[bioontology-support] Question about migrating ontologies from BioPortal to local VM

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[bioontology-support] Question about migrating ontologies from BioPortal to local VM

Koo, Jahoon

Hi BioPortal,

 

This is Jahoon, a student worker from Health Data Compass.

 

I have installed the virtual appliance and tried to migrate ontologies from BioPortal to the VM using the Ruby script provided.

It seems like many ontologies migrated have missing classes. On the UI, they have “no submission available”.

 

I have checked if my ontologies have fully parsed in the virtual appliance by following the instruction on your wiki:

https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#How_do_I_know_if_an_ontology_has_parsed.3F

I am currently using this URL: http://{your_appliance_ip_or_domain_name}:8080/ontologies/{ontology_acronym}/latest_submission?include=all to check parsing status.

I have migrated FB-CV ontology, and the submission status of FB-CV ontology is “Uploaded” at the REST service. However, when I click any other links, such as properties, classes, single class, etc, it has an error below.

 

·        errors": [

o   "Ontology FB-CV submission not found."

],

·        "status": 404

I have cleared the memcached-based UI cache, but it wasn’t helpful.

 

I also have checked parsing.log file in /srv/ncbo/repository/{ontology acronym}. It says,

“Starting to process http://data.bioontology.org /ontologies/FB-CV/submissions/8”

“Pull location found, but no file in the upload file path”

 

What should I do to fix this migration issue?

 

Respectfully,

Jahoon


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Re: [bioontology-support] Question about migrating ontologies from BioPortal to local VM

jvendetti
Hello Jahoon,

I looked at the ontology you mentioned below (FB-CV). It appears that it's configured in our production system to pull new versions from this URL:


However, this URL is no longer valid (results in a 404 error). This is why you see an error message in the parsing log file about “no file in the upload file path”. You could try contacting the ontology author to see if they have an updated URL for pulling new versions. Their contact information is available on the ontology summary page: http://bioportal.bioontology.org/ontologies/FB-CV. Alternatively, if you want to get this ontology into your appliance quickly, you could manually download the OWL file from our production site and upload it via your appliance UI.

I also noticed a GitHub repository that appears to be related:


It’s unclear to me which of their ontology entries maps to the dpo.owl file they originally entered in BioPortal.

If you can provide more specifics about the other ontologies you’re having trouble with, we can try to help further.

Kind regards,
Jennifer



On Feb 7, 2020, at 3:02 PM, Koo, Jahoon <[hidden email]> wrote:

Hi BioPortal,
 
This is Jahoon, a student worker from Health Data Compass.
 
I have installed the virtual appliance and tried to migrate ontologies from BioPortal to the VM using the Ruby script provided.
It seems like many ontologies migrated have missing classes. On the UI, they have “no submission available”.
 
I have checked if my ontologies have fully parsed in the virtual appliance by following the instruction on your wiki:
I am currently using this URL: <a href="http://{your_appliance_ip_or_domain_name}:8080/ontologies/%7bontology_acronym%7d/latest_submission?include=all" style="color: rgb(5, 99, 193); text-decoration: underline;" class="">http://{your_appliance_ip_or_domain_name}:8080/ontologies/{ontology_acronym}/latest_submission?include=all to check parsing status.
I have migrated FB-CV ontology, and the submission status of FB-CV ontology is “Uploaded” at the REST service. However, when I click any other links, such as properties, classes, single class, etc, it has an error below.
 
·        errors": [
o   "Ontology FB-CV submission not found."
],
·        "status": 404
I have cleared the memcached-based UI cache, but it wasn’t helpful.
 
I also have checked parsing.log file in /srv/ncbo/repository/{ontology acronym}. It says,
“Starting to process http://data.bioontology.org /ontologies/FB-CV/submissions/8”
“Pull location found, but no file in the upload file path”
 
What should I do to fix this migration issue? 
 
Respectfully,
Jahoon
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https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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Re: [bioontology-support] Question about migrating ontologies from BioPortal to local VM

jvendetti
One more thing to note here - I went ahead and entered an issue in their GitHub tracker to see if they can give us an updated pull URL:


Jennifer



On Feb 7, 2020, at 3:48 PM, Jennifer Leigh Vendetti <[hidden email]> wrote:

Hello Jahoon,

I looked at the ontology you mentioned below (FB-CV). It appears that it's configured in our production system to pull new versions from this URL:


However, this URL is no longer valid (results in a 404 error). This is why you see an error message in the parsing log file about “no file in the upload file path”. You could try contacting the ontology author to see if they have an updated URL for pulling new versions. Their contact information is available on the ontology summary page: http://bioportal.bioontology.org/ontologies/FB-CV. Alternatively, if you want to get this ontology into your appliance quickly, you could manually download the OWL file from our production site and upload it via your appliance UI.

I also noticed a GitHub repository that appears to be related:


It’s unclear to me which of their ontology entries maps to the dpo.owl file they originally entered in BioPortal.

If you can provide more specifics about the other ontologies you’re having trouble with, we can try to help further.

Kind regards,
Jennifer



On Feb 7, 2020, at 3:02 PM, Koo, Jahoon <[hidden email]> wrote:

Hi BioPortal,
 
This is Jahoon, a student worker from Health Data Compass.
 
I have installed the virtual appliance and tried to migrate ontologies from BioPortal to the VM using the Ruby script provided.
It seems like many ontologies migrated have missing classes. On the UI, they have “no submission available”.
 
I have checked if my ontologies have fully parsed in the virtual appliance by following the instruction on your wiki:
I am currently using this URL: <a href="http://{your_appliance_ip_or_domain_name}:8080/ontologies/%7bontology_acronym%7d/latest_submission?include=all" style="color: rgb(5, 99, 193); text-decoration: underline;" class="">http://{your_appliance_ip_or_domain_name}:8080/ontologies/{ontology_acronym}/latest_submission?include=all to check parsing status.
I have migrated FB-CV ontology, and the submission status of FB-CV ontology is “Uploaded” at the REST service. However, when I click any other links, such as properties, classes, single class, etc, it has an error below.
 
·        errors": [
o   "Ontology FB-CV submission not found."
],
·        "status": 404
I have cleared the memcached-based UI cache, but it wasn’t helpful.
 
I also have checked parsing.log file in /srv/ncbo/repository/{ontology acronym}. It says,
“Starting to process http://data.bioontology.org /ontologies/FB-CV/submissions/8”
“Pull location found, but no file in the upload file path”
 
What should I do to fix this migration issue? 
 
Respectfully,
Jahoon
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support