Re: OWL ontology database

>
> Is neo4j http://neo4j.org a good option to consider for this ?
>
Yes, it is a graph db not a triple store, worth exploring.

>  does it
>
provide seamless integration with dbpedia, free base etc?

 You should read up on it. It can consume LOD. I don't know how 'seemlessly'
- there would always be work to be done.
You should consider non-functional requirements as well.

Adam

On 21 June 2011 12:19, Aliabbas Petiwala <aliabbasjp@gmail.com> wrote:

> Is neo4j http://neo4j.org a good option to consider for this ? does it
> provide seamless integration with dbpedia, free base etc?
>
>
>
> On 6/19/11, Marco Brandizi <brandizi@ebi.ac.uk> wrote:
> > Hi Aliabbas,
> >
> > It all depends on what you want to represent and which tasks you want to
> > perform.
> > OWL-based models (and RDF/OWL triplestores) are useful when you have
> > heterogeneous data, for which you cannot define a schema a-priori (eg,
> > http://dc-research.eu/, OBI ontology).
> > OWL modelling can add useful inference capabilities to traditional OO or
> > relational modelling (eg, find automatically that the brother of my dad
> > is my uncle).
> > RDF/OWL world are particularly interesting if you want to integrate your
> > data with similar knowledge, which is increasingly being exported via
> > http and via RDF/OWL (ie, linked data, see eg, DBpedia, Freebase).
> > Relational DBs are useful to back object models (so, schema-based
> > models), you may want to consider NoSQL and Document-based stores too.
> > Exporting OWL from existing DB may make sense either, especially when
> > you have well-defined entities (ie, a schema), that you annotate with
> > ontologies or alike (eg, biomedical records, annotated with biomedical
> > ontologies, like MESH or GeneOntology).
> >
> > Also, keep in mind that in the case of OWL modelling you will typically
> > need to change your mindset completely. While a relational (or OO)
> > database is a closed dataset, which defines all (and only) the known
> > facts extesively, an OWL-based knowledge base is an open knowledge base,
> > where only what is known is defined by means of logical statements,
> > keeping the unknown as unknown, not as "not true", or "not existing".
> > For instance, in OWL it's difficult to establish that person1 and
> > person2 are two different individuals, cause usually nothing excludes
> > that they are the same real thing. Most straightforward way is to
> > explicitly say that they are owl:differentFrom (but, you need to do it
> > for all the pairs) and this is obviously different than a relational DB,
> > where two tuples are usually considered different by default (OWL-2 has
> > introduced identifier properties, but not sure they work so great). As
> > another example, it's difficult to use OWL for enforcing the equivalent
> > of relational integrity. For example, you may say that an employee must
> > have one boss, but this is an axiom, something that can be used to infer
> > that employee1 has such boss and we can call him/her emp1Boss. You
> > cannot say your KB is inconsistent just because you cannot find an
> > explicit declaration of a boss for an employee in that KB, ie, it may
> > have been declared somewhere else (or nowhere, but it still holds true
> > in reality). People often make confusion on this sort of things. For
> > instance, when one says that every protein has a standard international
> > name (it happens they do that in OWL), they actually mean that every
> > identified and classified protein that has a record in some
> > international biological database, has also an associated name in that
> > DB. That doesn't exclude proteins that exist, even if we know them and
> > we haven't named them yet. This comes from the fact that "has-name" is
> > not an inherent property of a protein, in the same sense "has-father" is
> > for a living being, since the former is just a conventional requirement
> > for the representation of the real thing.
> >
> > Hope it helps.
> >
> > Marco.
> >
> >
> >
> > On 18/06/2011 08:04, Aliabbas Petiwala wrote:
> >> we are looking forward to make an OWL ontology database as a mirror of
> >> a relational database for an upcoming social network semantic website
> >> is it a good decision to make?
> >>
> >> actually we can go for three options:
> >>
> >> 1. complete owl database, no relational db
> >> 2. owl mirror of relational db
> >> 3. only relational
> >>
> >> we are very much interested in the second option   is it wise to use
> >> mirror of ontology database as a relation database? how can owL
> >> Ontology database be efficient than a relational one considering that
> >> we will need to query a lot of external databases like
> >> dbpedia,freebase etc?
> >>
> >> for the second option,  ontological databases requires us to make a
> >> query against hundreds of different schemata and classes properties
> >> which seems to be a costly affair. And is it a wise decision to go for
> >> a complete ontological database for a social networking website ? The
> >> project is involves sharing of lot of small chunks of information
> >> across an array of distributed users building a personalized model of
> >> the user.
> >>
> >> ontotext, http://www.systap.com,http://www.opencalais.com/ provides a
> >> solution for semantic repositories , its really difficult to determine
> >> which is the best option for a STARTUP like us and we can't go in for
> >> these expensive paid consultations. so what are the options and
> >> solutions availaible for us?
> >>
> >>
> >
> > --
> >
> >
> ===============================================================================
> > Marco Brandizi<brandizi@ebi.ac.uk>
> >
> > Microarray Group - Sr Software Engineer
> > http://www.ebi.ac.uk/microarray
> >
> > European Bioinformatics Institute
> > Hinxton, CB10 1SD, United Kingdom
> > Office A3141
> >
> > Tel.: +44 (0)1223 492 613
> > Fax: +44 (0)1223 492 620
> >
> > http://www.marcobrandizi.info
> >
> >
>
>
> --
> Aliabbas Petiwala
> M.Tech CSE
>
>