Ontology meeting 2016-01-21: Difference between revisions
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because 'DNA demethylation' (and 'DNA methylation') is_a 'regulation of gene expression, epigenetic'. Should it be part_of instead? | because 'DNA demethylation' (and 'DNA methylation') is_a 'regulation of gene expression, epigenetic'. Should it be part_of instead? | ||
DOS: I have a mini project going on this topic. From [https://docs.google.com/document/d/1TDQvKK1uXZkdHyAiaVLLWzio4UD_njDQTnEGNVCRPn8/edit?disco=AAAAAjmQQMA&usp=comment_email_document discussion with Ruth and Karen], we agreed that a regulates relation should apply between 'chromatin modification' and 'epigenetic regulation of gene expression' | DOS: I have a mini project going on this topic. | ||
From [https://docs.google.com/document/d/1TDQvKK1uXZkdHyAiaVLLWzio4UD_njDQTnEGNVCRPn8/edit?disco=AAAAAjmQQMA&usp=comment_email_document discussion with Ruth and Karen], we agreed that a regulates relation | |||
should apply between 'chromatin modification' and 'epigenetic regulation of gene expression' | |||
Long confusing umbrella ticket here: https://github.com/geneontology/go-ontology/issues/11628 | Long confusing umbrella ticket here: https://github.com/geneontology/go-ontology/issues/11628 | ||
All agree that we are uncomfortable with DNA methylation is_a 'regulation of gene expression, epigenetic' | |||
DNA methylation | This is not intuitive to biologists. All more comfortable with using part_of. | ||
DOS: But if all DNA methylation regulates gene expression then it would be valid to add | |||
DNA methylation | DNA methylation SubClassOf: regulates some 'gene expression' and this would => inference that | ||
DNA methylation SubClassof 'regulation of gene expression'. It would also be consistent with the | |||
definition of 'regulation of gene expression' and with the fact the regulates is now transitive (so indirect regulation is | |||
allowed and will be inferred in many cases.) How can we avoid this? | |||
Suggestion: If we use causally_upstream_of, for cases like this, we can keep the causal link but prevent the odd inference. | |||
Also serves as a way of making breaks in causal chains to prevent inference of regulation going to far. | |||
DH: Just realised this is moot: restriction enzyme system in bacteria, methylation causes inability for REs to cut - DNA methylation | |||
is not always linked to 'regulation of gene expression, epigenetic' - Kills the part_of solution as this is not always true. | |||
PMID:6243774. Also means we can't use regulates or causally upstream of. Solution is to just delete the offending axiom. | |||
UPDATE 27/1/16 Done, deleted links: | |||
'DNA demethylation' is_a 'regulation of gene expression, epigenetic' | |||
'DNA methylation' is_a 'regulation of gene expression, epigenetic' | |||
'regulation of DNA demethylation' is_a 'regulation of gene expression' | |||
'regulation of DNA methylation' is_a 'regulation of gene expression' | |||
'''Separate topic: discussion of 'regulates o part_of.''' | |||
DH: Discomfort with regulates o part_of. Imagines that this will be disastrous in LEGO models. Where molecular functions | DH: Discomfort with regulates o part_of. Imagines that this will be disastrous in LEGO models. Where molecular functions | ||
that are part of the same signal transduction pathway may have a directly activates relation between them. We wouldn't want to | that are part of the same signal transduction pathway may have a directly activates relation between them. We wouldn't want to | ||
infer that they regulate the pathway. | infer that they regulate the pathway. | ||
DOS: Strongly agree. Definitely a problem for ST pathways. | |||
Consult with Val? | Consult with Val? | ||
Use 'causally upstream of' as a solution? More general than 'regulates' and won't | Poss solutions: | ||
Use 'causally upstream of' as a solution? More general than 'regulates' and no inference over part_of. | |||
But this won't work for direct -ve and +ve reg steps in ST | |||
DOS: suggest we remove the regulates o part_of axiom. | |||
Still very useful as a heuristic for finding potential regulates relationships. | |||
== Latest assertions == | == Latest assertions == | ||
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The reasoner would then look after classification completely. | The reasoner would then look after classification completely. | ||
AI: DOS will check with Val whether she's comfortable with 'occurs in' some cell. | AI: DOS will check with Val whether she's comfortable with 'occurs in' some cell. Then we'll run by Chris next week. | ||
== movement, transport, establishment of localization == | == movement, transport, establishment of localization == | ||
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which brings up issues with 'establishment of localization' and 'transport' | which brings up issues with 'establishment of localization' and 'transport' | ||
DOS' work in this area should clear up that issue as well. | DOS' work in this area should clear up that issue as well. | ||
