Towards a Linked Open Data Infrastructure for Science, Technology & Innovation Studies

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Towards a Linked Open Data Infrastructure
for Science, Technology & Innovation
Studies
Ali Khalili, PhD
Department of Computer Science/Artiﬁcial Intelligence
Knowledge Representation & Reasoning Research Group

Outline
• Linked (Open) Data
• RISIS Project
• Semantically Mapping Science (SMS) Platform
• Workﬂow
• Use Cases
• Adaptive Functional Urban Areas (FUAs) to Study Innovative Activities
• Gendered Dimensions in Grant Selection

Evolution of the Web
https://mcgratha.wordpress.com/

Linked (Open) Data
• A set of best practices for publishing data on the Web.
• Follows 4 simple principles:
https://www.ted.com/talks/tim_berners_lee_on_the_next_web
• Use HTTP URIs so that users can look up (dereference) those names.
• When someone looks up a URI, provide useful information, using the
open standards.
• Include links to other URIs, so that users can discover more things.
• Use URIs as names (identiﬁers) for conceptual things.

Linked (Open) Data: Principles
WWW World

5 Open Data
make your stuff available on the Web (whatever format)
under an open license
make it available as structured data
(e.g., Excel instead of image scan of a table)
make it available in a non-proprietary open format
(e.g., CSV instead of Excel)
use Linked Data format
(URIs to identify things, RDF to represent data)
link your data to other people’s data to provide context
http://5stardata.info/

Linked Open Data Cloud
8Linked Open DataAli Khalili
http://lod-cloud.net/

Linked Open Data Cloud
http://lod-cloud.net/

Linked Open Data: Statistics
http://lodlaundromat.org/
http://stats.lod2.eu/
more than 3426 datasets

Linked Open Data: Examples
https://en.wikipedia.org/wiki/Paris

Resource Property Value
https://en.wikipedia.org/wiki/Paris

http://dbpedia.org/resource/Paris

• Give me a list of capital cities in Europe with population more than 500,000
• Who are mayors of central European towns elevated more than 1000m?
• Which movies are starring both Brad Pitt and Angelina Jolie?
• All soccer players, who played as goalkeeper for a club that has a stadium with
more than 40.000 seats and who are born in a country with more than 10 million
inhabitants
• …

https://www.google.com/cse/

http://www.wolframalpha.com/

RISIS EU Project (http://risis.eu)
http://datasets.risis.eu/

RISIS Datasets: Entity Types
Organization Product Agreement
Person Policy
Policy
Evaluation Location
CIB ETER EUPRO JOREP Leiden-Ranking
MORE I Nano Proﬁle SIPER VICO
Higher
Education
Firm
Funding
Body
Publication
Patent
Project
Investment
Funding
Program

Semantically Mapping Science (SMS) Platform
http://sms.risis.eu

RISIS WP9 Vision
Proposing S&T map of Europe

defined by OECD in collaboration with EC/Eurostat
consider factors beyond the predefined city boundaries to better
reflect the economic geography of where people live and work
Functional Urban Areas (FUAs)
OECD Metropolitan eXplorer: http://measuringurban.oecd.org

defined by OECD in collaboration with EC/Eurostat
consider factors beyond the predefined city boundaries to better
reflect the economic geography of where people live and work
population
area
GDP
environment (CO2 emissions and air pollution)
labour market (employment and unemployment growth)
innovation (patent intensity)
urban form and territorial organization
Functional Urban Areas (FUAs)
OECD Metropolitan eXplorer: http://measuringurban.oecd.org

FUAs: Building Blocks
Municipalities

Problem
Address FUA
?
• Vrije Universiteit Amsterdam
• De Boelelaan 1105, 1081 HV Amsterdam
Amsterdam (NL002)

Problem
Address FUA
?
Amsterdam (NL002)
OECD FUAs List

Problem
Address FUA
?
Amsterdam (NL002)
- Geocode to LAU (municipality)
OECD FUAs List

Problem
Address FUA
?
Amsterdam (NL002)
- Geocode to LAU (municipality)
- Shapeﬁles for FUAs or LAUs?
OECD FUAs List

Linked Open Data 28Ali Khalili
Linked Open Data
Interlinking
Enrichment
Quality
Analysis
Evolution
Exploration
Extraction
Storage/
Querying
Authoring
Linked (Open) Data
Lifecycle
http://stack.linkeddata.org/

Linked Open Data Lifecycle
Exploration

• Search
• Browse
• Visualize
Exploration

Search for Linked Data
Linked Open Data Lifecycle Exploration
http://lov.okfn.org/

http://schema.org/
http://bl.ocks.org/danbri/1c121ea8bd2189cf411c

Data hub http://datahub.io
search for data, register published datasets, create and manage groups of datasets…
Exploration

http://lotus.lodlaundromat.org

• OpenStreepMap (OSM)
• Database of Global Administrative Areas (GADM)
• Flickr Shapeﬁles Dataset
• Published Shapeﬁles for Individual Countries
• Published Geospatial RDF Datasets
Example

OpenStreetMap (OSM)
• https://www.openstreetmap.org
• built by a community of mappers that contribute and
maintain data about roads, trails, cafés, railway
stations, and much more, all over the world.
• Administrative Boundaries
• Level 1: super-national administrations e.g. European Union.
• Level 2: country borders based on the political entities listed on
the ISO 3166 standard.
• Level 3 to 11: subnational borders such as ``state'', ``province'',
``region'' and ``district''.
• Data Access
• Nominatim Web API for querying OSM
• The Overpass API for fetching speciﬁc OSM data
• Planet.osm Data (over 617GB uncompressed!)

