Ontology meeting 2014-10-09: Difference between revisions
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Attendees: | Attendees: Jane, Paola, DavidH, Chris, Heiko, Harold, Tanya | ||
Minutes: | Minutes: Tanya | ||
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What is the most appropriate relation to use? See email thread '[go-ontology] cell migration templates' | What is the most appropriate relation to use? See email thread '[go-ontology] cell migration templates' | ||
Mix of 'has_input,' 'results in movement of,' and 'RO:0002313 transportsormaintainslocalizationof'. | |||
Action items: Check what UniProtKB has used in annotation extension, MGI uses 'results in movement of', update ontology to replace 'has_input' with | |||
'results in movement of' in the 'cell migration' children terms. Heiko to change relationship type in TermGenie for this template. | |||
=== GO into NCIt === | === GO into NCIt === |
Revision as of 11:46, 9 October 2014
Attendees: Jane, Paola, DavidH, Chris, Heiko, Harold, Tanya
Minutes: Tanya
TG template for 'cell migration'
What is the most appropriate relation to use? See email thread '[go-ontology] cell migration templates'
Mix of 'has_input,' 'results in movement of,' and 'RO:0002313 transportsormaintainslocalizationof'. Action items: Check what UniProtKB has used in annotation extension, MGI uses 'results in movement of', update ontology to replace 'has_input' with 'results in movement of' in the 'cell migration' children terms. Heiko to change relationship type in TermGenie for this template.
GO into NCIt
Follow-up on negatively_regulates o part_of/positively_regulates o part_of
We'll go ahead with these, right? Previous discussion copied below:
(Need them for SF 11166)
Chris made a correction. The new diff is attached to his email with subject 'reasoner diff before and after' and dated Sept. 25th. The list is quite long - did anyone get a chance to review it?
We also need to think of this in the context of the call on monday. See: http://go-genkisugi.rhcloud.com/seed/model/gomodel:542732ad0000005 Would NOS inhibitor activity classify under the negative regulation term here? Because that is implied by the classic GAF annotation
AI: Let's give it another week and look at at least sections of it... we will all look at random sections of it and comment/decide at next week's call. If we haven't had time, we'll go ahead all the same.
Discussion on direct/indirect regulation. AI: Some of us will look at examples and figure out suggestions. David H will submit Nikolai's work as an RO ticket, and will check his presentation/slides into svn.
Automatic Annotation Deepening
Also know as Fold-based prediction. This is currently the only 'experimental' prediction method.
Idea: use c16 information and equivalent class axioms to check for more specific classes. For example
GO:0008283 cell proliferation + acts_on_population_of(CL:0000037 hematopoietic stem cell) ==> GO:0071425 hematopoietic stem cell proliferation
GO:0009913 epidermal cell differentiation + results_in_acquisition_of_features_of(CL:0002187 basal cell of epidermis) ==> GO:0030216 keratinocyte differentiation
GO:0030182 neuron differentiation + results_in_acquisition_of_features_of(CL:0000617 GABAergic neuron) ==> GO:0097154 GABAergic neuron differentiation
GO:0001101 response to acid chemical + has_direct_input(CHEBI:3098 bile acid) ==> GO:1903412 response to bile acid
Activated for:
- goa_human http://build.berkeleybop.org/view/GAF/job/gaf-check-goa_human/
- MGI http://build.berkeleybop.org/view/GAF/job/gaf-check-mgi/
- Pombase http://build.berkeleybop.org/view/GAF/job/gaf-check-pombase/
- SGD (soon)
Look at 'gaf-prediction-experimental-report.txt' and 'gene_association.mgi.inf.experimental.gaf'
See SF issue 11241 In general, if a chemical is used as an analog of the biologically relevant chemical for an assay of MF/BP, should the corresponding MF/BP be represented by GO terms?
TG new curators?
Today, got a request to be a submitter in TG from Penelope Garmiri (UniProt Knowledgebase Content Team) What is the SOP?