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[bioontology-support] A few questions on Bioportal Sparql Endpoint

manuelso manuelso at stanford.edu
Wed Feb 20 10:26:34 PST 2013


(Hong Sun kindly agreed to have this response sent to the support list)

Hi Hong,

See inlined answers below ...

On Feb 18, 2013, at 8:53 AM, Hong Sun <hong.sun at agfa.com> wrote:

> This is Hong Sun, I am a researcher working on AGFA healthcare researching the semantic web in clinical domain. 
> I have read your paper: BioPortal as a Dataset of Linked Biomedical Ontologies and Terminologies in RDF, 
> and practiced your BioPortal SPARQL endpoint. It is great to have such a place where you can query different terminology and the mappings among them. 

Thanks!

> 
> I have three questions would like to check with you: 
> 1. As most properties in the endpoint uses SKOS properties, why do you chose the rdfs:subClassOf, instead of skos:broader, to represent the hierarchy?

The ontologies that BioPortal hosts have been mostly developed by other institutions.  It is the author's choice to use rdfs:subClassOf to represent the hierarchy. At the moment BioPortal only supports rdfs:subClassOf and that is why you probably will not see that many SKOS relations in the SPARQL endpoint. We are going to support SKOS very soon and that will probably change.

> 2. As the typed literals for skos:notation are stated as "best practice" of SKOS, is it possible to use typed literal to represent notation? 

We generate some skos:notation predicates but not all of them. The ones we generate are typed, we do not have control over the literals generated by others.

Our Web frontend (sparql.bioontology.org) hides the literal types, so probably you cannot see them there. If you query the endpoint programmatically you'll be able to see the literal typed.

Some example here: https://github.com/ncbo/sparql-code-examples

> 
> 3. As the mappings between different terminologies are submitted by different people, to which extent can I trust the mapping? 

Every mapping has its process/provenance information. You can look at that metadata and decide how much you can trust a single mapping or a collection of mappings--it is up to you or the application. Here there is a table with the types of mappings we host (http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal#mappings) .  REST mappings are submitted by users, CUI mappings are released with the UMLS database and are human-curated, LOOM are lexical mappings (terms with equals labels/synonyms), ...

> 
> 4. Is it possible to add skos:inScheme for instances like below? 
> http://sparql.bioontology.org/?query=PREFIX+maps%3A+%3Chttp%3A%2F%2Fprotege.stanford.edu%2Fontologies%2Fmappings%2Fmappings.rdfs%23%3E%0D%0ASELECT+*+%0D%0AFROM+%3Chttp%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FICD10%3E%0D%0AWHERE+%7B%0D%0A+++%3Chttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICD10%2FI21%3E+%3Fp+%3Fo+%7D&kboption=ontologies&csrfmiddlewaretoken=3d749d07c0ac5d0a0bff52fdcae2c04e 
> 

Sorry I cannot see the query there … can you copy & paste the query in an email.

Good questions! and thanks for the feedback.

Manuel


> Thank you very much in advance! 
> 
> Kind Regards,
> 
> Hong Sun | Agfa HealthCare
> Researcher | HE/Advanced Clinical Applications Research
> T  +32 3444 8108
> 
> http://www.agfahealthcare.com
> http://blog.agfahealthcare.com
> Click on link to read important disclaimer: http://www.agfahealthcare.com/maildisclaimer

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