1.
Mark D. Wilkinson
CBGP-UPM/INIA, Madrid
markw@illuminae.com
Data Interoperability and
FAIRness Through Existing
Web Technologies
DTL Partner Wkshp
November, 2016

2.
The Problem
...one recent survey of 18 microarray studies found that only
two were fully reproducible using the archived data. Another
study of 19 papers in population genetics found that 30% of
analyses could not be reproduced from the archived data and
that 35% of datasets were incorrectly or insufficiently
described.
“
”
Dominique G. Roche , Loeske E. B. Kruuk,
Robert Lanfear, Sandra A. Binning (2015)
http://dx.doi.org/10.1371/journal.pbio.1002295

3.
The Problem
We surveyed 100 datasets associated with nonmolecular
studies in journals that commonly publish ecological and
evolutionary research and have a strong PDA policy. Out of
these datasets, 56% were incomplete, and
64% were archived in a way that
partially or entirely prevented reuse.
“
”
Dominique G. Roche , Loeske E. B. Kruuk,
Robert Lanfear, Sandra A. Binning (2015)
http://dx.doi.org/10.1371/journal.pbio.1002295

4.
FAIR
Findable
→ Globally unique, resolvable, and persistent identifiers
→ Machine-actionable contextual information supporting discovery
Accessible
→ Clearly-defined access protocol
→ Clearly-defined rules for authorization/authentication
Interoperable
→ Use shared vocabularies and/or ontologies
→ Syntactically and semantically machine-accessible format
Reusable
→ Be compliant with the F, A, and I Principles
→ Contextual information, allowing proper interpretation
→ Rich provenance information facilitating accurate citation
The Four Principles

5.
“Skunkworks”
Task: Build a prototype

6.
Skunkworks Participants
● Mark Wilkinson
● Michel Dumontier
● Barend Mons
● Tim Clark
● Jun Zhao
● Paolo Ciccarese
● Paul Groth
● Erik van Mulligen
● Luiz Olavo Bonino da
Silva Santos
● Matthew Gamble
● Carole Goble
● Joël Kuiper
● Morris Swertz
● Erik Schultes
● Erik Schultes
● Mercè Crosas
● Adrian Garcia
● Philip Durbin
● Jeffrey Grethe
● Katy Wolstencroft
● Sudeshna Das
● M. Emily Merrill

7.
The Hourglass Concept
We want a large ecosystem of
apps that use FAIR Data

8.
The Hourglass Concept
We want to support a wide
range of source providers

9.
The Hourglass Concept
The FAIR solution between them must be THIN!

10.
Skunkworks
participants had tons of
experience v.v.
metadata around
scholarly publication

11.
Skunkworks
participants had tons of
experience v.v.
metadata around
scholarly publication
RDA,
Force11,
Dataverse,
Research
Objects,
NanoPubs,
Semantic
Science,
SADI,
AlzForum,
SWAN,
LSID,
…
…
…
...

12.
There was very little
disagreement
about F,
about A,
or about R

13.
The “I” is the big problem!

14.
Interoperability is
Hard!!
The “I” is the big problem!

15.
Keeping the history brief
A series of teleconferences led to the concept of putting
metadata into an iterative set of ~identical “containers”

16.
Skunkworks Hackathons
The “containers of containers of containers” idea
was elaborated by the belief that we should also
reject any solution that required a new API
ProgrammableWeb.com already catalogues
>16,000 different Web APIs!!!!!!

17.
Skunkworks Hackathons
The “containers of containers of containers” idea
was elaborated by the belief that we should also
reject any solution that required a new API
ProgrammableWeb.com already catalogues
>16,000 different Web APIs!!!!!!
APIs DO NOT MAKE YOU INTEROPERABLE!

