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[bioontology-support] [BioPortal] Feedback from VJHenry

John Graybeal jgraybeal at stanford.edu
Sun Apr 19 13:41:56 PDT 2020


Hi Vincent,

Here are some quick replies for now, please respond with whatever issues remain.

- the creation of "BiPOm-RPCC-instanciated" (https://bioportal.bioontology.org/ontologies/BIPOM-INST)

If you are asking to have this deleted, we can do that. Please confirm that is what you want.

- the description of "BiPOm inferences for Calvin cycle" (https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed instead of following

Descriptions can be modified by you; click on the pencil icon to edit the ontology metadata (at upper right) or the submission metadata (above the submission list).

- the acronym of "BiPOm E-Coli metabolism instantiation" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) BIPOM-ECMET-INST instead of BIPOM-ECMET-INF
and the the acronym of "BiPOm inferences for E-Coli metabolism" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF.

Acronyms can not be changed they are the index for everything in the system. To make this happen, you will need to re-submit your ontology(ies) under the new acronym you want to use, then tell us to delete the original ontology(ies). Unfortunately the history will be lost.

Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ?

I don't have time to look at the details at this moment, but the best way to figure this out is to try loading the ontology in Protege. If it is not parseable in BioPortal (which is what this indicates), it is almost always not parseable in Protege, for the same reasons because they use the same parser. And Protege actually shows you the errors, which makes it a much better tool for finding and fixing issues.

Hope this helps!

John


On Apr 18, 2020, at 6:25 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: VJHenry

Email: vincent643 at gmail.com<mailto:vincent643 at gmail.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FBIPOM-CC-INF

Feedback:

Hi,
I'm wondering if its possible to change some mistakes I made:
- the creation of "BiPOm-RPCC-instanciated" (https://bioportal.bioontology.org/ontologies/BIPOM-INST)
- the description of "BiPOm inferences for Calvin cycle" (https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed instead of following
- the acronym of "BiPOm E-Coli metabolism instantiation" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) BIPOM-ECMET-INST instead of BIPOM-ECMET-INF
and the the acronym of "BiPOm inferences for E-Coli metabolism" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF.

Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ?

Thank you very much for all,
Best regards,
Vincent (VJHenry; vincent643 at gmail.com<mailto:vincent643 at gmail.com>)

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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  | ORCID  0000-0001-6875-5360



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