Re: Are there EJB entities for BioSQL?
Andreas Prlic <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <CALthepznaGXHsY4VRZ=JSeXqsGDrPZZbwwypdughPgBt_bWZcQ@mail.gmail.com> |
Hi Jan, that really depends on what you want to do. My first response based on your comment would be to take a look at the Distributed Annotation System and the various DAS clients. We can say more if you tell us a bit more specific what your intention is. Andreas On Mon, Aug 6, 2012 at 2:10 AM, Jan T Kim <[email protected]> wrote: > Hi Andreas and All, > > On Fri, Aug 03, 2012 at 02:21:01PM -0700, Andreas Prlic wrote: >> Hi Jan, >> >> There is no biosql ORM mapping for biojava 3 currently. If you need >> something like that you would need to use biojava 1 or patch biojava >> 3... > > ok -- so is there any general suggestion / recommendation / best > practice for building applications that involve handling annotated > sequence data and a web UI? > > Best regards, Jan > > >> Andreas >> >> >> >> On Fri, Aug 3, 2012 at 5:47 AM, Jan T Kim <[email protected]> wrote: >> > Dear All, >> > >> > is there a set of EJB 3 entities that correspond to BioSQL available? >> > I've noticed that there are is a Hibernate mapping in biojavax [1, 2] -- >> > is that the recommended ORM solution? >> > >> > Personally, I'd prefer a set of classes, with the suitable annotations >> > from the javax.persistence package applied (@Entity, @Id etc.) to match >> > the BioSQL tables. >> > >> > Apparently there have been initiatives in this direction (e.g. [3]), has >> > any of these made it into mainstream BioJava? If not, why not? >> > >> > Best regards, Jan >> > >> > [1] http://biojava.org/wiki/BioJava:BioJavaXDocs >> > [2] http://www.biosql.org/wiki/BioJava_BioSQL_ORM >> > [3] http://www.biojava.org/pipermail/biojava-l/2008-October/006387.html >> > -- >> > +- Jan T. Kim -------------------------------------------------------+ >> > | email: [email protected] | >> > | WWW: http://www.jtkim.dreamhosters.com/ | >> > *-----=< hierarchical systems are for files, not for humans >=-----* >> > _______________________________________________ >> > Biojava-l mailing list - [email protected] >> > http://lists.open-bio.org/mailman/listinfo/biojava-l > > -- > +- Jan T. Kim -------------------------------------------------------+ > | email: [email protected] | > | WWW: http://www.jtkim.dreamhosters.com/ | > *-----=< hierarchical systems are for files, not for humans >=-----* > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l