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Annotation-checking by trigger File

Annotation-checking by trigger File. examples:. lactation --> only_in_taxon --> mammalia leaf development --> only_in_taxon --> Viridiplantae. File format. Purpose:. Check annotations Help disambiguate obscure language in the ontology. 562 triggers set up. First test - GOA.

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Annotation-checking by trigger File

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  1. Annotation-checking by trigger File

  2. examples: • lactation --> only_in_taxon --> mammalia • leaf development --> only_in_taxon --> Viridiplantae

  3. File format

  4. Purpose: • Check annotations • Help disambiguate obscure language in the ontology.

  5. 562 triggers set up

  6. First test - GOA 34,173,228 annotations present in GOA 47,471 conflicts flagged. = 0.14% conflicts

  7. Electronic annotations • 47,471 conflicts • 5 manual • 47466 IEA = 99.99% of conflicts were IEAs.

  8. 5 manual annotation conflicts • P97309 (Mus musculus) IMP annotation to ‘head involution’ by MGI. (Rule 24) • Q9CVV5 (Mus musculus) IMP annotation to ‘head involution’ by MGI. (Rule 24) • O61460 (Caenorhabditis elegans) IMP annotation to ‘dorsal closure’ by UniProt. (Rule 24) • Q9BMN8 (Caenorhabditis elegans) IMP annotation to ‘dorsal closure’ by UniProt. (Rule 24) • Q6RG02 (Fenneropenaeus merguiensis - Banana prawn) IEP annotation to ‘embryonic development via the syncytial blastoderm’ by UniProt. (Rule 24)

  9. head involution def: Movement of the anterior ectoderm to the interior of the embryo. dorsal closure def: The process during Drosophila embryogenesis whereby the ectodermal cells of the lateral epithelium stretch in a coordinated fashion to internalize the amnioserosa cells and close the embryo dorsally. embryonic development via the syncytial blastoderm def: The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva.

  10. IEA includes: • 1329 viral or prokaryote IEA to nucleus. • 2 human IEA to ‘head involution’. • 753 viral or bacterial IEA to ‘immune response’ or ‘innate immune response’. • 170 viral IEA to ‘antigen processing and presentation’. • 92 viral IEA to ‘negative regulation of complement activation’. • 736 viral IEA to ‘Golgi apparatus’. • 7479 bacterial IEA to ‘thylakoid light-harvesting complex’ • 339 non-fungal IEA to ‘1,3-beta-glucan biosynthetic process’

  11. Still to do: • Streamline trigger maintenance • Better filtered save in OBO-Edit. • Continue to add more triggers. • Start monthly trigger file runs.

  12. Should we: Implement this system? or B) Revert to just putting less rigorous taxon information in term names?

  13. Acknowledgements Jennifer Deegan Chris Mungall Jane Lomax Emily Dimmer Daniel Barrell Michelle Gwinn-Giglio David Binns Midori Harris Susan Tweedie Becky Foulger

  14. Spare slides

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