18.
Skunkworks Hackathons
The “containers of containers of containers” idea
was elaborated by the belief that we should also
reject any solution that required a new API

19.
Skunkworks Hackathons
The “containers of containers of containers” idea
was elaborated by the belief that we should also
reject any solution that required a new API
REST is an architectural style for software

20.
Skunkworks Hackathons
The “containers of containers of containers” idea
was elaborated by the belief that we should also
reject any solution that required a new API
Hypermedia-driven, NOT parameter-driven
The phrase “my REST API” makes almost no sense,
and in bioinformatics, is usually accompanied by a page explaining the
key/value pairs you should add to the URL to access various functions.
This Is Not REST!

21.
Skunkworks Hackathons
Are there existing standards that are
And have the properties of
?

22.
Uses machine-accessible standards and
representations, following a REST
paradigm
LDP
Useful Features
I
I + R
F + A
I
Defines HTTP-resolvable URIs for each of
these containers
Defines the concept of a “Container” - a
machine-actionable way to represent
repositories, data deposits, data files,
data points, and their metadata
Uses a widely accepted standard (DCAT)
to relate metadata to data →
machine-actionable data mining

23.
Caveats
We used LDP as “inspiration”
Some parts of LDP are not really “REST”
(in our opinion) so we stripped-out
those parts in favour of a 100%
API-free solution
For the moment we require
a read-only solution;
LDP defines a read-write platform
so we don’t use those portions either
(for now)

24.
The FAIR Accessor
In incremental detail
26

25.
What can we describe with
FAIR Accessors?
FAIR Accessors provide a machine-actionable, structured,
REST-oriented way to publish Metadata
about a wide range of scholarly “entities”

26.
What can we describe with
FAIR Accessors?
Warehouses (e.g. EBI)
Databases (e.g. UniProt)
Repositories (e.g. Zenodo, Dataverse, Leiden Repository, etc.)
Datasets (e.g. output from a workflow)
Research Objects (data a/o workflow a/o results a/o publications)
Data “slices” (e.g. the result of a database query)
Data Records (e.g. image, excel file, patient clinical record)
Other…

27.
Container
Resource HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource1
MetaRecordResource2
MetaRecordResource3
...
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
HTTP GET
What does a FAIR Accessor “look like”?

28.
Container
Resource HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource1
MetaRecordResource2
MetaRecordResource3
...
What does a FAIR Accessor “look like”?

29.
Container
Resource HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource1
MetaRecordResource2
MetaRecordResource3
...
What does a FAIR Accessor “look like”?
In REST, a “Resource” is
“anything that can be identified”
whether that is a single thing
or an identifiable collection of things,
and whether it exists in the real-world
or only in the network.
A “Resource” is identified by a URI

30.
Container
Resource HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource1
MetaRecordResource2
MetaRecordResource3
...
What does a FAIR Accessor “look like”?
Resources are manipulated using the HTTP
protocol on the Resource URI
For the FAIR Accessor, the only HTTP method
we currently require is HTTP GET

31.
Container
Resource HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource1
MetaRecordResource2
MetaRecordResource3
...
What does a FAIR Accessor “look like”?
What is returned is a document full of
metadata richly describing that Container
(warehouse, database, dataset, slice, etc.)
And a list of Resources (URIs) that represent
the contained “things”

32.
Container
Resource HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource1
MetaRecordResource2
MetaRecordResource3
...
What does a FAIR Accessor “look like”?
Looking more closely at one of those
contained things...

33.
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
HTTP GET
What does a FAIR Accessor “look like”?
The contained thing is a Resource

34.
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
HTTP GET
What does a FAIR Accessor “look like”?
That Resource can be resolved by HTTP GET

35.
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
HTTP GET
What does a FAIR Accessor “look like”?
To retrieve a Metadata document describing
that resource (e.g. a single record)

36.
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
HTTP GET
What does a FAIR Accessor “look like”?
Which record does this Metadata describe?
The foaf:primaryTopic attribute defines this

37.
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
HTTP GET
What does a FAIR Accessor “look like”?
Using the metadata structures defined by DCAT the
FAIR Accessor may also tell you how to get the
content of the record, and what formats are available

38.
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
HTTP GET
What does a FAIR Accessor “look like”?
In this case, the record is available in XML format
By calling HTTP GET on URL_U2

39.
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
HTTP GET
What does a FAIR Accessor “look like”?
Or in RDF format by calling HTTP GET on URL_U1

40.
Container
Resource HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource1
MetaRecordResource2
MetaRecordResource3
...
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
HTTP GET
What does a FAIR Accessor “look like”?

