1.
Data FAIRport Skunkworks
First Prototype Demo of Legacy Data Repository
Discovery and Interoperability
(Mark D Wilkinson, Presentation to Elsevier, Jul, 2015)

2.
This presentation is licensed CC-BY
Mark Wilkinson (markw@illuminae.com)
https://goo.gl/YEdwwB
@markmoby

3.
EU Lead
Mark Wilkinson
Isaac Peral Distinguished Researcher, CBGP-UPM, Madrid
USA Lead
Michel Dumontier
Associate Professor, Biomedical Informatics, Stanford, USA
FAIRport Project Lead
Barend Mons
Professor, Leiden University Medical Centre, Netherlands
Data FAIRport
Skunkworks
Common repository access via meta-meta-
descriptors and homogenous accessors

4.
What is a FAIRport?
● Findable - (meta)data should be uniquely and persistently
identifiable
● Accessible - identifiers should provide a mechanism for (meta)data
access, including authentication, access protocol, license, etc.
● Interoperable - (meta)data should be machine-accessible, using a
machine-parseable syntax and, where possible, shared common
vocabularies.
● Reusable - there should be sufficient machine-readable metadata
that it is possible to “integrate like-with-like”, and that component data
objects can be precisely and comprehensively cited post-integration.

5.
The Problem

6.
End-user view of “The Problem”
Tissue rejection experimental context. Today, I’m looking
for microarray data of human liver cells on a time-course
following liver transplant.
What repositories could contain such data?
● GEO? EUDat? FigShare? Dryad? Atlas?
● What fields in those repositories would I need to
search, using what vocabularies, to find the
microarray studies that are relevant?

7.
Dissecting the problem
There are a lot of repositories!
General Purpose: Dataverse, Dryad, EUDat, Figshare, etc.
Special Purpose: PDB, UniProt, NCBI, GEO, Atlas, EnsEMBL

8.
Dissecting the problem
Lack of harmonized metadata structures, or even rich
descriptions of the contents of these repositories, hinders
us from (for example):
● knowing where we can look for certain types of data
● knowing if two repositories contain records about the same thing
● Cross-referencing or “joining” across repositories to integrate
disparate data about the same thing
● Knowing which repository I could/should deposit my data to (and how)

9.
“Skunkworks” Challenge
If we wanted to enable this kind of FAIR discovery and
integration over myriad repositories, what infrastructure
(existing/new) would we need?

10.
If we wanted to enable this kind of FAIR discovery and
integration over myriad repositories, what infrastructure
(existing/new) would we need?
Discussions with Tim Clark revealed that the core
objectives of Skunkworks were very similar to those of
Force 11 Data Citation Implementation
Working Group Team 4 - “Common repository interfaces”
...so we joined forces :-)
“Skunkworks” Challenge

11.
The Solution?

12.
Shared Metadata Descriptors?
They already exist! (e.g. DCAT)
Are not (yet) widely implemented
But are not sufficiently rich...
...only describe “core” metadata
We need to query richer metadata like experimental
context and domain-specific data elements

13.
So... extend DCAT?

14.
So... extend DCAT?
...extend it where?...
too many specialist domains & data-types
resistance to harmonization
resistance to implementation
(time, money, expertise, ‘just don’t care’)
attempting to impose standards
is a Mug’s game!

15.
Common provider-implemented API?

16.
Common provider-implemented API?
a la TDWG/TAPIR and caBIO...
too many specialist domains & data-types
resistance to harmonization
resistance to implementation
(time, money, expertise, ‘just don’t care’)
attempting to impose standards
is a Mug’s game!

17.
Where else could the solution be?
What exactly *is* our problem?

18.
What exactly *is* our problem?
Data Record (e.g. XML, RDF)

19.
What exactly *is* our problem?
Data Record (e.g. XML, RDF)
Data Schema (e.g. XMLS, RDFS)
Defines

20.
What exactly *is* our problem?
Data Record (e.g. XML, RDF)
Data Schema (e.g. XMLS, RDFS)
Metadata Record (e.g. DCAT-compliant RDF)
Defines
Describes

21.
What exactly *is* our problem?
Data Record (e.g. XML, RDF)
Data Schema (e.g. XMLS, RDFS)
Metadata Record (e.g. DCAT-compliant RDF)
(IF the repository uses DCAT)
DCAT RDFS Schema
(IF the repository uses DCAT…)
Defines
Describes
Defines

22.
What exactly *is* our problem?
Data Record (e.g. XML, RDF)
Data Schema (e.g. XMLS, RDFS)
Metadata Record (e.g. DCAT-compliant RDF)
(IF the repository uses DCAT)
DCAT RDFS Schema
(IF the repository uses DCAT…)
Defines
Describes
Defines
If everyone used DCAT, we could at least query the
core metadata of all repositories…
...but they don’t...
...and core isn’t rich enough anyway...

