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obophenotype / human-phenotype-ontology

Ontology for the description of human clinical features
http://obophenotype.github.io/human-phenotype-ontology/
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EPIC: Harmonising HPO chemical phenotypes #10391

Open matentzn opened 8 months ago

matentzn commented 8 months ago
  1. Strategy is described here
  2. Curation is prepared here

@LCCarmody let me know if this works for you. I would suggest:

  1. Go through curation list I prepared in fill in column chemical_phenotype, basically saying "this is indeed a chemical phenotype" - there may be quite a few wrong ones.
  2. Go through list again and pick correct_pattern.
  3. Once this is done, we meet and make a strategy to harmonise everything

what do you think?

LCCarmody commented 8 months ago

Sorry for the delay (although I knew you were off)... overall, it looks good. I assume I can add terms to the list? I think this should be done in conjunction with Protege.

LCCarmody commented 8 months ago

And an additional comment as I am going through this, what is 'defined_class_label'? and how is it different from hpo_label?

Second: Could we have a way to add synonyms? One issue is that there is not consistency of labels, but adding synonyms could help that situation. It could also help decrease duplicate creation before the fact.

matentzn commented 8 months ago

@LCCarmody this is amazing work so far!!! Beautiful!

defined_class_label is the lingo used in DOSDP - its the same as hpo_label. You can hide this column for now if it annoys you - we will add it back when we start experimenting!

Second: Could we have a way to add synonyms?

Unless they are very specific synonyms, synonyms should not be manually curated. They should be added to the DOSDP pattern, and DOSDP tools will add them automatically. Does this make sense?

LCCarmody commented 8 months ago

Done with categorizing the patterns. Found one duplicate (will create ticket). What's next? Definitely would like some help pulling terms (protein/chemical).

pnrobinson commented 4 months ago

@LCCarmody Could we summarize progress to date and discuss prior to transition date?

LCCarmody commented 4 months ago

Yes! I am currently working through the current batches of patternized terms. Should we set up a time later this week? Early next? with or without @matentzn ?