60-minute FAIRification of a dataset

Daphne van Beek, Mark Thompson, Kees Burger, Rajaram Kaliyaperumal

https://fair-course.fair-dtls.surf-hosted.nl/fairifier

http://biosb.ubec.nl

http://biosb.ubec.nl

Findable:

F1. (meta)data are assigned a globally unique and persistent identifier;

F2. data are described with rich metadata;

F3. metadata clearly and explicitly include the identifier of the data it describes;

F4. (meta)data are registered or indexed in a searchable resource;

Accessible:

A1. (meta)data are retrievable by their identifier using a standardized communications protocol;

A1.1 the protocol is open, free, and universally implementable;

A1.2. the protocol allows for an authentication and authorization procedure, where necessary;

A2. metadata are accessible, even when the data are no longer available;

Interoperable:

I1. (meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation.

I2. (meta)data use vocabularies that follow FAIR principles;

I3. (meta)data include qualified references to other (meta)data;

Reusable:

R1. (meta)data are richly described with a plurality of accurate and relevant attributes;

R1.1. (meta)data are released with a clear and accessible data usage license;

R1.2. (meta)data are associated with detailed provenance;

R1.3. (meta)data meet domain-relevant community standards;

Principles allowing automatic interoperation of data

Why?

  • Good data stewardship is required for ‘better science’
  • Requirement funders and journals
  • Legal obligation
  • Integrate your data with external databases
  • Protect your scientific integrity
  • Get credit for the work you’ve done

http://biosb.ubec.nl

http://biosb.ubec.nl

How?

  • Generate a data model using identifiers
  • Use existing ontologies to describe your dataset
  • Convert your dataset into RDF triples
  • Expose your files as a SPARQL endpoint
  • Query your data!

Define driving user question(s)

Pre-
FAIRification analysis

Define semantic model

Define metadata

Transform data records

Deploy FAIR data resource

Query interface or user app

- Analyze question, data and prioritize essential data subset

- Conceptual model

- Available ontologies and data models

- Detailed instance model

- Principles for F, R: “rich metadata”

Includes usage policy/license

- Apply semantic model to original data

- FAIR-compliant, machine readable knowledge graph representation

- FAIR Data Point:
data and metadata (DTL)

http://biosb.ubec.nl

http://biosb.ubec.nl

What?

http://biosb.ubec.nl

http://biosb.ubec.nl

List of political parties in the Netherlands, wikipedia.

Identifiers

  • Uniquely and unambiguously identify data items
  • Linked Data implementation: URLs

Example:
http://www.wikidata.org/entity/Q57792

http://mydomainname.com/person/1

http://biosb.ubec.nl

http://biosb.ubec.nl

http://biosb.ubec.nl

http://biosb.ubec.nl

Triples

http://biosb.ubec.nl

Subject

Predicate

Object

http://biosb.ubec.nl

Triples

<http://mydomainname.com/person/1> foaf:name “Mark Rutte” .

http://biosb.ubec.nl

http://biosb.ubec.nl

Questions?

Foaf: PREFIX

What is RDF?

Triples

<http://mydomainname.com/person/1> foaf:name “Mark Rutte” .
<http://mydomainname.com/person/1> rdf:type <http://xmlns.com/foaf/0.1/Person> .

http://biosb.ubec.nl

http://biosb.ubec.nl

-> ontologies

-> machine readability

Full data model

http://biosb.ubec.nl

http://biosb.ubec.nl

Add simplified table

Link to wikidata

Query

Publish

Fairification

http://biosb.ubec.nl

Demo: query

What are the other occupations of political party leaders apart from politics?

http://biosb.ubec.nl

http://biosb.ubec.nl

Demo: query

What are the other occupations of political party leaders apart from politics?

http://biosb.ubec.nl

http://biosb.ubec.nl

Try it yourself: query and win!

In which dutch province were most political party leaders born?

https://tinyurl.com/fairquery

https://tinyurl.com/fairPrefixs

http://biosb.ubec.nl

http://biosb.ubec.nl

http://fair-course.fair-dtls.surf-hosted.nl:7200/sparql

In which dutch province were most political party leaders born?

http://biosb.ubec.nl

Person

Human

Place

province of the Netherlands

municipality

http://biosb.ubec.nl

In which dutch province were most political party leaders born?

http://biosb.ubec.nl

Person

Human

Place

province of the Netherlands

place of birth

closeMatch

located in the administrative territorial entity

Instance of

municipality

http://biosb.ubec.nl

Findable:

F1. (meta)data are assigned a globally unique and persistent identifier;

F2. data are described with rich metadata;

F3. metadata clearly and explicitly include the identifier of the data it describes;

F4. (meta)data are registered or indexed in a searchable resource;

Accessible:

A1. (meta)data are retrievable by their identifier using a standardized communications protocol;

A1.1 the protocol is open, free, and universally implementable;

A1.2. the protocol allows for an authentication and authorization procedure, where necessary;

A2. metadata are accessible, even when the data are no longer available;

Interoperable:

I1. (meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation.

I2. (meta)data use vocabularies that follow FAIR principles;

I3. (meta)data include qualified references to other (meta)data;

Reusable:

R1. (meta)data are richly described with a plurality of accurate and relevant attributes;

R1.1. (meta)data are released with a clear and accessible data usage license;

R1.2. (meta)data are associated with detailed provenance;

R1.3. (meta)data meet domain-relevant community standards;

Principles allowing automatic interoperation of data

References

http://biosb.ubec.nl

http://biosb.ubec.nl

http://biosb.ubec.nl

FAIR breakout session - Google Slides