semantic pipelines to molecular properties
DESCRIPTION
In our quest to replace answers in molecular sciences by recipes to get answers, the semantic web technologies play the important role of giving meaning to numbers and characters. The Resource Description Framework (RDF) complements (and not replaces) earlier work with eXtensible Markup Language (XML) applications by providing a more clear separation between syntax and meaning. This creates an environment where multiple serialization formats can be used, that grows and shrinks in complexity where needed, and, for example, that can be easily embedded in document formats like HTML. We here present recent work in the dissemination and prediction of molecular properties, where data is shared in RDF, read into statistical and life science software including Bioclipse and R, and where molecular properties are predicted.TRANSCRIPT
Department of Bioinformatics - BiGCaT 1
semantic pipelines to
Molecular Properties
Egon Willighagen (@egonwillighagen)
Dept. of Bioinformatics – BiGCaT, Maastricht University
#ACSPhilly 2012
Department of Bioinformatics - BiGCaT 2
Properties: Physical, chemical, biological
• From experiment–with experimental error: interlab
differences, method differences, …
• No experiment? Predict–with prediction error, originating
from experimental error, modeling error, incorrect interpretation, …
• Where does the predictionerror come from?
Predicted BPs →
Department of Bioinformatics - BiGCaT 3
Richer Property Prediction
1. Select training data (x,y)● experimental data with errors, detailed description of
what the data is
2. Find f(x) = y, minimizing error(y)● use as much as possible information from 1.
3. Validation● not just validate (and quantify) the statistics against a
test set, also compare with other data
How? → Semantic pipelines
E.L. Willighagen, et al. Molecular Chemometrics. Crit. Rev. Anal. Chem. 2006.
Department of Bioinformatics - BiGCaT 4
Semantic pipelines
Be clear in what you mean● Use (open) look-up lists,
dictionaries, ontologies● Be flexible and remove
format limitation● Link to other data →
from other domains● Calculation provenance
M. Samwald, et al. Linked open drug data for pharmaceutical research and development. J. Cheminf. 2011. 3:19
Department of Bioinformatics - BiGCaT 5
Semantic pipelines: what technology?
CML: semantic, flexible, embeddable in HTML, RSS, … but only in XMLRDF: ~10yrs before adopted! But JSON, XML, Turtle, … Also: linked data.
Department of Bioinformatics - BiGCaT 6
RDF and friends ...
• format independent (JSON, XML, ...)• db technology independent (RDB2RDF)• embeddable in HTML (e.g. RDFa)• Open Standard widely supported→
Querying • SPARQL: like SQL access• Federated SPARQL link multiple SPARQL endpoints and other RDF sources
→
Department of Bioinformatics - BiGCaT 7
App #1: Bioclipse speaks RDF and OpenTox
Department of Bioinformatics - BiGCaT 8
App #2: Nanotoxicity
Department of Bioinformatics - BiGCaT 9
What's next?
Department of Bioinformatics - BiGCaT 10
Collaborations / Thanx
Uppsala UniversityOla Spjuth et al.
Karolinska InstitutetRoland Grafström, Bengt Fadeel, Hanna Karlsson
W3C Heath Care and LifeScience interest group
CDK communityChristoph Steinbeck, Rajarshi Guha, many more
OpenTox communityNina Jeliazkova, Barry Hardy
CHEMINF communityNico Adams, Michel Dumontier, Janna Hastings
CML community (you know :)
Department of Bioinformatics - BiGCaT 11
Take home tweetImprove your property prediction training and validation by adopting semantic pipelines! Further examples:
blog: chem-bla-ics
twitter: @egonwillighagen
CiteULike: egonw
Mendeley: egon-willighagen
GScholar: u8SjMZ0AAAAJBlue Obelisk