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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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http://purl.obolibrary.org/obo/HP_0045077 #5493

Closed pnrobinson closed 4 years ago

pnrobinson commented 4 years ago

HPO term http://purl.obolibrary.org/obo/HP_0045077

this is the synonym type "abbreviation". Other synonyms have URLs like "http://purl.obolibrary.org/obo/hp#layperson" We should be consistent. @matentzn @drseb

matentzn commented 4 years ago

I can fix this in 1 second, but this is more a decision you need to make; do you want them all to be like http://purl.obolibrary.org/obo/hp#layperson or like http://purl.obolibrary.org/obo/HP_0045077?

In the following are all the HP specific annotation properties you use. We can either generate HP ids for all of them, or use syntax 2 everywhere.

Note: There is not technical need to unify these; its just cosmetic. Maybe @drseb can offer his opinion?

Syntax 1 Syntax 2
http://purl.obolibrary.org/obo/HP_0031859 obsolete synonym
http://purl.obolibrary.org/obo/HP_0031940 display label
http://purl.obolibrary.org/obo/HP_0045076 UK spelling
http://purl.obolibrary.org/obo/HP_0045077 abbreviation
http://purl.obolibrary.org/obo/HP_0045078 plural form
http://purl.obolibrary.org/obo/hp#hposlim_core
http://purl.obolibrary.org/obo/hp#secondary_consequence
http://purl.obolibrary.org/obo/hp.owl#layperson
mellybelly commented 4 years ago

I tend to prefer the # versions for human readability, unless they come from the OBO core annotation properties, in which case whatever syntax will be declared there should be used.

matentzn commented 4 years ago

Another consideration is compatibility with other ontology, and moving them all to IAO or some such (except from the slim declaration). Anyways its all as easy as 123 once the decision is made.

pnrobinson commented 4 years ago

http://purl.obolibrary.org/obo/HP_0045076 (UK spelling) http://purl.obolibrary.org/obo/HP_0045078 (plural form) http://purl.obolibrary.org/obo/HP_0031859 (obsolete synonym)

pnrobinson commented 4 years ago

I agree with @mellybelly that the # forms are nicer...

drseb commented 4 years ago

I agree with you. Let's make it consistent!

matentzn commented 4 years ago

@pnrobinson like this:

OLD NEW
http://purl.obolibrary.org/obo/HP_0031859 http://purl.obolibrary.org/obo/hp#obsolete_synonym
http://purl.obolibrary.org/obo/HP_0031940 http://purl.obolibrary.org/obo/hp#display_label
http://purl.obolibrary.org/obo/HP_0045076 http://purl.obolibrary.org/obo/hp#uk_spelling
http://purl.obolibrary.org/obo/HP_0045077 http://purl.obolibrary.org/obo/hp#abbreviation
http://purl.obolibrary.org/obo/HP_0045078 http://purl.obolibrary.org/obo/hp#plural_form
http://purl.obolibrary.org/obo/hp#hposlim_core
http://purl.obolibrary.org/obo/hp#secondary_consequence
http://purl.obolibrary.org/obo/hp.owl#layperson http://purl.obolibrary.org/obo/hp#layperson

?

matentzn commented 4 years ago

note the slide change in the laypersons IRI as well. (slide is a german way to say slight)

pnrobinson commented 4 years ago

The items under "NEW" work for me!

matentzn commented 4 years ago

Done; peter you have the HPO lock, just so you know.

matentzn commented 4 years ago

Passed the lock to @drseb

Annotation props not on current whitelist:

https://github.com/Phenomics/hpo-owl-qc/blob/a6c80c4547622911634fe963dade008a94c5e55e/src/main/java/de/phenomics/PerformHpoOwlQC.java#L227

matentzn commented 4 years ago

This should fix it: https://github.com/Phenomics/hpo-owl-qc/pull/1/files

Good night!