Presentación Prof. Maria Esther Vida. DataBootCampVE/31 octubre 2013

Impact of Open Data and
Linked Open Data
Venezuela

Maria-Esther Vidal

Universidad Simón Bolívar

mvidal@ldc.usb.ve

h1p://www.ldc.usb.ve/~mvidal

Twi1er
@Maria11576561

Skype:
mevs2006

1

Lights
around
the
London's
2012
Olympic
stadium
describe
Sir
Tim
Berners-‐Lee's
invenKon,
the

World
Wide
Web.
The
Open
Data
InsKtute,
which
he
co-‐founded,
declares
a
mandate
of

'Knowledge
for
Everyone'.

“The
ODI
announced
new
13
nodes:

US,
Canada,
France,
Dubai,
Italy,

Russia,
Sweden
and
ArgenKna.”

Oct
29

2103

Sir
Tim
Berners-‐Lee
(right)
and
Sir
Nigel
Shadbolt
(leT)

Agenda
Ø Open Data
Ø Linked Open Data
ü Linked Open Data in Journalism

Ø Linked Open Data Applications
ü Linked Open Data at USB

Ø Conclusions and Future Directions

Open Data
Deﬁnition http://opendeﬁnition.org/:
“A piece of data or content is open if anyone is
free to use, reuse, and redistribute it — subject
only, at most, to the requirement to attribute
and/or share-alike.”
Open_Data_stickers.jpg 1,024×768 pixels

7/1/13 9:33 PM

Availability and access
Reuse and Distribution
Universal Participation
6

Open Data

Availability and Access:
Data should be available as a whole,
preferably downloading via the Internet.
Data should be available in a convenient
format.
Should be free or at most at a reproduction
cost.

7

Open Data

Reuse and Distribution:
Data should be offered in a way that it can be
reused, distributed and be interrelated with
other datasets.

8

Open Data

Universal Participation:
Any person should be able to use, reuse and
distribute.
NO discrimination:
Commercial vs. NOT commercial
Educational vs. NOT educational
Proﬁt vs. No Proﬁt

9

Why Open Data?

Interoperability

Transparency

11

Why Open Data?
Avoid
CorrupKon

Wealth

Only
in
Europe
over
140
billion
of
euros
per
year

h1p://www.economist.com/news/business/21578084-‐making-‐oﬃcial-‐data-‐publi
could-‐spur-‐lots-‐innovaKon-‐new-‐goldmine

12

Why Open Data?

Research
and
Development

Quality
of
Life

13

Why Open Data?

Improve
Public
AdministraKon

Data
Quality

14

Why Open Data?

Citizens can express themselves and unite so that their
voices can be heard.
15

h1p://www.ted.com/talks/sanjay_pradhan_how_open_data_is_changing_internaKonal_aid.html

Open

Licenses

Open
Data

Open

ParKcipaKon

Open
Source

Open

Standards

What is and what is not Open Data
Open
Data.

“A piece of content or data is open if you are free to use,
reuse, and redistribute it — subject only, at most, to the
requirement to attribute and share-alike.”
Difference between open data and data that is publicly available lies in the use of
formats that may be read, used and redistributed by any citizen.
Examples of public data that is not open data: data in spreadsheets, pdf, etc. Usually
open data are csv.
h1p://opensource.com/government/10/12/what-‐“open-‐data”-‐means-‐–-‐and-‐what-‐it-‐doesn’t

Opening Up Data
Rules
Ø  Keep it simple
Ø  Engage early and
engage often
Ø  Address common fears
and misunderstandings

Four Steps
Ø  Choose your Dataset(s)
Ø  Apply an Open License
Ø  Make the data available
Ø  Make it discoverable

Open Data Conditions
Data Providers Requirements

Distributing Open Data

Ø  Attribution: data
providers may require to
receive credit.
Ø  Integrity: data providers
may require that users
indicate if data change.
Ø  Share-alike: data
providers may impose
that any dataset created
using their data are also
open.

