Accelerating Biomedical Research with the Emerging Internet of FAIR Data and Services

Accelerating Biomedical Research
with the Emerging Internet of FAIR Data and Services
@micheldumontier::Montpellier:2019-05-271
Michel Dumontier, Ph.D.
Distinguished Professor of Data Science
Director, Institute of Data Science

An increasing number of discoveries
are data-driven

3
A common rejection module (CRM) for acute rejection across multiple organs identifies novel
therapeutics for organ transplantation
Khatri et al. JEM. 210 (11): 2205
DOI: 10.1084/jem.20122709
Main Findings:
1. CRM genes predicted future injury to a graft
2. Mice treated with drugs against the CRM genes extended graft survival
3. Retrospective EHR analysis supports treatment prediction
Key Observations:
1. Meta-analysis offers a more reliable estimate of the magnitude of the effect
2. Data can be used to generate and support/dispute new hypotheses

However, significant effort is
still needed to find the right
datasets, make sense of them,
and ultimately use them for a
new purpose

metadata is key to find and evaluate content

Poor quality experimental metadata frustrates reuse

7 @micheldumontier::Montpellier:2019-05-27
Reproducing landmark studies remains challenging:
39% (39/100) in psychology1
21% (14/67) in pharmacology2
11% (6/53) in cancer3
1doi:10.1038/nature.2015.17433 2doi:10.1038/nrd3439-c1 3doi:10.1038/483531a

we need to completely rethink
how we perform
biomedical research

Lambin et al. Radiother Oncol. 2013. 109(1):159-64. doi: 10.1016/j.radonc.2013.07.007

The Future is Human Machine Collaboration

We need a new social contract,
supported by legal and technological
infrastructure to make digital
resources available to
people and the machines they use

An international, bottom-up paradigm for
the discovery and reuse of digital content
for people and the machines that they use

http://www.nature.com/articles/sdata201618

FAIR: Impact

FAIR in a nutshell
FAIR aims to create social and economic impact by facilitating the
discovery and reuse of digital resources through a set of basic
requirements:
– unique identifiers to retrieve all forms of digital content and knowledge
– high quality meta(data) to enhance discovery of digital resources
– use of common vocabularies to create shared meaning and facilitate search
– adherence to community standards for common representations
– detailed provenance to provide context and facilitate reproducibility
– registered in appropriate repositories to make sure they can be found
– social and technological commitments to realize reliable access
– simpler terms of use to clarify expectations and intensify innovation

FAIR does not imply Open.
Open as possible
closed as is necessary

Improving the FAIRness of digital resources will
increase their potential for reuse

Let’s build the Internet of FAIR data and services

Your invitation to participate
https://osf.io/n7uwp/
erik.schultes@go-fair.org
22

The Semantic Web
is a portal to the web of knowledge
standards for publishing, sharing and querying
facts, expert knowledge and services
scalable approach for the discovery
of independently constructed,
collaboratively described,
distributed knowledge

The semantic web community has built a massive
open and decentralized knowledge graph

• 30+ biomedical data sources
• 10B+ interlinked statements
• EBI, SIB, NCBI, DBCLS, NCBO, and many others
produce this content
chemicals/drugs/formulations,
genomes/genes/proteins, domains
Interactions, complexes & pathways
animal models and phenotypes
Disease, genetic markers, treatments
Terminologies & publications
27
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
Linked Data for the Life Sciences
Bio2RDF is an open source project that uses semantic web
technologies to make it easier to reuse biomedical data

Query the distributed web of data
Phenotypes of
knock-out
mouse models
for the targets
of a selected
drug (Imatinib)

Find and explore data with effective user interfaces
Disclosure: I’m an advisor to OntoForce

Examine the provenance behind the facts
Disclosure: I’m an advisor to OntoForce

Make your work easier to reproduce
AUC 0.91 across all therapeutic indications
Scripts not available. Feature tables available.

Result: ROCAUC 0.831 doesn’t quite match

Find new uses for existing drugs
Finding melanoma drugs through a probabilistic knowledge graph.
PeerJ Computer Science. 2017. 3:e106 https://doi.org/10.7717/peerj-cs.106
by exploring a probabilistic
semantic knowledge graph
And validate them against
pipelines for drug discovery

Analyzing partitioned FAIR health data responsibly
Maastricht Study + MUMC CBS
Goal is to learn high confidence determinants of health in a privacy preserving
manner over vertically partitioned FAIR data from the Maastricht Study and
Statistics Netherlands.
Establish a new social, legal, ethical and technological infrastructure for discovery
science in and across health and non-health settings, including scalable
governance and flexible consent to underpin the responsible use of Big Data.

Unifying API data
with Linked Open Data
API
API

Towards Genuine Semantic Publishing

Automated FAIRness Assessments
• Powered using smartAPI and
semantic web technologies
• Harvests a diverse set of
metadata through HTTP
operations and links in
documents
• Open source and extensible!
39
http://W3id.org/AmIFAIR

Things to think about
• Making data FAIR suffers from a lack of incentives. Maybe data needs to be
stored, before it can be analyzed? How can data generators readily see the
impact of their contributions?
• Making data FAIR is time consuming. To what extent can we automate
this? Can non-expert workers reduce the time? Can we make more data
FAIR at the moment it is generated?
• Making data FAIR requires collaboration. How can we more efficiently
create and sustain communities to establish and disseminate best
practices?
• Making data FAIR is expensive. Some funding agencies (e.g. Horizon2020)
are exploring how to make research data management a budget line item

Summary
• FAIR represents a global initiative to enhance the discovery and reuse of all
kinds of digital resources which will also help address the reproducibility crisis
• It demands a new social, legal and technological infrastructure that currently
doesn’t exist in whole, but has to be built for and tested by various
communities!
• The FAIR concept is transforming into new processes, behaviours and
platforms.
• Huge benefits to be had, particularly in augmenting existing research
programs and in automated machine processing, but needs to be coupled
with the proper technical and ethical training.
@micheldumontier::FAIR:2019-05-2441

michel.dumontier@maastrichtuniversity.nl
Website: http://maastrichtuniversity.nl/ids
42 @micheldumontier::FAIR:2019-05-24
The mission of the Institute of Data Science at Maastricht University is to foster a
collaborative environment for multi-disciplinary data science research,
interdisciplinary training, and data-driven innovation .
We tackle key scientific, technical, social, legal, ethical issues that advance our
understanding across a variety of disciplines and strengthen our communities in the
face of these developments.

Accelerating Biomedical Research with the Emerging Internet of FAIR Data and Services

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