nodalpoint.org - ISMB2005 - Comments

Conference updates

chris — Wed, 29 Jun 2005 05:42:45 -0400

Agreed. We should have a little section for people to blog from venues of interest (not necessarily just conferences, either). I could hack into the taxonomy (again)?

Thanks for the effort

PedroBeltrao — Tue, 28 Jun 2005 11:26:49 -0400

I think it is an interesting an useful experiment. It has been for me very informative, even if you bias the coverage to your scientific interest :). What do you think about setting up a "section" for this type of event coverage ?

Good point. Scalability of tr

Greg — Tue, 28 Jun 2005 11:07:22 -0400

Good point. Scalability of triple stores for biological applications (or in general) is clearly something that will need to be addressed. There is a report from SWAD-Europe here on RDF scalability. Relevant quote:

Other important storage issues that arose were were with scalability of the current systems available. Stores that can handle 10-20M triples are readily available and the current state of the art is around 40M; the development community is considering the next 10x increase in storage requirements, and their affect on indexing, which has tended to be O(n) for triples. Novel dedicated storage approaches such as in RDFStore were shown to avoid this. The dedicated non-relational stores can outperform the relational ones in such scaling, although the relational databases continue to perform well.

My understanding is that both DB2 and Oracle 10g do graphs on top of their relational dbs.

Oracle are active in this space too

Matt Cockerill — Tue, 28 Jun 2005 10:35:45 -0400

I bumped into Susie Stephens, from Oracle's Life Science marketing group, here at ISMB.
Oracle are active in this space too. e.g. they are a participant in the BioDASH project.

Oracle already has support for graphs (or in oracle's terminology, networks) built into it's database, allowing various types of topological query to be done on the network connections that are stored in the db.

Apparently in 10g release 2 (due out any time now) there will be explicit support for RDF, built on top of this underlying network representation/querying technology.

Earlier presentations at ISMB have mentioned how poorly most current RDF storage/querying technologies perform, as the number of 'facts' scales up. Will be interesting to see how the various technologies in this space evolve, as they start to be thrown at non-toy problems.

User created content

PedroBeltrao — Tue, 28 Jun 2005 09:32:38 -0400

I'm going to digress on the unrelated topic of gaming. I don't game to much now that I have very little time but I still like to follow the advances of the industry and the impact games can have on society. One common theme that is starting to pick up a lot is user created content. Some gaming experts have noticed that users love to create and share their own content , amazing examples of "games" based on this idea are The Sims, Second life and the upcoming Spore.
What is the point ? I think the problem with a lot of the standards for bio-ontologies is that they are made by people disconnected from the biological activities that they are trying to capture in the ontologies. More than defining the standards there should be more effort into building tools that would facilitate the creation and use of ontologies in biology, like these games have focused on empowering the user. In the end there might not be enough critical mass for this user driven mentality to work yet, I don't know.

I just caught Eric as he was

Greg — Sun, 26 Jun 2005 11:49:04 -0400

I just caught Eric as he was walking out of the conference hall. The slides he used were from Tim BL's talk at Bio-it world. Now reading back over the notes I see that he mentioned exactly that (I think the problem for me right now is there is just too much information to consume here at ISMB).

The ontologies slide is available here, along with the rest of the talk.

I can see where the confussio

Greg — Sun, 26 Jun 2005 11:32:11 -0400

I can see where the confussion is here: bad notes. That was actually suposed to read "EN: Multiple bio-ontolgoies (existing) used together right now..." ME: My poster (not EN's) discusses this.

Eric Neumann had some slides that he put up at the end of the disucssion, one of those was the multiple ontologies slide. There we also references to BioDash although I couldn't find the presentation on the website. I've emailed him and asked if they are available online but his email is not working, I'll ask him when I go to the W3C Semantic Web BOF.

I was referring to "EN: Multi

alf — Sat, 25 Jun 2005 11:23:21 -0400

I was referring to "EN: Multiple bio-ontolgoies (existing) used together right now... My poster discusses this (note to self to put this online)." ... and was hoping it might be a summary of existing ontologies, which would be useful.

Poster

Greg — Fri, 24 Jun 2005 23:50:48 -0400

If you are referring to the poster that I presented (at the AS-SIG not bio-ontologies) it is available here. This was something I only put together shortly before the conference so I don't think I articulated the point very well. The general idea was to take current tools and data sets and see if the semantic web delivered for bioinformatics data integration.

If you are referring to the bio-ontologies meeting poster session, there was no mention made about putting them online.

ontologies summary

alf — Fri, 24 Jun 2005 17:53:49 -0400

It would be good to see the bio-ontologies poster, if you can get it online.