OSM: Nominatim Web API
• a tool to search OSM data by name and address and to
generate synthetic addresses of OSM points (reverse
geocoding)
• Several companies provide hosted instances of Nominatim
query API, e.g MapQuest Open Initiative, PickPoint or the
OpenCage Geocoder
• API documentation
• Example usage:
• http://nominatim.openstreetmap.org/search.php?
q=amsterdam&polygon=1&country=Netherlands&format=
json&addressdetails=1
• MapQuest API

GADM (Global Administrative Areas)
• http://www.gadm.org
• GADM is developed by University of California, Berkeley
Museum of Vertebrate Zoology, the International Rice
Research Institute and the University of California, Davis, and
with contributions of many others.
• uses other existing sources: http://www.gadm.org/links
• Administrative Boundaries
• Level 0: countries.
• Level 1 to 5: lower level subdivisions such as provinces, departments,
counties, etc. depending on the size and availability of data for the
underlying country.
• Data Access
• data is available globally and for each individual country, in different
formats: geopackage,R SpatialPolygonsDataFrame, ESRI ﬁle geodatabase, Google Earth

Flickr geo-tagged pictures
• Data from 190M geo-tagged photos on Flickr
• new smart phone do not only have a camera but also the ability to capture
location information.
• plotted all the geotagged photos associated with a particular place to
generate a mostly accurate contour of that place (something more fine-
grained than a bounding box!).
• Where On Earth (WOE) IDs
• correspond to the hierarchy of places where a photo was taken: from
country (level 1), region (level 2) county (level 3), locality (level 4) to
neighborhood (level 5).
• for a given WOE entity, approximate shape of that place is inferred.
• shapes in GeoJSON format
• view shapes at http://polymaps.org/ex/flickr.html
• download at http://www.flickr.com/services/shapefiles/2.0.1/
• more info: http://code.flickr.net/2012/10/24/2273/

Published Shapefiles for Individual Countries
• Local administrative offices or Geo-related research
centres might provide shape files specific to a country.
• E.g. for the Netherlands, shapefiles are provided by
Centraal Bureau voor de Statistiek (CBS)
• Data collection needs to be done by a group of people
in contact with Geo-related organization in countries.
• Current status

Published Geospatial RDF Datasets
•http://linkedgeodata.org and http://geoknow.eu
•a large spatial knowledge base (>400m geo elements)
which has been derived from OpenStreetMap.
•provides unique URIs and has Mappings to DBpedia.
•GeoVocab.org
• GADM-RDF: Global Administrative Areas
• NUTS-RDF: EU's Nomenclature of Territorial Units for
Statistics

Published Geospatial RDF Datasets
•http://linkedgeodata.org and http://geoknow.eu
•a large spatial knowledge base (>400m geo elements)
which has been derived from OpenStreetMap.
•provides unique URIs and has Mappings to DBpedia.
•GeoVocab.org
• GADM-RDF: Global Administrative Areas
• NUTS-RDF: EU's Nomenclature of Territorial Units for
Statistics Outdated!
No Shapeﬁles!

Extraction

from Semi-structured sources
Linked Open Data Lifecycle Extraction
Resource Property Value

Linked Open Data Lifecycle Extraction DBpedia

Persian DBpedia?

Persian DBpedia (mapping Wiki)

• Ad-hoc
• DBpedia extraction framework
• Generic
• OpenReﬁne
from Semi-structured sources

from Unstructured sources
…After leaving Apple, Jobs took a few of its members with him to
found NeXT, a computer platform development company based in
Redwood City, specializing in state-of-the-art computers for higher-
education and business markets. In addition, Jobs helped to initiate
the development of the visual effects industry when he funded the
spinout of the computer graphics division of George Lucas's
company Lucasfilm in 1986. The new company, Pixar, would
eventually produce the first fully computer-animated film, Toy Story…
NLP, Text mining, Annotation

Named Entity Recognition

foundedBy
Relation Extraction

http://spotlight.dbpedia.org
http://bioportal.bioontology.org/annotator

from Structured sources: Tripliﬁcation
• Relational Database to RDF
R2RML: RDB to RDF Mapping Language
http://www.w3.org/TR/r2rml/
• D2R Server: Accessing databases with SPARQL &
as Linked Data
http://d2rq.org/
• Sparqlify
deﬁning RDF views on relational databases
http://sparqlify.org/

DATA EXTRACTION & CONVERSION
GeoJSON
Enrichment
Functions
Mapping
Conﬁgurations
OSM XML
PBF
ESRI shapes
triplify
mapshaper
osmtogeojson
osmosis

DATA EXTRACTION & CONVERSION
Metadata about different levels provided by OSM
http://wiki.openstreetmap.org/wiki/Tag:boundary%3Dadministrative

Storage & Querying

Relational Databases vs. Triple Stores
Linked Open Data Lifecycle Storage/Querying
• A relational databases’ (e.g. MySQL, PostgreSQL, Oracle)
natural representation is a collection interlinked tables.
• A triple stores’ (e.g. OpenSesame, AllegroGraph, Neo4j)
natural representation is a multi-relational network, or graph.
* Triple Store: it is called a triple store because in RDF, the facts
are represented in form of a triple (Subject-Predicate-Object).

