Supporting Dataset Descriptions in the Life Sciences

Alasdair J G GrayHeriot-Watt University www.macs.hw.ac.uk/~ajg33A.J.G.Gray@hw.ac.uk@gray_alasdair

FAIR Data Principles

5 April 2017 @gray_alasdair www.macs.hw.ac.uk/~ajg33 2

Wilkinson, M. D. et al. The FAIR Guiding Principles for scientific data management and stewardship Authors. Nature Scientific Data 3, 1–15 (2016). DOI: 10.1038/sdata.2016.18

Degrees of FAIRness

@gray_alasdairwww.macs.hw.ac.uk/~ajg33 4

Open PHACTS Explorer

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Data Cache (Triple Store)

Semantic Workflow Engine

Linked Data API (RDF/XML, TTL, JSON) DomainSpecificServices

Identity Resolution

Service

IdentifierManagement

Service

“Adenosine receptor 2a”

EC2.43.4CS4532

P12374

ChEMBL-RDF

ChEMBLv13

Chem2Bio2RDF

v13v12

v2 or v8

Which ChEMBL version?

5 April 2017 @gray_alasdair www.macs.hw.ac.uk/~ajg33

Historic Use Case~January 2012

Open PHACTS v2.1ChEMBL 20

http://tiny.cc/ops-datasets

Open PHACTS Provenance

5 April 2017 @gray_alasdair www.macs.hw.ac.uk/~ajg33

Open PHACTS FAIR Data

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Data Reuse 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– Can be out-of-date– Can contain conflicting information

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Scientists require data provenance!

Goal: To be FAIR

Open PHACTS Dataset Description Guidelines

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Challenging for Publishers:• Datasets are complex• Evolve over time• Another publishing burden• Requires RDF knowledge• Descriptions are complex• Metadata precision

Tooling support required!

Open PHACTS Dataset Description Model

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Open PHACTS Dataset Description Guidelines

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Help me describe my data!

No! Use the Open PHACTS VoID Editor

Thanks for converting my data to RDF, can you help me make it findable by creating a VoID dataset description?

Dataset description Metadata Boring

Here are the guidelines, just write the terms in a text document.

Characters reproduced from Piled Higher and Deeper by Jorge Cham, http://phdcomics.com

Open PHACTS VoID Editor

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Open PHACTS Validator

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(Some) Life Sciences Metadata Specifications

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HCLS DataDesc

Bioschemas

Schema.org for biologyMinimum properties for • Finding data• Presenting search results

<div> <h1>Classic potato salad</h1> <div> Nutrition facts: <span>144 kcal</span>, </div>

Ingredients: - <span>800g small new potato</span> - <span>3 shallot</span> . . .

Structured data markup for web pages

Without markup

<div> <h1>Classic potato salad</h1> <div> Nutrition facts: <span>144 kcal</span>, </div>

Ingredients: - <span>800g small new potato</span> - <span>3 shallot</span> . . .

Recipe

Nutrition

Calories

Ingridients

Without markup

<div itemscope itemtype="http://schema.org/Recipe"> <h1 itemprop="name">Classic potato salad</h1> <div itemprop="nutrition” itemscope

itemtype="http://schema.org/NutritionInformation"> Nutrition facts: <span itemprop="calories">144 kcal</span>, </div>

Ingredients: - <span itemprop="recipeIngredient">800g small new potato</span> - <span itemprop="recipeIngredient">3 shallot</span> . . .

RDFaJSON-LD

Microdata With markup

Minimum informationControlled vocabularies

Cardinality

Data model

New properties24

The ELIXIR Implementation Study

1. Data Repositories

2. Datasets

3. Beacons4. Samples

6. Protein

Annotations

7. Bioschemas registry

8. Validation

Henning Hermjakob

Susanna A Sansone

Serena ScollenHelen Parkinson

Rafa Jimenez

Maria Martin

Audald Lloret

Alasdair Gray

Planning

Agreement

Adoption

Application

March-April 2017

May-June 2017

July-Oct 2017

Nov-Feb 2018

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HCLS DataDesc

W3C HCLS GroupDumontier, M. et al. The health care and life sciences community profile for dataset descriptions. PeerJ 4, e2331 (2016). DOI:10.7717/peerj.2331

Use Case Requirements

Standard metadata requirements plus:

1. Resolvable identifiers for metadata

2. Descriptions of data identifiers

3. Data provenance

4. Data statistics

HCLS Dataset Descriptions

61 Metadata properties from 18 vocabularies5 Modules: Core, Identifiers, Provenance, Distributions, Stats

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Prescribed UsageElement Property Value Summary

LevelVersion Level

Distribution Level

Core MetadataType declaration rdf:type dctypes:Dataset MUST MUST SHOULD

Type declaration rdf:type void:Dataset or

dcat:DistributionMUST NOT

MUST NOT MUST

Title dct:title rdf:langString MUST MUST MUSTAlternative titles dct:alternative rdf:langString MAY MAY MAY

Description dct:description rdf:langString MUST MUST MUST

… … … … … …

ChEMBL: Summary Level

Implementations

RDF Platform

More coming…5 April 2017

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HCLS DataDesc

Layered Descriptions

Minimal dataset description More detailed

description

Dataset

Sketch of content

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HCLS DataDesc

Configurable Tooling

Creation Validation

✗ ✓

Creation Validation

✓ ✓

Constraint LanguagesShEx SHACL JSON Schema

Status W3C Draft CG Report

W3C Working Draft IETF Internet-Draft v5

Notation Concise notation Extended SPARQL JSONData model RDF RDF JSON (JSON-LD?)Open/closed Supported Supported ClosedResult format Defined DefinedConstraint types supported• Domain ✓ ✓ ✓• Values ✓ ✓ ✓• Cardinality ✓ ✓ ✓• Vocabulary ✓ ✓ ✗• Recursion ✓ ✗ ✗• Conformance

levels Extension Fixed ✗

Example Constraint

• Shape

• A Dataset– MUST be declared to be of type dctype:Dataset– MUST have a dcterms:title as a language typed string– MUST NOT have dcterms:created date

<Dataset> rdf:langString

Dates are associated with versions in HCLS

Example Validation

• Shape

• Data

Example Validation

• Shape

• Data

Not Valid

Example Validation

• Shape

• Data

<Dataset> { rdf:type (dctypes:Dataset), dct:title rdf:langString, dct:alternative rdf:langString+, !dct:created .}

Shape Expressions (ShEx)

ShEx: Validation<Dataset> { rdf:type (dctypes:Dataset), dct:title rdf:langString, dct:alternative rdf:langString+, !dct:created .}

<Dataset> { rdf:type (dctypes:Dataset), dct:title rdf:langString, dct:alternative rdf:langString+, !dct:created .}

Validator can’t warn of missing property

Example data

<Dataset> { `MUST` rdf:type (dctypes:Dataset), `MUST` dct:title rdf:langString, `MAY` dct:alternative rdf:langString+, `MUST` !dct:created .}

Requirement Levels

Validator can warn of missing property

Implementation

Validata• Web app front end• Javascript + HTML• Relies on ShEx-validator

– Validates documents– Returns report

https://github.com/HW-SWeL/Validata

ShEx-validator• Validation system• Validation API• Javascript

– nodejs engine• Reuses

– n3: RDF Library– ShExParser

https://github.com/HW-SWeL/ShEx-validator

http://hw-swel.github.io/Validata/ VALIDATA DEMO

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HCLS DataDesc

Creation Validation

✓ ✓

AcknowledgementsBioSchemas• Carole Gobel• Rafael JimenezFAIR Data• FAIRdom project• Jun ZhaoOpen PHACTS• Christian Brenninkmeijer• Lefteris Tatakis• Andra Waagmeester

Validata (MEng 2015)• Andrew Beveridge• Jacob Baungard Hansen• Johnny Val• Leif Gehrmann• Roisin Farmer• Sunil Khutan• Tomas Robertson

• Eric Prud’hommeaux

5 April 2017

QuestionsValidata https://github.com/HW-SWeL/Validata• RDF constraint validation tool

– Configurable to any profile• Shape Expression (ShEx) constraints

Dumontier, M. et al. The health care and life sciences community profile for dataset descriptions. PeerJ 4, e2331 (2016). DOI:10.7717/peerj.2331

Wilkinson, M. D. et al. The FAIR Guiding Principles for scientific data management and stewardship. Nature Scientific Data 3, 1–15 (2016). DOI: 10.1038/sdata.2016.18

www.macs.hw.ac.uk/~ajg33/A.J.G.Gray@hw.ac.uk@gray_alasdair

5 April 2017

Supporting Dataset Descriptions in the Life Sciences

Data & Analytics

Transcript of Supporting Dataset Descriptions in the Life Sciences

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