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[bioontology-support] [BioPortal] Feedback from Bryce Mecum

Michael Dorf mdorf at stanford.edu
Thu Jul 18 11:35:45 PDT 2019


Hi Bryce,

Thank you for your question. I don’t believe our documentation offers details on how we extract these attributes. I can give you a few pointers.  Our class/term model defines several built-in attributes, which we then populate using the values of a number of properties defined within the ontology. These built-in properties are:

label
prefLabel
synonym
definition

These are defined here: https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/models/class.rb#L44
The values used to populate these are contained in: https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/utils/triples.rb

The attribute label is populated using a property: http://www.w3.org/2000/01/rdf-schema#label
The attribute prefLabel is populated using the following logic:

1. Look for a prefLabel property supplied by the user when the ontology is created. If exists, use it to populate prefLabel attribute of the model.
2. If the user has not supplied a prefLabel property, use one of these (in the order of priority):

http://www.w3.org/2004/02/skos/core#prefLabel
http://www.w3.org/2000/01/rdf-schema#label
http://data.bioontology.org/metadata/def/prefLabel

The attribute synonym is populated using the following logic:

1. Look for a synonym property supplied by the user when the ontology is created. If exists, use it to populate synonym attribute of the model.
2. If the user has not supplied a synonym property, use one of these (in the order of priority):

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

The attribute definition is populated using the following logic:

1. Look for a definition property supplied by the user when the ontology is created. If exists, use it to populate definition attribute of the model.
2. If the user has not supplied a definition property, use one of these (in the order of priority):

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

Hope this helps. Feel free to contact us if you require further elaboration.

Michael


On Jul 17, 2019, at 4:00 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Bryce Mecum

Email: mecum at nceas.ucsb.edu<mailto:mecum at nceas.ucsb.edu>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FECSO%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.dataone.org<http://252Fpurl.dataone.org>%252Fodo%252FECSO_00000536

Feedback:

I'm trying to figure out if there's documentation on how Bioportal extracts definitions, synonyms, etc. from ontology terms. I can kinda guess (SKOS definition, altLabel, etc) but a comprehensive mapping would be handy.

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