23.
What exactly *is* our problem?
XML
Data Record
XMLS
Data Schema
DCAT RDF
Metadata Record
RDF
Data Record
RDFS
Data Schema
UniProt RDF
Metadata Record
ACEDB
Data Record
ACEDB
Data Schema
DragonDB Form
Metadata Record
DCAT
RDFS Schema
UniProt RDFS
MetadataSchema
DragonDB Form
Metadata Schema
REALITY

24.
What exactly *is* our problem?
XML
Data Record
XMLS
Data Schema
DCAT RDF
Metadata Record
RDF
Data Record
RDFS
Data Schema
UniProt RDF
Metadata Record
ACEDB
Data Record
ACEDB
Data Schema
DragonDB Form
Metadata Record
DCAT
RDFS Schema
UniProt RDFS
MetadataSchema
DragonDB Form
Metadata Schema
Repositories don’t all use DCAT Schema

25.
What exactly *is* our problem?
XML
Data Record
XMLS
Data Schema
DCAT RDF
Metadata Record
RDF
Data Record
RDFS
Data Schema
UniProt RDF
Metadata Record
ACEDB
Data Record
ACEDB
Data Schema
DragonDB Form
Metadata Record
DCAT
RDFS Schema
UniProt RDFS
MetadataSchema
DragonDB Form
Metadata Schema
Those that use DCAT Schema, use only parts of it

26.
What exactly *is* our problem?
XML
Data Record
XMLS
Data Schema
DCAT RDF
Metadata Record
RDF
Data Record
RDFS
Data Schema
UniProt RDF
Metadata Record
ACEDB
Data Record
ACEDB
Data Schema
DragonDB Form
Metadata Record
DCAT
RDFS Schema
UniProt RDFS
MetadataSchema
DragonDB Form
Metadata Schema
Those that don’t use DCAT
use a myriad of alternatives (some very loosely defined)

27.
What exactly *is* our problem?
XML
Data Record
XMLS
Data Schema
DCAT RDF
Metadata Record
RDF
Data Record
RDFS
Data Schema
UniProt RDF
Metadata Record
ACEDB
Data Record
ACEDB
Data Schema
DragonDB Form
Metadata Record
DCAT
RDFS Schema
UniProt RDFS
MetadataSchema
DragonDB Form
Metadata Schema
And don’t necessarily use
all elements of those alternatives either

28.
What exactly *is* our problem?
XML
Data Record
XMLS
Data Schema
DCAT RDF
Metadata Record
RDF
Data Record
RDFS
Data Schema
UniProt RDF
Metadata Record
ACEDB
Data Record
ACEDB
Data Schema
DragonDB Form
Metadata Record
DCAT
RDFS Schema
UniProt RDFS
MetadataSchema
DragonDB Form
Metadata Schema
So we need to find a way to do RICH queries
over all of these?

29.
What exactly *is* our problem?
XML
Data Record
XMLS
Data Schema
DCAT RDF
Metadata Record
RDF
Data Record
RDFS
Data Schema
UniProt RDF
Metadata Record
ACEDB
Data Record
ACEDB
Data Schema
DragonDB Form
Metadata Record
DCAT
RDFS Schema
UniProt RDFS
MetadataSchema
DragonDB Form
Metadata Schema
We need a way to describe the descriptors...

30.
Desiderata of meta-meta descriptors
● Must describe legacy data (i.e. not just DCAT or other “modern” data)
● Must describe a multitude of data formats (XML, RDF, Key/Value, etc.)
● Must be capable of describing any kind of value constraint, e.g. plain text,
numerical, arbitrary CV, rdf:range, or equivalent OWL construct
● Must be modular, identifiable, shareable, and reusable (to stem the
proliferation of new formats)
● Must be hierarchical to allow composite re-use of shared descriptors
● Must use standard technologies, and re-use existing vocabularies if poss.
● Must be extremely lightweight and “trivial” to create
● Must NOT require the participation of the repository host (no buy-in required)

31.
The Solution?
(or at least, our best attempt to date!)

32.
Exemplar use-cases:
● A piece of software that can generate a “sensible”
data submission form for any repository
(at the Force 2015 meeting a few months ago I gave a presentation of a working
example of this… so I won’t repeat that today…)
● A piece of software that can generate a “sensible”
query form/interface for any repository
(demonstration of this today!)
Skunkworks Task #1 - [F]indable
Invent harmonized cross-repository meta-
descriptors

33.
“FAIR Profiles”
FAIR Profiles provide a common way to describe
a repository’s metadata
(and data, for that matter!)

34.
XML
Data Record
XMLS
Data Schema
DCAT RDF
Metadata Record
RDF
Data Record
RDFS
Data Schema
UniProt RDF
Metadata Record
ACEDB
Data Record
ACEDB
Data Schema
DragonDB Form
Metadata Record
DCAT
RDFS Schema
UniProt RDFS
MetadataSchema
DragonDB Form
Metadata Schema
What FAIR Profiles do

35.
XML
Data Record
XMLS
Data Schema
DCAT RDF
Metadata Record
RDF
Data Record
RDFS
Data Schema
UniProt RDF
Metadata Record
ACEDB
Data Record
ACEDB
Data Schema
DragonDB Form
Metadata Record
DCAT
RDFS Schema
UniProt RDFS
MetadataSchema
DragonDB Form
Metadata Schema
FAIR Profile of
DCAT Schema
FAIR Profile of
UniProt Metadata
Schema
FAIR Profile of
DragDB Metadata
Schema
What FAIR Profiles do

36.
XML
Data Record
XMLS
Data Schema
DCAT RDF
Metadata Record
RDF
Data Record
RDFS
Data Schema
UniProt RDF
Metadata Record
ACEDB
Data Record
ACEDB
Data Schema
DragonDB Form
Metadata Record
DCAT
RDFS Schema
UniProt RDFS
MetadataSchema
DragonDB Form
Metadata Schema
FAIR Profile
DCAT Schema
FAIR Profile
UniProt Metadata
Schema
FAIR Profile
DragDB Metadata
Schema
Though they are potentially describing very different things
(from Web FORM fields to OWL Ontologies!)
all FAIR Profiles are written using the same vocabulary and structure, defined by...

