Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Help with Submission

Jennifer Leigh Vendetti vendetti at
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="">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=""><a href="">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:

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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: phenx.diff
Type: application/octet-stream
Size: 15464 bytes
Desc: phenx.diff
URL: <>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the bioontology-support mailing list