Richard White

Biodiversity Informatics

What is biodiversity informatics?

• The preceding project, among others, shows that the challenges facing biodiversity informatics include not only– Describing the diversity of life at all levels of

organisation, so that biologists can understand, conserve and exploit it,

• But also– Inventing ways to describe the ever-increasing

diversity of information resources and analysis tools available, so that users can find and use them

A challenge to link resources

• It is potentially very difficult to link all these resources together

• Much attention is currently being given to:– Providing unique identifiers for data objects

– Which can return metadata about themselves

– Which can be stitched together into a distributed collaborative information system: see the biodiversity informatics organisations TDWG and GBIF (later)

Biodiversity organisationsExamples include: • Database level: ILDIS (International Legume Database and

Information Service) - www.ildis.org• Data portal level:

– Catalogue of Life - www.sp2000.org

– Encyclopedia of Life – www.eol.org

– GBIF (Global Biodiversity Information Facility) - www.gbif.org

• Standards, etc.: TDWG (Taxonomic Database Working Group) – www.tdwg.org

• International agencies: CBD, CITES, WCMC, etc. ...

• Lots more

Current developments

• Encyclopedia of Life

• Biodiversity Heritage Library

• DNA barcoding

• Persistent identifiers

Encyclopedia of Life

• “A new project to create an online reference source and database for every one of the 1.8 million species that are named and known on this planet”

• http://www.eol.org/

Biodiversity Heritage Library

• Ten major natural history museum libraries, botanical libraries, and research institutions • digitising the published literature of biodiversity held in

their collections• available through a global “biodiversity commons”

• The data can be accessed using Web Services• now online:

• 1,479 titles• 4,607 volumes• 2,017,577 pages

http://biodiversitylibrary.org

DNA barcoding

• “DNA barcoding is a new technique that uses a short DNA sequence from a standardized and agreed-upon position in the genome as a molecular diagnostic for species-level identification”

• “DNA barcode sequences are very short relative to the entire genome and they can be obtained reasonably quickly and cheaply”

• The “Folmer region” at the 5' end of the cytochrome c oxidase subunit 1 mitochondrial region (COI)

DNA barcoding organisations

• Consortium for the Barcode of Life (CBOL)– http://barcoding.si.edu

• Barcode sequences are submitted to GenBank

• Barcode of Life Data Systems (BOLD)– “an online workbench that aids collection, management,

analysis, and use of DNA barcodes”

– http://www.barcodinglife.org

– “as of 28 January 2008, there are 341,825 barcode records from 35,798 species in the Barcode of Life Database”

Persistent identifiers

• GBIF’s “LSID-GUID Task Group”

• Introduction (Riccardi, White & Ó Tuama, 2009): www.tdwg.org/proceedings/article/view/568

• Report: “Adoption of Persistent Identifiers for Biodiversity Informatics”, Cryer, Hyam, Miller, Nicolson, Ó Tuama, Page, Rees, Riccardi, Richards, White, 2009: www2.gbif.org/Persistent-Identifiers.pdf

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