Automation of Natural History Collections and Bioinformatics: Rapid Optical Data Acquisition and Automated Computerization at INHS

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This project will digitize and computerize approximately 489,000 specimens of Collembola (springtails), Thysanoptera (thrips), Phthiraptera (lice), and Psocoptera (book and bark lice) into a rapid data acquisition imaging/database workflow recently developed in the entomology collections at the Illinois Natural History Survey. Digitization and computerization will be achieved by optical scanning of glass slide preparations and collection labels from ethanol-preserved material (vials). Upon batch scanning, programming language scripts will be used to a) automate capture of each collection object image into the database as an individual specimen record; and b) semi-automate data entry into relational database fields. The first pass of semi-automated parsing of specimen data results in an average of 60% of the complete individual record automatically parsed into the database. A second pass using computer scripts and interactive data entry, recovers the remaining collection object data. An important contribution of this proposed natural history collections digitization solution is the implementation of a database/software workflow that allows integration of verbatim label data (imaged) with the traditional specimen-level database. This newly developed imaging/database solution will transform the way, and accurately accelerate the rate, in which invaluable natural history collections are digitized. The workflow will be integrated with the NSF-supported Specify collections management software and be made available for broader use in the natural history collections community. Application of this workflow solution will facilitate complete curation for the groups of INHS insects listed, making available a wealth of critical historical and modern-day collections data to researchers and the public, worldwide. The project will provide training for two graduate students, one database technician, and select undergraduates in biodiversity informatics. Availability of this solution will benefit the greater biological collections community with efforts to rapidly digitize, integrate, and mobilize collections data. This project is part of a 10-year effort to digitize and mobilize the scientific information associated with biological specimens held in U.S. research collections. The images and digitized data from this project will be integrated into the online national resource as outlined in the community strategic plan available at http://digbiocol.files.wordpress.com/2010/05/digistratplanfinaldraft.pdf.