Addresses #364 NTR for BioData#428
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#364) Group A - entity_attribute_location (OBA:2100006-2100013): - OBA:2100006: 8-epi-prostaglandin F2alpha amount in urine (CHEBI:34505) - OBA:2100007: aspartate aminotransferase (human) amount in blood (PR:000050353) - OBA:2100008: D-dimer (human) amount in blood (PR:000050369) - OBA:2100009: hemoglobin A1c amount in blood (PR:000050469) - OBA:2100010: intercellular adhesion molecule 1 amount in blood (PR:000001467) - OBA:2100011: interleukin-10 amount in blood (PR:000001471) - OBA:2100012: interleukin-18 amount in blood (PR:000001376) - OBA:2100013: troponin complex amount in blood (GO:0005861) Group B - attribute_ratio (OBA:2100014-2100016): - OBA:2100014: waist to hip ratio (OBA:1001085 / OBA:1000032) - OBA:2100015: albumin to creatinine ratio in urine (OBA:VT0002871 / OBA:VT0010540; CMO:0000384) - OBA:2100016: urea nitrogen to creatinine ratio in blood (OBA:VT0005265 / OBA:VT0005328) Closes part of #364
Refresh imports and definitions.owl
These two terms (interleukin-10 amount in blood and interleukin-18 amount in blood) were already created in the ontology, so removed them from this branch to avoid duplication.
Add a new term for the amount of lipid in blood during fasting (OBA:2090011). Changes: append new row to src/patterns/data/default/attribute_location_during_activity.tsv (and fix newline on the insulin row), update src/patterns/definitions.owl release IRI and versionInfo to 2026-05-29, add Declaration for OBA_2090011 and its annotations (label, definition, dbxref/exact synonym) and an EquivalentClasses axiom linking the PATO amount to CHEBI:18059 located in blood during fasting.
New pattern: combined_process_attribute_during_activity - Models traits that capture the rate/frequency of two combined processes during a specific activity (e.g. apnea + hypopnea events per hour of sleep) - Uses subClassOf (not equivalentTo) to avoid OWL union semantic issue: an equivalence axiom would incorrectly classify a rate of only one process (apnea-only) as a subtype of AHI - Vars: entity1, entity2 (owl:Thing), attribute (quality), activity (GO:0008150) - Relation: characteristic_of (RO:0000052), happens_during (RO:0002092) New term: OBA:2100017 apnea-hypopnea index (AHI) - entity1: HP:0002104 (apnea), entity2: HP:0040213 (hypopnea) - attribute: PATO:0050000 (rate of occurence) - activity: GO:0030431 (sleep) - Synonyms: AHI, apnoea-hypopnoea index; related: apnea index, hypopnea index - Xref: SNOMED:774099003 - Note: happens_during sleep is retained because HP:0002104 and HP:0040213 are not sleep-specific phenotypes; there is no HP term for sleep hypopnea to encode sleep context in the entity itself Import updates: - Add HP:0002104 and HP:0040213 to hp_terms.txt seed - Regenerate merged_import.owl (now includes HP:0040213) - Regenerate definitions.owl and components Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Update the apnea-hypopnea index ID from OBA:2100017 to OBA:2100012. The TSV row in combined_process_attribute_during_activity.tsv was updated and the OWL definitions were adjusted accordingly: a Declaration and annotation/class axioms for OBA_2100012 were added, and the previous OBA_2100017 class block was removed to keep ontology IDs consistent with the pattern data.
…e_during_activity_ratio - Renamed YAML pattern file - Renamed TSV data file - Updated internal pattern_name, pattern_iri, and xref annotation in YAML - Updated xref annotation in definitions.owl Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
I want to use this commit as a checkpoint, but it has many inconsistencies described in the next commit
Delete the attribute_during_activity_ratio pattern. The pattern was created for a particular term but it doesn't represent well the term. The ratio shouldn't be between phenotypes but the count of occurrences for each phenotype.
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Hi @MeeSiing @diatomsRcool I need to fix some issues, but I have created some terms and I have suggested some existent terms from other ontologies. There are two more terms that can be created in other ontologies. The rest of the terms I need to think a bit more about them, but at the moment non of the existent patterns would be able to create them. Also, please let me know if there is any extra term you think is missing (you commented about having some analytes during fasting). |
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For food servings/week, there are some terms that could be useful such as 'food portion' (FOODON:00003336). However, I'm not sure if in your context portion and serving are exact synonyms. |
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I agree that the consumption terms do not belong in OBA. For all of the terms that need to be requested, I think we can hold off on those and use OMOP identifiers. If I request Lipoprotein-Associated Phospholipase A2 activity in GO, will you then be able to make an OBA term for Lipoprotein-Associated Phospholipase A2 activity in blood? |
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Thank you for your answer.
Ok, if in the future you need one of the 5 terms that could be created in EFO let me know.
Yes, once I have the GO term I can import and generate the OBA term.
I can create easily the
Yes please, a list would be very useful.
That would be preferable. However, if it is a new issue, please do not include the terms that are already part of this issue. I would prefer as well that the fasting non-fasting terms are part of the new issue, and keep this PR for the terms requested. I will finish with the terms that are already created to be ready for the next release, thank you. |
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Regarding the fasting terms, I think just leaving off the process would be fine. No need to specifically say "non-fasting". I will make the lists and then put them in a new issue. Thanks! |
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New term requested in GO...... |
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This is the GO term we need: GO:0003847 1-alkyl-2-acetylglycerophosphocholine esterase activity. Just needed some synonyms. |
That's great, thank you! |
3 participants
New terms for #364
Existing terms:
Needs to be requested in another ontology: