Integration of oreChem with the eCrystals repository for crystal structures
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This document discusses integrating the oreChem ontology for representing scientific experiments and their provenance with the eCrystals repository for crystallography data. It describes how eCrystals represents crystallography experiments and data, the motivation for open access to research, and the oreChem ontology's concepts for representing methodologies, enactments, and provenance. It then outlines a proposed plugin for eCrystals that would map eCrystals data to oreChem concepts to capture the provenance of experiments and link data to the methods used.
![ProvenanceThe 7 W’s [Goble 2002]Who, What, Where, Why, When, Which, & (W)HowThe Why aspect is usually ignored Rational, intent, hypothesis, protocol, methodology, workflow, etc.11“Diana and Actaeon by Titian has a full provenance covering its passage through several owners and four countries since it was painted for Philip II of Spain in the 1550s.”Source: http://en.wikipedia.org/wiki/Diana_and_Actaeon_%28Titian%29](https://image.slidesharecdn.com/integrationoforechemwiththeecrystalsrepositoryforcrystalstructures-100917044518-phpapp01/85/Integration-of-oreChem-with-the-eCrystals-repository-for-crystal-structures-11-320.jpg)
Integration of oreChem with the eCrystals repository for crystal structures
- 1. Integration of oreChemwith the eCrystals repository for crystal structuresMark Borkum, Simon Coles and Jeremy Frey15 September 2010
- 3. Current Practice in CrystallographyCrystallography data is highly structuredThe de facto standard adopted by the community is the CIF (Crystallographic Information File)Relatively few crystal structures are openly published3http://www.rin.ac.uk/our-work/data-management-and-curation/share-or-not-share-research-data-outputs
- 4. Open Access JournalsAdvantages:Rapid publicationHighly citedData is available to downloadDisadvantages:Electronic onlyNot all data is of primary importance to the underlying chemistryBy-products, unexpected results, tracking reactions, etc.4
- 6. The eCrystals FederationJISC project to establish a network of crystallography resources on the Internet, with metadata that is harvested by a number of aggregation servicesLed by the UK National Crystallography Service (NCS)With core partners at UKOLN, the Digital Curation Centre, and the Unilever Centre for Molecular Science Informatics6
- 7. eCrystals – University of SouthamptonLocated @ http://ecrystals.chem.soton.ac.ukArchive for crystal structures that are generated by:Southampton Chemical Crystallography GroupUK National Crystallography Service (NCS)Modified version of EPrints 3.1OAI-PMH compliantExtensible platform (with plug-ins architecture)7
- 8. What is an eCrystal?“all the fundamental and derived data resulting from a single crystal X-ray structure determination”“the information supplied should enable any reader to check the reliability and validity”8http://www.ukoln.ac.uk/projects/ebank-uk/images/collage-web.gif
- 10. The Data Deluge10In Haiku:Lots of producers;Generating more datathan ever before.40 years ago, a PhD student would determine 3 structures over the entire course of their study!The Great Wave off Kanagawa by Katsushika Hokusai
- 11. ProvenanceThe 7 W’s [Goble 2002]Who, What, Where, Why, When, Which, & (W)HowThe Why aspect is usually ignored Rational, intent, hypothesis, protocol, methodology, workflow, etc.11“Diana and Actaeon by Titian has a full provenance covering its passage through several owners and four countries since it was painted for Philip II of Spain in the 1550s.”Source: http://en.wikipedia.org/wiki/Diana_and_Actaeon_%28Titian%29
- 12. “In theory, there is no difference between theory and practice.But, in practice, there is.” Unknown (possibly Yogi Berra)12
- 13. Why “Why” MattersIt is the reason for the data’s existenceIt gives us the ability to interpret the data in the correct contextIt allows us to align the data with the big picture13http://www.myexperiment.org/workflows/16.html
- 14. The oreChem Core OntologyDescribes three concepts:The methodology (planned method) of a scientific experimentThe enactment of methodologiesThe provenance of realised artefacts14
- 15. Methodology (Planned Method)The “plan” is modelled as a directed graphTwo node types:Plan Stagedescription of an activity that will be enactedPlan Objectdescription of an artefact that will be realised15
- 16. Enactment (of a Methodology)Each “run” (of a plan) is modelled as a directed graph Two node types:Stagedescription of an activity that has been enactedObjectdescription of an artefact that has been realised16
- 17. ProvenanceProspectiveThe plan describes a scientific experiment that will be enactedRetrospectiveThe run describes a scientific experiment that hasbeen enactedEvery ‘run thing’ is linked to exactly one ‘plan thing’17
- 18. oreChem Plug-in for eCrystalsThree components:orechem:Plan (the eCrystals methodology) “eCrystalorechem:Run” mapping “orechem:Run provenance graph” pipeline18
- 21. SPARQL RequestPREFIX orechem: <http://www.openarchives.org/2010/05/24-orechem-ns#>PREFIX ecrystals: <http://ecrystals.chem.soton.ac.uk/plan.rdf#>SELECT ?run ?raw ?derived ?reportedWHERE { ?run a orechem:Run ;orechem:hasPlanecrystals:Ecrystals ;orechem:containsObject ?raw ;orechem:containsObject ?derived ;orechem:containsObject ?reported . ?raw a orechem:File ;orechem:hasPlanObjectecrystals:HKL . ?derived a orechem:File ;orechem:derivedFrom ?raw . ?reported a orechem:File ;orechem:hasPlanObjectecrystals:CIF ;orechem:derivedFrom ?derived .}21
- 22. SPARQL Response (for eCrystal #643)22?run?reported?derived?raw
- 24. AcknowledgmentsoreChem is funded by Microsoft External ResearcheCrystals is funded by both EPSRC and JISCThe oreChem project team:Nico Adams, Mark Borkum, William Brouwer, RameswaraSashiKiranChalla, Simon Coles, Nick Day, Jim Downing, Jeremy Frey, C. Lee Giles, Carl Lagoze (PI), Na Li, PrasenjitMitra, Karl Meuller, Peter Murray-Rust, Marlon Pierce, Joe Townsend, and Theresa Velden.24