Presentation given during the Mendeley Data FAIR hackathon in London on November 18th 2016.

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

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

3. WHAT IS FAIR DATA?

4. 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

5. WHAT IS FAIR DATA?

6. 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

7. WHAT IS FAIR DATA?

8. 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;
■ http://www.nature.com/articles/sdata201618

9. WHAT IS FAIR DATA?

10. 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;
■ http://www.nature.com/articles/sdata201618

11. NETHERLANDS
FAIR transformation FAIR transformation
Analysis transformation Analysis transformation

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

13. FAIR DATA TOOLS

15. 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

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

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

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

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

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

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

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

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

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

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

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

27. FAIR DATA POINT
Here
is my data.
FAIR Data

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

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

31. 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> .

32. FAIR Data Point metadata
Catalog metadata
Title
Theme taxonomy
Issued date
…

33. 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> .

34. FAIR Data Point metadata
Catalog 1 metadata
Dataset metadata
Title
Publisher
License
Theme(s)
Version
…

35. 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:issued "2016-02-01"^^xsd:date ;
dct:language lang:en ;
dct:modified "2016-08-01"^^xsd:date ;
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> …

36. FAIR Data Point metadata
Catalog 1 metadata
Dataset 1 metadata
Distribution metadata
Title
Media type
Download/access URL
License
…

37. DISTRIBUTION METADATA
<http://dev-vm.fair-dtls.surf-hosted.nl:8082/fdp/biobank/77350-collection1/
distributionTurtle> dct:description "Ring14 biobank turtle distribution"@en ;
dct:hasVersion "1.0" ;
dct:identifier "distributionTurtle" ;
dct:issued "2016-02-01"^^xsd:date ;
dct:license <http://rdflicense.appspot.com/rdflicense/cc-by-nc-nd3.0> ;
dct:modified "2016-07-07"^^xsd:date ;
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:hasVersion "1.0" ;
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> .

38. FAIR Data Point metadata
Catalog metadata
Dataset metadata
Distribution
metadata
Data record
metadata
Type
Domain
Range
…

39. 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:issued "2016-02-01"^^xsd:date ;
dct:language lang:en ;
dct:modified "2016-08-01"^^xsd:date ;
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>
];

40. FAIR Data Point metadata
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

41. 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

42. 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

43. 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

44. FAIR DATA POINT
Metadata
Provider
FAIR Accessor
Metrics Gatherer Security Enforcer

45. EXISTING DATA REPOSITORIES
Metadata
Provider
FAIR Accessor
Metrics Gatherer Security Enforcer

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

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

48. 0110011
1100101
1001100
Development started in October 2016

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

50. 0110011
1100101
1001100

51. Development started in October 2016
Based on OpenRefine

52. 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

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

54. 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

55. 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

56. FAIRIFIER

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

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

59. FAIRIFICATION - NEW DATASET TYPE
Original dataset
FAIR Data Resource
FAIR Format
Metadata Licensesubmit generate
FAIR Data
Model Registry
store
Non-FAIR
- FAIR
mapping

60. FAIRIFICATION - RECURRING DATASET TYPE
Original dataset
FAIR Data Resource
FAIR Format
Metadata Licensesubmit generate
FAIR Data
Model Registry
query
Non-FAIR
- FAIR
mapping
retrieve

61. ■ 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

62. 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

63. 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
Ex. *APInatomy, BRAIN,
etc)
Data Consumer Apps
Ex. *APInatomy, BRAIN,
etc)
Data Consumer Apps
Ex. *APInatomy, BRAIN,
etc)Data Mgmt AppData Mgmt App
Data
Stewardship
Apps

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

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

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

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

68. 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

69. 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

70. TECHNOLOGY TRANSFER EVENTS

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

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

73. 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;

74. FAIR HACKATHONS
RDRF

75. MOLGENIS FAIR HACKATHON

76. MOLGENIS FAIR HACKATHON

77. MOLGENIS FAIR HACKATHON

78. 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, …

79. 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

80. NETHERLANDS
Domain Expert
Data Owner FAIR Data Expert
BYOD

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

82. NETHERLANDS
BYOD Planning
Preparation Execution Follow Up

83. 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

84. 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

85. 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

86. BYOD
F
A
I
R
FAIR HACKATHON

87. 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

88. RELATED PROJECTS
ODEX4all
FAIR-dICT
myFAIR

89. QUESTIONS?