TDWG VoMaG Vocabulary management workflow, 2013-10-31


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Presentation of the VoMaG Vocabulary management workflow at TDWG 2013 in Firenze, 2013-10-31.

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TDWG VoMaG Vocabulary management workflow, 2013-10-31

  1. 1.     A framework for managing vocabularies Outcomes of the TDWG Vocabulary Management Task Group TDWG 2013 Annual Conference, Florence, Italy Dag Endresen*, Éamonn O Tuama, Gregor Hagedorn and Steve Baskauf * GBIF-Norway, Natural History Museum of the University in Oslo Global Biodiversity Information Facility (GBIF) 31 October 2013
  2. 2. VoMaG  report   Three  main  sec,ons   •  Status  of  the  TDWG  ontology   •  Seman4c  MediaWiki  as  a  development   pla<orm   •  Requirements  for  a  framework  for   managing  vocabularies  
  3. 3. ries ula cab g vo agin /   man 101 /29 view es/ fra n: pag ssio /pg/ scu .org Di gbif ity. un omm ://c h9p for ork mew
  4. 4. Vocabulary  management   • Vocabularies/ontologies  are  one  of   the  three  core  components  in  the   TDWG  technical  architecture.  
  5. 5. Vocabularies/ontologies   • Provide  a  shared  understanding  of   what  we  mean  when  describing   biodiversity  en44es.   • What  kind  of  thing  or  property.   • A  list  of  things  we  as  a  community   can  agree  upon  the  meaning  of.   • “Concept  repository”  with  terms   iden4fied  by  URIs.   TDWG Technical Roadmap 2008. (TDWG TAG, convened by Roger Hyam).
  6. 6. Vocabulary  governance   •  Development,  management  and   governance  remain  a  challenge.   •  Maintenance  requires  efforts.   •  Challenge:  Lack  of  resources  -­‐  No  TDWG   Ontology  coordinator  (since  2007).   •  Experiment:  Possible  as  a  collabora4ve   community  approach  coordinated  using   a  Seman4c  Wiki…???  
  7. 7. Term  Wiki
  8. 8. Concept  vocabularies   •  Collabora4ve  development  of  terms  at:   h[p://  [?  ?]   •  Terms  grouped  into  “concept   vocabularies”  each  controlled  by  a   TDWG  task  group.   •  REUSE  terms  (and  term  URI)  whenever   possible!!  
  9. 9. Data  standards   Important principle: Re-use of terms from standardized terminologies wherever possible. 9 The cartoon is from XKCD: CC-BY-NC
  10. 10. 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 (….) concepts – units of thought – and distinguishes these from the terms that are used to label these concepts. 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. 10
  11. 11. Vocabularies/ontologies   • What  kind  of  thing  or  property   •  Concept  (skos:Concept)   • Reused  as:   •  Class  (rdf:Class)    [?]   •  Property  (rdfs:Property)   •  Controlled  element  values  
  12. 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. 13. Darwin Core – a glossary of terms Wieczorek J, Bloom D, Guralnick R, Blum S, Döring M, De Giovanni R, Robertson T, and Vieglais D (2012) Darwin Core: An Evolving Community-Developed Biodiversity Data Standard. PLoS ONE 7(1): e29715. doi: 10.1371/journal.pone.0029715
  14. 14. Vocabulary  repository   •  Establish  a  repository  for   “concept  vocabularies”.   •  Example  at:          h[p://          [?  ?]   Photo CC-by-3.0 by Hannes Grobe/AWI. Palaeoclimate archives: Core repository of AWI,
  15. 15. Work-flow for Vocabulary management 1.  Mint and maintain concepts and terms, in domain-expert working groups. Using e.g. the as a collaboration platform. 2. Release final version as a Concept Vocabulary. E.g. publish vocabulary at the GBIF or a TDWG Resources Repository. REUSE terms from published concept vocabularies and other ontologies when designing new application schema such as DwC-A controlled term and value vocabularies. Term Wiki For vocabulary development 15 Concept Vocabulary (rdf, skos) Resources Repository
  16. 16. Example: master SKOS/RDF resource en [ es [ zh [ ja [ 16
  17. 17. Biodiversity ontology development Concept Vocabulary (rdf, skos) REUSE terms from concept vocabularies whenever possible. Ontologies (rdf, owl) Biodiversity ontology repository. 17
  18. 18. BioPortal ontology repository A biodiversity “slice” was established at the NCBO BioPortal. •  Loading biodiversity ontologies into the NCBO BioPortal promotes mapping (and reuse of terms) between bio-medical and biodiversity ontologies. h9p:// por 18 tal.bioo ntology .org/on tologie s?filter =BIS  
  19. 19. Agenda   Time   Title/Presenter   09.00  –  09.05   Introduc,on  to  VoMaG   Éamonn  Ó  Tuama         09.05  –  09.20   The  TDWG  Ontologies   Steve  Baskauf       09.20  –  09.35   A  framework  for  managing  vocabularies   Dag  Endresen   09.35  –  09.45   Seman,c  MediaWiki    -­‐  a  community  plaWorm  for  vocabulary   development     Gregor  Hagedorn     09.45  –  09.55   Developing  a  vocabulary:    the  SINP  use  case   Julie  Chataigner  &  Laurent  Poncet   09.55  –  10.05   Modeling  property  values:  Is  SKOS  part  of  the  solu,on  or  part  of  the   problem?       Robert  A.  Morris   10.05  –  10.30   General  discussion