37.
XML
Data Record
XMLS
Data Schema
DCAT RDF
Metadata Record
RDF
Data Record
RDFS
Data Schema
UniProt RDF
Metadata Record
ACEDB
Data Record
ACEDB
Data Schema
DragonDB Form
Metadata Record
DCAT
RDFS Schema
UniProt RDFS
MetadataSchema
DragonDB Form
Metadata Schema
FAIR Profile
DCAT Schema
FAIR Profile
UniProt Metadata
Schema
FAIR Profile
DragDB Metadata
Schema

38.
The FAIR Profile
Schema

39.
Repo. Data Record (e.g. XML, RDF)
Repo. Data Schema (e.g. XMLS, RDFS)
Repository Metadata Record
Repository Metadata Schema
Defines
Describes
Defines
Defines
~~Describes**
Repository’s FAIR Profile
FAIR Profile Schema

40.
Repo. Data Record (e.g. XML, RDF)
Repo. Data Schema (e.g. XMLS, RDFS)
Repository Metadata Record
Repository Metadata Schema
Defines
Defines
~~Describes**
Repository’s FAIR Profile
FAIR Profile Schema

41.
FAIR Profile Schema
A very small OWL Vocabulary for writing meta-meta-
descriptors
FAIR Profile
Metadata
FAIR Class
dc:
provenance
hasProperty
owl:Class
(URI or de
novo
definition)
rdf:Property
owl:ObjectProperty or
owl:DatatypeProperty
describes property
minCount
xsd:anyURI
xsd:integer
xsd:integer
maxCount
allowedValues
FAIR
Property
describes class
rdf:langString
skos:preferredLabel skos:preferredLabel
rdf:langString
http://datafairport.org/schema/FAIR-schema.owl

42.
FAIR Profile Schema
A very small OWL Vocabulary for writing meta-meta-
descriptors
http://datafairport.org/schema/FAIR-schema.owl
FAIR Profile
Metadata
FAIR Class
dc:
provenance
hasProperty
owl:Class
(URI or de
novo
definition)
rdf:Property
owl:ObjectProperty or
owl:DatatypeProperty
describes property
minCount
xsd:anyURI
xsd:integer
xsd:integer
maxCount
allowedValues
FAIR
Property
describes class
rdf:langString
skos:preferredLabel skos:preferredLabel
rdf:langString

43.
xsd:anyURI
allowedValues

44.
URI must resolve to a
SKOS Concept Scheme
Describes the constraints on the possible
values for a predicate in the target-
Repository’s metadata Schema
xsd:anyURI
allowedValues

45.
URI must resolve to a
SKOS Concept Scheme
Describes the constraints on the possible
values for a predicate in the target-
Repository’s metadata Schema
NOTE: we cannot use rdfs:range because
we are meta-modelling a schema! The
predicate is a CLASS at the meta-model
level, so use of rdfs:range is not appropriate.
xsd:anyURI
allowedValues

46.
A FAIR Profile
(an RDF document that follows the FAIR Profile Schema)
This
Metadata Record
Metadata Schema
Fair Profile
Fair Profile Schema

47.
A FAIR Profile
(an RDF document that follows the FAIR Profile Schema)
This
Metadata Record
Metadata Schema
Fair Profile
Fair Profile Schema
(as an aside, This is a document that, we believe, is
an implementation of the ISO11179 standard for
metadata descriptors; however we have not formally
made the mapping between our concepts and theirs.
This will happen soon, and this mapping alone is
sufficient to become ISO11179-compliant. As such, the
Fair Profile Schema is a schema for creating ISO11179-
compliant descriptors…)

48.
What a FAIR Profile is:
A meta-description of the (meta)data
in a repository

49.
What a FAIR Profile is:
A meta-description of the (meta)data
in a repository
What a FAIR Profile is NOT:
THE meta-description of the (meta)data
in a repository

50.
What a FAIR Profile is:
A meta-description of the (meta)data
in a repository
if you were to view it
from a particular “perspective”
(also known as a “lens*” over the data)
* Scientific Lenses to Support Multiple Views over Linked Chemistry
Data; DOI:10.1007/978-3-319-11964-9_7

51.
What a FAIR Profile is:
A meta-description of the (meta)data
in a repository
if you were to view it
from a particular “perspective”
(also known as a “lens*” over the data)
this is where the FAIRport approach becomes
distinctly powerful!

52.
What a FAIR Profile is:
A meta-description of the (meta)data
in a repository
if you were to view it
from a particular “perspective”
(also known as a “lens*” over the data)
but first, look at the other
FAIRport components

53.
Skunkworks Task #2 - [A]cessible
Are there already access layer definitions?

54.
remind myself to say that many of
these components are standalone
you don’t have to implement
everything, all at once.

55.
A set of behaviors for providing a unified (albeit simplistic!)
access layer for “records” contained in any Web resource
Skunkworks Task #2 - [A]cessible
Are there already access layer definitions?

56.
LDP sits at a URL waiting

57.
GET
Client calls HTTP GET
on the URL
(that’s all!)

58.
??
LDP communicates
with the repository
(how? entirely up to you!)

