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[bioontology-support] Questions about SPARQL endpoint

Josh Mandel jmandel at gmail.com
Wed May 23 15:52:06 PDT 2012


First off, congratulations!  sparql.bioontology.org is shaping up to
be a really great resource. I love the built-in examples, slick UI,
and (most important) substantial content!

A few of questions / issues:

0.  Having the UMLS in one place makes for some very convenient
queries!  For example, I'm using http://bit.ly/got-statins-sparql as
an example to figure out whether a medication list contains any
statins.   Hierarchical queries (e.g. to sort a problem list by body
system) would get much easier with support for either subclass
inferences *or* SPARQL 1.1 property paths (?a rdfs:subClassOf* ?b.)

1.  The documentation (and examples) don't make it clear what the
default graph is for queries.  It looks like the default graph is the
union of all named graphs; is that right?  Are any triples asserted
directly into the default graph?

2.  It's my understanding that https://github.com/ncbo/umls2rdf
generates a strict subset of the triples that
http://sparql.bioontology.org/ hosts.  Is this right?  Is there any
way to generate or obtain the entire set?

3.  The sparql endpoint ignores the `output` GET variable (but pays
attention to the Accept: header).

4.  The sparql endpoint fails to set Access-Control-Allow-Origin: *
when there is an error (missing apikey; typo in query, etc).  This
make debugging a browser-based app difficult (because the error
message doesn't make it to the client code; the request simply
aborts).

5.  Because of (3) (and also because it appears to time out against
alphasparql.bioontology.otg) the JS sparql client fails:
https://github.com/ncbo/sparql-code-examples/blob/master/javascript/index.html

I've submitted a pull request with a simplified (working) example:
https://github.com/ncbo/sparql-code-examples/pull/2

6.  github SPARQL examples still point to alphasparql

Best,

  Josh


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