Difference between revisions of "Publications, Talks, Posters 2007-2009"

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2007 Computing on Development. Society for Developmental Biology Annual Meeting, Cancun, Mexico (Hill)
 
2007 Computing on Development. Society for Developmental Biology Annual Meeting, Cancun, Mexico (Hill)
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2007 The Comprehensive Functional Annotation of Mouse Genes and Gene Products Using The Gene Ontology (GO). Genome Informatics Meeting, Cold Spring Harbor, NY. (Ni) (November)
  
 
===2007 Fliers/literature created ===
 
===2007 Fliers/literature created ===

Revision as of 12:35, 26 September 2008

GO publications, Tutorials and Workshops, Presentations, and Posters
For the GO grant HG –02273
2003 – 2006

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

2008

2008 Publications

Harris MA. 2008. Developing an ontology. Methods Mol Biol. 452: 111-124.

Harris MA, Feltrin E. 2008. Browsing and searching Gene Ontology resources using AmiGO. EMBnet News 14(1): 17-21.

Dimmer E. The GOA@EBI resource. EMBnet News 14(1): 22-27.

Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA., Mouse Genome Database Group. 2008. The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res. 36(Database):D724-8.

The Gene Ontology Consortium*. 2008. The Gene Ontology (GO) Project in 2008. Nucleic Acids Res. [Epub ahead of print].

2008 Talks

2008 Keynote speaker: Plant and Animal Genomes Conference, San Diego. (Ashburner) (January)

2008 Invited speaker: Ontology workshop, Plant and Animal Genomes Conference, San Diego. (Ashburner) (January)

2008 Organiser and speaker: Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives. Dagstuhl, Germany. March 24-28th. (Ashburner) (March)

2008 Invited talk. Introduction to the Gene Ontology. Making Small Facts Travel: Labels, Packages and Vehicles workshop, London School of Economics and Political Science, UK. (Harris) (March)

2008 Invited Speaker. Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives. Dagstuhl, Germany. March 24-28, 2008. Talk: What makes text mining useful. (Blake)(March)

2008 Invited speaker. Royal Society Discussion Meeting, Environmental eScience. (Ashburner) (April)

2008 Keynote speaker. European Bioinfomatics Institute, Chemi-Informatics Meeting. Hinxton. (Ashburner) (May)

2008 Plenary Speaker. International Conference: Delivering Value from Avian Genomics. Mississippi State University, Starkville, Mississippi. May 19-20, 2008. Talk: Ontologies for Biology. (Blake)(May)

2008 Invited speaker. Royal Society of Chemistry, Cambridge, UK. The Gene Ontology Project. (Harris) (June)

2008 Invited Seminar speaker. Universität Bonn, B-IT. (Ashburner) (July)

2008 Keynote speaker. German Conference on Bioinformatics -2008 - Dresden. (Ashburner) (September)

2008 Workshops

2008 Avian gene Ontology Workshop, Starksville, MI. What is the GO? GO Annotation. (Drabkin) (May)

2008 Posters

2008 Describing Biological Regulations In The Gene Ontology. Biology of Genomes, Cold Spring Harbor, NY. (Dolan) (May)

2008 Data Management and Biological Knowledge Representation in the Mouse, ISMB 2008 Conference, Toronto, CA. (Ni) (July)

2007

2007 Publications

Blake, J.A., Harris, M. The Gene Ontology (GO) Project: Structured Vocabularies for Molecular Biology and Their Application to Genome and Expression Analysis. In /Current Protocals in Bioinformatics. [In Press].

de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcantara, R., Guedj, M., Ashburner, M., and Degtyarenko, K. 2008. ChEBI; A database and ontology for chemical entities of biological interest. Nucleic Acids Res. [In Press].

Diehl A.D., Lee J.A., Scheuermann R.H., Blake J.A. 2007. Ontology development for biological systems: immunology. Bioinformatics. 23(7):913-5.

Dimmer, E., Berardini, T. Z., Barrell, D., Camon, E. Methods for Gene Ontology Annotation. Plant Bioinformatics: Methods and Protocols, Ed. D. Edwards. Published by Humana Press: Series Methods in Molecular Biology 31 July 2007.

