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Knowledge Organization System for GBIF
Virtual Biodiversity Research and Access Network for Taxonomy (ViBRANT)




Dag Endresen
Knowledge Systems Engineer

Éamonn Ó Tuama
Senior Programme Officer, Inventory, Discovery, Access (IDA)


Global Biodiversity Information Facility (GBIF)

31 August 2012
Enabling interoperability for the GBIF
network and beyond                     GEO
                                           BON,
“The ability of two or more systems or          IPBE
                                                    S
components to exchange information and to
use the information that has been exchanged”
(ref: IEEE Standard Computer Dictionary: Compilation of IEEE Standard Computer Glossaries, ISBN:155937079)



 Key requirement:
  Common exchange standards and protocols
  for biodiversity data …
         necessitate agreement on use of common
         vocabularies for the classes of objects and
         their properties
    Knowledge Organisation Systems (KOS)
                                               - can help us manage our vocabularies
Knowledge Organisation Systems
... to manage the vocabularies used for
sharing biodiversity information.

- Term lists: glossaries, dictionaries, gazetteers

- Classifications / categorisations: taxonomies
                           e.g., Dewey Decimal Classification


- Relationships: thesauri, ontologies


    simple relationships           a model of a domain
Darwin Core – a glossary of terms


       higherClassification
         coordinatePosition
          specificEpithet
            geodeticDatum
             collectionCode
               taxonConceptID
                 taxonRank
collectionCode: The name, acronym, coden, or initialism identifying the
collection or data set from which the record was derived. Examples:
"Mammals", "Hildebrandt", "eBird".
AgroVoc vocabulary – a thesaurus
            bt   Resources
                  nt Natural resources

                      nt Biological resources

                           nt Genetic resources

                                 nt   Germplasm
                                   uf Genetic            material
                                    uf Germplasm resources
                                    rt Protoplasm
 bt = broader term
 nt = narrower term                 rt Genes
 uf = used for
                                    rt Gene pools
 rt = related term
                                    rt Biodiversity
                                    rt Germplasm collections
                                    rt Gametes
                          http://aims.fao.org/standards/agrovoc/functionalities/hierarchy
Ontology – a model of a domain
                           collectors take samples

                                   inverseOf
             samples are taken by collectors                                                   William
                                                                                               Jefferson
                                                                                               Clinton


           NHM, Los Angeles County                                                        sameAs
               differentFrom                                                                   Bill Clinton

                               NHM, London


                                                                             transitiveProperty
                                                          A hasAncestor B                B hasAncestor C

                                                                                 hasAncestor
Clinton image source: http://www.whitehouse.gov/sites/default/files/first-
family/masthead_image/42bc_header_sm.jpg?1250887359




                               ontologies = computable dictionaries
Term	
  versus	
  Concept
                                                  	
  
“The SKOS (simple knowledge organization system) format is designed to present
KOS data in a format that is suitable for machine inferencing and particularly for use
in the Semantic Web (….) The model [ISO 25964] is based on the understanding that
thesauri show the relationships between concepts – units of thought – and
distinguishes these from the terms that are used to label these concepts. These terms
may be in one or more languages, and one term per language is chosen as a
preferred term for each concept. One or more additional terms for the same concept
may be recorded in the thesaurus as non-preferred terms.”
Will, L. (2012). The ISO 25964 Data Model for the Structure of an Information Retrieval Thesaurus. Bulletin of the American
Society for Information Science and Technology 38(4): 48-51.




Dextre Clarke, S.G. and L. Zeng (2012). From ISO 2788 to ISO 25964: the evolution of thesaurus Standards towards
Interoperability and data modeling. ISQ Information Standards Quarterly 24(1): 20-26.
Knowledge Organisation Systems
Key requirement: a platform to support the
development, maintenance and governance of
vocabularies for the biodiversity community
- New dedicated position at GBIF funded through          KOS
                                                               activi
  external projects (ViBRANT, i4Life)                   in GB         ties
                                                              IF wo
                                                       progr         rk
- Review recommendations in KOS task group                   amm
  report and develop implementation roadmap                        e
- Review GBIF Vocabularies Service and develop
  vocabulary management system

-  Engage with wider community:
     -  participation in Dublin Core workshop, Sept 2011
     -  KOS symposium at TDWG 2011 Conf, Oct 2011
     -  TDWG Vocabulary Management Task Group, 2012
ViBRANT: Task 4.1 Ontology platform (GBIF, JKI)
Description of work:
•  “[F]lexible, user-friendly ontology management
   environment, enabling users to create, define, extent
   and share their own terms and concepts where
   needed, providing options for discussions and
   annotation, while supporting re-use of terms from
   standardized ontologies wherever possible”.
    •  Extent the functionalities of existing vocabulary services (like
       GBIF).

    •  Collaborative community interface for users and user-
       networks, bottom-up, user-friendly and non-technical.

    •  Flexibility for biologists to express their knowledge regardless
       of whether the terminology has been standardized yet or not.
      Text from the ViBRANT project summary, page 13 (my highlighting).




