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[bioontology-support] [BioPortal] Feedback from brycemecum

Bryce Mecum mecum at nceas.ucsb.edu
Fri Aug 2 10:44:15 PDT 2019


Hey John, thanks for following up on this.

We're building out user-facing tools for Ecological Metadata Language's
(EML) new (in v2.2.0) semantic annotation module that allows metadata
authors to annotate specific sections of their metadata records with RDF
properties and OWL classes. For example, a free-text variable name can be
annotated with a specific OWL class to give it a much higher degree of
clarity and specificity. The EML record only stores bare term URIs (and
user-specified labels) so we're using the BioPortal API to make a rich,
scientist-appropriate display of the bare term URIs on our websites. See
the following, for an example:

[image: Screen Shot 2019-08-02 at 9.31.20 AM.png]

What brought me to wanting to know the ontology a term comes from was
wanting to make the above tooltip say "Chlorophyll-a Concentration is
defined as.... in the *ECSO* ontology as..." but, in a few cases for other
ontologies, the term is found in a more popular ontology than the ontology
of origin and I don't have a way with the current API response to determine
which. A specific example is searching for
http://purl.obolibrary.org/obo/UO_0000301 which returns a hit from the EFO
ontology before the UO ontology. See
https://data.bioontology.org/search?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000301&apikey=5c385237-ec28-4ef6-8ba1-f5bcfb752142
.

This isn't a deal breaker at all for us and I totally understand the need
to prioritize. Let me know if you have any questions or would like to chat
more about what we're doing. The BioPortal API has been a huge help in
bootstrapping the above and other parts of our implementation.
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