Dolan, M.E., and Blake, J.A., Using ontology visualization to facilitate access to knowledge about human disease genes (in press: Applied Ontology).

Field, D., Garrity, G., Gray, T., Morrison, N., Selengut, J., Sterk, P., Tatusova, T., Thomson, N., Allen, M.J., Angiuolii, S.V., Ashburner, M., Axelrod, N., Baldauf, S., Ballard, S., Boore, J., Cochrane, G., Cole, J., Dawyndt, P., de Vos, P., dePamphilis, C., Edwards, R., Faruque, N., Feldman, R., Gilbert, J., Gilna, P., Glöckner, F.O., Goldstein, P., Guralnick, R., Haft, D., Hancock, D., Hermjakob, H., Hertz-Fowler, C., Hugenholtz, P., Joint, I., Kagan, L., Kane, M., Kennedy, J., Kowalchuk, G., Kottmann, R., Kolker, E., Kravitz, S., Kyrpides, N., Leebens-Mack, J., Lewis, S.E., Li, K., Lister, A., Lord, P., Maltsev, N., Markowitz, V., Martiny, J., Methe, B., Moxon, R., Nelson, K., Parkhill, J., Proctor, L., Sansone, S.-A., Spiers, A., Stevens, R., Swift, P., Taylor, C., Tateno, Y., Tett, A., Turner, S., Ussery, D., Vaughan, B., Ward, N., Whetzel, T. Wilson, G., and Wipat, A. 2007. Towards a richer description of our complete collection of genomes and metagenomes: the “Minimum Information about a Genome Sequence” (MIGS) specification. Nature Biotechnology [In Press].

Hill, D., Smith, B. McAndrews-Hill, M., Blake, J.A., Gene Ontology Annotations: What they mean and where they come from. (submitted for publication).

Mabee, P.M., Ashburner, M., Cronk, Q., Gkoutos, G.V., Haendel, M., Segerdell, E., Mungall, C. and Westerfield, M. 2007. Phenotype ontologies: the bridge between genomics and evolution. Trends in Ecology and Evolution 22(7): 345—350.

Natale DA, Arighi CN, Barker WC, Blake JA, Chang T-C, Hu Z, Liu H, Smith B, Wu CH. 2007. Framework for a Protein Ontology. BMC Bioinformatics 8(Suppl 9):S1.

Smith, B., Ashburner, M., Ceusters, W., Mungall, C.J., Musen, M.A., Shah, N.H., Bard, J., Eilbeck, K., Ireland, A., Leontis, N., Rocca-Serra, P., Rosse, C., Lewis, S.E. 2007. The OBO Foundry: Remoulding Ontology to Support Data Integration. Nature Biotechnology 25: 1251-1255.

Taylor, C.F., Field, D., Sansone, S.-A., Apweiler, R., Ashburner, M., Ball, C., Binz, P.-A. Brazma, A., Brinkman, R., Deutsch, E., Fiehn, O., Fostel, J., Ghazal, P., Grimes, G., Hardy, N., Hermjakob, H., Randall, J., Kolker, E., Kuiper, M., Le Novère, N., Leebens-Mack, J., Lewis, S., McNally, R., Mehrle, A., Morrison, N., Paton, N.W., Quackenbush, J., Robertson, D., Rocca-Serra, P., Smith, B., Snape, J., Wiemann, S. 2007. MICheck: A Minimum Information Checklist Resource. Nature Biotech. [In Press].

The Gene Ontology Consortium. 2007. The Gene Ontology (GO) project in 2008. Nucleic Acids Res. Epub 2007 Nov 4.

Zhong, W., Sternberg P.W. Automated data integration for developmental biological research. Development. 2007 Sep;134(18):3227-38. Epub 2007 Aug 8.


