Dear Gregor,

Various comments:

Relationship to ER -------------------------

In many ways RDF is very like ER-modelling (e.g., http://bit.csc.lsu.edu/~chen/pdf/Chen_Pioneers.pdf), indeed the W3C states that "RDF is a member of the Entity-Relationship modelling family." One could think of the modelling the link between two entities as a triple.

There's also a comment on this on Danny Ayers' blog (http://dannyayers.com/2005/03/16/xml-andor-rdf/) - embedded in some other extraneous stuff.

You might also want to look at D2R Map (http://www.wiwiss.fu-berlin.de/suhl/bizer/d2rmap/D2Rmap.htm) for mapping between database schema and RDF.

One way I like to think of this is that I think RDMS are geared towards locally held data, hence the emphasis on primary keys and normalisation. If, however, much of the data is elsewhere (as I believe it is in biodiversity informatics) then you need ways to refer to remotely held objects (i.e., URIs, which is another way of saying GUIDs). Hence, instead of locally defined primary keys you start to store GUIDs (which, by definition, are unique). If you then start to think about relationships between the objects identified by GUIDs, then you've pretty much got RDF. I would also say that in terms of managing local data, RDBMS are not going away. RDF, in my opinion, only really becomes relevant once you want to make the data available to others, and once you want to enable people to be able to aggregate that data.

RDMS and triple stores -------------------------------

Regarding triple stores, most ones that I'm aware of are actually built on top of a RDBMS. For example, I use 3store, which uses MySQL as the backend.

Would we be first in line? ---------------------------------- Well, I've been serving RDF for taxonomic names since mid-2005, uBio are serving their own LSIDs, and DiGIR is moving that way. So, there are functioning examples to play with, and people making a start in this area.

Does bioinformatics use it? ------------------------------------

The biggest use I've seen is the port of UniProt to RDF (http://expasy3.isb-sib.ch/~ejain//rdf/) by Eric Bain. The EBI has some interest in RDF via the BioMoby project. Another project is BioPax (see commentary at Nodalpoint - http://www.nodalpoint.org/2006/03/12/ integrating_biopax_compliant_pathway_data).

GML/SVG not RDFS -------------------------- (no idea)

Importing RDF ------------------- Well, this is sort of what triple stores do. Given that RDF is composed of triples the trivial mapping to a relational database is to store the triples in one table with three columns (subject, predicate, object). I guess for most people the issue is getting data out of RDBMS into RDF, not the other way around.

Tools -------

As one who positively hates the diagrams XMLSpy produces I'm biased, but when I played with Altova SemanticWorks I was distinctly underwhelmed.

Hope this helps,

Regards

Rod

On 24 Mar 2006, at 17:36, Gregor Hagedorn wrote:

Hi all,

RDF to me appears on a level of abstraction making it very hard for me to follow the documentation and discussion. Most of the examples are embedded in an artificial intelligence / reasoning use cases that I have no experience with.

I am a biologist and I feel comfortable with UML, ER-modeling, xml-schema- modeling, and - surprise - relational databases. I believe many others are as well - how many datastores are actually build upon RDBMS technology?

To me xml-schema maps nicely to both UML-like OO-modeling and Relational DBMS. I can guess about the advantages of opening this all up and seeing the world as a huge set of unstructured statement tupels. But it also scares me.

Angst is a bad advisor. But then if only a minority of the current few people involved can follow on the RDF abstraction level. A few questions I have:

• Would we be first in line to try rdf for such complex models as

biodiversity informatics?

• Do Genbank/EMBL with their hundreds of employees and programmers use

rdf? Internally/externally? The molecular bioinformatics is probably 1000 times larger than our biodiversity informatics.

• Why are GML, SVG etc. based on xml schema and not RDFS? Is this just

historical?

• Are there any tools around that let me import RDF into a relational

database (simple tools for xml-schema-based import/export are almost standard part of databases now, or you can use comfortable graphical tools like Altova MapForce).

-- I am just trying to test some tools to help me to visualize RDFS productions (like Roger has send around) on a level comparable with the UML-like xml-schema editors (Spy, Stylus, Oracle, etc.) I will try Altova SemanticWorks and Protege over the next week. The screenshot seem to be about AI and semantic web much more than about information models (those creatures where you try to simplify the world to make it manageable...).

Gregor---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn@bba.de) Institute for Plant Virology, Microbiology, and Biosafety Federal Research Center for Agriculture and Forestry (BBA) Königin-Luise-Str. 19 Tel: +49-30-8304-2220 14195 Berlin, Germany Fax: +49-30-8304-2203

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