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Weaving repository contents into the Semantic Web 
Pascal-Nicolas Becker | Technische Universität Berlin | SWIB14 | Bonn, December 1-3, 2014
Digital Repositories 
Source: The Directory of Open Access Repositories, 
http://www.opendoar.org, retrieved June 06, 2014. 
Repositories are systems to safely store 
and publish digital objects and their 
descriptive metadata. 
Not in the meaning of software repositories. 
Examples: 
• Digital archives 
• Institutional repositories (preprints, 
postprints, open access publications, …) 
• Digital image libraries 
• Research data repositories 
• … 
More than 2500 Open Access repositories 
worldwide. 
Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 
Slide 2
Repository contents are particularly suited 
The data stored in repositories are 
particularly suited to be used in the 
Semantic Web: 
• Metadata already exist in a structured 
form. 
• They do not have to be generated or 
entered manually for publication as 
Linked Data. 
• “Just” convert the data in RDF, add links 
and publish them respecting the Linked 
Data Principles. 
Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 
Slide 3
xxx.lanl.org / ArXiv.org 
Source: Paul Ginsparg, First Steps Towards Electronic Research Communication. In: Computer in Physics, Vol. 8, No. 4, 1994, pp. 390-396. 
Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 
Slide 4 
“Although the WorldWideWeb still 
represents only a small fraction of the 
overall usage, this access mode is expected 
to become dominant in the near future.” 
Paul Ginsparg 1994
Current data exchange with Repositories 
• OAI-PMH (Open Archive Initiative – Protocol for Metadata Harvesting): 
de facto standard in the context of repositories 
• But: limited to that context 
• Google retired support for OAI-PMH in 2008 
(used before as alternative to the sitemap protocol) 
• “Just” an interface, not a format 
 Linked Data is a generic, native way of data exchange, 
not only in the field of repositories 
 Data published following the Linked Data Principles is self-descriptive 
 Linked Data simplifies data exchange with repositories 
Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 
Slide 5
Characteristics of repositories 
• Different repositories may use different metadata schemas. 
 Conversion must be highly configurable and extendable. 
• Metadata may use already existing vocabularies (e.g. Dublin Core, LCSH, …). 
 Convert metadata values to URIs / links. 
• Repository contents change rarely (to be citable and reliable). 
Conversion may be time intensive. 
 Convert data and store converted data in a cache. 
• Repositories generate URIs that shall be used to address their content. 
 Reuse those URIs, add content negotiation to them. 
• Persistent Identifiers (handle, DOI, …) violate the Linked Data Principles. 
 Use Persistent Identifiers in form of HTTP(S) URIs (http://dx.doi.org/...). 
Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 
Slide 6
Extending Repositories 
• Add a Triple Store. 
• Use it as cache for converted data. 
• Use it to provide a SPARQL endpoint. 
• Add methods to convert data into RDF and to add links. 
• Add a module to serve data as RDF serializations. 
• Add content negotiation. 
RDF Conversion 
Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 
Slide 7 
File System 
Relational 
Database 
Triple Store 
Authorization 
System 
Browse and 
Search 
Persistent 
Identifier Mgt. 
Event System 
User 
Administration 
... 
Web UI 
OAI-PMH 
Interface 
REST 
SWORD ... 
RDF 
Serialization 
Interfaces 
Business Logic 
Storage Layer
What do Repositories store? 
“Repositories are systems to safely store and publish digital objects and 
• Digital objects 
their descriptive metadata.” 
 We can‘t convert the files (technical problems, far too much work). 
 But we can convert the metadata and link to the files! 
Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 
Slide 8 
 One or several files: 
Documents (PDF, Text, …), Tables (CSV, …), 
Images (PNG, Tiff …), Audio (Wave, …), 
Video, File Archives, … 
• Descriptive metadata 
 Structured metadata as key – value: 
dc.title, dc.contributor.author, dc.description, 
dc.date.available, dc.subject.lcsh, 
dc.subject.ddc, …
Convert existing metadata to RDF 
• Repository software can be extended to support more or other metadata fields. 
• Dublin Core is used often, but there are other metadata schemas as well. 
 Make the conversion highly configurable! 
 Use RDF for the configuration (so all features of RDF can be used in the configuration 
easily). 
