Difference between revisions of "GO 2009 Publications, Tutorials & Workshops, Presentations, Posters, and Resources"

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#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 <b>PAMGO</b>
 
#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 <b>PAMGO</b>
 
#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) <b>SGD</b>
 
#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) <b>SGD</b>
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#Eilbeck K, Moore B, Holt C and Yandell M. Quantitative measures for the management and comparison of annotated genomes. BMC Bioinformatics 2009, 10:67doi:10.1186/1471-2105-10-67. PMCID: PMC2653490 <b>SO</b>
 
#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 <b>EBI, MGI, ...</b>
 
#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 <b>EBI, MGI, ...</b>
 
#Gaudet P, 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 <b>DictyBase, ALL</b>
 
#Gaudet P, 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 <b>DictyBase, ALL</b>
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#Korves T. Colosimo ME. 2009. Controlled vocabularies for microbial virulence factors. Trends in Microbiology. 17(7): 279-285. (July)  
 
#Korves T. Colosimo ME. 2009. Controlled vocabularies for microbial virulence factors. Trends in Microbiology. 17(7): 279-285. (July)  
 
#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 <b>PAMGO</b>
 
#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 <b>PAMGO</b>
#Lovering R.C., Dimmer E.C., Talmud P.J. 2009 Improvements to cardiovascular Gene Ontology. Atherosclerosis. 205(1): 9-14. (July) PMC2706316 <b>BHF-UCL, GOA</b> pdfs available at [[www.cardiovasculargeneontology.com]].
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#Lovering R.C., Dimmer E.C., Talmud P.J. 2009 Improvements to cardiovascular Gene Ontology. Atherosclerosis. 205(1): 9-14. (July) PMC2706316 <b>BHF-UCL, GOA</b> pdfs available at http://www.ucl.ac.uk/silva/cardiovasculargeneontology.
 
#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 <b>PAMGO</b>
 
#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 <b>PAMGO</b>
 
# Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG. 2009. An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC Bioinformatics, 10:70. <b>MGI, LBNL, ...</b>
 
# Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG. 2009. An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC Bioinformatics, 10:70. <b>MGI, LBNL, ...</b>
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#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 <b>PAMGO</b>
 
#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 <b>PAMGO</b>
 
# 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 <b>LBNL, TAIR, EBI, MGI, ...</b>
 
# 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 <b>LBNL, TAIR, EBI, MGI, ...</b>
#Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B. (2009) FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. Nucleic Acids Res. [Epub ahead of print] PMID:19884132 <b>FlyBase</b>
 
 
#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<b>MGI, ...</b>
 
#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<b>MGI, ...</b>
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#Shimoyama M, Hayman GT, Laulederkind SJ, Nigam R, Lowry TF, Petri V, Smith JR, Wang SJ, Munzenmaier DH, Dwinell MR, Twigger SN, Jacob HJ; RGD Team. 2009. The rat genome database curators: who, what, where, why. PLoS Comput Biol. 5(11):e1000582.
 
#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 <b>PAMGO</b>
 
#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 <b>PAMGO</b>
 
#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 <b>PAMGO</b>
 
#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 <b>PAMGO</b>
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#<b>JCVI: </b>Linda Hannick presented an hour-long Introduction to GO to the participants in the JCVI Eukaryotic Genome Annotation and Analysis Course, presented March 3-5, April 1-3, and June 10-12, 2009. Another course will be presented September 23-25, 2009.
 
#<b>JCVI: </b>Linda Hannick presented an hour-long Introduction to GO to the participants in the JCVI Eukaryotic Genome Annotation and Analysis Course, presented March 3-5, April 1-3, and June 10-12, 2009. Another course will be presented September 23-25, 2009.
 
#<b>GOA - March 21st: </b>Perspectives in Stem Cell Proteomics Training Workshop, EBI (Emily GO/GOA talk and tutorial)
 
#<b>GOA - March 21st: </b>Perspectives in Stem Cell Proteomics Training Workshop, EBI (Emily GO/GOA talk and tutorial)
#<b>E.Coli - April 13th: </b>Jim Hu and Debby Siegele attended the American Society for Microbiology Conference on Undergraduate Education (ASMCUE), where they discussed the importance of GO for microbiology, and using GONUTS in education.
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#<b>EcoliWiki - April 8th-May 3rd: </b> Pilot course - CACAO (Community Assessment of Community Annotation with Ontologies) (Brenley McIntosh, Debby Siegele and Jim Hu)
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#<b>EcoliWiki - May 20th: </b>Jim Hu, Debby Siegele & Brenley McIntosh attended the American Society for Microbiology Conference on Undergraduate Education (ASMCUE), where they discussed the importance of GO for microbiology, and using GONUTS in education.
 