9
ViBRANT WP4: GBIF tasks and deliverables

 Deliverable	
  4.2:	
  Ontology	
  tools:	
  	
  
 •  “Develop	
  the	
  GBIF	
  ontology	
  tool	
  and	
  
    produce	
  an	
  equivalent	
  tool	
  based	
  on	
  a	
  
    seman<c	
  wiki.	
  Deliver	
  a	
  single	
  user	
  
    interface	
  for	
  ontology	
  crea<on	
  and	
  
    edi<ng	
  based	
  on	
  user-­‐acceptance	
  of	
  the	
  
    alterna<ve	
  technologies.”	
  
     Text from the ViBRANT project summary, page 14 (my highlighting).




10
Governance structure (TDWG VoMaG)




                       h=p://community.gbif.org/pg/groups/21382/	
  	
  




11
Why use a flat vocabulary ?
 •  Maximize the reuse of terms, focus on the definition
    and labels for basic terms.
 •  Low threshold for non-technical biologists and
    biodiversity domain experts to access terms and
    contribute (compared to richer ontologies).
 •  Preferred technology: RDF (resource description
    framework) and SKOS (simple knowledge organization
    system).
 •  Construction and maintenance of OWL ontologies are
    demanding in respect to expertise, effort and costs.
 •  Maintaining SKOS vocabularies are less demanding.
 •  RDF resources are designed to be easily extended.
 •  Ontologies (OWL) can be based on (extend) terms
    declared by a RDF/SKOS vocabulary.
 •  SKOS became a W3C recommendation in 2009.
12
Why use OWL (web ontology language) ?
•  OWL DL supports machine reasoning through machine
   accessible formal semantics.
•  OWL provides by default an URI as identifier for classes,
   properties, relations and instances.
•  E.g. OBO target practical solutions in the biomedical /
   biology domain, while OWL is more generic and provide
   cross-domain interoperability.
•  OWL 1.0 became a W3C recommendation in 2004,
•  OWL 2.0 in 2009.
•  http://www.w3.org/2007/OWL/

•  Recommendation:
      •  REUSE terms declared by flat vocabularies…
      •  Start with SKOS - then explore OWL…

 13
Vocabulary management
                            1.  Mint and maintain concepts and terms, in domain-
 Wiki                           expert working groups.
 Vocabulary                 2.  Release final version as a Concept Vocabulary.
                            3.  REUSE terms from published concept vocabularies
 Management                     and ontologies when designing new DwC-A
                1               extensions & controlled value vocabularies.              4
                            4.  Publish at the GBIF Resources Repository.
                            5.  Browse at the GBIF Resources Browser.                    Resources
                                                                                         Repository
                                                          2
  ISOcat                                        Concept
  Vocabulary                                   Vocabulary                                           GBIF      5
  Management                                   (rdf, skos)                                          Resources
                1                                                                                   Browser
                                 proposed
                             template
                          processor
                                                                         DwC-A
                                                                         extensions &
                                                                                             GBIF Vocabularies
Excel, text, etc…                                                        controlled
                                                                                             as a collaborative
Template for            Evaluation of
                        collaborative
                                                              3          vocabularies
                                                                                             management tool for
Vocabularies                                                                                 Darwin Core Archive
                    1   management tools
                        http://kos.gbif.org/                                                 extensions and controlled
                                                              GBIF	
  Vocabularies	
  
                                                                                             vocabularies.
 14
GBIF Vocabulary Server (Drupal)

   Wiki
   Vocabulary
   Management
                                       Concept
                                      Vocabulary                                 Resources
          ISOcat
                                      (rdf, skos)
          Vocabulary
          Management                                                             Repository                GBIF IPT
                       MS Excel
                       Template for
                       Vocabularies
                                                                                                     ?
  Evaluation of various tools for                                 DwC-A
                                                                  extensions &                             Scratchpads
  collaborative management of
                                                                  controlled
   concept vocabularies (RDF).
                                                                  vocabularies




GBIF Vocabularies                               GBIF	
  Vocabularies	
  
                                                                                   GBIF Vocab Server is based on
  as a collaborative                                                               Drupal 6 / Scratchpads (v1)
                                      Darwin Core Archive
management tool for                   extensions and controlled
Darwin Core Archive                   value vocabularies                            --> Drupal 7/Scratchpads2
     extensions and                                                                 --> Drupal 8 ?
    controlled value
                                                                                   Integration with Scratchpads2?
       vocabularies.
                                                                                   Integration with the NPT?
  15
Semantic wiki forum for terms

 Wiki
 Vocabulary
 Management
                                     Concept
                                    Vocabulary
        ISOcat
        Vocabulary
                                    (rdf, skos)
                                                                       Resources
        Management

                     MS Excel
                                                                       Repository   GBIF IPT
                     Template for
                     Vocabularies




Evaluation of various tools for
                                                           DwC-A
collaborative management of                                                         Scratchpads
 concept vocabularies (RDF).                            extensions &
                                                         controlled
                                                        vocabularies

                                                  ?

                                                  Wiki forum for terms as an
                                                  open community platform for
                     Wiki Forum                   description and maintenance
                     for Terms                    of existing terms.

