GO publications 2009

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Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members during 2009 reporting year.

2009 Publications

  1. Alterovitz, G., Xiang, M., Hill, D., Lomax, J., Liu, J., Mungall, C., Harris, M., Dolan, M.E., Blake, J.A., Ramoni, M.F. Engineering Biomedical Ontologies: The Gene Ontology [Accepted, In Press, Nature Biotechnology]
  2. Barrell D., Dimmer E., Huntley R.P., Binns D., O'Donovan C., Apweiler R. 2009. The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res. Jan;37(Database issue):D396-403. (January) PMC2686469
  3. Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R. 2009 QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics. doi:10.1093/bioinformatics/btp536 (September) Nov 15;25(22) 3045-3046 PMC2773257
  4. Alexander D. Diehl, Alison Deckhut Augustine, Judith A. Blake, Lindsay G. Cowell, Elizabeth S. Gold, Timothy A. Gondré-Lewis, Anna Maria Masci, Terrence F. Meehan, Penelope A. Morel, NIAID Cell Ontology Working Group, Anastasia Nijnik, Bjoern Peters, Bali Pulendran, Richard H. Scheuerman, Q. Alison Yao, Martin S. Zand, and Christopher J. Mungall. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. In Proceedings of the First International Conference on Biomedical Ontology, 2009
  5. Meng S, Torto-Alalibo T, Chibucos MC, Tyler BM, Dean RA. Common Processes in Pathogenesis by Fungal and Oomycete Plant Pathogens, described with Gene Ontology Terms. BMC Microbiology 2009, 9(Suppl 1):S7 (19 February 2009) PMC2654667
  6. Blake, J.A., Bult, C.J., Eppig, J.T., Kadin, J.A., Richardson, J.E.; Mouse Genome Database Group. 2009. The Mouse Genome Database genotypes::phenotypes. Nucleic Acids Res. (Database issue):D712-9. (January) PMC2686566
  7. Christie KR, Hong EL, Cherry JM. 2009. Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends in Microbiology. 17(7): 286-294. (July)
  8. Chibucos MC, Tseng T-T, Setubal JC. 2009. Describing commonalities in microbial effector delivery using the Gene Ontology. Trends in Microbiology. 17(7): 312-319. (July)
  9. Chibucos MC, Collmer CW, Torto-Alalibo T, Gwinn-Giglio M, Lindeberg M, Li D, Tyler BM. Programmed Cell Death in Host-symbiont Associations, viewed through the Gene Ontology. BMC Microbiology 2009, 9(Suppl 1):S5 (19 February 2009) PMC2654665
  10. Chibucos MC, Tyler BM. Common Themes in Nutrient Acquisition by Plant Symbiotic Microbes, described by The Gene Ontology. BMC Microbiology 2009, 9(Suppl 1):S6 (19 February 2009) PMC2654666
  11. Feltrin E., Campanaro, S., Diehl A.D., Ehler, E., Faulkner, G., Fordham, J., Gardin, C., Harris, M., Hill, D., Knoell, R., Laveder, P., Mittempergher, L., Nori, A., Reggiani, C., Sorrentino V., Volpe P., Zara I., Valle G., Deegan J. 2009. Muscle Research and Gene Ontology: New standards for improved data integration. BMC Medical Genomics 2:6 dpo10.1186/1755-8794-2-6. (January) PMC2657163
  12. Giglio MG, Collmer C.W. Lomax J. Ireland A. 2009. Applying the Gene Ontology in microbial annotation. Trends in Microbiology. 17(7): 262-268. (July)
  13. Hill DP, Berardini TZ, Howe DG, Van Auken KM. Representing Ontogeny Through Ontology: A Developmental Biologist’s Guide to The Gene Ontology. Molecular Reproduction and Development. (November) NIHMS163751, PMID 19921742
  14. Hu JC. Karp PD. Keseler, IM. Krummenacker M. Siegele DA. What we can learn about Escherichia coli through application of Gene Ontology. Trends in Microbiology. 17(7): 269-278. (July)
  15. Korves T. Colosimo ME. 2009. Controlled vocabularies for microbial virulence factors. Trends in Microbiology. 17(7): 279-285. (July)
  16. Huntley RP; Binns D; Dimmer E; Barrell D; O'Donovan C; Apweiler R. 2009 QuickGO: a user tutorial for the web-based Gene Ontology browser. Database. doi: 10.1093/database/bap010 (September) PMC2773257
  17. Lindeberg M, Biehl BS, Glasner JD, Perna NT, Collmer A, Collmer CW. Gene Ontology Annotation highlights Shared and Divergent Pathogenic Strategies of Type III Effector Proteins deployed by the Plant Pathogen Pseudomonas syringae pv tomato DC3000 and Animal Pathogenic Escherichia coli Strains. BMC Microbiology 2009, 9(Suppl 1):S4 (19 February 2009) PMC2654664
  18. Lovering R.C., Dimmer E.C., Talmud P.J. 2009 Improvements to cardiovascular Gene Ontology. Atherosclerosis. 205(1): 9-14. (July) PMC2706316
