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The Nature.com ontologies portal - Linked Science 2015

Presentation outlining the resources available at nature.com/ontologies Part of LISC 2015 - http://linkedscience.org/events/lisc2015/

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The nature.com
ontologies portal
nature.com/ontologies
Tony Hammond, Michele Pasin
Macmillan Science and Education
Who we are
We are both part of Macmillan Science and Education*
-  Macmillan S&E is a global STM publisher
-  Tony Hammond is Data Architect, Technology
@tonyhammond
-  Michele Pasin is Information Architect, Product Office
@lambdaman
* We merged earlier this year (May 2015) with Springer Science+Business Media
to become Springer Nature. We are currently actively engaged in integrating our
businesses.
Macmillan: science and education brands
May 2015
We publish a lot of science! (1845-2015)
http://www.nature.com/developers/hacks/articles/by-year
1,2 million articles in total
Why we’re here today: to ask some questions
We have been making semantic data available in RDF models for a number of
years through our data.nature.com portal (2012–2015)
Big questions:
-  Is this data of any use to the Linked Science community?
-  Should Springer Nature continue to invest in LOD sharing?
More specifically:
-  Does the data contain enough items of interest? [Content]
-  Are the vocabularies understandable and useful? [Structure]
-  Are the data easy to get and to reuse? [Accessibility]
-  Is dereference / download / query the preferred option?
Our work so far
-  Step 1: Linked Data Platform (2012–2014)
-  datasets
-  downloads + SPARQL endpoint
-  linked data dereference
-  Step 2: Ontologies Portal (2015–)
-  datasets + models (core, domain)
-  downloads
-  extensive documentation

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The Nature.com ontologies portal - Linked Science 2015