                                                  Replacement tool also for the
                                                  GBIF Vocabulary Server?
16
GBIF Term browser

 Wiki
 Vocabulary
 Management
                                         Concept
                                                                     Concept vocabularies
                                        Vocabulary
        ISOcat
        Vocabulary
                                        (rdf, skos)
                                                        Resources    stored/deposited at
        Management                                                   http://rs.gbif.org/terms/
                     MS Excel
                                                        Repository
                     Template for
                     Vocabularies




Evaluation of various tools for
collaborative management of
 concept vocabularies (RDF).




            The GBIF Term Browser
           allows a user to browse for
         terms defined in widely used
        concept vocabularies such as
           Darwin Core, Dublin Core,
            FOAF, etc., including where
                        available, translations.
              http://kos.gbif.org/termbrowser/


17
Biodiversity ontology management

                  REUSE terms from
   Concept        RDF vocabularies   Ontologies
  Vocabulary                          (rdf, owl)
  (rdf, skos)




 Evaluation of                         Evaluation of
  tools for the                         biodiversity
development                                ontology
of biodiversity                         repository
   ontologies.                            solutions.
                  Wiki tool inc.                       Resources
       1                                           2
                  Ontology                             Repository
                  Management ??                        (incl. ontologies?)

18
BioPortal ontology repository
Proposal: establish a biodiversity “slice” at the NCBO BioPortal.
•     Loading biodiversity ontologies into the NCBO BioPortal promotes
      mapping (and reuse of terms) between bio-medical and biodiversity
      ontologies.
•     An instance of the BioPortal software for biodiversity requires long-term
      obligations to host and maintain the resource – does e.g. GBIF have the
      resources to offer to host a BioPortal instance?




                                        h=p://bioportal.bioontology.org/projects/168	
  	
  




 19
GBIF KOS resources
 Concept vocabularies (skos:conceptSchema, RDF)
 •  Darwin Core, Darwin Core “extensions”, NCD, GNA,
    Audubon Core (and other vocabularies of concepts).

              as a basis and foundation for


 Software application schema (XML, XML schema)
 •  Darwin Core Archive (DwC-A) extensions and
    controlled value vocabularies.
 •  Resources such as the DwC-A extensions and
    controlled value vocabularies REUSE terms (URI)
    from a vocabulary of terms.

20
Biodiversity KOS (based on Darwin Core)
Darwin Core (DwC) is a flat list of terms, expressed using RDF.

     à DwC “extensions” (flat vocabularies for declaration of concepts).
     à Reuse concepts from other vocabularies whenever possible.



Darwin Core Archive (DwC-A) has a star schema model.

•      DwC-A core(s), extensions and controlled value vocabularies
        •    declared as XML lists of terms.
•      DwC-A resources should REUSE terms from Darwin Core and other flat
       concept vocabularies.
        •    New DwC-A core types (data types), eg. sample? Formalize class
             entities (ontology). [Current types: Taxon & Occurrence]

à  Formalize a governance structure for maintaining KOS resources
    based on the principles established for Darwin Core (towards TDWG
    VoMaG).

 21
Darwin Core Archive (DwC-A)
v    DwC-A publish DwC records including terms
      from DwC-A extensions.
v    Simple text based format.
v    Zipped single file archive.




                  Germplasm.txt




22
Darwin Core Archive extension (XML term list)




  23                   http://rs.gbif.org/sandbox/extension/audubon.xml
Concept vocabulary (RDF/SKOS)




                                                                  In progress:
                                                                  XSLT -> HTML for
                                                                  human readable
                                                                  version.




24          http://rs.gbif.org/terms/geotime/geotimeConcept.rdf
GBIF Vocabulary Server
                                     The GBIF Vocabulary
                                     Server can assist a
                                     user to create and
                                     manage DwC-A
                                     extensions or
                                     controlled value
                                     vocabularies.

                                     However, it is not
                                     designed to create
                                     RDF/SKOS concept
                                     vocabulary resources
                                     with reusable
                                     concepts.

                    edit interface   It can export XML, but
                                     not RDF.

                                     It is based on
     XML export                      Scratchpads (v1), aka.
                                     Drupal v 6.


25
Global Names Architecture (GNA)




Many of the GNA term URI identifiers does
not resolve (404 not found).

The rowType identifiers simply resolve to
the software application schema (to the
DwC-A extension).

We propose to formalize the GNA concept
declarations using RDF/SKOS for
improved re-usability of the GNA terms
and concepts.


26
Global Names Architecture (GNA)

                                                                                      RDF/SKOS	
  	
  


XML	
  




          The Global Names Architecture (GNA) terms were originally simply declared
          by the DwC-A extension. We propose to formalize the GNA concept
 27       declarations using RDF/SKOS for improved re-usability of the GNA terms.
Global Names Architecture (GNA)


                                                                          RDF/SKOS	
  




        We propose to formalize the GNA concept declarations using RDF/
        SKOS for improved re-usability of the GNA terms.
28
Darwin Core Archive extensions
     •    Global Names Architecture (GNA)
     •    Audubon Core (multimedia)
     •    Invasive species (GISIN)
     •    Genetic Resources (Germplasm)
     •    Natural Collections Description (NCD)
     •    Metadata profile (EML)
     •    EOL species profile
     •    Taxonomic Concept Schema (TCS)
     •    Genomics Standards Consortium (GSC)
     •    Meta-genomics (?)
     •    ABCD (?)
     •    …

29
Controlled value vocabularies
 •  Geological time periods
      •  chronostratigraphy
      •  magnetostratigraphy
 •  Species interactions
      •  saproxylic interactions
      •  pollinators
 •    Country codes
 •    Language
 •    Basis of record
 •    Taxonomic rank
 •    Nomenclatural status
 •    Life form
 •    Life stage
 •    …
30
a	
  proposed	
  workflow	
  /	
  brainstorming	
  
Versioning	
  resources
                      	
  



        Move outdated vocabularies to a
        separated folder named “deprecated”? No
        versions?

        Will IPT be aware of this folder?

        Note that previous DwC-A datasets could
        be mapped to deprecated vocabulary
        resources…!
Versioning	
  resources
                      	
  




       Version the DwC-A vocabularies and extensions
       using a [_DATE] postfix.

       Could IPT be made aware of this postfix?

       Note that previous DwC-A datasets could be
       mapped to outdated vocabulary resources…!
Versioning	
  RDF	
  vocabularies
                                	
  




              Move outdated vocabularies to a
              subfolder named “archive/[DATE]”?

              Same versioning model for extensions
              and vocabularies…?
Versioning	
  RDF	
  vocabularies
                                   	
  




Deprecated and outdated vocabularies and DwC-A resources could
declare their status, eg. using dcterms:isReplacedBy…?

Drawback: the XML document is required to be accessed and parsed to
read resource status.
Versioning	
  vocabulary	
  resources
                                    	
  

•  Separated folder named “deprecated”?

•  Postfix using [_DATE]?

•  Subfolder named “archive/[DATE]”?

•  dcterms:isReplacedBy

•  Other ideas, solutions?
a	
  proposed	
  workflow	
  
TranslaTon	
  of	
  vocabulary	
  term	
  descripTons
                                                          	
  




                                     Expert working groups or a
                                     collaborative expert
                                     community develop new
                                     translations or refine previous
                                     translations.                                The expert group
     Export working file
                                                                                  provides their output as
     format from the SKOS
                                                                                  a CSV file, XML data or
     file (RDF/SKOS à
                                                                                  as a SKOS/RDF
     CSV).
                                                                                  resource.



 Archive (SKOS/RDF)                    Term translations
 [DATE]/dwc_translations.rdf                                           Translations for a given
                                       (SKOS/RDF)                      vocabulary of terms are
                                       dwc_translations.rdf            maintained and published as a
                                                                       SKOS/RDF file at the GBIF
Archive the translations each time                                     Resources Repository
the “active” SKOS file is updated.                                     (http://rs.gbif.org/terms/).
Example: master SKOS/RDF resource


en   [
es
     [
zh   [
ja   [




         http://rs.gbif.org/terms/dwc/dwc_translations.rdf
Workflow	
  for	
  term	
  translaTon	
  
                                                                                       dwc_translations_de.csv
                                                                                       dwc_translations_es.csv
                                                                                       dwc_translations_fr.csv
                                                                                       dwc_translations_jp.csv
                                                           XSLT	
  
                                                                                       dwc_translations_ru.csv
                                                                                       dwc_translations_zh_Hans.csv
                                                                                       …
                                                                                                                                expert group
  Term translations
  (SKOS/RDF)                                            XSLT split
  dwc_translations.rdf                                  and merge
                                                          cycle

                                                                                       dwc_translations_de.csv
                                                                                       dwc_translations_es.csv
                                                                                       dwc_translations_fr.csv (*)
                                                          XSLT	
                       dwc_translations_jp.csv
                                                                                       dwc_translations_ru.csv
                                                                                       dwc_translations_zh_Hans.csv
                                                                                       …                                      dwc_translations_fr.csv (*)
                                                                                       dwc_translations_pt.csv (**)                   updated



Adding new term translations or updating previous term translations always
starts and ends with the “active” SKOS/RDF resource for translations.
(*) Updated CSV files with translations simply replace extracted previous translations – in the XSLT split and merge cycle.
(**) Adding translations to a new language simply by adding the CSV resource into the XSLT cycle.
New data types?

Genomic level observations
Ecological measurements
associated with observations

- complement, not duplicate work    A roa
                                          dmap
                                   deve
- GBIF as premier gateway to            loped
                                   Q1 20      by
 discovery, access                       13
                                      - gen
                                            o
                                     - eco mic data
                                          logica
                                                 l data
Metadata
Essential for discovery and
access to new data types
The GBIF metadata catalogue
system allows interoperability
across distributed metadata
repositories
        http://metadata.gbif.org

The challenge ahead ...
  populating the catalogue
  with high quality, complete
  metadata
GBIF KOS work-program
Some	
  suggested	
  next	
  steps	
  
•     GBIF	
  Resources	
  Repository	
  (h=p://rs.gbif.org/)	
  
        •  Further	
  development	
  of	
  new	
  DwC-­‐A	
  extensions	
  and	
  controlled	
  value	
  vocabularies.	
  