41.
Or you may add additional layers...
Metadata
Metadata
Metadata
Metadata
DATA - format 1
DATA - format 2

42.
Features of the FAIR Accessor
1: There is no API
GET
Interpret the Metadata
Select the desired Resource
GET

43.
Features of the FAIR Accessor
1: There is no API
GET
Interpret the Metadata
Select the desired Resource
GET
ANY Web agent can explore/index a FAIR Accessor
(e.g. Google)
An agent that understands globally-accepted vocabularies
can explore it “intelligently”!

44.
Features of the FAIR Accessor
46
1: There is no API
It’s difficult to get thinner than nothing ;-)

45.
Features of the FAIR Accessor
2: Identifiers for unidentifi-ed/-able things
HTTP GET
<FAIR metadata/>
This is the ArrayExpress query
I did for paper doi:10/1234.56
Results:
MetaRecordResource1
MetaRecordResource2
MetaRecordResource3
...

46.
Features of the FAIR Accessor
2: Identifiers for unidentifi-ed/-able things
HTTP GET
<FAIR metadata/>
This is the ArrayExpress query
I did for paper doi:10/1234.56
Results:
MetaRecordResource1
MetaRecordResource2
MetaRecordResource3
...
Should assist with reproducibility and transparency

47.
Features of the FAIR Accessor
3: A predictable “place” for metadata
MetaRecordURL
PrimaryTopic: record 1A445
Metadata...
DATA - format 1
DATA - format 2
Different “kinds” of metadata have distinct ontological types, and
distinct document structures. There is no ambiguity regarding
what the metadata is describing - a repository or a record.
Repository metadata
MetaRecordURL

48.
Features of the FAIR Accessor
3: Symmetry & predictable path to citation
XXX
Part of dataset XXX
Metadata...
DATA - format 1
DATA - format 2
The record metadata contains an “upward” link to the
Repository-level metadata, which should contain license and
citation information
Repository metadata:
Cite: doi:10/8847.384
License: cc-by

49.
Features of the FAIR Accessor
4: Granularity of Access/Privacy/Security
Container
Resource HTTP GET
<FAIR metadata/>
Contains
<<184 Records>>
Contact Mark Wilkinson
For more information about
These records

50.
Features of the FAIR Accessor
4: Granularity of Access/Privacy/Security
Container
Resource HTTP GET
<FAIR metadata/>
Contains
<<184 Records>>
Contact Mark Wilkinson
For more information about
These records

51.
Features of the FAIR Accessor
Container HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource3
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:distribution
<<NONE>>
HTTP GET
4: Granularity of Access/Privacy/Security

52.
Features of the FAIR Accessor
Container HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource3
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:distribution
<<NONE>>
HTTP GET
4: Granularity of Access/Privacy/Security

53.
Container HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource3
...
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
HTTP GET
Features of the FAIR Accessor
4: Granularity of Access/Privacy/Security

54.
Container HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource3
...
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
HTTP GET
Features of the FAIR Accessor
4: Granularity of Access/Privacy/Security

55.
Features of the FAIR Accessor
4: Granularity of Access/Privacy/Security
Thin solution - if it’s private, do nothing! Literally!

56.
The Real Thing
A working FAIR Accessor
Serving a “Slice” of UniProt

57.
A real-world scenario...
Imagine you are publishing a paper
describing the evolution of proteins
involved in the RNA Processing machineries
of the fungus Aspergillus nidulans.
If you want to be a “good” scholarly publisher,
interested in transparency and reproducibility,
what is the first thing you need to explain
to your readers and reviewers?

