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ACCELERATING RARE DISEASE RESEARCH BY CONTRIBUTING TO GLOBAL DATA INFRASTRUCTURE
M a r c o R o o s , a c k n o w l e d g i n g E l i x i r, R D - C o n n e c t , B B M R I , O D E X 4 A l l , FA I R D i c t a n d m a n y c o l l e a g u e s
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Audience
Patient organisation
Research
Policy
Before I start…
14 June 2016
3
Who is generating genomics data?
Who is managing a rare disease registry?
Who is managing a sample collection?
Before I start
14 June 2016
5
Roles
between biology and computer science group leader Biosemantics knowledge discovery
group, Human Genetics, LUMC co-lead rare disease use case in Elixir:
European life science data infrastructure member RD-Connect chair rare disease linked data and ontology task force
Who is talking…
14 June 2016
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Example: drug prioritization for Huntington’s DiseaseEleni Mina, Kristina Hettne, Eelke van der Horst, Katerina Nosikova, Elizaveta Besedina, Katy Wolstencroft , Peter-Bram ‘t Hoen, Marco Roos
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Select genes by phenotype matching in
Monarch
Select drug compounds in OpenPHACTS
Filter on feasibility for treating HD
Prioritized drug compounds
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Example: drug prioritization for Huntington’s DiseaseEleni Mina, Kristina Hettne, Eelke van der Horst, Katerina Nosikova, Elizaveta Besedina, Katy Wolstencroft , Peter-Bram ‘t Hoen, Marco Roos
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Select genes by phenotype matching in
Monarch
Select drug compounds in OpenPHACTS
Filter on feasibility for treating HD
Prioritized drug compounds
Eleni combines
Gene expression information from HD patientsChemical information about drug compounds
Literature (gene-disease relations) Recorded phenotypes of Huntington’s disease patients
Phenotypes of humans and model organisms (Monarch)
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Who knows the data best?
Eleni
The data generator/collector
Other
…
Who knows…
14 June 2016
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F: Eleni can easily find all relevant data
A: It is clear how Eleni can access the data
I: The data is interoperable with other
data sets (structure of data, not content)
R: Eleni and others can reuse the data
Proposition: data is FAIR?
14 June 2016
10
Who should be responsible for making data FAIR?
Eleni
The data generator/collector
Other
…
Who is responsible
14 June 2016
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When data is not prepared for cross-resource analysis
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Back of an envelope calculation
6 months per data set
Reuse: 5x on average, 6x5=30 Months
For every RD: 6000x(6x5) = 180000 M
How much time do researchers spend on preparing data for integration
14 June 2016
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Data linkable at the source
6 months once
Reuse: 5x on average, +1M, 1x5=5 M (30)
For every RD: 6000x(6+1x5) = 66000 M
How much time do researchers spend on preparing data for integration
14 June 2016
(180000)
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Benefits for cross-resource analysis
- 66% efficiency gain (more time for research)
- Researchers can start analysing 6x faster
How much time do researchers spend on preparing data for integration
14 June 2016
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Example: proof-of-concept rare disease
registries and biobanks
But how
14 June 2016
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DISCLAIMER
Demo based on dummyfied data derived
from real data. Results do not reflect
actual data.
14/06/201616
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As a researcher…
In addition, I would like to see in which
biobanks I can find the samples, the
phenotypes associated with them, and
information about the organisation(s)
behind the biobanks or registries
I would like to know the number of samples of
donors with an abnormality in head or neck in a
specific region of Italy, in order to check if
exposure to environmental factors is important
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Claudio requested information that is in multiple sources
• Sample information in biobanks
• Patient information in registries
What just happened?
