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Describing Scientific Datasets: The HCLS Community Profile
@micheldumontier::CEDAR:Jan 20151
Michel Dumontier, Ph.D.
Associate Professor of Medicine (Biomedical Informatics)Stanford University
World Wide Web Consortium (W3C)
• The W3C is the main international standards organization for the World Wide Web.
• The W3C is made up of over 400 member organizations for the purpose of working together in the development of standards for the World Wide Web.
@micheldumontier::CEDAR:Jan 20152
The Semantic Webis the new global web of knowledge
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It involves standards for publishing, sharing and querying facts, expert knowledge and services
It is a scalable approach to thediscovery of independently formulated
and distributed knowledge
Resource Description Framework
• It’s a language to represent knowledge– Logic-based formalism -> automated reasoning– graph-like properties -> data analysis
• Good for– Describing in terms of type, attributes, relations– Integrating data from different sources– Sharing the data (W3C standard)– Reusing what is available, developing what you need,
and contributing back to the web of data.
@micheldumontier::CEDAR:Jan 20154
@micheldumontier::CEDAR:Jan 2015
drugbank:DB00586
drugbank_vocabulary:Drug
rdf:type
drugbank:290
drugbank_vocabulary:Target
rdf:type
drugbank_vocabulary:targets
rdfs:label
Prostaglandin G/H synthase 2 [drugbank_target:290]
rdfs:label
Diclofenac [drugbank:DB00586]
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PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX rdfs: http://www.w3.org/2000/01/rdf-schema#PREFIX drugbank: <http://bio2rdf.org/drugbank:>PREFIX drugbank_vocabulary: <http://bio2rdf.org/drugbank_vocabulary:>
The linked data network expands with every reference
@micheldumontier::CEDAR:Jan 2015
drugbank:DB00586
pharmgkb_vocabulary:Drug
rdf:type
rdfs:labeldiclofenac [drugbank:DB00586]
pharmgkb:PA449293
drugbank_vocabulary:Drug
pharmgkb_vocabulary:x-drugbank
diclofenac [pharmgkb:PA449293]rdfs:label
DrugBank
PharmGKB
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We are building a massive network of linked open data
7Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. http://lod-cloud.net/”
@micheldumontier::CEDAR:Jan 2015
Linked Data for the Life Sciences
• Free and open source• Leverages Semantic Web standards• 10B+ interlinked statements from 30+
conventional and high value datasets• Partnerships with EBI, SIB, NCBI, DBCLS, NCBO,
OpenPHACTS, and many others
chemicals/drugs/formulations, genomes/genes/proteins, domainsInteractions, complexes & pathwaysanimal models and phenotypesDisease, genetic markers, treatmentsTerminologies & publications
@micheldumontier::CEDAR:Jan 20158
Alison Callahan, Jose Cruz-Toledo, Peter Ansell, Michel Dumontier:
Bio2RDF Release 2: Improved Coverage, Interoperability and Provenance of Life Science Linked Data. ESWC 2013: 200-212
Semantic Web for Health Care and Life Sciences Interest Group (HCLS)
• Mission: to develop, advocate for, and support the use of Semantic Web technologies across health care, life sciences, clinical research and translational medicine.
• Since 2001. 86 members from 29 organizations.
• Chairs: Michel Dumontier and Charlie Mead
• Objectives:
– Develop high level and architectural vocabularies.
– Implement proof-of-concept demonstrations and industry-ready code.
– Document guidelines to accelerate the adoption of the technology.
– Disseminate information about the group's work at government, industry, academic events and by participating in community initiatives.
@micheldumontier::CEDAR:Jan 20159
Challenge: Working with Web Data
• Often have inadequate descriptions so we don’t know what they are about or how they were constructed.
• datasets change over time, but often don’t come with versioning information
• may have been constructed using other data, but it’s not clear which version of data was used or whether these were modified
• Data may be available in a variety of formats
• There may be multiple copies of data from different providers, but it’s unclear if they are exact copies or derivatives
@micheldumontier::CEDAR:Jan 201510
Data registries aren’t in sync
– Identifiers.org, Bio2RDF.org, BioSharing.org, etc.
– May be concerned about only some data elements i.e. incomplete
– May be out-of-date and there is no easy way to exchange data descriptions
– May contain conflicting information, unclear the sources used.
