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Catalog of Fishes 2.0

Catalog of Fishes 2.0. Improving user services and preparing for community participation. Principal Collaborators. Stanley Blum William Eschmeyer Carl Ferraris Richard Pyle. History and Status of the Catalog.

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Catalog of Fishes 2.0

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  1. Catalog of Fishes 2.0 Improving user services and preparing for community participation

  2. Principal Collaborators • Stanley Blum • William Eschmeyer • Carl Ferraris • Richard Pyle

  3. History and Status of the Catalog • Initial purpose: to produce a printed catalog: Eschmeyer, W.N., 1998. 3 Volumes, ~1,000 pp. • DB has nearly doubled since printing • 1998: 32 MB • 2006: 58 MB • Queries from external IP addresses • 12/2001: 10,000 queries / month • 06/2006: 260,000 queries / month • Eschmeyer continues to add content

  4. Long-Term Goals & Planning • What do we really want to do with taxonomic data? • Maintenance requires effort • How can this resource be sustained and improved? • Alternative models • Single editor • Multi-editor • Community maintained • Wikipedia

  5. Single Editor Scenarios • Unfunded • Volunteer (more likely = institutional support) • Funded • Staffing models: • Editor only ~60-80% FTE • Editor (25%) and data entry (50%) • Funding • Institutional • Government • Endowment

  6. Wikipedia Model • Institutional host for server (minimal support) • Content by volunteers • Volunteer editor(s) • Volunteer contributors • Quality concerns • Accuracy / correctness • Completeness

  7. Required Elements • Managing entity • Editorial board • Technical board • Institutional commitment to host • Episodic funding to advance technology

  8. Editorial Board • Establish policies based on principles • Facts of publication • opinions & interpretations explicit and attributable • Develop criteria for determining consensus • Single emergent view, but existence of alternatives signaled and only “one click away” • Review • Data model • Interfaces, workflow • Outputs • Engage community • Monitor and assure quality

  9. Technical Board Review: • Technology selection • Data model • Application architecture • Specification of services

  10. Editorial Board • Carl Ferraris – chair • Bruce Collette • Sven Kullander • Keiichi Matsuura • Roberto Reis • Andrew Polaszek • +2 to be appointed

  11. Technical Advisory Board • Richard Pyle – chair • Rainer Froese (FishBase rep.) • Robert Hanner (FishBoL) • Tom Orrell (ITIS, Sp2000 • David Remsen (GBIF, UBIO) • David Vieglais (KU, SEEK) • +2 to be appointed

  12. Goals for CoF 2.0 Preparation • Modernize data model • Apply Life Science Identifiers (LSID); in conjunction with ZooBank • Develop web application for access and maintenance • Develop web services (interoperability) • “Do no harm”

  13. Names and Taxonomic Concepts • Taxonomic Concept Schema (TCS)Taxonomic Databases Working Group (TDWG) • Definitions of taxa • Contents: • types (taxa, specimens) • specimens examined • Circumscription (characters) • Phylocode • Publication reference

  14. CoF: from Names to Concepts • Primary name record: original name, author, date, type desig., type localities, etc. • Add subsequent uses, identified by ref. concept = name according to reference • Not comparable by machine except by contained types (assumed by synonyms)

  15. Parse the Status Records • Status references contain • Treatments by subsequent authors

  16. Parsing Status Records • Status references contain • Treatments by subsequent authors • Normalizing will • Promote consistency in multi-contributor mode • Enable greater variety of views • More efficient workflow • Compare concepts/classfication by relationships taxa/types • Round-trip validation to ensure loss-less conversion

  17. Data Models Current Planned

  18. Improving services • User interface • Better searching and browsing • Multiple ways to view / organize content • Structured downloads (TCS) • Subscriptions based on query or full replication

  19. Facilitating Collaboration • Eliminate duplicate data entry • Make verification and correction integral part of data (metadata) • Queue for entry and proofing • Electronic documents makes this much easier • Explore automated extraction tools • Tools to help authors construct classifications

  20. Motivations • Benefits to end-user / contributor • Self promotion • Better re-use of existing data; better efficiency, fewer errors • Benefits for collaborating databases • Efficiency • Consistency across DBs; interoperability

  21. General Issues • Transforming name-usages to concepts • Annotation framework: queue, action, feedback to originator, credit, lineage/audit trail; not email • Sharing data and LSID policy • New adaptations of protocols; OAI, RSS

  22. Feedback & Collaboration Please let us know if you have similar problems, goals, tools, etc. sblum@calacademy.org deepreef@bishopmuseum.org

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