58.
A real-world scenario...
Imagine you are publishing a paper
describing the evolution of proteins
involved in the RNA Processing machineries
of the fungus Aspergillus nidulans.
If you want to be a “good” scholarly publisher,
interested in transparency and reproducibility,
what is the first thing you need to explain
to your readers and reviewers?
The list of proteins and their inclusion/exclusion criteria
How would this usually be done today?

59.
The query that returns the relevant proteins
WHERE
{
?protein a up:Protein .
?protein up:organism ?organism .
?organism rdfs:subClassOf taxon:162425 .
?protein up:classifiedWith ?go .
?go rdfs:subClassOf* <http://purl.obolibrary.org/obo/GO_0006396> .
bind(replace(str(?protein),
"http://purl.uniprot.org/uniprot/", "", "i") as ?id)
}

60.
The query that returns the relevant proteins
WHERE
{
?protein a up:Protein .
?protein up:organism ?organism .
?organism rdfs:subClassOf taxon:162425 .
?protein up:classifiedWith ?go .
?go rdfs:subClassOf* <http://purl.obolibrary.org/obo/GO_0006396> .
bind(replace(str(?protein),
"http://purl.uniprot.org/uniprot/", "", "i") as ?id)
}
NCBI Taxonomy:
Aspergillus nidulans

61.
The query that returns the relevant proteins
WHERE
{
?protein a up:Protein .
?protein up:organism ?organism .
?organism rdfs:subClassOf taxon:162425 .
?protein up:classifiedWith ?go .
?go rdfs:subClassOf* <http://purl.obolibrary.org/obo/GO_0006396> .
bind(replace(str(?protein),
"http://purl.uniprot.org/uniprot/", "", "i") as ?id)
}
Gene Ontology:
RNA Processing

62.
Create and publish a FAIR Accessor for that query
http://linkeddata.systems/Accessors/UniProtAccessor
Container
Resource HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource1
MetaRecordResource2
MetaRecordResource3
...

63.
Create and publish a FAIR Accessor for that query
http://linkeddata.systems/Accessors/UniProtAccessor
Container
Resource HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource1
MetaRecordResource2
MetaRecordResource3
...
Resolve the URI
(in software or in your
browser)

64.
Create and publish a FAIR Accessor for that query
Returns a page of metadata (in this example, in RDF)
Container
Resource HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource1
MetaRecordResource2
MetaRecordResource3
...

65.
68

66.
69
Note that this Metadata is about ME! I am the creator of this dataset, and may be credited for it.

67.
I have a script that
generates these…
not a significant barrier!

68.
Container Resource HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource1
MetaRecordResource2
MetaRecordResource3
...

69.
Container
Resource HTTP GET
<FAIR metadata/>
Contains
MetaRecordResource1
MetaRecordResource2
MetaRecordResource3
...
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
HTTP GET
Step down to individual Record metadata

70.
Step down to individual Record metadata
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
HTTP GET
Software calls HTTP GET on the URL
representing the MetaRecord Resource
for the desired record in the Container
(or just click on it, or type it into your browser)

71.
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
The document that is returned

72.
Note the change in metadata focus!
This metadata is about the UniProt Record
(not about Mark Wilkinson).
The record described in this metadata was
created by UniProt, so the citation and
authorship information is now THEIRS, not
MINE.

