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An Introduction to Specify 6 for Entomology Collections

An Introduction to Specify 6 for Entomology Collections. Jennifer Thomas Division of Entomology University of Kansas. Specify 6 . Over 10 major releases in 17 years with extensive upgrades and new features. Supported by the U.S. National Science Foundation since 1987.

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An Introduction to Specify 6 for Entomology Collections

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  1. An Introduction to Specify 6 for Entomology Collections Jennifer Thomas Division of Entomology University of Kansas

  2. Specify 6 • Over 10 major releases in 17 years with extensive upgrades and new features. • Supported by the U.S. National Science Foundation since 1987. • Staff of 8 people attending to programming, development, conversions, web, DiGIR and user issues.

  3. Norway Denmark Germany (6) Canada (2) Poland UK (2) Hungary Portugal Spain Mexico India Guatemala (2) Venezuela Colombia (3) Malaysia Ecuador Kenya Peru Brazil (9) New Zealand Chile (3) South Africa (3) Australia (6) • Representation of all Natural History disciplines • Over 375 collections in 26 countries • Over 140 US institutions in 43 states • Over 10 million specimens cataloged • Increasing all the time

  4. Overview • Brief History of the SEMC database • Capturing historical specimen data with associated label image • Proactive capture – straight from the field • Specify 6 Georeferencing tools • Sharing data • Specify 6 museum management tools • Acknowledgements

  5. A Brief History of our database • Started in FoxPro – 1998 • Migrated to Specify – NSF North American/Mexican bee project • Duplication of collecting events, localities, collectors • 2008 – EPSCoR funds to capture SEMC Orthoptera • Launched first effort to clean up/standardize the database • Smallest Table = Agents (~3000 Collectors/Determiners) • Collection Event table – most duplication here • Solution = Retroactive Collecting Event #s • SK.PadrZ1959.07.23 001 • NSF – A specimen-level database of the world’s bees (Apoidea) at the University of Kansas

  6. It takes a village to raise a collection?

  7. Overview • Brief History of the SEMC database • Capturing historical specimen data with associated label image • Proactive capture – straight from the field • Specify 6 Georeferencing tools • Web-access • Specify 6 museum management tools • The future of Specify 6 for Entomology

  8. Recuration

  9. Retroactive Capture - arrange/barcode • Within each species, specimens are arranged by collecting event: • Collector • Date • Locality • Elevation, host plant, habitat data… • Then barcodes are attached in that order.

  10. Image Capture - file name = collecting event # SK.PadrZ1959.07.23 001

  11. Query – Collecting Events/Attach Image

  12. Retroactive Capture

  13. Overview • Brief History of the SEMC database • Capturing historical specimen data with associated label image • Proactive capture – straight from the field • Specify 6 Georeferencing tools • Web-access • Specify 6 museum management tools • The future of Specify 6 for Entomology

  14. Proactive Capture

  15. Overview • Brief History of the SEMC database • Capturing historical specimen data with associated label image • Proactive capture – straight from the field • Specify 6 Georeferencing tools • Web-access • Specify 6 museum management tools • The future of Specify 6 for Entomology

  16. Georeferencing

  17. Overview • Brief History of the SEMC database • Capturing historical specimen data with associated label image • Proactive capture – straight from the field • Specify 6 Georeferencing tools • Sharing Data • Specify 6 museum management tools • The future of Specify 6 for Entomology

  18. KU Biodiversity Institute choose to leverage the GBIF-developed IPT Ease of mapping Darwin Core concepts Ease of mobilizing data through IPT to GBIF Integrated Publishing Toolkit http://www.gbif.org/informatics/primary-data/publishing/

  19. Specify - DC schema selection Specify - query mapping Specify - export tool Export data from Specify 6

  20. Discover data • Thematic portals • InvertNet • MaNIS: http://www.manisnet.org • HerpNET: http://www.herpnet.org • ORNIS: http://www.ornisnet.org • FishNet2: http://www.fishnet2.net • GBIF data portal • http://portal.gbif.org • Available 4-6 weeks after initial publication

  21. Overview • Brief History of the SEMC database • Capturing historical specimen data with associated label image • Proactive capture – straight from the field • Specify 6 Georeferencing tools • Web-access • Specify 6 museum management tools and security features • Acknowledgements

  22. Specify 6 Museum Management tools

  23. Where to from here? • We’ll continue to work with the Specify team to customize our database. • Functionality to allow all types of barcodes • Batch-editing tools like we had in Specify 5 • Form customizer • Web interface

  24. Acknowledgements • Dr. Michael Engel, Dr. Zack Falin • Our CA’s - Crystal Maier & Mabel Alvarado • Our Undergrads – Erin, Alexa, Shayna, and Dan • The Specify Team – Andy Bentley, Theresa Miller, Tim Noble, Rod Spears, & Jim Beach. • Laura Russell – KU Informatics programmer, and GBIF extraordinaire • NSF DBI – 1057366: A specimen-level database of the world’s bees (Apoidea) at the University of Kansas PI – Dr. Michael Engel

  25. Specify6 • Written in Java • PC, Mac and LINUX • compatible • Database agnostic – MySQL • Open source – all source code available under FOSS (GPL2)

  26. Specify6 • Collections management platform – pluggable components • Multi-collection/discipline capable • 3rd party applications - GEOLocate, Google Earth • Web services and online providers – ITIS, Fishbase, Lifemapper • Strategic Partnerships – Filtered push (Harvard), botanical OCR (Michigan), image bank (MorphBank) and DNA (BCoL) • Staged, frequent releases with added functionality – smart update

  27. Specify6 • Many other systems out there – KeEmu, • Past Perfect, Index Kentukiensis, Collections Space, Mantis, Multi-Mimsyetc. • All have limitations or cost prohibitions for small to medium sized museums • Cost • Flexibility and customization • All disciplines * • Open source – community driven • Wealth of features • Support and longevity

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