2 posts tagged “vansemweb”
Michel Dumontier, assistant Professor of Bioinformatics at Carleton University, was visiting Vancouver just before the Canadian Semantic Web Working Symposium and kindly offered to present his work during our third Vancouver Semantic Web Meetup.
During his talk,
he used several examples illustrating some of the issues he currently
faces when trying to unambiguously reference a specific chemical
molecule, whether generic or modified, and how we are currently lacking
efficient way to represent one molecule in different conformation or
different states (i.e. phosphorylated for example).
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, . 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!
Deep Dhillon, CTO of Evri, was in Vancouver yesterday to talk at the Vancouver Semantic Web group second meetup.
Evri aims at exposing entities on the web, entities being anything that can be expressed using natural language.
They create their knowledge based based on various resources (e.g. Freebase and Wikipedia) and some manual curation, and then use this to parse, index and analyze web documents.Deep spent some time showing us various demos and queries that can be performed via the Evri API.
You can use the Evri Search Query System with for example a query like company > acquire > company (figure on the right).
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!