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monarch-initiative / HPO-UMLS-Integration

Repository for HPO UMLS integration QA code and tracking issues
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Microcephaly #30

Closed mirandajarnot closed 8 years ago

mirandajarnot commented 8 years ago

The concepts Microcephaly (HP:0000252) and Decreased head circumference (HP:0040195) have very similar strings between them. Do all the synonyms in Microcephaly refer specifically to the syndrome, and not to the finding of small head size?

A similar situation exists with Macrocephaly (HP:0000256) and Increased head circumference (HP:0040194).

Thanks, Miranda Jarnot

markengelstad commented 8 years ago

i think the way microcephaly is modeled now, it is representing both the syndrome and the finding of a skull that is very small -- so you are seeing a lot of synonyms in there.

That's because, right now, microcephaly is the only class for representing an overall small skull (not just in circumference).

we should add another term 'Decreased size of skull' to capture some of the more non-specific terms that are currently synonyms of microcephaly, like 'small skull'.

and microcephaly should be reserved for certain type of small skull defined by particular head circumference values

On Fri, Feb 12, 2016 at 9:46 AM mirandajarnot notifications@github.com wrote:

The concepts Microcephaly (HP:0000252) and Decreased head circumference (HP:0040195) have very similar strings between them. Do all the synonyms in Microcephaly refer specifically to the syndrome, and not to the finding of small head size?

Thanks, Miranda Jarnot

— Reply to this email directly or view it on GitHub https://github.com/monarch-initiative/HPO-UMLS-Integration/issues/30.

drseb commented 8 years ago

please have a look at https://github.com/obophenotype/human-phenotype-ontology/issues/497 for further information on the current solution for this part of HPO.

may be true that some synonyms should be moved. will look at this later

mirandajarnot commented 8 years ago

Thank you, Seb, this is very helpful. It’s good to see how you (HPO) view things and how they are considered, and makes it easier for editing HPO in the UMLS.

Miranda

From: Sebastian Köhler [mailto:notifications@github.com] Sent: Thursday, February 18, 2016 2:06 PM To: monarch-initiative/HPO-UMLS-Integration HPO-UMLS-Integration@noreply.github.com Cc: Jarnot, Miranda (NIH/NLM) [E] jarnotm@mail.nlm.nih.gov Subject: Re: [HPO-UMLS-Integration] Microcephaly (#30)

please have a look at obophenotype/human-phenotype-ontology#497https://github.com/obophenotype/human-phenotype-ontology/issues/497 for further information on the current solution for this part of HPO.

may be true that some synonyms should be moved. will look at this later

— Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/HPO-UMLS-Integration/issues/30#issuecomment-185864610.

pnrobinson commented 8 years ago

This issue seems to be closed? Note that the HPO class microcephaly is refering to the phenotypic finding of a small skull, not the disease known as microcephaly (this disease typically also is characterized by intellectual disability and perhaps other abnormalities).

mirandajarnot commented 8 years ago

Thanks Peter – this is exactly what I needed to know to make sure we have this edited correctly in the Metathesaurus.

Thanks, Miranda Jarnot

From: Peter Robinson [mailto:notifications@github.com] Sent: Saturday, February 27, 2016 2:15 AM To: monarch-initiative/HPO-UMLS-Integration HPO-UMLS-Integration@noreply.github.com Cc: Jarnot, Miranda (NIH/NLM) [E] jarnotm@mail.nlm.nih.gov Subject: Re: [HPO-UMLS-Integration] Microcephaly (#30)

This issue seems to be closed? Note that the HPO class microcephaly is refering to the phenotypic finding of a small skull, not the disease known as microcephaly (this disease typically also is characterized by intellectual disability and perhaps other abnormalities).

— Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/HPO-UMLS-Integration/issues/30#issuecomment-189599417.