Download - Life Sciences Linked Data
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Life Sciences Linked Data
Máster Bioinformática UM
Mikel Egaña Aranguren
/
Biological Informatics Group ( ), CBGP, UPM, Madridhttp://mikeleganaaranguren.com [email protected]
http://wilkinsonlab.info
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Life Sciences Linked Data
https://mikeleganaaranguren.wordpress.com/teaching/
http://biordf.org:8080/UM_LSLD/Clases/UM_Bioinformatics_LD.html
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¿Qué es Linked Data?
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Video divulgativo
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¿Qué es Linked Data (LD)?
Un método para ofrecer datos directamente en la web
Una propuesta del : W3C http://www.w3.org/standards/semanticweb/data
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Un primer paso hacia la Web Semántica
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Pila tecnologías Web Semántica
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Un primer paso hacia la Web Semántica
LD utiliza la tecnología ya existente (URI, HTTP, ...) para ofrecer una primeraversión de la Web Semántica
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Pila tecnologías Web Semántica y LD
BNODE
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Principios LD
1. Usar URIs para identificar entidades2. Usar URIs HTTP para que se pueda acceder a esas entidades3. Cuando un usuario o agente accede a una URI, proveer información útil mediante
estándares (RDF, SPARQL)4. Incluir enlaces a otras URIs para que se puedan descubrir más entidades
http://www.w3.org/DesignIssues/LinkedData.html
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Con LD publicamos datos de manera ...
... semántica
... enlazada
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Semántica
RDF ofrece el triple, un modelo de datos explícito y homogéneo: una "frase"estándar que los ordenadores pueden "entender"
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Enlaces
En el triple, cada entidad (sujeto, predicado, objeto) tiene una URI que lo identifica
Los datos son enlazados a otros datos a través de la web, con enlaces explícitos
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Red global de datos enlazados
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Red global de datos enlazados
Internet de datos, en vez de documentos: "Base de Datos universal":
Es más fácil construir aplicaciones que exploten los datos, incluyendorazonamiento automáticoEncontramos justo lo que buscamos: consultas directas (SPARQL) en vez deprocesar texto
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Red global de datos enlazados
Navegamos directamente por las datos (RDF), en vez de navegar a través dedocumentos que representan esos datos en lenguaje natural (HTML)
Enlazar datos nuevos es tan fácil como enlazar páginas web: crecimiento orgánicode la red
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Linked Open Data (LOD) cloud
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http://richard.cyganiak.de/2007/10/lod/
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Datasets de interés
(¡UM!)
**
LOD cloud ...
Bio2RDFOGOLODLinkedLifeDataHyQueArrayExpress and Gene expression atlasUniProt
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RDF
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RDF (Resource Description Framework)
RDF es un estándar oficial del para representar información en la webW3C
www.w3.org/standards/techs/rdf
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Triple RDF
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Grafo RDF
Un grafo RDF es un conjunto de triples
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Grafo RDF
Algunos objetos pueden ser valores literales (Cadenas de caracteres)
Sujetos y predicados sólo pueden ser recursos
Los valores literales pueden tener tipo ( )XML Schema datatypes
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Elementos RDF
rdf:type: agrupar recursos en clases
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Elementos RDF
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URIs en RDF
Cada recurso (Sujeto, predicado, objeto) tiene una URI
URI: Uniform Resource Identifier ( )
Reference URI: URI + fragment (http://foo/bar#frag)(En Linked Data, las URIs se pueden resolver, es decir dereferenciar)
RFC3986
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Espacios de nombres XML
RDF usa espacios de nombres XML mediante "qualified names"
Vocabulario: URIs bajo un espacio de nombre
rdfs="http://www.w3.org/2000/01/rdfschema#"obo="http://purl.org/obo/owl/GO#"owl="http://www.w3.org/2002/07/owl#"...
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Serializar RDF
RDF es un modelo para representar datos
Ese modelo abstracto se puede representar con diferentes sintaxis: "Serializar"(escribir) en un archivo
Una de esas sintaxis es RDF/XML
No confundir el modelo con la sintaxis: ¡RDF es mucho más que un archivo XML!
