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CAAB and taxon management at CSIRO Marine Research Tony Rees Divisional Data Centre

CAAB and taxon management at CSIRO Marine Research Tony Rees Divisional Data Centre CSIRO Marine Research, Hobart http://www.marine.csiro.au/caab/. Linking taxonomic resources. db A (e.g. field surveys) Taxon 1 ----- Taxon 2 ----- etc. User searches by scientific or other name.

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CAAB and taxon management at CSIRO Marine Research Tony Rees Divisional Data Centre

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  1. CAAB and taxon management at CSIRO Marine Research Tony Rees Divisional Data Centre CSIRO Marine Research, Hobart http://www.marine.csiro.au/caab/

  2. Linking taxonomic resources db A(e.g. field surveys) Taxon 1 ----- Taxon 2 ----- etc. User searches by scientific or other name db query db B (e.g. specimen coll.) Taxon 1 ----- Taxon 2 ----- etc. Master query system db query db query db C (e.g. supporting info) Taxon 1 ----- Taxon 2 ----- etc. Available for any taxon: - scientific name (may or may not be consistent across db’s) - internal ID in database (may or may not be common across db’s) - possibly 1 or more external ID’s Organisation 1 Organisation 2 Organisation 3 ...

  3. Name-based system • Names may vary across db’s (different opinions, old data, typographic errors, variant spellings, authorities present/absent, subgenera present/absent, etc.) • Names may change in future db A(e.g. field surveys) Taxon 1 ----- Taxon 2 ----- etc. db query db B (e.g. specimen coll.) Taxon 1 ----- Taxon 2 ----- etc. Master query system name 1a = name 1b = name 1c etc. db query db query (all possible names) db C (e.g. supporting info) Taxon 1 ----- Taxon 2 ----- etc. (high maintenance overhead at master db level) poss. name 1d not found Organisation 1 Organisation 2 Organisation 3 ...

  4. Example (doughboy scallop) Chlamys asperrimum Chlamys asperrima Chlamys (Mimamachlamys) asperrimum Chlamys (Mimamachlamys) asperrima Mimachlamys asperrimum Mimachlamys asperrima - not really a synonymy, just a partial “potential variants” list; a full list would include versions with/without authors, any other synonyms, “near” matches (possible typographic errors), etc…

  5. Name-based system • Names may vary across db’s (different opinions, old data, typographic errors, variant spellings, authorities present/absent, subgenera present/absent, etc.) • Names may change in future db A(e.g. field surveys) Taxon 1 ----- Taxon 2 ----- etc. db query db B (e.g. specimen coll.) Taxon 1 ----- Taxon 2 ----- etc. Master query system name 1a = name 1b = name 1c etc. db query db query (all possible names) db C (e.g. supporting info) Taxon 1 ----- Taxon 2 ----- etc. (high maintenance overhead at master db level) poss. name 1d not found Organisation 1 Organisation 2 Organisation 3 ...

  6. External ID-based system db A(e.g. field surveys) Taxon 1 ----- (ID1) Taxon 2 ----- (ID2) etc. Master query system name 1 = ID1 etc. db query db B (e.g. specimen coll.) Taxon 1 ----- (ID1) Taxon 2 ----- (ID2) etc. db query (low maintenance overhead at master db level) db query (single ID) db C (e.g. supporting info) Taxon 1 ----- (ID1) Taxon 2 ----- (ID2) etc. • Data searching is name independent (user agencies can follow own wishes re consistency, formats, timing of updates etc.) Organisation 1 Organisation 2 Organisation 3 ...

  7. Essential/desirable properties of external taxon identifiers • Essential • ability to cover all taxonomic groups of interest • ability to cope with numbers of taxa potentially required • translation system (codes:names) readily accessible • codes can be created in realistic time frame for taxa needed • Desirable • systematic/meaningful approach to code allocation (cf. telephone numbering system) - understandable to humans • not too many digits • codes are stable (preferably NOT dependent on genus/species name) • taxon names are reliable (i.e., content is subject to ongoing QC and maintenance as needed) • compatibility/interoperability with emerging global standards

  8. CMR’s “CAAB” system” • able to cover all taxonomic groups • up to 999,999 codes (optionally 3 million) per “major category” (phylum or similar) • web interface for codes/names access • local (i.e. Australian) control of content (rapid data addition possible) • systematic/meaningful approach to code allocation (category number, family number and species/taxon number) • not too many digits (2 digits for category and 6 for family+species) • codes are stable (not dependent on genus/species name) • taxon name maintenance can be devolved to relevant specialists • cross-mapping to ITIS and other codes incorporated in current database structure • possible candidate or model for a national system?

  9. Other CAAB features • searchable by scientific or common name synonyms/variants, as entered in the database (useful as entry point) • comments fields available for external display and/or admin use • holds custom links for database querying at CMR via the web • holds on-line links to other information resources • CAAB administration and data entry can be carried out remotely by relevant persons (uses web access tools and user/domain authentication) • special sections of CAAB are available to deal with family-level groups, other species groupings as needed, and informal/agency-designated taxa

  10. Portion of main “taxon details” table in CAAB

  11. ITIS codes - another option • Pluses... • possibly a global standard in the future • able to cover all taxonomic groups • no limit to number of taxa which can be covered • web interface for codes/names access • not too many digits (typically 5 or 6) • Minuses... • codes are non meaningful (just a number, semi-random allocation) • codes are fixed to genus/species name, however, cross-mapping is maintained within the database for synonyms, where held on the system • would need to investigate how locally supplied content might be able to be added to the master system, in a realistic time frame

  12. Topics arising -for consideration for “Australian virtual museum”... • Names or (name independent) taxon ID’s to be used for database linkages? • If names, is a master list achievable in real time? Who will undertake continuous update required? What performance implications may arise? • If taxon ID’s, what is the best route, e.g…. • ITIS (with upgraded Australian content)? • CAAB or other existing Austr. system (extended)? • A new system designed from the ground up? • If any of the above, what is the best way to manage and resource the process? What time frame is realistic?

  13. Sample scientific name search (NB: also searches synonyms as held in the database)

  14. Sample scientific name search (go to demo if available)

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