Ø  Data is machine-readable
Ø  Data is available in bulk
more than using an API.

h1p://opendatahandbook.org/en/

OPEN
DATA
APPLICATIONS

OPEN
DATA
AND
GOVERNMENT

Some Open Data Applications

Al
menos
77
países
cumplen
nivel
>
2

h1p://wheredoesmymoneygo.org/

22

Why Open
Data?
Citizens may
unite so that
their voices can
be heard

Why Open Data?

Monrovia
África


Why Open Data?

Tanzanía


h1p://www.tableausoTware.com/public/gallery/london-‐deprivaKon

OPEN
DATA
AND
PUBLIC
HEALTH

Vaccines and Immunisation in Australia

h1p://www.theguardian.com/society/datablog/interacKve/2013/oct/16/children-‐vaccinaKon-‐australia-‐map

h1p://www.cfr.org/interacKves/GH_Vaccine_Map/index.html#map

Applications of Open Data

h1p://pinterest.com/socrata/open-‐data-‐applicaKons/

Kenia

OPEN
DATA
AND
SOCIETY

ApplicaKons
of
Open
Data

h1p://www.crimemapping.com/

h1p://www.tableausoTware.com/public/gallery/tcc13friends

OPEN
DATA
AND
FINANCES

h1p://opencorporates.com/viz/ﬁnancial/index.html#bankofamerica/ch/934

Who Owns Who

h1p://opencorporates.com/viz/ﬁnancial/index.html#goldman/ch/2213

Who Owns Who

OPEN
DATA
AND
ENVIRONMENT

Why Open Data?
Improve
Public
Services

Smart
CiKes

Mejorar
la

Administración
Pública

40

h1p://visualizaKon.geblogs.com/visualizaKon/co2/

h1p://www.visualizing.org/full-‐screen/27036

Applications of Open Data

h1p://opendatachallenge.org/

LINKED
OPEN
DATA

h1p://www.ted.com/talks/lang/en/Km_berners_lee_the_year_open_data_went_worldwide.html

What to do with Open Data?

46


At
least
77
countries
comply
level
>
2

h1p://www.slideshare.net/mgarrigap/opendata-‐en-‐el-‐ararteko

47


At least 11 countries comply level > 4
h1p://www.slideshare.net/mgarrigap/opendata-‐en-‐el-‐ararteko

48


h1p://www.theguardian.com/news/datablog/2013/oct/28/uk-‐top-‐open-‐data-‐index-‐how-‐countries-‐compare#!

Bottom 10 by Open Data Index Score

h1p://www.theguardian.com/news/datablog/2013/oct/28/uk-‐top-‐open-‐data-‐index-‐how-‐countries-‐compare

Local
Governments
must
use

Open
Data
to
stay
connected

with
the
ciKzens!

MoKvaKon
SemanKc
Web
EvoluKon

The Linked Open Data cloud, using the
Web to connect related data that was not
previously linked!
Published Data are enhanced with semantics!
Standards to annotate and describe data:
XML, RDF, RDFS, OWL.
Standards to query data: SPARQL.
Ontologies representing almost any domain.
Hyperlink-based systems.
Protocols: http, uri, html
Documents and data were published
Arpanet: four servers connected
Files were transferred
Tools: ftp, telnet, e-mail
80’s

IRMLs
2010-‐ESWC
2010

90’s

00’s

Now

The Linked Open Data Cloud
• Explosion in the number of:

– Linking Open Data
resources and databases
– Different quality
parameters.
Molecular databases 1170, 95 more

– Controlledthan 2008 and 110 more than the year before !

vocabularies:
– MeSH, GO, PO… tools published

Services and
– Highly interconnected
by these databases follow a similar progression!

data sources:
In October 2007, Cloud of Linked Data

Different Sizes
datasets consisted of over two billion RDF triples,

Many links

which were interlinked by over two million RDF links.

