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Dataflow

Dataflow. Karyn Mégy. VectorBase http://www.vectorbase.org. Who?. EBI Dan Lawson Karyn Megy Notre Dame Dave Campbell Harvard Dave Emmert Pinglei Zhou Lynn Crosby Susan Russo UNM Phil Baker. Aim. Improve automatic annotation

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Dataflow

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  1. Dataflow Karyn Mégy VectorBase http://www.vectorbase.org

  2. Who? • EBI • Dan Lawson • Karyn Megy • Notre Dame • Dave Campbell • Harvard • Dave Emmert • Pinglei Zhou • Lynn Crosby • Susan Russo • UNM • Phil Baker

  3. Aim • Improve automatic annotation • Resolve conflictive community annotations (same locus)

  4. Manual/Community Annotation DataflowImproving the gene set ChadoXML Harvard UNM ChadoXML ChadoXML(gff) ChadoXML Apollo EBI ChadoXML Ensembl DB NotreDame (CAP) gff DAS ChadoXML CAP Community

  5. Potential issues • New gene build Generating vs. annotating 2. Patch build issues = Conflict in manual annotation (1 locus, > 1 gene submitted) 3. Modifying submitted models

  6. 1a. Generate a new genebuild E.g. Anopheles AgamP3.6 -> AgamP3.7 ChadoXML Harvard UNM 2 AgamP3.6 ChadoXML 1 ChadoXML(gff) ChadoXML Apollo EBI DATA FREEZE 3 5 ChadoXML Ensembl DB AgamP3.7 NotreDame (CAP) 4 gff ChadoXML => Data freeze

  7. 1b. Annotate a new genebuild E.g. Anopheles AgamP3.6 -> AgamP3.7 ChadoXML Harvard UNM 2 ChadoXML 1 ChadoXML(gff) ChadoXML Apollo EBI 3 0 ChadoXML Ensembl DB AgamP3.7 NotreDame (CAP) 4 gff ChadoXML => New dump

  8. Patch build issues

  9. 2. Patch build issues E.g. Anopheles AgamP3.6 -> AgamP3.7 ChadoXML Harvard UNM 2 ChadoXML 1 ChadoXML(gff) ChadoXML Apollo EBI 3 DAS/gff ChadoXML Ensembl DB AgamP3.x NotreDame (CAP) 4 gff ChadoXML

  10. 3. Modifying submitted gene models Harvard UNM ChadoXML Apollo If pass this point: - Harvard trick EBI • If pass this point: • Submit as new model • Integration of new model • (EBI trick) Ensembl DB NotreDame (CAP) If pass this point: - No integration new model - Submit as new model ChadoXML

  11. Considerations • Timeline • Bulk data from UNM every x months? = New gene set every x months • Manual model revision • More and newer data for automatic predictions • Should we revise manual annotations? • When/should manual annotations loose their golden label?

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