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[bioontology-support] Downloading Mappings in Bulk

John Graybeal jgraybeal at stanford.edu
Wed Feb 1 09:57:14 PST 2017


I'm a little unclear about which mappings you will find at the SPARQL endpoint for BIoPortal, but if this post is correct, it could work for you. But you'd still have to iterate over all the ontologies:
    https://github.com/agroportal/documentation/wiki/Mappings 

Note that we haven't updated the content in the Beta SPARQL endpoint for some time, hopefully will get to do that soon.

John


> On Jan 31, 2017, at 11:09 PM, Erik Fäßler <erik.faessler at uni-jena.de> wrote:
> 
> Hi again,
> 
> I understand and I sympathise with the challenge you have there (data scaling is always bigger an issue than is initially expected…).
> I will just continue to use the REST API, then.
> Or could it be worthwhile to have a look at the SPARQL endpoint? Could it, by any chance, be quicker than the REST API?
> 
> Best,
> 
> Erik
> 
>> On 01 Feb 2017, at 03:28, John Graybeal <jgraybeal at stanford.edu> wrote:
>> 
>> Hello Erik,
>> 
>>> Is there a way to get some kind of mapping files, containing many mappings in one large chunk? 
>> 
>> 
>> I'm afraid the short answer is 'no'. Again with input from Manuel: 
>> 
>> The syntactic mappings of type LOOM and CUI do not live anywhere, they are generated at query time (on the fly) using the mapping LOOM predicate (for LOOM mappings) or the CUI predicates (for CUI mappings). You cannot get a dump unless you traverse all ontologies and request them with the API or the SPARQL queries implemented in the API. 
>> 
>> At some point the materialized version of LOOM and CUI mappings was growing so quickly that we decided to make this change.
>> 
>> The REST mappings are indexed in 4store (our backend) because they are submitted by users and we cannot implement queries that generate these on the fly.
>> 
>> I appreciate your interest in this, and it would seem advantages. With BioPortal having over 33.7 million mappings, I think we would have to implement a batch job to run at user request (with user credentials), then post the results to an FTP site or similar. It wouldn't be a trivial thing, sorry to say.
>> 
>> John
>> 
>> 
>>> 
>>> On Jan 26, 2017, at 1:48 AM, Erik Fäßler <erik.faessler at uni-jena.de> wrote:
>>> 
>>> Dear Bio-Ontologies Team,
>>> 
>>> I have been downloading and extracting class names from the original ontology files, circumventing the classes/ endpoint, thanks to your help.
>>> 
>>> Now I’d also be interested into the mappings. Currently, I still use the REST API to get the mappings. This causes a lot of paging on your side and slows things done significantly for ontologies with many mappings.
>>> Is there a way to get some kind of mapping files, containing many mappings in one large chunk? This would speed up downloading for me, avoid gateway timeouts, which I experienced in the past, and probably even reduce the load on your servers. Is there a good way?
>>> 
>>> Best,
>>> 
>>> 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
>> 
>> 
> 

========================
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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