From 7f431edd107215386662ec5dba33c1285d4e4803 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Tue, 19 Sep 2023 17:04:41 +0300 Subject: [PATCH 1/3] Update 2023-16-15-second-issue-newsletter.md --- _posts/2023-16-15-second-issue-newsletter.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_posts/2023-16-15-second-issue-newsletter.md b/_posts/2023-16-15-second-issue-newsletter.md index 93461471c..a25d0fb83 100644 --- a/_posts/2023-16-15-second-issue-newsletter.md +++ b/_posts/2023-16-15-second-issue-newsletter.md @@ -1,7 +1,7 @@ --- layout: post categories: newsletter -title: "The OBO Foundry Newsletter: Advancing Bio-Ontologies for Enhanced Data Integration" +title: "2nd OBO Foundry Newsletter: In Memoriam - Remembering Michael Ashburner" date: 2023-09-15 author: - Leila Kiani From 43b582ec901cffca491fca4976af5a2f6433727a Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Tue, 19 Sep 2023 17:29:07 +0300 Subject: [PATCH 2/3] Update tables and title --- _posts/2023-16-15-second-issue-newsletter.md | 54 ++++++-------------- 1 file changed, 17 insertions(+), 37 deletions(-) diff --git a/_posts/2023-16-15-second-issue-newsletter.md b/_posts/2023-16-15-second-issue-newsletter.md index a25d0fb83..ba1aca03a 100644 --- a/_posts/2023-16-15-second-issue-newsletter.md +++ b/_posts/2023-16-15-second-issue-newsletter.md @@ -1,7 +1,7 @@ --- layout: post categories: newsletter -title: "2nd OBO Foundry Newsletter: In Memoriam - Remembering Michael Ashburner" +title: "OBO Foundry Newsletter issue 2" date: 2023-09-15 author: - Leila Kiani @@ -145,48 +145,28 @@ Starting from this issue, we spotlight essential software tools that form the fo - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + +
Software Package - Links - Language(s) - Core Features - Software PackageLinksLanguage(s)Core Features
curies / curies4j - cthoyt/curies, cthoyt/curies4j - Python, Java - The core library for conversion between URIs and Compact URIs (CURIEs). An essential addon for all Semantic Software Engineers. - curies / curies4jcthoyt/curies, cthoyt/curies4jPython, JavaThe core library for conversion between URIs and Compact URIs (CURIEs). An essential addon for all Semantic Software Engineers.
ROBOT - https://github.com/ontodev/robot -

-http://robot.obolibrary.org/ -

Java, CLI - The Swiss Army Knife of Ontology Engineering. Transform your ontologies, manage them with templates and check them for errors! A must have for all ontology engineers! - ROBOThttps://github.com/ontodev/robotJava, CLIThe Swiss Army Knife of Ontology Engineering. Transform your ontologies, manage them with templates and check them for errors! A must have for all ontology engineers!
Ontology Access Kit (OAK) - https://incatools.github.io/ontology-access-kit -

- -

Python - User-facing Python library and CLI tool suite for accessing ontologies, including visualization, mapping and annotation. Indispensable for data scientists that work with ontologies. - Ontology Access Kit (OAK)https://incatools.github.io/ontology-access-kitPythonUser-facing Python library and CLI tool suite for accessing ontologies, including visualization, mapping and annotation. Indispensable for data scientists that work with ontologies.
From 04e9da6bbe1e403f8b6d399152d57ba421a415ec Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Tue, 19 Sep 2023 17:57:02 +0300 Subject: [PATCH 3/3] Update 2023-16-15-second-issue-newsletter.md --- _posts/2023-16-15-second-issue-newsletter.md | 33 ++++---------------- 1 file changed, 6 insertions(+), 27 deletions(-) diff --git a/_posts/2023-16-15-second-issue-newsletter.md b/_posts/2023-16-15-second-issue-newsletter.md index ba1aca03a..9753f0c91 100644 --- a/_posts/2023-16-15-second-issue-newsletter.md +++ b/_posts/2023-16-15-second-issue-newsletter.md @@ -143,33 +143,12 @@ It is essential to use the same license to ensure consistency and clarity within Starting from this issue, we spotlight essential software tools that form the foundation of the Open Biomedical Ontologies (OBO) Foundry community. These tools play a central role in facilitating collaboration, upholding data integrity, and editing and validating ontologies. The table below lists some of the tools that are frequently used by (and, in some cases, developed by) members of the OBO Foundry community. - - - - - - - - - - - - - - - - - - - - - - - - - -
Software PackageLinksLanguage(s)Core Features
curies / curies4jcthoyt/curies, cthoyt/curies4jPython, JavaThe core library for conversion between URIs and Compact URIs (CURIEs). An essential addon for all Semantic Software Engineers.
ROBOThttps://github.com/ontodev/robotJava, CLIThe Swiss Army Knife of Ontology Engineering. Transform your ontologies, manage them with templates and check them for errors! A must have for all ontology engineers!
Ontology Access Kit (OAK)https://incatools.github.io/ontology-access-kitPythonUser-facing Python library and CLI tool suite for accessing ontologies, including visualization, mapping and annotation. Indispensable for data scientists that work with ontologies.
- +| Software Package | Links | Language(s) | Core Features | +|---------------------------|-------------------------------------------------|--------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| curies / curies4j | cthoyt/curies, cthoyt/curies4j | Python, Java | The core library for conversion between URIs and Compact URIs (CURIEs). An essential addon for all Semantic Software Engineers. | +| ROBOT | https://github.com/ontodev/robot | Java, CLI | The Swiss Army Knife of Ontology Engineering. Transform your ontologies, manage them with templates and check them for errors! A must have for all ontology engineers! | +| Ontology Access Kit (OAK) | https://incatools.github.io/ontology-access-kit | Python | User-facing Python library and CLI tool suite for accessing ontologies, including visualization, mapping and annotation. Indispensable for data scientists that work with ontologies. | + --- ## Events