Increasingly Accurate Representation of Biochemistry
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 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, . 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!
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).
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!