#<b>FlyBase - May 29: </b>FlyBase/FlyMine 1 day workshop - Dept. of Genetics, University of Cambridge, UK (Peter McQuilton)
 
#<b>FlyBase - May 29: </b>FlyBase/FlyMine 1 day workshop - Dept. of Genetics, University of Cambridge, UK (Peter McQuilton)
 
#<b>GOA - June 22nd: </b> - Presentation of GOA and the Renal Annotation Initiative at Edinburgh University (GUDMAP Consortium) Introduction to Gene Ontology Annotation (GOA) and The Renal GOA Initiative’. Yasmin Alam-Faruque
 
#<b>GOA - June 22nd: </b> - Presentation of GOA and the Renal Annotation Initiative at Edinburgh University (GUDMAP Consortium) Introduction to Gene Ontology Annotation (GOA) and The Renal GOA Initiative’. Yasmin Alam-Faruque
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#<b>University of Maryland - July 28-31: </b>Michelle Gwinn-Giglio gave a GO workshop for 20 people at the University of Maryland. IGS Genomics Workshop included a 2-hour lecture on the GO and then was followed by hands-on manual annotation exercises where part of what attendees had to do was attach GO terms to the exercise genes. The workshop was attended by 17 people and held on the IGS University of Maryland Campus. Two more workshops are planned for September and November.
 
#<b>University of Maryland - July 28-31: </b>Michelle Gwinn-Giglio gave a GO workshop for 20 people at the University of Maryland. IGS Genomics Workshop included a 2-hour lecture on the GO and then was followed by hands-on manual annotation exercises where part of what attendees had to do was attach GO terms to the exercise genes. The workshop was attended by 17 people and held on the IGS University of Maryland Campus. Two more workshops are planned for September and November.
 
#<b>GOA - July 29th: </b> Presentation of the Renal GOA Initiative to Wellcome Trust Genome Campus-wide curators. Title of talk: ‘Introduction to The Renal Gene Ontology Annotation (GOA) Initiative’. Yasmin Alam-Faruque
 
#<b>GOA - July 29th: </b> Presentation of the Renal GOA Initiative to Wellcome Trust Genome Campus-wide curators. Title of talk: ‘Introduction to The Renal Gene Ontology Annotation (GOA) Initiative’. Yasmin Alam-Faruque
#<b>GOA - September 17-18th: </b>'Meet the experts: Gene Ontology' at the British Atherosclerosis Society Autumn meeting 'Genetics of Complex Diseases'. Cambridge, UK. (Ruth Lovering, Emily Dimmer)
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#<b>EcoliWiki & BHF-UCL - Sept-Dec </b> CACAO (Community Assessment of Community Annotation with Ontologies) competition (Brenley McIntosh, Jim Hu, Adrienne Zweifel, Debby Siegele, Ruth Lovering, Varsha Khodiyar)
#<b>SO - October: </b>Invited speaker - 'Ontologies for genomics' Biomedical Informatics Seminar Series, University of Utah, (Eilbeck).  
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#<b>SO - October: </b>Invited speaker - 'Ontologies and genomics' Biomedical Informatics Seminar Series, University of Utah, (Eilbeck).  
 
#<b>GOA - November 9-13th: </b>Wellcome Trust Advanced Courses Proteomics Bioinformatics course. 'Introduction to the Gene Ontology and GO annotation resources'. Emily Dimmer
 
#<b>GOA - November 9-13th: </b>Wellcome Trust Advanced Courses Proteomics Bioinformatics course. 'Introduction to the Gene Ontology and GO annotation resources'. Emily Dimmer
 
#<b>PathEpigen - November: </b> Ana Barat and colleagues visited GOA and the GO Editorial Office at the EBI to discuss annotation systems. They are making manual literature annotations with genes involved in cancer.
 
#<b>PathEpigen - November: </b> Ana Barat and colleagues visited GOA and the GO Editorial Office at the EBI to discuss annotation systems. They are making manual literature annotations with genes involved in cancer.
#<b>GOA - December : </b> Hands-on training at EBI - Joint EBI-Wellcome Trust Proteomics workshop 'Gene Ontology as a data classification tool' (Huntley; GO/GOA talk and tutorial)
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#<b>SO - November: </b>“Managing genomics data” Human Genetics Faculty Research in Progress Series, University of Utah.
 
#<b>Fission Yeast Community Curation: </b> Valerie Wood ran a community curation pilot project for fission yeast, by sending forms to researchers to complete for a recent publication. The initial trial of 20 publications had a 95% response rate demonstrating that the fission yeast community is willing to participate actively in the curation process. See the pilot summary at http://www.sanger.ac.uk/Projects/S_pombe/community_curation.shtml. Eight SF items were also raised for new biology, or ontology issues. The pilot will be extended to 50 laboratories within one month. The hope is to get funding to develop a simple community curation interface as part of the fission yeast grant proposal. We believe that this initiative presents a significant cost-effective opportunity to enhance the efforts of core curation staff at low cost.
 