I would like to know the number of samples of
donors with an abnormality in head or neck in a
specific region of Italy, in order to check if
exposure to environmental factors is important
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PreFAIR data
14 June 2016
Disease Phenotype Consent code label
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood Health/medical/biomedical research use and clinical care, No “general methods” research
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Mild to moderate developmental delay and difficulty with learning No restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood General research use and clinical care, No “general methods” research
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Difficulties with eyesight General research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood Health/medical/biomedical research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Difficulties with eyesight No restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood General research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood No restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Difficulties with eyesight General research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Chorea Population origins/ancestry research, Other research specific restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Mild to moderate developmental delay and difficulty with learning No restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Hypotonia Health/medical/biomedical research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood General research use and clinical care, No “general methods” research
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Hypotonia Health/medical/biomedical research use and clinical care, No “general methods” research
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood Disease specific research use and clinical care, No “general methods” research
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Hypotonia Health/medical/biomedical research use and clinical care, No “general methods” research
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Difficulties with eyesight General research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Difficulties with eyesight Population origins/ancestry research, Other research specific restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Mild to moderate developmental delay and difficulty with learning Disease specific research use and clinical care, No “general methods” research
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Hypotonia Population origins/ancestry research, Other research specific restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Hypotonia Disease specific research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Hypotonia No restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood Population origins/ancestry research, Other research specific restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood Disease specific research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Hypotonia Disease specific research use and clinical care, Research use only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood Population origins/ancestry research, Research use only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Mild to moderate developmental delay and difficulty with learning General research use and clinical care, Research use only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Mild to moderate developmental delay and difficulty with learning General research use and clinical care, Research use only
Disease Phenotype Consent code label
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood Health/medical/biomedical research use and clinical care, No “general methods” research
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Mild to moderate developmental delay and difficulty with learning No restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood General research use and clinical care, No “general methods” research
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Difficulties with eyesight General research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood Health/medical/biomedical research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Difficulties with eyesight No restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood General research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood No restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Difficulties with eyesight General research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Chorea Population origins/ancestry research, Other research specific restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Mild to moderate developmental delay and difficulty with learning No restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Hypotonia Health/medical/biomedical research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood General research use and clinical care, No “general methods” research
