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Buffington ecn 2012
1. Digitization efforts and products
from the USNM Hymenoptera Unit
Matthew L. Buffington & Michael Gates
Systematic Entomology Lab, ARS-USDA
NMNH, Smithsonian Institution
2. Whole Drawer Imaging: Giga
panning the USNM gall wasps
Type digitization in the
Hymenoptera Unit
3. USNM Hymenoptera Types
Online Database: www.usnmhymtypes.com
7,267 primary types included.
Four images per type,
incl. labels (~3,200)
All types being affixed
with unique matrix code
label.
5. Value Added I
Zoobank: www.zoobank.org
Working with Rich Pyle to assign Life Science
Identifiers to all Hymenoptera type species in
USNM.
Cross check in advance
with Hym. Name Server.
Provide link to LSID on
USNMHymtypes.
6. Value Added II
Global Names Interface for Taxonomic
Editing: www.gnite.org
Name-based cyberinfrastructure for
interconnecting all online information
about any species.
Ultimately, link all
USNMhymtypes
information.
7. Value Added III
CiteBank: www.citebank.org
Our contractor and CiteBankstaff:
Provide links on USNMHymtypes
to each publication (click volume).
Provide link to page on which species
was originally described (click page).
All original citations are/will
be available through BHL
portal.
8. Whole Drawer Imaging: Giga
panning the USNM gall wasps
NMNH Contains ca 35 million specimens, in:
132,354 drawers, stored in 5200 cabinets
Specimen-level databasing limited
How can we quickly ‘digitize’ the collection?
How can we better serve the research community?
“Bugs on pins” Smithsonian Castle project.
9. Whole Drawer Imaging: Giga
panning the USNM gall wasps
Cost-effective way to digitize whole drawers with
200+ megapixel images
High-end setup: $5000 USD; ‘budget’ setup ca.
$2500 USD
Setup: 30 sec; capture: 90 sec; stitching: 90-100
sec. Time to capture: 3.5-4min
Metadata management (e.g. species names)
time-intensive: 5-10 min/drawer
14 min/drawer x 140 drawers = 32.6 hours
21. Any collection curated in drawers can be digitized via the
Gigapan system. In this case, dinosaurs.
22. Future Directions of the Gigapan
Project
Research cameras that are better designed for this
application (e.g. battery compartment on the side;
wireless file transfer)
Determine a better file management system
Determine the best delivery system: will SI agree to have
Gigapan ‘host’ the images?
Metadata management (e.g. species names) time-
intensive: 5-10 min/drawer; can this be improved?
14 min/drawer x 140 drawers = 32.6 hours; can this be
improved?
23. Acknowledgements
SI DigiComm committee, SI Women’s
Committee, SI Collections Care Fund and Alma
Solis (SEL) for helping to finance the
USNMHymTypes and Gigapan projects
Matt Bertone and Andy Deans (NCSU) for
Gigapan inspiration, ideas and hints
Patricia Gentille-Poole (SI Entomology) Gino
Nearns (recent PhD!; our web designer),
Jolearra Tshiteya (SI/RIT imaging intern) and
Yaz Sarraj (SI gigapan intern)
Editor's Notes
We must vet all hym type names to make sure LSIDs are not already extant before proceeding with generating them for all.
GN is the US component of the international Global Names Architecture (GNA). It will become a multi-agent enterprise level names-based cyberinfrastructure that will act primarily behind the scenes, like the Domain Name System (DNS) for the internet, providing quick, effective and persistent services that use scientific names as the key to a virtual layer that interconnects distributed information about any species; indexing, organizing and making data discoverable for reuse. We are also collaborators on GN2 NSF proposal of Pyle, Patterson, Franz to: We will develop stable enterprise level services in six areas: (1) Names discovery and recognition software to index documents, databases, and other electronic sources allowing discovery of and linking to myriad biodiversity resources. (2) Names reconciliation - our solution to the many-names-for-one-taxon problem - and resolution services to returns the current name(s) for taxa. Reconciliation and resolution map alternative names for the same taxa together and keep the infrastructure up to date with current taxonomic knowledge. By standardizing names in multiple data sources, data are interconnectable and can thereby facilitate the transition (translation?) of the long tail of biology to the Big Data world. (3) Improved access to content by expansion of the Global Names Usage Bank (GNUB) indexing environment, its web services, and exposure of its metadata to the Linked Open Data Cloud. (4) Enhancement of ZooBank for nomenclaturalists and extension to non-animals. (5) Increased engagement with taxonomy, integration of synonymy information for reconciliation, and taxonomic concept and classification provenance management. We will offer a registry and clearing house for classifications and add classification integration based on the Euler and CleanTax software. We will expand the data model and GNITE editing environment to cover more classes of annotations of taxa and be more fully interoperable with other taxonomic workbench software. We will integrate Filtered Push logic to improve synchrony among initiatives and to enhance data quality control. (6) Integration of insufficiently named taxa identified in reference to short gene sequences. A final component is our sustainability agenda, through which we will establish GNA as an integral part of an international infrastructure, and will develop mirrors to remove the risk of single-point-of-failure. We will identify elements of our efforts that can be monetized in a not-for-profit enterprise to sustain the core functions.
Had to modifiy our original spreadsheet to make it palatable (EndNote fields/format) to bulk upload by CiteBank. We will need to locate PDFs already avaialable at BHL and can include those pub and page URLs in USNMHymtypes. Those original citations that cannot be located as original scans anywhere online will need to be scanned (by BHL staff on NMNH) and uploaded to BHL.
