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[bioontology-support] [BioPortal] Feedback from brycemecum

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Sep 17 15:55:16 PDT 2019


Hello Bryce,

I’ve provided some background information below on how BioPortal operates to assist in understanding why you see definition listed twice in the class Details pane.


On Sep 17, 2019, at 10:27 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


After making a change to our ontology and re-uploading to BioPortal, we're seeing our definition show up twice on our landing page for this term: http://bioportal.bioontology.org/ontologies/ECSO/?p=classes&conceptid=http%3A%2F%2Fpurl.dataone.org%2Fodo%2FECSO_00002092.

The RDF/XML for this term can be found in this diff: https://github.com/DataONEorg/sem-prov-ontologies/commit/694957803cf77f5723ddd6ff1b7c88e810cc8c75#diff-3aac6f836ca99404f3acabd594fa36d3L16842.

Our ontology isn't configured with a custom term URI For the definition field. This isn't really a huge deal but it would be nice to only show the definition once. Is there something we can do on our end to change this?




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

BioPortal often looks at more than one user defined property to populate each of the above properties. As a concrete example, to follow is the declaration for the “d14C” class in your ontology:

<!-- http://purl.dataone.org/odo/ECSO_00003112 -->

<owl:Class rdf:about="http://purl.dataone.org/odo/ECSO_00003112">
  <rdfs:subClassOf rdf:resource="http://purl.dataone.org/odo/ECSO_00001514"/>
  <obo:IAO_0000115>The per mille depletion in sample carbon 14 prior to isotopic fractionation correction.</obo:IAO_0000115>
  <dc:creator rdf:resource="http://orcid.org/0000-0003-1264-1166"/>
  <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2019-09-11T23:51:31Z</dc:date>
  <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">delta C 14</oboInOwl:hasExactSynonym>
  <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">δ14C</oboInOwl:hasExactSynonym>
  <rdfs:comment>Note that this measurement uses the lower case Greek letter delta (δ).</rdfs:comment>
  <rdfs:label xml:lang="en">d14C</rdfs:label>
  <skos:altLabel rdf:datatype="http://www.w3.org/2001/XMLSchema#string">delta C 14</skos:altLabel>
  <skos:altLabel rdf:datatype="http://www.w3.org/2001/XMLSchema#string">δ14C</skos:altLabel>
</owl:Class>

When you issue a call to the BioPortal REST API to retrieve this class (http://data.bioontology.org/ontologies/ECSO/classes/http%3A%2F%2Fpurl.dataone.org%2Fodo%2FECSO_00003112?display_links=false&display_context=false<http://data.bioontology.org/ontologies/ECSO/classes/http://purl.dataone.org/odo/ECSO_00003112?display_links=false&display_context=false>), you’ll see that the BioPortal standard definition property is populated with an array of two values (one from the obo:IAO_0000115 property, and one from the rdfs:comment property):


[cid:E1523485-CEF9-41A0-B2CE-5D3054275C98 at stanford.edu]


If you want to see a list of user defined properties for a class exactly as they are declared in the ontology, you can add “include=properties” to the query string (http://data.bioontology.org/ontologies/ECSO/classes/http%3A%2F%2Fpurl.dataone.org%2Fodo%2FECSO_00003112?display_links=false&display_context=false&include=prefLabel,definition,properties<http://data.bioontology.org/ontologies/ECSO/classes/http://purl.dataone.org/odo/ECSO_00003112?display_links=false&display_context=false&include=prefLabel,definition,properties>):


[cid:8D0A688F-D9B8-4061-BA11-92E81A2D6644 at stanford.edu]

All of this is to say that the BioPortal user interface first displays the set of BioPortal standard properties, then concatenates all other user defined properties in the class Details pane. A lot of ontologies have a user defined property with a label of “definition”, which results in the same kind of display as ECSO with two entries in the table for definition display. Someone asked a similar question on the support list before regarding synonyms and altLabel: http://ncbo-support.2288202.n4.nabble.com/Re-bioontology-support-SNOMED-ttl-file-tp4656300.html.

The Details pane could certainly use improvement. There should be a clear visual indication of which properties are BioPortal standard vs. user defined. In addition, when the Definitions field contains multiples values, they aren’t separated by a newline, but rather just concatenated into one long string.

Hope that information helps.

Kind regards,
Jennifer










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