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Hypotonia Health/medical/biomedical research use and clinical care, No “general methods” research
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood Disease specific research use and clinical care, No “general methods” research
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Hypotonia Health/medical/biomedical research use and clinical care, No “general methods” research
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Difficulties with eyesight General research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Difficulties with eyesight Population origins/ancestry research, Other research specific restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Mild to moderate developmental delay and difficulty with learning Disease specific research use and clinical care, No “general methods” research
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Hypotonia Population origins/ancestry research, Other research specific restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Hypotonia Disease specific research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Hypotonia No restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood Population origins/ancestry research, Other research specific restrictions
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood Disease specific research use and clinical care, Genetic studies only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Hypotonia Disease specific research use and clinical care, Research use only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Frequent infections in early childhood Population origins/ancestry research, Research use only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Mild to moderate developmental delay and difficulty with learning General research use and clinical care, Research use only
Partial deletion of the long arm of chromosome 14 (ORPHA262110)Mild to moderate developmental delay and difficulty with learning General research use and clinical care, Research use only
34
Step 1: coding data
14 June 2016
Disease Phenotype Consent code
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0100543,HP_0000232,HP_0000733,HP_0008207,HP_0002714,HP_0006101,HP_0100543HMB(CC), NMDS
ORPHA262110 HP_0100543,HP_0005469,HP_0005280,HP_0000580NRES, GSO
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0008207,HP_0002714,HP_0006101,HP_0100543GRU(CC), NMDS
ORPHA262110 HP_0002307,HP_0001250,HP_0005469,HP_0005280,HP_0000580,HP_0000470,HP_0000316,HP_0000369,HP_0000463,HP_0000494,HP_0001252,HP_0001510GRU(CC), GSO
ORPHA262110 HP_0008207,HP_0002714,HP_0006101,HP_0100543HMB(CC), GSO
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0008207NRES, GSO
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0100543,HP_0000232,HP_0000733,HP_0008207GRU(CC), GSO
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0100543,HP_0000232,HP_0000733,HP_0008207,HP_0002714,HP_0006101,HP_0100543NRES, NMDS
ORPHA262110 HP_0100543 GRU(CC), GSO
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0008207,HP_0002714,HP_0006101,HP_0100543POA, RS-[XX]
ORPHA262110 HP_0002307,HP_0001250 NRES, RUO
ORPHA262110 HP_0008207,HP_0002714,HP_0006101,HP_0100543HMB(CC), GSO
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0008207GRU(CC), NMDS
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0100543,HP_0000232,HP_0000733,HP_0008207HMB(CC), NMDS
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0100543,HP_0000232,HP_0000733,HP_0008207,HP_0002714,HP_0006101,HP_0100543DS-[XX](CC), NMDS
ORPHA262110 HP_0100543,HP_0005469,HP_0005280,HP_0000580,HP_0000470,HP_0000316,HP_0000369HMB(CC), NMDS
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0008207,HP_0002714,HP_0006101,HP_0100543GRU(CC), GSO
ORPHA262110 HP_0002307,HP_0001250 POA, RS-[XX]
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0100543,HP_0000232,HP_0000733,HP_0008207,HP_0002714,HP_0006101,HP_0100543DS-[XX](CC), NMDS
ORPHA262110 HP_0100543 POA, RS-[XX]
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0008207,HP_0002714,HP_0006101,HP_0100543DS-[XX](CC), GSO
ORPHA262110 HP_0002307,HP_0001250 NRES, RS-[XX]
ORPHA262110 HP_0008207,HP_0002714,HP_0006101,HP_0100543POA, RS-[XX]
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0008207DS-[XX](CC), GSO
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0100543,HP_0000232,HP_0000733,HP_0008207DS-[XX](CC), RUO
Disease Phenotype Consent code
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0100543,HP_0000232,HP_0000733,HP_0008207,HP_0002714,HP_0006101,HP_0100543HMB(CC), NMDS
ORPHA262110 HP_0100543,HP_0005469,HP_0005280,HP_0000580NRES, GSO
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0008207,HP_0002714,HP_0006101,HP_0100543GRU(CC), NMDS
ORPHA262110 HP_0002307,HP_0001250,HP_0005469,HP_0005280,HP_0000580,HP_0000470,HP_0000316,HP_0000369,HP_0000463,HP_0000494,HP_0001252,HP_0001510GRU(CC), GSO
ORPHA262110 HP_0008207,HP_0002714,HP_0006101,HP_0100543HMB(CC), GSO
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0008207NRES, GSO
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0100543,HP_0000232,HP_0000733,HP_0008207GRU(CC), GSO
