Mendeley Data FAIR hackathon

MENDELEY FAIR HACKATHON
Luiz Olavo Bonino - luiz.bonino@dtls.nl

WHAT IS FAIR DATA?
I need data.
What should I do?

WHAT IS FAIR DATA?
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;
http://www.nature.com/articles/sdata201618

WHAT IS FAIR DATA?
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;
■ http://www.nature.com/articles/sdata201618

WHAT IS FAIR DATA?
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;

WHAT IS FAIR 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;

NETHERLANDS
FAIR transformation FAIR transformation
Analysis transformation Analysis transformation

FAIRNESS LEVELS
PID
Metadata (intrinsic)
'provenance' (user defined)
Data (elements)
Non-FAIR
PID
Data (elements)
Findable
Usable for Humans
PID
Data (elements)
FAIR metadata
PID
Data (elements)
FAIR data-
restricted access
PID
Data (elements)
FAIR data-
Open Access
PID
Data (elements)
FAIR data-
Open Access/Functionally Linked

FAIR DATA POINT
A particular class of FAIR Data System that provides access to
datasets in a FAIR manner. The datasets can be external or
internal to the FAIR Data Point. Also, the source data can be a
non-FAIR dataset or a FAIR Data Resource. If the source data is
non-FAIR, the FAIR Data Point needs to made the necessary FAIR
transformations on the fly.
FAIR Data Resource
non-FAIR Data Resource

FAIR DATA POINT
Who
are you? Can I
trust you?

FAIR DATA POINT
Here
is information about
myself
FDP
Metadata
Who is responsible?
FDP license?
Description?

FAIR DATA POINT Ok,
now that I know
you, tell me what you
have to offer
reads
FDP
Metadata

FAIR DATA POINT
Here is
information about my
catalog of datasets
Catalog
Metadata

FAIR DATA POINT
Tell
me more about your
genomic dataset
reads
Catalog
Metadata

FAIR DATA POINT
This
is the information about the
genomic dataset
Dataset
Metadata
License?
Publisher?
Last modified date?
Theme?

FAIR DATA POINT
In
which forms the
dataset is available?
reads
Dataset
Metadata

FAIR DATA POINT
This
is the information about the
dataset distributions
Distribution
Metadata
Access or download URL?
Format?
Size?
Media type?

FAIR DATA POINT
Tell
me more about the
dataset content
reads
Dataset
Metadata

FAIR DATA POINT
This
is the information about the data
record of the dataset
Data record
Metadata
Types?
Domain?
Range?

FAIR DATA POINT Ok,
now that I know
what you have, give
me the data.
reads
Dataset, distribution,
data record metadata

FAIR DATA POINT
Here
is my data.
FAIR Data

FAIR DATA POINT - ARCHITECTURE
FAIR API / GUI
Metadata
Provider
FAIR Accessor
Metrics Gatherer Security Enforcer
FAIR Metadata FAIR Data

FAIR Data Point metadata
Title
Responsible institution(s)
Contact
FAIR API version
License
…

FDP METADATA
<http://dev-vm.fair-dtls.surf-hosted.nl:8082/fdp> dct:alternative "DTL FDP"@en ;
dct:description "The DTL FAIR Data Point hosts the FAIR Data versions of datasets that
have been made FAIR during BYODs as well as other relevant life sciences datasets"@en ;
dct:subject "FAIR Data" , "Life Sciences" ;
dct:title "DTL FAIR Data Point"@en ;
<http://www.re3data.org/schema/3-0#api> <http://dtls.nl/fdp#api=1> ;
<http://www.re3data.org/schema/3-0#catalog> <http://dev-vm.fair-dtls.surf-hosted.nl:
8082/fdp/biobank> , <http://dev-vm.fair-dtls.surf-hosted.nl:8082/fdp/comparativeGenomics> ,
<http://dev-vm.fair-dtls.surf-hosted.nl:8082/fdp/patient-registry> , <http://dev-vm.fair-
dtls.surf-hosted.nl:8082/fdp/textmining> , <http://dev-vm.fair-dtls.surf-hosted.nl:8082/fdp/
transcriptomics> ;
<http://www.re3data.org/schema/3-0#institution> <http://dtls.nl> ;
<http://www.re3data.org/schema/3-0#institutionCountry> <http://lexvo.org/id/iso3166/NL>
;
<http://www.re3data.org/schema/3-0#lastUpdate> "2016-10-27"^^xsd:date ;
<http://www.re3data.org/schema/3-0#software> "FAIR Data Point" ;
<http://www.re3data.org/schema/3-0#startDate> "2016-10-27"^^xsd:date ;
a <http://www.re3data.org/schema/3-0#Repository> ;
rdfs:label "DTL FAIR Data Point"@en ;
<http://xmlns.com/foaf/0.1/landingpage> <http://dev-vm.fair-dtls.surf-hosted.nl:8082/
fdp/swagger-ui.html> .

