Richard White Biodiversity Data

Outline Biodiversity: what is it? – Definitions: is biodiversity: A resource? Something which can be measured? How to measure it – Who is it for? Data providers Researchers Users Biodiversity Informatics – Research into techniques for handling data

Threats to the planet Human activities Legal issues Economics ConservationManagement Exploitation Habitat conservation Species conservation Ecological diversity Species diversity Genetic diversity Ecology Evolution Genetics Molecular biology Genetic resources Information services

Biodiversity data types Kinds of biodiversity information: – Data about areas, habitats, etc. – Data about individual specimens – Data about species Biodiversity data dimensions – Species – Diverse information types Descriptive, geographical, chemical, genomic etc.

Data about areas, habitats, etc. Species lists, for –Conservation –Management –Legal obligations Ecological processes –Modelling ecosystems –Predicting impacts

Information about individual specimens Curatorial data about the management of each specimen Data describing characteristics of the specimen itself (which can also describe an entire species)

Curatorial information Collection event – Date and place of collection – Collector’s name Identifications (determinations) – Species name (see data about individual specimens and species) – Who identified it, date, etc. Management information – Location within the specimen collection (storage) – Treatments given to specimen, etc.

Data about specimens and species curatorial data nomenclatural data descriptive data geographical data, maps images bibliographic data

Data describing specimens and species (1) Genetic diversity –Allele and chromosome frequencies Molecular bioinformatics –Molecular data – enzyme properties, etc. –Molecular sequences – DNA, protein, polysaccharides, etc. “Traditional” data used in taxonomy etc. –See next slide

Data describing specimens and species (2) Nomenclature – accepted name, synonyms Taxonomy – higher taxa Geographical data – distribution (range) Chemical constituents (especially in plants) Behavioural information (animals) Descriptive data –Anatomical and morphological descriptors –Images Bibliographic data (source references, especially for species data)

Geographical data - storage Database may store: –Individual locations of specimens or sightings –Status in an area based on a number of specimens or sightings: (present, absent, introduced, etc.) Locations may be stored as –Area names (languages, synonyms, hierarchies, overlaps) –Grid coordinates (various systems)

Geographical data - use May be used to generate –summary distributions (e.g. for species distribution from specimen data) –Maps (point locations or shaded areas) May be used to allow searching by location or area – user may specify a point or an area name

Descriptive data Should be carefully designed, because it is complex and may be used for many purposes It should be –Structured –Consistently applied It may include data types suitable for statistical and multivariate analysis Special problems exist

Descriptive data Structured, for Querying Classification, phylogenetic analysis Identification Documentation and dissemination

Descriptive data Consistency and comparability: Consistent terminology (c.f. attempts to standardise terms for indexing purposes, as in BioCASE Thesaurus) Same characters for all specimens or taxa Characters precisely defined –Discontinuous - set of character states –Continuous – units, precision

Descriptive data – special problems Variability –specimens within a species –repeated structures within a specimen Character dependence (inapplicable characters) Taxonomic hierarchy issues, e.g. –Is the data for a species in agreement with the data for a genus? –Can the data be stored at the appropriate taxonomic level only?

Images Type –Bitmap files, e.g. JPEG –Vector graphics, e.g. drawings, diagrams Location –In the local database –Elsewhere in a separate image bank The Web makes the latter option easy – just store the URL in the database

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