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[bioontology-support] Filtering minor terms on Bioportal Annotator REST API

Ray Fergerson ray.fergerson at stanford.edu
Wed Jul 3 16:12:57 PDT 2013


My guess would be that you are not using the default "stop words". There
is a flag on the API call to "withDefaultStopWords". Unfortunately by
default this flag is set to "false" in the REST API but the UI overrides
this to set it to true. The REST API has quite a strange choice for a
default I will admit.

 

Ray

 

From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Pieter Sheth-Voss
Sent: Wednesday, July 03, 2013 10:20 AM
To: support at bioontology.org
Subject: [bioontology-support] Filtering minor terms on Bioportal
Annotator REST API

 

 

 

In using the Bioportal Annotator REST API, it often returns matches for
relatively minor terms like "And" and "With".

 

For instance, consider "headache with dizziness and fever" against just
the SNOMEDCT ontology. 

 

In the annotator web client, it matches only "Headache", "Dizziness" and
"Fever".  Which for our immediate purpose is ideal.  

 

However, the REST API returns many more matches (attached), e.g.:

.         "With"   

o    fullId: http://purl.bioontology.org/ontology/SNOMEDCT/421463005

o    synonyms: "With - dosing instruction fragment", ...

o    semanticType: "T170" ("Intellectual Product")

.         "With"   

o    fullId: http://purl.bioontology.org/ontology/SNOMEDCT/20401003

o    synonyms: "In addition to", ...

o    semanticType: "T080" ("Qualitative Concept")

.         "And"   

o    fullId: http://purl.bioontology.org/ontology/SNOMEDCT/421829000

o    synonyms: "And - dosing instruction fragment", ...

o    semanticType: "T170" ("Intellectual Product")

 

How does the web service filter these words out?

 

If for expedient, we filter out T080 and T710, would we be missing other
arguably more important Intellectual Products or Qualitative Concepts?

 

Thanks!

 

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