Chemical terms in GO

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Revision as of 10:26, 6 March 2010 by Midori (talk | contribs)
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Goal: make terms that refer to chemicals internally consistent in GO prior to alignment with ChEBI

Meeting March 5-6, 2010

Chris generated ontology of chemicals named in GO terms, with Chebi IDs - GOCHE

Going through GOCHE; for each chemical 'X'

see if terms exist for

  • X metabolic process
  • X biosynthetic process
  • X catabolic process
  • X transport
  • X transporter
  • X binding

adjust parentage in GOCHE based on GO paths; add GOCHE terms as needed

GOCHE ends up with union of all paths

March 5th: got through CDP-diacylglycerol
resume at monoglyceride

March 6th: modified approach:

  • skip noting which terms exist in GOCHE file
  • mark GOCHE terms we've looked at with 'chem_mtg' def dbxref
  • note all parents from GO paths as before
  • also filled in more chemicals that GO has but ChEBI doesn't; we don't know what they are!

Concentrated on high-level terms, because that's where most problems crop up; easier to sort out more specific terms without meeting face-to-face

Notes:

  • at present, GO doesn't have paths from nucleoside/tide/base terms to 'aromatic compound' terms, but we will want to add back in GOCHE
  • 'response to chemical substance' branch isn't consistent with the rest of GOCHE at all
  • Note that we have made a few fixes, but have not consistently fixed all problems we've spotted.


GOCHE changes done Sat 6th:

  • merged 'organic alcohol' into 'alcohol'
  • merged hydroxyproline into 4-hydroxyproline; made L-hydroxyproline is_a hydroxyproline

Rules for GOCHE

  • if you are X biosynthesis or X catabolism, you only follow is_a paths up the graph via X metabolism
    • use MF-BP links to capture links between (e.g.) pyruvate and glucose
  • use ChEBI '-ic acid' ID for '-ate' GO terms - it's the ionized form that's biologically relevant
  • a part_of link in GO should not translate into an is_a link in GOCHE
  • ignore modification terms for building GOCHE paths
  • every chemical with a path to 'small molecule' MUST also have a path classifying it based on structure

Action items:

  • find chemicals named in GO missing from GOCHE
    • look at children of GO terms that do have corresponding GOCHE entries
  • organic alcohol = alcohol, so fix transport term name - DONE.
  • clean up 'heterocycle' vs 'heterocyclic compound' in both GO & GOCHE
  • clean up hyphenation inconsistency
  • DNA binding & RNA binding
    • separate out hierarchies based on chemistry from those based on SO terms
    • don't forget ncRNA
  • missing synonyms for *acylglycerol B & C