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Describing Scientific Datasets: The HCLS Community Profile
The document discusses the complexities of describing scientific datasets within the Health Care and Life Sciences (HCLS) community, highlighting challenges like versioning, format discrepancies, and the need for data provenance. It emphasizes the inadequacies of existing metadata standards and introduces W3C's HCLS group initiatives aimed at creating a more effective dataset description framework. Future visions include ensuring accurate data provenance, developing automatic pipelines for dataset registration, and promoting FAIR data principles.
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Describing Scientific Datasets: The HCLS Community Profile
- 1. Describing Scientific Datasets: TheHCLS Community Profile Alasdair J G Gray A.J.G.Gray@hw.ac.uk alasdairjggray.co.uk @gray_alasdair Michel Dumontier Stanford University M. Scott Marshall MAASTRO Clinic
- 4. Data Cache (Triple Store) SemanticWorkflow Engine Linked Data API (RDF/XML, TTL, JSON) Domain Specific Services Identity Resolution Service Identifier Management Service “Adenosine receptor 2a” EC2.43.4 CS4532 P12374 CorePlatform ChEMBL- RDF ChEMBL v13 Chem2 Bio2RDF SD v13 v12 v2 or v8
- 5. Data Cache (Triple Store) SemanticWorkflow Engine Linked Data API (RDF/XML, TTL, JSON) Domain Specific Services Identity Resolution Service Identifier Management Service “Adenosine receptor 2a” EC2.43.4 CS4532 P12374 CorePlatform ChEMBL- RDF ChEMBL v13 Chem2 Bio2RDF SD v13 v12 v2 or v8 Open PHACTS Discovery PlatformHistoric Use Case ~January 2012 Open PHACTS v1.3 ChEMBL 16 http://tiny.cc/ops-datasets
- 6. Challenges Datasets available In many versions over time In different formats From many mirrors/registries Datasets build on each other Files do not carry metadata Registries Can be out-of-date Can contain conflicting information 25 September 2014 EUON - HCLS Dataset Description 5 Scientists require data provenance!
- 7. Dublin Core MetadataInitiative Widely used Broadly applicable Documents Datasets ✗Generic terms ✗Not comprehensive ✗No required properties 25 September 2014 EUON - HCLS Dataset Description 6 “Date: A point or period of time associated with an event in the lifecycle of the resource.”
- 8. 7EUON - HCLSDataset Description Metadata carried with data Directly embedded: void:inDataset ✗No versioning ✗No checklist of requisite fields ✗Only for RDF data VoID: Vocabulary of Interlinked Datasets 25 September 2014
- 9. DCAT: Data Catalog Separates Dataset and Distribution ✗No versioning ✗No prescribed properties 25 September 2014 EUON - HCLS Dataset Description 8
- 10. W3C HCLS Group 25September 2014 EUON - HCLS Dataset Description 9
- 11. HCLS Dataset Descriptions 25September 2014 EUON - HCLS Dataset Description 10
- 12. VoID Editor 25 September2014 EUON - HCLS Dataset Description 12
- 13. Validator 25 September 2014EUON - HCLS Dataset Description 13 New version using ShEx in development
- 14. Future Vision Providerich and accurate provenance trail of data Write once, use many times Automatic pipeline from description file to registries FAIR Data 25 September 2014 EUON - HCLS Dataset Description 14
- 15. Thank you Editors’ Draft: http://tiny.cc/hcls-datadesc-ed W3CInterest Group Note: http://tiny.cc/hcls-datadesc Acknowledgements to W3C HCLS Group www.alasdairjggray.co.uk A.J.G.Gray@hw.ac.uk @gray_alasdair 25 September 2014 EUON - HCLS Dataset Description 15
Editor's Notes
- #3 Open PHACTS as a use case; data integration platform Explorer screenshot returning compound information
- #4 Key element is provenance of where the data has come from Enabled by having detailed descriptions of the sources
- #5 Behind the scenes! ChemSpider: EBI SDF file ChEMBL 13 Data Cache: Chem2Bio2RDF ChEMBL RDF File downloaded May 2011 Chem2Bio2RDF metadata webpages: ChEMBL 8 File contents: ChEMBL 2 Mapping Server: Kasabi ChEMBL RDF file ChEMBL 12
- #6 Behind the scenes! ChemSpider: EBI SDF file ChEMBL 13 Data Cache: Chem2Bio2RDF ChEMBL RDF File downloaded May 2011 Chem2Bio2RDF metadata webpages: ChEMBL 8 File contents: ChEMBL 2 Mapping Server: Kasabi ChEMBL RDF file ChEMBL 12
- #10 We reuse several properties
- #11 Large community buy in – Including EBI Builds on OPS document: Checklist and guidance notes! Wide range of use cases Should be finalised by end of May – not final URL
- #12 Summary level: time unchanging information, e.g. name, description, publisher Version level: version specific information, e.g. version number, creator, etc Distribution level: file specific information, e.g. file location and format, number of triples Reuse vocabularies: DCTerms, DCAT, VoID, FOAF, … Prescribed properties: MUST, SHOULD, MAY, MUST NOT for each level
- #14 Dataset description creator Generates outline description through web form Allows you to see generated content
- #15 Given a dataset description, does it conform to the OPS guidelines Generates error (red) and warning (orange) reports Error for MUST properties Warning for SHOULD properties Information for MAY properties