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[bioontology-support] [BioPortal] Feedback from nporto

Clement Jonquet jonquet at lirmm.fr
Fri Feb 26 11:26:47 PST 2016


Hi Nporto, 

 

1)      Yes the documentation explicity says « ontologies » and not “ontology” for the name of the parameter. And comma separate them if you have more than once.

 

2)      There is not parameter explicitly to limit a search to a UMLS CUI, because it’s a “keyword” search web service. However, you can search for the CUI string itself and if you include the properties in your seach you will have responses e.g.

http://bioportal.bioontology.org/search?q=C0010678 <http://bioportal.bioontology.org/search?q=C0010678&ontologies=ICD10,MESH&include_properties=true&include_views=false&includeObsolete=false&require_definition=false&exact_match=false> &ontologies=ICD10,MESH&include_properties=true&include_views=false&includeObsolete=false&require_definition=false&exact_match=false

3)      For your current list, you would have to do for each CUI

a.       /search, limiting to ICD10,

b.      Select the most appropriate concept if several results

e.g., http://data.bioontology.org/ontologies/ICD10/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICD10%2FB69.9

 

c.       Follow the links.ancestors. property to get all the parents concepts

e.g., 

http://data.bioontology.org/ontologies/ICD10/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICD10%2FB69.9/ancestors

 

d.      Get the last concepts in the list… 

e.g., “Certain infectious and parasitic diseases”

 

3 bis) The SPARQL endpoint is outdated. 

 

Hope it helps

Clement

 

De : bioontology-support [mailto:bioontology-support-bounces at lists.stanford.edu] De la part de support at bioontology.org
Envoyé : vendredi 26 février 2016 06:21
À : support at bioontology.org; portokallidis at gmail.com
Objet : [bioontology-support] [BioPortal] Feedback from nporto

 

Name: nporto 

Email: portokallidis at gmail.com <mailto:portokallidis at gmail.com>  

Location: https://bioportal.bioontology.org/help 


Feedback: 

Hello, I am facing a problem using the API - search method. 
1) In the documentaion ( <http://data.bioontology.org/documentation#nav_search> http://data.bioontology.org/documentation#nav_search) You describe that in order to limit the search by ontology i have to provide a param &ontology=ICD10 , which doesnt work , instead i tried ontologies=ICD10 and it does work! 
2) I cant figure out how to limit the search by cui , e.g &cui=C0001783 doesnt return any results

3) This is a more broad question. I have a list of cui's (ICD10) and i want to get all the corresponding Root ICD10 categories (subClassOf #Thing) in only one request. Is something like this possible from the api? Also can i use the SPARQL endpoint. 

Thank you so much for the Bioportal service

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