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[bioontology-support] BioPortal Question

Michael Dorf mdorf at
Wed Sep 4 17:23:20 PDT 2019

Hi Matt,

Thank you for your inquiry. We don’t have a document that details the algorithm that we use for our class search. It is relatively straightforward, however. We index a the following fields from each class:

1. Term id (resource_id)
2. Preferred Label (prefLabel)
3. Synonyms (synonym)
4. Definition (definition)
5. Ontology Acronym (submissionAcronym)
6. Notation (notation - last fragment of id)
7. CUI (cui - for UMLS ontologies)
8. Semantic types (semanticType)

The rest of the fields are indexed as a bulk in a field called “property”. You can view our index schema here:

The search is performed on the fields above, using match ranking in the following order or priority:

prefLabelExact (match on the full pref label)
prefLabel (match on partial pref label)
synonymExact (match on the full synonym(s))
synonym (match on the partial synonym(s))
notation (last fragment of id)
cui (for UMLS ontologies)

You can refer to this code for the exact algorithm:

The instructions for getting a BioPortal API key are found on our Wiki:

Hope this helps! Feel free to reach out if you have further questions.


Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at<mailto:mdorf at>
O: 650-723-0357
M: 650-995-4374

On Sep 3, 2019, at 6:17 PM, Matthew Johnson <johnsm21 at<mailto:johnsm21 at>> wrote:


I’m interested in learning a bit more about your class search algorithm, is there any documentation available that you could share. I’m also interested in potentially getting an api key to make direct calls, what’s the process involved in that?

Thank You,
bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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