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/
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
Linked (Open) Data: Principles
WWW World
Linked (Open) Data: Principles
WWW World
Linked (Open) Data: Principles
WWW World
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/
5 Open Data
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
Linked Open Data: Examples
Resource Property Value
https://en.wikipedia.org/wiki/Paris
Linked Open Data: Examples• 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
• …
Linked Open Data: Examples• 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
• …
Linked Open Data: Examples
Linked Open Data: Examples
RISIS EU Project (http://risis.eu)
http://datasets.risis.eu/
RISIS Datasets: Entity Types
Organization Product Agreement
Person PolicyPolicy
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
RISIS Datasets: Entity Types
Organization Product Agreement
Person PolicyPolicy
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
RISIS WP9 Vision
ProposingS&TmapofEurope
Functional Urban Areas (FUAs)
Functional Urban Areas (FUAs)
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
Functional Urban Areas (FUAs)
FUAs Example: Netherlands
FUAs: Building Blocks
Municipalities
Problem
Address FUA?
Problem
Address FUA?
• Vrije Universiteit Amsterdam • De Boelelaan 1105, 1081 HV Amsterdam Amsterdam (NL002)
Problem
Address FUA?
• Vrije Universiteit Amsterdam • De Boelelaan 1105, 1081 HV Amsterdam Amsterdam (NL002)
OECD FUAs List
Problem
Address FUA?
• Vrije Universiteit Amsterdam • De Boelelaan 1105, 1081 HV Amsterdam Amsterdam (NL002)
- Geocode to LAU (municipality)
OECD FUAs List
Problem
Address FUA?
• Vrije Universiteit Amsterdam • De Boelelaan 1105, 1081 HV Amsterdam Amsterdam (NL002)
- Geocode to LAU (municipality)
OECD FUAs List
Problem
Address FUA?
• Vrije Universiteit Amsterdam • De Boelelaan 1105, 1081 HV Amsterdam Amsterdam (NL002)
- Geocode to LAU (municipality)
- Shapefiles for FUAs or LAUs?OECD FUAs List
Problem
Address FUA?
• Vrije Universiteit Amsterdam • De Boelelaan 1105, 1081 HV Amsterdam 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 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 29Ali Khalili
Linked Open Data Lifecycle
Exploration
Linked Open Data 29Ali Khalili
Linked Open Data Lifecycle
• Search • Browse • Visualize
Exploration
Search for Linked Data
Linked Open Data 30Ali Khalili
Linked Open Data Lifecycle Exploration
http://lov.okfn.org/
Search for Linked Data
Linked Open Data 31Ali Khalili
Linked Open Data Lifecycle Exploration
http://schema.org/
http://bl.ocks.org/danbri/1c121ea8bd2189cf411c
Search for Linked Data
Linked Open Data 32Ali Khalili
Linked Open Data Lifecycle
Data hub http://datahub.io search for data, register published datasets, create and manage groups of datasets…
Exploration
Search for Linked Data
Linked Open Data 33Ali Khalili
Linked Open Data Lifecycle Exploration
http://lotus.lodlaundromat.org
Search for Linked Data
Linked Open Data 34Ali Khalili
Linked Open Data Lifecycle Exploration
• 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
OSM Data: Example
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
Linked Open Data 42Ali Khalili
Linked Open Data Lifecycle
from Semi-structured sources
Linked Open Data 43Ali Khalili
Linked Open Data Lifecycle Extraction
Resource Property Value
Linked Open Data 44Ali Khalili
Linked Open Data Lifecycle Extraction DBpedia
Linked Open Data 44Ali Khalili
Linked Open Data Lifecycle Extraction DBpedia
Persian DBpedia?
