Dag Endresen (dendresen@gbif.org)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 (dendresen@gbif.org)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