59.
Repository returns data
“about available records”
(how? entirely up to you!)
??

60.
LDP returns you an
RDF representation of the
list of records’ URLs
<RDF>
URL1
URL2
URL3
URL4
URL5
URL6
…
…
...
</RDF>

61.
GET URL6
The URLs (should) point
back to the LDP server

62.
??
LDP communicates with the
repository about that record
??

63.
LDP returns you
DCAT Distributions for all
available formats of that record
that the repo provides
<RDF>
<dcat:Dist.>
<format xml>
URL6a
<dcat:Dist.>
<format html>
URL6b
</RDF>

64.
You directly call the
repository using the URL of
your choice
GET URL6a

65.
Repository returns you the
data you requested
Content-type: application/xml
<data>
<data>
Yummy Data Here!
</data>
</data>
….
(Note: most repositories already do this part!
So we’re half-way there :-) )

66.
The first time I wrote one of these from scratch,
it was about 170 lines of code,
and took less than 4 hours
(including reading the W3C documentation!)

67.
The first time I wrote one of these from scratch,
it was about 170 lines of code,
and took less than 4 hours
(including reading the W3C documentation!)
These may exist completely independently of any other FAIRport component
as a way of fulfilling the “A” (Accessible) aspect of the FAIR Data Principles
https://www.force11.org/group/fairgroup/fairprinciples

68.
The first time I wrote one of these from scratch,
it was about 170 lines of code,
and took less than 4 hours
(including reading the W3C documentation!)
However, when one of these is associated with a FAIR Profile we call it a
“FAIR Accessor”

69.
The first time I wrote one of these from scratch,
it was about 170 lines of code,
and took less than 4 hours
(including reading the W3C documentation!)
**** As of July 8, 2015, there are now support libraries (in Perl)
for this part of the implementation: https://goo.gl/NB13Fz (the
location of this code will change soon, sorry!)

70.
Live Demo….
http://biordf.org/cgi-bin/RD_Connect/EHDN_Accessor
DISCLAIMER: This demonstration was written during an RD Connect
workshop, and the demonstration references various aspects of the RD
Connect project (including having ‘RD_Connect’ in the URL). HOWEVER, I am
not affiliated with RD Connect, I do not speak for RD Connect in any way,
and RD Connect does not endorse any of these ideas, products,
behaviours, or anything else presented in this talk. In addition, the data
and metadata presented here is all completely fake, and this public demo
raises no privacy concerns.
The demo is presented using the Tabulator extension to Chrome, in order to
nicely format the RDF for human readability.

71.
These elements
are defined by
the LDP
Specification

72.
A SKOS Concept Scheme describing the
“nature” of the data in the repository

73.
Optional - the link to the
meta-descriptors of each
record in the repository
(paginated using HTTP
headers defined by LDP)

74.
The Record’s Meta-descriptor

75.
The Record’s Meta-descriptor
Metadata about the
record (which metadata
is completely at the
discretion of the data
owner!)

76.
The Record’s Meta-descriptor
Ontological information
about the type of
record… click through to:

77.
rdf:type SIO:SIO_001027 (Medical Health Record)

78.
The Record’s Meta-descriptor
There are 3 DCAT
Distributions for this
record

79.
The Record’s Meta-descriptor
Each distribution has its own
format and download URL
(distributions are completely
optional, and up to the provider)
This would also be the place to
put license, accessibility, or
authentication metadata!

80.
This provides an API-free way of accessing any record
in any dataset
Every step is just HTTP GET with
standard metadata following the DCAT ontology
Incremental drill-down from repository-level all the way to an
individual record
Useful metadata at all levels
Access is 100% under provider-control at all levels

81.
This is NOT intended to be “efficient”!!
However, the alternative is to invent a query API, and then
force all repositories to implement it…
Not Gonna Happen!
This is lightweight, and easy to implement
Trade power for (hopefully) wider adoption...

