From 513c54730071694104fb8e32a141dffb66a1a7a5 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Thu, 30 May 2024 13:43:16 -0700 Subject: [PATCH 1/2] Update resources.md - Fixed typo - Adding links to OAK and obofoundry github tag --- resources.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/resources.md b/resources.md index 284082ca4..96ade1d97 100644 --- a/resources.md +++ b/resources.md @@ -23,6 +23,7 @@ title: Ontology Tools and Resources - [Cell Ontology Tutorial](https://github.com/obophenotype/cell-ontology-training/blob/master/README.md): Led by David Osumi-Sutherland, Alex Diehl, Nico Matentzoglu and Nicole Vasilevsky - [ROBOT tutorial](https://ontodev.github.io/robot-tutorial/#/title-slide) by James Overton - [OBO Academy](https://www.youtube.com/channel/UCKAkmAIIfPZc5kjdait-MdQ): A YouTube channel with presentations and tutorials relevant to the OBO Foundry +- [The OAK Guide](https://incatools.github.io/ontology-access-kit/guide/index.html): Hands-on guide to programmatically working with OBO ontologies - [Pizza Tutorial for Protégé 5](https://drive.google.com/file/d/1UqI19JiGnJwzKx_JQ7qRAz7bmCzyqZpj/view) by Michael DeBellis. [More info](https://www.michaeldebellis.com/post/new-protege-pizza-tutorial). - [Introduction to Biomedical Ontologies](http://ontology.buffalo.edu/smith/BioOntology_Course.html): A training course in eight lectures by [Barry Smith](http://ontology.buffalo.edu/smith/) - [Building Ontologies with Basic Formal Ontology](http://ontology.buffalo.edu/BOBFO/detailed-table-of-contents.html): By Robert Arp, Barry Smith, and Andrew Spear @@ -37,12 +38,14 @@ title: Ontology Tools and Resources - [Karma Data Integration](http://usc-isi-i2.github.io/karma/): A data integration tool - [Ontofox](http://ontofox.hegroup.org/): An ontology term and relation extraction and reuse tool - [Ubergraph](https://github.com/INCATools/ubergraph): A sparql endpoint with many OBO ontologies loaded and pre-reasoned with simple triples materialized +- [Ontology Access Kit (OAK)](https://github.com/INCATools/ontology-access-kit): A python library and command-line tool for working with ontologies and ontology-annotated data +- [obofoundry-tagged repositories in GitHub](https://github.com/topics/obofoundry) ## Ontology Analysis - [OBO Dashboard](https://dashboard.obofoundry.org): An assesment of OBO Foundry ontologies' conformance to OBO Foundry principles - [OBO Community Health Report](https://cthoyt.com/obo-community-health): A self-updating assessment of the quality of metadata, responsiveness of the maintainers, and the overall community engagement for each OBO Foundry ontology. -- [Ontology Quality Assessment](https://cthoyt.com/oquat): A self-updating assesment of the semantic quality of OBO Foundry ontologies and beyond (using known prefixes, using standard identifiers, etc.) +- [Ontology Quality Assessment](https://cthoyt.com/oquat): A self-updating assessment of the semantic quality of OBO Foundry ontologies and beyond (using known prefixes, using standard identifiers, etc.) - [Current Ontology Versions](https://psiotwo.github.io/ontology-version-extractor/output.html): A daily refreshed list of OBO ontology versions and their compatibility with OBO Foundry Identifier Policy. ## Relevant Publications/blogs From 161391fe8dbe1ea70d458615b61978e94158857a Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Fri, 31 May 2024 13:30:22 +0300 Subject: [PATCH 2/2] Update resources.md --- resources.md | 1 - 1 file changed, 1 deletion(-) diff --git a/resources.md b/resources.md index 96ade1d97..d16bc24f4 100644 --- a/resources.md +++ b/resources.md @@ -45,7 +45,6 @@ title: Ontology Tools and Resources - [OBO Dashboard](https://dashboard.obofoundry.org): An assesment of OBO Foundry ontologies' conformance to OBO Foundry principles - [OBO Community Health Report](https://cthoyt.com/obo-community-health): A self-updating assessment of the quality of metadata, responsiveness of the maintainers, and the overall community engagement for each OBO Foundry ontology. -- [Ontology Quality Assessment](https://cthoyt.com/oquat): A self-updating assessment of the semantic quality of OBO Foundry ontologies and beyond (using known prefixes, using standard identifiers, etc.) - [Current Ontology Versions](https://psiotwo.github.io/ontology-version-extractor/output.html): A daily refreshed list of OBO ontology versions and their compatibility with OBO Foundry Identifier Policy. ## Relevant Publications/blogs