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[bioontology-support] LOOM for custom use

Erik Fäßler erik.faessler at uni-jena.de
Tue Jan 31 23:05:48 PST 2017


Hi John,

I’ll have a look into it, thanks a lot!

Best,

Erik

> On 01 Feb 2017, at 03:02, John Graybeal <jgraybeal at stanford.edu> wrote:
> 
> Sorry, Erik, it appears that's the code that instantiates the mappings.  I obtained a more accurate answer from one of the extended team:
> 
>> This is the ruby method that does the literal transformation that we use to generate loom labels.
>> 
>> https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/models/ontology_submission.rb#L1271
>> 
>> Also we only generate loom literales when the length after the transformation is 3 or more characters:
>> 
>> https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/models/ontology_submission.rb#L565
>> 
>> I hope this helps,
>> Manuel
> 
> 
>> On Jan 31, 2017, at 12:16 PM, John Graybeal <jgraybeal at stanford.edu> wrote:
>> 
>> Hello Erik,
>> 
>> Please have a look at the bioportal_mappings repository in the NCBO github project: https://github.com/ncbo/bioportal_mappings. In particular, https://github.com/ncbo/bioportal_mappings/blob/master/src/main/java/org/ncbo/stanford/mappings/LoomMappings.java seems to have the source code for the LOOM mapping generation.
>> 
>> I just looked at the repository quickly, so let me know if you have trouble accessing or this is not what you want. It seems that this repository has all the code related to LOOM mappings, based on a search for LOOM.
>> 
>> John
>> 
>>> On Jan 30, 2017, at 7:06 AM, Erik Fäßler <erik.faessler at uni-jena.de> wrote:
>>> 
>>> Dear support team,
>>> 
>>> I would be interested to use the LOOM ontology mapping algorithm for a custom use. More specifically, I am interested in a mapping between MeSH headings and NCBI Gene or UniProt database entries (if someone knows a respective resource I would be delighted to learn about it!).
>>> I did not manage to find a LOOM distribution or even a web service that I could use for this. There is also seemingly no code for it on your GitHub page. Is it published in a way I could use it on my own?
>>> 
>>> Thanks!
>>> 
>>> Erik
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> 
>> ========================
>> John Graybeal
>> Technical Program Manager
>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>> Stanford Center for Biomedical Informatics Research
>> 650-736-1632  
>> skype: graybealski
>> 
>> 
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
> ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 650-736-1632  
> skype: graybealski
> 
> 



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