        •  Workflow	
  for	
  the	
  translaTon	
  of	
  term	
  descripTons.	
  
•     ConTnue	
  the	
  evaluaTon	
  of	
  collaboraTve	
  tools	
  for	
  management	
  of	
  flat	
  
      vocabularies	
  of	
  terms	
  (RDF/SKOS).	
  
        •  SemanTc	
  Wiki,	
  ISOcat,	
  Protégé	
  (web-­‐protégé),	
  …	
  
•     New	
  semanTc	
  Wiki	
  for	
  descripTon	
  of	
  terms	
  /	
  glossary	
  of	
  terms	
  /	
  community-­‐
      driven	
  discussion	
  forum	
  (with	
  JKI,	
  Gregor	
  Hagedorn).	
  
        •  Discussion,	
  discovery	
  and	
  REUSE	
  of	
  exisTng	
  terms.	
  
•     NCBO	
  BioPortal	
  as	
  a	
  repository	
  for	
  biodiversity	
  ontologies.	
  
•     Will	
  GBIF	
  contribute	
  to	
  mint	
  new	
  biodiversity	
  ontologies?	
  
        •    BFO	
  based	
  OWL	
  version	
  of	
  Darwin	
  Core…?	
  

•     KOS	
  governance	
  structure	
  developed	
  and	
  formalized	
  by	
  the	
  (TDWG)	
  
      Vocabulary	
  Management	
  Task	
  Group	
  (VoMaG).	
  
•     Roadmap	
  for	
  KOS	
  into	
  the	
  GBIF	
  infrastructure,	
  portal,	
  …!	
  

 43
Furthermore,
     I think that
     we need
     persistent
     identifiers!




           Cato the Elder ended all his speeches in
                the senate of Rome with: "Ceterum
                  autem censeo Carthaginem esse
               delendam" (English: "Furthermore, I
               think Carthage must be destroyed").




44

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Knowledge Organization System (KOS) for biodiversity information resources, GBIF KOS work program (Dag and Eamonn, 2012).

