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

Pan, Huaqin (Helen) hpan at rti.org
Mon Jan 22 13:59:27 PST 2018


Hi Jennifer,

I am working on another project that developed an ontology that I will submit soon. It’s currently available at our project site, https://lungmap.net/breath-ontology-browser/.

Here is my questions. Due to the fact that owl/Protégé display the hierarchical relation only for “subclass-of”, not “part-of”, I have developed 2 versions of the ontology in .owl for each ontology, and I need your guidance on which version to submit. I have seen both on BioPortal.

  *   Version 1 with exclusive “subclass_of” – Pros: display the hierarchical relationships among the classes, Cons: lacks the biological distinction of “part-of” and “subclass_of”
  *   Version 2 with mix of “part-of” and “subclass_of” – Cons: lacks the display of hierarchical relationships among the classes, Pros: captures the biological distinction of “part-of” and “subclass_of”

We used version 2 (part-of and subclass-of) for the project site, with some rules to enable the display properly for “part-of”.

Best regards,
Helen

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Tuesday, March 29, 2016 3:17 PM
To: Pan, Huaqin (Helen) <hpan at rti.org>
Cc: Qin, Ying <yingqin at rti.org>; NCBO User Support <support at bioontology.org>
Subject: Re: [bioontology-support] Help with Submission

Hi Helen,

I uploaded the new version of the ontology that you attached.  It’s now available in BioPortal:

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

Best,
Jennifer


On Mar 29, 2016, at 6:55 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I reviewed the current version at bioportal and found a handful of classes missing subclass relation. I attached an updated owl. Would you please help loading this version to replace the existing one?

Many thanks!
Helen

From: Pan, Huaqin (Helen)
Sent: Tuesday, March 29, 2016 9:31 AM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: Qin, Ying <yingqin at rti.org<mailto:yingqin at rti.org>>
Subject: RE: [bioontology-support] Help with Submission

Hi Jennifer,

I replied too soon ☺ As I read through the end of email, I realized that you have already fixed the syntax errors and uploaded the file for us. I appreciate your help!

Best regards,
Helen

From: Pan, Huaqin (Helen)
Sent: Tuesday, March 29, 2016 9:01 AM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: Qin, Ying <yingqin at rti.org<mailto:yingqin at rti.org>>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] Help with Submission

Hi Jennifer,

I will look into the error messages you summarized, update and test in Protégé, and upload.

Thank you for your help!

Best,
Helen

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Monday, March 28, 2016 7:57 PM
To: Qin, Ying <yingqin at rti.org<mailto:yingqin at rti.org>>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Help with Submission

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


<phenXOnto_v1_0.owl>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20180122/9b5f9695/attachment-0001.html>


More information about the bioontology-support mailing list