Ontology meeting 2014-09-18: Difference between revisions
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Following up on http://wiki.geneontology.org/index.php/Ontology_meeting_2014-09-04#Trello_Items | Following up on http://wiki.geneontology.org/index.php/Ontology_meeting_2014-09-04#Trello_Items | ||
Paul: anyone added comments on web protege ; Jane: no, we need to review the comments and proposal. | |||
Paola: new need something clearer about waht are the aims; Is there a white paper? | |||
We need to be clear in light of the recent discussions of GO changing. | |||
Compound fuctions, like "cell adhesion mediator" ?? | |||
See: http://purl.obolibrary.org/obo/GO_0098631 protein binding involved in cell adhesion" | |||
How is this different from 'cell-adhesion mediator' | |||
Is cell-adhesion mediator a compound? | |||
=== Removing 'unknown' synonyms from the GO root terms (MF, BP, CC) === | === Removing 'unknown' synonyms from the GO root terms (MF, BP, CC) === | ||
Tanya thinks it does no harm. But we agreed to remove the synonyms. | |||
From Chris, see https://sourceforge.net/p/geneontology/ontology-requests/11167/ | From Chris, see https://sourceforge.net/p/geneontology/ontology-requests/11167/ | ||
=== Property chains for regulates/part_of === | === Property chains for regulates/part_of === | ||
Do these property chains always make sense? | Do these property chains always make sense? | ||
| Line 22: | Line 30: | ||
positively regulates o part_of = positively regulates | positively regulates o part_of = positively regulates | ||
So if you regulate a part of a process are you regulating the whole process? | |||
http://sourceforge.net/p/geneontology/ontology-requests/11164/ | |||
http://sourceforge.net/p/geneontology/ontology-requests/11166/ | |||
Chris thinks we should add them. | |||
=== SF items === | === SF items === | ||
* Modified amino acids in ChEBI are is_a amino acid. This is causing weird parentage in the metabolism part of the graph. | * Modified amino acids in ChEBI are is_a amino acid. This is causing weird parentage in the metabolism part of the graph. | ||
Will discuss with CHEBI on site | |||
* Please have a look at SF#11108, discussion about protein complexes. | * Please have a look at SF#11108, discussion about protein complexes. | ||
Macromolecular assembly? for actin, chromatin. Supermolecular structure? | |||
=== 'intracellular transport' does not apply to 'plasma membrane' === | === 'intracellular transport' does not apply to 'plasma membrane' === | ||
Revision as of 13:24, 18 September 2014
Attendees:
Minutes:
Molecular Function refactoring
Following up on http://wiki.geneontology.org/index.php/Ontology_meeting_2014-09-04#Trello_Items
Paul: anyone added comments on web protege ; Jane: no, we need to review the comments and proposal.
Paola: new need something clearer about waht are the aims; Is there a white paper?
We need to be clear in light of the recent discussions of GO changing.
Compound fuctions, like "cell adhesion mediator" ??
See: http://purl.obolibrary.org/obo/GO_0098631 protein binding involved in cell adhesion"
How is this different from 'cell-adhesion mediator'
Is cell-adhesion mediator a compound?
Removing 'unknown' synonyms from the GO root terms (MF, BP, CC)
Tanya thinks it does no harm. But we agreed to remove the synonyms.
From Chris, see https://sourceforge.net/p/geneontology/ontology-requests/11167/
Property chains for regulates/part_of
Do these property chains always make sense?
For SF11164 and SF11166
regulates o part_of = regulates
negatively regulates o part_of = negatively regulates
positively regulates o part_of = positively regulates
So if you regulate a part of a process are you regulating the whole process?
http://sourceforge.net/p/geneontology/ontology-requests/11164/
http://sourceforge.net/p/geneontology/ontology-requests/11166/
Chris thinks we should add them.
SF items
- Modified amino acids in ChEBI are is_a amino acid. This is causing weird parentage in the metabolism part of the graph.
Will discuss with CHEBI on site
- Please have a look at SF#11108, discussion about protein complexes.
Macromolecular assembly? for actin, chromatin. Supermolecular structure?
'intracellular transport' does not apply to 'plasma membrane'
Should we relax the logical def. to point to 'cell' rather than 'intracellular', or do we need new terms?
See https://sourceforge.net/p/geneontology/ontology-requests/11158/
Following email discussion, we may need a new cc that is intracellular + plasma membrane only. Is there one already? If not, what should we call it?
TG template for 'cell migration'
It's out there in TG, does it need testing? Any necessary AIs?