#<b>Fission Yeast Community Curation: </b> Valerie Wood ran a community curation pilot project for fission yeast, by sending forms to researchers to complete for a recent publication. The initial trial of 20 publications had a 95% response rate demonstrating that the fission yeast community is willing to participate actively in the curation process. See the pilot summary at http://www.sanger.ac.uk/Projects/S_pombe/community_curation.shtml. Eight SF items were also raised for new biology, or ontology issues. The pilot will be extended to 50 laboratories within one month. The hope is to get funding to develop a simple community curation interface as part of the fission yeast grant proposal. We believe that this initiative presents a significant cost-effective opportunity to enhance the efforts of core curation staff at low cost.
 
#<b>Pombe Database: </b>Val Wood gave a talk and workshop on GO Tools for pombe researchers at a Wellcome Trust Advanced Course: Genome-Wide Approaches With Fission Yeast.
 
#<b>Pombe Database: </b>Val Wood gave a talk and workshop on GO Tools for pombe researchers at a Wellcome Trust Advanced Course: Genome-Wide Approaches With Fission Yeast.
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#<b>WormBase: </b>The sea urchin database staff are in touch with WormBase (they are on the same campus at Caltech). To begin with, they are interested in doing InterPro2GO mappings for their proteins, and intend later to submit a gene association file.
 
#<b>WormBase: </b>The sea urchin database staff are in touch with WormBase (they are on the same campus at Caltech). To begin with, they are interested in doing InterPro2GO mappings for their proteins, and intend later to submit a gene association file.
 
#<b>RGD: </b>Jennifer Smith at RGD produced and released an introductory video tutorial entitled "Introduction to Biomedical Ontologies #1: What is an Ontology?". It is available on both SciVee (http://www.scivee.tv/node/11759) and Vimeo (http://www.vimeo.com/5344028). The intended target audience is researchers and students who are largely, or completely, unfamiliar with ontologies, and the example that is used to illustrate ontologies, ontology annotations and ontology browsers (including AmiGO) is GO.
 
#<b>RGD: </b>Jennifer Smith at RGD produced and released an introductory video tutorial entitled "Introduction to Biomedical Ontologies #1: What is an Ontology?". It is available on both SciVee (http://www.scivee.tv/node/11759) and Vimeo (http://www.vimeo.com/5344028). The intended target audience is researchers and students who are largely, or completely, unfamiliar with ontologies, and the example that is used to illustrate ontologies, ontology annotations and ontology browsers (including AmiGO) is GO.
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#<b>BHF-UCL: </b>10 week core module for the new UCL MSc course, Genetics of Human Diseases, http://www.ucl.ac.uk/ugi/education/msc.
  
 
=== Talks (chronological) ===
 
=== Talks (chronological) ===
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#<b>SO, LBNL - January: </b>Invited Speaker/Participant, SO was represented by KE and CJM at the January RNAO content meeting in Cambridge. The division of labor between SO and RNAO was worked out.
 
#<b>MGI - February: </b>Invited Speaker-' Evidence and Inference: Comparative Biology in the Age of Genomics' University of Chicago, Chicago, Illinois. (Blake).  
 
#<b>MGI - February: </b>Invited Speaker-' Evidence and Inference: Comparative Biology in the Age of Genomics' University of Chicago, Chicago, Illinois. (Blake).  
#<b>GOA - February: </b>Invited speaker-'GO for it! Gene Ontology - an essential resource'. Department of Medicine, University College London, UK. (Lovering).
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#<b>BHF-UCL - February: </b>Invited speaker-'GO for it! Gene Ontology - an essential resource'. Department of Medicine, University College London, UK. (Lovering).
 
#<b>MGI - March: </b>Invited Speaker-Gene Ontology Recapitulates Ontogeny: Using the Gene Ontology to Study Development. Molecular Reproduction and Development Meeting, Brown University, RI. (Hill).
 
#<b>MGI - March: </b>Invited Speaker-Gene Ontology Recapitulates Ontogeny: Using the Gene Ontology to Study Development. Molecular Reproduction and Development Meeting, Brown University, RI. (Hill).
 
#<b>WormBase - April 16-19th: </b>Conference talk - Using Textpresso for Information Retrieval, Fact Extraction, and Database Entry. Third International Biocuration Conference, 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).  
 
#<b>WormBase - April 16-19th: </b>Conference talk - Using Textpresso for Information Retrieval, Fact Extraction, and Database Entry. Third International Biocuration Conference, 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).  
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#<b>DictyBase - July 3-5th: </b>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).
 
#<b>DictyBase - July 3-5th: </b>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).
 