Persian DBpedia (mapping Wiki)
Linked Open Data 45Ali Khalili
Linked Open Data Lifecycle Extraction DBpedia
Linked Open Data 46Ali Khalili
Linked Open Data Lifecycle Extraction
• Ad-hoc• DBpedia extraction framework
• Generic• OpenRefine
from Semi-structured sources
from Unstructured sources
Linked Open Data 47Ali Khalili
Linked Open Data Lifecycle Extraction
…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
from Unstructured sources
Linked Open Data 47Ali Khalili
Linked Open Data Lifecycle Extraction
…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
from Unstructured sources
Linked Open Data 47Ali Khalili
Linked Open Data Lifecycle Extraction
…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
Named Entity Recognition
Linked Open Data 48Ali Khalili
Linked Open Data Lifecycle Extraction
http://spotlight.dbpedia.org
http://bioportal.bioontology.org/annotator
from Structured sources: Triplification
Linked Open Data 49Ali Khalili
Linked Open Data Lifecycle Extraction
• Relational Database to RDFR2RML: RDB to RDF Mapping Languagehttp://www.w3.org/TR/r2rml/
• D2R Server: Accessing databases with SPARQL & as Linked Datahttp://d2rq.org/
• Sparqlifydefining RDF views on relational databaseshttp://sparqlify.org/
DATA EXTRACTION & CONVERSION
GeoJSON
Enrichment Functions
MappingConfigurations
OSM XML
PBF
ESRI shapes
triplify
mapshaper
osmtogeojson
osmosis
DATA EXTRACTION & CONVERSION
Metadata about different levels provided by OSMhttp://wiki.openstreetmap.org/wiki/Tag:boundary%3Dadministrative
Storage & Querying
Linked Open Data 52Ali Khalili
Linked Open Data Lifecycle
Relational Databases vs. Triple Stores
Linked Open Data 53Ali Khalili
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
Linked Open Data 54Ali Khalili
Linked Open Data Lifecycle Storage/Querying
• Native triple stores4Store, AllegroGraph, BigData, Jena TDB, Sesame, Stardog, OWLIM and uRiKa
• RDBMS-backed triple storesJena SDB, IBM DB2 and OpenLink Virtuoso
• NoSQL triplestoresCumulusRDF
DATA STORAGE & QUERYING
Virtuoso Geo Spatial Geometry as SMS
internal representation for Geo-data in RDF
SPARQL – SQL for the Linked Data
Linked Open Data 56Ali Khalili
Linked Open Data Lifecycle Storage/Querying
What can be done with SPARQL that can't be done with SQL?
SPARQL – SQL for the Linked Data
Linked Open Data 56Ali Khalili
Linked Open Data Lifecycle Storage/Querying
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 – SQL for the Linked Data
Linked Open Data 56Ali Khalili
Linked Open Data Lifecycle Storage/Querying
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 – SQL for the Linked Data
Linked Open Data 57Ali Khalili
Linked Open Data Lifecycle Storage/Querying
• SPARQL allows the conceptual data model to be fully explored through queries.
SPARQL – SQL for the Linked Data
Linked Open Data 57Ali Khalili
Linked Open Data Lifecycle Storage/Querying
• 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
SPARQL – SQL for the Linked Data
Linked Open Data 58Ali Khalili
Linked Open Data Lifecycle Storage/Querying
• Queries that have to traverse a chain of connections are particularly complex in SQL while very simple in SPARQL.
SPARQL – SQL for the Linked Data
Linked Open Data 58Ali Khalili
Linked Open Data Lifecycle Storage/Querying
• Queries that have to traverse a chain of connections are particularly complex in SQL while very simple in SPARQL.
SPARQL – SQL for the Linked Data
Linked Open Data 59Ali Khalili
Linked Open Data Lifecycle Storage/Querying
• 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
Linked Open Data 60Ali Khalili
Linked Open Data Lifecycle Storage/Querying
http://yasgui.org/
Interlinking
Linked Open Data 61Ali Khalili
Linked Open Data Lifecycle
Interlinking
Linked Open Data 62Ali Khalili
Linked Open Data Lifecycle
• 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
Linked Open Data 63Ali Khalili
Linked Open Data Lifecycle
• 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
OECDFUAs
DBpedia
GeoNames
WikiData
GADM
FlickrShapes
OpenStreetMapAdministrative
Boundaries
DATA LINKAGE
OECDFUAs
DBpedia
GeoNames
WikiData
GADM
FlickrShapes
OpenStreetMapAdministrative
Boundaries
DATA LINKAGE
OECDFUAs
DBpedia
GeoNames
WikiData
GADM
FlickrShapes
OpenStreetMapAdministrative
Boundaries
Scientific Lenses
DBpedia
Wikidata
OrgRef
GRID FundRef
Geoname
ISNI
VIAF
Cordis
?
SERVICE TO APPLICATIONhttps://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 administrative boundaries
Collaboration between Universities and Companies
Properties of Universities and Companies
Use Cases
Universities + Companies + Projects + BoundariesRVO-NL
DBpedia OpenStreetMap
GADMFlickr
OECD FUAs
CBS-NL
Properties of container administrative boundaries
Collaboration between Universities and Companies
Properties of Universities and Companies
Use Cases
Universities + Companies + Projects + BoundariesRVO-NL
DBpediaLeiden-Ranking
ETER
OrgRef Cordis OpenStreetMap
GADMFlickr
OECD FUAs
Grid
CBS-NL
Properties of container administrative boundaries
Collaboration between Universities and Companies
Properties of Universities and Companies
Eurostat
Summary of the Use Case
Address
FUA
Administrative Boundaries
Coordinates
geocode
Summary of the Use Case
Address
FUA
Administrative Boundaries
Coordinates
geocode
References
Linked Open Data 77Ali Khalili
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/
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