Catalog metadata
Title
Theme taxonomy
Issued date
…

CATALOG METADATA
<http://dev-vm.fair-dtls.surf-hosted.nl:8082/fdp/biobank> dct:hasVersion "1.0" ;
dct:identifier "biobank" ;
dct:issued "2016-02-01"^^xsd:date ;
dct:language lang:en ;
dct:modified "2016-08-01"^^xsd:date ;
dct:title "Rd connect's biobank catalog"@en ;
a dcat:Catalog ;
rdfs:label "Rd connect's biobank catalog"@en ;
dcat:dataset <http://dev-vm.fair-dtls.surf-hosted.nl:8082/fdp/biobank/77350-
collection1> ;
dcat:themeTaxonomy <http://dbpedia.org/resource/Biobank> , <http://edamontology.org/
topic_3337> .

Catalog 1 metadata
Dataset metadata
Title
Publisher
License
Theme(s)
Version
…

DATASET METADATA
<http://dev-vm.fair-dtls.surf-hosted.nl:8082/fdp/biobank/77350-collection1>
dct:creator <http://orcid.org/0000-0002-1215-167X> ;
dct:hasVersion "1.0" ;
dct:identifier "77350-collection1" ;
dct:publisher <http://orcid.org/0000-0002-1215-167X> ;
dct:title "Galliera Genetic Bank"@en ;
<http://rdf.biosemantics.org/ontologies/fdp-o#dataRecord> <http://dev-
vm.fair-dtls.surf-hosted.nl:8082/fdp/datarecord/77350-collection1-
datarecord-1> ;
a dcat:Dataset ;
rdfs:label "Galliera Genetic Bank"@en ;
rdfs:seeAlso <http://catalogue.rd-connect.eu/web/galliera-genetic-bank/
bb_home> ;
dcat:distribution <http://dev-vm.fair-dtls.surf-hosted.nl:8082/fdp/
biobank/77350-collection1/csv> , <http://dev-vm.fair-dtls.surf-hosted.nl:8082/
fdp/biobank/77350-collection1/distributionTurtle> , <http://dev-vm.fair-
dtls.surf-hosted.nl:8082/fdp/biobank/77350-collection1/ldf> ;
dcat:keyword "Galliera Genetic Bank" , "biobank" ;
dcat:landingPage <http://ggb.galliera.it> ;
dcat:theme <http://dbpedia.org/resource/Biobank> , <http://
edamontology.org/topic_3337> , <http://www.orpha.net/ORDO/Orphanet_1023> …

Catalog 1 metadata
Dataset 1 metadata
Distribution metadata
Title
Media type
Download/access URL
License
…

DISTRIBUTION METADATA
<http://dev-vm.fair-dtls.surf-hosted.nl:8082/fdp/biobank/77350-collection1/
distributionTurtle> dct:description "Ring14 biobank turtle distribution"@en ;
dct:identifier "distributionTurtle" ;
dct:license <http://rdflicense.appspot.com/rdflicense/cc-by-nc-nd3.0> ;
dct:title "Ring14 biobank turtle distribution"@en ;
a dcat:Distribution ;
rdfs:label "Ring14 biobank turtle distribution"@en ;
dcat:downloadURL <http://semlab1.liacs.nl:8080/rdc-demo-dataset/RING_14_dummy-
Biobank.ttl> ;
dcat:mediaType "text/turtle" .
<http://dev-vm.fair-dtls.surf-hosted.nl:8082/fdp/biobank/77350-collection1/ldf>
dct:description "Ring14 biobank linked data fragment distribution"@en ;
dct:identifier "ldf" ;
dct:license <http://rdflicense.appspot.com/rdflicense/cc-by-nc-nd3.0> ;
dct:title "Ring14 biobank linked data fragment distribution"@en ;
a dcat:Distribution ;
rdfs:label "Ring14 biobank linked data fragment distribution"@en ;
dcat:accessURL <http://dev-vm.fair-dtls.surf-hosted.nl:5050/ring14-biosample> .

Catalog metadata
Dataset metadata
Distribution
metadata
Data record
metadata
Type
Domain
Range
…

DATA RECORD METADATA
<http://dev-vm.fair-dtls.surf-hosted.nl:8082/fdp/datarecord/77350-collection1-
datarecord-1> dct:hasVersion "1.0" ;
dct:identifier "77350-collection1-datarecord-1" ;
dct:publisher <http://orcid.org/0000-0002-1215-167X> ;
dct:title "Galliera Genetic Bank datarecord metadata" ;
<http://rdf.biosemantics.org/ontologies/fdp-o#refersTo> <http://dev-vm.fair-
dtls.surf-hosted.nl:8082/fdp/biobank/77350-collection1/csv> ;
<http://rdf.biosemantics.org/ontologies/fdp-o#rmlMapping> <https://git.lumc.nl/
biosemantics/ring14-fdp-metadata/raw/bd01b84fb792ae3860fdda646e9cb96a1a11205c/rml/bioban
RING_14_biobank_mapping.ttl> ;
a <http://rdf.biosemantics.org/ontologies/fdp-o#DataRecord> ;
rdfs:label "Galliera Genetic Bank datarecord metadata" .
<#ring14-biobank-id-resource>
rml:logicalSource <#inputFile>;
rr:subjectMap [
rr:template "http://rdf.biosemantics.org/dataset/ring14/resource/identifier/
{Sample ID}" ;
rr:class <http://rdf.biosemantics.org/ontologies/rd-connect/
21f6df30_1f72_45fb_bfc1_2b3d1af1410a>
];

Catalog 2
metadata
Catalog 1 metadata
Dataset 1
metadata
Distribution
1.a metadata
Data record
metadata
Distribution
1.b metadata
Dataset 2
metadata
Distribution
2.a metadata
Data record
metadata
Distribution
2.b metadata
Dataset 3
metadata
Distribution
3.a metadata
Data record
metadata

FAIR DATA POINT
B
iobank
FA
IR
D
ata
Point
Biobank
D
atabase
Patient
R
egistry
FA
IR
D
ata
Point
U
N
IP
R
O
T
FA
IR
D
ata
Point
H
PA
FA
IR
D
ata
Point

METADATA LAYERS
Layer Description Example Standard
FDP (Data
repository)
Information about the FDP as
a data repository
PID, title, description,
license, owner, API
version, etc.
RE3Data
Catalog Information about the
catalog of datasets offered
PID, title, description,
publisher, etc.
W3C DCAT
#Catalog
Dataset Information about each of
the offered datasets
Publisher, issue date,
theme, etc.
W3C DCAT
#Dataset,
Distribution Information about how the
dataset is distributed
AccessURL,
downloadURL, format,
mediaType, etc.
W3C DCAT
#Distribution
Data record Information about the actual
data, types, identifiers, etc.
Data items types,
identifiers, domain,
range, etc.
RML
OAI-PMH

DEMO FAIR DATA POINT
http://dev-vm.fair-dtls.surf-hosted.nl:8082/fdp/swagger-ui.html
http://dev-vm.fair-dtls.surf-hosted.nl:8082/fdp/
API
GUI

