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To create a common 'look and feel' for browsing phenotype ontologies, we would like to start thinking about what kind of standard upper-level distinctions we can recommend for phenotype concepts. [Her…
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This section of the documentation links to the Ontology Lookup Service (OLS):
https://obophenotype.github.io/upheno/reference/core-concepts/
The link behind the text "[Unified Phenotype On…
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We will apply these templates to taxon-specific phenotype ontologies, improving inter-ontology alignment and automated classification (Figure 10B,D) within individual ontologies. During the course of …
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E.g. current translation, obo writer warns:
```
Oct 06, 2015 9:00:31 AM org.obolibrary.oboformat.parser.OBOFormatParser warn
WARNING: LINE: 29927 Empty value for qualifier in trailing qualifier bloc…
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## Desiderata
- [ ] All pheno ontologies (at least MP and HP) should use the same design pattern _approach_
- [ ] design patterns in MP and HP should be _coordinated_
- they may diverge in terms of …
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Per convo with @deepakunni3 @matentzn
As an improvement on our current ingest of ontologies, Nico will ingest and perform a transform of ontologies of interest (HPO, GO, MONDO), make links between …
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## Summary
We will apply these templates to rebuild the species-neutral core uPheno, using a combination of automated mechanisms and manual selection to choose appropriate terms to group phenotypes…
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@manulera
>However, I am not sure variant -> phenotype is the most meaningful link. Probably the user would like to see which alleles give a certain phenotype, rather than what a particular sequen…
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Not sure how best to organize this, so it is stream of consciousness for now. Feel free to flesh out. @mellybelly
### Phenotype Standards:
- phenopackets
- minimum phenotype standard
- Annotation suf…
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To start sorting out the disease vs phenotype business, we suggest the following plan:
1. Update our HPO - Mondo mapping by running the OAK lexmatch matching pipeline to HPO.
2. Implement a review…