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Linked Data in ScholarlyCommunicationAAHEP5 Information Provider Summit, Sept. 22nd 2011Bernhard Haslhofer | Cornell University, Information Science

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Overview • Linked Data Vision and Goals • Enabling Technologies (by example) • Publishing and Consuming Linked Data • The SciLink ProjectAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Web Architecture HTML HTML HTML hyperlinks hyperlinksAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Web Architecture HTML HTML HTML HTML HTMLAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Web Architecture • A set of simple standards • Uniform document encoding (HTML) • Uniform global (!) addressing (URI) • Uniform transportation (HTTP) • Hyperlinks connecting documents • Works pretty well for accessing and exchanging documentsAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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But sometimes we need to access to the underlying (meta)data.AAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Web Services and Web APIs API API API API APIAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Web Services and Web APIs • Each Web API has a proprietary interface • Datasources must be known in advance • Information entities (papers, authors, subjects, etc.) are not linkedAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Linked Data Vision • Create a single global data space based on the Architecture of the World Wide Web RDF RDF RDF RDF links RDF linksAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Linked Data Principles • Use URIs as names for things • Use HTTP URIs so that people can look up those names • When someone looks up a URI, provide useful information, using standards (RDF, SPARQL) • Include links to other URIs, so that they can discover more thingsAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Web of Linked Data • A set of simple standards • Uniform data model (RDF) • Uniform global (!) addressing (URI) • Uniform transportation (HTTP) • RDF links connecting entities • Forms a global dataspace and facilitates accessing and exchanging dataAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Web of Linked Data • Data publishers • assign URIs to their information entities • publish RDF instance data about these entities • publish schemas / vocabularies on the Web • link their entities with other entities on the Data Web • can provide query access to their dataAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Linking Open Data Project • Open Data: a philosophy, practice, or policy that data are freely available to everyone without restrictions from copyright, patents, a.s.o • Linked Data: method / best practices for exposing, sharing, and connecting data using URI and RDF • Linking Open Data: a W3C community project with the goal to extend the Web with a data commons by publishing various open data sets as RDF on the Web and by setting links between data items from different sourcesAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Linked Data in the IndustryAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Linked Data in Libraries • Strong uptake in recent years • Library of Congress (vocabularies) • German / Swedish / Hungarian National Library (authorities and/or catalogue data) • Europeana (metadata about ~4M items) • W3C Library Linked Data Incubator GroupAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Overview • Linked Data Vision and Goals • Enabling Technologies (by example) • Publishing and Consuming Linked Data • The SciLink ProjectAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Uniform Resource Identifiers (URIs) • Name and identify things (resources) • Dereferencable HTTP URIs http://springerlink.com/ http://arxiv.org/authors/ author/xyzafbea Haslhofer_B http://eprints.cs.univie.ac.at/ creator/xyzafbea http://arxiv.org/abs/ 1106.5178 http://eprints.cs.univie.ac.at/ 2871AAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Resource Description Framework (RDF) • A data model for representing data on the Web • Sets of statements (triples) form a graph http://xmlns.com/foaf/ spec/#term_Person rdf:type http://arxiv.org/authors/ Haslhofer_B Bernhard Haslhofer http://purl.org/ontology/ bibo/Article dcterms:creator foaf:name http://arxiv.org/abs/ dcterms:created rdf:type 1106.5178 2011-06-25T22:55:17 dc:title The Open Annotation Collaboration (OAC) ModelAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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RDF Serialization (RDF/XML, Turtle, N- Triples, RDF/JSON) • Data formats for