Merge pull request #568 from NFDI4BIOIMAGE/git-bob-mod-SfANo3Fb0r

Add content from communities: nfdi4bioimage, gerbi, euro-bioimaging, neubias, bio-formats, globias, rdm4mic

resources/nfdi4bioimage.yml

@@ -9131,4 +9131,198 @@ resources:
   - GitHub Repository
   - Slides
   url: https://github.com/jatkinson1000/rse-skills-workshop
-
+  - authors:
+  - Haase, Robert
+  description: 'This slide deck introduces Large Language Models to an audience of
+    life-scientists. We first dive into terminology: Different kinds of Language Models
+    and what they can be used for. The remaining slides are optional slides to allow
+    us to dive deeper into topics such as tools for using LLMs in Science, Quality
+    Assurance, Techniques such as Retrieval Augmented Generation and Prompt Engineering.'
+  license: cc-by-4.0
+  name: 'Large Language Models: An Introduction for Life Scientists'
+  num_downloads: 24
+  publication_date: '2024-12-12'
+  submission_date: '2024-12-24T11:17:37.842980'
+  url:
+  - https://zenodo.org/records/14418209
+  - https://doi.org/10.5281/zenodo.14418209
+- authors:
+  - Becker, Markus M.
+  - Chaerony Siffa, Ihda
+  - Baum, Roman
+  description: "Abstract: \nTerminology services (TS) [1,2] play a pivotal role in\
+    \ achieving structured metadata by providing controlled vocabularies and ontologies\
+    \ that standardize the description of data. This is a crucial aspect of research\
+    \ data management (RDM) in all scientific disciplines. In addition, TS facilitate\
+    \ the use of a common vocabulary within a scientific community also in a more\
+    \ general context, e.g. to annotate scientific papers, patents or other content\
+    \ for better discoverability, as envisaged by the Open Research Knowledge Graph\
+    \ (ORKG) [3] or the Patents4Science project [4]. \nTo make use of these opportunities,\
+    \ terminologies, ontologies and knowledge graphs must be developed and made available\
+    \ as TS where they do not yet exist. This step is currently being taken by the\
+    \ research community in low-temperature plasma (LTP) physics. LTP physics explores\
+    \ partially ionized gases and its technological applications. This vibrant field\
+    \ offers innovative solutions for societal challenges, ranging from developing\
+    \ efficient lighting and solar cells to revolutionizing healthcare through plasma\
+    \ medicine. Various activities and projects have been started in the past years\
+    \ to support the RDM in LTP research and development and to facilitate the application\
+    \ of data-driven research methods. These activities are supported in parts by\
+    \ the NFDI4BIOIMAGE consortium, active work in the NFDI section “(Meta)data,\
+    \ Terminologies, Provenance”, and the basic service Terminology Services\
+    \ 4 NFDI (TS4NFDI) funded by Base4NFDI. \nRecently, the ontology Plasma-O\
+    \ [5–7] for LTP physics has been developed at INP in collaboration with\
+    \ FIZ Karlsruhe – Leibniz Institute for Information Infrastructure, providing\
+    \ a framework for structuring metadata and building a knowledge graph for scientific\
+    \ information within the field. The present contribution will show how a TS utilizing\
+    \ this resource can support different aspects of RDM and knowledge discovery using\
+    \ concrete examples. The application cases include (i) standardizing data annotation:\
+    \ By providing researchers with a controlled vocabulary of LTP-specific terms\
+    \ and their relationships, ensuring consistent and unambiguous data descriptions;\
+    \ (ii) enabling semantic search: Moving beyond keyword-based searches, TS allow\
+    \ for complex queries based on the relationships between concepts, significantly\
+    \ improving data discoverability; (iii) facilitating data integration: By mapping\
+    \ data from different sources to a common ontology, TS enable seamless integration\
+    \ and analysis of heterogeneous datasets, which is crucial for data-driven research\
+    \ and development. The TS Suite of TS4NFDI with the provided widgets [8] fits\
+    \ perfectly to the requirements of these three application cases and will support\
+    \ the harmonization of metadata in LTP physics. The implementation of a public\
+    \ TS is required to provide the domain-specific metadata in a standardized format\
+    \ and will be instrumental in unlocking the full potential of the TS widgets for\
+    \ RDM and knowledge discovery by LTP researchers. Furthermore, the results can\
+    \ provide insights to other domains on how to apply TS to their specific needs.\n\
+     The work was supported in parts by the Deutsche Forschungsgemeinschaft (DFG,\
+    \ German Research Foundation) under the National Research Data Infrastructure\
+    \ – [NFDI46/1] – 501864659 and project number 496963457 as well as\
+    \ by the Federal Ministry of Education and Research (BMBF), project number 16KOA013A.\n\
+    References:\n\n\n\n\n[1]\n\n\nS. Jupp, T. Burdett, C. Leroy, H. Parkinson, “A\
+    \ new Ontology Lookup Service at EMBL-EBI”, Workshop on Semantic Web Applications\
+    \ and Tools for Life Sciences (2015), https://ceur-ws.org/Vol-1546/paper_29.pdf\
+    \ (accessed: 2024-09-20).\n\n\n\n\n[2]\n\n\nP. L. Whetzel, N. F. Noy, N. H. Shah,\
+    \ P. R. Alexander, C. Nyulas, T. Tudorache, M. A. Musen, “BioPortal: enhanced\
+    \ functionality via new Web services from the National Center for Biomedical Ontology\
+    \ to access and use ontologies in software applications”, Nucleic Acids\
+    \ Res. 39 (2011) W541–W545, https://doi.org/10.1093/nar/gkr469. \n\n\n\n\
+    \n[3]\n\n\nOpen Research Knowledge Graph, https://orkg.org/ (accessed: 2024-09-20).\n\
+    \n\n\n\n[4]\n\n\nPatents4Science – Establishing an Information Infrastructure\
+    \ for the Use of Patent Knowledge in Science, https://www.patents4science.org/\
+    \ (accessed: 2024-09-20).\n\n\n\n\n[5]\n\n\nH. Sack, F. Hoppe, “Verbundprojekt:\
+    \ Qualitätssicherung und Vernetzung von Forschungsdaten in der Plasmatechnologie\
+    \ - QPTDat; Teilvorhaben: Wissensgraph und Ontologieentwicklung zur Vernetzung\
+    \ von Metadaten : Schlussbericht des Teilvorhabens”, 2023, https://doi.org/10.2314/KXP:1883436974.\n\
+    \n\n\n\n[6]\n\n\nI. Chaerony Siffa, R. Wagner, L. Vilardell Scholten, M. M. Becker,\
+    \ “Semantic Information Management in Low-Temperature Plasma Science and\
+    \ Technology with VIVO”, 2024, preprint, https://doi.org/10.48550/arXiv.2409.11065.\n\
+    \n\n\n\n[7]\n\n\nI. Chaerony Siffa, R. Wagner, L. Vilardell Scholten, M. M. Becker,\
+    \ “Plasma Ontology and Knowledge Graph Initial Release v0.5.0”, 2024,\
+    \ Zenodo, https://doi.org/10.5281/zenodo.13325226. \n\n\n\n\n[8]\n\n\nJ. Sasse,\
+    \ V. Kneip, R. Baum, P. Zimmermann, J. Darms, J. Schneider, V. Clemens, P. Oladazimi,\
+    \ L. Kühnel, “ts4nfdi/terminology-service-suite: v2.6.0”, 2024,\
+    \ Zenodo, https://doi.org/10.5281/zenodo.13692297. \n\n\n\n"
+  license: cc-by-4.0
+  name: Terminology service for research data management and knowledge discovery in
+    low-temperature plasma physics
+  num_downloads: 73
+  publication_date: '2024-12-11'
+  submission_date: '2024-12-24T11:17:38.438350'
+  url:
+  - https://zenodo.org/records/14381522
+  - https://doi.org/10.5281/zenodo.14381522
+- authors:
+  - NFDI4BIOIMAGE Consortium
+  description: 'These illustrations were contracted by the Heinrich Heine University
+    Düsseldorf in the frame of the consortium NFDI4BIOIMAGE from Henning Falk
+    for the purpose of education and public outreach. The illustrations are free to
+    use under a CC-BY 4.0 license.AttributionPlease include an attribution similar
+    to: "Data annoation matters", NFDI4BIOIMAGE Consortium (2024): NFDI4BIOIMAGE data
+    management illustrations by Henning Falk, Zenodo, https://doi.org/10.5281/zenodo.14186100,
+    is used under a CC-BY 4.0 license. Modifications to this illustration include
+    cropping.