  • 1.     Knowledge Organization System for GBIF Virtual Biodiversity Research and Access Network for Taxonomy (ViBRANT) Dag Endresen Knowledge Systems Engineer Éamonn Ó Tuama Senior Programme Officer, Inventory, Discovery, Access (IDA) Global Biodiversity Information Facility (GBIF) 31 August 2012
  • 2. Enabling interoperability for the GBIF network and beyond GEO BON, “The ability of two or more systems or IPBE S components to exchange information and to use the information that has been exchanged” (ref: IEEE Standard Computer Dictionary: Compilation of IEEE Standard Computer Glossaries, ISBN:155937079) Key requirement: Common exchange standards and protocols for biodiversity data … necessitate agreement on use of common vocabularies for the classes of objects and their properties Knowledge Organisation Systems (KOS) - can help us manage our vocabularies
  • 3. Knowledge Organisation Systems ... to manage the vocabularies used for sharing biodiversity information. - Term lists: glossaries, dictionaries, gazetteers - Classifications / categorisations: taxonomies e.g., Dewey Decimal Classification - Relationships: thesauri, ontologies simple relationships a model of a domain
  • 4. Darwin Core – a glossary of terms higherClassification coordinatePosition specificEpithet geodeticDatum collectionCode taxonConceptID taxonRank collectionCode: The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived. Examples: "Mammals", "Hildebrandt", "eBird".
  • 5. AgroVoc vocabulary – a thesaurus bt Resources nt Natural resources nt Biological resources nt Genetic resources nt Germplasm uf Genetic material uf Germplasm resources rt Protoplasm bt = broader term nt = narrower term rt Genes uf = used for rt Gene pools rt = related term rt Biodiversity rt Germplasm collections rt Gametes http://aims.fao.org/standards/agrovoc/functionalities/hierarchy
  • 6. Ontology – a model of a domain collectors take samples inverseOf samples are taken by collectors William Jefferson Clinton NHM, Los Angeles County sameAs differentFrom Bill Clinton NHM, London transitiveProperty A hasAncestor B B hasAncestor C hasAncestor Clinton image source: http://www.whitehouse.gov/sites/default/files/first- family/masthead_image/42bc_header_sm.jpg?1250887359 ontologies = computable dictionaries
  • 7. Term  versus  Concept   “The SKOS (simple knowledge organization system) format is designed to present KOS data in a format that is suitable for machine inferencing and particularly for use in the Semantic Web (….) The model [ISO 25964] is based on the understanding that thesauri show the relationships between concepts – units of thought – and distinguishes these from the terms that are used to label these concepts. These terms may be in one or more languages, and one term per language is chosen as a preferred term for each concept. One or more additional terms for the same concept may be recorded in the thesaurus as non-preferred terms.” Will, L. (2012). The ISO 25964 Data Model for the Structure of an Information Retrieval Thesaurus. Bulletin of the American Society for Information Science and Technology 38(4): 48-51. Dextre Clarke, S.G. and L. Zeng (2012). From ISO 2788 to ISO 25964: the evolution of thesaurus Standards towards Interoperability and data modeling. ISQ Information Standards Quarterly 24(1): 20-26.
  • 8. Knowledge Organisation Systems Key requirement: a platform to support the development, maintenance and governance of vocabularies for the biodiversity community - New dedicated position at GBIF funded through KOS activi external projects (ViBRANT, i4Life) in GB ties IF wo progr rk - Review recommendations in KOS task group amm report and develop implementation roadmap e - Review GBIF Vocabularies Service and develop vocabulary management system -  Engage with wider community: -  participation in Dublin Core workshop, Sept 2011 -  KOS symposium at TDWG 2011 Conf, Oct 2011 -  TDWG Vocabulary Management Task Group, 2012
  • 9. ViBRANT: Task 4.1 Ontology platform (GBIF, JKI) Description of work: •  “[F]lexible, user-friendly ontology management environment, enabling users to create, define, extent and share their own terms and concepts where needed, providing options for discussions and annotation, while supporting re-use of terms from standardized ontologies wherever possible”. •  Extent the functionalities of existing vocabulary services (like GBIF). •  Collaborative community interface for users and user- networks, bottom-up, user-friendly and non-technical. •  Flexibility for biologists to express their knowledge regardless of whether the terminology has been standardized yet or not. Text from the ViBRANT project summary, page 13 (my highlighting). 9
  • 10. ViBRANT WP4: GBIF tasks and deliverables Deliverable  4.2:  Ontology  tools:     •  “Develop  the  GBIF  ontology  tool  and   produce  an  equivalent  tool  based  on  a   seman<c  wiki.  Deliver  a  single  user   interface  for  ontology  crea<on  and   edi<ng  based  on  user-­‐acceptance  of  the   alterna<ve  technologies.”   Text from the ViBRANT project summary, page 14 (my highlighting). 10
  • 11. Governance structure (TDWG VoMaG) h=p://community.gbif.org/pg/groups/21382/     11
  • 12. Why use a flat vocabulary ? •  Maximize the reuse of terms, focus on the definition and labels for basic terms. •  Low threshold for non-technical biologists and biodiversity domain experts to access terms and contribute (compared to richer ontologies). •  Preferred technology: RDF (resource description framework) and SKOS (simple knowledge organization system). •  Construction and maintenance of OWL ontologies are demanding in respect to expertise, effort and costs. •  Maintaining SKOS vocabularies are less demanding. •  RDF resources are designed to be easily extended. •  Ontologies (OWL) can be based on (extend) terms declared by a RDF/SKOS vocabulary. •  SKOS became a W3C recommendation in 2009. 12