serializing RDF graphs • Used to transfer RDF data between apps <http://arxiv.org/abs/1106.5178> dc:title “The Open Annotation Collaboration Model” . ...AAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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RDF Vocabulary Description Language (RDFS) • A language for describing the syntax and semantics of vocabularies in a machine understandable way http://xmlns.com/foaf/ rdf:type rdfs:Class spec/#term_Agent rdfs:subclassOf rdf:type rdf:type http://xmlns.com/foaf/ http://purl.org/ontology/ spec/#term_Person bibo/ArticleAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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OWL Web Ontology Language • A more expressive (formal) language for defining the syntax and semantics of vocabularies owl:DatatypeProperty owl:ObjectProperty owl:FunctionalProperty rdf:type rdf:type rdf:type http://xmlns.com/foaf/0.1/ http://xmlns.com/foaf/0.1/ http://xmlns.com/foaf/0.1/ name homepage genderAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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OWL Web Ontology Language • Defines properties for linking resources owl:sameAs http://arxiv.org/authors/ http://springerlink.com/ Haslhofer_B author/xyzafbea owl:sameAs owl:sameAs http://arxiv.org/abs/ 1106.5178 http://eprints.cs.univie.ac.at/ creator/xyzafbea owl:sameAs http://eprints.cs.univie.ac.at/ 2871NOTE: owl:sameAs is NOT the only linking property.AAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Simple Knowledge Organization System (SKOS) • A language for describing controlled vocabularies (taxonomies, thesauri, etc) skos:closeMatch http://springerlink.com/ http://arxiv.org/subjects/ vocab/computer-science skos.rdf#cs skos:broadMatch skos:broadMatch skos:broader http://arxiv.org/subjects/ http://eprints.cs.univie.ac.at/ skos.rdf#cs.DL subjects/multimedia dcterms:subject dcterms:subject http://arxiv.org/abs/ http://eprints.cs.univie.ac.at/ 1106.5178 2871AAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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SPARQL • A query language and protocol for accessing RDF data on the Web SELECT DISTINCT ?x WHERE { ?x skos:subject <http://arxiv.org/subjects/skos.rdf#cs> } LIMIT 10AAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Overview • Linked Data Vision and Goals • Enabling Technologies (by example) • Publishing and Consuming Linked Data • The SciLink ProjectAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Information vs. Non-Information Resource • Information Resource • web pages, images, pdf documents, etc. • all their essential characteristics can be conveyed in a message • e.g., http://arxiv.org/pdf/1106.5178v1 • Non-Information Resource • other things such as people, this meeting, concepts • their essence is not information • e.g., http://arxiv.org/authors/Haslhofer_BAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Publishing Data • Distinguish between non-information and information resource • Sample NIR • http://arxiv.org/resource/1106.5178 • Sample IRs • http://arxiv.org/abs/1106.5178 (HTML) • http://arxiv.org/data/1106.5178 (RDF)AAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Publishing Data GET http://arxiv.org/resource/1106.5187 Accept: application/rdf+xml 303 See Other Location: http://arxiv.org/data/1106.5187 GET http://arxiv.org/data/1106.5187 Accept: application/rdf+xml 200 OK ... <?xml version="1.0" encoding="utf-8"?> <rdf:RDF ...AAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Publishing Data GET http://arxiv.org/resource/1106.5187 Accept: application/rdf+xml 303 See Other Location: http://arxiv.org/data/1106.5187 Oh dear! GET http://arxiv.org/data/1106.5187 Accept: application/rdf+xml 200 OK ... <?xml version="1.0" encoding="utf-8"?> <rdf:RDF ...AAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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RDFa / Microformats / Microdata • Mechanisms for embedding structured data in Web documents • Define or use a set of attributes to augmented presentation-oriented (HTML) documents with structured data • User agents can extract data from Web documentsAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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RDFa Example<div typeof=”bibo:Article” xmlns:bibo=”http://purl.org/ontology/bibo”> <div xmlns:dc=”http://purl.org/dc/elements/1.1/”> <h1 property=”dc:title”>The Open Annotation Collaboration (OAC) Model</h1> .... </div></div>AAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Microformats Example <head profile=”http://www.w3.org/2006/03/hcard”> ... </head> <div class=”vcard”> <div class=”fn”>Bernhard