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[bioontology-support] searching for synonyms (was: How to handle imported ontologies on bioportal)

John Graybeal jbgmeta1 at stanford.edu
Sun Dec 27 23:51:38 PST 2015


Sridevi, a quick follow-on — I’ve created the task "can't search NMOSP by synonym” as task NCBO-1605 in our ticket tracking system, and started this new thread with a different title for this topic.

Also as an aside, I see that a proposed fix has been created for the previous issue (NCBO-1490, ’the synonym bug’); we will release it and confirm it fixes the issue in the new year.

John

Sridevi,

Sorry for the delay getting back to you.

The short answer is, you will likely need to wait until after the new year before we can provide the additional information about schedule.

I know that some new software is being tested which may fix one of the earlier problems (not seeing multiple synonyms under certain conditions, referred to as ‘the synonym bug’; this is internally tracked as ticket NCBO-1490).

I have confirmed that displaying ‘pan troglodytes’ class from NMOSP, shows that both ‘chimpanzee' and 'common chimpanzee’ are synonyms; but that searching for ‘chimpanzee’ will not bring up NMOSP as containing that class.

It is not clear to me that fixing the problem with multiple synonyms, will also fix the problem with searches on synonyms within NMOSP not returning any hits. Already we are seeing MESH hits for ‘chimpanzee’ but not NMOSP; and MESH and NMOBR hits for cerebellum, but not NMOSP. (I suspect this secton issue will be a less challenging problem, since it seems to work in other cases already.)

I will confer with our developers and consultants when they return in January, to figure out further information about the schedule for the original issue, and whether this or an additional issue may be causing the problem with searching on synonyms in NMOSP.

john


On Dec 23, 2015, at 1:39 PM, sridevi polavaram <spolavar at gmail.com<mailto:spolavar at gmail.com>> wrote:

Hi Michael,
 I just uploaded a newer version of NMOSp on the bioportal at: https://bioportal.bioontology.org/ontologies/NMOSP?p=classes

but the synonyms are not searchable, e.g., "common chimpanzee" says no match!

Do you have any idea when this can be fixed? I will be using this in my PhD dissertation defense, which is scheduled in less than two months time. It would be helpful to know the status so i can plan for it accordingly.

Wish you Happy holidays!

Thank you
Sridevi
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