73.
Container
Resource
Symmetrical Link
back upward to the Accessor
Container
(possibly relevant metadata
up there… about Me :-) )

74.
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml

75.
Two ways to retrieve the record - RDF or HTML
(in REST-speak, two Representations
of that Resource)

76.
Note that this metadata record is
somewhat more FAIR, than what you
can (easily) retrieve from UniProt itself!
e.g. the UniProt record does not include
the citation or license information - you
have to manually surf around the
UniProt Web page to find that.
So the Accessor makes UniProt’s
already notably FAIR data, even more
FAIR (with respect to “R”)

77.
How FAIR are we now?
What does the Accessor give us?

78.
What we have achieved
We have created a FAIR record for something - i.e. a slice of a database - that was,
historically, un-recordable and un-identifiable in any formal way.F
F + A
F + R
Accessors are a standard approach to providing human & machine accessible metadata
to facilitate appropriate discovery (contextual, biological), proper usage (license) and
proper citation for any kind of data.
The discovery, accessibility, and drill-down/up behaviors do not require any novel
API, rather simply rely on global Web standards; this allows them to be indexed by
existing Web search engines

79.
What we have achieved
F + AI
The metadata itself uses machine-accessible syntaxes, and widely adopted ontologies
and vocabularies, thus easily integrates with other metadata
A
Accessors provide a lightweight means to protect privacy while still providing the
maximum degree of transparency possible
+
Accessors can be static, or dynamic. i.e. we can provide template Accessor file(s)
that are edited in Notepad, then published together with the data; or Accessors can
dynamically generate their output from code (e.g. layered on a database server)

80.
Can we be FAIRer?

81.
Not good enough
for the Skunk!
So far we have only addressed
Interoperability and FAIRness of Metadata
The Holy Grail of Interoperability is to
provide interoperable Data.

82.
FAIR Projection:
Providing FAIR Data
from non-FAIR Data

83.
This is going to be a bit complicated, but
please be patient
Interoperability is Hard!!

84.
Imagine the data
we need to integrate
is in a CSV file
In FigShare or Zenodo
How do we discover and integrate that data?
CSV (usually) has no inherent semantics
and semantics is ~impossible to automatically guess

85.
Things we need to do:
We need a way to query “opaque” data blobs (like CSV) about their content
We need a way to retrieve that content in a FAIR format
We need, therefore, to model semantics for that opaque data content
We need to model various semantics for that content (one “size” doesn’t fit all!)
We need to associate those semantic models with a record or record-sets
We need a way to query those semantics determine which “size” fits our req’s
We would like to reuse semantic definitions as much as possible
We need to do all of this without creating a new API :-)

86.
Triple Pattern Fragments
+
RDF Modeling/Mapping Language
Ruben Verborgh
Ghent University
Anastasia Dimou
Ghent University

87.
Triple Pattern Fragments (TPF)
A REST interface for requesting/retrieving RDF Triples
(from any source)
Ruben Verborgh
“Slices” of data, from any source, are considered Resources
and are therefore represented by a distinct URL:
http://some.database.org/dataset?s=___;p=___;o=___
Calling HTTP GET on a TPF URL returns the set of Triples matching {?s, ?p, ?o}
PLUS hypermedia instructions and Resource URLs for other relevant slices.

88.
Triple Pattern Fragments (TPF)
A REST interface for retrieving RDF Triples
(from any source)
Ruben Verborgh
For example, the “BMI” column from a patient registry is a Resource with the URL:
http://my.registry.org/patients?p=CMO:0000105 (CMO:0000105 = “body mass index””)
HTTP GET gives me all BMI triples in the registry, together with other Resource URLs
representing other “slices” that might be useful, for example:
http://my.registry.org/patients?p=CMO:0000004 (CMO:0000004 = “systolic B.P.”)

89.
Triple Pattern Fragments (TPF)
A REST interface for retrieving RDF Triples
(from any source)
Ruben Verborgh
For example, the “BMI” column from a patient registry is a Resource with the URL:
http://my.registry.org/patients?p=CMO:0000105 (CMO:0000105 = “body mass index””)
HTTP GET gives me all BMI triples in the registry, together with other Resource URLs
representing other “slices” that might be useful, for example:
http://my.registry.org/patients?p=CMO:0000004 (CMO:0000004 = “systolic B.P.”)

