Chemical terms in GO: Difference between revisions
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*ignore modification terms for building GOCHE paths | *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 | *every chemical with a path to 'small molecule' MUST also have a path classifying it based on structure | ||
*if GO term is not plural, but GOCHE term points the ID for a Chebi plural, then GO should use an 'and derivative' term. | |||
==Action items:== | ==Action items:== |
Revision as of 10:35, 6 March 2010
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
- if GO term is not plural, but GOCHE term points the ID for a Chebi plural, then GO should use an 'and derivative' term.
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