2007 Talks

2007 Gene Ontology Annotation (GOA) at the EBI: Update. EBI Sequence Database group, EBI, Cambridge, UK. (Huntley)(January)

2007 What's New in GO? Chicken and Cow Meeting, Hinxton, UK. (Clark)(January)

2007 The Gene Ontology Project. CRIBI, University of Padua, Italy (Clark)(January)

2007 Plant-Associated Microbe Gene Ontology (PAMGO): A community resource of Gene Ontology (GO) terms describing gene products involved in microbe-host interactions. Plant and Animal Genome XV Conference. San Diego. CA. USA. (Gwinn-Giglio, Collmer, Torto-Alalibo) (January)

2007 Sharing immunological knowledge with Gene Ontology. St. Vincents Hospital Research Centre, Dublin. (Camon)(February)

2007 Invited seminar. Ontologies for all. Babraham Institute, Cambridge. (Ashburner)(February)

2007 Invited Speaker and Participant. Alignment of Ontologies for Biological Research. Dagstuhl Seminar: Towards Interoperability of Biomedical Ontologies. Wadern, Germany. (Blake)(March)

2007 Invited talk. SO and Biological Sequence. Towards interoperability of biomedical ontologies, Schloss Dagstuhl, Germany. (Eilbeck)(March)

2007 Real-life Ontology Development: Lessons from the Gene Ontology. Ontogenesis Meeting, Manchester, UK. (Lomax) (March)

2007 Invited seminar. The Gene Ontology, Department of Biology, University of Cyprus. (Ashburner)(April)

2007 Presentation on ontologies. GAIA Workshop, Gournadis GAIA Centre, Athens. (Ashburner)(April)

2007 Invited seminar. Ontologies and biological knowledge. Max-Plank Institute for Cell Biology, Dresden. (Ashburner)(April)

2007 Presentation on ontologies. EU-US Workshop on Infrastructure Needs of Systems Biology, Boston. (Ashburner)(May)

2007 Invited Participant. US-EU Workshop on Infrastructure Needs of Systems Biology. US-EC Task Force on Biotechnology Research: NSF, NIH, and Research Directorate of the European Commission. Boston, MA. (Blake)(May)

2007 Invited talk. Representing Immunology in the GO: Ontology Development and Annotation. DAIT Bioinformatics Summit 2007, Gaithersburg, MD. (Diehl)(May)

2007 Invited talk. Gene Ontology for Immunology: an Overview. 94th Annual Meeting of the The American Association of Immunologists, Miami Beach, FL.(Diehl)(May)

2007 Invited talk. SO meets RNAO. RNA Ontology Consortium meeting, Madison. (Eilbeck)(May)

2007 Introduction to the Gene Ontology and GOA projects, and an overview of other ontology developments at the EBI. Boehringer-Ingelheim, Biberach an der Riss, Germany. (Dimmer)(May)

2007 Introduction to the Gene Ontology and GOA projects, EMBO/SPINE2 Conference on Intrinsically Unstructured Proteins, Budapest, Hungary. (Camon)(May)

2007 Immune Gene Classification Using Gene Ontology, Bovine & Avian Immunogenomics Workshop, Dublin, Ireland. (Dimmer)(May)

2007 Using Ontology to Represent Biological Knowledge, Dept. of Physiology, Medical College of Wisconsin, Milwaukee, WI (Hill)(May)

2007 Sharing Knowledge with Gene Ontology Annotation: An Immunology Update. Institute for Animal Health (IAH), Compton, Berkshire, England, UK. (Camon)(June)

2007 Gene Ontology in WormBase. WormBase Workshop. 16th International C. elegans Meeting, University of California at Los Angeles. (Kishore)(June).

2007 Presentation on ontologies. Drosophila Neuroinformatics Workshop. HHMI, Janelia Farm Research Campus. (Ashburner)(July)

2007 Gene Ontology Annotation Database, Almac Group Ltd., Craigavon, Northern Ireland. (Camon)(July)

2007 GO and GOA. Royal Society of Chemistry, Cambridge, UK. (Dimmer)(July)

2007 GOA database Project. Swiss Institute of Bioinformatics, Geneva, Switzerland. (Dimmer and Barrell)(July)

2007 GOA: Looking after GO annotations, International Workshop on Genomic Databases, Rio de Janeiro, Brazil. (Foulger)(August)

2007 Presentation on ontologies. Infectious Disease Ontology Meeting, Cold Spring Harbor. (Ashburner)(September)

2007 Invited talk. Ontologies for all. ESF-EMBO Symposium on Comparative Genomics, Spain. (Ashburner)(September)

2007 Presentation on ontologies. Expanding the Genetic Toolkit in Drosophila, HHMI, Janelia Farm Research Campus. (Ashburner)(September)

