Grant Progress Reports December 2009: Difference between revisions
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=== [https://docs.google.com/document/d/1w8nR5llrexyqCKk3NTlj3v3s7gKBA-DPtAT3LiIe5jo/edit#heading=h.q5pvr82zaw65 GO 2009 Publications, Tutorials & Workshops, Presentations, Posters, and Resources] === | |||
=== Working Groups === | === Working Groups === | ||
[[Ontology Development Progress Report December 2009]] | [[Ontology Development Progress Report December 2009]] | ||
[[Outreach and Advocacy Progress Report December 2009]] | |||
[[Software Group progress report for 2009]] | |||
[[Reference Genome progress report for 2009]] | |||
=== MODs and Annotation Projects === | === MODs and Annotation Projects === | ||
[[MGI]] | |||
[[WormBase]] | |||
[[EcoliWiki]] | |||
[[RGD]] | |||
[[dictyBase Progress Report December 2009]] | |||
[[FlyBase]] | |||
[[TAIR December 2009]] | |||
[[GOA December 2009]] | |||
[[SGD_December_2009]] | |||
[[BHF-UCL_December_2009]] | |||
=== Supplements === | === Supplements === | ||
[[Princeton Progress Report December 2009]] | [[Princeton Progress Report December 2009]] | ||
[[Sequence Ontology Progress Report December 2009]] | |||
[[Cell Ontology Progress Report December 2009]] | |||
===Project-Generated Resources=== | |||
* The Gene Ontologies: As of Dec. 2009, the Gene Ontologies include Molecular Function (8,657 terms), Biological Process (17, 553 terms), and Cellular Component (2,613 terms). The ontologies including definitions are available at the GO Web site in a variety of formats including OWL, RDF, XML, and OBO. | |||
* The Sequence Ontology is provided for download in 4 different forms. It is provided for editing as so-xp.obo which includes the raw cross product terms, and is intended for use with a reasoner. It is provided fully reasoned with the implicit links fully written out, for use without a reasoner as so.obo. Two subsets of SO are maintained for specialized uses: a version for natural language programming (l_s_f.obo) and subset of SO feature for automated annotation pipelines (sofa.obo). | |||
* GO Associations files for the major model organisms are provided in OBO, tab delimited and XML formats that include evidence assertions, citations, synonyms and other accIDs and Xrefs. | |||
* The GO Database is developed and maintained by software engineers located in the Stanford and LBNL GO groups. The MySQL database, API documentation, schema diagrams and full descriptions of all tables are freely available at http://www.godatabase.org/dev/database/. GO monthly releases are available in RDF XML or a MySQL database dump. | |||
* GO Consortium Tools are the AmiGO browser for the GO database resource and the OBO-Edit ontology editing tool; both are open-source applications (http://www.geneontology.org/GO.tools.html). | |||
* Many GO Tools for mining GO data have been developed and can be accessed from the GO Web Site. Tools can map granular GO terms to more general parent terms, and can facilitate the access to GO information from gene-set input files. Several are particularly useful for analysis of microarray data. | |||
* GO Browsers: Several browsing tools have been developed and are available via the GO Web site. The AmiGO browser is provided by the GOC for access to the GO database. | |||
* GO Teaching Resources include tutorials, presentations and posters provided by members of the GO Consortium (http://www.geneontology.org/GO.teaching.resources.html). | |||
* Indices mapping other classification systems to the GO provided at the GO Web site include translations of Swiss-Prot keywords, TIGR/EGAD, GenProtEC, InterPro keywords, and the Enzyme Commission set. (http://www.geneontology.org/GO.indices.html). |
Latest revision as of 11:49, 10 February 2023
GO 2009 Publications, Tutorials & Workshops, Presentations, Posters, and Resources
Working Groups
Ontology Development Progress Report December 2009
Outreach and Advocacy Progress Report December 2009
Software Group progress report for 2009
Reference Genome progress report for 2009
MODs and Annotation Projects
dictyBase Progress Report December 2009
Supplements
Princeton Progress Report December 2009
Sequence Ontology Progress Report December 2009
Cell Ontology Progress Report December 2009
Project-Generated Resources
- The Gene Ontologies: As of Dec. 2009, the Gene Ontologies include Molecular Function (8,657 terms), Biological Process (17, 553 terms), and Cellular Component (2,613 terms). The ontologies including definitions are available at the GO Web site in a variety of formats including OWL, RDF, XML, and OBO.
- The Sequence Ontology is provided for download in 4 different forms. It is provided for editing as so-xp.obo which includes the raw cross product terms, and is intended for use with a reasoner. It is provided fully reasoned with the implicit links fully written out, for use without a reasoner as so.obo. Two subsets of SO are maintained for specialized uses: a version for natural language programming (l_s_f.obo) and subset of SO feature for automated annotation pipelines (sofa.obo).
- GO Associations files for the major model organisms are provided in OBO, tab delimited and XML formats that include evidence assertions, citations, synonyms and other accIDs and Xrefs.
- The GO Database is developed and maintained by software engineers located in the Stanford and LBNL GO groups. The MySQL database, API documentation, schema diagrams and full descriptions of all tables are freely available at http://www.godatabase.org/dev/database/. GO monthly releases are available in RDF XML or a MySQL database dump.
- GO Consortium Tools are the AmiGO browser for the GO database resource and the OBO-Edit ontology editing tool; both are open-source applications (http://www.geneontology.org/GO.tools.html).
- Many GO Tools for mining GO data have been developed and can be accessed from the GO Web Site. Tools can map granular GO terms to more general parent terms, and can facilitate the access to GO information from gene-set input files. Several are particularly useful for analysis of microarray data.
- GO Browsers: Several browsing tools have been developed and are available via the GO Web site. The AmiGO browser is provided by the GOC for access to the GO database.
- GO Teaching Resources include tutorials, presentations and posters provided by members of the GO Consortium (http://www.geneontology.org/GO.teaching.resources.html).
- Indices mapping other classification systems to the GO provided at the GO Web site include translations of Swiss-Prot keywords, TIGR/EGAD, GenProtEC, InterPro keywords, and the Enzyme Commission set. (http://www.geneontology.org/GO.indices.html).