  19. Tyler, BM. 2009. Viewing the microbial world through the lens of the Gene Ontology. Trends in Microbiology. 17(7): 259-261. (July) PMC2654664
  20. Anna Maria Masci, Cecilia Arighi, Alexander Diehl, Anne Lieberman, Chris Mungall, Richard Scheuermann, Barry Smith, and Lindsay Cowell. An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC Bioinformatics, 10(1):70, 2009
  21. Meng S, Brown DE, Ebbole DJ, Torto-Alalibo T, Oh YY, Deng J, Mitchell TK, Dean RA. Gene Ontology Annotation of Magnaporthe oryzae. BMC Microbiology 2009, 9(Suppl 1):S8 (19 February 2009) PMC2654668
  22. Meng S, Torto-Alalibo T, Chibucos MC, Tyler BM, Dean RA. Common Processes in Pathogenesis by Fungal and Oomycete Plant Pathogens, described with Gene Ontology Terms. BMC Microbiology 2009, 9(Suppl 1):S7 (19 February 2009) PMC2654667
  23. Christopher J. Mungall, Michael Bada, Tanya Z. Berardini, Jennifer Deegan, Amelia Ireland, Midori A. Harris, David P. Hill, and Jane Lomax. Cross-Product Extensions of the Gene Ontology. In Proceeeings of the First International Conference on Biomedical Ontology, July 2009
  24. Sam LT, Mendonca EA, Li J, Blake J, Friedman C, Lussier YA. 2009. PhenoGO: an integrated resource for the multiscale mining of clinical and biological data. BMC Bioinformatics 10(Suppl 2):S8. PMC2646241
  25. The Reference Genome Group of the Gene Ontology Consortium (2009) The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species. PLoS Comput Biol 5(7): e1000431. doi:10.1371/journal.pcbi.1000431 PMC2699109
  26. Torto-Alalibo T, Meng S, Dean RA. 2009. Infection strategies of filamentous microbes described with the Gene Ontology. Trends in Microbiology. 17(7): 320-327. (July) PMID: 19577927
  27. Torto-Alalibo, T, Collmer, CW, Gwinn-Giglio, M. The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium: Community Development of New Gene Ontology Terms Describing Biological Processes Involved in Microbe-Host Interactions. BMC Microbiology 2009, 9(Suppl 1):S1 (19 February 2009) PMC2654661
  28. Torto-Alalibo TA, Collmer CW, Lindeberg M, Bird D, Collmer A, Tyler BM. Common and Contrasting Themes in Host Cell-targeted Effectors from Bacterial, Fungal, Oomycete and Nematode Plant Symbionts described using the Gene Ontology. BMC Microbiology 2009, 9(Suppl 1):S3 (19 February 2009) PMC2654663
  29. Tseng, T-T, Tyler, BM, Setubal, JC. Protein Secretion Systems in Bacterial-Host Associations, and their Description in the Gene Ontology. BMC Microbiology 2009, 9(Suppl 1):S2 (19 February 2009) PMC2654662
  30. Tweedie, S., Ashburner, M., Falls, K., Leyland, P., McQuilton, P., Marygold, S., Millburn, G., Osumi-Sutherland, D., Schroeder, A., Seal, R., Zhang, H.; FlyBase Consortium. 2009. FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res. Jan; 37(Database issue): D555-9. PMC2686450
  31. Van Auken K, Jaffery J, Chan J, Müller HM, Sternberg PW. Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation. BMC Bioinformatics 2009, Jul 21;10:228. PMC2719631
  32. Schober D, Smith B, Lewis SE, Kusnierczyk W, Lomax J, Mungall C, Taylor CF, Rocca-Serra P, Sansone SA. Survey-based naming conventions for use in OBO Foundry ontology development. BMC Bioinformatics. 2009 Apr 27;10(1):125. (April) PMC2684543
  33. Wortman J.R., Gilsenan J.M., Joardar V., Deegan J.I., Clutterbuck J., Andersen M.R., Archer D., Bencina M., Braus G., Coutinho P., von Döhren H., Doonan J., Driessen A.J., Durek P., Espeso E., Fekete E., Flipphi M., Estrada C.G., Geysens S., Goldman G., de Groot P.W., Hansen K., Harris S.D., Heinekamp T., Helmstaedt K., Henrissat B., Hofmann G., Homan T., Horio T., Horiuchi H., James S., Jones M., Karaffa L., Karányi Z., Kato M., Keller N., Kelly D.E., Kiel J.A., Kim J.M., van der Klei I.J., Klis F.M., Kovalchuk A., Krasevec N., Kubicek C.P., Liu B., Maccabe A., Meyer V., Mirabito P., Miskei M., Mos M., Mullins J., Nelson D.R., Nielsen J., Oakley B.R., Osmani S.A., Pakula T., Paszewski A., Paulsen I., Pilsyk S., Pócsi I., Punt P.J., Ram A.F., Ren Q., Robellet X., Robson G., Seiboth B., van Solingen P., Specht T., Sun J., Taheri-Talesh N., Takeshita N., Ussery D., vanKuyk P.A., Visser H., van de Vondervoort P.J., de Vries R.P., Walton J., Xiang X., Xiong Y., Zeng A.P., Brandt B.W., Cornell M.J., van den Hondel C.A., Visser J., Oliver S.G., Turner G. The 2008 update of the Aspergillus nidulans genome annotation: A community effort. Fungal Genetics and Biology. 46 (2009) S2–S13.

