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CAAB - Codes for Australian Aquatic Biota Tony Rees Divisional Data Centre

CAAB - Codes for Australian Aquatic Biota Tony Rees Divisional Data Centre CSIRO Marine Research, Hobart http://www.marine.csiro.au/caab/. CAAB purpose. Use of taxon codes simplifies / standardises data recording and storage

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CAAB - Codes for Australian Aquatic Biota Tony Rees Divisional Data Centre

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  1. CAAB - Codes for Australian Aquatic Biota Tony Rees Divisional Data Centre CSIRO Marine Research, Hobart http://www.marine.csiro.au/caab/

  2. CAAB purpose • Use of taxon codes simplifies / standardises data recording and storage • Decouples maintenance of the stored data from maintenance of taxon names (scientific names or common names) • Taxonomic position (down to family level) can be deduced from the code alone • The encoded taxonomic information can be used for data sorting or simplified retrieval of target data CAAB is not alone - other coding systems are in use elesewhere or available for some groups - e.g. ITIS (+ predecessor NODC codes), CAVS, others CAAB is specifically targeted for marine data users within Australia

  3. CMR and other users CAAB in relation to other taxonomic resources Regional Monographs, Floras, etc. Research publications CAAB database Expert advice Global treatments Local checklists CSIRO survey data • CAAB provides ... • master list of currently endorsed scientific names and taxon codes, for CMR use (and other agencies as requested) • cross-referenced searching by selected alternative scientific names (recent synonyms), previous codes (if any), and common names where available • links to other coding systems • ancillary information, on-line links, etc. for any taxon

  4. CAAB history • Early 1970s -late 1980s: FISHLIST (6-digit codes) • 3-digits for family, 3 digits for species number … e.g. 020004 - Deania quadrispina(longsnout dogfish) - family 020 (Squalidae) • 1990-1995: development of CAAB v.1 - 8-digit codes • prefix “37” added for fish species (e.g. 020004 becomes 37 020004 ) • prefix “00” added for non-fish codes pending systematic recoding • 1998-99: development of CAAB v2 • review and recoding of non-fish taxa from FISHLIST and CAAB v1 • incorporation of more taxa, e.g. marine vertebrates, based on CAVS list and others • new information incorporated for many taxa • new database structure and web access set up

  5. CAAB functions • Primary function: • lookup table (taxon names to codes and vice versa) with variety of search methods • Secondary functions: • storage of additional taxon-related information (e.g. voucher specimen references, photo references, on-line links) - selected attributes available as “taxon report” • translation system (old codes to new codes, other identifiers to CAAB codes) • checklist generator - e.g. by category or family • taxon sorting / grouping mechanism • “tree” or index of taxa which can be used for other purposes in future (entry point to other systems)

  6. Features of CAAB v2 (Sept 1999 onwards) • On-line search of the database via www • search by sci. name (current or past), common name (including alternatives if entered), taxon code • old (superseded) codes redirected to new code if required • www report on any taxon, including on-line links as entered • can generate taxon lists - by family, major category (e.g. fishes, molluscs), or all groups • can search by partial names (e.g. “N. macropterus”) • can search by other organisations’ identifiers, if held in the database (e.g. ABRS codes, ITIS numbers, etc.) • Review latest additions/changes to database • Generate export files (selected data) for upload to other systems

  7. CAAB search interface (ex. 1)

  8. CAAB search interface (ex. 2)

  9. CAAB search interface (ex. 3)

  10. CAAB search interface (ex. 4)

  11. Example CAAB taxon report -user-accessible detailshttp://strait.hba.marine.csiro.au:7272/CAAB/search/caab_search.caab_report?spcode=28786002

  12. CAAB family listing

  13. Data review facility

  14. Data export facility

  15. CAAB present status • Fish species - • c. 4500 fish species presently recognised - includes c. 200 undescribed taxa • maintained independently from “Zoological Catalogue” list, will be checked against the latter when complete • Other vertebrates (mammals, reptiles, aquatic birds) - • taxa included are marine representatives from ABRS and CSIRO (ANWC) lists - c. 260 species • CAVS codes are included as cross reference • Invertebrates - • taxa included are species of commercial importance, plus species from CMR research cruises (I.e., not a comprehensive list) • Other groups - • Marine angiosperms (mangroves, seagrasses) have been compiled from literature sources • Macroalgae, microalgae: yet to be addressed

  16. CAAB future ... • Maintenance - • CSIRO Marine Research will maintain current CAAB content as resources are available, and extend it in accordance with Divisional needs • Development - • Database and www access application are currently “bedding down” - no more development planned at present • Funding may be sought to incorporate/standardise common names for fish species to a more complete level • Funding/IP protocols for incorporating links to CSIRO photographs, distr. maps, etc. -- still to be worked through • Documentation - • Updated report on CAAB structure and content yet to be produced (2000?). No funding at present allocated • Other ... • “Wish lists” from other users ??

  17. Past/current contributiors to CAAB CMR Fish Taxonomy Section: - Design and content of CAAB v1 (with contribution from FRDC) - Maintenance of fish data in CAAB v2 - Design and maintenance of CAAB v2 (database structure and user interfaces) - User administration for CAAB v2 (e.g. controlling access/update privileges, etc.) - Upgrade of old non-fish codes from CAAB v1 - Maintenance of vertebrates section of CAAB v2 from available data (ABRS + other sources) CMR Data Centre: CMR Invertebrates collection manager (CRIMP/MUMEEZ funded): - Extension of CAAB coverage to further invertebrate taxa as needed - Ongoing maintenance of invertebrates section of CAAB

  18. MS Access interface for admin-level review/editing

  19. CMR’s databases and data recording systems CAAB rationale CAAB master database Taxon list Common taxon code (semi-continuous maintenance) Other agency 1database/s Other agency 2database/s • Key features: • code remains constant independent of name changes • master list of names is maintained in a single location • code can be allocated to “taxonomic units” at any level (e.g. undescribed taxa, aggregate taxa, morphotypes) • codes indicate taxonomic affinity of the organism • codes can be sorted numerically so that related taxa are grouped together

  20. Improvements over CAAB v1 ... • Much more sophisticated searching, cross-linkages, etc. • Increased information held on any taxon • Users gain live access to latest information in the database on a “self serve” basis • Facility for incorporation of www links to other documents, sites or systems, as desired • Pre-existing system for invertebrate coding has been completely overhauled and put on “sound” systematic footing • New taxa being added to the system as requirements grow • New data review and data download facility available to specialist users

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