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[bioontology-support] [BioPortal] Feedback from Roberto Mosca

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Sep 14 15:09:04 PDT 2015


Hello Roberto,


On Sep 14, 2015, at 2:03 AM, roberto.mosca at thomsonreuters.com<mailto:roberto.mosca at thomsonreuters.com> wrote:

Dear Jennifer,

thanks for your answer and for your help! Based on what you say I believe the following query

http://data.bioontology.org/search?q=autosomal+dominant+form&also_search_obsolete=True&ontologies=HP

should also return the entry

"http://purl.obolibrary.org/obo/HP_0000113”

which has the following definition

definition": [

  *   "The presence of multiple cysts in both kidneys.",
  *   "Polycystic kidney disease (PKD) is a leading cause of end-stage renal disease. Most commonly, PKD arises as an inherited trait. Tremendous enlargement of both kidneys is characteristic of the autosomal dominant form of PKD, with up to hundreds or thousands of renal cysts. This term does not refer to the disease entity but rather to the finding of numerous cysts in both kidneys."

],


Nevertheless, this entry is not in the set of results returned by the previous query.

Is it correct? Did I misinterpret the way the search function works?


No, you didn’t misinterpret the search functionality.  You are correct that the result set should include the entry you listed above.  This is a bug on our side and I will file an issue today.  In the mean time (as a workaround) you could add the “also_search_properties” parameter to the query string.  This will generate a result set that includes the entry above, e.g.:

http://data.bioontology.org/search?q=autosomal+dominant+form&also_search_obsolete=True&ontologies=HP&also_search_properties=true

Best,
Jennifer



On 12 Sep 2015, at 00:56, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Roberto,


On Sep 10, 2015, at 1:14 AM, roberto.mosca at thomsonreuters.com<mailto:roberto.mosca at thomsonreuters.com> wrote:

any news on this issue?


Apologies for the late reply.


Name: Roberto Mosca

Email: roberto.mosca at thomsonreuters.com<mailto:roberto.mosca at thomsonreuters.com>

Location: http://bioportal.bioontology.org/ontologies/HP?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHP_0000006

Feedback:

Dear Support,

I have a question about the REST API. When doing a search through the search API (/search?q=) which fields are specifically searched? For example, is the "description" used for the search? Is it just the prefLabel? Do you also search in the "synonym"?



The default set of fields used for searches are class id, prefLabel, synonym, definition, notation, cui, and semanticType.


I think listing the fields that are actually searched would be a nice addition to the documentation :)



Thanks for the suggestion.  I’ll enter an issue today to get the documentation updated.

Best,
Jennifer



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