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[bioontology-support] BioPortal Question

Michael Dorf mdorf at stanford.edu
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:

https://github.com/ncbo/ontologies_linked_data/blob/master/config/solr/term_search/schema.xml#L131

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

id
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)
semantic_types

You can refer to this code for the exact algorithm:

https://github.com/ncbo/ontologies_api/blob/master/helpers/search_helper.rb#L105

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

https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key

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

Michael


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



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

Hello,

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,
Matt
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