Open PHACTS Explorer

Ian Dunlop1, Rishi Ramgolam2, Stephen Pettifer1,
Alasdair JG Gray3, James Eales4, Carole Goble1,
Jan...
Datasets

www.openphacts.org
Architecture

Explorer
OPS.js
Linked Data API

Linked Data Cache

Datasets

Identity
Mapping
Service

Identity
Resolution
...
Search
Compound Info
Compound Pharmacology
Compound Pathways
Pathway Info
Target Info
Target Pharmacology
Target Class Hierarchy
Acknowledgements

Ian Dunlop1, Rishi Ramgolam2, Stephen
Pettifer1, Alasdair JG Gray3, James Eales4, Carole
Goble1, Jan Vel...
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SWAT4LS Open PHACTS Explorer demonstration

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Open PHACTS Explorer demonstration and talk given at SWAT4LS, Edinburgh, 2013. The Explorer is an Ember JS MVC web application used to navigate the Open PHACTS Linked Data Cache without requiring any knowledge of RDF or SPARQL

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  • Some of the datasets added to the openphacts linked data cache.
  • The Open PHACTS architecture. No SPARQL endpoint is exposed, instead an API is used to answer various chemistry questions based on the URI of an entity eg. Given a URI which represents Aspirin can you return the pharmacology data. The OPS.js library abstracts this API for javascript users and is used by the explorer. The explorer is an Ember JS browser based MVC application to allow users to navigate the linked data without requiring them to use the API. IMS = which uris are equivalentIRS = text search to uriDatasets = chemspideretcDataset Descriptions = voidsOPS.js = javascript library used to access the Linked data APIExplorer – Browser based GUI for searching over the linked data cache
  • Enter a search term in to the box and hit enter. Any concepts which solr thinks are of relevance are then displayed.
  • Information about a compound is displayed when clicking on the label of a search result. The provenance of where each fact is from can also be toggled. Links to other facts about this compound are also shown.
  • Compound pharmacology results are loaded on demand as the table is scrolled. Provenance can be shown. Results can be filtered and sorted.
  • Pathways for a compound with links to the pathways in the left of the table. Link outs to the source of many of the facts are available
  • A pathway reached by clicking on a link in the compound pathways table. Link outs to source facts are shown
  • A target with provenance shown as icons beside each fact.
  • Target pharmacology with links to compounds. Results are loaded on demand and can be filtered and sorted.
  • Target class hierarchies for enzymes, chembl, chebi and go can be navigated by clicking on nodes which then reveals the children. Each target class can be clicked on which loads the pharmacology data for it.
  • SWAT4LS Open PHACTS Explorer demonstration

    1. 1. Open PHACTS Explorer Ian Dunlop1, Rishi Ramgolam2, Stephen Pettifer1, Alasdair JG Gray3, James Eales4, Carole Goble1, Jan Velterop2 1 University of Manchester (ian.dunlop, steve.pettifer, carole.goble@manchester.ac.uk) 2 AQnowledge Ltd. (ramgolam, velterop@aqnowledge.com) 3 Heriot-Watt University (A.J.G.Gray@hw.ac.uk) 4 University of Leicester (jme25@leicester.ac.uk)
    2. 2. Datasets www.openphacts.org
    3. 3. Architecture Explorer OPS.js Linked Data API Linked Data Cache Datasets Identity Mapping Service Identity Resolution Service Data Descriptions
    4. 4. Search
    5. 5. Compound Info
    6. 6. Compound Pharmacology
    7. 7. Compound Pathways
    8. 8. Pathway Info
    9. 9. Target Info
    10. 10. Target Pharmacology
    11. 11. Target Class Hierarchy
    12. 12. Acknowledgements Ian Dunlop1, Rishi Ramgolam2, Stephen Pettifer1, Alasdair JG Gray3, James Eales4, Carole Goble1, Jan Velterop2 1 University of Manchester (ian.dunlop, steve.pettifer, carole.goble@manchester.ac.uk) 2 AQnowledge Ltd. (ramgolam, velterop@aqnowledge.com) 3 Heriot-Watt University (A.J.G.Gray@hw.ac.uk) 4 University of Leicester (jme25@leicester.ac.uk)

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