82.
package EHDN_Accessor; # this should be the same as your filename!
use strict;
use warnings;
use JSON;
use base 'FAIR::Accessor';
my $config = { title => 'European Huntington Disease Network Data Accessor',
serviceTextualDescription => 'Server for some ERDN Data',
textualAccessibilityInfo => "The information from this server requries no authentication", # this could also be a $URI describing the accessibiltiy
mechanizedAccessibilityInfo => "", # this must be a URI to an RDF document
textualLicenseInfo => "CC-BY", # this could also be a URI to the license info
mechanizedLicenseInfo => "", # this must be a URI to an RDF document
baseURI => "", # I don't know what this is used for yet, but I have a feeling I will need it!
ETAG_Base => "EHDN_Accessor_For_RegInfo",
localNamespaces => {ehdn => 'http://ehdn.org/some/items/', ehdnpred => 'http://ehdn.org/some/predicates/'},
localMetadataElements => [qw(erdnpred:fromHospital erdnpred:lastevaluatedDate) ], };
my $service = EHDN_Accessor->new(%$config);
$service->handle_requests;
sub get_all_meta_URIs {
my ($starting_at_record, $path_info) = @_;
$path_info ||="";
my %result = ( 'dc:title' => "EHDN Accessor Server",
'dcat:description' => "the prototype Accessor server for EHDN",
'dcat:identifier' => "handle:12345566798",
'dcat:keyword' => ["medical records", "rare diseases", "EHDN", "Linked Data Platform", 'HTT', 'huntington'],
'dcat:landingPage' => 'http://www.euro-hd.net/html/network',
'dcat:language' => 'en',
'dcat:publisher' => 'http://www.euro-hd.net',
'dcat:temporal' => 'http://reference.data.gov.uk/id/quarter/2006-Q1',
'dcat:theme' => 'http://biordf.org/DataFairPort/ConceptSchemes/Huntingtons.rdf',
'daml:has-Technical-Lead' => "Summer Student Joe",
'daml:has-Administrative-Contact' => "John Doe",
'daml:has-Program-Manager' => "Jane Doe",
'daml:has-Principle-Investigator' => "Big Doctor", );
my $BASE_URL = "http://" . $ENV{'SERVER_NAME'} . $ENV{'REQUEST_URI'} . $path_info;
my @known_records = ($BASE_URL . "/479-467-29X", $BASE_URL . "/768-599-467", );
$result{'void:entities'} = scalar(@known_records); # THE TOTAL *NUMBER* OF RECORDS THAT CAN BE SERVED
$result{'ldp:contains'} = @known_records; # the listref of record ids
return encode_json(%result);
}
sub get_distribution_URIs {
my ($self, $ID, $PATH_INFO) = @_;
my (%response, %formats, %metadata);
$formats{'text/html'} = 'http://myserver.org/ThisScript/record/479-467-29X.html';
$formats{'application/rdf+xml'} = 'http://myserver.org/ThisScript/record/479-467-29X.rdf';
$metadata{'rdf:type'} = ['edam:data_0006', 'sio:SIO_000088'];
extractDataFromSpreadsheet(%metadata, $ID);
$response{distributions} = %formats;
$response{metadata} = %metadata if (keys %metadata); # only set it if you can provided something
my $response = encode_json(%response);
return $response;
}
sub extractDataFromSpreadsheet{
my ($metadata, $ID) = @_;
use Spreadsheet::XLSX::Reader::LibXML;
my $db_file = "registry3-enrolment.xlsx.xlsx";
my $excel = Spreadsheet::XLSX::Reader::LibXML->new();
my $workbook = $excel->parse($db_file);
my ($sheet) = $workbook->worksheets;
my ($first, $last) = $sheet->row_range;
foreach my $row ($first .. $last) {
next unless ($sheet->get_cell($row, 0)->value eq $ID);
my $cell = $sheet->get_cell($row, 5);
$metadata->{'dcat:updateDate'} = $cell->value;
$cell = $sheet->get_cell($row, 1);
$metadata->{'dcat:releaseDate'} = $cell->value;
$cell = $sheet->get_cell($row, 3);
This is the only code that a provider
must implement… and much (almost
half!) of it is just tag/value definitions
If they don’t want to implement the full
set of drill-down behaviors then the
code is even smaller!
(This is the actual code - 68 lines -
running the demo you just saw. Most
of the heavy-lifting is handled by the
libraries I published yesterday)

83.
Skunkworks Task #3 - [I]nteroperable
This is “the holy grail”!!

84.
Skunkworks Task #3 - [I]nteroperable
This is “the holy grail”!!
This is where the FAIR Profile reveals its utility
“what it IS” vs. “what it IS NOT”

85.
What a FAIR Profile is:
A meta-description of the (meta)data
in a repository
if you were to view it
from a particular “perspective”
(also known as a “lens” over the data)

86.
Skunkworks Task #3 - [I]nteroperable
“FAIR Projectors”
A FAIR Projector is a (potentially) small, modular,
reusable Web based service that “projects” data
from a repository into the format
described by a FAIR Profile

87.
Skunkworks Task #3 - [I]nteroperable
“FAIR Projectors”
A FAIR Projector is a (potentially) small, modular,
reusable Web based service that “projects” data
from a repository into the format
described by a FAIR Profile
http://linkeddatafragments.org/

88.
RESTful access to RDF data resources
RESTful hypermedia controls (e.g. pagination)
defined by Hydra W3C Community Group
http://www.hydra-cg.com/

89.
implementedBy

90.
implementedBy
GET

91.
implementedBy
2 Options for a projector:

92.
implementedBy
2 Options for a projector:
Direct Access to Repository

93.
implementedBy
2 Options for a projector:
OR access via a FAIR Accessor

94.
implementedBy
Client receives

95.
Stage 1: Kinds of questions we can ask
● How do I access the records in Repo X?
→ HTTP GET (Accessor URL)
● How do I access the records in Repo X in XML?
→ HTTP GET (Accessor URL)
→ HTTP GET (DCAT Dist URL)
● Can I please have the “biological tissue” field in Repository X
as FMA Ontology terms?
→ Search FAIRport Registry
→ Find matching FAIR Profile + Projector
→ HTTP GET (Projector URL)

96.
FAIR Projector:
The first time I wrote one of these from scratch,
it was about 300 lines of Perl code,
and took about 6 hours
(including reading the LDF documentation!)
and it projected three different FAIR Profiles
The next thing on my TODO list is to write libraries to make this
easier; however, this is a much trickier thing to do!