• Different in- and outBy May 2009 this had grown to 4.2 billion RDF triples,

degrees, etc
interlinked by around 142 billions RDF links! Today

• Biological Web: large
the Linked Open Data cloud has at least 295 datasets,
datasets of linking data.
31,634,213,770
triples, and 503,998,829
links.

• Genes, Diseases,
Clinical Drugs, Proteins,
and so on.

LINKED
DATA
IN
JOURNALISM

Open Data in Journalism

Ø It may be trendy but not new.
Ø Open Data implies Open Data Journalism.
Ø Data is not necessarily curated.
Ø Bigger Datasets and Small Things.
Ø Data Journalism is 80% perspiration, 10% great
ideas, 10% output.
Ø Long and short-form.
Ø Anyone can do it.
Ø Visualization is important.
Ø Data publishers do not have to be programmers.
Ø It is all about stories.
h1p://www.theguardian.com/news/datablog/2011/jul/28/data-‐journalism

Breaking

News

Open

Data

Running

Events

Shared
Data

Open Data in
Journalism

Breaking

News

Open

Data

Open Data in
Journalism

Running

Events

Shared
Data

•  Data Cleansing
•  Conﬂict Resolution

Data
IntegraKon

SemanKﬁcaKon

•  Meta-Data
Annotation
•  Vocabularies

•  Visualization
•  Publishing the Story

PublicaKon

Meta-Data
BBC News

This will help users to
ﬁnd news content about
the stories they want to
know about and
ultimately help to open
up references to the
data contained in
those stories.

h1p://www.bbc.co.uk/blogs/internet/posts/News-‐Linked-‐Data-‐Ontology

Data Management ToolsBBC News

h1p://www.bbc.co.uk/blogs/internet/posts/Linked-‐Data-‐ConnecKng-‐together-‐the-‐BBCs-‐Online-‐Content

h1p://www.slideshare.net/moustaki/linked-‐data-‐on-‐the-‐bbc-‐2638734

More

Ontologies
to

represent

Meta-‐Data

VISUALIZING
LINKED
OPEN
DATA

Challenges
for

Linked
Data

Visualization

•  Enabling
user
interacKon

–  Users
must
be
able
to
navigate
through
the
data
by
exploiKng
the

connecKons
between
Linked
Data
resources

–  The
user
might
edit
the
underlying
data
to
enrich
it
by:

•  CreaKng
addiKonal
metadata

•  HighlighKng
or
correcKng
errors

•  ValidaKng
data

•  SupporKng
data
reusability

–  The
output
(the
plo1ed
data
or
the
visualizaKon
itself)
might
be

encoded
using
standard
ontologies
and
vocabularies

•  Scalability

–  Linked
Data
visualizaKon
techniques
should
support
the
display
of

large
amount
of
data
in
an
eﬃcient
way

EUCLID
–
InteracKon
with
Linked
Data

74

Challenges
for

Linked
Open

Data
Visualization

•  ExtracKng
data
from
different
repositories

–  A
Linked
Data
set
might
be
parKKoned
into
several
repositories

–  The
region
of
interest
(ROI)
might
include
data
from
different
data

sets,
requiring
the
access
to
distributed
repositories

•  Handling
heterogeneous
data

–  The
same
data
(concepts)
might
be
modeled
differently,
for
example,

using
different
vocabularies

–  Certain
values
might
have
different
formats,
for
example,
dates

represented
as
DD-‐MM-‐YYYY,
MM-‐DD-‐YYYY
or
just
YYYY

•  Dealing
with
missing
values

–  Due
to
the
semi-‐structuredness
of
Linked
Data,
some
instances
might

have
missing
values
for
certain
properKes

EUCLID
–
InteracKon
with
Linked
Data

75

Linked
Open
Data
VisualizaKon
Techniques

View

EUCLID
–
InteracKon
with
Linked
Data

76

Comparison
of

A1ributes
/
Values

Bar/column
chart

Pie
chart

Allows
the
comparison
of
values
of

different
categories.

