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] Missing metrics in HORD ontology

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Aug 7 09:46:53 PDT 2017


Hello Laia,

I looked at your latest ontology source file (HORD_all_2017_08_07_scenarios.owl). There are still a number of problems with the import statements.

1). It’s not valid to use a BioPortal REST API call as a download URL for the location of an ontology that you’d like to import. The import statements on lines 21 and 23 in your ontology file will result in not found errors:

<owl:imports rdf:resource="http://data.bioontology.org/ontologies/ICF/submissions/3/download?apikey=eb8ef13c-ae88-42a5-b6f5-39c93d736688"/>
…
<owl:imports rdf:resource="http://data.bioontology.org/ontologies/ORDO/submissions/11/download?apikey=eb8ef13c-ae88-42a5-b6f5-39c93d736688”/>

This is true not only for BioPortal, but for other ontology editing environments as well. If I open your ontology in the Protege ontology editing environment [1], you will see errors for both of those imports:


[cid:F229D349-E469-46E9-A15B-5D1CC5550BFA at stanford.edu][cid:27C78D6C-8B9A-4ADD-8CD1-A07D94EB0713 at stanford.edu]



2). Line 26 contains another invalid import statement:

<owl:imports rdf:resource="http://www.owl-ontologies.com/unnamed.owl"/>

… which has a URL that doesn’t resolve to anything.

Kind regards,
Jennifer

[1] http://protege.stanford.edu/products.php



On Aug 6, 2017, at 10:21 PM, Laia Subirats <laia.subirats at gmail.com<mailto:laia.subirats at gmail.com>> wrote:

Hi John,

I changed the references and now there is not a parsing problem anymore. However, the metrics do not appear.

Cheers,

Laia Subirats
On Mon, Aug 7, 2017 at 1:40 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:
Hi Laia,

Sorry for the trouble you are having.  Usually that message indicates there has been a problem parsing the ontology, and you can try verifying the ontology parses with Protege or WebProtege as a next step.

In this case, a quick look at the error log indicated two issues:
* "OWL_IMPORT_MISSING: http://who.int/icf"
* "OWL_IMPORT_MISSING: http://www.orpha.net/version2.4"

A quick suggestion (sorry, no time today to verify myself) is to check to confirm that those two ontologies are indeed at those locations, and if they are not, change the references in the source ontology to point to correct locations.

If you are still having trouble after that, please send another note indicating your latest understanding, and our team will try to help. Thanks.

John


On Aug 5, 2017, at 9:52 PM, Laia Subirats <laia.subirats at gmail.com<mailto:laia.subirats at gmail.com>> wrote:

Dear Sir/Madam,

I would like to see the metrics of my ontology in http://bioportal.bioontology.org/ontologies/HORD<http://bioportal.bioontology.org/ontologies/PMR>, I do not know if there is any problem. I see that there is a "(Uploaded, Error Rdf)" but I do not see the problem.

Yours faithfully,
--
Laia Subirats
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research



--
Laia Subirats
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20170807/c43f033b/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2017-08-07 09.20.54.png
Type: image/png
Size: 37932 bytes
Desc: Screenshot 2017-08-07 09.20.54.png
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20170807/c43f033b/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2017-08-07 09.21.22.png
Type: image/png
Size: 39093 bytes
Desc: Screenshot 2017-08-07 09.21.22.png
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20170807/c43f033b/attachment-0003.png>


More information about the bioontology-support mailing list