#<b>MGI, LBNL -  July 24-26th: </b>Invited Speaker, “Hematopoietic Cell Types: Prototype for a Revised Cell Ontology,” at the International Conference on Biomedical Ontology, July 24-26, Buffalo, NY. (Diehl).
 
#<b>MGI, LBNL -  July 24-26th: </b>Invited Speaker, “Hematopoietic Cell Types: Prototype for a Revised Cell Ontology,” at the International Conference on Biomedical Ontology, July 24-26, Buffalo, NY. (Diehl).
#<b>SO -  July 24-26th: </b>Conference talk - 'The evolution of Sequence Ontology Terms and Relationships' International Conference for Biomedical Ontology, Buffalo NY. (Eilbeck).
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#<b>SO, LBNL -  July 24-26th: </b>Conference talk & paper - 'The evolution of Sequence Ontology Terms and Relationships' International Conference for Biomedical Ontology, Buffalo NY. (Eilbeck). Manuscript submitted to Journal of Biomedical Informatics.
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#<b>BHF-UCL, GOA - September 17-18th: </b>Invited Speakers 'Meet the experts: Gene Ontology' at the British Atherosclerosis Society Autumn meeting 'Genetics of Complex Diseases'. Cambridge, UK. (Lovering and Dimmer)
 
#<b>SO -  October: </b>Invited speaker - 'Genome Annotation and the Sequence Ontology' at the Idaho State University Bioinformatics Workshop, Lava Hot Springs, Idaho, (Eilbeck).
 
#<b>SO -  October: </b>Invited speaker - 'Genome Annotation and the Sequence Ontology' at the Idaho State University Bioinformatics Workshop, Lava Hot Springs, Idaho, (Eilbeck).
 
#<b>MGI -  October: </b>Plenary Speaker- 'Biomedical Literature in the Clouds: Ontologies, Data, and the Semantic Web' North Atlantic Health Sciences Libraries Meeting. (Blake).
 
#<b>MGI -  October: </b>Plenary Speaker- 'Biomedical Literature in the Clouds: Ontologies, Data, and the Semantic Web' North Atlantic Health Sciences Libraries Meeting. (Blake).
 
#<b>MGI -  October: </b>Invited Speaker- ' Digital Annotation for Production Bioinformatics Systems' BioCreative 11.5 Workshop, Madrid, Spain. (Blake).
 
#<b>MGI -  October: </b>Invited Speaker- ' Digital Annotation for Production Bioinformatics Systems' BioCreative 11.5 Workshop, Madrid, Spain. (Blake).
#<b>DictyBase, LBNL, SRI, Princeton - October 27-30th: </b>Invited Speaker - LARGE-SCALE ANNOTATION OF GENE ONTOLOGY TERMS ACROSS MULTIPLE ORGANISMS, USING PHYLOGENETIC TREES. (Cold Spring Harbor LaboratoryGenome Informatics, Cold Spring Harbor, NY. Pascale Gaudet, Kara Dolinski, Stan Dong, Suzanna E. Lewis, Michael S. Livstone, Anushya Muruganujan, and Paul D. Thomas*).  
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#<b>DictyBase, LBNL, SRI, Princeton - October 27-30th: </b>Invited Speaker - LARGE-SCALE ANNOTATION OF GENE ONTOLOGY TERMS ACROSS MULTIPLE ORGANISMS, USING PHYLOGENETIC TREES. (Cold Spring Harbor LaboratoryGenome Informatics, Cold Spring Harbor, NY. Pascale Gaudet, Kara Dolinski, Stan Dong, Suzanna E. Lewis, Michael S. Livstone, Anushya Muruganujan, and Paul D. Thomas*).
#<b>GOA - December: </b>Invited speaker - 'Gene Ontology and Heart Development' at 8th London Heart Development Meeting, Institute for Child Health, London (Varsha Khodiyar).
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#<b>EcoliWiki - Nov 11: </b>Invited speaker - 'Contains 100% CACAO: Functional Annotation with Undergraduates' at 3rd National Meeting of Urban Biology, Nilton Lins University, Manaus, Brazil (Brenley McIntosh)
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#<b>BHF-UCL - December: </b>Invited speaker - 'Gene Ontology and Heart Development' at 8th London Heart Development Meeting, Institute for Child Health, London (Varsha Khodiyar).
  
 
=== Posters (chronological) ===
 
=== Posters (chronological) ===
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#  <b>GOA -  April 16-19th: </b>The GO Annotation (GOA) Project. Third International Biocuration Conference, Berlin, Germany. (Rachael Huntley*, Emily Dimmer, Daniel Barrell, David Binns and Rolf Apweiler) (April).  
 
#  <b>GOA -  April 16-19th: </b>The GO Annotation (GOA) Project. Third International Biocuration Conference, Berlin, Germany. (Rachael Huntley*, Emily Dimmer, Daniel Barrell, David Binns and Rolf Apweiler) (April).  
 
