2 posts tagged “vansemweb”

He also showed how current information from various biological databases (using UniProt and Reactome as examples) was incomplete by having for example one unique identifier referencing different isoforms of the same entry, or in the latter case referencing the same external resource from those different coumpounds.

He aims at assigning a unique identifier for each description, changing this identifier as the description changes. He introduced some of the currently existing systems, like the IUPAC International Chemical Identifier (InCHI), the Chemical Markup Language (CML) or the Structure Data Format (SDF) chemical file format.
He then showed how OWL DL can be used to describe funstional groups, and how those group can be modeled using a Chemical Ontology, thus allowing reasoning and classification.

His group worked on integrating PubChem, DrugBank and DBPedia, and exploit this to answer some queries.
For example, the DLQuery: isQualityOf some (Molecule and pubchemcompoundid value 3911) will return the set of descriptors for leuprolide.
The query DLQuery: Alcohol and BiotechDrug and eliminationHalfLife  value "Hour" will leverage the 3 resources and fetch chemical that are biotech drugs (DrugBank), have and alcohol moiety (PubChem) and are eliminated within an hour (DBpedia).

Finally he described what he himself calls a "crazy idea": using OWL to describe the molecule, and then using that to generate its identifier. His group started implementing that idea and developed the Biological Identifier Service, which given information like sequence, position of the modifications and species will generate a unique ID.





It was great seeing Michel, and as usual he delivered a great talk. Only drawback? Realizing that my biochemistry knowledge fades with years... :)


Resources:
- Chemical Knowledge for the Semantic Web, Mykola Konyk, Alexander De Leon, and Michel Dumontier.  Data Integration in the Life Sciences (DILS2008). Evry, France. Lecture Notes in Computer Science. 2008. Springer Berlin / Heidelberg. ISBN:978-3-540-69827-2. [PDF]
- Increasingly Accurate Representation of Biochemistry (v2) Slideshare of the talk (above pictures where created by Michel as part of his talk)
- SemanticScience several resources developed by Michel and his collaborators
- DumontierLab Michel's lab webpage
- Michel in action - picture taken by Jim Pick during the meetup.


Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else's. I'm happy to correct any errors you may spot - just let me know!

An other example presented was shark > attack  > [Person]. In this case [Person] is the entity type Person, and the results will pull up all entities recognized as being of type person, in this case "diver", "woman" or individuals identified by their name. In the figure on the left, you can also see that Bettina Pereira has been identified as having been attacked by a shark by the system, even though nowhere is it stated explicitly in the article, and instead the system interprets pronouns and dependencies in the text ("her son says she has been...")

Evri also teams up with the Washington Post to add to their articles. You would need to register with the journal to see the results by yourself, but here is a summary. Whenever you browse an article, an embedded Evri widget will automatically parse the text and suggest further reading. I just used a random news, entitled "Conservatives plans to question Obama's Supreme Court pick on gay marriage"

At the bottom of the page you will find the Evri generated extra information. Above left shows that the article is associated with the entities Barack Obama, Supreme Court, Congress etc. You can then browse further any of those by simply clicking on it, in the above right figure I chose to follow information related to Supreme Court, which in turns pull out links towards other entities, like Senate or Judiciary Committee.

More widgets can be found in the Widget Gallery.  An Evri toolbar is also available, and the Evri blog is a good source of information. Finally, being able to play with EvriVerse may be my next official excuse to get an iPhone :)

Update [May 18th 2009]: The slides used during the presentation are posted at http://is.gd/B2FH

Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else's. I'm happy to correct any errors you may spot - just let me know!