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0100543,HP_0000232,HP_0000733,HP_0008207,HP_0002714,HP_0006101,HP_0100543NRES, NMDS
ORPHA262110 HP_0100543 GRU(CC), GSO
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0008207,HP_0002714,HP_0006101,HP_0100543POA, RS-[XX]
ORPHA262110 HP_0002307,HP_0001250 NRES, RUO
ORPHA262110 HP_0008207,HP_0002714,HP_0006101,HP_0100543HMB(CC), GSO
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0008207GRU(CC), NMDS
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0100543,HP_0000232,HP_0000733,HP_0008207HMB(CC), NMDS
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0100543,HP_0000232,HP_0000733,HP_0008207,HP_0002714,HP_0006101,HP_0100543DS-[XX](CC), NMDS
ORPHA262110 HP_0100543,HP_0005469,HP_0005280,HP_0000580,HP_0000470,HP_0000316,HP_0000369HMB(CC), NMDS
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0008207,HP_0002714,HP_0006101,HP_0100543GRU(CC), GSO
ORPHA262110 HP_0002307,HP_0001250 POA, RS-[XX]
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0100543,HP_0000232,HP_0000733,HP_0008207,HP_0002714,HP_0006101,HP_0100543DS-[XX](CC), NMDS
ORPHA262110 HP_0100543 POA, RS-[XX]
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0008207,HP_0002714,HP_0006101,HP_0100543DS-[XX](CC), GSO
ORPHA262110 HP_0002307,HP_0001250 NRES, RS-[XX]
ORPHA262110 HP_0008207,HP_0002714,HP_0006101,HP_0100543POA, RS-[XX]
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0008207DS-[XX](CC), GSO
ORPHA262110 HP_0002307,HP_0001250,HP_0005280,HP_0002376,HP_0002650,HP_0100543,HP_0000232,HP_0000733,HP_0008207DS-[XX](CC), RUO
35
Step 2: machine readable codes
14 June 2016
Disease Phenotype Primary consent code
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/HMB_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/NRES>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0000316>, <http://purl.obofoundry.org/obo/HP_0000369><http://www.mylinkeddata.org/CCODE/HMB_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/NRES>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/NRES>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/POA>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/NRES>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/HMB_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0000316>, <http://purl.obofoundry.org/obo/HP_0000369><http://www.mylinkeddata.org/CCODE/HMB_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/DS-_XX__CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/><http://www.mylinkeddata.org/CCODE/HMB_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/POA>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/DS-_XX__CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/POA>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/DS-_XX__CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/NRES>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/POA>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0000316>, <http://purl.obofoundry.org/obo/HP_0000369><http://www.mylinkeddata.org/CCODE/DS-_XX__CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/DS-_XX__CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/><http://www.mylinkeddata.org/CCODE/POA>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
Disease Phenotype Primary consent code
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/HMB_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/NRES>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0000316>, <http://purl.obofoundry.org/obo/HP_0000369><http://www.mylinkeddata.org/CCODE/HMB_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/NRES>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/NRES>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/POA>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/NRES>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/HMB_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0000316>, <http://purl.obofoundry.org/obo/HP_0000369><http://www.mylinkeddata.org/CCODE/HMB_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/DS-_XX__CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/><http://www.mylinkeddata.org/CCODE/HMB_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/POA>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/DS-_XX__CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/POA>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/DS-_XX__CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/NRES>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/POA>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0000316>, <http://purl.obofoundry.org/obo/HP_0000369><http://www.mylinkeddata.org/CCODE/DS-_XX__CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/DS-_XX__CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/><http://www.mylinkeddata.org/CCODE/POA>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
36
Step 3: machine readable relations
14 June 2016
Disease Phenotype Primary consent code
