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The HCLS Community Profile: Describing Datasets, Versions, and Distributions
This document describes the need for standardized metadata to describe datasets in the health and life sciences domain. It summarizes challenges with current practices, such as datasets having multiple versions and formats without consistent metadata. The document then introduces the Health Care and Life Sciences Community Profile for Dataset Descriptions, which defines a set of core and optional metadata properties from existing vocabularies to provide comprehensive, standardized descriptions of datasets. Implementing this profile will help address scientists' need for clear provenance about the data they use.
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The HCLS Community Profile: Describing Datasets, Versions, and Distributions
- 1. The HCLS CommunityProfile: Describing Datasets, Versions, and Distributions Alasdair J G Gray Heriot-Watt University www.macs.hw.ac.uk/~ajg33 A.J.G.Gray@hw.ac.uk @gray_alasdair Michel Dumontier Stanford University M. Scott Marshall MAASTRO Clinic 30/11/2016 @gray_alasdair www.macs.hw.ac.uk/~ajg33 1
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- 3. 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 Which ChEMBL version? @gray_alasdair www.macs.hw.ac.uk/~ajg33 3
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- 6. 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 v2.1 ChEMBL 20 http://tiny.cc/ops-datasets Which ChEMBL version? @gray_alasdair www.macs.hw.ac.uk/~ajg33 6
- 7. 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– From many mirrors/registries • Datasets build on each other • Files do not carry metadata • Registries – Can be out-of-date – Can contain conflicting information 30/11/2016 @gray_alasdair www.macs.hw.ac.uk/~ajg33 7 Scientists require data provenance!
- 8. Dublin Core MetadataInitiative Widely used Broadly applicable – Documents – Datasets ✗Generic terms ✗Not comprehensive ✗No required properties 30/11/2016 @gray_alasdair www.macs.hw.ac.uk/~ajg33 8 “Date: A point or period of time associated with an event in the lifecycle of the resource.”
- 9. 9 @gray_alasdair www.macs.hw.ac.uk/~ajg33 Metadata carriedwith data – Directly embedded: void:inDataset ✗No versioning ✗No checklist of requisite fields ✗Only for RDF data VoID: Vocabulary of Interlinked Datasets 30/11/2016
- 10. DCAT: Data Catalog Separates Dataset and Distribution ✗No versioning ✗No prescribed properties 30/11/2016 @gray_alasdair www.macs.hw.ac.uk/~ajg33 10
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- 12. HCLS Dataset Descriptions 61Metadata properties from 18 vocabularies 5 Modules: Core, Identifiers, Provenance, Distributions, Stats
- 13. Prescribed Usage Element PropertyValue Summary Level Version Level Distribution Level Core Metadata Type declaration rdf:type dctypes:Dataset MUST MUST SHOULD Type declaration rdf:type void:Dataset or dcat:Distribution MUST NOT MUST NOT MUST Title dct:title rdf:langString MUST MUST MUST Alternative titles dct:alternative rdf:langString MAY MAY MAY Description dct:description rdf:langString MUST MUST MUST … … … … … …
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- 17. HCLS Dataset Descriptions https://www.w3.org/TR/hcls-dataset/ DumontierM, Gray AJG, Marshall MS, et al. (2016) The health care and life sciences community profile for dataset descriptions. PeerJ 4:e2331 https://doi.org/10.7717/peerj.2331 A.J.G.Gray@hw.ac.uk @gray_alasdair
Editor's Notes
- #3 OPS Explorer screenshot returning compound information Open PHACTS as a use case; data integration platform One of many use cases gathered in HCLSIG
- #4 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
- #5 OPS Explorer screenshot returning compound information Open PHACTS as a use case; data integration platform One of many use cases gathered in HCLSIG
- #6 Key element is provenance of where the data has come from Enabled by having detailed descriptions of the sources
- #7 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
- #11 We reuse several properties
- #12 Large community buy in - 27 authors – Major data providers EBI, RIKEN, SIB Weekly telcons, collaborative editing 2-3 year process Wide range of use cases
- #14 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
- #15 61 properties from 18 vocabularies Minimised number of MUST/SHOULD to those for interoperability MAYs are recommended terms
- #16 21 Properties 4 MUST 4 SHOULD 13 May
- #20 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 Acknowledge W3C HCLS IG