Open PHACTS: meaningful linking ofpreclinical drug discovery knowledgehttp://www.openphacts.org/ACS 2013, New OrleansAckno...
#1 Introduction"To reduce the barriers to drug discovery in industry,academia and for small businesses, the Open PHACTScon...
#1.1 Scientific questions
Example scientific questions1. All oxido,reductase inhibitors active < 100 nM inboth human and mouse.2. Given a target fin...
#1.2 Architecture
Architecture: zooming in
Linking Datahttp://www.openphacts.org/specs/datadesc/
Linking data: statisticsAck: Alasdair, Christian (Manchester)
Units
WikiPathwaysPico, AR et al. PLoS biology 6.7 (2008): e184.
#1.3 Linked Data API
Example LDA callREST-basedhttp://ops2.example.org/compound?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F38932552-111f-...
Open PHACTS timeline• Explorer went open early 2013• LDA goes open in 2013• Open PHACTS (1) ends in 2014Specifications (CC...
Conclusion & Thanx● Joined effort of many partners– I only have a small (1 FTE) role in this● Several partners around here...
Associate Partner Program
Workshop in 2013
Open PHACTS: meaningful linking of preclinical drug discovery knowledge
Open PHACTS: meaningful linking of preclinical drug discovery knowledge
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Open PHACTS: meaningful linking of preclinical drug discovery knowledge

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Authors: E. Willighagen, C. Brenninkmeijer, C. Evelo, L. Harland, A. Gray, C. Goble, A. Waagmeester, A. Williams

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Open PHACTS: meaningful linking of preclinical drug discovery knowledge

  1. 1. Open PHACTS: meaningful linking ofpreclinical drug discovery knowledgehttp://www.openphacts.org/ACS 2013, New OrleansAcknowledgements: Contains contributions from across the OpenPHACTS partners.
  2. 2. #1 Introduction"To reduce the barriers to drug discovery in industry,academia and for small businesses, the Open PHACTSconsortium is building an Open Pharmacological Space(OPS). This will be a freely available platform, integratingpharmacological data from a variety of informationresources and providing tools and services to question thisintegrated data to support pharmacological research."
  3. 3. #1.1 Scientific questions
  4. 4. Example scientific questions1. All oxido,reductase inhibitors active < 100 nM inboth human and mouse.2. Given a target find me all actives against thattarget. Find/predict polypharmacology of actives.Determine ADMET profile of actives.3. Retrieve all experimental and clinical data for agiven list of compounds defined by theirchemical structure (with options to matchstereochemistry or not).4. Identify all known protein-protein interactioninhibitors.
  5. 5. #1.2 Architecture
  6. 6. Architecture: zooming in
  7. 7. Linking Datahttp://www.openphacts.org/specs/datadesc/
  8. 8. Linking data: statisticsAck: Alasdair, Christian (Manchester)
  9. 9. Units
  10. 10. WikiPathwaysPico, AR et al. PLoS biology 6.7 (2008): e184.
  11. 11. #1.3 Linked Data API
  12. 12. Example LDA callREST-basedhttp://ops2.example.org/compound?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F38932552-111f-4a4e-a46a-4ed1d7bdf9d5... calls SPARQL?ops_item skos:exactMatch ?cw_uri .?cw_uri skos:prefLabel ?compound_name ;void:inDataset<http://www.conceptwiki.org> .?ops_item skos:exactMatch ?cs_uri .?cs_uri chemspider:smiles ?smiles ;chemspider:inchi ?inchi ;chemspider:inchikey ?inchiKey ;ops:logp ?alogp ;ops:hba ?hba ;ops:hbd ?hbd ;ops:ro5_violations ?num_ro5_violations ;ops:psa ?psa;void:inDataset<http://www.chemspider.com> .?ops_item skos:exactMatch ?equiv_compound .?equiv_compound ?bNode1 ?molformula ;?bNode2 ?molweight ;?bNode3 ?mw_freebase ;?bNode4 ?rtb ;void:inDataset<http://data.kasabi.com/dataset/chembl-rdf>.?ops_item skos:exactMatch ?db_uri .
  13. 13. Open PHACTS timeline• Explorer went open early 2013• LDA goes open in 2013• Open PHACTS (1) ends in 2014Specifications (CC-BY-SA)http://www.openphacts.org/specs/Source code at (various Open licenses)http://github.com/openphacts/Data (mixed/open)various locations
  14. 14. Conclusion & Thanx● Joined effort of many partners– I only have a small (1 FTE) role in this● Several partners around here at ACS– Let me know if you like to meet any ofthem● Details– http://www.openphacts.org/– http://explorer.openphacts.org/– Posters: http://www.openphacts.org/docs/173-posters
  15. 15. Associate Partner Program
  16. 16. Workshop in 2013

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