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Annotation Checking System for Improved Ontology Clarity

This system checks annotations to disambiguate complex language in the ontology, identifies conflicts, and helps maintain accuracy. Includes examples of annotation triggers and conflict resolutions.

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Annotation Checking System for Improved Ontology Clarity

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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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