2009 Talks

  1. Invited speaker - 'Gene Ontology and Heart Development' at 8th London Heart Development Meeting, Institute for Child Health, London (Varsha Khodiyar) (December)
  2. Invited speaker - 'Genome Annotation and the Sequence Ontology' at the Idaho State University Bioinformatics Workshop, Lava Hot Springs, Idaho, (Eilbeck) (October).
  3. Plenary Speaker- 'Biomedical Literature in the Clouds: Ontologies, Data, and the Semantic Web' North Atlantic Health Sciences Libraries Meeting. (Blake) (October).
  4. Invited Speaker- ' Digital Annotation for Production Bioinformatics Systems' BioCreative 11.5 Workshop, Madrid, Spain. (Blake) (October).
  5. Invited speaker - 'Ontologies for genomics' Biomedical Informatics Seminar Series, University of Utah, (Eilbeck) (October).
  6. Invited speakers - 'Meet the experts: Gene Ontology' at the British Atherosclerosis Society Autumn meeting 'Genetics of Complex Diseases'. Cambridge, UK. (Ruth Lovering, Emily Dimmer) (September)
  7. Conference talk - 'The evolution of Sequence Ontology Terms and Relationships' International Conference for Biomedical Ontology, Buffalo NY. (Eilbeck) (July).
  8. Invited conference talk- ' PAINT:The GO Workbench for Protein Family Annotation' Special Session on Orthology Inference at ISMB-2009 Stockholm, Sweden (Lewis) (July).
  9. Invited Participant/Speaker- 'PAINT: THE GO WORKBENCH FOR PROTEIN FAMILY ANNOTATION' Quest for Orthologs Meeting, Cambridge-Hinxton Genome Center, U.K. (Lewis) (July).
  10. Invited Participant/Speaker- 'Orthologs, Paralogs, and Functional Annotations using the Gene Ontology' Quest for Orthologs Meeting, Cambridge-Hinxton Genome Center, U.K. (Blake) (July).
  11. Invited Participant/Speaker- 'The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species' Quest for Orthologs Meeting, Cambridge-Hinxton Genome Center, U.K. (Gaudet) (July).
  12. Invited Speaker and Workshop -'Searching, querying, browsing, downloading and analysing data using GeneDB and the Gene Ontology annotation' Molecular Genetics of the Fission Yeast Schizosaccharomyces pombe. EMBO Workshop. Manchester. (Wood) (June).
  13. Invited Speaker- 'Functional Annotation and the Gene Ontology" 2009 Oomycete Bioinformatics Resources Training Workshop. Virginia Bioinformatics Institute, Virginia Tech. (Torto-Alalibo) (June).
  14. Invited Speaker-Introduction to Gene Ontology Annotation (GOA) and The Renal GOA Initiative, GenitoUrinary Development Molecular Anatomy Project (GUDMAP), MRC Human Genetics Unit (HGU), Western General Hospital, Edinburgh (Alam-Faruque) (June).
  15. Invited Speaker-Introduction to the Gene Ontology. Cell Behavior Ontology Workshop, National Institutes of Health, Bethesda, MD. (Diehl) (May).
  16. Invited speaker-'Microbe-Plant Interactions through the Lens of Gene Ontology'. Research Centre for Plant Biotechnology and Genomics, Madrid, Spain (CW Collmer) (May).
  17. Conference talk - Using Textpresso for Information Retrieval, Fact Extraction, and Database Entry. Third International Biocuration Conference, April 16-19, 2009, Berlin, Germany. Available from Nature Proceedings: http://precedings.nature.com/documents/3302/version/1 (Yook K, Van Auken KM, Sternberg P, and the WormBase Consortium) (April).
  18. Conference talk - The reference genome project. International Biocurator Meeting 2009. (Gaudet) (April).
  19. Invited Speaker-Gene Ontology Recapitulates Ontogeny: Using the Gene Ontology to Study Development. Molecular Reproduction and Development Meeting, Brown University, RI. (Hill) (March).
  20. Invited speaker-Introduction to GO and other Biomedical Ontologies. European Bioinformatics Institute Primer for Predocs Course, Hinxton, UK. (Lomax) (Feb).
  21. Invited Speaker-' Evidence and Inference: Comparative Biology in the Age of Genomics' University of Chicago, Chicago, Illinois. (Blake) (Feb).
  22. Invited speaker-'GO for it! Gene Ontology - an essential resource'. Department of Medicine, University College London, UK. (Lovering) (Feb).