Existing Triple Stores
• Native triple stores
4Store, AllegroGraph, BigData, Jena TDB, Sesame,
Stardog, OWLIM and uRiKa
• RDBMS-backed triple stores
Jena SDB, IBM DB2 and OpenLink Virtuoso
• NoSQL triplestores
CumulusRDF

DATA STORAGE & QUERYING
Virtuoso Geo Spatial
Geometry as SMS
internal representation
for Geo-data in RDF

SPARQL – SQL for the Linked Data
What can be done with SPARQL that can't be done with SQL?

What can be done with SPARQL that can't be done with SQL?
• SPARQL queries are considerably better aligned with users’ mental
models of a domain.

• SPARQL allows the conceptual data model to be fully explored
through queries.

• SPARQL allows the conceptual data model to be fully explored
through queries.
- example:workPhone rdfs:subPropertyOf example:phone

- example:cellPhone rdfs:subPropertyOf example:phone

- example:homePhone rdfs:subPropertyOf example:phone

• Queries that have to traverse a chain of connections are
particularly complex in SQL while very simple in SPARQL.

• In addition to SELECT, INSERT and DELETE, SPARQL supports
ASK queries.
• SPARQL includes syntax (i.e. SERVICE) to call two or more data
sources within a single query.
• …

SPARQL Query Interface
http://yasgui.org/

Interlinking

Interlinking
• The degree to which entities that represent the same
concepts are linked to each other.
• “Connecting things that are somehow related”
• Methods
• Automatic, Semi-automatic, Manual
• Universal, Domain-speciﬁc
<http://dbpedia.org/resource/VU_University_Amsterdam>
<https://www.wikidata.org/entity/Q1065414>
SameAs

Interlinking Methods
• Ontology Matching
• establish links between ontologies underlying two
data sources.
• Instance Matching (Link Discovery)
• discover links between instances contained in two
data sources.

DATA LINKAGE
- Query on metadata about the
administrative boundaries
- Find the alignment between levels
in different datasets

DATA LINKAGE
- used the possible mappings between datasets at different levels.
- check the overlaps of areas at the similar level, and for the matching areas apply
string matching to make sure that they refer to the same administrative boundary.

DATA LINKAGE
OECD
FUAs
DBpedia
GeoNames
WikiData
GADM
Flickr
Shapes
OpenStreetMap
Administrative
Boundaries

Scientiﬁc Lenses
DBpedia
Wikidata
OrgRef
GRID FundRef
Geoname
ISNI
VIAF
Cordis
?

Linked Data Services
http://api.sms.risis.eu/

SERVICE TO APPLICATION
http://sms.risis.eu/demos

SERVICE TO APPLICATION
https://docs.google.com/spreadsheets/d/1XhXzdAf-veqHPj0kIaeZoXE3AJa8nwNugW_nOHH1jtk/edit?usp=sharing

Use Cases
https://hyperir.cartodb.com/viz/13b5f3da-4356-11e6-a365-0e5db1731f59/public_map
(research) and innovation subsidies for organizations and
companies in the Netherlands

Use Cases
(research) and innovation subsidies for organizations and companies in the Netherlands
People Hybrid OECD FUAsBusinesses
People Hybrid OECD FUAsBusinesses

Use Cases
Universities + Companies + Projects + Boundaries
Properties of container
Collaboration between
Universities and Companies
Properties of Universities
and Companies

Use Cases
RVO-NL
DBpedia OpenStreetMap
GADM
Flickr
OECD FUAs
CBS-NL
and Companies

Use Cases
RVO-NL
DBpedia
Leiden-Ranking
ETER
OrgRef Cordis OpenStreetMap
GADM
Flickr
OECD FUAs
Grid
CBS-NL
and Companies
Eurostat

Summary of the Use Case
Address
FUA
Administrative Boundaries
Coordinates
geocode

References
Linked Open Data
• http://slidewiki.org/deck/11936_semantic-data-web-lecture-series
• Introduction to linked data and its lifecycle on the web
• http://euclid-project.eu/
• http://videolectures.net/wims2011_auer_interlinked/
• https://vimeo.com/76257120
• http://www.slideshare.net/slidarko/evolving-the-web-into-a-giant-global-
database-3880018
• http://www.dataversity.net/introduction-to-triplestores/
• http://www.topquadrant.com/2014/05/05/comparing-sparql-with-sql/

Towards a Linked Open Data Infrastructure for Science, Technology & Innovation Studies

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