@micheldumontier::CEDAR:Jan 201511
no single vocabulary provides all key metadata fields
@micheldumontier::CEDAR:Jan 201512
Key Use Cases
1. Dataset Identification, Description, Licensing and Provenance
2. Dataset Discovery (via Catalog)
3. Exchange of Dataset Descriptions
4. Dataset Linking
5. Content Summary
6. Monitoring of Dataset Changes
@micheldumontier::CEDAR:Jan 201513
Objective
• Develop a guidance note for reusing existing vocabularies to describe datasets with RDF– Mandatory, recommended, optional descriptors– Identifiers– Versioning– Attribution– Provenance– Content summarization
• Recommend vocabulary-linked attributes and value sets
• Provide reference editor and validation
@micheldumontier::CEDAR:Jan 201514
Dublin Core Metadata Initiative
Widely used
Broadly applicable– Documents
– Datasets
✗Generic terms
✗Not comprehensive
✗No required properties
@micheldumontier::CEDAR:Jan 2015
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“Date: A point or period of time associated with an event in the lifecycle of the resource.”
DCAT: Data Catalog
Separates Dataset and Distribution
✗No versioning
✗No prescribed properties
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2015
VoID: Vocabulary of Interlinked Datasets
Metadata carried with data
– Directly embedded: void:inDataset
✗No versioning
✗No checklist of requisite fields
✗Only for RDF data
We compiled a list of metadata fields used across the community
@micheldumontier::CEDAR:Jan 201518
and then surveyed over 20 vocabularies to see if they provided relevant metadata elements or value sets
To produce a big spreadsheet that maps metadata needs with existing vocabularies
@micheldumontier::CEDAR:Jan 201519
@micheldumontier::CEDAR:Jan 201520
Dataset
“A collection of data, available for access or download in one or more formats”
– DCAT
@micheldumontier::CEDAR:Jan 201521
Included Vocabularies
@micheldumontier::CEDAR:Jan 201522
Three Component Metadata Model:description – version - distribution
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Example of Use
@micheldumontier::CEDAR:Jan 201524
61 metadata elements
@micheldumontier::CEDAR:Jan 201525
Metadata element, description, and example of use
@micheldumontier::CEDAR:Jan 201526
Metadata Specificationconstrained property:value pairs
@micheldumontier::CEDAR:Jan 201527
The key words "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL
NOT", "SHOULD", "SHOULD NOT", "RECOMMENDED", "MAY", and
"OPTIONAL" in this document are to be interpreted as described in
RFC 2119 [RFC2119].
Description
• Identifiers• Title• Description• Homepage• License• Language• Keywords• Concepts and vocabularies used• Standards• Publication
@micheldumontier::CEDAR:Jan 201528
Attribution
• Simple Model– Individuals are related to roles using specific
propertiese.g. dct:creator, pav:createdBy, pav:curatedBy
• Expandable Model– Individuals are related to roles and dates by
associated object– PROV, ViVo
@micheldumontier::CEDAR:Jan 201529
Provenance and Change
• Version number
• Source
• Provenance: retrieved from, derived from, created with
• Frequency of change
@micheldumontier::CEDAR:Jan 201530
Availability
• Format
• Download URL
• Landing page
• SPARQL endpoint
@micheldumontier::CEDAR:Jan 201531
RDF Dataset Statistics
Basic Statistics
• # of triples
• # of typed entities
• # of distinct subjects
• # of distinct predicates
• # of distinct objects
• # of classes
• # of literals
Enhanced Statistics
• Classes + #
• Properties + triples
• Subject Types + # Property + triples
• Object Types + # Property + triples
• Literals + # Property + triples
• Dataset-Dataset links
@micheldumontier::CEDAR:Jan 201532
Application scenarios
@micheldumontier::CEDAR:Jan 201533
VoID Editor
@micheldumontier::CEDAR:Jan 201534
Validator
@micheldumontier::CEDAR:Jan 201535
New version using ShEx in development
Towards Semantic Interoperability
@micheldumontier::CEDAR:Jan 201536
dumontierlab.com
@micheldumontier::CEDAR:Jan 2015
Website: http://dumontierlab.comPresentations: http://slideshare.com/micheldumontier
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HCLS:http://www.w3.org/blog/hcls/
Mailing list:http://lists.w3.org/Archives/Public/public-semweb-lifesci/
Editors’ Draft: http://tiny.cc/hcls-datadesc-ed
W3C Interest Group Note:http://tiny.cc/hcls-datadesc
Special thanks to Alasdair Gray, Scott Marshall, Joachim BaranThanks to all other contributors to the HCLS note