# <b>DictyBase, LBNL, SRI, Princeton - October 27-30th: </b>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)  
 
# <b>DictyBase, LBNL, SRI, Princeton - October 27-30th: </b>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)  
# <b>GOA - April: </b> 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).  
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# <b>BHF-UCL, GOA - April: </b> 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).  
 
# <b>EBI, TAIR, MGI, LBNL, ... - May: </b> 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)
 
# <b>EBI, TAIR, MGI, LBNL, ... - May: </b> 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)
 
#<b>DictyBase - August: </b> 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).  
 
#<b>DictyBase - August: </b> 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).  
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#<b>EcoliWiki - Aug 24-28th </b> Community Assessment of Community Annotation with Ontologies (CACAO): Functional annotation with undergraduates.  61st Meeting on Molecular Genetics of Bacteria and Phages, Cold Spring Harbor, NY.  (Brenley McIntosh*, Debby Siegele, Daniel Renfro, Jim Hu).
 
# <b>GOA - September: </b>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).  
 
# <b>GOA - September: </b>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).  
#  <b>GOA - October: </b>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).
+
#  <b>BHF-UCL, GOA - October: </b>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).
# <b>GOA - November: </b>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).
+
# <b>BHF-UCL, GOA - November: </b>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).
# <b>E.coli: </b>Members of the EcoliWiki team presented posters about Gene Ontology and GONUTS at the annual symposium of the Program in the Biology of Filamentous Fungi at Texas A&M and at the Texas Protein Folders Conference.
+
# <b>EcoliWiki: </b>Members of the EcoliWiki team presented posters about Gene Ontology and GONUTS at the annual symposium of the Program in the Biology of Filamentous Fungi at Texas A&M and at the Texas Protein Folders Conference.
 
# <b>MGI: </b>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).
 
# <b>MGI: </b>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).
 +
# David Osumi-Sutherland's poster at the 3rd International Boicuration Conference in Berlin, April 2009: [[Media:Berlin_poster_final.pdf]]
  
 
=== Project-Generated Resources ===
 
=== Project-Generated Resources ===
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[[Grant Progress Reports December 2009 | return to 2009 Progress Reports]]
 
[[Grant Progress Reports December 2009 | return to 2009 Progress Reports]]
  
[[Category:Reports]]
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[[Category:Publications]]

Latest revision as of 07:03, 15 April 2019

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.

Publications (alphabetical)

  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] MGI, LBNL, EBI, ...
  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 GOA
  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 GOA
  4. Diehl AD, Deckhut Augustine A, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, NIAID Cell Ontology Working Group, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. 2009. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. Proceeding of the International Conference on Biomedical Ontology, July 24-26, 2009, University of Buffalo, NY. MGI, LBNL, ...
  5. Dolan ME, Blake JA. 2009. Using ontology visualization to facilitate access to knowledge about human disease genes. Applied Ontology 4(1):35-49. MGI
  6. 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) PAMGO
  7. 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 PAMGO
  8. 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 PAMGO
  9. 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) SGD
  10. Eilbeck K, Moore B, Holt C and Yandell M. Quantitative measures for the management and comparison of annotated genomes. BMC Bioinformatics 2009, 10:67doi:10.1186/1471-2105-10-67. PMCID: PMC2653490 SO
  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 EBI, MGI, ...
  12. Gaudet P, 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 DictyBase, ALL
  13. 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) Univ. of Maryland, PAMGO, EBI
  14. 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 MGI, TAIR, ZFIN, WormBase
  15. 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) E.coli
  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 GOA
  17. Korves T. Colosimo ME. 2009. Controlled vocabularies for microbial virulence factors. Trends in Microbiology. 17(7): 279-285. (July)
  18. 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 PAMGO
  19. Lovering R.C., Dimmer E.C., Talmud P.J. 2009 Improvements to cardiovascular Gene Ontology. Atherosclerosis. 205(1): 9-14. (July) PMC2706316 BHF-UCL, GOA pdfs available at http://www.ucl.ac.uk/silva/cardiovasculargeneontology.
  20. 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 PAMGO
  21. Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG. 2009. An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC Bioinformatics, 10:70. MGI, LBNL, ...
  22. 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 PAMGO
  23. 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 PAMGO
  24. 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 LBNL, TAIR, EBI, MGI, ...
  25. 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. PMC2646241MGI, ...
  26. Shimoyama M, Hayman GT, Laulederkind SJ, Nigam R, Lowry TF, Petri V, Smith JR, Wang SJ, Munzenmaier DH, Dwinell MR, Twigger SN, Jacob HJ; RGD Team. 2009. The rat genome database curators: who, what, where, why. PLoS Comput Biol. 5(11):e1000582.
  27. 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 PAMGO
  28. 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 PAMGO
  29. 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 PAMGO
  30. 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 PAMGO
  31. 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 FlyBase
  32. Tyler, BM. 2009. Viewing the microbial world through the lens of the Gene Ontology. Trends in Microbiology. 17(7): 259-261. (July) PMC2654664 PAMGO
  33. 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 WormBase
  34. 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 LBNL, EBI, ...
  35. 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. Univ. of Maryland, EBI, ...