Haslhofer</div> </div>AAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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RDFa vs. Microformats Microformats RDFa flat namespace XML namespaces support HTML4, XHTML 1.1, and support for XHTML 1.1, HTML 5 HTML 5 use latent HTML attributes introduces new metadata attributes vocabulary defined by one open to any RDF-based vocabulary organization/communityAlso see: http://evan.prodromou.name/RDFa_vs_microformatsAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Microdata • A very young HTML proposition that extends Microformats and addresses its shortcomings <div itemscope itemtype="http://schema.org/Article"> <span itemprop="name">The Open Annotation Collaboration (OAC) Model</span> by <span itemprop="author">Bernhard Haslhofer</span>, <span itemprop=”author”>Rainer Simon</span>, <span itemprop=”author”>Robert Sanderson</span> and <span itemprop=”author”>Herbert Van De Sompel</span> This article has been tweeted 1 times and contains 0 user comments. <meta itemprop="interactionCount" content="UserTweets:1"/> <meta itemprop="interactionCount" content="UserComments:0"/> </div>AAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Web Data Publishing Approaches Pro Con Separates data / Technical complexity Linked Data presentation markup Conneg IR / NIR Communication Web Architecture overhead Mixes data / RDFa / Easy to implement presentation markup Microformats / Microdata Search Engines Becomes messyAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Consuming Linked Data curl -H “Accept: application/rdf+xml” http://arxiv.org/data/1105.5178 rapper http://arxiv.org/resource/1105.5178 ... any RDF libraryAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Overview • Linked Data Vision and Goals • Enabling Technologies (by example) • Publishing and Consuming Linked Data • The SciLink ProjectAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Motivation • Current research articles • are mostly PDFs (a kind of BLOB) • point to supplemental or related information by textual references, DOIs, or embedded hypertext links HTML HTML HTML HTML HTMLAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Motivation • But a publication is more: • data sets, conference presentations • blog / wiki entries, software libraries, etc • There is related information on the Web (e.g., Wikipedia)AAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Overall Goal Publication Document (PDF) Aggregation for the Document foaf:firstname Jennifer dbpedia: dbpedia: Drosphila Category: dblp: Genome-wide analysis of Notch jmummery Mummery- Signal_transduction signaling in Drosphila by Widmer transgenic RNAi rdfs:seeAlso foaf:lastname skos:subject dcterms: creator Jennifer Mummery-Widmer, .... Outer context Here we report the use of a library of Inner context Drosphila strains...we identified 6 new genes involved in asymmetric cell ore: division. Aggregation Genome-wide dc:title analysis... rdf:type A total of 20,262 transgenic RNAi lines were ex:agg1 screened...Ten flies were recorded in an online database... ore: aggregates ore: aggregates ex: ex: figure4.jpg ore: aggregates ore: aggregates nature07936.pdf ex: ex: movie1.avi database.zip Figure 4. An interaction network for Notch dctype: signalling Dataset Asymmmetric dc:title rdf:type cell division http://www.nature.com/nature/journal/ vaop/ncurrent/pdf/nature07936.pdfAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Methodology • Aggregation/Data Extraction: create aggregations from available information (PDFs, metadata) • Analysis: combine aggregations and learn about established research and publication practices in different areas (focus on linking) • Tool design and Implementation • link discovery • resource synchronization / link maintenance • demonstrator applications operating on data graphAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Aggregation / Data Extraction • scilink-extract library • takes PDFs and metadata as input • creates ORE Aggregations / CSV files • currently implemented for arXiv.org • https://github.com/behas/scilink-extractAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Analysis • How did HTTP linkage evolve in the past? • Where in their papers do scholars make use of HTTP links? • What are the linking to? • Are the links still operational? • ....AAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011

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Status • Extraction for arxiv.org finished (~ 700K ) PDFs • We need access to further corpora covering different research areas !!! Work in ProgressAAHEP5 Information Provider Summit | Ithaca, NY | Sept. 22nd, 2011