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[bioontology-support] [BioPortal] Feedback from rose.lau

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Mar 25 10:50:01 PDT 2020


Hello Rose,

http://ncbo-support.2288202.n4.nabble.com/bioontology-support-BioPortal-Feedback-from-Bryce-Mecum-td4657320.html#a4657322


On Mar 25, 2020, at 5:55 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Dear Sir/Madam

I am writing on behalf of Databiology HK. We have found that there are some differentiations between the BioPortal UI and API response which make users confused.

For example, for this term (http://bioportal.bioontology.org/ontologies/PCAO?p=classes&conceptid=http%3A%2F%2Fwww.semanticweb.org%2Fontologies%2F2018%2F1%2FProstateCancer.owl%23pT3), We could observe there are information provided by isDefinedBy and synonyms fields.
However, from the API response (http://data.bioontology.org/ontologies/PCAO/classes/http%3A%2F%2Fwww.semanticweb.org%2Fontologies%2F2018%2F1%2FProstateCancer.owl%23pT3)
, there are empty brackets for definition and synonym fields.



BioPortal accepts ontologies in multiple different formats including OBO, OWL, and SKOS. When the system consumes an ontology, we have a set of eight “BioPortal standard properties" that we attempt to populate for each class, regardless of ontology format. The set of standard properties are:

ID
Preferred Name
Synonyms
Definitions
CUI
Semantic Types
Obsolete
Parents

With specific regard to population of definitions and synonyms, BioPortal looks for the following properties in the ontology sources:

Definitions

http://purl.obolibrary.org/obo/IAO_0000115
http://www.w3.org/2004/02/skos/core#definition

Synonyms

http://www.w3.org/2004/02/skos/core#altLabel
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
http://purl.obolibrary.org/obo/synonym
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym

I looked at your ontology source file and it appears that definitions and synonyms were declared using properties that don’t match anything in the lists above, i.e., definitions are declared using the property:

http://www.w3.org/2000/01/rdf-schema#isDefinedBy

… and synonyms are declared using the property:

http://www.semanticweb.org/ontologies/2018/1/ProstateCancer.owl#synonyms

You may be interested to read this question/answer set in our mailing list archive for a more detailed explanation of how BioPortal extracts definitions, synonyms, etc.:

http://ncbo-support.2288202.n4.nabble.com/bioontology-support-BioPortal-Feedback-from-Bryce-Mecum-td4657320.html#a4657322

You can still use our REST API to retrieve the desired data though. Please see below.



Could you please tell us how we could obtain the same data provided in UI by REST API?

From the documentation (http://data.bioontology.org/documentation), we understand that the fields we could request by performing Term Search are prefLabel, synonym, definition, notation, cui and semanticType.
If isDefinedBy is a field which is not included, may please help to extend the API and add this field? And for synonym field, we suspect this could be a bug.



All of the properties on a class that fall outside of the BioPortal standard properties mentioned above are extracted into what we refer to as “user defined properties”. You can access these properties using the “properties” parameter. For example, if you want to use the /search endpoint, the following call will include all of the user defined properties for the “pT3” class:

http://data.bioontology.org/search?q=pT3&ontologies=PCAO&include=prefLabel,properties

Alternatively, you can also use the /classes endpoint to retrieve user defined properties on a class. This can be achieved by adding the “include=all” key value pair to the query string:

http://data.bioontology.org/ontologies/PCAO/classes/http%3A%2F%2Fwww.semanticweb.org%2Fontologies%2F2018%2F1%2FProstateCancer.owl%23pT3?include=all<http://data.bioontology.org/ontologies/PCAO/classes/http://www.semanticweb.org/ontologies/2018/1/ProstateCancer.owl#pT3?include=all>

… or you can use any desired combination of comma separated values for the include parameter, e.g.:

http://data.bioontology.org/ontologies/PCAO/classes/http%3A%2F%2Fwww.semanticweb.org%2Fontologies%2F2018%2F1%2FProstateCancer.owl%23pT3?include=prefLabel,properties<http://data.bioontology.org/ontologies/PCAO/classes/http://www.semanticweb.org/ontologies/2018/1/ProstateCancer.owl#pT3?include=prefLabel,properties>

I’ve included screenshots of the results of a couple of these calls below.

Kind regards,
Jennifer


[cid:063C7E84-13E2-4455-8D5C-BCCB025CB25A at stanford.edu][cid:55AABCC3-0486-4B82-B756-B2B11BC72E4F at stanford.edu]
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