global biodiversity

GLOBALBIODIVERSITY

INFORMATIONFACILITY

David Remsen

ECAT Program Officer

September 2010

WWW.GBIF.ORG

A Darwin-Core Archive solution to publishing and indexing taxonomic data within the GBIF network

Thanks: Peter Desmet, Canadensys- (graphics)

GBIF - A global discovery point for biodiversity data

GBIF: Extend global discovery to taxonomic data

Enabling global discovery: Objectives

• Develop capacity to document and publish taxonomic data– A simple exchange format– Suite of publication tools

• Promote the publication of taxonomic data in a common format

• Build and maintain an index of published checklists

• Build services on this index that address user needs in the GBIF network

Enabling global discovery: Outcomes

• Embed taxonomy into large-scale biodiversity data/info. management– Improved Interoperability among resources– Improved Precision and Recall within resources

• Increase efficiencies in taxon-related linking, mapping, data-mining, and data management

• Increased recognition of the value and relevance of taxonomy within all biodiversity information interchange (large and small)

Darwin Core Archive

Data Format

Darwin Core

• Ratified in 2009• Significant additions/refinements• Set of terms– http://rs.tdwg.org/dwc/terms/index.htm

• Simple Darwin Core (Subset)• Express as Text– http://

rs.tdwg.org/dwc/terms/guides/text/index.htm

Core components – single file

Taxon

• Classification• Synonymy• Publication Details

• Simple to Export• Simple to Manage• Comma-Separated Values Text File

Extending Darwin Core

Taxon

Types and Specimens

Bibliography

one-to-m

any

one-to-many

• Extensions defined via simple schema• Darwin Core or other terms• Linked to controlled vocabularies• One taxa – many extension records

• Simple to Export• Simple to Manage• Comma-Separated Values Text File

Metafile describes the set

Metafile Core

Describes

Types and Specimens

Bibliography

one-to-m

any

one-to-many

Describes

Describes

Core + Set of Extensions

MetafileTaxa

Types and Specimens

Bibliography

one-to-m

any

one-to-many

VernacularNames

Distribution

one-to-many

one-to-m

any

describes

“GNA Simple Exchange Format”

Metadata documents resource

MetafileTaxa

Types and Specimens

Bibliography

one-to-m

any

one-to-many

VernacularNames

Distribution

one-to-many

one-to-m

any

describes

GBIF EML profile

documents

A Darwin Core Archive

Validator

http://tools.gbif.org/dwca-validator/Status: Under Evaluation

Darwin Core Archive

Publishing Options

Integrated Publishing Toolkit

• Compose EML Metadata

• Connect to database• Upload Data• Transform to DWCA• Publish via GBIF

Status: Stable release – end 2010 http://ipt.gbif.org

Guidelines and Best Practices

• DB Admin skills• Database export• No tools required• Successful pilots• Ireland• NBN UK• Norway• Avian Knowledge

network• IPNI• IRMNG

Status: Drafts for November campaign (see roadmap)

Authoring Descriptor XML

Status: Ready for Review

Metafile

http://tools.gbif.org/dwca-assistant/

Excel Spreadsheet Templates

Status: Ready for Review/Testing

Spreadsheet Processor

http://tools.gbif.org/spreadsheet-processor/Status: Ready for Review

Checklist Bank

Status: Dev version in place. Integration with GBIF data portal 2011

http://ecat-dev.gbif.org/

Roadmap

• Evaluation and testing and refinement Q4 2010

• Consolidate docs and publishing for ver. 1 Simple Exchange Format using DWC-A

• Target current taxonomic data export publishers– Small grants to pilot DWC-A exports

• Seed funds to GBIF Nodes– Publish regional and thematic species checklists– Evaluate 1.0 extensions and vocabularies