Hi, I would like to come back to you about some points in this email. On Tue, 16 Mar 2004, Marc Dumontier wrote: > Hi, > > So this is in regards to the current development efforts for the BIND > database. > > The main reasoning for data being stored in an XML blob is that the BIND > data model is very large and complex, and hierarchical (i believe the > current spec. has approximately 2200 individual fields). > > We use JAXB (Java API For XML Binding) to do the marshalling and > unmarshalling of the XML document into auto-generated data structures. > This allows us to work with the data in a very simple way without > dealing directly with DOM or SAX. This is used extensively by the BIND > Submission System. > > We have also developed a module which takes the XML, and text indexes > the document with the help of Lucene (http://jakarta.apache.org/lucene). > This framework allows us to only worry about what to index, but also > provides the query engine, file handling, etc. We use this code for our > BIND Browsing System. We can do most searches under 1 millisecond, > stream the data to the browser, and never touch the database. > > We believe this was the best way to deal with a highly complex data > model to provide not only field-specific searching which is very fast, > but also an easy to generate API for working with the data. > > I can't imagine dealing with a 3000 table relational database..scary. How does the use of XML make the data model less scary? I see how the XML is convenient for your read / write API, and how the hierarchical data model is more naturally encoded in XML. I see that it is because you use XML that you have access to the fast indexing technology. But how do you deal with issues of data integrity? I get the feeling I should learn XML schema... Does the BIND datamodel have an XML schema with constraints on the data? I can't help feeling that a big / complex data model is probelmatic for any system, nomater what the format. Thanks very much for the feedback, Cheers, Dan. > we should be releasing a beta of this software in a short while...please > visit http://www.bind.ca periodically for more information. > > Marc Dumontier > BIND Software Developer > Blueprint Initiative > Mt. Sinai Hospital > Toronto,ON > > Dan Bolser wrote: > > >On Tue, 16 Mar 2004, Michel Dumontier wrote: > > > > > > > >>>Same goes for BIND, they plan to use RDB, but not in a conventional way > >>>(so far as I understand). > >>> > >>> > >>> > >>BIND (http://bind.ca) stores bind-objects based on ASN.1 specification > >>(ftp://ftp.blueprint.org/pub/BIND/spec/, also available as XML DTD and > >>Schema), as ASN.1/XML in BLOB fields in the database table. BIND makes use > >>of field-specific indexing to be able to search for any particular object or > >>set of objects that match the search criteria. The relational aspect is > >>really more for curatorial work and tracking, afaik... > >> > >> > > > > > >So it wont be like an XML query system? Sorry if I misunderstand, but it > >sounds like you just do plain text index on an XML blob, but is is more > >than that? > > > >Generally, can anyone tell me what is the point of XML schema when > >relational schema have existed for years with well understood maths, query > >language and theories of relational design? I understand XML as a > >transport medium, but why make it the basis for your object model over the > >RDB relational schema? Perhaps object orented datamodeling can do things > >relational modeling can't, but at what cost? I hate sounding old, but what > >was wrong with the RDB that we have to invent X-path and the like? > > > >Anyone on the list remember when relational databases were 'the new > >thing'? > > > >Dan. > > > > > > > >>Michel Dumontier > >>PhD Candidate > >>Samuel Lunenfeld Research Institute, Mt. Sinai Hospital > >>Department of Biochemistry, University of Toronto > >>Toronto, ON M5G1X5 > >>micheld at mshri.on.ca > >>http://blueprint.org > >> > >> > >> > >>_______________________________________________ > >>Biodevelopers mailing list > >>Biodevelopers at bioinformatics.org > >>https://bioinformatics.org/mailman/listinfo/biodevelopers > >> > >> > >> > > > >_______________________________________________ > >Biodevelopers mailing list > >Biodevelopers at bioinformatics.org > >https://bioinformatics.org/mailman/listinfo/biodevelopers > > > > > > _______________________________________________ > Biodevelopers mailing list > Biodevelopers at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biodevelopers >