W3C HCLS Dataset Description Guidelines

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.


The Semantic Webis the new global web of knowledge

3 @micheldumontier::CEDAR:Jan 2015

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.



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:>

http://www.w3.org/2000/01/rdf-schema

The linked data network expands with every reference


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

6

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/”


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


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.


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


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.


no single vocabulary provides all key metadata fields


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


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


Dublin Core Metadata Initiative

Widely used

Broadly applicable– Documents

– Datasets

✗Generic terms

✗Not comprehensive

✗No required properties


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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


17@micheldumontier::CEDAR:Jan

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


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



Dataset

“A collection of data, available for access or download in one or more formats”

– DCAT


Included Vocabularies


Three Component Metadata Model:description – version - distribution


Example of Use


61 metadata elements


Metadata element, description, and example of use


Metadata Specificationconstrained property:value pairs


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].

http://htmlpreview.github.io/?https://github.com/joejimbo/HCLSDatasetDescriptions/blob/master/Overview.html#RFC2119

Description

• Identifiers• Title• Description• Homepage• License• Language• Keywords• Concepts and vocabularies used• Standards• Publication


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


Provenance and Change

• Version number

• Source

• Provenance: retrieved from, derived from, created with

• Frequency of change


Availability

• Format

• Download URL

• Landing page

• SPARQL endpoint


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


Application scenarios


VoID Editor


Validator


New version using ShEx in development

Towards Semantic Interoperability


dumontierlab.com

[email protected]


Website: http://dumontierlab.comPresentations: http://slideshare.com/micheldumontier

37

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

http://dumontierlab.com/

http://slideshare.com/micheldumontier

http://www.w3.org/blog/hcls/

http://lists.w3.org/Archives/Public/public-semweb-lifesci/

http://tiny.cc/hcls-datadesc-ed

http://tiny.cc/hcls-datadesc

W3C HCLS Dataset Description Guidelines

Internet

web of data

linked data network

relationsintegrating

prefix drugbank

data w3c standardreusing

labeldiclofenac drugbank

labeldi drugbank

new global web of knowledge