Major problem: the branch under organelle transport is a TPV. | |||
By current def, transport is for 'substances' not big things like organelles, vesicles. | |||
But biologists use term transport for many classes under here (esp for vesicular transport along axons) | |||
Poss solutions: | |||
1. Redefine transport? But then how does it differ from 'establishment of loc' ? Merge? | |||
2. Use a different term in this branch (tracfficking?), and move it up from under transport. | |||
BUT TRAFFICKING USED MORE NARROWLY BY BIOLOGISTS? NOT FOR TRANSPORT ALONG AXON. | |||
3. Keep the term transport, but move term under establishment of loc | |||
WOULD THIS BE TOO CONFUSING? | |||
Melanie suggests using synonyms and using 'community of usage' as a property. "you can them extract specific slims for your users | Melanie suggests using synonyms and using 'community of usage' as a property. "you can them extract specific slims for your users | ||
with their preferred labels" Might that be a solution? | with their preferred labels" Might that be a solution? | ||
DOS: Could be part of solution, but don't think there's a community that uses anything but transport for vesicles moving along axons. | |||
More discussion needed. | |||
[[Category:Ontology]] | [[Category:Ontology]] | ||
[[Category:Meetings]] | [[Category:Meetings]] |
Latest revision as of 04:56, 27 January 2016
Attendees: DavidH, DavidOS, Harold, Heiko, Melanie, Paola, Tanya
Minutes: Tanya
Fun with regulates axioms
https://github.com/geneontology/go-ontology/issues/12235
400 some new inferences after Chris added some regulates axioms before the holiday break. After fixing what was causing the build to break, we can now examine them. The problem described in https://github.com/geneontology/go-ontology/issues/12235 was one result that was troubling. See this ticket. Basic pattern is 'negative regulation of xx by negative regulation of yy' inferred SubClassOf: positive regulation of xx. This was due to a badly designed TG template (since removed by Heiko). But the bigger problem is that this is just too much complexity to pack into a term. All agreed ee should get rid of the terms we have and not allow more.
There are 22 terms following this pattern. We have decided to obsolete all that have no annotations ASAP. For those that have annotations, as a temporary measure we will delete the Equivalence axioms that cause the problem and manually assert classification. We will then request re-annotation for all existing annotations, preferably via construction of a LEGO model -> production of inferred annotations in GAF would give annotation to the relevant parent classes. Discussion of practicality of doing this in LEGO: When will be able to do this? GAF from LEGO status: Basic inference already works. This is probably sufficient for the models we need for this issue. But sometimes we want more than just the basic inference. T The whole part where we go to deeper terms, use inferencing features, is taking longer. What do we state in the model and what do we infer? Needs discussion. Something stable is needed by the end of the month will be out for KMW to consume. Less than 2 weeks to the basic version.
DNA methylation and gene expression
Stemming from latest assert report (the same one with the negative by negative terms)
ADD GO:1901535 'regulation of DNA demethylation' GO:0010468 'regulation of gene expression'
because 'DNA demethylation' (and 'DNA methylation') is_a 'regulation of gene expression, epigenetic'. Should it be part_of instead?
DOS: I have a mini project going on this topic. From discussion with Ruth and Karen, we agreed that a regulates relation should apply between 'chromatin modification' and 'epigenetic regulation of gene expression' Long confusing umbrella ticket here: https://github.com/geneontology/go-ontology/issues/11628
All agree that we are uncomfortable with DNA methylation is_a 'regulation of gene expression, epigenetic' This is not intuitive to biologists. All more comfortable with using part_of. DOS: But if all DNA methylation regulates gene expression then it would be valid to add DNA methylation SubClassOf: regulates some 'gene expression' and this would => inference that DNA methylation SubClassof 'regulation of gene expression'. It would also be consistent with the definition of 'regulation of gene expression' and with the fact the regulates is now transitive (so indirect regulation is allowed and will be inferred in many cases.) How can we avoid this? Suggestion: If we use causally_upstream_of, for cases like this, we can keep the causal link but prevent the odd inference. Also serves as a way of making breaks in causal chains to prevent inference of regulation going to far. DH: Just realised this is moot: restriction enzyme system in bacteria, methylation causes inability for REs to cut - DNA methylation is not always linked to 'regulation of gene expression, epigenetic' - Kills the part_of solution as this is not always true. PMID:6243774. Also means we can't use regulates or causally upstream of. Solution is to just delete the offending axiom.
