Transcript 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/

Specify - DC schema selection

Specify - query mapping

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





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