Useful
for
performing
comparison

of
percentages
or
proporKons.

Image
source:
h1p://musicbrainz.fluidops.net

Image
source:
h1p://mbostock.github.io/protovis/

Line
chart

Histogram

Allows
visualizing
data
as
a
series
of

data
points,
where
the
measurement

points
(x-‐axis)
are
ordered.

Graphical
representaKon
of
the

distribuKon
of
the
data.

Image
source:

Image
source:
h1p://musicbrainz.fluidops.net

EUCLID
–
InteracKon
with
Linked
Data

77

Analysis
of

RelaKonships
and

Hierarchies

Graph

Arc
diagram

The
data
entries
are
represented
as

nodes
and
the
links
as
edges.

The
nodes
are
displayed
in
one

dimension,
and
the
arcs
represent

the
connecKons.

Adjacency
Matrix
diagram

Node-‐link
visualizaKons

The
nodes
are
displayed
as
rows
and

columns,
and
the
links
between
the

nodes
are
entries
in
the
matrix.

The
data
is
organized
in
hierarchies.

Source
of
images:

EUCLID
–
InteracKon
with
Linked
Data

78

Analysis
of

RelaKonships
and

Hierarchies
(2)

Space-‐ﬁlling
techniques

Treemaps

Icicles
and
sunburst

Subdivide
area
into
rectangles.

Hierarchies
are
represented
by

adjacencies.

Circle-‐packing

Rose
diagrams

Containment
is
used
to
represent
the

hierarchies.

Areas
are
equal
angles
and
the
data

is
represented
by

the
extension
of

the
area.

Source
of
images:

EUCLID
–
InteracKon
with
Linked
Data

79

Analysis
of

Temporal
or
Geographical

Events

ConKnuous
data
in
Kme

Timeline

Discrete
data
points
in
Kme

Source:
h1p//musicbrainz.fluidops.net

Source:
h1p://www.ko1ke.org/08/08/2008-‐movie-‐box-‐office-‐chart

Display
geo-‐points
on
a
map

Choropleth
maps

Dorling
cartograms

Aggregate
data
by

geographical
area

Aggregate
data
and
replace

each
area
with
a
circle

Maps

LocaKon
maps

Source:
Google
Map
API

Source:
h1p//musicbrainz.fluidops.net

EUCLID
–
InteracKon
with
Linked
Data

Source:

80

Libraries

h1ps://github.com/mbostock/d3/wiki/Gallery

Tasks
to
be
Solved
…

Traverse and Consume
Linked Data from the LOD cloud or
locally.

SPARQL endpoints have been developed to access data from the LOD cloud.
83

select
disKnct
*
where
{<h1p://dbpedia.org/resource/Venezuela>
?p
?o}

h1p://dbpedia.org/sparql

All
the
informaKon
related
to
Venezuela

SPARQL
Query

h1p://worldbank.270a.info/about.html

SPARQL
Endpoint

URL

SPARQL
Query

Data:

foaf:made

dbpedia:

The_Beatles

foaf:made

foaf:made

<h1p://

musicbrainz.org/
record/...>

dc:Ktle

<h1p://

musicbrainz.org/
record/...>

dc:Ktle

"Help!"

"Abbey
Road"

<h1p://

musicbrainz.org/
record/...>

dc:Ktle

"Let
It
Be"

SELECT
?x
?name
?mbox
?country
?reviewer
?product
?title

WHERE
{

<http://www4.wiwiss.fu-‐berlin.de/bizer/bsbm/v01/instances/dataFromRatingSite293/
Review2883011>
rev:reviewer
?x
.

?x
<http://www.w3.org/1999/02/22-‐rdf-‐syntax-‐ns#type>
<http://xmlns.com/foaf/0.1/Person>
.

?x
<http://xmlns.com/foaf/0.1/name>
?name
.

