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[bioontology-support] How to handle imported ontologies on bioportal

John Graybeal jbgmeta1 at stanford.edu
Sun Dec 27 23:37:58 PST 2015


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

On Mon, Nov 23, 2015 at 8:23 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Hi Sridevi,

We have an active tracker open on this issue.  An engineer is working on the problem, but as Ray had mentioned, this turned out to be a tricky issue to address. We'll keep you posted when we've deployed the fix.

Meanwhile, I am wondering whether setting the "SYNONYM PROPERTY" for the latest submission to:

http://www.geneontology.org/formats/oboInOwl#hasExactSynonym

would help this particular issue. We'll need to re-parse/re-index the ontology for this change to take effect.

Thanks,

Michael



On Nov 22, 2015, at 07:18, sridevi polavaram <spolavar at gmail.com<mailto:spolavar at gmail.com>> wrote:

Hi Mike,
 The problem i was referring to is when i search for synonyms i am getting inconsistent results. The NMOSP ontology right now seems to be working fine, as it is able to fetch the term when i search for "zebra fish". The REST service is also working fine in this regard.

However, when i search in NMOBR for a synonym e.g., "isocortex", it fails, i won't get the term 'neocortex'. The difference between the two ontologies is the format, NMOBR is in owl and uses oboInOWL:has_exact_synonym for the synonyms.

Do you see the problem now? If this bug gets fixed, I will be able to use both formats seamlessly.

Thank you
Sridevi

On Fri, Nov 20, 2015 at 8:29 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Hi Sridevi,

Just FYI, Ray Fergerson is no longer at Stanford. I tried the search you mentioned (Cerebellum in NMOBR ontology) and I get a result within seconds. I've also tried the REST service directly (which is used by BioPortal UI), and it too returned results (single result) without a hitch:

http://data.bioontology.org/search?q=Cerebellum&ontologies=NMOBR

You'll need to append "&apikey=<your API key> to this query for it to work.

The difficult part here is that if I am unable to reproduce the problem on my end, it would be hard for me to troubleshoot it. Do you see issues with other search queries as well?

Thanks!

Michael Dorf


On Nov 20, 2015, at 11:05, sridevi polavaram <spolavar at gmail.com<mailto:spolavar at gmail.com>> wrote:

Cerebellum





========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632
skype: graybealski


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