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[bioontology-support] metadata treeview error message

Pete Rivett pete.rivett at adaptive.com
Thu Mar 14 03:01:42 PDT 2019


Helen,
The message means you've used a namespace prefix "metadata:" without defining it. For example at line 253 you have:
        <metadata:treeView rdf:resource="http://www.lungmap.net/ontologies/human_anatomy#LMHA0000000211"/>

To fix it, add the following line in the block of namespace definitions, e.g. line 14:
     xmlns:metadata="http://data.bioontology.org/metadata/"

It then seemed to load OK into Protégé (I'm on 5.2).

Pete


Pete  Rivett (pete.rivett at adaptive.com<mailto:pete.rivett at adaptive.com>)
CTO, Adaptive Inc
65 Enterprise, Aliso Viejo, CA 92656
cell: +1 949 338 3794
Follow me on Twitter @rivettp or http://twitter.com/rivettp





From: bioontology-support <bioontology-support-bounces at lists.stanford.edu> On Behalf Of Pan, Huaqin (Helen)
Sent: Wednesday, March 13, 2019 8:40 PM
To: John Graybeal <jgraybeal at stanford.edu>
Cc: support at bioontology.org
Subject: [bioontology-support] metadata treeview error message

Hi John,

I got an error message "The prefix "metadata" for element "metadata:treeView" is not bound" when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

Thank you for your help!

Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Saturday, March 24, 2018 5:51 PM
To: 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] problem with ontology submission - please help!

Helen,

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

Thanks,

John

[1]  Results of submission:

Thank you for submitting your ontology to BioPortal.
We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.
When your ontology is ready for viewing, it will be available here:
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at support at bioontology.org<mailto:support at bioontology.org>

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hello,

Hello, I tried several times to submit an ontology:

initial submission always got
<image002.jpg>
Another try always got
<image004.jpg>

It repeats that when I tried different name/acronyms on different web browsers.

Would you please help me create the ontology?
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy

Owl is attached.

Thanks!
Helen


<Human_bioportal.owl>_______________________________________________
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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632

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