Toward a Unified Gene Page GMOD Meeting, April 2004 Don Gilbert,

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Presentation transcript:

Toward a Unified Gene Page GMOD Meeting, April 2004 Don Gilbert,

Bionet news ( needs new home Used by celegans, yeast, chlamydomonas, drosophila, zebrafish, maize, urodeles; genbank, embl, software, others. Letters of Support? TeraGrid (NSF Shared Cyberinfrastructure) wants to help MOD genome computes BLAST for FlyBase and euGenes this fall - others? -See Don Gilbert for details Extraneous announcements

Common parts of MOD gene pages What could/should be unified? Who will benefit? Costs? Common Web Reports and XML ? You: discuss, design common gene page Gene Pages

Names, symbols/IDs, synonyms Map locations Sequences Reagents Gene ontology Similar Genes Database cross-refs, External links Common gene attributes, pt1

Alleles, Transcripts Expression and Mutant Phenotypes Proteins, Structure and Domains Gene Interactions Literature references Summary Text... others... Common gene attributes, pt2

Labels - are these same things? Gene / locus / orf Homolog / ortholog / relationship / similarity Citation / publication / reference Organization of document Section headers Important at top, common ordering Should these be unified?

Structure and size of default document Tabular, text, document-like, … One screen or long report Graphics (maps, icons,...) Further Detail options Layout and Design (colors, formatting, fonts..) Should these be unified?

MOD customizations Look and Feel Details & Extensions Customer choices Best for organism community (org. standard) or for general reader (general standard) Best for beginners or experts (simple,complex) What is customizable?

Computable text of gene page ? "what you see (web page) is also what your computer can read" simple and human-readable, or complex and detailed XML variants, tabular, other? Ace2XML, NCBI XML, others Samples (Web -> XML) Common Gene XML?

Fly Gene Page as XML

Yeast Gene Page as XML

Mouse Gene Page as XML

Worm Gene Page as XML

Now: Design your common gene page Cut/paste sample XML pages into one Comment on what should be unified Comment on best parts of MOD pages After: Talk MODs into generating these HTML and XML Tasks

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