Publications, Talks, Posters 2010-2012
Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members during 2010 reporting year.
Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF. 2010. Ontology Engineering. Nat Biotechnol. Feb;28(2):128-30.
Mungall C, Gkoutos G, Smith C, Haendel M, Lewis S, Ashburner M. Integrating phenotype ontologies across multiple species. Genome Biology, 11(1):R2, 2010.
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold TS, GondrÃ-Lewis TA, Masci AM, Meehan TF, Morel PA, NIAID Cell Ontology Working Group, Nijnik A, Peters B, Pulendran B, Scheuerman RH, Yao QA, Zand MS, and Mungall CJ. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. Journal of Biomedical Informatics, (accepted), 2010.
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. Cross-Product Extensions of the Gene Ontology. Journal of Biomedical Informatics, In Press, Uncorrected Proof, 2010. PDF.
Deegan et al is accepted pending acceptance of minor revisions
Gene Ontology Consortium. 2010. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2010 January; 38(Database issue): D331–D335.
- Fisk D et al (SGD), Title: "Annotation Across Species: SGD and the Reference Genome Project"; Model Organism to Human Biology Conference (June 2010)
- 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).