term ids

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term ids

Cynthia Grondin

Hi, 


Our group currently has an ontology containing 81 terms with sequential ids (e.g. ExO:0000001 - ExO:0000081) registered with the OBO Foundry and uploaded to Github.  These appear to be OBO ids.  We’ve updated the ontology in Protégé to include 67 new terms, and ids were automatically generated,  (e.g. id: OWLClass_f77c921c_654c_4ab9_a50d_083637e05482).  How can we change these new ids to continue sequentially from where the original ones left off?  In other words, is it possible to assign OBO ids to these terms that will continue sequentially from the original term ids, or can we reassign OWL ids to the original terms so that everything is consistent?


Thanks,


Cindy



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Re: term ids

Chris Mungall-2
Hi Cindy,

We have some instructions on setting up Protege to add IDs your ID
range. This is relatively straightforward (provided you don't need to
switch between ontologies)
https://github.com/Planteome/protege-tutorial/blob/master/presentations/protege_planteome_tutorial.doc?raw=true

We also recommend that each curator get an ID range. I'm not sure if you
managed to have success with the ontology starter kit, but this
auto-generated curator documentation and the relevant files:
https://github.com/cmungall/ontology-starter-kit/blob/master/template/src/ontology/README-editors.md

For mapping existing IDs, this may have to be done programmatically. The
quick and hacky way is to dump the list of temp IDs and make a perl
regular expression that will switch everything. It should be fairly easy
for a programmer to do this without knowing anything about the
complexities of OWL encoding.

Also, just a note about OBO and OWL ids. There isn't really such a thing
as OWL ids per se. In OWL, everything is identified by a URI. So in
exo.owl, your classes are identifier by URLs like
http://purl.obolibrary.org/obo/ExO_0000013 - when this is converted to
OBO the ID will be ExO:0000013

(confusingly, the owl to obo conversion injects an additional
oboInOwl#id property, but this can be ignored)

On 27 Oct 2016, at 13:16, Cynthia Grondin wrote:

> Hi,
>
> Our group currently has an ontology containing 81 terms with
> sequential ids
> (e.g. ExO:0000001 - ExO:0000081) registered with the OBO Foundry and
> uploaded to Github.  These appear to be OBO ids.  We’ve updated the
> ontology in Protégé to include 67 new terms, and ids were
> automatically
> generated,  (e.g. id: OWLClass_f77c921c_654c_4ab9_a50d_083637e05482).  
> How
> can we change these new ids to continue sequentially from where the
> original ones left off?  In other words, is it possible to assign OBO
> ids
> to these terms that will continue sequentially from the original term
> ids,
> or can we reassign OWL ids to the original terms so that everything is
> consistent?
>
> Thanks,
>
> Cindy
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: term ids

Cynthia Grondin
Thanks, Chris.  I will check out the tutorial link you provide above.  I will also read the starter kit documentation, though I don't have a Mac, so I was under the impression that I wouldn't be able to use the starter kit.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cynthia J. Grondin, PhD
Biocurator
Comparative Toxicogenomics Database
http://ctdbase.org


On Thu, Oct 27, 2016 at 4:52 PM, Chris Mungall <[hidden email]> wrote:
Hi Cindy,

We have some instructions on setting up Protege to add IDs your ID range. This is relatively straightforward (provided you don't need to switch between ontologies)
https://github.com/Planteome/protege-tutorial/blob/master/presentations/protege_planteome_tutorial.doc?raw=true

We also recommend that each curator get an ID range. I'm not sure if you managed to have success with the ontology starter kit, but this auto-generated curator documentation and the relevant files:
https://github.com/cmungall/ontology-starter-kit/blob/master/template/src/ontology/README-editors.md

For mapping existing IDs, this may have to be done programmatically. The quick and hacky way is to dump the list of temp IDs and make a perl regular expression that will switch everything. It should be fairly easy for a programmer to do this without knowing anything about the complexities of OWL encoding.

Also, just a note about OBO and OWL ids. There isn't really such a thing as OWL ids per se. In OWL, everything is identified by a URI. So in exo.owl, your classes are identifier by URLs like http://purl.obolibrary.org/obo/ExO_0000013 - when this is converted to OBO the ID will be ExO:0000013

(confusingly, the owl to obo conversion injects an additional oboInOwl#id property, but this can be ignored)


On 27 Oct 2016, at 13:16, Cynthia Grondin wrote:

Hi,

Our group currently has an ontology containing 81 terms with sequential ids
(e.g. ExO:0000001 - ExO:0000081) registered with the OBO Foundry and
uploaded to Github.  These appear to be OBO ids.  We’ve updated the
ontology in Protégé to include 67 new terms, and ids were automatically
generated,  (e.g. id: OWLClass_f77c921c_654c_4ab9_a50d_083637e05482).  How
can we change these new ids to continue sequentially from where the
original ones left off?  In other words, is it possible to assign OBO ids
to these terms that will continue sequentially from the original term ids,
or can we reassign OWL ids to the original terms so that everything is
consistent?

Thanks,

Cindy
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


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[hidden email]
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