An Introduction to Specify 6 for entomology collections

Jennifer Thomas Division of Entomology University of Kansas

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.

Norway Denmark Canada (2)

Germany (6) Poland

UK (2)

Hungary Portugal

Spain

Mexico Guatemala (2) Colombia (3)

Venezuela

India 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

 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

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

 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

 Within each species,

specimens are arranged by collecting event:  Collector  Date  Locality  Elevation, host plant,

habitat data…  Then barcodes are attached in that order.

SK.PadrZ1959.07.23 001

 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

 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

 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

Integrated Publishing Toolkit

KU Biodiversity Institute choose to leverage the GBIF-developed IPT  Ease of mapping Darwin

Core concepts  Ease of mobilizing data through IPT to GBIF

http://www.gbif.org/informatics/primary-data/publishing/

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Specify - DC schema selection

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Specify - query mapping

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Specify - export tool

 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

 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

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

 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

 Written in Java  PC, Mac and LINUX compatible

 Database agnostic – MySQL  Open source – all source code available under FOSS (GPL2)

 Collections management platform – pluggable  

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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

 Many other systems out there – KeEmu, Past Perfect, Index Kentukiensis, Collections Space, Mantis, Multi-Mimsy etc.  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