Re: Direct Mapping

On Mon, Sep 6, 2010 at 8:44 PM, Eric Prud'hommeaux <eric@w3.org> wrote:

> * Juan Sequeda <juanfederico@gmail.com> [2010-09-06 18:58-0500]
> > On Mon, Sep 6, 2010 at 5:15 PM, Eric Prud'hommeaux <eric@w3.org> wrote:
> >
> > > * Juan Sequeda <juanfederico@gmail.com> [2010-09-06 16:57-0500]
> > > > >
> > > > >
> > > > >
> > > > > Let's see if I understand the implied mechanics. Option 1 directly
> > > > > specifies the RDF graph implied by a database (for any tuple in the
> > > > > database, you can say exactly what triples are in the direct
> > > > > graph). Option 2 specifies a mapping language, with certain mapping
> > > > > semantics, and with a default configuration. The default graph is
> the
> > > > > products of applying the mapping semantics for a default
> configuration
> > > > > to a database.
> > > > >
> > > > >
> > > > Option 2 uses R2RML.
> > > >
> > > > I see the two options this way
> > > >
> > > > Option 1:
> > > >
> > > > 1) We (the WG) present the direct mapping rules in order to generate
> a
> > > > direct RDF graph from a RDB
> > > > 2) Database vendors (oracle, db2, etc) implement these mapping rules
> OR
> > > > RDB2RDF systems on top of a RDB can read the database dictionary and
> run
> > > > these mapping rules
> > > > 3) You click the button "Generate Direct RDF"
> > >
> > > Or you say
> > >  dbview --serve http://localhost:8888/proteins --user XXX --password
> YYY
> > > db2pro.rif db2biopax.rif
> > > and issue SPARQL queries against http://localhost:8888/proteins .
> > >
> > > > 4) Outcomes your RDF
> > > > 5) Use RDF to RDF tools (sparql constructs, etc) to map to other
> > > > vocabularies
> > >
> >
> >
> > What is db2pro.rif and db2biopax.rif ?
>
> just some maps for the example scenario where you have a relational
> database of proteins and you want to share with the world in two
> popular ontologies, PRO and BioPAX.
>

But this is out of the scope of this WG. We are chartered to present a
mapping language

>
> > The whole idea is for this to be completely automated. No input at all
> from
> > the user, right?
> >
> > If the rif file is the RDF to RDF, then that is not part of the direct
> > mapping.
>
> Right, the direct mapping provides a standard graph and someone (not
> necessarily the custodian of the data) uses RDF rules to produce other
> graphs in popular formats. In the SPASQL scenario, this all happens in
> one database, but it can also be multi-agent, with e.g. the uniprot
> MySQL database at genome-mysql.cse.ucsc.edu offering SQL and someone
> grabbing some rif files to offer a SPARQL interface in e.g. BioPAX.
> The common requirement is a defined RDF view so that folks can write
> the RDF rules to map to whatever the like.
>
>
Ok, but again, this is out of scope of this WG

>
> > >  In the server scenario, they're part of the query transformation
> > > configuration, but yes, the effec is the same; the SPARQL queries
> > > operate over the same (virtual) graphs.
> > >
> > > > Option 2:
> > > >
> > > > 1) We (the WG) present the direct mapping rules in order to generate
> a
> > > > direct RDF graph from a RDB
> > > > 2) Database vendors (oracle, db2, etc) implement these mapping rules
> OR
> > > > RDB2RDF systems on top of a RDB can read the database dictionary and
> run
> > > > these mapping rules
> > > > 3) You click the button "Generate Direct RDF"
> > > > 4) Outcomes your RDF
> > > > 5) Out comes the R2RML mapping file that generated the Direct RDF
> Graph
> > > > 6) A user can modify the R2RML mapping file in order to change
> > > vocabularies,
> > > > etc
> > > >
> > > >
> > > > So.. if we agree on this.. we are practically then talking about the
> same
> > > > thing. Only difference is that in Option 2 we are outputing the
> direct
> > > > mapping also in R2RML. Otherwise.. why would we need R2RML??????
> > >
> > > I think the main reason folks want R2ML is to have an alternative to
> > > writing RIF rules for defining the e.g. biopax view.
> >
> > Both approaches
> > > can be used to:
> > >  • generate SQL views on the server
> > >  • configure some intermediate agent to present the appropriate graph
> > >  • produce a materialized view
> > >
> >
> >
> > I still don't understand then why we are not expecting from the direct
> > mapping a R2RML mapping file that will produce the direct RDF graph
>
> The community who want to use RDF rules engines will be best served by
> a terse, direct definition of the RDF graph. Once we hand them that,
> we've met their needs.
>
>
> > > > > > So you think that a direct mapping shouldn't output the R2RML
> file? I
> > > > > think
> > > > > > it should because this file is the basis for people to work on
> and
> > > start
> > > > > > customizing it.
> > > > >
> > > > > The RDF rules folks will have everything they need with option 1.
> They
> > > > > can write/share rules in RIF, SPIN, n3, ... which transform the
> > > > > default graph to popular ontologies. Simple implementations will
> > > > > materialize these graphs, and arguably cooler implementations will
> > > > > work directly on the relational data, but that's really
> implementation
> > > > > detail; all they need is the default graph.
> > > > >
> > > > >
> > > > > > > Hence I'm with Eric here.
> > > > > > >
> > > > > > >
> > > > > > >  The automatic mapping file that is generated in D2R is
> equivalent
> > > to
> > > > > the
> > > > > > >> Direct Mapping (right Richard?).
> > > > > > >>
> > > > > > >
> > > > > > > Well I'd say the *graph* produced by an auto-generated D2R
> mapping
> > > file
> > > > > is
> > > > > > > equivalent to the direct mapping.
> > > > > > >
> > > > > >
> > > > > > and I'd call the auto-generated D2R mapping file the Direct
> Mapping
> > > file.
> > > > > So
> > > > > > D2R does option 2 then.
> > > > > >
> > > > > > >
> > > > > > > Best,
> > > > > > > Richard
> > > > >
> > > > > --
> > > > > -ericP
> > > > >
> > >
> > > --
> > > -ericP
> > >
>
> --
> -ericP
>