi4chem_Data_Publication_white.svg",
+            link: "/docs/data_publishing",
+        },
+    ],
+    domains: [
+        {
+            title: <Translate>Synthetic Chemistry</Translate>,
+            svg: "/img/nfdi4chem_Synthetic_Chemistry.svg",
+            link: "/docs/synthetic_chemistry",
+        },
+        {
+            title: <Translate>Analytical Chemistry</Translate>,
+            svg: "/img/nfdi4chem_Analytical_Chemistry.svg",
+            link: "/docs/analytical_chemistry",
+        },
+        {
+            title: <Translate>Physical Chemistry</Translate>,
+            svg: "/img/nfdi4chem_Physial_Chemistry.svg",
+            link: "/docs/physical_chemistry",
+        },
+        // {
+        //   "title": <Translate>Polymer Chemistry</Translate>,
+        //   "svg": "/img/nfdi4chem_Polymer_Chemistry.svg",
+        //   "link":  "/docs/polymer_chemistry"
+        // },
+        {
+            title: <Translate>Pharmaceutical Chemistry</Translate>,
+            svg: "/img/nfdi4chem_Medicinal-Pharmaceutical_Chemistry.svg",
+            link: "/docs/pharmaceutical_chemistry",
+        },
+    ],
+    roles: [
+        {
+            title: <Translate>Research Group Leader</Translate>,
+            svg: "/img/nfdi4chem_Research_Group_Leader.svg",
+            link: "/docs/research_group_leader",
+        },
+        {
+            title: <Translate>Research Group Member</Translate>,
+            svg: "/img/nfdi4chem_Research_Group_Member.svg",
+            link: "/docs/research_group_member",
+        },
+        {
+            title: <Translate>Student</Translate>,
+            svg: "/img/nfdi4chem_Student.svg",
+            link: "/docs/student",
+        },
+        {
+            title: <Translate>Data Steward</Translate>,
+            svg: "/img/nfdi4chem_Data_Steward.svg",
+            link: "/docs/data_steward",
+        },
+        {
+            title: <Translate>Core Facility Manager</Translate>,
+            svg: "/img/nfdi4chem_Core_Facility_Manager.svg",
+            link: "/docs/core_facility_manager",
+        },
+    ],
+    stakeholders_data_publishing: [
+        {
+            title: <Translate>Authors</Translate>,
+            svg: "/img/nfdi4chem_Research_Group_Member.svg",
+            link: "/docs/publishing_standards_authors",
+        },
+        {
+            title: <Translate>Academic Publishers</Translate>,
+            svg: "/img/nfdi4chem_Data_Publication.svg",
+            link: "/docs/publishing_standards_publishers",
+        },
+        {
+            title: <Translate>Infrastructure Providers</Translate>,
+            svg: "/img/nfdi4chem_Core_Facility_Manager.svg",
+            link: "/docs/publishing_standards_infrastructure",
+        },
+    ],
 };
 
 function Feature({ title, svg, link, style }) {
-
-  return (
-    <div className='col feature__col'>
-    <div className='text--center'>
-      {link ? (
-        <Link
-          className={style} 
-          // ? <Link className={clsx('')}
-          to={link}>
-            <img className="featureSvg" alt={title} src={useBaseUrl(svg)} /><br/>
-          {title}
-        </Link>
-      ) : (
-        <p>{title}</p>
-      )}
-    </div>
-    </div>
-  );
+    return (
+        <div className="col feature__col">
+            <div className="text--center">
+                {link ? (
+                    <Link
+                        className={style}
+                        // ? <Link className={clsx('')}
+                        to={link}
+                    >
+                        <img
+                            className="featureSvg"
+                            alt={title}
+                            src={useBaseUrl(svg)}
+                        />
+                        <br />
+                        {title}
+                    </Link>
+                ) : (
+                    <p>{title}</p>
+                )}
+            </div>
+        </div>
+    );
 }
 
-export default function N4CFeatures( { feature } ) {
-
-  var style = "";
-  const featureList = features[feature];
+export default function N4CFeatures({ feature }) {
+    var style = "";
+    const featureList = features[feature];
 
-  if (feature == "entry") {
-    style="button button--primary feature__button";
-  } else {
-    style="button button--secondary feature__button--secondary";
-  }
+    if (feature == "entry") {
+        style = "button button--primary feature__button";
+    } else {
+        style = "button button--secondary feature__button--secondary";
+    }
 
-  return (
-    <section className='features'>
-      <div className='container'>
-        <div className='row'>
-          {featureList.map((props, idx) => (
-            <Feature key={idx} {...props} style={style} />
-          ))}
-        </div>
-      </div>
-    </section>
-  );
-}
\ No newline at end of file
+    return (
+        <section className="features">
+            <div className="container">
+                <div className="row">
+                    {featureList.map((props, idx) => (
+                        <Feature key={idx} {...props} style={style} />
+                    ))}
+                </div>
+            </div>
+        </section>
+    );
+}