?x
<http://xmlns.com/foaf/0.1/mbox_sha1sum>
?mbox
.

?x
<http://www4.wiwiss.fu-‐berlin.de/bizer/bsbm/v01/vocabulary/country>
?country
.

?reviewer
<http://purl.org/stuff/rev#reviewer>
?x
.

?reviewer
<http://www4.wiwiss.fu-‐berlin.de/bizer/bsbm/v01/vocabulary/reviewFor>
?product
.

?reviewer
<http://purl.org/dc/elements/1.1/title>
?title
}

APPLICATIONS
DEVELOPED
AT
USB

FEDERATED
QUERIES

ANAPSID

SPARQL-DQP

Federations of Endpoints

h1ps://github.com/anapsid/anapsid

Federated Queries

ANAPSID

“Genes and diseases that have been studied
for drugs tested in clinical trials where Breast Cancer was studied”

SELECT
DISTINCT
?D1?TGD
?GN1
?GN2

WHERE
{

?CT1
<http://data.linkedct.org/resource/linkedct/condition>
?C1
.

?CT1<http://data.linkedct.org/resource/linkedct/intervention>
?I
.

?CT1<http://data.linkedct.org/resource/linkedct/intervention>
?I
.

?I<http://data.linkedct.org/resource/linkedct/intervention_type>
"Drug"
.

?C1
<http://www.w3.org/2000/01/rdf-‐schema#seeAlso>
?D1
.

?I
?I1
.

?C
<http://data.linkedct.org/resource/linkedct/condition_name>
"Breast
Cancer"
.

?CT
<http://data.linkedct.org/resource/linkedct/intervention>
?I
.

?CT
?A4
.

?II
<http://www4.wiwiss.fu-‐berlin.de/drugbank/resource/drugbank/target>
?TGD
.

?TGD
<http://www4.wiwiss.fu-‐berlin.de/drugbank/resource/drugbank/genbankIdGene>
?GN1
.

?D1
<http://www4.wiwiss.fu-‐berlin.de/diseasome/resource/diseasome/associatedGene>
?GN2
.

}

Life
Sciences
Query:

97

Federated Queries


ANAPSID

SELECT
DISTINCT
?D1
?TGD
?GN1
?GN2

WHERE
{

{
SERVICE
<http://virtuoso.bd.cesma.usb.ve/sparql>
{

?C1
"Breast
Cancer"
.

?C1
?D1
.

?C3
?D1
.

?CT3
?C3
}}
.

{
SERVICE
{

?C1
"Breast
Cancer"
.

?I
<http://data.linkedct.org/resource/linkedct/intervention_type>
"Drug"
.

?CT1
?C1
.

?CT1
?I
}}
.

{
SERVICE
<http://www4.wiwiss.fu-‐berlin.de/drugbank/>
{

?I1
<http://www4.wiwiss.fu-‐berlin.de/drugbank/resource/drugbank/target>
?TGD
.

?TGD
<http://www4.wiwiss.fu-‐berlin.de/drugbank/resource/drugbank/genbankIdGene>
?GN1
}}
.

{
SERVICE
{

?I
<http://data.linkedct.org/resource/linkedct/intervention_type>
"Drug"
.

?I
?I1
.

?CT3
?I
.

?CT3
?C3
}}
.

}

S1:

S2:

S3:

S4:

98

Federated Queries


ANAPSID

S1

S2

S3

S4

99

ANAPSID

ANAPSID

ANAPSID

h1p://silurian.thalassa.cbm.usb.ve/

“Drugs that possibly target Leukemia”
SELECT
DISTINCT
?drug1

WHERE
{

?drug1
drugbank:possibleDiseaseTarget

diseasome:673
.

?drug1
drugbank:target
?o.

?o
drugbank:genbankIdGene
?g.

?o
drugbank:locus
?l.

?o
drugbank:molecularWeight
?mw.

?o
drugbank:hprdId
?hp.

?o
drugbank:swissprotName
?sn.