90.
We have a standard, RESTful way to
request triples from any data source
i.e. every slice of every dataset will be considered a distinct Resource
→ simply call HTTP GET on that Resource to get the Triples

91.
But it’s a disaster!
We have no way to know what Resources are
available for any given dataset
or what those Resources “are”
(proteins? genes? patients? articles?)
...and still no defined way to generate the associated Triples

92.
RML
A way to describe the structure of an RDF document
Anastasia Dimou
RML allows us to create models of (meta)data structures
“What could this (meta)data look like?”
RML fulfills similar objectives to DCAT Profiles, the Dublin Core
Application Profile, and ISO 11179 - Metadata Registries;
but has added advantages!
http://rml.io/RMLmappingLanguage.html

93.
Using RML to describe the structure
and semantics of a single Triple
Map1
Predicate
Object Map
Subject
Map
Object
Map
ex:Patient
Record
subjectMap template
“http://example.org/patient/{id}”
predicateObjectMap
predicate ex:has
Variant
objectM
ap
class
Map2
parentTriplesMap
Subject
Map2
SO:0000694
(“SNP”)
subjectMap template
“http://identifiers.org/dbsnp/{snp}”
class
T
H
E
M
O
D
E
L

94.
Using RML to describe the structure
(and semantics) of a single triple
Map1
Predicate
Object Map
Subject
Map
Object
Map
ex:Patient
Record
subjectMap template
“http://example.org/patient/{id}”
predicateObjectMap
predicate ex:has
Variant
objectM
ap
class
Map2
parentTriplesMap
Subject
Map2
SO:0000694
(“SNP”)
subjectMap template
“http://identifiers.org/dbsnp/{snp}”
class
T
H
E
M
O
D
E
L
We call this a “Triple Descriptor”
These are used to describe the
structure of data “slices” in which all
Triples have the same structure

95.
T
H
E
M
O
D
E
L
Using RML to describe the structure
(and semantics) of a single triple
Map1
Predicate
Object Map
Subject
Map
Object
Map
ex:Patient
Record
subjectMap template
“http://example.org/patient/{id}”
predicateObjectMap
predicate ex:has
Variant
objectM
ap
class
Map2
parentTriplesMap
Subject
Map2
SO:0000694
(“SNP”)
subjectMap template
“http://identifiers.org/dbsnp/{snp}”
class
Patient:123
rdf:type
ex:Patient
Record
snp:
rs0020394
ex:hasVariant
rdf:type
ex:Patient
Record
The Data

96.
Where are we now?
TPF - A standard, RESTful way to request Triples
Triple Descriptors - A standard way to describe
the structure and meaning of a Triple

97.
Where are we now?
TPF - A standard, RESTful way to request Triples
Triple Descriptors - A standard way to describe
the structure and meaning of a Triple
There is still no way to associate these with the dataset that they represent
There is still no way to make these triples “real”

98.
Wait… that’s not right!
“There is still no way to associate these
with the dataset that they represent”
???!!!
Of course there is!
We already have that!

99.
MetaRecord
Resource3
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
HTTP GET
The FAIR Accessor carries this information
Using the metadata structures defined by DCAT the
FAIR Accessor also tells you how to get the content of
the record, and what formats are available

100.
If we consider the TPF Resource URL to be just another
DCAT Distribution, we get...
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
dcat:Distribution_3
Source TPFrag_URL_1
format rdf+xml

101.
If we consider the TPF Resource URL to be just another
DCAT Distribution, we get...
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
dcat:Distribution_3
Source TPFrag_URL_1
format rdf+xml
URL to the
Triple Pattern
Fragment
Server

102.
If we consider the TPF Resource URL to be just another
DCAT Distribution, we get… now add the Triple Descriptor
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
dcat:Distribution_3
Source TPFrag_URL_1
format rdf+xml
Model: Triple_Desc_URL