  • 1. The nature.com ontologies portal nature.com/ontologies Tony Hammond, Michele Pasin Macmillan Science and Education
  • 2. Who we are We are both part of Macmillan Science and Education* -  Macmillan S&E is a global STM publisher -  Tony Hammond is Data Architect, Technology @tonyhammond -  Michele Pasin is Information Architect, Product Office @lambdaman * We merged earlier this year (May 2015) with Springer Science+Business Media to become Springer Nature. We are currently actively engaged in integrating our businesses.
  • 3. Macmillan: science and education brands May 2015
  • 4. We publish a lot of science! (1845-2015) http://www.nature.com/developers/hacks/articles/by-year 1,2 million articles in total
  • 5. Why we’re here today: to ask some questions We have been making semantic data available in RDF models for a number of years through our data.nature.com portal (2012–2015) Big questions: -  Is this data of any use to the Linked Science community? -  Should Springer Nature continue to invest in LOD sharing? More specifically: -  Does the data contain enough items of interest? [Content] -  Are the vocabularies understandable and useful? [Structure] -  Are the data easy to get and to reuse? [Accessibility] -  Is dereference / download / query the preferred option?
  • 6. Our work so far -  Step 1: Linked Data Platform (2012–2014) -  datasets -  downloads + SPARQL endpoint -  linked data dereference -  Step 2: Ontologies Portal (2015–) -  datasets + models (core, domain) -  downloads -  extensive documentation
  • 8. Our goals and rationale -  Semantic technologies are an effective way to do enterprise metadata management at web scale -  Initially used primarily for data publishing / sharing (data.nature.com, 2011) -  Since 2013, a core component of our digital publishing workflow (see ISWC14 paper) -  Contributing to an emerging web of linked science data -  As a major publisher since 1845, ideally positioned to bootstrap a science ‘publications hub’ -  Building on the fundamental ties that exist between the actual research works and the publications that tell the story about it
  • 9. The vision of a science graph
  • 11. The core ontology -  Language: OWL 2, Profile: ALCHI(D) -  Entities: ~50 classes, ~140 properties -  Principles: Incremental Formalization/ Enterprise Integration / Model Coherence http://www.nature.com/ontologies/core/
  • 12. The core ontology: mappings :Asset :Thing :Publication :Concept :Event :Subject :Type :Agent :ArticleType :Publishing Event :Aggregation Event :Component :Document :Serial cidoc-crm: Information_Carrier cidoc-crm: Conceptual_Object dbpedia:Agent dc:Agent dcterms:Agent cidoc-crm:Agent vcard:Agent foaf:Agent event:Event bibo:Event schema:Event cidoc-crm: TemporalEntity cidoc-crm:Type vcard:Type fabio:SubjectTerm bibo:Document cidoc-crm:Document foaf:Document bibo:Periodical fabio:Periodical schema:Periodical bibo:DocumentPart fabio:Expression cidoc-crm:InformationObject = owl:equivalentClass http://www.nature.com/ontologies/linksets/core/
  • 13. Domain models: subjects ontology -  Structure: SKOS, multi hierarchical tree, 6 branches, 7 levels of depth -  Entities: ~2500 concepts -  Mappings: 100% of terms, using skos:broadMatch or skos:closeMatch, (Dbpedia and MESH) www.nature.com/ontologies/models/subjects/
  • 15. Datasets -  Articles: 25m records (for 1.2m articles) with metadata like title, publication etc.. except authors -  Contributors: 11m records (for 2.7m contributors) i.e. the article’s authors, structured and ordered but not disambiguated -  Citations: 218m records (for 9.3m citations) – from an earlier release
  • 16. Datasets: articles-wikipedia links How: data extracted using wikipedia search API, 51,309 links over 145 years Quality: only ~900 were links to nature.com without a DOI, rest all use DOIs correctly Encoding: cito:isCitedBy => wiki URL, foaf:topic => dbPedia URI http://www.nature.com/developers/hacks/wikilinks
  • 17. Data publishing: sources Sources: Ontologies (small scale; RDF native) -  mastered as RDF data (Turtle) -  managed in GitHub -  in-memory RDF models built using Apache Jena -  models augmented at build time using SPIN rules -  deployed to MarkLogic as RDF/XML for query -  exported as RDF dataset (Turtle) and as CSV Documents (large scale; XML native) -  mastered as XML data -  managed in MarkLogic XML database -  data mined from XML documents (1.2m articles) using Scala -  in-memory RDF models built using Apache Jena -  injected as RDF/XML sections into XML documents for query -  exported as RDF dataset (N-Quads) Organization: Named graphs – one graph per class
  • 19. Data publishing: rules (enrichment) construct { ?s npg:publicationStartYear ?xds1 . ?s npg:publicationStartYearMonth ?xds2 . ?s npg:publicationStartDate ?xds3 . ?s npg:publicationEndYear ?xde1 . ?s npg:publicationEndYearMonth ?xde2 . ?s npg:publicationEndDate ?xde3 . } where { ?s a npg:Journal . optional { ?s npg:dateStart ?dateStart } optional { ?s npg:dateEnd ?dateEnd } { bind (if(regex(?dateStart, "^d{4}"), substr(?dateStart,1,4), "") as ?ds1) bind (xsd:gYear(?ds1) as ?xds1) } union { bind (if(regex(?dateStart, "^d{4}-d{2}"), substr(?dateStart,1,7), "") as ?ds2) bind (xsd:gYearMonth(?ds2) as ?xds2) } union { bind (if(regex(?dateStart, "^d{4}-d{2}-d{2}$"), substr(?dateStart,1,10), "") as ?ds3) bind (xsd:date(?ds3) as ?xds3) } union { … } filter (?xds1 != "" || ?xds2 != "" || ?xds3 != "" || ?xde1 != "" || ?xde2 != "" || ?xde3 != "") }
  • 20. Data publishing: rules (validation) construct { npgg:journals npg:hasConstraintViolation [ a spin:ConstraintViolation ; npg:severityLevel "Warning" ; rdfs:label ?message ; spin:rule [ a sp:Construct ; sp:text ?query ; ] ; ] . } where { { select (count(?s) as ?count) where { ?s a npg:Journal . filter ( not exists { ?s bibo:shortTitle ?h . } ) } } bind (concat("! Found ", str(?count), " journals with no short title") as ?message) bind (""” construct { npgg:journals npg:hasConstraintViolation [ a spin:ConstraintViolation ; spin:violationRoot ?s ; … ] . } where { … } """ as ?query) }
  • 21. Data publishing: rules (contracts) knowledge-bases:public ... npg:hasContract [ rdfs:comment "Contract for ArticleTypes Ontology" ; npg:graph npgg:article-types ; npg:hasBinding [ npg:onOntology article-types: ; npg:allowsPredicate dc:creator , dc:date , dc:publisher , dc:rights , dcterms:license , npg:webpage , owl:imports , owl:versionInfo , rdf:type , rdfs:comment , skos:definition , skos:prefLabel , skos:note , vann:preferredNamespacePrefix , vann:preferredNamespaceUri ; ] , [ npg:onInstanceOf npg:ArticleType ; npg:allowsPredicate npg:hasRoot , npg:isPrimaryArticleType , npg:id , npg:isLeaf , npg:isRoot , npg:treeDepth , rdf:type , rdfs:isDefinedBy , rdfs:seeAlso , skos:broadMatch , skos:broader , skos:closeMatch , skos:definition , skos:exactMatch , skos:inScheme , skos:narrower , skos:prefLabel , skos:relatedMatch , skos:topConceptOf ; ] ; ] ; ...
  • 22. Data publishing: rules (contracts)
  • 23. Next steps More features: -  Linked data dereference -  Richer dataset descriptions (VoID, PROV, HCLS Profile, etc.) -  SPARQL endpoint? -  JSON-LD API? More data: -  Adding extra data points (funding info, affiliations, …) -  Revamp citations dataset -  Longer term: extending archive to include Springer content More feedback: -  User testing around data accessibility -  Surveying communities/users for this data
  • 24. Looking ahead: how can a publisher make linked science happen? From a business perspective: -  Finding adequate licensing solutions -  Justifying the effort to publishers -  What’s the ROI? From a communities perspective: -  Do we actually know who are the users? -  How do we get more feedback/uptake? -  Should we work more with non-linked-data communities?