Tag Archives: semantic web

Agile SPARQL

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I’m attending the BioHackathon 2010, the topic is “Semantic Web”.

Everthing is fantastic, yeah you need a dozen of servers to crunch your data but that’s not the real problem. The real problem is how can we use that stuff ?

There are different answers to this simple question.

You can build a fancy/functional  interface like BioGateway Semantic Systems Biology by Erick Antezana . Actually this is a great work that puts in the hands of “scientists” the power of Semantic Web. The facade is just a pice of the huge work done by Eric.

Then there are the programs that need to consume this information and this has been solved by Mark Wilkinson , Luke McCarthy and Paul Gordon with thier SADI project.

Then there are the people in the middle, blue helments of the OpenBio* projects like BioRuby, BioPython, BioPerl, BioJava that need to come up with a way to use the so called Semantic Web.

I’m a BioRuby and I was in charge to consume this SemWeb. Googling around I found ActiveRDF a very cute library which solved part of my/our problems. After some days of panic and bugs now BioRuby can consume in an Agile way every SPARQL endpoints. Thanks Eyal Oren, Renaud Delbru, Sebastian Gerke, and Benjamin Heitmann for your great work.

Query Bio2RDF GeneId endpoint.
I know, the cose is messy but it’s just a test…

Hey, but where is the agile stuff? Right there :-D

myGeneSemWeb is an array of triplettes. Just grab the first one:

Not yet agile, yessss I know… but now?

AGILE NOW!!!!!!

At this point you can browse your object dinamically, the only limitation is moving from one domain to the other. We are using the geneid endpoint if you want to move to kegg it’s not yet possiblem but is something we want to do.

There are a lot of things to do:
* design the integration with bioruby
* handle multiple endpoints
* test federation and create federated queries
* provide to the end user a friendly api.
* We all are very happy to have met Brad Chapman and Peter Cock from BioPython Dev Team, we plan to develop the same/similar API and work together. You can find Brad’s work here
* I’d like to implement this by default as autocompletion into irb
* Map RDFS classes to BioRuby objects.

Brilliant Bright Smart

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First of all, i drunk a lot, actually not so much.

This evening I had a very good dinner with Alberto. We went in a resturant near Ueno, without japanese, so we were alone in this adventure. Obviously we choosen a very tipical no japanese resturant, very raw but particular. In the middle of the table the were a stone with fire inside and a fence over which you can cook your raw stuffs like vegetable and meat. Menu in japanese. Random choise.

I thing was clear two big big glasses of beer.

We discussed a lot sharing experiences but mostly imporant ideas.

I’m attending a meeting, in Tokyo, on Semantic Web. I have saw  video’ of Tim Berners-Lee very inspiring but … with just things that we can have today, it’s just a matter of a good like style. Evolution admin and tollerate jumps but not so frequently.

Discussing discussing and discussing I see a lot more behind that video.

I see objects without shape and for shape I mean format without the way we are used to exchange them, just objects. We say each other that we must not care about our color, but actually we care, the same is with the files.

I imagine objects there are in something similar of a cloud (old concept) that can move and follow  me that can host by themself what I need to have them, like friends.

What does it happend with friends ? You care about then and there are there near you but with the time ? Someone stay there because you still care about him, other go away just because you don’t care about them. Objects can mashup and become something different but with the same knowledge they had before, at least.

We discussed about comunication, about life style and we moved… around… around… around

If you don’t comunicate, problems came up and you can’t stop them anymore, you can apply patches and as everyone is in the informatic field knows that patches are always worst than a good intial design.

It’s not over…