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

Hong Sun hong.sun at agfa.com
Thu Mar 7 01:41:30 PST 2013


Hi Manuel, 

Thank you very much for your detailed explanations! I now have a much 
better understanding, and yet still a few questions would like to check 
with you concerning the matching. 

First, in my last email, I mentioned that Is it possible to add 
skos:inScheme for instances like below? 
You can open the URL I enclosed, the query I executed is : 
Query1: 
PREFIX maps: <
http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#> 
SELECT * 
FROM <http://bioportal.bioontology.org/ontologies/ICD10> 
WHERE { 
   <http://purl.bioontology.org/ontology/ICD10/I21> ?p ?o } 
I am wondering it would be nice to have a skos:inScheme property for this 
instance, is it possible to add? 

Second, a few questions concerning mapping. 
1. 
Your answer below well explained my question, 
"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), ..." 
I get the explanation from the web page: 

<Mail Attachment.gif> 
I found the graph name is implicitly stated in each mapping instance, 
e.g. a mapping instance <
http://purl.bioontology.org/mapping/umls_cui/9edef869c7003a554b6e0a59547c451b
> tells it is from umls_cui graph. 
Is there any explicit way to retrieve the mapping type in the above table? 

Is it possible to add a property in the mapping ontology to 
directly/explicitly state these different mapping types? 

2. I queried the following query at the endpoint, 
Query2: 
PREFIX map: <
http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#> 
SELECT * WHERE { 
      ?m map:source <http://purl.bioontology.org/ontology/ICD10/I21> ; 
             map:target  <
http://purl.bioontology.org/ontology/SNOMEDCT/194796000> . 
  ?m ?p ?o. 
} 

I get a triple 
<
http://purl.bioontology.org/mapping/umls_cui/9edef869c7003a554b6e0a59547c451b
>         <
http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#dependency> 
        <
http://purl.bioontology.org/mapping/umls_cui/7f5ffe5eb1e0db2536db9bf810ac6c55
> 
What does <
http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#dependency> 
mean? 

3. I found that in the published mapping ontology 
http://protege.stanford.edu/ontologies/mappings/mappings.rdfs# 
there are many interesting properties, like mappings:confidence 
mappings:authority mappings:verified mappings:submittedBy 
mappings:verified_by 
query these properties in the endpoint does not return any result yet, 
would they be supported in the later versions? 

4. I found there are some inconsistence with the ontologies among the 
published ontology, 
http://protege.stanford.edu/ontologies/mappings/mappings.rdfs# 
introduction webpage,  
http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal#mappings 
and the endpoint. 

e.g. 
in the introduction web page, there is a mapping instance 
@prefix maps: <
http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#> .

<http://purl.bioontology.org/mapping/2767e8e0-001b-012e-749f-005056bd0010>
   maps:has_process_info <.../procinfo/2008-04-23-38138> ;
   maps:comment "Manual mappings between Mouse anatomy and NCIT." ;
   maps:relation skos:closeMatch ;
   maps:target <http://purl.org/obo/owl/MA#MA_0001096> ;
   maps:source <
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Olfactory_Nerve> ;
   maps:source_ontology_id <
http://bioportal.bioontology.org/ontologies/1032> ;
   maps:target_ontology_id <
http://bioportal.bioontology.org/ontologies/1000> ;
   a maps:One_To_One_Mapping . 

It uses maps:source_ontology_id 

In the endpoint, it uses mappings:target_ontology 
e.g. below is a triple returned from Query2 
<http://purl.bioontology.org/mapping/loom/9edef869c7003a554b6e0a59547c451b
>         <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#
target_ontology>         <http://bioportal.bioontology.org/ontologies/1353
> 

And in the published ontology 
http://protege.stanford.edu/ontologies/mappings/mappings.rdfs# 
neither maps:source_ontology_id nor mappings:target_ontology  is mentioned 
as a property. 

Again, thank you very much for your kind help! 

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 



From:   manuelso <manuelso at stanford.edu>
To:     Hong Sun/AXIFX/AGFA at AGFA
Cc:     "support at bioontology.org Support" <support at bioontology.org>
Date:   02/20/2013 07:26 PM
Subject:        Re: A few questions on Bioportal Sparql Endpoint



(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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