2007 Gene Ontology Annotation for Immune System Genes. Irish Society of Immunology, Annual Symposium, Dublin, Ireland. (Camon)(September)

2007 Invited seminar. Center for Molecular and Biomolecular Informatics, Radboud University, Nijmegen. (Ashburner)(October)

2007 Plenary Speaker. Evidence and Influence: Paths to Curation. Second International Biocurator Meeting, San Jose (Blake)(October)

2007 Good habits in Ontology Development, a GO perspective. 2nd International Biocurator Meeting, San Jose (Hill)(October)

2007 Invited talk. Introduction to the Gene Ontology. EMBRACE workshop on Applied GO, Bari, Italy. (Harris) (November)

2007 Invited talk. Introduction to GOA. EMBRACE workshop on Applied GO, Bari, Italy. (Dimmer)(November)

2007 Seminar and tutorial: Introduction to GOA. Wellcome Trust Advanced Courses Proteomics Workshop, EBI, Cambridge, UK. (Dimmer and Huntley)(November)

2007 Cardiovascular GO annotation initiative. Centre for Cardiovascular Genetics, University College London, UK. (Lovering)(November)

2007 Invited talk. Protein features in SO. The inaugural meeting of the Protein Ontology project, Georgetown University, Washington DC. (Eilbeck)(December)


2007 Workshops and Tutorials

2007 Browsing and Searching Gene Ontology Resources Using AmiGO: A Tutorial. EMBRACE workshop on Applied GO, Bari, Italy. (Harris, Feltrin)

2007 The Gene Ontology project and its application to fission yeast functional genomics data. Wellcome Trust fission yeast functional genomics workshop. Hinxton, UK (Wood)

2007 The Gene Ontology (GO) Project. GO tutorial at Interactome Networks meeting, Hinxton, UK. (Deegan, Hitz)

2007 Using GO for Analysis of Gene Expression Data. Talk and demo on GO at Wellcome Trust Advanced Course on Functional Genomics, Hinxton, UK. (Lomax)

2007 Gene Ontology (GO) Project. Talk and demo on GO at Agro-genomics workshop on plant annotation, Ghent, Belgium. (Lomax)

2007 GO demonstration at MSc student open day at EBI, Hinxton, UK. (Clark)

2007 Gene Ontology Project. GO tutorial at Royal Society of Chemistry, Cambridge, UK. (Lomax, Clark)

2007 Making Gene Ontology Annotations for Fungal Genomes. GO Workshop at 24th Fungal Genetics Conference, Asilomar, Pacific Grove, CA. (Christie, Balakrishnan, Costanzo)

2007 Arabidopsis gene function annotation using controlled vocabularies. Part of the TAIR workshop. Plant and Animal Genome Conference, San Diego, CA. (Donghui) (January)

2007 TAIR/Gramene/SGN Workshop I: Gene Ontology and Plant Metabolic Databases. American Society of Plant Biologists Plant Biology and Botany Joint Congress, Chicago, IL (Tanya) (July)

2007 Invited workshop. Getting started with PAMGO: Theory and practice of creating new GO terms. XIII International Congress on Molecular Plant-Microbe Interactions. Sorrento, Italy. (Collmer)(July)

2007. Invited workshop. GO annotation of experimentally characterized genes from Pseudomonas syringae. XIII International Congress on Molecular Plant-Microbe Interactions. Sorrento, Italy. (Lindeberg) (July)

2007. Invited workshop. GO annotation of oomycete genomes: bioinformatic approaches. XIII International Congress on Molecular Plant-Microbe Interactions. Sorrento, Italy. (Chibucos) (July)

2007. Invited workshop. Overview of ontology-based comparative genomics of microbes and their hosts. XIII International Congress on Molecular Plant-Microbe Interactions. Sorrento, Italy. (Torto-Alalibo) (July)

2007. Introduction to Functional Annotation. PAMGO Workshop at the Virginia Bioinformatics Institute, Virginia Tech. Blacksburg VA. USA. (Hannick) (August)

2007. The Gene Ontology. PAMGO Workshop at the Virginia Bioinformatics Institute, Virginia Tech. Blacksburg VA. USA. (Gwinn-Giglio)(August)

