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[bioontology-support] a list of related terms to a specific term

Clement Jonquet jonquet at lirmm.fr
Mon Apr 3 19:41:21 PDT 2017


Hi  Sara, 

 

To comple Misha’s answer:

 

Developing a « semantic similarity” service is an old request NCBO had in the past. But it’s quite complex for not a lot of use. 

We had a prototype a long time ago :)

 

I recommend to check out : http://www.semantic-measures-library.org/sml/ as this is a state of the art framework for computing similarities. 

 

As a complement, you could also consider looking at the hierarchy (parents/children) of a class, once you identify it. 

 

In your example: dystonia

One you have a match in SNOMED-CT (thanks to /search or /annotator):

http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F15802004?display=all <http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F15802004?display=all&display_links=false&display_context=false> &display_links=false&display_context=false 

then 

you can look up “parents” or “children “cf JSON

 

Bye

Clement

 

 

Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
University of Montpellier

Coordinator of the SIFR <http://www.lirmm.fr/sifr/>  and AgroPortal <http://agroportal.lirmm.fr/>  projects

Visiting scholar, Stanford University (EU Marie Curie fellow)

 

jonquet at lirmm.fr <mailto:jonquet at lirmm.fr> 

http://www.lirmm.fr/~jonquet 

 

@Montpellier : +33/4 67 14 97 43

@Stanford       : +1 650 723 6725

 

 

 

De : bioontology-support [mailto:bioontology-support-bounces at lists.stanford.edu] De la part de Michael Dorf
Envoyé : vendredi 31 mars 2017 16:35
À : Sara ArabYarmohammadi <s.yarmohammadi at icloud.com>
Cc : bioontology-support at lists.stanford.edu
Objet : Re: [bioontology-support] a list of related terms to a specific term

 

Hi Sara, 

 

Thank you for getting in touch with us! Unfortunately, at present we don’t offer a service that would render a list of related terms.  Such a service actually has been discussed within our team, and we may consider implementing it in the near future. Meanwhile, below is a list of the existing services that may be of help in your case:

 

1. Mapping service for a specific term. This allows you to find the mappings to terms that are related. Here is a sample request for mappings for the NCIT ontology term  <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C82956> http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C82956 (Odontogenesis):

 

 <http://data.bioontology.org/ontologies/NCIT/classes/http:/ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C82956/mappings?apikey=> http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C82956/mappings?apikey=<your apikey> 

 

2. Search service. You can use the prefLabel of your source term to search for terms with similar prefLabels/synonyms/definitions:

 

 <http://data.bioontology.org/search?q=Odontogenesis&apikey=> http://data.bioontology.org/search?q=Odontogenesis&apikey=<your apikey>

 

3. The Annotator service. Similarly to search, you can use the prefLabel of your source term as the input to the Annotator to see what other terms from other ontologies are annotated with the same text:

 

 <http://data.bioontology.org/annotator?text=Odontogenesis&apikey=> http://data.bioontology.org/annotator?text=Odontogenesis&apikey=<your apikey>

 

If you have specific ontologies in mind that you are pursuing, you can always limit your REST call to that set by passing in the ontologies=NCIT,GO,NCBITAXON parameter. This works for both the Search and Annotator services:

 

 <http://data.bioontology.org/annotator?text=Odontogenesis&ontologies=NCIT,GO,NCBITAXON&apikey=> http://data.bioontology.org/annotator?text=Odontogenesis&ontologies=NCIT,GO,NCBITAXON&apikey=<your apikey>

 

Sorry for not getting exactly what you are looking for, but I hope that one or a combination of the above options will help you achieve your goal. For the complete list of available parameters and other services available through our REST API, please browse our docs here:

 

 <http://data.bioontology.org/documentation> http://data.bioontology.org/documentation

 

Sincerely,

 

Michael

 

 

 

On Mar 31, 2017, at 12:51 PM, Sara ArabYarmohammadi < <mailto:s.yarmohammadi at icloud.com> s.yarmohammadi at icloud.com> wrote:

 

Dear Team, 

I have a term and I want to have a list of all related terms using NCBO API. Would you please provide me a sample code or help me find a good source to get help? Is it possible to do so using the API?

I searched a lot trying to figure out the API and how it works but still no success.

Thank you,

 

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