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[bioontology-support] Help with Submission

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Mar 28 16:57:24 PDT 2016


Hello Ying Qin,

I’ve had a chance to look at your ontology in detail and have some information for you about why it didn’t load in BioPortal.  There were a number of syntax errors in your ontology, i.e.:

1).  Unescaped embedded HTML.  If you want to embed HTML in your ontology, you need to either escape the HTML, or use the XML Literal parse type.  For example, the following is valid because the parse type is Literal:

<Definition rdf:parseType="Literal"><a href="http://www.phenxtoolkit.org/toolkit_content/supplemental_info/anthropometrics/additional_info/Body_Composition_Guidance.doc">Body Composition Guidance</a></Definition>

… and the following is also valid because the parse type is string, but the HTML is properly escaped:

<Definition rdf:datatype="http://www.w3.org/2001/XMLSchema#string"><a href="http://www.phenxtoolkit.org/toolkit_content/supplemental_info/anthropometrics/additional_info/Body_Composition_Guidance.doc">Body Composition Guidance</a></Definition>

2).  The ® and — entities were undeclared.

3).  There were unescaped ampersands.

I took the liberty of fixing these errors and re-submitted your ontology to BioPortal, which uploaded and parsed successfully:

http://bioportal.bioontology.org/ontologies/PHENX

If you want to see the exact edits I made to the OWL file, I’ve attached a diff (generated by the git version control system).

For future submissions of your ontology to be successful, you’ll need to incorporate these fixes.  On a related note, I’m wondering how you are generating your ontology file?  These sorts of syntax errors generally aren’t present if you’re using one of the popular ontology editing tools like Protege to maintain your ontology.

Best,
Jennifer


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