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Establishing a support infrastructure for Knowledge Organisation Systems (KOS) in biodiversity informatics. Eamonn O Tuama, Dag Terje Filip Endresen, and David Remsen (GBIF) Vocabularies and ontologies are types of Knowledge Organisation System (KOS) that range from simple glossaries and dictionaries through classification schemes, taxonomies, thesauri and ontologies [1]. As such, they are an essential foundation for data interoperability within the biodiversity informatics domain. Recent TDWG conferences have acknowledged the need to adopt principles and best practices for developing ontologies and to draw, wherever possible, on available community resources [2]. GBIF also recognises this need by including KOS related activities in the GBIF Strategic Plan 2012-2016 [3] and in its ongoing work programmes. Key activities to date have been the establishment of the prototype GBIF Vocabularies Service [4] and the publication of a white paper Recommendations for the use of Knowledge Organisation Systems by GBIF [5]. The focus of this symposium is on identifying key actors and activities that will enable TDWG, GBIF and related communities of practice to develop a road map on how to engage all players in creating a global infrastructure for the development, maintenance and governance of such vocabularies (the term “vocabularies” is used here in a generic sense to represent the various types of KOS). Several brief presentations will set the background for our discussions. After introducing the broader GBIF context, the recommendations of the GBIF KOS task group and their uptake in the GBIF work programme will be outlined. Two systems for managing vocabularies and ontologies will then be introduced – the GBIF Vocabularies Service [4] and the BioPortal [6]. This will be followed by a summary of the history, management and plans for the TDWG vocabularies which form the foundation for KOS in biodiversity informatics, and conclude with an account of experiences in managing the Darwin Core as an example of a widely used set of terms under active discussion in the community. [1] http://www.clir.org/pubs/reports/pub91/contents.htm [2] http://imsgbif.gbif.org/CMS/DMS_.php?ID=1057 [3] http://links.gbif.org/sp2012_2016.pdf [4] http://vocabularies.gbif.org [5] http://links.gbif.org/gbif_kos_whitepaper_v1.pdf [6] http://bioportal.bioontology.org/
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Dag Endresen ([email protected])Knowledge Systems EngineerGBIF
New Orleans (Louisiana, USA)20 October 2011
Biodiversity Information Standards, TDWGAnnual Meeting 2011, New Orleans
The GBIF KOS Work Program:Prioritized Requirements and Proposed Solutions
Outline
Element vocabularies and value vocabularies
Vocabulary management tools Vocabularies exchange format (SKOS) Vocabulary registry (portal) New data types
Standards
Biodiversity Information Standards (TDWG), Dublin Core Metadata Initiative (DCMI), Genomics Standards Consortium (GSC), etc... provide domain standards. We want to reuse, map and relate terms across these standards.
Why: Gain understanding across domains
Element vocabulary (glossary)
Darwin Core (DwC), Dublin Core (DCMI), Ecological Metadata Language (EML), Gene Ontology (GO), TDWG Ontology, etc... provide definitions for conceptual terms. We want to reuse, map and relate terms from basic vocabularies with concept definitions.
Why: reuse terms and share a common definitions and understanding of biodiversity concepts.
Vocabulary management tools GBIF Vocabularies
Custom Scratchpad Tool (Drupal)
Semantic Wiki (SpeciesID, Key to Nature) Protégé (collaborative Protégé)
SKOSEd plugin, Web-Protégé Top Quadrant EVN (commercial) Pool Party (commercial) ThManager (open source) ISOcat (Clarin, linguistics) iQvoc (open source) TemaTres (open source, Spanish)
GBIF Vocabularieshttp://vocabularies.gbif.org
Collaborative development of community terminology, including biodiversity concept definitions and controlled value lists.
Controlled Vocabularies
The “Vocabularies” are Value Vocabularies (authority files) of accepted values for terms where controlled values are already available - or appropriate to develop.
dwc:basisOfRecordPreservedSpecimenFossilSpecimenLivingSpecimenHumanObservationMachineObservationNomenclaturalChecklistOccurrenceTaxonLocation
dc:TypeCollectionDatasetEventImageInteractiveResourceServiceSoftwareSoundTextPhysicalObjectStillImageMovingImage
gbif:nomenclatural_codeICBNICZNICVCNICNBICNCPBioCode
Why: standardize how biodiversity data is provided when controlled values are appropriate
Controlled Vocabularies
“Extensions” are Element Vocabularies defining new terms organized as extensions to Core Types (dwc: Taxon and dwc: Occurrence).
•Audubon Core (multimedia/images)•DwC-Germplasm (plant genetic resources)•EOL Data Object (species profiles)•GISIN Species Status (invasive species)•…etc
Why: Provide a mechanism for thematic communities to define their own specific terms.
GBIF Vocabularies
Core types – could be more than DwC: Taxon and DwC: Occurrence •habitat, spatial areas, lines, grid, places, images/multimedia, literature, people, institutes, collections, collection specimens, etc…?
“Extensions” = element/attribute vocabulary, definition of terms•Separate the definition of terminology from application models•Is “extensions” the appropriate label?
