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Catalog of Fishes 2.0

Catalog of Fishes 2.0

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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