Ticket #68 (closed defect: fixed)

Opened 3 years ago

Last modified 3 years ago

Change the expected value of health_disease_stat

Reported by: pyilmaz Owned by: pyilmaz
Priority: minor Component: MIxS general
Version: 4.1 Keywords:
Cc: mcourtot@…, lschriml@… Sensitive: no


Hi Lynn and Pelin,

I was wondering if you could help us with the values for the field “health_disease_stat” in the MIxS specification? Definition is “Health or disease status of specific host at time of collection. This field accepts PATO (v 2013-10-28) terms, for a browser please see http://purl.bioontology.org/ontology/PATO”, and accepted values should come from PATO.
Do you have an example of a PATO term that would be appropriate, or a list of different values that could be expected? I was browsing through PATO, but couldn’t find anything such as “healthy” or “diseased”.

Hi Melanie,

I looked at how submitters have used this qualifier so far in NCBI Bioprojects. The result is somewhat of a mix; health, healthy, diseased, injured, IDIOP(?)...
And you're right that PATO doesn't really have the right terms. The only semi-fitting terms I could find were under the viability class:

I searched a little in bioportal, and I found that NCIT terms are perhaps a little better suited for this purpose:

a small set of terms is good idea.

healthy, diseased, dead, or disease-free,

NCI thesaurus terms:
undetermined, recovering or resolving, pre-existing condition, pathological, life threatening, healthy, congenital,

Change History

comment:1 Changed 3 years ago by pyilmaz

  • Status changed from new to assigned

comment:2 Changed 3 years ago by pyilmaz

  • Status changed from assigned to closed
  • Resolution set to fixed

expected value > CV
syntax > [healthy|diseased|dead|disease-free|undetermined|recovering|resolving|pre-existing condition|pathological|life threatening|healthy|congenital]

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