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SOFG Post Conference

SOFG -- Standards and Ontologies for Functional Genomics

17th to 20th November, 2002
Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

[Wellcome Trust Sponsored]

NEW SOFG WEBSITE AT http://www.sofg.org/

The Standards and Ontologies for Functional Genomics (SOFG) conference was held at Hinxton on 17-20 Nov 2002.

Oral presentations and a .pdf of the abstract book are all available to download from our FTP server. In addition, please checkout this section for a review by Comparative and Functional Genomics journal.

Oral Presentations
Michael Ashburner Global Open Biology Ontologies - GOBO  
Christian Blaschke A literature based ontology construction aiding system “BLASTing” the literature [html]
Sean Bechhofer Reasoning: Who Gives a Hoot? [pdf] [ppt]
Ken Buetow    
Albert Burger XSPAN:A cross-species anatomy network [pdf] [ppt]
Gregory Butler Intelligent use of ontologies: Towards a semantic web  
Chris Catton Making sense of images - ontologies and the BioImage Database  
Duncan Davidson The Mouse Atlas - an ontology for mapping gene function data to the mouse embryo  
Tony Davies Data standards and ontologies in chemistry and the unification efforts of the International Union of Pure and Applied Chemistry  
Kirill Degtyarenko Ontologies in biological chemistry [pdf] [ppt]
Frehiwot Fisseha (cancelled)  
Ken-Ichiro Fukuda Annotating Signal Transduction Pathways with Bioprocesses using hierarchical multi-layered structures [pdf]
Winston Hide Challenges in developing and
implementing standards-based
approaches in bioinformatics
[pdf] [ppt]
Martin Hoffman Establishing Local Ontologies by Means of Text Mining [pdf]
Peter Hunter    
Andrew Jones XML Standards for Proteomics Data [pdf] [ppt]
Peter Karp The Pathway Tools Ontology and Inferencing Layer [pdf] [ppt]
Per Kraulis Towards a unified hierarchical representation of biological structures and processes  
Raymond Lee Building a C. elegans Cell and
Anatomy Ontology
[pdf] [ppt]
Suzanna Lewis A Sequence Ontology [pdf] [ppt]
Jane Lomax The Gene Ontology and its insertion into UMLS [pdf] [ppt]
Bernardo Magnini The WordNet Lexical Database [pdf] [ppt]
Alexa McCray Sharing Sharing Ontologies Ontologies in the Biomedical Biomedical Domain [pdf] [ppt]
Robin McEntire Standards and Ontologies to Enable Discovery Data and Information Integration [pdf] [ppt]
Huaiyu Mi Assessment of genome-wide protein function classification for Drosophila melanogaster [pdf] [ppt]
Mark Musen It Takes a Village: The Role of an International User Community in Support of the Protégé-2000 Ontology
Development System
[pdf] [ppt]
Diane Oliver Genes, Drugs, and Diseases
for a Pharmacogenetics
Knowledge Base
[pdf] [ppt]
Steve Oliver From genotype to phenotype: Bioinformatic tools for functional genomics  
Alan Rector Scale and Context: Issues in Ontologies to Scale and Context: Issues in Ontologies to link Health- and Bio-Informatics [pdf] [ppt]
Sue Rhee Development and Use of Controlled Vocabularies at the Arabidopsis Information Resource (TAIR) [pdf] [ppt]
Martin Ringwald Integration and correlation of expression and phenotype data [pdf] [ppt]
Bo Servenius Implementation of Gene Ontology in the drug discovery process [pdf]
Lincoln Stein Linnaeus, Ashburner, Pokémon [pdf] [ppt]
Robert Stevens GOing GOing GONG (cancelled)  
Chris Stoeckert The MGED Ontology: A framework for describing functional genomics experiments [pdf] [ppt]
Leszek Vincent The Plant Ontology The Plant OntologyTM TM Consortium Consortium (POC) and an Ontology for Maize/Corn (Zea mays) Plant
Structure
[pdf] [ppt]
Mike Waters Chemical effects in biological systems - database standards and ontologies  
Tingting Zhang A framework for abstracting system behavior from experiments  

Comparative and Functional Genomics Review

In addition this meeting was reviewed in Comparative and Functional Genomics, this meeting review and three invited reviews on ontologies and their use in biology will be in the January 2003 issue, which has several other articles on biology.

Comparative and Functional Genomics is offering SOFG delegates
a Special Discounted Single Issue Price of US$ 17.00 (£11.50)
for a print copy of CFG Volume 4 issue 1 'Ontologies and Standards'. This issue includes special sections on SOFG and the ESF Functional
Genomics Programme workshop 'Ontology for Biology', with 12 articles
contributed by invited speakers, plus a detailed report on each meeting.

Simply print and fill out the pdf order form and return it, by post
or fax, to the address given on the form.

Conference Special Section - SOFG

  • Parkinson + Harris SOFG report
  • Lee & Sternberg A C. elegans cell and anatomy ontology
  • Stoeckert & Parkinson The MGED ontology
  • Stevens R et al Building ontologies in DAML+OIL

Conference Special Section - ESF: Ontology for Biology

  • Bernardi et al Official meeting report
  • Camon E et al The GO Annotation project (GOA)
  • Blaschke & Valencia Automated classification of protein function from literature
  • McCray A An Upper Level Ontology for the Biomedical Domain
  • Ratch E Developing a protein interaction ontology
  • Williams Bringing Ontology to GO
  • Hahn U Ontology engineering in thesaurus re-engineering
  • Staab S The Semantic Web
  • Gangemi A Tools and methods for building domain ontologies
  • Von Wachter D A Philosophical theory of causation for ontology engineering
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