Ontology meeting 2012-11-15: Difference between revisions
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All done from last week? (http://wiki.geneontology.org/index.php/Ontology_meeting_2012-11-08#FOLLOW-UP:_import.2Fexport_template) | All done from last week? (http://wiki.geneontology.org/index.php/Ontology_meeting_2012-11-08#FOLLOW-UP:_import.2Fexport_template) | ||
RELATED: | |||
Just working on the non-entailed transport and localization links. For these ones: | |||
EXISTS, NOT-ENTAILED SubClassOf(GO:0032974 'amino acid export from vacuole' GO:0034487 'vacuolar amino acid transmembrane transport') | |||
EXISTS, NOT-ENTAILED SubClassOf(GO:0032975 'amino acid import into vacuole' GO:0034487 'vacuolar amino acid transmembrane transport') | |||
I ended up adding new genus terms, but looking at the xps they're still not right: | |||
[Term] | |||
id: GO:0032974 ! amino acid transmembrane export from vacuole | |||
intersection_of: GO:0044746 ! amino acid transmembrane export | |||
intersection_of: results_in_transport_or_localization_to GO:0005773 ! vacuole | |||
[Term] | |||
id: GO:0032975 ! amino acid transmembrane import into vacuole | |||
intersection_of: GO:0044745 ! amino acid transmembrane import | |||
intersection_of: results_in_transport_or_localization_to GO:0005773 ! vacuole | |||
export is obviously from, and not to the vacuole. The import one might be okay logically, but it still doesn't across that it's into rather than to the vacuole. | |||
Using the imports/exports relations doesn't solve the problem because it's the location that we need to capture. | |||
===FOLLOW-UP: instantiating inferred/removing redundant links=== | ===FOLLOW-UP: instantiating inferred/removing redundant links=== |
Revision as of 11:54, 15 November 2012
MINUTES: Harold
ATTENDEES:
FOLLOW-UP: ChEBI paper
Follow-up on action items from last week (http://wiki.geneontology.org/index.php?title=Ontology_meeting_2012-11-08)
Tanya sent Dropbox invite to authors. Deadline for comments: Friday 16th. People have started commenting.
FOLLOW-UP: import/export template
All done from last week? (http://wiki.geneontology.org/index.php/Ontology_meeting_2012-11-08#FOLLOW-UP:_import.2Fexport_template)
RELATED:
Just working on the non-entailed transport and localization links. For these ones:
EXISTS, NOT-ENTAILED SubClassOf(GO:0032974 'amino acid export from vacuole' GO:0034487 'vacuolar amino acid transmembrane transport') EXISTS, NOT-ENTAILED SubClassOf(GO:0032975 'amino acid import into vacuole' GO:0034487 'vacuolar amino acid transmembrane transport')
I ended up adding new genus terms, but looking at the xps they're still not right:
[Term] id: GO:0032974 ! amino acid transmembrane export from vacuole intersection_of: GO:0044746 ! amino acid transmembrane export intersection_of: results_in_transport_or_localization_to GO:0005773 ! vacuole
[Term] id: GO:0032975 ! amino acid transmembrane import into vacuole intersection_of: GO:0044745 ! amino acid transmembrane import intersection_of: results_in_transport_or_localization_to GO:0005773 ! vacuole
export is obviously from, and not to the vacuole. The import one might be okay logically, but it still doesn't across that it's into rather than to the vacuole.
Using the imports/exports relations doesn't solve the problem because it's the location that we need to capture.
FOLLOW-UP: instantiating inferred/removing redundant links
Heiko has provided script. Editors have looked at the results. Tanya has added the implied links and removed the redundant links. She's also added the instructions to this Curator Guide page on the Wiki:
http://wiki.geneontology.org/index.php/Curator_Guide:_Ontology_Editing
FOLLOW-UP: TermGenie template for 'cellular response to'
All done from last week? (http://wiki.geneontology.org/index.php/Ontology_meeting_2012-11-08#TermGenie_template_for_.27cellular_response_to.27)
- File created, reviewed. Cross-products added to go_xp_chebi.obo.
FOLLOW-UP: Endosomal transport
All done from last week? (http://wiki.geneontology.org/index.php/Ontology_meeting_2012-11-08#Endosomal_transport)
Plan was: create vesicle-mediated endosomal transport as of endosomal transport, put all current kids under this (parent can be removed from vesicle-mediated parentage), send email to dbs to either move or leave in place, still correct
Did this: removed vesicle-mediated transport (VMT) as parent of endosomal transport, revisited all kids, copied those that referred to transport using vesicles to VMT. No new term created. Annotators can annotate to 'endosomal transport' or more specific kids, as they see fit.
Chris created xp for endosomal transport with new relationship:
[Term] id: GO:0016197 ! endosomal transport intersection_of: GO:0006810 ! transport intersection_of: results_in_transport_to_from_or_mediated_by GO:0005768 ! endosome
[Typedef] id: results_in_transport_to_from_or_mediated_by name: results_in_transport_to_from_or_mediated_by comment: This relation is so far only used for one class, 'endosomal transport' (GO:0016197), which groups together disparate roles the participants can play - it is defined as 'The directed movement of substances into, out of *or mediated by* an endosome...' is_a: has_participant
involved_in template
Can we extend this to include MFs involved_in BPs?
Jenkins check?
Not catching term with definitions but not def references? Used to be fatal error in OE but isn't anymore.
EC numbers in GO - feasibility study
Carried over from a previous meeting: see Action Items and background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2012-08-08#FOLLOW-UP:_EC_numbers_in_GO_-_feasibility_study
Capturing explicit cell lineage in GO
Stemming from this paper:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048527
But also see:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2830379/
Annotations to part terms
Stemming from thread on go-discuss