FAIR DATA POINT
Metadata
Provider
FAIR Accessor

EXISTING DATA REPOSITORIES
Metadata
Provider
FAIR Accessor

EXTENDING EXISTING DATA REPOSITORIES
Metadata
Provider
FAIR Accessor
+
Metadata
Provider
FAIR Data
Accessor
Metrics Gatherer Access Controller
EUDAT Current
Components
EUDAT Current
Components
EUDAT Current
Components
Current
Solution
Components

FAIR DATA ECOSYSTEM
Create Publish AnnotateFind
0110011
1100101
1001100
Open RDF
Knowledge AnnotatorORKA
DataFAIRport

0110011
1100101
1001100
Development started in October 2016

FAIR Metadata FAIR Metadata FAIR Metadata FAIR Metadata
0110011
1100101
1001100
metadata
index
retrieves
metadata
search
interfaces
(GUI and API)

Development started in October 2016
Based on OpenRefine

FAIRIFICATION PROCESS
■ Retrieve original data
■ Dataset identification and analysis
■ Definition of the semantic model
■ Data transformation
■ License assignment
■ Metadata definition
■ FAIR Data resource (data, metadata, license)
deployment

FAIRIFICATION
Original dataset
FAIR Data Resource
FAIR Format
Metadata Licensesubmit generate
Generic
semantic
model

Resolution ServicesInput
Non-FAIR Dataset
Metadata
License
ARTA Service
Identiﬁer Service
Vocabulary Service
FAIR Data Resource
FAIR Format
Metadata License
output
FAIR Data
Model Registry

FAIRIFIER
■ Transform non-FAIR datasets into FAIR Data Resources
(dataset in FAIR format, license and metadata)
■ Data munging
■ Semantic modeling
■ License definition
■ Metadata definition and extraction
■ Data publication

FAIR DATA MODEL REGISTRY
FAIR Data
Model Registry
Dataset
Data Model
Dataset
Data Model
Dataset
Data Model

FAIRIFICATION - NEW DATASET TYPE
Original dataset
FAIR Data Resource
FAIR Format
FAIR Data
Model Registry
store
Non-FAIR
- FAIR
mapping

FAIRIFICATION - RECURRING DATASET TYPE
Original dataset
FAIR Data Resource
FAIR Format
FAIR Data
Model Registry
query
Non-FAIR
- FAIR
mapping
retrieve

■ A particular class of FAIR Data System to provide
support for data interoperability;
■ Supports publication and access to FAIR data.
■ Fosters an ecosystems of applications and services;
■ Federated architecture: different FAIRports (and other
FAIR Data Systems) are interconnectable;
■ Supports citations of datasets and data items;
■ Provides metrics for data usage and citation;
DataFAIRport

FAIR Data Search
Engine
FAIRiﬁer +
(Meta)Data
Publication
Metadata storage
Data storage
(optional)
Transformation
Services Registry
(optional)
FAIR Data Point
DataFAIRport
DTL
FAIR Data PointFAIR Data Point
F A I
R

FAIRPORT
DataFAIRportFind,&Access,&Interoperate&&&Re3use&Data
Stewardship API FAIR Data API
(Meta)Data Storage component
Metadata storage
Data storage
DataVerse EUDAT Data Repository
Semantic resolver Ontology storage
Data storage API / FAIR Data API
Data usage policy
Management component
GUI (Data publishing, search, mgmt)
Data Mgmt App
FAIR Data System
Metrics storage
Data Consumer
Data Producer
Data Consumer Apps
Ex. *APInatomy, BRAIN,
etc)
Data Consumer Apps
etc)
Data Consumer Apps
etc)
Data Consumer Apps
etc)Data Mgmt AppData Mgmt App
Data
Stewardship
Apps

■ Allow third-party annotation on existing knowledge
bases
■ Capture the provenance of the annotator and the
original statement
Open RDF
Knowledge AnnotatorORKA