  • 13. Why use OWL (web ontology language) ? •  OWL DL supports machine reasoning through machine accessible formal semantics. •  OWL provides by default an URI as identifier for classes, properties, relations and instances. •  E.g. OBO target practical solutions in the biomedical / biology domain, while OWL is more generic and provide cross-domain interoperability. •  OWL 1.0 became a W3C recommendation in 2004, •  OWL 2.0 in 2009. •  http://www.w3.org/2007/OWL/ •  Recommendation: •  REUSE terms declared by flat vocabularies… •  Start with SKOS - then explore OWL… 13
  • 14. Vocabulary management 1.  Mint and maintain concepts and terms, in domain- Wiki expert working groups. Vocabulary 2.  Release final version as a Concept Vocabulary. 3.  REUSE terms from published concept vocabularies Management and ontologies when designing new DwC-A 1 extensions & controlled value vocabularies. 4 4.  Publish at the GBIF Resources Repository. 5.  Browse at the GBIF Resources Browser. Resources Repository 2 ISOcat Concept Vocabulary Vocabulary GBIF 5 Management (rdf, skos) Resources 1 Browser proposed template processor DwC-A extensions & GBIF Vocabularies Excel, text, etc… controlled as a collaborative Template for Evaluation of collaborative 3 vocabularies management tool for Vocabularies Darwin Core Archive 1 management tools http://kos.gbif.org/ extensions and controlled GBIF  Vocabularies   vocabularies. 14
  • 15. GBIF Vocabulary Server (Drupal) Wiki Vocabulary Management Concept Vocabulary Resources ISOcat (rdf, skos) Vocabulary Management Repository GBIF IPT MS Excel Template for Vocabularies ? Evaluation of various tools for DwC-A extensions & Scratchpads collaborative management of controlled concept vocabularies (RDF). vocabularies GBIF Vocabularies GBIF  Vocabularies   GBIF Vocab Server is based on as a collaborative Drupal 6 / Scratchpads (v1) Darwin Core Archive management tool for extensions and controlled Darwin Core Archive value vocabularies --> Drupal 7/Scratchpads2 extensions and --> Drupal 8 ? controlled value Integration with Scratchpads2? vocabularies. Integration with the NPT? 15
  • 16. Semantic wiki forum for terms Wiki Vocabulary Management Concept Vocabulary ISOcat Vocabulary (rdf, skos) Resources Management MS Excel Repository GBIF IPT Template for Vocabularies Evaluation of various tools for DwC-A collaborative management of Scratchpads concept vocabularies (RDF). extensions & controlled vocabularies ? Wiki forum for terms as an open community platform for Wiki Forum description and maintenance for Terms of existing terms. Replacement tool also for the GBIF Vocabulary Server? 16
  • 17. GBIF Term browser Wiki Vocabulary Management Concept Concept vocabularies Vocabulary ISOcat Vocabulary (rdf, skos) Resources stored/deposited at Management http://rs.gbif.org/terms/ MS Excel Repository Template for Vocabularies Evaluation of various tools for collaborative management of concept vocabularies (RDF). The GBIF Term Browser allows a user to browse for terms defined in widely used concept vocabularies such as Darwin Core, Dublin Core, FOAF, etc., including where available, translations. http://kos.gbif.org/termbrowser/ 17
  • 18. Biodiversity ontology management REUSE terms from Concept RDF vocabularies Ontologies Vocabulary (rdf, owl) (rdf, skos) Evaluation of Evaluation of tools for the biodiversity development ontology of biodiversity repository ontologies. solutions. Wiki tool inc. Resources 1 2 Ontology Repository Management ?? (incl. ontologies?) 18
  • 19. BioPortal ontology repository Proposal: establish a biodiversity “slice” at the NCBO BioPortal. •  Loading biodiversity ontologies into the NCBO BioPortal promotes mapping (and reuse of terms) between bio-medical and biodiversity ontologies. •  An instance of the BioPortal software for biodiversity requires long-term obligations to host and maintain the resource – does e.g. GBIF have the resources to offer to host a BioPortal instance? h=p://bioportal.bioontology.org/projects/168     19
  • 20. GBIF KOS resources Concept vocabularies (skos:conceptSchema, RDF) •  Darwin Core, Darwin Core “extensions”, NCD, GNA, Audubon Core (and other vocabularies of concepts). as a basis and foundation for Software application schema (XML, XML schema) •  Darwin Core Archive (DwC-A) extensions and controlled value vocabularies. •  Resources such as the DwC-A extensions and controlled value vocabularies REUSE terms (URI) from a vocabulary of terms. 20
  • 21. Biodiversity KOS (based on Darwin Core) Darwin Core (DwC) is a flat list of terms, expressed using RDF. à DwC “extensions” (flat vocabularies for declaration of concepts). à Reuse concepts from other vocabularies whenever possible. Darwin Core Archive (DwC-A) has a star schema model. •  DwC-A core(s), extensions and controlled value vocabularies •  declared as XML lists of terms. •  DwC-A resources should REUSE terms from Darwin Core and other flat concept vocabularies. •  New DwC-A core types (data types), eg. sample? Formalize class entities (ontology). [Current types: Taxon & Occurrence] à  Formalize a governance structure for maintaining KOS resources based on the principles established for Darwin Core (towards TDWG VoMaG). 21
  • 22. Darwin Core Archive (DwC-A) v  DwC-A publish DwC records including terms from DwC-A extensions. v  Simple text based format. v  Zipped single file archive. Germplasm.txt 22
  • 23. Darwin Core Archive extension (XML term list) 23 http://rs.gbif.org/sandbox/extension/audubon.xml
  • 24. Concept vocabulary (RDF/SKOS) In progress: XSLT -> HTML for human readable version. 24 http://rs.gbif.org/terms/geotime/geotimeConcept.rdf
  • 25. GBIF Vocabulary Server The GBIF Vocabulary Server can assist a user to create and manage DwC-A extensions or controlled value vocabularies. However, it is not designed to create RDF/SKOS concept vocabulary resources with reusable concepts. edit interface It can export XML, but not RDF. It is based on XML export Scratchpads (v1), aka. Drupal v 6. 25