103.
If we consider the TPF Resource URL to be just another
DCAT Distribution, we get… now add the Triple Descriptor
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
dcat:Distribution_3
Source TPFrag_URL_1
format rdf+xml
Model: Triple_Desc_URL
HTTP GET on that
URL returns:

104.
If we consider the TPF Resource URL to be just another
DCAT Distribution, we get… now add the Triple Descriptor
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
dcat:Distribution_3
Source TPFrag_URL_1
format rdf+xml
Model: Triple_Desc_URL
When a TPF Server
is associated with a
Record and a Triple
Descriptor, we call
the combination of
technologies a
FAIR
Projector

105.
If we consider the TPF Resource URL to be just another
DCAT Distribution, we get… now add the Triple Descriptor
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
dcat:Distribution_3
Source TPFrag_URL_1
format rdf+xml
Model: Triple_Desc_URL
Calling HTTP GET on TPFrag_URL_1
will give you rdf+xml triples from
Record R
That look like
VOILA!!
Interoperability
from

106.
I hear you objecting… I skipped something important!!!
There is still no way to
make these triples “real”

107.
I hear you objecting… I skipped something important!!!
There is still no way to
make these triples “real”
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
dcat:Distribution_3
Source TPFrag_URL_1
format rdf+xml
Model: Triple_Desc_URL
What is this??

108.
Sadly, there is no magic wand to create interoperability

109.
Sadly, there is no magic wand to create interoperability
Someone has to write the TPF server, and host it somewhere
Interoperability will never come “for free”
(because semantics will never come “for free”)

110.
However, there are reasons for optimism!
1. People must transform data anyway in order to integrate it - this is a daily
routine in most bioinformatics labs
2. For the most common file formats (e.g. CSV or Excel), there are RML-based
tools to automate these transformations; simply create an RML model of
what you want/need, and point the tool at the file.
3. Investing time into creating an RML model, vs. ad hoc “re-useless”
transformation, makes it ~trivial to create a TPF server, and therefore to create
a FAIR Projector for your own data transformation needs… and it is reusable!
AND
4. Because the RML of Triple Descriptors is itself so simple (one triple!), we can
also templatize their construction, making the entire process even more trivial
5. Citations Citations Citations! FAIR Accessors/Projectors are FAIR objects! You
can get credit if other people use your Projector for their own analyses!

111.
Summary of FAIR Projectors
FAIR Projectors create interoperable data, associated with
interoperable metadata, that can be discovered by querying a FAIR
Port (or potentially Google, when/if Google properly indexes RDF)
F+I+R
A + I
I
FAIR Projectors can convert non-FAIR data into FAIR data, or can change
the structure, URL format, or semantics of existing FAIR data sources
FAIR Projectors can be deployed over, and provide a common interface to:
- Static Data Deposits (in any format!)
- Databases
- Triplestores
- Certain (common) types of Web Services
R+++
Triple Descriptors are FAIR entities, intended for reuse, &
None of this required a new API

112.
How does the FAIR Projector fit into the Data FAIR Port?

113.
How does the FAIR Projector fit into the Data FAIR Port?
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
dcat:Distribution_3
Source TPFrag_URL_1
format rdf+xml
Model: Triple_Desc_URL

114.
How does the FAIR Projector fit into the Data FAIR Port?
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_1
Source URL_U1
format rdf+xml
dcat:Distribution_2
Source URL_U2
format application/xml
dcat:Distribution_3
Source TPFrag_URL_1
format rdf+xml
Model: Triple_Desc_URL HTTP GET on that
URL returns:
We know that this is
about Record R in
some repository
We know one possible
representation of a slice
of the data in Record R

115.
Or different Accessors published
by different individuals…
Anyone can publish an Accessor
for any publicly-visible data!
Every possible representation for
Record R
Can be used simply for discovery of
the “type” of content inside of
Record R, or can be used to
discover a FAIR Projector that
executes the transformation

116.
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
Index all possible
representations for
Record R
(and for every other
record)
FAIR Profile
Map of all semantic
representations for
Record R