DEMO: HTTP://DEV-VM.FAIR-DTLS.SURF-HOSTED.NL:8080/#/

DEMO: HTTP://DEV-VM.FAIR-DTLS.SURF-HOSTED.NL:8080/#/
ANNOTATIONS GO TO NANOPUB STORE

TOOLS ROADMAP
Dec 16 Jan 17 Feb 17 Mar 17
FAIR Data
Point
Version 1
Metadata editor,
release metadata,
POST, FAIR
accessor
Version 1.1
Reintroduce OAI-
PMH compliance
Version 1.2
Update
notification
FAIR Data
Search
Engine
Beta 1
Crawler,
metadata index
and search GUI
Beta 2
Improved search
GUI, search API
FAIRifier
Beta 1
OpenRefine + RDF
plugin, publication
to FAIR Data Point
Beta 2
Metadata
definition and
extraction (RML),
license picker

TOOLS ROADMAP
Dec 16 Jan 17 Feb 17 Mar 17
FAIR Data
Model
Registry
Alpha 1
Start of the
integration work
ORKA
Beta 1
Definition of 2-3
use cases
Beta 2
Extended with
features required
by the use cases
Data
FAIRport
Alpha 1
Start of the
integration work

FAIR HACKATHON - GOALS
■ Align solutions with FAIR Data Point specifications.
■ Metadata content
■ API
■ Data

FAIR HACKATHON OUTCOME
■ FAIR data model for solutions content;
■ Architecture of the required adjustments/extensions;
■ Technical specification of the adjustments/extensions;
■ Proof-of-concept of the adjusted solution;

DTL’S FAIR HACKATHONS ROADMAP
■ EUDAT (pilot project ongoing)
■ EGA (July 6-8 2016)
■ Molgenis (Oct 19-20 2016)
■ Patient registry solution providers (Oct 25-27 2016)
■ Mendeley (Nov 18 2016)
■ Quaero Systems (Nov 24 2016)
■ tranSMART (TBD)
■ phenotypeDB (TBD)
■ Euretos Knowledge Platform (TBD)
■ NIH, Australian National Data Services, Brazilian open government
data, …

BRING YOUR OWN DATA - BYOD
■ Goals:
■ Learn how to make data linkable “hands-on” with experts
■ Create a “telling story” to demonstrate its use
■ Make FAIR Data at the source
■ Composition:
■ Data owners – specialists on given datasets
■ Data interoperability experts
■ Domain experts
Source: Marcos Roos

NETHERLANDS
Domain Expert
Data Owner FAIR Data Expert
BYOD

NETHERLANDS
BYOD
Non-FAIR Dataset
Metadata
Non-FAIR Dataset
FAIR Data
Transformation
Ontology
Ontology
FAIR datasets
FAIR datasets

NETHERLANDS
BYOD Planning
Preparation Execution Follow Up

NETHERLANDS
BYOD Planning
Preparation
Identify Plan
Datasets
Attendees' profile
Output data access
Tentative dates
Tentative venue
Costs
Funds
Coordination
Set date
Invite attendees
Set venue
Catering
Lodging
Financial planning
Publicity
Working document
Preparatory calls
Data hosting
Software hosting
Documentation hosting

NETHERLANDS
BYOD Planning
Execution
Day One
Introduction
SW, LD, Ontology intro
Use case intro
Workgroups division
Working sessions
WWW/TTTALA
Day Two
Progress report
Working sessions
Groups reports
WWW/TTTALA
Day Three
Data integration
Answer driving question
Explore data
Demo improvement
Final report
WWW/TTTALA

NETHERLANDS
BYOD Planning
Follow-Up
D+15
Report difficulties
Clarifications
Next steps
D+45
Report difficulties
Clarifications
Next steps
Implementation
Expand FAIRification
Implement solution
Scale-up solution
Deploy

BBMRI
2.0
FAIR
dICT
RD
Connectt
ODEX4ALL
myFAIR
Elixir
Excellerate
Core FAIR
Technology
FAIR Data E.T.
FAIR Data E.T.
FAIR Data E.T.
FAIR Data E.T.
FAIR Data E.T.
FAIR Data E.T.
DTL

RELATED PROJECTS
ODEX4all
FAIR-dICT
myFAIR

Mendeley Data FAIR hackathon

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