97.
Live Demo of a FAIR Projector
This demo is done over my own database:
http://antirrhinum.net
it will project the “Allele” slice of that database into three
different forms, using 3 different profiles. The demo uses a
FAIR Accessor (as described in the previous demo)

98.
<?xml version="1.0" standalone="yes"?>
<Allele class="Allele" value="cho">
<Source>
<gene class="Locus" value="CHO" />
</Source>
<Location class="Laboratory" value="Schwarz-Sommer" />
<Description>
<Phenotype class="#Text" value="Habit:" />
<Phenotype class="#Text" value="Leaves: Thin and narrow starting from the 6th leaf. Buckled and warped along the axis of the leaf." />
<Phenotype class="#Text" value="Seedlings:" />
<Phenotype class="#Text" value="Cotyledons: no obvious change" />
<Phenotype class="#Text" value="Hypocotyl:" />
<Phenotype class="#Text" value="Inflorescence:" />
<Phenotype class="#Text" value="Flowers: Conspicuous sepal to petal transformations, particularly in 165E genetic background. Petals unfused. Carpel sometimes unfused and stunted." />
<Phenotype class="#Text" value="_____________" />
<Phenotype class="#Text" value="Upper lip:" />
<Phenotype class="#Text" value="Lower lip:" />
<Phenotype class="#Text" value="Bumps:" />
<Phenotype class="#Text" value="Seed: reduced germimation of mutant seed." />
<Phenotype class="#Text" value="Roots: root growth retarded; roots sometimes absent." />
<Phenotype class="#Text" value="Remarks: F2 74:25, though usually mutants are under-represented in F2 populations." />
<Phenotype class="#Text" value="Remarks: Identical phenotype to Des (Despenteado)" />
<Recessive />
</Description>
<Phenotype_picture class="Phenotype_Picture" value="cho~a" />
<Phenotype_picture class="Phenotype_Picture" value="cho~b" />
<Phenotype_picture class="Phenotype_Picture" value="cho-0" />
<Phenotype_picture class="Phenotype_Picture" value="cho-1" />
<Phenotype_picture class="Phenotype_Picture" value="zss_pict0027" />
<Phenotype_picture class="Phenotype_Picture" value="zss_pict0028" />
<Phenotype_picture class="Phenotype_Picture" value="zss_pict0029" />
<Expression_pattern_of class="Locus" value="FIM">
<Description class="#Text" value="FIM extends to first whorl" />
<Pick_me_to_call class="#txt" value="FIM_in_cho">
<Pick_me_to_call-2 class="#txt" value="FIM_in_cho.jpg" />
</Pick_me_to_call>
<Photo_by class="Author" value="Wilkinson MD" />
</Expression_pattern_of>
<Expression_pattern_of class="Locus" value="GLO">
<Description class="#Text" value="GLO expression in first whorl organs that ectopically express FIM" />
<Pick_me_to_call class="#txt" value="GLO_in_cho">
<Pick_me_to_call-2 class="#txt" value="GLO_in_cho.jpg" />
</Pick_me_to_call>
<Photo_by class="Author" value="Wilkinson MD" />
</Expression_pattern_of>
<Multi_mutant class="Multi_mutant" value="cho_fim-679" />
<Multi_mutant class="Multi_mutant" value="cho_fim-1" />
<Multi_mutant class="Multi_mutant" value="cho_fis" />
<Multi_mutant class="Multi_mutant" value="cho_def-gli" />
<Multi_mutant class="Multi_mutant" value="cho_inco" />
<Multi_mutant class="Multi_mutant" value="cho_glo-1" />
<Multi_mutant class="Multi_mutant" value="cho_glo-3D" />
</Allele>
The raw data, from
the repository

99.
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:FAI="http://datafairport.org/schemas/FAIR-schema.owl#"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:s="http://www.w3.org/2000/01/rdf-schema#">
<FAI:FAIRClass rdf:about="">
<FAI:hasProperty rdf:resource="http://datafairport.org/sampledata/profileschemaproperty/0c0c0c3c-5ce1-4df6-98d3-4c22a75748ea"/>
<FAI:hasProperty rdf:resource="http://datafairport.org/sampledata/profileschemaproperty/94037d0d-3d8e-4fc4-bd24-dafb85520089"/>
<FAI:onClassType rdf:resource="http://purl.obolibrary.org/obo/SO_0001023"/>
<dcterms:provenance rdf:resource="#Profile"/>
<s:label>FAIR Class of Allele</s:label>
</FAI:FAIRClass>
<FAI:FAIRProfile rdf:about="#Profile">
<FAI:hasClass rdf:resource=""/>
<dcterms:description>FAIR Profile Allele record properties, using textual descriptions and links to Gene Records</dcterms:description>
<dcterms:identifier>doi:Mark.Dragon.P1</dcterms:identifier>
<dcterms:license>Anyone may use this freely</dcterms:license>
<dcterms:organization>wilkinsonlab.info</dcterms:organization>
<dcterms:title>FAIR Profile of Descriptive Allele records</dcterms:title>
<rdf:type rdf:resource="http://purl.org/dc/terms/ProvenanceStatement"/>
<s:label>FAIR Profile Allele</s:label>
</FAI:FAIRProfile>
<FAI:FAIRProperty rdf:about="http://datafairport.org/sampledata/profileschemaproperty/0c0c0c3c-5ce1-4df6-98d3-4c22a75748ea">
<FAI:allowedValues rdf:resource="../ConceptSchemes/xsdstring"/>
<FAI:onPropertyType rdf:resource="http://purl.org/dc/terms/description"/>
<s:label>description</s:label>
</FAI:FAIRProperty>
<FAI:FAIRProperty rdf:about="http://datafairport.org/sampledata/profileschemaproperty/94037d0d-3d8e-4fc4-bd24-dafb85520089">
<FAI:allowedValues rdf:resource="../ConceptSchemes/SequenceOntologyGene704"/>
<FAI:maxCount>1</FAI:maxCount>
<FAI:minCount>1</FAI:minCount>
<FAI:onPropertyType rdf:resource="http://purl.obolibrary.org/obo/so_variant_of"/>
<s:label>variant of</s:label>
</FAI:FAIRProperty>
</rdf:RDF>
FAIR Profile #1 - “Descriptive”