+
+     '
+  license: cc-by-4.0
+  name: NFDI4BIOIMAGE data management illustrations by Henning Falk
+  num_downloads: 136
+  publication_date: '2024-11-29'
+  submission_date: '2024-12-24T11:17:39.796497'
+  url:
+  - https://zenodo.org/records/14186101
+  - https://doi.org/10.5281/zenodo.14186101
+- authors:
+  - Engel, Judith
+  - Helling, Patrick
+  - "Herrenbr\xFCck, Robert"
+  - Lemaire, Marina
+  - Mehrtens, Hela
+  - Schmidt, Marcus
+  - Stellmacher, Martha
+  - Weimer, Lukas
+  - Wiljes, Cord
+  - Zinke, Wolf
+  description: 'Support is an essential component of an efficient infrastructure for
+    research data management (RDM). Helpdesks guide researchers through this complex
+    landscape and provide reliable support about all questions regarding research
+    data management, including support for technical services, best practices, requirements
+    of funding organizations and legal topics. In NFDI, most consortia have already
+    established or are planning to establish helpdesks to support their specific communities.
+    On a local level, many institutions have set up RDM helpdesks that provide support
+    for the researchers of their own institution. Additional RDM support services
+    are offered by RDM federal state initiatives, by research data centers, by specialist
+    libraries, by the EOSC, and by providers of RDM-relevant tools. Helpdesks cover
+    a wide range of institutions, disciplines, topics, methodologies and target audiences.
+    However, the individual helpdesks are not yet interconnected and therefore cannot
+    complement one another in an efficient way: Given the wide and constantly increasing
+    complexity of RDM, no single helpdesk can provide the expertise for all potential
+    support requests. Therefore, we see great potential in combining the efforts and
+    resources of the existing RDM helpdesks into an efficient and comprehensive national
+    RDM support network in order to provide optimal and tailored RDM support to all
+    researchers and research-related institutions in Germany and in an international
+    context.'
+  license: cc-by-4.0
+  name: Working Group Charter. RDM Helpdesk Network
+  num_downloads: 215
+  publication_date: '2024-11-04'
+  submission_date: '2024-12-24T11:17:41.996394'
+  url:
+  - https://zenodo.org/records/14035822
+  - https://doi.org/10.5281/zenodo.14035822
+- authors:
+  - Schmidt, Christian
+  - Boissonnet, Tom
+  - Bortolomeazzi, Michele
+  - "Kroo\xDF, Ksenia"
+  description: 'Research Data Management for Microscopy and BioImage Analysis
+
+
+    Introduction to BioImaging Research Data Management, NFDI4BIOIMAGE and I3D:bioChristian
+    Schmidt /DKFZ Heidelberg
+
+    OMERO as a tool for bioimaging data managementTom Boissonnet /Heinrich-Heine Universität
+    Düsseldorf
+
+    Reproducible image analysis workflows with OMERO software APIsMichele Bortolomeazzi
+    /DKFZ Heidelberg
+
+    Publishing datasets in public archives for bioimage dataKsenia Krooß /Heinrich-Heine
+    Universität Düsseldorf
+
+
+    Date & Venue:Thursday, Sept. 26, 5.30 p.m.Haus 22 / Paul Ehrlich Lecture Hall
+    (H22-1)University Hospital Frankfurt'
+  license: cc-by-4.0
+  name: '[Workshop] Research Data Management for Microscopy and BioImage Analysis'
+  num_downloads: 159
+  publication_date: '2024-09-30'
+  submission_date: '2024-12-24T11:17:45.069538'
+  url:
+  - https://zenodo.org/records/13861026
+  - https://doi.org/10.5281/zenodo.13861026
+- authors:
+  - Salama Lab Fred Hutchinson Cancer Center
+  license: cc-by-4.0
+  name: LSM example J. Dubrulle
+  num_downloads: 23
+  publication_date: '2024-12-17'
+  submission_date: '2024-12-24T11:18:35.007394'
+  url:
+  - https://zenodo.org/records/14510432
+  - https://doi.org/10.5281/zenodo.14510432