  • 26. Global Names Architecture (GNA) Many of the GNA term URI identifiers does not resolve (404 not found). The rowType identifiers simply resolve to the software application schema (to the DwC-A extension). We propose to formalize the GNA concept declarations using RDF/SKOS for improved re-usability of the GNA terms and concepts. 26
  • 27. Global Names Architecture (GNA) RDF/SKOS     XML   The Global Names Architecture (GNA) terms were originally simply declared by the DwC-A extension. We propose to formalize the GNA concept 27 declarations using RDF/SKOS for improved re-usability of the GNA terms.
  • 28. Global Names Architecture (GNA) RDF/SKOS   We propose to formalize the GNA concept declarations using RDF/ SKOS for improved re-usability of the GNA terms. 28
  • 29. Darwin Core Archive extensions •  Global Names Architecture (GNA) •  Audubon Core (multimedia) •  Invasive species (GISIN) •  Genetic Resources (Germplasm) •  Natural Collections Description (NCD) •  Metadata profile (EML) •  EOL species profile •  Taxonomic Concept Schema (TCS) •  Genomics Standards Consortium (GSC) •  Meta-genomics (?) •  ABCD (?) •  … 29
  • 30. Controlled value vocabularies •  Geological time periods •  chronostratigraphy •  magnetostratigraphy •  Species interactions •  saproxylic interactions •  pollinators •  Country codes •  Language •  Basis of record •  Taxonomic rank •  Nomenclatural status •  Life form •  Life stage •  … 30
  • 31. a  proposed  workflow  /  brainstorming  
  • 32. Versioning  resources   Move outdated vocabularies to a separated folder named “deprecated”? No versions? Will IPT be aware of this folder? Note that previous DwC-A datasets could be mapped to deprecated vocabulary resources…!
  • 33. Versioning  resources   Version the DwC-A vocabularies and extensions using a [_DATE] postfix. Could IPT be made aware of this postfix? Note that previous DwC-A datasets could be mapped to outdated vocabulary resources…!
  • 34. Versioning  RDF  vocabularies   Move outdated vocabularies to a subfolder named “archive/[DATE]”? Same versioning model for extensions and vocabularies…?
  • 35. Versioning  RDF  vocabularies   Deprecated and outdated vocabularies and DwC-A resources could declare their status, eg. using dcterms:isReplacedBy…? Drawback: the XML document is required to be accessed and parsed to read resource status.
  • 36. Versioning  vocabulary  resources   •  Separated folder named “deprecated”? •  Postfix using [_DATE]? •  Subfolder named “archive/[DATE]”? •  dcterms:isReplacedBy •  Other ideas, solutions?
  • 38. TranslaTon  of  vocabulary  term  descripTons   Expert working groups or a collaborative expert community develop new translations or refine previous translations. The expert group Export working file provides their output as format from the SKOS a CSV file, XML data or file (RDF/SKOS à as a SKOS/RDF CSV). resource. Archive (SKOS/RDF) Term translations [DATE]/dwc_translations.rdf Translations for a given (SKOS/RDF) vocabulary of terms are dwc_translations.rdf maintained and published as a SKOS/RDF file at the GBIF Archive the translations each time Resources Repository the “active” SKOS file is updated. (http://rs.gbif.org/terms/).
  • 39. Example: master SKOS/RDF resource en [ es [ zh [ ja [ http://rs.gbif.org/terms/dwc/dwc_translations.rdf
  • 40. Workflow  for  term  translaTon   dwc_translations_de.csv dwc_translations_es.csv dwc_translations_fr.csv dwc_translations_jp.csv XSLT   dwc_translations_ru.csv dwc_translations_zh_Hans.csv … expert group Term translations (SKOS/RDF) XSLT split dwc_translations.rdf and merge cycle dwc_translations_de.csv dwc_translations_es.csv dwc_translations_fr.csv (*) XSLT   dwc_translations_jp.csv dwc_translations_ru.csv dwc_translations_zh_Hans.csv … dwc_translations_fr.csv (*) dwc_translations_pt.csv (**) updated Adding new term translations or updating previous term translations always starts and ends with the “active” SKOS/RDF resource for translations. (*) Updated CSV files with translations simply replace extracted previous translations – in the XSLT split and merge cycle. (**) Adding translations to a new language simply by adding the CSV resource into the XSLT cycle.
  • 41. New data types? Genomic level observations Ecological measurements associated with observations - complement, not duplicate work A roa dmap deve - GBIF as premier gateway to loped Q1 20 by discovery, access 13 - gen o - eco mic data logica l data
  • 42. Metadata Essential for discovery and access to new data types The GBIF metadata catalogue system allows interoperability across distributed metadata repositories http://metadata.gbif.org The challenge ahead ... populating the catalogue with high quality, complete metadata
  • 43. GBIF KOS work-program Some  suggested  next  steps   •  GBIF  Resources  Repository  (h=p://rs.gbif.org/)   •  Further  development  of  new  DwC-­‐A  extensions  and  controlled  value  vocabularies.   •  Workflow  for  the  translaTon  of  term  descripTons.   •  ConTnue  the  evaluaTon  of  collaboraTve  tools  for  management  of  flat   vocabularies  of  terms  (RDF/SKOS).   •  SemanTc  Wiki,  ISOcat,  Protégé  (web-­‐protégé),  …   •  New  semanTc  Wiki  for  descripTon  of  terms  /  glossary  of  terms  /  community-­‐ driven  discussion  forum  (with  JKI,  Gregor  Hagedorn).   •  Discussion,  discovery  and  REUSE  of  exisTng  terms.   •  NCBO  BioPortal  as  a  repository  for  biodiversity  ontologies.   •  Will  GBIF  contribute  to  mint  new  biodiversity  ontologies?   •  BFO  based  OWL  version  of  Darwin  Core…?   •  KOS  governance  structure  developed  and  formalized  by  the  (TDWG)   Vocabulary  Management  Task  Group  (VoMaG).   •  Roadmap  for  KOS  into  the  GBIF  infrastructure,  portal,  …!   43
  • 44. Furthermore, I think that we need persistent identifiers! Cato the Elder ended all his speeches in the senate of Rome with: "Ceterum autem censeo Carthaginem esse delendam" (English: "Furthermore, I think Carthage must be destroyed"). 44