100.
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:FAI="http://datafairport.org/schemas/FAIR-schema.owl#"
xmlns:dc="http://purl.org/dc/terms/"
xmlns:s="http://www.w3.org/2000/01/rdf-schema#">
<FAI:FAIRClass rdf:about="">
<FAI:hasProperty rdf:resource="http://datafairport.org/sampledata/profileschemaproperty/6e35cbde-3e6a-430d-be22-
e87507c71827"/>
<FAI:onClassType rdf:resource="http://purl.obolibrary.org/obo/SO_0001023"/>
<dc:provenance rdf:resource="#Profile"/>
<s:label>FAIR Class of Allele</s:label>
</FAI:FAIRClass>
<FAI:FAIRProfile rdf:about="#Profile">
<FAI:hasClass rdf:resource=""/>
<dc:description>FAIR Profile the Image portion of an Allele record using SIO:Image classification</dc:description>
<dc:identifier>doi:Mark.Dragon.P2</dc:identifier>
<dc:license>Anyone may use this freely</dc:license>
<dc:organization>wilkinsonlab.info</dc:organization>
<dc:title>FAIR Profile the Image portion of an Allele record</dc:title>
<rdf:type rdf:resource="http://purl.org/dc/terms/ProvenanceStatement"/>
<s:label>FAIR Profile of Allele Images(SIO)</s:label>
</FAI:FAIRProfile>
<FAI:FAIRProperty rdf:about="http://datafairport.org/sampledata/profileschemaproperty/6e35cbde-3e6a-430d-be22-e87507c71827">
<FAI:allowedValues rdf:resource="../ConceptSchemes/SIOOntologyImage81"/>
<FAI:onPropertyType rdf:resource="http://semanticscience.org/ontology/SIO_000205"/>
<s:label>is represented by</s:label>
</FAI:FAIRProperty>
</rdf:RDF>
FAIR Profile #2 - “Image using SIO ontology”

101.
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:FAI="http://datafairport.org/schemas/FAIR-schema.owl#"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:s="http://www.w3.org/2000/01/rdf-schema#">
<FAI:FAIRClass rdf:about="">
<FAI:hasProperty rdf:resource="http://datafairport.org/sampledata/profileschemaproperty/4fbb6c39-1bbe-49bf-af36-
c966c3e233a1"/>
<FAI:onClassType rdf:resource="http://purl.obolibrary.org/obo/SO_0001023"/>
<dcterms:provenance rdf:resource="#Profile"/>
<s:label>FAIR Class of Allele</s:label>
</FAI:FAIRClass>
<FAI:FAIRProfile rdf:about="#Profile">
<FAI:hasClass rdf:resource=""/>
<dcterms:description>FAIR Profile the Image portion of an Allele record using EDAM:Image classification</dcterms:description>
<dcterms:identifier>doi:Mark.Dragon.P3</dcterms:identifier>
<dcterms:license>Anyone may use this freely</dcterms:license>
<dcterms:organization>wilkinsonlab.info</dcterms:organization>
<dcterms:title>FAIR Profile the Image portion of an Allele record</dcterms:title>
<rdf:type rdf:resource="http://purl.org/dc/terms/ProvenanceStatement"/>
<s:label>FAIR Profile Allele Images (EDAM)</s:label>
</FAI:FAIRProfile>
<FAI:FAIRProperty rdf:about="http://datafairport.org/sampledata/profileschemaproperty/4fbb6c39-1bbe-49bf-af36-c966c3e233a1">
<FAI:allowedValues rdf:resource="../ConceptSchemes/EDAMOntologyImage2968"/>
<FAI:onPropertyType rdf:resource="http://semanticscience.org/ontology/SIO_000205"/>
<s:label>is represented by</s:label>
</FAI:FAIRProperty>
</rdf:RDF>
FAIR Profile #3 - “Image using EDAM ontology”

102.
FAIR Accessor Step 1
(http://antirrhinum.net/cgi-bin/LDP/Alleles)

103.
FAIR Accessor Step 2
(click on “cho” in the list of alleles)
The Projector takes the application/xml distribution and projects it...

104.
XML of the Allele records
projected using the “descriptive” FAIR Profile
http://biordf.org/cgi-bin/DataFairPort/DragonDB_LDF_Profiler/DragonDB_Allele_ProfileAlleleDescriptions/

105.
XML of the Allele records (SAME XML!)
projected using the “SIO Image” FAIR Profile
http://biordf.org/cgi-bin/DataFairPort/DragonDB_LDF_Profiler/DragonDB_Allele_ProfileImagesSIO/
http://semanticscience.org/resource/SIO_000081

106.
XML of the Allele records (SAME XML!)
projected using the “EDAM Image” FAIR Profile
http://biordf.org/cgi-bin/DataFairPort/DragonDB_LDF_Profiler/DragonDB_Allele_ProfileImagesSIO/
http://edamontology.org/data_2968

107.
XML of the Allele records (SAME XML!)
projected using the “EDAM Image” FAIR Profile
http://biordf.org/cgi-bin/DataFairPort/DragonDB_LDF_Profiler/DragonDB_Allele_ProfileImagesSIO/
Pagination controls from
the Hydra ontology...