UPDATE 27/1/16 Done, deleted links: 'DNA demethylation' is_a 'regulation of gene expression, epigenetic' 'DNA methylation' is_a 'regulation of gene expression, epigenetic' 'regulation of DNA demethylation' is_a 'regulation of gene expression' 'regulation of DNA methylation' is_a 'regulation of gene expression'
Separate topic: discussion of 'regulates o part_of.
DH: Discomfort with regulates o part_of. Imagines that this will be disastrous in LEGO models. Where molecular functions that are part of the same signal transduction pathway may have a directly activates relation between them. We wouldn't want to infer that they regulate the pathway. DOS: Strongly agree. Definitely a problem for ST pathways. Consult with Val? Poss solutions: Use 'causally upstream of' as a solution? More general than 'regulates' and no inference over part_of. But this won't work for direct -ve and +ve reg steps in ST DOS: suggest we remove the regulates o part_of axiom. Still very useful as a heuristic for finding potential regulates relationships.
Latest assertions
The list in yesterday's assert report (email "[go-ontology] build-go-assert-inferences - Build # 173 - Fixed!") is really long, 402 added axioms presumably as a result of the synapse branch merge. Has anyone had a chance to review them all?
DOS: Inferences from synapse branch merge reviewed. Many inferences also come from the change to regulation axiomatisation. I have reviewed these briefly. Some problematic ones are flagged in https://github.com/geneontology/go-ontology/issues/12235
AI: Everyone else look through report for odd references.
Logical definitions for 'response to chemical' terms
Logical defs for 'response to chemical' terms point to 'response to stimulus', while 'cellular response to chemical' points to 'cellular response to chemical stimulus':
id: GO:1903842
name: response to arsenite ion
intersection_of: GO:0050896 ! response to stimulus
intersection_of: has_input CHEBI:22633 ! arsenite ion
relationship: has_input CHEBI:22633 {is_inferred="true"} ! arsenite ion
but
id: GO:1903843
name: cellular response to arsenite ion
intersection_of: GO:0070887 ! cellular response to chemical stimulus
intersection_of: has_input CHEBI:22633 ! arsenite ion
relationship: has_input CHEBI:22633 {is_inferred="true"} ! arsenite ion
Was this intentional - shouldn't the former point more specifically to 'response to chemical'? (which is_a 'response to stimulus') Of course, the 'response to chemical' parentage is inferred anyway.
DOS RESPONSE: [note - DH suggested the same]
Non-redundant classification is correct:
This equivalence axioms takes care of the correct classification of 'response to arsenite ion' under 'response to chemical':
- 'response to chemical' EquivalentTo 'response to stimulus' and ('has input' some 'chemical entity')
We don't yet have axiomatisation to deal with the 'cellular bit' - hence the more specific genus in this case. But if we agree that all cellular response occurs in some cell we could have:
- 'cellular response to stimulus' EquivalentTo: 'response to stimulus' and occurs in some cell
- 'cellular response to chemical stimulus' EquivalentTo: 'response to stimulus' and occurs in some cell and has_input some 'chemical entity'
- 'cellular response to arsenite ion' EquivalentTo: 'response to stimulus' and occurs in some cell and has_input some 'arsenite ion'
The reasoner would then look after classification completely.
AI: DOS will check with Val whether she's comfortable with 'occurs in' some cell. Then we'll run by Chris next week.
movement, transport, establishment of localization
See this document that DOS put together: https://docs.google.com/document/d/1mLuIbLGo9MApOVBeELzqaalKDcLG0xZthWnporGVkCg/edit?usp=sharing
also:
https://github.com/geneontology/go-ontology/issues/9189 which brings up issues with 'establishment of localization' and 'transport'
DOS' work in this area should clear up that issue as well.
Major problem: the branch under organelle transport is a TPV. By current def, transport is for 'substances' not big things like organelles, vesicles. But biologists use term transport for many classes under here (esp for vesicular transport along axons) Poss solutions: 1. Redefine transport? But then how does it differ from 'establishment of loc' ? Merge? 2. Use a different term in this branch (tracfficking?), and move it up from under transport. BUT TRAFFICKING USED MORE NARROWLY BY BIOLOGISTS? NOT FOR TRANSPORT ALONG AXON. 3. Keep the term transport, but move term under establishment of loc WOULD THIS BE TOO CONFUSING?
Melanie suggests using synonyms and using 'community of usage' as a property. "you can them extract specific slims for your users with their preferred labels" Might that be a solution? DOS: Could be part of solution, but don't think there's a community that uses anything but transport for vesicles moving along axons.
More discussion needed.