Tutorials (chronological)

  1. GOA - between January and November: Emily Dimmer, Rachael Huntley have trained 30 SIB curators in manual GO annotation. Emily and Rachael have visited SIB in Geneva 5 times to train curators over 2009. The last set of curators will be trained in February 2010.
  2. E.Coli - January: Jim Hu gave a computer demo at the Plant and Animal Genome meeting in San Diego. This included using GONUTS to do community GO annotation.
  3. GOA - January 22nd: Transcriptomics workshop (Rachael GO/GOA talk and tutorial)
  4. GO Editorial Office - February 13th: Invited speaker-Introduction to GO and other Biomedical Ontologies. European Bioinformatics Institute Primer for Predocs Course, Hinxton, UK. (Lomax) (Feb).
  5. GO Editorial Office - February 18th: Jennifer Deegan took part in an EBI Roadshow at John Innes Centre, Norwich, UK. She gave a 2 hour hands-on tutorial for 20 people, covering a general introduction to GO Project.
  6. JCVI: Linda Hannick presented an hour-long Introduction to GO to the participants in the JCVI Eukaryotic Genome Annotation and Analysis Course, presented March 3-5, April 1-3, and June 10-12, 2009. Another course will be presented September 23-25, 2009.
  7. GOA - March 21st: Perspectives in Stem Cell Proteomics Training Workshop, EBI (Emily GO/GOA talk and tutorial)
  8. EcoliWiki - April 8th-May 3rd: Pilot course - CACAO (Community Assessment of Community Annotation with Ontologies) (Brenley McIntosh, Debby Siegele and Jim Hu)
  9. EcoliWiki - May 20th: Jim Hu, Debby Siegele & Brenley McIntosh attended the American Society for Microbiology Conference on Undergraduate Education (ASMCUE), where they discussed the importance of GO for microbiology, and using GONUTS in education.
  10. FlyBase - May 29: FlyBase/FlyMine 1 day workshop - Dept. of Genetics, University of Cambridge, UK (Peter McQuilton)
  11. GOA - June 22nd: - Presentation of GOA and the Renal Annotation Initiative at Edinburgh University (GUDMAP Consortium) Introduction to Gene Ontology Annotation (GOA) and The Renal GOA Initiative’. Yasmin Alam-Faruque
  12. DictyBase - June: Annotation in Model Organism Databases, Concordia University, Montreal (Pascale Gaudet)
  13. TAIR - June: Extracting Information from Scientific Papers: Challenges and Opportunities for Researchers and Curators. June 2009. Carnegie Institution, Stanford CA (Kate Dreher).
  14. FlyBase - July 20-23rd: Osumi-Sutherland D. OBO-Edit2 tutorial - Outlines theory of OBO relations and how they relate to definitions: specifying necessary vs necessary and sufficient conditions for class membership. Also covers: hidden assertions, redundancy, using terms from foreign ontologies, using the reasoners, reasoner enabled searching, asserting inferred classifications. Given at the International Conference for Biomedical Ontology, Buffalo NY.
  15. University of Maryland - July 28-31: Michelle Gwinn-Giglio gave a GO workshop for 20 people at the University of Maryland. IGS Genomics Workshop included a 2-hour lecture on the GO and then was followed by hands-on manual annotation exercises where part of what attendees had to do was attach GO terms to the exercise genes. The workshop was attended by 17 people and held on the IGS University of Maryland Campus. Two more workshops are planned for September and November.
  16. GOA - July 29th: Presentation of the Renal GOA Initiative to Wellcome Trust Genome Campus-wide curators. Title of talk: ‘Introduction to The Renal Gene Ontology Annotation (GOA) Initiative’. Yasmin Alam-Faruque
  17. EcoliWiki & BHF-UCL - Sept-Dec CACAO (Community Assessment of Community Annotation with Ontologies) competition (Brenley McIntosh, Jim Hu, Adrienne Zweifel, Debby Siegele, Ruth Lovering, Varsha Khodiyar)
  18. SO - October: Invited speaker - 'Ontologies and genomics' Biomedical Informatics Seminar Series, University of Utah, (Eilbeck).
  19. GOA - November 9-13th: Wellcome Trust Advanced Courses Proteomics Bioinformatics course. 'Introduction to the Gene Ontology and GO annotation resources'. Emily Dimmer
  20. PathEpigen - November: Ana Barat and colleagues visited GOA and the GO Editorial Office at the EBI to discuss annotation systems. They are making manual literature annotations with genes involved in cancer.
  21. SO - November: “Managing genomics data” Human Genetics Faculty Research in Progress Series, University of Utah.
  22. Fission Yeast Community Curation: Valerie Wood ran a community curation pilot project for fission yeast, by sending forms to researchers to complete for a recent publication. The initial trial of 20 publications had a 95% response rate demonstrating that the fission yeast community is willing to participate actively in the curation process. See the pilot summary at http://www.sanger.ac.uk/Projects/S_pombe/community_curation.shtml. Eight SF items were also raised for new biology, or ontology issues. The pilot will be extended to 50 laboratories within one month. The hope is to get funding to develop a simple community curation interface as part of the fission yeast grant proposal. We believe that this initiative presents a significant cost-effective opportunity to enhance the efforts of core curation staff at low cost.
  23. Pombe Database: Val Wood gave a talk and workshop on GO Tools for pombe researchers at a Wellcome Trust Advanced Course: Genome-Wide Approaches With Fission Yeast.
  24. GO Editorial Office: Jennifer Deegan taught general GO at a Master's students outreach day at the EBI.
  25. Peach Genome: Bryon Sosinski (sosinski at ncsu.edu) wrote to say that he is coordinating the sequencing of the peach genome, and is writing a USDA-SCRI proposal to employ GO for the initial annotation of the sequence. He also wishes to offer workshops to the community on how to do the higher level annotations in their respective regions of interest. He has been put in contact with Tanya Berardini at TAIR and Fiona McCarthy as AgBase to follow this up.
  26. WormBase: The sea urchin database staff are in touch with WormBase (they are on the same campus at Caltech). To begin with, they are interested in doing InterPro2GO mappings for their proteins, and intend later to submit a gene association file.
  27. RGD: Jennifer Smith at RGD produced and released an introductory video tutorial entitled "Introduction to Biomedical Ontologies #1: What is an Ontology?". It is available on both SciVee (http://www.scivee.tv/node/11759) and Vimeo (http://www.vimeo.com/5344028). The intended target audience is researchers and students who are largely, or completely, unfamiliar with ontologies, and the example that is used to illustrate ontologies, ontology annotations and ontology browsers (including AmiGO) is GO.
  28. BHF-UCL: 10 week core module for the new UCL MSc course, Genetics of Human Diseases, http://www.ucl.ac.uk/ugi/education/msc.

