Transcript 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
34,173,228 annotations present in GOA
47,471 conflicts flagged.
= 0.14% conflicts
Electronic annotations
• 47,471 conflicts
• 5 manual
• 47466 IEA
= 99.99% of conflicts were IEAs.
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)
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.
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’
Still to do:
• Streamline trigger maintenance
– Better filtered save in OBO-Edit.
• Continue to add more triggers.
• Start monthly trigger file runs.
Should we:
A) Implement this system?
or
B) Revert to just putting less
rigorous taxon information in
term names?
Acknowledgements
Jennifer Deegan
Chris Mungall
Jane Lomax
Emily Dimmer
Daniel Barrell
Michelle Gwinn-Giglio
David Binns
Midori Harris
Susan Tweedie
Becky Foulger
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