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Serializar RDF
RDF/XML ( )RDFa ( )Turtle ( )N3 ( )...
http://www.w3.org/TR/rdfsyntaxgrammar/http://www.w3.org/TR/rdfacore/http://www.w3.org/TR/turtle/
http://www.w3.org/DesignIssues/Notation3.html
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Serializar RDF: RDF/XML
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Vocabulario (ontología) / triples
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Más información
RDF primer
RDF validator
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RDFS (RDF Schema)
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RDFS
RDFS es un estándar oficial del para describir clases de recursos RDF y suspropiedades: definir vocabularios para RDF
W3C
http://www.w3.org/TR/rdfschema/
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RDFS
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OWL (Web Ontology Language)
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OWL
OWL es un estándar oficial del para crear ontologías en la web con unsemántica precisa y formal
W3C
http://www.w3.org/standards/techs/owl
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OWL
OWL se basa en Lógica Descriptiva (DL)
Representación computacional de un dominio de conocimiento:
Razonamiento automático: inferir conocimiento "nuevo" (*), consultas,consistencia, clasificar entidades contra la ontología, ...Integrar conocimiento disperso
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Sintaxis OWL
Para ordenadores: RDF/XML, OWL/XML, ...
Para humanos: Manchester OWL Syntax, functional, ...
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Semántica OWL
Una ontología OWL esta compuesta de:
Entidades: las entidades del dominio de conocimiento, identificadas con URIs,introducidas por el desarrollador ("proteina", "participa_en", ...)Axiomas: relacionan las entidades mediante el vocabulario lógico que ofreceOWL
Una ontología puede importar otra (owl:import) y hacer referencia a sus entidadesmediante axiomas
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Entidades OWL
IndividuosClasesPropiedades
ObjetoAnotaciónDatos
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Semántica OWL
Una ontología OWL formada por individuos y clases es una "Base deConocimiento" (KB) formada por:
TBox (Terminological Box): clases (~ "esquema")Abox (Assertional Box): individuos (~ "datos")
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Clases
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Clase subclase
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Clases equivalentes
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Jerarquía de clases (Taxonomía)
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Condiciones necesarias
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Condiciones necesarias y suficientes
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Restricción existencial (some)
Manchester tutorial
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Restricción universal (only)
Manchester tutorial
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Restricción a un individuo (value)
Manchester tutorial
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Restricciones cardinales
(+ QCR!) Manchester tutorial
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Más axiomas para clases
disjointFrom
booleanos: not, or, and
Manchester tutorial
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Expresiones complejas
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Propiedades OWL
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Jerarquía propiedades
Jerarquía propiedadsubpropiedad (~taxonomía pero con propiedades), ej:
interacciona conmata a
estrangula a
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Características propiedades objeto
Manchester tutorial
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Características propiedades objeto
Manchester tutorial
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Características propiedades objeto
Manchester tutorial
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Características propiedades datos
Solo funcional
Dominio clases, rango datatypes
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Propiedades anotación
Anotar con lenguaje natural entidades (propiedades, clases, individuos), axiomas,ontologías
Fuera de la semántica
rdfs:label, rdfs:comment, dublin core, a medida
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Individuos
Miembro de una o más clases (Types)
Igual (SameAs) o diferente (DifferentFrom) a otro individuo
Relaciones binarias con otros individuos o datos (triples), positivas o negativas
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Razonamiento automático
Un razonador infiere los "nuevos" axiomas que implican los axiomas que hemosintroducido en la ontología
El razonador infiere todos los axiomas; es útil para tratar con conocimientocomplejo
Open World Assumption (OWA)
(Falta de) Unique Name Assumption (¡owl:sameAs!)
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Tareas más comunes razonamiento automático
Mantener taxonomía
Consistencia
Clasificar entidades y consultas
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Mantener una taxonomía
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Consistencia
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Clasificar entidades, consultas
Clasificar entidades: dada una entidad nueva, como se relaciona con las demasentidades (types, equivalentTo, subClassOf, triples)
Una consulta es una clase anónima que clasificamos contra la ontología como sifuese una entidad
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Ejercicios
Ejercicios:
Soluciones:
,
owl_assignment.pdf
cars.owlnormalisation.owl normalisation.pnganswers_3_4.pdf
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SPARQL
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SPARQL
Lenguaje para hacer consultas sobre grafos RDF (~"El SQL para RDF")
http://www.w3.org/standards/techs/sparql
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SPARQL
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SPARQL
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SPARQL
Tutorial: ( )SPARQL by example Cambridge Semantics
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SPARQL
Ejercicio práctico:
Ejercicio práctico:
http://linkedlifedata.com/sparql
BioGateway
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SPARQL
Ejercicio práctico:
search for the human genetic diseases related to the gene Brca1 of the Mus musculusspecies stored in bio2rdf.org datasets
http://miuras.inf.um.es/sparql
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SPARQL
PREFIX ogolod: <http://miuras.inf.um.es/ogolod/ontology/>SELECT DISTINCT ?bio2rdf_omim ?titleWHERE ?gene owl:sameAs <http://bio2rdf.org/page/geneid:12189> .?cluster ogolod:hasOrtholog ?gene .?cluster ogolod:hasOrtholog ?ortholog .?disease ogolod:causedBy ?ortholog .?disease owl:sameAs ?bio2rdf_omim .?disease ogolod:Name ?title .
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SPARQL
Ejercicio práctico:
orthologs related to genes involved in lung cancer and belonging to RattusNorvegicus
http://miuras.inf.um.es/sparql
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SPARQL
PREFIX ogolod: <http://miuras.inf.um.es/ogolod/ontology/>PREFIX ogolodr: <http://miuras.inf.um.es/ogolod/resource/>SELECT DISTINCT ?gene2WHERE ?ortholog ogolod:fromSpecies<http://miuras.inf.um.es/ogolod/resource/NCBITaxon_10116/NCBITaxon_10116> .?ortholog owl:sameAs ?gene2 .?cluster ogolod:hasOrtholog ?gene .?cluster ogolod:hasOrtholog ?ortholog .?disease ogolod:causedBy ?gene .?disease owl:sameAs <http://bio2rdf.org/page/omim:211980> .
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Cómo funciona LD
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Grafos y triple stores
Un "triple store" contiene diferentes grafos
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Consultas
Solo recibiremos los triples de ese triple store (¡Pero nosotros o nuestro agenteautomático podemos seguir los enlaces! "Follow your nose")
Alternativa: federated queries ()
http://www.w3.org/TR/sparql11federatedquery/
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Negociacion contenido
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Negociacion contenido
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Negociacion contenido
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Diseño URIs
HTTP URIs dereferenciables: cuando se busca una URI, deberia devolver unadescripción del objeto que identifica esa URI
Descripción del objeto (documento RDF) ≠ objeto
303 URIs vs Hash URIs
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Diseño URIs
Base URI: http://geo.linkeddata.es/TBox URIs:
http://geo.linkeddata.es/ontology/concept|propertyhttp://geo.linkeddata.es/ontology/Provincia
ABox URIs:http://geo.linkeddata.es/resource/r. type/r. namehttp://geo.linkeddata.es/resource/Provincia/Madrid
http://www.slideshare.net/boricles/
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Inferencia en LD
Para producir el dataset: materializar triples y asegurar consistencia
En consultas
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Consumir LD
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Navegadores LD
...
DiscoTabulatorOpenLink
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Buscadores LD
( )
...
Sig.ma CYCBSWSE
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Aplicaciones (Mashups)
...
RevyuTalis aspireNYT
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Publicar datos en LD
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¿Por qué publicar datos en LD?
Enlaces al exterior:Publicar solo nuestros datos, referancias al resto, no hay que replicar datosexternos:Los datos externos se actualizan independientemente, y nuestro dataset va "aremolque" sin esfuerzo
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¿Por qué publicar datos en LD?
Enlaces a nuestro dataset:Es facil enlazar a nuestro dataset, ya que usamos HTTP URIsPor lo tanto, aumenta la capacidad de nuestro dataset de ser descubiertomediante enlaces
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¿Por qué publicar datos en LD?
Semántica: el significado de nuestro datos es explícito y claro, debido a RDF(instancias) + OWL ("esquema"): es fácil crear aplicaciones, incluyendorazonamiento automático (ej. agentes)
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Publicar datos en LD
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Publicar datos en LD
Crear el datasetOntología OWL: reusar lo más posible de otras ontologías parainteroperabilidadInstancias RDF
Añadir enlaces a otros datasetsManualmente o con herramientas como SILKA nivel de instancias (owl:sameAs, predicados, ...) y a nivel de vocabulario(owl:equivalentClass, ...)
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Publicar datos en LD
Almacenar el dataset en triple storePublicar el dataset mediante servidor webRegistrar el dataset en Generar archivo voiD (Vocabulary of Interlinked Datasets):
Generar archivo (con ) y enviarlo a Semantic Webindex ( ) y Google
Data Hub
http://www.w3.org/TR/void/sitemap.xml sitemap4RDF
http://sindice.com/
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Publicar datos en LD
Ejercicio práctico: recrear todo el proceso de publicar un dataset Linked Data
Crear el dataset y "publicarlo" en una infraestructura ya lista (Life Sciences LinkedData)
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Life Sciences Linked Data
"Pack" ya listo y configurado para publicar Linked Data en localhost (Solo paraGNU/Linux)
http://github.com/mikeleganaaranguren/LSLD
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Life Sciences Linked Data
: triple store
: servidor web
: negociacioncontenido etc.