Talks (chronological)

  1. SO, LBNL - January: Invited Speaker/Participant, SO was represented by KE and CJM at the January RNAO content meeting in Cambridge. The division of labor between SO and RNAO was worked out.
  2. MGI - February: Invited Speaker-' Evidence and Inference: Comparative Biology in the Age of Genomics' University of Chicago, Chicago, Illinois. (Blake).
  3. BHF-UCL - February: Invited speaker-'GO for it! Gene Ontology - an essential resource'. Department of Medicine, University College London, UK. (Lovering).
  4. MGI - March: Invited Speaker-Gene Ontology Recapitulates Ontogeny: Using the Gene Ontology to Study Development. Molecular Reproduction and Development Meeting, Brown University, RI. (Hill).
  5. WormBase - April 16-19th: Conference talk - Using Textpresso for Information Retrieval, Fact Extraction, and Database Entry. Third International Biocuration Conference, 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).
  6. DictyBase - April 16-19th: Conference talk - The reference genome project. International Biocurator Meeting 2009. (Gaudet).
  7. MGI - May: Invited Speaker-Introduction to the Gene Ontology. Cell Behavior Ontology Workshop, National Institutes of Health, Bethesda, MD. (Diehl).
  8. PAMGO - May: Invited speaker-'Microbe-Plant Interactions through the Lens of Gene Ontology'. Research Centre for Plant Biotechnology and Genomics, Madrid, Spain (CW Collmer).
  9. Pombe - June: 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).
  10. PAMGO - June: Invited Speaker- 'Functional Annotation and the Gene Ontology" 2009 Oomycete Bioinformatics Resources Training Workshop. Virginia Bioinformatics Institute, Virginia Tech. (Torto-Alalibo).
  11. LBNL - June 29th: Invited Conference Talk- ' PAINT:The GO Workbench for Protein Family Annotation' Special Session on Orthology Inference at ISMB-2009 Stockholm, Sweden (Lewis).
  12. LBNL - July 3-5th: Invited Participant/Speaker- 'PAINT: THE GO WORKBENCH FOR PROTEIN FAMILY ANNOTATION' Quest for Orthologs Meeting, Cambridge-Hinxton Genome Center, U.K. (Lewis).
  13. MGI - July 3-5th: Invited Participant/Speaker- 'Orthologs, Paralogs, and Functional Annotations using the Gene Ontology' Quest for Orthologs Meeting, Cambridge-Hinxton Genome Center, U.K. (Blake).
  14. DictyBase - July 3-5th: 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).
  15. MGI, LBNL - July 24-26th: Invited Speaker, “Hematopoietic Cell Types: Prototype for a Revised Cell Ontology,” at the International Conference on Biomedical Ontology, July 24-26, Buffalo, NY. (Diehl).
  16. SO, LBNL - July 24-26th: Conference talk & paper - 'The evolution of Sequence Ontology Terms and Relationships' International Conference for Biomedical Ontology, Buffalo NY. (Eilbeck). Manuscript submitted to Journal of Biomedical Informatics.
  17. BHF-UCL, GOA - September 17-18th: Invited Speakers 'Meet the experts: Gene Ontology' at the British Atherosclerosis Society Autumn meeting 'Genetics of Complex Diseases'. Cambridge, UK. (Lovering and Dimmer)
  18. SO - October: Invited speaker - 'Genome Annotation and the Sequence Ontology' at the Idaho State University Bioinformatics Workshop, Lava Hot Springs, Idaho, (Eilbeck).
  19. MGI - October: Plenary Speaker- 'Biomedical Literature in the Clouds: Ontologies, Data, and the Semantic Web' North Atlantic Health Sciences Libraries Meeting. (Blake).
