scientific lenses over linked data - open phacts
TRANSCRIPT
Scientific Lenses: Supporting Alternative Views of the Data
Alasdair J G Gray University of Manchester
Authors: Christian Y. A. Brenninkmeijer, Chris Evelo, Carole Goble, Alasdair J. G. Gray, Paul Groth, Steve Pettifer, Robert Stevens, Antony Williams and Egon L. Willighagen
http://c745.r45.cf2.rackcdn.com/img/2009/lens_filter_coasters.jpg
Filters Change our Perceptions
23 April 2013 Scientific Lenses – A. Gray
© Alasdair J. G. Gray, November 2012
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Resolving Multiple Identities
P12047 X31045
GB:29384
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Multiple Points of View
Chem-informatition
• Chemicals must be the same isomer
• Target can be gene or protein
Bio-informatition
• Chemicals can match only at structure
• Target is a protein, distinct from genes
• Sometimes I want to match across species
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Linked Data Cloud
http://lod-cloud.net/
Gleevec® = Imatinib Mesylate
Drugbank ChemSpider PubChem
Imatinib
Mesylate Imatinib Mesylate YLMAHDNUQAMNNX-UHFFFAOYSA-N
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Multiple Links: Different Reasons
Link: skos:closeMatch Reason: non-salt form
Link: skos:exactMatch Reason: drug name
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InChI Key Match { chemspider:imantinib_mesylate skos:exactMatch chembl: imantinib_mesylate } Salt-forms { chemspider:imantinib_mesylate skos:closeMatch drugbank:imatinib } Enantiomer { (+)Staurosporine skos:exactMatch (-)Staurosporine }
Lenses: Operational Equivalence
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InChI Key Match { chemspider:imantinib_mesylate skos:exactMatch chembl: imantinib_mesylate } Salt-forms { chemspider:imantinib_mesylate skos:closeMatch drugbank:imatinib } Enantiomer { (+)Staurosporine skos:exactMatch (-)Staurosporine }
Profile P1 “Stereo”
Lenses: P1 stereo-chemistry
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InChI Key Match { chemspider:imantinib_mesylate skos:exactMatch chembl: imantinib_mesylate } Salt-forms { chemspider:imantinib_mesylate skos:closeMatch drugbank:imatinib } Enantiomer { (+)Staurosporine skos:exactMatch (-)Staurosporine }
Profile P1 “Stereo”
Profile P2 “Salts”
Lenses: P2 salt-forms
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InChI Key Match { chemspider:imantinib_mesylate skos:exactMatch chembl: imantinib_mesylate } Salt-forms { chemspider:imantinib_mesylate skos:closeMatch drugbank:imatinib } Enantiomer { (+)Staurosporine skos:exactMatch (-)Staurosporine }
Profile P1 “Stereo”
Profile P2 “Salts”
Profile P3 “Strict”
Lenses: P3 strict equivalence
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Lenses in the Explorer
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Lenses Support Dynamic Equality
• Tuneable (same data, different questions)
• Data & entity specific • User driven • Traceable
Strict Relaxed
Analysing Browsing
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OPS Lenses
• Compound Drugs
• Salt-form Drugs
• Parent/child Chemical Relationships
• Genes/proteins
Ideas for other lenses?
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Thank you
• Paper: Christian Y. A. Brenninkmeijer, Chris Evelo, Carole Goble, Alasdair J. G. Gray, Paul Groth, Steve Pettifer, Robert Stevens, Antony Williams, and Egon L. Willighagen. Scientific Lenses over Linked Data: An approach to support task specific views of the data. A vision. In 2nd International Workshop on Linked Science 2012—Tackling Big Data (LISC2012) co-located with 11th International Semantic Web Conference (ISWC2012), Boston, MA, USA, November 2012.
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