The Royal Society of Chemistry and its adoption of semantic web technologies for chemistry at the epoch of a federated world Antony Williams, Valery Tkachenko, Ken Karapetyan, Alexey Pshenichnov ACS, 248th National Meeting San Francisco, CA August 11 th 2014
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The Royal Society of Chemistry and its adoption of semantic web technologies for chemistry at the epoch of a federated world
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The Royal Society of Chemistry and its adoption of semantic web technologies for chemistry at the epoch of a federated world
Antony Williams, Valery Tkachenko, Ken Karapetyan, Alexey Pshenichnov
ACS, 248th National Meeting
San Francisco, CAAugust 11th 2014
Who is involved?
29 partners
Research questions
Research questions
ChEMBL DrugBank Gene Ontology Wikipathways
UniProt
ChemSpider
UMLS
ConceptWiki
ChEBI
TrialTrove
GVKBio
GeneGo
TR Integrity
“Find me compounds that inhibit targets in NFkB pathway assayed in only functional assays with a potency <1 μM”
“What is the selectivity profile of known p38 inhibitors?”
“Let me compare MW, logP and PSA for known oxidoreductase inhibitors”
Open PHACTS Explorer Web based searching
interfaceexplorer.openphacts.org
Discovery Platform
Open PHACTS API dev.openphacts.org
Applications can query the pharmacological data within Open PHACTS
Micro-articleCompoundsReactionAnalytical DataText and References
Technical view - unification
Chemistry Validation and Standardization Platform
DrugBank dataset (6516 records)
J. Brechner, IUPACGraphical Representation of stereochem. configurationsSection: ST-1.1.10
DB06287
PubChemDrugbankChemSpider
Imatinib
Mesylate
What Is Gleevec?
Ambiguities
How is this a semantic web problem? Why can’t people just be clear?
People may be working with faulty data.
Salts, say, may make little difference to the effects of an active ingredient.
People may assume a one-to-one mapping between a gene and the gene product (protein, ncRNA) that it codes for.
What’s in a lens?
IdentifierTitle (dct:title)Description (dct:description)Documentation link (dcat:landingPage)Creator (pav:createdBy)Timestamp (pav:createdOn)
Equivalence rules (bdb:linksetJustification)
Equivalence rules
The BridgeDB vocabulary adds metadata that provides a justification for treating two URIs alike, thus allowing the researcher to determine whether their circumstances fit.
has component with uncharged counterparthas counterpart molecular entity
has normalized counterparthas OPS normalized counterparthas PubChem normalized counterpart
has uncharged counterpartsimilar to
similar to by PubChem 2D similarity algorithmsimilar to by PubChem 3D similarity algorithm
has same connectivity asis isotopologue ofis stereoisomer of
subClassOf (standard relation in RDF)has isotopically unspecified parenthas stereoundefined parent
Link: skos:closeMatchReason: non-salt form
Link: skos:exactMatchReason: drug name
Strict Relaxed
Analysing Browsing
skos:exactMatch(InChI)
Strict Relaxed
Analysing Exploring
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skos:closeMatch(Drug Name)
skos:closeMatch(Drug Name)
skos:exactMatch(InChI)
What does the Open PHACTS Chemistry Registration System do?
Takes in structures from ChEMBL, ChEBI, DrugBank, PDB, Thomson Reuters.Normalizes structures according to rules based on FDA guidelines.Generates counterpart molecules: without charge, fragments