  20. MGI - October: Invited Speaker- ' Digital Annotation for Production Bioinformatics Systems' BioCreative 11.5 Workshop, Madrid, Spain. (Blake).
  21. DictyBase, LBNL, SRI, Princeton - October 27-30th: Invited Speaker - LARGE-SCALE ANNOTATION OF GENE ONTOLOGY TERMS ACROSS MULTIPLE ORGANISMS, USING PHYLOGENETIC TREES. (Cold Spring Harbor LaboratoryGenome Informatics, Cold Spring Harbor, NY. Pascale Gaudet, Kara Dolinski, Stan Dong, Suzanna E. Lewis, Michael S. Livstone, Anushya Muruganujan, and Paul D. Thomas*).
  22. EcoliWiki - Nov 11: Invited speaker - 'Contains 100% CACAO: Functional Annotation with Undergraduates' at 3rd National Meeting of Urban Biology, Nilton Lins University, Manaus, Brazil (Brenley McIntosh)
  23. BHF-UCL - December: Invited speaker - 'Gene Ontology and Heart Development' at 8th London Heart Development Meeting, Institute for Child Health, London (Varsha Khodiyar).

Posters (chronological)

  1. FlyBase - April 16-19th: Improving functional annotation of Drosophila transcription factors in FlyTF and FlyBase. Third International Biocuration Conference, Berlin, Germany. Susan Tweedie, Ulrike Pfreundt and Boris Adryan FlyBase-Cambridge, Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, UK
  2. TAIR, EBI, MGI, LBNL - April 16-19th: Improving Logical Relationship in the Gene Ontology. Third International Biocuration Conference, Berlin, Germany. (Berardini, Harris*, Hill, Lomax, Mungall).
  3. EBI, LBNL, SGD - April 16-19th: Gene Ontology: Serving the Community. Third International Biocuration Conference, Berlin, Germany. (Lomax*, Carbon, Hitz, Ireland, the Gene Ontology web-presence WG) (April).
  4. GOA - April 16-19th: The GO Annotation (GOA) Project. Third International Biocuration Conference, Berlin, Germany. (Rachael Huntley*, Emily Dimmer, Daniel Barrell, David Binns and Rolf Apweiler) (April).
  5. DictyBase, LBNL, SRI, Princeton - October 27-30th: 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)
  6. BHF-UCL, GOA - April: 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).
  7. EBI, TAIR, MGI, LBNL, ... - May: 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)
  8. DictyBase - August: 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).
  9. EcoliWiki - Aug 24-28th Community Assessment of Community Annotation with Ontologies (CACAO): Functional annotation with undergraduates. 61st Meeting on Molecular Genetics of Bacteria and Phages, Cold Spring Harbor, NY. (Brenley McIntosh*, Debby Siegele, Daniel Renfro, Jim Hu).
  10. GOA - September: 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).
  11. BHF-UCL, GOA - October: 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).
  12. BHF-UCL, GOA - November: 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).
  13. EcoliWiki: Members of the EcoliWiki team presented posters about Gene Ontology and GONUTS at the annual symposium of the Program in the Biology of Filamentous Fungi at Texas A&M and at the Texas Protein Folders Conference.
  14. MGI: 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).
  15.  David Osumi-Sutherland's poster at the 3rd International Boicuration Conference in Berlin, April 2009: Media:Berlin_poster_final.pdf

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).
  9. 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).

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