2009 Posters

  1. Hill DP, Sitnikov D, Blake JA. 2009. Using gene ontology to study branching morphogenesis in mice. Society for Developmental Biology, San Francisco (Hill, Sitnikov, Blake).
  2. PAINTing GO Annotations Across Genomes. Cold Spring Harbor Laboratory Genome Informatics, Cold Spring Harbor, NY. (Michael S. Livstone*, Kara Dolinski, Pascale Gaudet, Suzanna E. Lewis, Anushya Muruganujan and Paul D. Thomas).
  3. Improving Logical Relationship in the Gene Ontology. Third International Biocuration Conference, Berlin, Germany. (Berardini, Harris*, Hill, Lomax, Mungall) (April).
  4. Gene Ontology: Serving the Community. Third International Biocuration Conference, Berlin, Germany. (Lomax*, Carbon, Hitz, Ireland, the Gene Ontology web-presence WG) (April).
  5. The GO Annotation (GOA) Project. Third International Biocuration Conference, Berlin, Germany. (Rachael Huntley*, Emily Dimmer, Daniel Barrell, David Binns and Rolf Apweiler) (April).
  6. The Cardiovascular Gene Ontology Initiative. Third International Biocuration Conference, Berlin, Germany. (Varsha Khodiyar*, Daniel Barrell, Peter Scambler, Mike Hubank, Rolf Apweiler, Philippa Talmud and Ruth Lovering) (April).
  7. The Gene Ontology: Making Biomedical language Computable. The Hopper Colloquium, British Computer Society, London. (Jennifer I. Deegan*, Michael Bada, Tanya Z. Berardini, Amelia Ireland, Midori A. Harris, David P. Hill, Jane Lomax, Wacek Kusnierczyk, Christopher J. Mungall) (May).
  8. The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species, Pascale Gaudet for the Reference Genome Group of the Gene Ontology Consortium, Dicty Annual International Meeting, Estes Park, CO (Gaudet) (August).
  9. The Renal Gene Ontology Annotation Initiative. Kidney Research UK Fellows Day, Heley Business School, Henley-on-Thames. (Yasmin Alam-Faruque*, Emily Dimmer, Peter Scambler, Rolf Apweiler) (September).
  10. Gene Ontology - a way forwards, UCL Institute of Stroke Research - Scientific meeting, London, UK. (Ruth Lovering*, Varsha Khodiyar, Daniel Barrell, Peter Scambler, Mike Hubank, Rolf Apweiler, Philippa Talmud) (October).
  11. Gene Ontology - a way forwards, UCL Genetics Institute - Public launch, London, UK. (Ruth Lovering*, Varsha Khodiyar, Daniel Barrell, Peter Scambler, Mike Hubank, Rolf Apweiler, Philippa Talmud) (November).

Project-Generated Resources

  1. 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.
  2. 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).
  3. 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.
  4. 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.
  5. 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).
  6. 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.
  7. 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.
  8. GO Teaching Resources include tutorials, presentations and posters provided by members of

the GO Consortium (http://www.geneontology.org/GO.teaching.resources.html).

  1. 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).