108.
This was a very “lightweight” demo,
but it showed the point
Same data, different lenses (FAIR Profiles)
In the case of this demo, all three Projections used the
same FAIR Accessor
It is obviously more efficient to reach-into the database
directly and skip the Accessor altogether. Yes!
However, the point of this demo was to show the
“worst case scenario” where you need to FAIR Project
something that you have absolutely no control over

109.
Stage 2: Leverage the Modularity
implementedBy

110.
Stage 2: Leverage the Modularity
implementedByimplementedBy

111.
Stage 2: Leverage the Modularity
implementedByimplementedBy
Repository X
Repository Y

112.
Stage 2: Leverage the Modularity
implementedByimplementedBy

113.
Stage 2: Leverage the Modularity
implementedByimplementedBy
Merged data to be cross-queried

114.
Main features of FAIR Profiles
● Do not require repository participation - anyone can write a Profile. Most of
the time it should be possible to write an accessor too, even by screen-
scraping!
● Provides a end-user-purpose-driven, potentially non-comprehensive “view”
on a repository
● FAIR Profiles of any given repository facet may be different! May use
different vocabularies or may interpret fields differently, depending on the
needs of the Profile author
● FAIR profiles can/should be indexed and shared (e.g. in a FAIRport
Registry), to facilitate cross-repository interoperability and integration
● There is no (obvious) reason why a FAIR profile could not be used to
describe the DATA in the repository, not just the metadata…
o my Antirrhinum Allele example does exactly that!
● FAIR Profiles can be used both at the “read” and at the “write” end of data
publishing… (Force 11 Oxford meeting demo was for “write” interfaces)

115.
Main features of FAIRPort Platform
● GET GET GET!! We didn’t invent any new technology or API :-) :-)
● All components modular, re-usable, and often will be written by 3rd parties
o → encourages the creation of an ecosystem of these lightweight,
discoverable little data transformers
● All components identified by URL, and can be “cobbled together” in whatever
way a client needs on a particular day (and this can happen automatically!)
● Because everything is identified by a URL, and we only use HTTP GET,
components can be “chained” (e.g. the Projector calls GET on the URL of
another Projector)
→ i.e. I don’t care how the Projector or Accessor work “under the hood”,
it’s all the same GET to me!

116.
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

117.
Working Examples
- One (small) dataset (the Allele slice of my own DragonDB): http://antirrhinum.net An example record in the Repository's native format is
here: http://antirrhinum.net/cgi-bin/ace/generic/xml/DragonDB?name=cho;class=Allele
- Three different FAIR Profiles that could be applied to Allele records (from ANY repository) - one with textual descriptions and gene cross-
references, the other two with phenotypic images described using the SIO ontology, or the EDAM ontology (respectively). This is the "F" in
FAIR, since these can (in principle) be searched and queried in order to find various representations of your data of interest. Profiles are
associated - in a many-to-many relationship - with specific repositories via “Projectors” (see below). A Repository may project into many
different Profiles, and many Repositories may project their data into the same Profile.
* http://biordf.org/DataFairPort/ProfileSchemas/Allele_Profile_Descriptive.rdf
* http://biordf.org/DataFairPort/ProfileSchemas/Allele_Profile_EDAM.rdf
* http://biordf.org/DataFairPort/ProfileSchemas/Allele_ProfileSIO.rdf
- a "FAIR Accessor" that provides a Linked Data Platform-compliant way to retrieve all of the URIs for the Allele records, as well as their
various representations (described as DCAT Distributions). This is the "A" in FAIR. http://antirrhinum.net/cgi-bin/LDP/Alleles
- a "FAIR Projector" that takes the data from the Allele records and "projects" it as RDF that is compliant with whichever Profile you chose.
This is the 'I" in FAIR. http://biordf.org/cgi-bin/DataFairPort/DragonDB_LDF_Profiler If you call HTTP GET on that URL, it will report to
you what FAIR Profiles it is capable of projecting, using which FAIR Accessor (if any) In this example, all three Projections use an Accesor,
and use the same Accessor in each case. This is the ‘worst case scenario’, as it represents the slowest, most roundabout way to access
a Repository’s records - it would generally only be used if the Repository provides no externally-facing API of its own! (that’s why the
demo runs so slowly…) I did the demo this way so that everyone could see every component “working together”.
Three “Projections” of the DragonDB Allele Data (note that most of the process above is achieved simply by called GET on the URLs
below!!)
http://biordf.org/cgi-bin/DataFairPort/DragonDB_LDF_Profiler/DragonDB_Allele_ProfileAlleleDescriptions
http://biordf.org/cgi-bin/DataFairPort/DragonDB_LDF_Profiler/DragonDB_Allele_ProfileImagesSIO
http://biordf.org/cgi-bin/DataFairPort/DragonDB_LDF_Profiler/DragonDB_Allele_ProfileImagesEDAM

118.
This presentation is licensed CC-BY
Mark Wilkinson (markw@illuminae.com)
https://goo.gl/YEdwwB
@markmoby