 Use Reification to describe the results. 
 Use Placeholders where necessary, e.g. URIs used by the repository. 
 Use Regular Expressions to generate Literals and/or URIs from a metadata value. 
 Create a vocabulary to write such configurations. 
Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 
Slide 9
Example: DSpace Metadata RDF Mapping Vocabulary 
http://digital-repositories.org/ontologies/dspace-metadata-mapping/ 
• One Mapping describes how to convert one metadata field in RDF. 
• Can detect the metadata field by its name (key) and a regular expression used on its 
value. 
• Creates one or several triples. 
• Can use a placeholder for the URI of the object being converted currently. 
• Can create Literals or Resources as needed. 
• Can specify value types and language tags. 
• Can use the language tag DSpace stores for some metadata fields. 
• Can reuse the metadata value, of course. 
• May use regular expressions to modify metadata values used as Literals or Resource 
URIs. 
Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 
Slide 10
Example: DSpace Metadata RDF Mapping Vocabulary 
@prefix dc: <http://purl.org/dc/elements/1.1/> . 
@prefix dm: <http://digital-repositories.org/ontologies/dspace-metadata-mapping/0.2.0#> . 
@prefix : <#> . 
:title 
dm:metadataName "dc.title" ; 
dm:creates [ 
dm:subject dm:DSpaceObjectIRI ; 
dm:predicate dcterms:title ; 
dm:object dm:DSpaceValue ; 
] ; 
. 
Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 
Slide 11
Example: DSpace Metadata RDF Mapping Vocabulary 
:doi 
dm:metadataName „dc.identifier.doi" ; 
dm:condition „^doi:“ ; 
dm:creates [ 
dm:subject dm:DSpaceObjectIRI ; 
dm:predicate dc:identifier; 
dm:object [ 
a dm:ResourceGenerator ; 
dm:modifier [ 
dm:matcher „^doi:(.*)$“ ; 
dm:replacement „http://dx.doi.org/$1“ ; 
] ; 
dm:pattern „$DSpaceValue“ ; 
] ; 
] ; 
. 
Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 
Slide 12
Describing Repositories 
• Beside converting metadata it is worth describing the repository itself. 
• Who is running the repository? Does it have an OAI-PMH interface? Where can I find 
a SPARQL endpoint? How is the content structured? … 
• A vocabulary to link to the digital objects (files) is needed as well. 
• For DSpace, I created the DSpace Repository Ontology: 
http://digital-repositories.org/ontologies/dspace/ 
• A Digital Repositories Ontology would be great, describing repositories independent 
from the software used to create them. 
• A mapping between such an ontology and the DSpace Repository Ontology, the 
EPrints Ontology or any other would be great! 
• If you are interested in creating such an Ontology as well: please contact me. 
Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 
Slide 13
Things to mention, even if they should be clear 
• Reuse existing URIs wherever possible, don’t create your own URI if there already 
exists one. 
• E.g.: For classifications like the Library of Congress Subject Headings URIs 
already exists. 
• Create URIs only for you own entities or if you have enough information. 
• Do not create URIs for authors unless you can distinguish different authors with 
the same name! 
• Think about whether the author should create his or her own URI or if it is really 
up to you to create one. 
• But create URIs for the objects in your repository. 
• Create links wherever possible. 
Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 
Slide 14
DSpace 5 
• DSpace is the most often used software for Open Access Repositories worldwide 
• Release of DSpace version 5.0 planned for December 2014 
(release candidates are out, testathon is running) 
• Will contain support for Linked Data (RDF/XML, Turtle, N-Triples, SPARQL) 
• Will support content negotiation 
• Highly configurable, good default configuration included 
• Test it yourself: 
http://demo.dspace.org/data/handle/10673/5/ttl 
http://demo.dspace.org/data/handle/10673/5/ttl?text 
wget -O - --header=‘Accept: text/turtle’ http://demo.dspace.org/jspui/handle/10673/5 
or download and install a release candidate 
If you’re about to use DSpace 5.0 or above 
please consider switching Linked Data Support on. 
Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 
Slide 15
Technische Universität Berlin 
Universitätsbibliothek 
Pascal-Nicolas Becker 
p.becker@tu-berlin.de 
Servicezentrum Forschungsdaten und –publikationen 
http://www.szf.tu-berlin.de 
Repository DepositOnce 
http://depositonce.tu-berlin.de 
Thesis „Repositorien und das Semantic Web“ (in German) 
http://www.pnjb.de/uni/diplomarbeit/ 
Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 
Slide 16

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SWIB14 Weaving repository contents into the Semantic Web

  • 1. Weaving repository contents into the Semantic Web Pascal-Nicolas Becker | Technische Universität Berlin | SWIB14 | Bonn, December 1-3, 2014
  • 2. Digital Repositories Source: The Directory of Open Access Repositories, http://www.opendoar.org, retrieved June 06, 2014. Repositories are systems to safely store and publish digital objects and their descriptive metadata. Not in the meaning of software repositories. Examples: • Digital archives • Institutional repositories (preprints, postprints, open access publications, …) • Digital image libraries • Research data repositories • … More than 2500 Open Access repositories worldwide. Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 Slide 2
  • 3. Repository contents are particularly suited The data stored in repositories are particularly suited to be used in the Semantic Web: • Metadata already exist in a structured form. • They do not have to be generated or entered manually for publication as Linked Data. • “Just” convert the data in RDF, add links and publish them respecting the Linked Data Principles. Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 Slide 3
  • 4. xxx.lanl.org / ArXiv.org Source: Paul Ginsparg, First Steps Towards Electronic Research Communication. In: Computer in Physics, Vol. 8, No. 4, 1994, pp. 390-396. Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 Slide 4 “Although the WorldWideWeb still represents only a small fraction of the overall usage, this access mode is expected to become dominant in the near future.” Paul Ginsparg 1994
  • 5. Current data exchange with Repositories • OAI-PMH (Open Archive Initiative – Protocol for Metadata Harvesting): de facto standard in the context of repositories • But: limited to that context • Google retired support for OAI-PMH in 2008 (used before as alternative to the sitemap protocol) • “Just” an interface, not a format  Linked Data is a generic, native way of data exchange, not only in the field of repositories  Data published following the Linked Data Principles is self-descriptive  Linked Data simplifies data exchange with repositories Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 Slide 5
  • 6. Characteristics of repositories • Different repositories may use different metadata schemas.  Conversion must be highly configurable and extendable. • Metadata may use already existing vocabularies (e.g. Dublin Core, LCSH, …).  Convert metadata values to URIs / links. • Repository contents change rarely (to be citable and reliable). Conversion may be time intensive.  Convert data and store converted data in a cache. • Repositories generate URIs that shall be used to address their content.  Reuse those URIs, add content negotiation to them. • Persistent Identifiers (handle, DOI, …) violate the Linked Data Principles.  Use Persistent Identifiers in form of HTTP(S) URIs (http://dx.doi.org/...). Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 Slide 6
  • 7. Extending Repositories • Add a Triple Store. • Use it as cache for converted data. • Use it to provide a SPARQL endpoint. • Add methods to convert data into RDF and to add links. • Add a module to serve data as RDF serializations. • Add content negotiation. RDF Conversion Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 Slide 7 File System Relational Database Triple Store Authorization System Browse and Search Persistent Identifier Mgt. Event System User Administration ... Web UI OAI-PMH Interface REST SWORD ... RDF Serialization Interfaces Business Logic Storage Layer
  • 8. What do Repositories store? “Repositories are systems to safely store and publish digital objects and • Digital objects their descriptive metadata.”  We can‘t convert the files (technical problems, far too much work).  But we can convert the metadata and link to the files! Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 Slide 8  One or several files: Documents (PDF, Text, …), Tables (CSV, …), Images (PNG, Tiff …), Audio (Wave, …), Video, File Archives, … • Descriptive metadata  Structured metadata as key – value: dc.title, dc.contributor.author, dc.description, dc.date.available, dc.subject.lcsh, dc.subject.ddc, …