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/HMB_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/NRES>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0000316>, <http://purl.obofoundry.org/obo/HP_0000369><http://www.mylinkeddata.org/CCODE/HMB_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/NRES>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/NRES>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/POA>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/NRES>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/HMB_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0000316>, <http://purl.obofoundry.org/obo/HP_0000369><http://www.mylinkeddata.org/CCODE/HMB_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/DS-_XX__CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/><http://www.mylinkeddata.org/CCODE/HMB_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/POA>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/DS-_XX__CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/POA>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/DS-_XX__CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/NRES>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/POA>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0000316>, <http://purl.obofoundry.org/obo/HP_0000369><http://www.mylinkeddata.org/CCODE/DS-_XX__CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/DS-_XX__CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/><http://www.mylinkeddata.org/CCODE/POA>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<http://www.orpha.net/ORDO/ORPHA262110> <http://purl.obofoundry.org/obo/HP_0005469>, <http://purl.obofoundry.org/obo/HP_0005280><http://www.mylinkeddata.org/CCODE/GRU_CC>
<…>
<http://purl.obolibrary.org/obo/ERO_0002100> <http://purl.obolibrary.org/obo/RO_0002200>
“has phenotype”“has diagnosis”
Anonymous person ID
37
Demonstrated answering questions
across biobanks and registries using
linkable data at the source
Data was made linkable using global
standards (ontologies) and computer
readable identifiers
Hard work at source, integration trivial
Summary
14 June 2016
38
Emerging FAIR data ecosystem
Hemangiome
Osteogenesisimperfecta
Cystic Fibrosis
ChEBI
OrphaNet
UniProt
Predicted gene-disease relations
RS-virus
Epilepsy
Predicted chromatin states
Human Protein Atlas
Ring-14
Huntington’s Disease
WikiPathways
39
Traditional warehouse
Hemangiome
Osteogenesisimperfecta
Cystic Fibrosis
ChEBI
OrphaNet
UniProt
Predicted gene-disease relations
RS-virus
Neck cancer
Predicted chromatin states
Human Protein Atlas
Ring-14
Huntington’s Disease
WikiPathways
Data warehouse
40
Traditional warehouse
Hemangiome
Osteogenesisimperfecta
Cystic Fibrosis
ChEBI
OrphaNet
UniProt
Predicted gene-disease relations
RS-virus
Neck cancer
Predicted chromatin states
Human Protein Atlas
Ring-14
Huntington’s Disease
WikiPathways
41
Emerging FAIR data ecosystem
Hemangiome
Osteogenesisimperfecta
Cystic Fibrosis
ChEBI
OrphaNet
UniProt
Predicted gene-disease relations
RS-virus
Epilepsy
Predicted chromatin states
Human Protein Atlas
Ring-14
Huntington’s Disease
Drug discovery (OpenPHACTS)
WikiPathways
42
Emerging FAIR data ecosystem
Hemangiome
Osteogenesisimperfecta
Cystic Fibrosis
ChEBI
OrphaNet
UniProt
Predicted gene-disease relations
RS-virus
Epilepsy
Predicted chromatin states
Human Protein Atlas
Ring-14
Huntington’s Disease
Cystic fibrosis
WikiPathways
43
Emerging FAIR data ecosystem
Hemangiome
Osteogenesisimperfecta
Cystic Fibrosis
ChEBI
OrphaNet
UniProt
Predicted gene-disease relations
RS-virus
Epilepsy
Predicted chromatin states
Human Protein Atlas
Ring-14
Huntington’s Disease
Drug repurposing for Ring-14 symptoms
WikiPathways
44
Emerging FAIR data ecosystem
Hemangiome
Osteogenesisimperfecta
Cystic Fibrosis
ChEBI
OrphaNet
UniProt
Predicted gene-disease relations
RS-virus
Epilepsy
Predicted chromatin states
Human Protein Atlas
Ring-14
Huntington’s Disease
WikiPathways
No warehouse
Robust infrastructure
45
Make at least 7 rare disease resources FAIR: biobanks, registries, molecular data with support from
RD-Connect, BBMRI, ADOPT, Elixir, FAIRDict, ODEX4All
Engaging with patient organisations (and vice versa)
E.g. Ring-14, Hemangiome (VSOP)
Engaging with registry companies
E.g. OpenApps, PatientCrossroads
How about you / your organisation / RD?
Next steps
14 June 2016
46
Data owners bring their datae.g. rare disease registries, biobanks, omics
FAIR data experts + source data experts make data FAIR
Pre: two webinarsBYOD: 2+1 dayPost: two follow-up teleconferencesLearning experience: FAIR Data SOP
Contact DTL/Elixir-NL or Marco for BYODs and FAIR data projects
http://www.dtls.nl/fair-data/
Bring Your Own Data workshops
14 June 2016
47
Registry summerschool and Bring Your Own Data workshopRome, September 26-28, 29-30
14 June 2016
https://www.elixir-
europe.org/events/rare-
disease-byod-workshop
http://www.iss.it/cnmr/
48
Support from stakeholder projects to get
things started (RD-Connect, BBMRI, Elixir, and more)
Shared responsibility, including patient organisations
5% rule: 5% of every data generating project to FAIR data management European Open Science Cloud
Similar endorsement from NIH
Funding
14 June 2016
Thank you
14-jun-16
49
http://www.iss.it/cnmr/
http://www.dtls.nl/fair-data/
50