2007. Introduction to PAMGO. PAMGO Workshop at the Virginia Bioinformatics Institute, Virginia Tech. Blacksburg VA. USA. (Collmer)(August)

2007. Introduction to GO tools. PAMGO Workshop at the Virginia Bioinformatics Institute, Virginia Tech. Blacksburg VA. USA. (Torto-Alalibo)(August)

2007. Faculty, Graduate Course in Functional Genomics. UMaine-Orono and The Jackson Laboratory, Bar Harbor, ME. (Blake)

2007 Posters

2007 Does your species show in GO? Therapeutic Applications of Computational Biology and Chemistry meeting, Hinxton, UK. (Clark)

2007 The Cardiovascular Gene Ontology Initiative, University College London Cardiovascular Science and Medicine Day, London, UK. (Talmud, Lovering, Khodiyar)

2007 The Cardiovascular Gene Ontology Initiative, Genomics of Common Diseases, Wellcome Trust Genome Campus, Cambridge, UK (Talmud, Dimmer)

2007 The GO Reference Genome Annotation Project. Second International Biocurator Meeting, San Jose, CA, US. (Tweedie)

2007 PAMGO: A Community Resource for Gene Ontology (GO) Term Development and Annotation of Gene Products Involved in Microbe-Host Interactions. 107th American Society for Microbiology. Toronto, Canada. (Torto-Alalibo)

2007 Gene Ontology (GO) for microbe-host interactions and its use in ongoing annotation of three Pseudomonas syringae genomes. 7th International Conference on Pseudomonas syringae Pathovars and Related Pathogens (ICPSPRP), Agadir, Morocco. (Collmer)

2007 Ortholog detection and transfer of Gene Ontology annotations in related oomycete genomes. Oomycete Molecular Genetics Network Workshop, Pacific Grove, CA. USA.(Chibucos)

2007 Computing on Development. Society for Developmental Biology Annual Meeting, Cancun, Mexico (Hill)

2007 The Comprehensive Functional Annotation of Mouse Genes and Gene Products Using The Gene Ontology (GO). Genome Informatics Meeting, Cold Spring Harbor, NY. (Ni) (November)

2007 Fliers/literature created

University College London Cardiovascular Science and Medicine Day, May 2007, London, UK: Distributed a one-page flyer titled ‘The Cardiovascular Gene Ontology Initiative’ (P Talmud, P Scambler, M Hubank, R Apweiler, R Lovering and V Khodiyar)

76th European Atherosclerosis Society Meeting, June 2007, Helsinki, Finland: Distributed a one-page flyer titled ‘The Cardiovascular Gene Ontology Initiative’ (P Talmud, P Scambler, M Hubank, R Apweiler, R Lovering and V Khodiyar)

Genomics of Common Diseases, July 2007, Wellcome Trust Genome Campus, Cambridge, UK: Distributed a one-page flyer titled ‘The Cardiovascular Gene Ontology Initiative’ (P Talmud, P Scambler, M Hubank, R Apweiler, R Lovering and V Khodiyar)


All Years

Course Lectures on GO in the following courses

2007 Faculty, Graduate Course in Bioinformatics. Nanjing Agricultural University, China (Tyler)

2004 Faculty, Graduate Course in Functional Genomics. University of Maine and The Jackson Laboratory, Bar Harbor, ME (Blake).

2004 Faculty, Assessing gene function using the GO and MGI, Short Course on Gene Microarray Development and Analysis: Approaches to Heart, Lung, Blood and Sleep Disorders.(Blake).

2002-2004 Faculty, Short Course on Genome Sequence Analysis: Theory and Practice. Bar Harbor, ME. (Blake, Lewis)

2002-2004 Faculty, Short Course on Gene Microarray Development and Analysis: Approach to Heart, Lung, Blood and Sleep Disorders. Bar Harbor, ME. (Blake)

2003 Faculty, Toxicogenomics. Gordon Research Conference. Bates College, Lewiston, ME.(Blake).

2003, 2004 Invited speaker Advances in Genome Technology and Bioinformatics. Co-Sponsored by the Marine Biological Laboratory and The Institute for Genomic Research. Woods Hole, MA (Blake).