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[bioontology-support] Bioportal Rest API - Term search results

Ozge Yurtsever ozge at stanford.edu
Fri Nov 20 17:53:59 PST 2020


Hi all,

We are using Bioportal Rest API for one of the WEB applications that we are currently building. This application is going to be the new version of ATB (Aim Template Builder).

In the current ATB, to save a term user does a search in Bioportal and copies the fields I marked red on the screenshot below manually. If the user has dozens of terms to search, creating a template may become a tedious task. Therefore, we wanted to make search and select easier by showing the search results in our web application and copying the necessary information for users with one click.

We are using Bioportal Rest API to search terms and list the results, so when a user clicks on an item, we can copy the information. However, data attributes may be different for different ontologies. For instance, result we get for “lung” from NCIT includes a “prefLabel” attribute, which can be used for “Preferred Name,” but I don’t see any unique code value. However, in the screenshot below, there is one.

On the other hand, there are some results with both cui and notation attributes like OMIM - Online Mendelian Inheritance in Man.

Our issue regarding getting the correct and unique code value of a term arises in the following cases:

  1.  If there are both notation and cui, which info should we use for code value?
  2.  If there are more than one cui and no notation, how should we decide which one to use?
  3.  If there isn’t any code value at all, from which attribute we can acquire the correct code value? (Like NCIT example)

Thank you,

Ozge Yurtsever
Software Developer – ePAD team
Stanford University Department of Biomedical Data Science


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