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[bioontology-support] omeprazole

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue May 24 12:23:41 PDT 2016


Hi Alexander,


On May 23, 2016, at 10:57 AM, Alexander Garcia Castro <alexgarciac at gmail.com<mailto:alexgarciac at gmail.com>> wrote:

Hi Jennifer, I am not complaining about the ncbo annotator, it works. I am complaining about the ontologies. the ncbo works as advertised, the ontologies are the ones making it hard.


I’m sorry about your frustration regarding some of the ontology content in BioPortal.  We’re always open to suggestions from our user community on how to make BioPortal better.

Currently there are 516 ontologies with just over 8 million classes in our system.  It’s not feasible based on our current level of staffing to manually curate a dataset of this size.  From a computational standpoint, I’m aware of tools like the OOPS! (OntOlogy Pitfall Scanner!) REST service [1], but there doesn’t appear to be a de facto standard in the ontology community for highlighting quality issues.  Perhaps because determining what makes an ontology good or bad is somewhat subjective.

I looked at the Protege & WebProtege ontology editors as potential guides for integrating ontology quality plug-ins into BioPortal, but their software doesn’t include any services of this nature either.

It’s worth mentioning that we offer a review system in BioPortal where users can rate several aspects of a given ontology, including quality, usability, coverage, formality, correctness, and documentation.  Although admittedly, this system has not been widely used/adopted by BioPortal users.

Jennifer


[1] http://oops-ws.oeg-upm.net/


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