117.
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
FAIR
Port
Registry/
Broker
Index of all FAIR
Profiles in one or more
of the FAIR Ports

118.
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic Record R
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
FAIR
Port
Registry/
Broker
“I need the blood creatinine levels for patient
Record R using Clinical Measurement
Ontology format”
?
http://hosp.nl/recs/R?s.CMO.o

119.
http://hosp.nl/recs/R?s.CMO.o

120.
http://hosp.nl/recs/R?s.CMO.o
The data you want,
in the format you
want!
Go ahead and
integrate it with
your other data!

121.
<FAIR metadata/>
foaf:primaryTopic u:Q2348Y
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic u:Q2348Y
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic u:Q2348Y
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic u:Q2348Y
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic u:Q2348Y
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic u:Q2348Y
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
<FAIR metadata/>
foaf:primaryTopic u:Q2348Y
dcat:Distribution_3
Source TPFrag_URL
format rdf+xml
Model: Triple_Desc_URL
FAIR
Port
Registry/
Broker
“I need the functional annotations for UniProt
Q2348Y, using EDAM ontology”
?
Exactly the same process for any
data you are trying to retrieve...
http://linkdd.sys/UP/Q2348Y?s.fa.o

122.
With all of this in-place, what will we be able to do?

123.
With all of this in-place, what will we be able to do?
Siri?
Yes, master!
Please find me all known low molecular weight inhibitors of the
Human p65 Protein. Please separate the list based on those
that were found in curated databases, and those that were
found in self-deposited data archives. Also, keep track of the
license and citation information for each one. If you find data
that is relevant, but not public, please provide me with the
contact information for the person I need to request the data
from.

124.
Thanks to:
Michel Dumontier - Stanford Center for Biomedical Informatics Research, Stanford, California.
Ruben Verborgh – Ghent University – imec, Ghent, Belgium
Luiz Olavo Bonino da Silva Santos - Dutch Techcentre for Life Sciences, Utrecht, The Netherlands -
Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
Tim Clark - Department of Neurology, Massachusetts General Hospital Boston MA and Harvard Medical
School, Boston, MA, USA
Morris A. Swertz - Genomics Coordination Center and Department of Genetics, University Medical
Center Groningen, Groningen, The Netherlands
Fleur D.L. Kelpin - Genomics Coordination Center and Department of Genetics, University Medical
Center Groningen, Groningen, The Netherlands
Alasdair J. G. Gray - Department of Computer Science, School of Mathematical and Computer Sciences,
Heriot-Watt University, Edinburgh, UK
Erik A. Schultes - Department of Human Genetics, Leiden University Medical Center, The Netherlands
Erik M. van Mulligen - Department of Medical Informatics, Erasmus University Medical Center
Rotterdam, The Netherlands
Paolo Ciccarese - Perkin Elmer Innovation Lab, Cambridge MA and Harvard Medical School, Boston
MA, USA
Mark Thompson - Leiden University Medical Center, Leiden, The Netherlands
Jerven T. Bolleman - Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical
Universitaire, Geneva, Switzerland

125.
Funding for Mark Wilkinson from:
Fundacion BBVA and the UPM Isaac Peral programme, and the
Spanish Ministerio de Economía y Competitividad grant number
TIN2014-55993-R.
Additional support for FAIR Skunkworks members comes from:
European Union funded projects ELIXIR-EXCELERATE (H2020 no. 676559),
ADOPT BBMRI-ERIC (H2020 no. 676550)
CORBEL (H2020 no. 654248)
Netherlands Organisation for Scientific Research (Odex4all project)
Stichting Topconsortium voor Kennis en Innovatie High Tech Systemen en Materialen
(FAIRdICT project)
BBMRI-NL
RD-Connect and ELIXIR (Rare disease implementation study FP7 no. 305444).

126.
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...You are encouraged to!

127.
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