Presentation by Luiz Olavo Bonino about the current state of the developments on FAIR Data supporting tools at the Dutch Techcentre for Life Sciences Partners Event on November 3-4 2016.

1. FAIR DATA TECHNOLOGY UPDATE
Luiz Olavo Bonino - luiz.bonino@dtls.nl

2. DTL

4. Mark Wilkinson
UP Madrid
Michel Dumontier
Stanford /
Maastricht U.

5. DTL

6. Jan 2014
SWT
1st Skunkworks hackathon
Maastricht - NL
W3C DCAT - FAIR Profiles
Apr 2014 Sept 2014
FAIR Data Principles
@ FORCE 11

7. Mar 2015 Apr 2015 Aug 2015
DFDET
ODEX4all project
SWT
2nd Skunkworks hackathon
Hinxton - UK
FAIR Profiles, Beacons,
Molgenis
DFDET
Released first beta version of
ORKA
DTL

8. Sept 2015 Feb 2016 Jun 2016
The FAIR Guiding Principles
paper on Scientific Data *
SWT
Skunkworks @ Biohackathon
Final version of the Principles
First attempt FAIR Projection
DFDET
Starts the work on
FAIR Data Point
DFDET + SWT
FAIR Data Point paper **
* http://www.nature.com/articles/sdata201618
** http://www.iste.co.uk/index.php?f=a&ACTION=View&id=1073
Mar 2016
SWT + DFDET + others
Starts work group
on FAIR metrics for
data and services

9. Sept 2016
DFDET
Starts the work on the
FAIR Data Search Engine
and on the FAIRifier.
FAIR Data Point incorporates
RML
Oct 2016 Nov 2016
SWT + DFDET
FAIR Technologies paper
LDP, LDF, RML,
FAIR Projectors
DFDET
First FAIR Hackathons with
Molgenis, Castor EDC,
RDRF and OSSE
FAIR Data Point
DFDET
FAIR Hackathons with
Mendeley and Quaero Systems
FAIR Data Point
DFDET
FAIR Data Point v. 1.0
FAIR Data Point
DFDET + SWT
FAIR Data workshop
@ ECCB 2016
The Hague - NL

10. FAIR transformation FAIR transformation
Analysis transformation Analysis transformation

11. 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

12. WHAT?
HOW?
WHO?
BYODs, FAIR hackathons, FAIR Data Points,
FAIR Search Engine, FAIRifier, FAIR Data Model
Registry, Data FAIRport, …
Training, capacity building;

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.

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.

28. FAIR DATA POINT - ARCHITECTURE

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/biobank/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 metadataCatalog 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

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

45. EXISTING DATA REPOSITORIES

46. EXTENDING EXISTING DATA REPOSITORIES
+

47. 0110011
1100101
1001100
Development started in October 2016

48. 0110011
1100101
1001100
metadata
index
retrieves
metadata
search
interfaces
(GUI and API)

49. 0110011
1100101
1001100

50. Development started in October 2016
Based on OpenRefine

51. 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

52. FAIRIFICATION
FAIR Data Resource
submit generate
Generic
semantic
model

54. 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

55. FAIRIFIER

56. FAIR DATA MODEL REGISTRY

57. FAIRIFICATION
FAIR Data Resource
submit generate
Generic
semantic
model

58. FAIRIFICATION - NEW DATASET TYPE
FAIR Data Resource
submit generate
FAIR Data Model
Registry
store
Non-FAIR
- FAIR
mapping

59. FAIRIFICATION - RECURRING DATASET TYPE
FAIR Data Resource
submit generate
FAIR Data Model
Registry
query
Non-FAIR
- FAIR
mapping
retrieve

60.  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;

61. F A I
R

62. FAIRPORT

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

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

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

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

67. 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

68. 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

69. TECHNOLOGY TRANSFER EVENTS

70. EXTENDING EXISTING DATA REPOSITORIES
+

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

72. 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;

73. FAIR HACKATHONS
RDRF

74. MOLGENIS FAIR HACKATHON

75. MOLGENIS FAIR HACKATHON

76. MOLGENIS FAIR HACKATHON

77. 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, …

78. 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

79. Domain Expert
Data Owner FAIR Data Expert
BYOD

80. BYOD

81. BYOD Planning
Preparation Execution Follow Up

82. 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

83. 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

84. 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

85. BYOD
F
A
I
R
FAIR HACKATHON

86. FAIR
dICT
RD
Connectt
Core
FAIR
Technol
ogyFAIR Data E.T.
FAIR Data E.T.
FAIR Data E.T.
FAIR Data E.T.
FAIR Data E.T.
FAIR Data E.T.
DTL

87. RELATED PROJECTS
ODEX4all
FAIR-dICT
myFAIR

88. QUESTIONS?