Fuseki
Jetty
Pubby
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Life Sciences Linked Data
Probar con el dataset por defecto
Instrucciones: lifescienceslinkeddata/LSLD/README, "Standard running"
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Life Sciences Linked Data
/jena-fuseki-0.2.6-SNAPSHOTchmod +x fuseki-server s-*./fuseki-server --update --mem /ds
./s-put http://localhost:3030/ds/data defaultData/books.ttl
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Life Sciences Linked Data
jetty-distribution-9.0.0.M3/webapps/ROOT/WEB-INF/web.xml
/jetty-distribution-9.0.0.M3java -jar start.jar jetty.port=8080http://localhost:8080/book1
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Life Sciences Linked Data
Publicar el dataset de ejemplo con enlaces a otros datasets LOD
Instrucciones: lifescienceslinkeddata/LSLD/README, "Using a differentdataset"
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Life Sciences Linked Data
1. /jena-fuseki-0.2.6-SNAPSHOT2. mkdir lslddb3. ./fuseki-server --update --loc=./lslddb /dataset
4. ./s-put http://localhost:3030/dataset/data lsldData/LSLD_example.owl
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Life Sciences Linked Data
jetty-distribution-9.0.0.M3/webapps/ROOT/WEB-INF/web.xml
/jetty-distribution-9.0.0.M3java -jar start.jar jetty.port=8080http://localhost:8080/Protein_A
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Life Sciences Linked Data
Crear vuestro propio dataset con Protégé 4 ( ) (DemoProtégé?)
Con enlaces a otros datasets
Publicar el dataset en localhost (Usar "Using a different dataset" como guía)
http://protege.stanford.edu/
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Life Sciences Linked Data
Silk ...
Inferencia con P4: materializar triples ...
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Programación para LD
Generar RDF con Jena
Model model = ModelFactory.createDefaultModel();
Resource prot_a = model.createResource("http://cbgp.upm.es/lsld.rdf#prot_a");
Resource cell_cycle = model.createResource("http://cbgp.upm.es/lsld.rdf#cell_cycle");
Property participates_in = model.createProperty("http://cbgp.upm.es/lsld.rdf#participates_in");
model.add(prot_a, participates_in,cell_cycle);
model.write(System.out);
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Aplicaciones Linked Data
Consulta SPARQL endpoint con JENA (Juan F. Sequeda)
import com.hp.hpl.jena.query.*;
String service = "..."; // address of the SPARQL endpoint String query = "SELECT ..."; // your SPARQL query QueryExecution e = QueryExecutionFactory.sparqlService(service, query)
ResultSet results = e.execSelect(); while ( results.hasNext() ) QuerySolution s = results.nextSolution(); // ...
e.close();
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Sumario herramientas para LD
Triple strores y APIs: , , , , ...Editores ontologías: , , ...Publicar LD: , , ...Validadores: , , , ......
Jena Virtuoso Sesame OWL APIProtégé TopBraid composer
Silk PubbyVapour RDF:Alerts Sindice inspector
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Más información, agradecimientos, etc.
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Más información
(Christian Bizer, Tom Heath, Tim BernersLee)
(Christian Bizer, TomHeath)
Semantic Web Health Care and Life Sciences Interest Group ( ):
Linked Data, the story so far
Linked Data: Evolving the Web into a Global Data Space
W3C HCLS IGHealth Care and Life Science (HCLS) Linked Data Guide
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Más información
José Antonio MiñarroGiménez, Mikel Egaña Aranguren, Boris VillazónTerrazasand Jesualdo Tomás FernándezBreis. Publishing Orthology and DiseasesInformation in the Linked Open Data cloud. Current Bioinformatics 2012, 7 (3),255266. [ ] [ ]Bentham science pdf
Linked Data Patterns
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Inspiración
: Raúl García Castro, University of Texas: Juan F.
Sequeda: Boris Villazón Terrazas
: Mark Wilkinson: Evolving the Web into a Global Data Space (Christian Bizer, Tom
Heath)
Ontology engineering Group (UPM)Bioinformatics and Semantic Web Group
IsocoBiological Informatics Group (CBGP, UPM)Linked Data
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