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[bioontology-support] Missing metrics in HORD ontology

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Aug 17 18:06:41 PDT 2017


Hi Laia,

You’re including the ORDO ontology, which doesn’t parse in BioPortal at the moment. Unfortunately, the problem is a bug in the OWL API, which is 3rd party software that we use to load / parse ontologies. I’ve been corresponding with the developer of the OWL API and he has released a bug fix version that may address the problem with ORDO. I plan to integrate this new version of the OWL API into BioPortal, but haven’t been able to get to it yet due to some other work that is higher priority at the moment.

I apologize that I don’t have an exact date for you when the problem with ORDO will be resolved, but it should be in the near future.

Kind regards,
Jennifer



On Aug 17, 2017, at 3:32 AM, Laia Subirats <laia.subirats at gmail.com<mailto:laia.subirats at gmail.com>> wrote:

Dear Jennifer,

I would like to ask you help about this issue. I am still lost about how can I solve this error.

Best,

Laia

On Tue, Aug 8, 2017 at 1:00 PM, Laia Subirats <laia.subirats at gmail.com<mailto:laia.subirats at gmail.com>> wrote:
Hello Jennifer,

I change the imports. I uploaded the external ontologies in my Github webpage and pointed my ontology to them. I also changed the unamed.owl import.

However, now I have this error: "(Uploaded, Error Rdf)".

I have uploaded to webprotege and it works properly, and in my local Protégé as well.

Sorry for making you spend time helping me.

Best,

Laia
On Mon, Aug 7, 2017 at 6:46 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
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”/<http://data.bioontology.org/ontologies/ORDO/submissions/11/download?apikey=eb8ef13c-ae88-42a5-b6f5-39c93d736688%E2%80%9D/>>

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:


<Screenshot 2017-08-07 09.20.54.png><Screenshot 2017-08-07 09.21.22.png>



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



--
Laia Subirats
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--
Laia Subirats



--
Laia Subirats

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