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Short Course on Biological Specimen Informatics

posted Aug 15, 2013, 1:05 PM by Katja Seltmann   [ updated Aug 15, 2013, 2:29 PM ]

The Tri-Tropic Database Thematic Collection Network recently finished up an exciting course about present best practices for specimen-level data management. The two-week Short Course on Biological Specimen Informatics (Specimen Short Course; syllabus and more information: tcn.amnh.org/home/specimen-course) was designed as a first introduction to biological informatics with early career graduates students in mind. The Specimen Short Course gathered individuals from 18 different institutions across the United States at the Richard Gilder Graduate School (American Museum of Natural History  - rggs.amnh.org) in order to specifically address research specimen data capture issues through training, from the field to preserved collections. Instructors for the course were staff were Mike Bevins (Information Manager, NYBG), Christine Johnson (TTD co-PI, AMNH), Rob Naczi (TTD  PI, NYBG), Randall Schuh (TTD PI, AMNH), Katja Seltmann (TTD Project Manager, AMNH), Steve Thurston (Image Specialist, AMNH), Melissa Tulig (TTD co-PI, NYBG), and Kim Watson (TTD Project Manager, NYBG).

Unarguably, biological research generates a great deal of specimen level data. These data can be complex and include familiar collection level data (the focus of many broad museum digitization efforts) as well as highly specific data depending on the research question/s. Researchers have the additional need of high accessibility to all of their data, either through bulk download, or by direct database access, in order to perform analysis. The results of early training for students is mutually beneficial, as improved specimen handling techniques facilitates research, and well-managed data according to community standards allows for greater dissemination of the end products. In order to create a workflow that fits their research needs, participants in the Short Course learned about, and worked on, projects with several tools including: Arthropod Easy Capture (sourceforge.net/projects/arthropodeasy), Specify (specifysoftware.org), ScratchPads (scratchpads.eu), SimpleMappr (simplemappr.net) and others. At the same time students gained valuable expertise mapping datasets to DarwinCore, manipulating data with Open Refine (openrefine.org), Excel, and MySQL.

Enabling students to manage research was one aspect of the Specimen Short Course. The second was to place these efforts in the context of the larger biodiversity informatics community. The course involved visiting research areas at the American Museum of Natural History and the New York Botanical Garden, allowing participants to gain a sense of what the various workflows at these institutions are like, as well as the collection requirements for vouchering specimens at the end of a research project. These experiences helped participants develop techniques and collecting protocols that they could use in their own research.

Imaging was another important component discussed as a means of data capture. At the New York Botanical Garden, participants in the course got hands-on experience photographing plant specimens. At AMNH, insect specimens were the focus. Participants got to see how high-quality images of small insects are taken, and visited the museum’s imaging lab to learn about the technology at work there.  They also learned about how images could be incorporated into their databases to strengthen specimen records.

            As the course progressed participants began to plan how they will use databasing techniques and other resources discovered through the Specimen Short Course. Each participant brought some of his or her data to the course and began to develop a workflow that best matches their individual research needs. As a culmination of the course, each participant delivered a presentation on how they will continue to incorporate the techniques they had learned into their own research.

            By the end of the course, each participant had gained not only a better understanding of specimen informatics techniques, but also a sense of how they could apply these techniques to their own research. The goal of the course was to train students in present best practices for specimen-level data management from the field to preserved collections, and how a specimen management plan can facilitate addressing research questions. The experiences they gained through the course will aid them in producing and making available datasets that will be of great use to them and countless other researchers.


Authors: Jeremy Frank (Short Course Participant) & Katja Seltmann (TTD Project Manager, AMNH)

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