?o
drugbank:proteinSequence
?ps.

?o
drugbank:generalReference
?gr.

?drug
drugbank:target?o.

?drug
drugbank:synonym?o1
.

OPTIONAL
{

?drug
owl:sameAs
?drug5
.

?drug5
rdf:type
dbcategory:Drug
.

?drug
drugbank:keggCompoundId
?cpd
.

?enzyme
kegg:xSubstrate
?cpd
.

?enzyme
rdf:type
kegg:Enzyme
.

?reaction
kegg:xEnzyme
?enzyme
.

?reaction
kegg:equation
?equation
.

}
}


101

SELECT
DISTINCT
?drug1

WHERE
{

?drug1

diseasome:673
.

?drug1
drugbank:target
?o.

?o
?g.

?o
drugbank:locus
?l.

?o
?mw.

?o
drugbank:hprdId
?hp.

?o
?sn.

?o
?ps.

?o
?gr.

?drug
drugbank:target?o.

?drug
drugbank:synonym?o1
.

OPTIONAL
{

?drug
owl:sameAs
?drug5
.

?drug5
rdf:type
dbcategory:Drug
.

?drug
?cpd
.

?enzyme
kegg:xSubstrate
?cpd
.

?enzyme
rdf:type
kegg:Enzyme
.

?reaction
kegg:xEnzyme
?enzyme
.

?reaction
kegg:equation
?equation
.

}
}


102

SELECT
DISTINCT
?drug1

WHERE
{

?drug1

diseasome:673
.

?drug1
drugbank:target
?o.

?o
?g.

?o
drugbank:locus
?l.

?o
?mw.

?o
drugbank:hprdId
?hp.

?o
?sn.

?o
?ps.

?o
?gr.

?drug
drugbank:target?o.

?drug
drugbank:synonym?o1
.

OPTIONAL
{

?drug
owl:sameAs
?drug5
.

?drug5
rdf:type
dbcategory:Drug
.

?drug
?cpd
.

?enzyme
kegg:xSubstrate
?cpd
.

?enzyme
rdf:type
kegg:Enzyme
.

?reaction
kegg:xEnzyme
?enzyme
.

?reaction
kegg:equation
?equation
.

}
}


103

APPLICATIONS-‐

LINK
PREDICTION
AND
PATTERN

DISCOVERY

Tasks
to
be
Solved
…(2)

Patterns of connections
between people to understand
functioning of society.

Topological properties
of graphs can be used to identify
patterns that reveal phenomena,
anomalies and potentially lead to
a discovery.

A signiﬁcant increase of graph data in the form of social biological information.
105

Pa1erns
or
Signatures

Brentuzumab_vedoKn

And
Catumaxomab

108

Annotation Similarity between two
genes based on shared GO
annotations
Vacuolar

GO
Paths

Membrane

Vacuolar

Membrane

Golgi

apparatus

Plant-‐type

vacuole

Chloroplast

Gene

AtVHA-‐C5

Vacuole

proton-‐

TransporKng

V-‐type

ATPase
,
V1

domain

Gene

AtVHA-‐C

Chloroplast

Vacuole

GO
Terms

Vacuole

GO
Terms

109

Pa1erns
or
Signatures
between

genes
AtVHA-‐C5
and
AtVHA-‐C

110

Drug-Target Interaction Network

Pa1erns

Between

InteracKons

PotenKal
new

interacKon

112

Patterns of connections
between people to understand
functioning of society.

113

Conclusions
Ø  Open Data:
ü  Transparency
ü  Interoperability
ü  Avoid Corruption
ü  Impulse research and development
ü  Data Quality

Ø  Linked Open Data:
ü  RDF data
ü  Linked to existing datasets
ü  Endpoints can be used to access data

116

Presentación Prof. Maria Esther Vida. DataBootCampVE/31 octubre 2013

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Presentación Prof. Maria Esther Vida. DataBootCampVE/31 octubre 2013