Create DOSDP entity_response_quality_in_location#399
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Introduces a new DOSDP pattern for traits describing the quality of an entity in response to a stimulus and location. Adds corresponding TSV data for anti-Helicobacter pylori IgG in blood.
Changed NCIT import references to use the new GitHub raw URL
Replaced the use of RO_0002503 ('in_response_to') with RO_0020329 ('indicates_response_to') in ontology definitions and DOSDP pattern.
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| text: "%s and 'characteristic_of' some (%s and ('indicates_response_to' some %s) and ('part_of' some %s))" |
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I am not sure that indicates_response_to is the best object property I can use, but I could not find a better one. Ideally I would like in_response _to. @ar-ibrahim @matentzn any ideas?
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indicates_response_to is defined by RO as "A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to show that a biological response to 'e' has occurred." and comments that 'the exposure agent' can be an organism. And this fits with the terms we want to create with this new pattern: 'biomarker' IgG released as a biological response to 'exposure agent' Helicobacter pylori, a bacterial organism. We can also ask for suggestions in RO slack but I think indicates_response_to is an appropriate relation to use in this context.
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In order to not block the universe from doing good work, I stay out of RO discussions. Looks good enough.
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Looking at the pattern I think would want to use it for something like 'liver Cyp1a1 level after dioxin exposure' and based on the RO term label I think that would be okay. The one thing that gives me pause is that indicates_response_to sits under indicates_clinical_effect_of but I think this is more of an issue with RO. I would consider indicates_response_to to be broader than 'clinical effect'. But I also don't see anything in the clinical effect parent that specifies what 'clinical' means so possibly its just a bad label in RO.
TL/DR - I don't see anything better.
matentzn
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matentzn
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I am fine with this - but I am not a great person to review such things. Ray was the best, now he is of the project, I think you could do a friendly reach out to Sue Bello on slack.
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| equivalentTo: | ||
| text: "%s and 'characteristic_of' some (%s and ('indicates_response_to' some %s) and ('part_of' some %s))" |
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In order to not block the universe from doing good work, I stay out of RO discussions. Looks good enough.
sbello
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sbello
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I think this looks good. I don't see a better RO term to use
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| equivalentTo: | ||
| text: "%s and 'characteristic_of' some (%s and ('indicates_response_to' some %s) and ('part_of' some %s))" |
There was a problem hiding this comment.
Looking at the pattern I think would want to use it for something like 'liver Cyp1a1 level after dioxin exposure' and based on the RO term label I think that would be okay. The one thing that gives me pause is that indicates_response_to sits under indicates_clinical_effect_of but I think this is more of an issue with RO. I would consider indicates_response_to to be broader than 'clinical effect'. But I also don't see anything in the clinical effect parent that specifies what 'clinical' means so possibly its just a bad label in RO.
TL/DR - I don't see anything better.
ar-ibrahim
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ar-ibrahim
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No further comments to add. All looks good Aleix.
Thank you for the feedback! |
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Create DOSDP entity_response_quality_in_location and use to add new term OBA:2090002 'level of anti-Helicobacter pylori IgG in blood'.
Fixes #391