  • 9. Convert existing metadata to RDF • Repository software can be extended to support more or other metadata fields. • Dublin Core is used often, but there are other metadata schemas as well.  Make the conversion highly configurable!  Use RDF for the configuration (so all features of RDF can be used in the configuration easily).  Use Reification to describe the results.  Use Placeholders where necessary, e.g. URIs used by the repository.  Use Regular Expressions to generate Literals and/or URIs from a metadata value.  Create a vocabulary to write such configurations. Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 Slide 9
  • 10. Example: DSpace Metadata RDF Mapping Vocabulary http://digital-repositories.org/ontologies/dspace-metadata-mapping/ • One Mapping describes how to convert one metadata field in RDF. • Can detect the metadata field by its name (key) and a regular expression used on its value. • Creates one or several triples. • Can use a placeholder for the URI of the object being converted currently. • Can create Literals or Resources as needed. • Can specify value types and language tags. • Can use the language tag DSpace stores for some metadata fields. • Can reuse the metadata value, of course. • May use regular expressions to modify metadata values used as Literals or Resource URIs. Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 Slide 10
  • 11. Example: DSpace Metadata RDF Mapping Vocabulary @prefix dc: <http://purl.org/dc/elements/1.1/> . @prefix dm: <http://digital-repositories.org/ontologies/dspace-metadata-mapping/0.2.0#> . @prefix : <#> . :title dm:metadataName "dc.title" ; dm:creates [ dm:subject dm:DSpaceObjectIRI ; dm:predicate dcterms:title ; dm:object dm:DSpaceValue ; ] ; . Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 Slide 11
  • 12. Example: DSpace Metadata RDF Mapping Vocabulary :doi dm:metadataName „dc.identifier.doi" ; dm:condition „^doi:“ ; dm:creates [ dm:subject dm:DSpaceObjectIRI ; dm:predicate dc:identifier; dm:object [ a dm:ResourceGenerator ; dm:modifier [ dm:matcher „^doi:(.*)$“ ; dm:replacement „http://dx.doi.org/$1“ ; ] ; dm:pattern „$DSpaceValue“ ; ] ; ] ; . Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 Slide 12
  • 13. Describing Repositories • Beside converting metadata it is worth describing the repository itself. • Who is running the repository? Does it have an OAI-PMH interface? Where can I find a SPARQL endpoint? How is the content structured? … • A vocabulary to link to the digital objects (files) is needed as well. • For DSpace, I created the DSpace Repository Ontology: http://digital-repositories.org/ontologies/dspace/ • A Digital Repositories Ontology would be great, describing repositories independent from the software used to create them. • A mapping between such an ontology and the DSpace Repository Ontology, the EPrints Ontology or any other would be great! • If you are interested in creating such an Ontology as well: please contact me. Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 Slide 13
  • 14. Things to mention, even if they should be clear • Reuse existing URIs wherever possible, don’t create your own URI if there already exists one. • E.g.: For classifications like the Library of Congress Subject Headings URIs already exists. • Create URIs only for you own entities or if you have enough information. • Do not create URIs for authors unless you can distinguish different authors with the same name! • Think about whether the author should create his or her own URI or if it is really up to you to create one. • But create URIs for the objects in your repository. • Create links wherever possible. Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 Slide 14
  • 15. DSpace 5 • DSpace is the most often used software for Open Access Repositories worldwide • Release of DSpace version 5.0 planned for December 2014 (release candidates are out, testathon is running) • Will contain support for Linked Data (RDF/XML, Turtle, N-Triples, SPARQL) • Will support content negotiation • Highly configurable, good default configuration included • Test it yourself: http://demo.dspace.org/data/handle/10673/5/ttl http://demo.dspace.org/data/handle/10673/5/ttl?text wget -O - --header=‘Accept: text/turtle’ http://demo.dspace.org/jspui/handle/10673/5 or download and install a release candidate If you’re about to use DSpace 5.0 or above please consider switching Linked Data Support on. Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 Slide 15
  • 16. Technische Universität Berlin Universitätsbibliothek Pascal-Nicolas Becker p.becker@tu-berlin.de Servicezentrum Forschungsdaten und –publikationen http://www.szf.tu-berlin.de Repository DepositOnce http://depositonce.tu-berlin.de Thesis „Repositorien und das Semantic Web“ (in German) http://www.pnjb.de/uni/diplomarbeit/ Weaving repository contents into the Semantic Web | Pascal-Nicolas Becker | SWIB14 | Bonn, December 3, 2014 Slide 16