“Vocabularies” = value vocabulary, authority files•external examples: countries, languages, …•biodiversity domain: taxonRank, basisOfRecord, …
http://vocabularies.gbif.org
GBIF VocabulariesGBIF Vocabularies is hosted by the Scratchpads server in London• Install the GBIF Vocabulary Service in Copenhagen?• Further developments are needed.• Package the Vocabulary Service as an open-source tool?• Develop as Drupal modules, migrate to Drupal 7?
Element vocabularies are not always an “extension” of Darwin Core…?• Add management interface with definitions for new core types?• Rename “Extensions” to “Element-” or ”Attribute Vocabularies”?• Rename “Vocabularies” to “Value Vocabularies” or “Authority files”…?
Export and import of vocabularies to and from other management systems (SKOS, RDF, OWL as vocabulary exchange format?)• SKOS import and export features to be developed?
Improved Human readable interface• Export to HTML/PDF format for human readable documentation of a vocabulary?
Vocabulary Registry/Portal GBIF Vocabulary Registry
Is the present registry sufficient?
GBIF Vocabularies Develop the Scratchpads solution further
as a vocabulary registry?
NCBO BioPortal alternative Start using the NCBO BioPortal software
Why: Support the discovery of biodiversity terminology and standard vocabularies.
GBIF Vocabulary Registry
The official versions of the “vocabularies” and “extensions” for deployment are available from the GBIF Registry (http://rs.gbif.org). They are used from here by the GBIF infrastructure such as the IPT and HIT.
Separate service for discovery – different service from the GBIF Vocabulary site (management ≠ discovery).
GBIF Vocabulary Registry
Promote SKOS as the preferred vocabulary (exchange) format? Gradually replace XML Schema for defining standards?
Why: Promote ease of vocabulary exchange, import and export.
http://rs.gbif.org
Simple Knowledge Organization System (SKOS)
GBIF Vocabulary Registry Add human interface to explore SKOS
documents at the GBIF Registry? OWLDoc (CO-ODE, static HTML) OWL Ontology Browser (CO-ODE, dynamic)
Using the BioPortal Registry
GBIF KOS Task Group:
“GBIF should deploy an instance of the BioPortal platform for biodiversity ontologies as a complement to the GBIF Vocabularies Server.”
Using the BioPortal Registry Include Biodiversity Vocabularies to the
NCBO BioPortal…? Will support the mapping of terms to the
major Genomics Vocabularies.
Establish a “GBIF BioPortal” using the same BioPortal software? Will focus on Biodiversity Community identity
and relevance.
WorkflowDraft vocabulary
Review version
Published version
Approve?
… and other SKOS compliant vocabulary management tools.
-> Uptake by the GBIF infrastructure including the IPT and the data portal.
“In anticipation of the integration and serving of future data types, GBIF will work closely with partners to enable data integration and interoperability across phenotypic, genomic, taxonomic, geospatial and ecosystem domains.”
GBIF Strategic Plan 2012-2016:
“Further activities as part of the Plan will include improving the Data Portal system and expanding the depth and range of data types“
“specimen, observation, descriptive, literature, name/concept, image, character, OGC, etc”
GBIF Strategic Plan 2007-2011:
New Core Types?
DwC: Taxon DwC: Occurrence
Aububon Core (images/multimedia) Invasive Species (invasive in region/country) New Spatial Objects (from point locations to include
polygon, poly-line and grid objects) etc…
Is the general principle on Extension of Core Types also suitable for new data types?
Data typesdwc:identificationIDdwc:dateIdentifieddwc:identifiedBydwc:taxonIDdwc:scientificNameIDdwc:scientificName…
dwc:measurementIDdwc:measurementValuedwc:measurementUnitdwc:measurementDeterminedBy…
dwc:taxonIDdwc:scientificNameIDdwc:scientificNamedwc:taxonConceptIDdwc:kingdomdwc:familydwc:genusdwc:specificEpithet…
dwc:occurrenceIDdwc:basisOfRecorddwc:eventIDdwc:eventDatedwc:locationIDdwc:decimalLongitudedwc:decimalLatitudedwc:taxonIDdwc:scientificNameIDdwc:scientificName…
dc:identifierdc:bibliographicCitationdc:titledc:creatordc:datedc:sourcedc:languagedwc:taxonRemarks…
dc = http://purl.org/dc/terms/dwc = http://rs.tdwg.org/dwc/terms/ gbif = http://rs.gbif.org/terms/1.0/
etc…
dwc:vernacularNamedc:languagedc:temporaldwc:locality…
Star schema
dc = http://purl.org/dc/terms/dwc = http://rs.tdwg.org/dwc/terms/ gbif = http://rs.gbif.org/terms/1.0/ audubon: http://rs.tdwg.org/ac/terms/
Star schema (??)
dc = http://purl.org/dc/terms/dwc = http://rs.tdwg.org/dwc/terms/ gbif = http://rs.gbif.org/terms/1.0/ audubon: http://rs.tdwg.org/ac/terms/
etc…
Dag Endresen ([email protected])Knowledge Systems EngineerGBIF
New Orleans (Louisiana, USA)20 October 2011
Biodiversity Information Standards, TDWGAnnual Meeting 2011, New Orleans
The GBIF KOS Work Program:Prioritized Requirements and Proposed Solutions
