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    Specimen Short Course

    Short Course on Biological Specimen Informatics at the American Museum of Natural History

     Richard Gilder Graduate School

    May 13–24, 2013



    Participant Information:

    Participant Information and suggested readings page with information for course participants, guidelines for installation of Arthropod Easy Capture, housing, and getting around New York.


            


    Faculty:

                      Randall Schuh, TTD-TCN PI (AMNH)

                      Christine Johnson, TTD-TCN co-PI (AMNH)

                      Katja Seltmann, TTD-TCN Project Manager (AMNH)

                      Rob Naczi, PI (NYBG)

                      Melissa Tulig, TTD-TCN co-PI (NYBG)

                      Kim Watson, TTD-TCN Project Manager (NYBG)

                      Steve Thurston, Imaging Specialist (AMNH)

                      Mike Bevins, Information Manager (NYBG)


    Lecture/Lab Schedule: 

    No.   Date              Topic

     

    1

    May 13



    Lecture: (Toby Schuh & Rob Naczi)

    • Overview of biodiversity informatics and the importance of considering biodiversity informatics when developing a research plan

    • Best practices in specimen collecting, recording collecting events, preparation, handling, labeling, vouchering, imaging and workflow

    • Basic nomenclature (zoology, botany)

    • Incorporating specimen data capture into your research regimen

    • Introduction to specimen publication workflow, including data examination through mapping

    Lab:  (Toby Schuh) Introduction to relational databases (Arthropod Easy Capture); discussion of requirements of last day presentation

    Suggested Reading:


    Johnson, N. Biodiversity Informatics. Annu. Rev. Entomol. 2007. 52:421–38


    Meier, R. & Dikow, T. Significance of Specimen Databases from Taonomic Revisions for Estimating and Mapping the Global Species Diversity of Invertebrates and Repatriating Reliable Specimen Data. 2004. Conservation Biology. Volume 18, No 2.


    Schuh, R.T.. 2012. Integrating specimen databases and revisionary systematics.  Publication part of ZooKeys 209 (2012) : Special issue: No specimen left behind: mass digitization of natural history collections. doi: 10.3897/zookeys.209.3288


    Schuh, R.T., Hewson-Smith, S., and Asher, J. 2010. Specimen Databases: A Case Study in Entomology using Web-based Software. American Entomologist. Winter.

    Naczi, Rob & Schuh, Randall. Collecting Best Practices

    Naczi, Rob & Schuh, Randall. Labeling Best Practices


    2

    May 14



    Lecture: (Melissa Tulig)

    • Introduction to museum collections

    • Introduction to specimen database management and specimen digitization

    • Introduction to authority files for taxonomy, people, geography

    • Data aggregators and common data standards (e.g., Darwin Core) for biological data

    • Unique specimen identification for specimens and in databases (barcodes, GUIDs)

    • Managing derivatives of specimens

    Lab: (Melissa Tulig)



    Suggested Reading:


    Chapman - Principles of Data Quality (http://www.gbif.org/orc/?doc_id=1229)

    Chapman - Guide to Best Practices for Generalising Sensitive Species Occurence Data (http://www.gbif.org/orc/?doc_id=1233)

    3

    May 15


    Lab: (Christine Johnson)

    • Relational databases continued (Specify, Symbiota, EMU, Access)
    • Data input, import (database, Excel)
    • What data should you be collecting and how?
    • Methods of database data management for different higher zoological taxa

    Lecture: (AMNH Staff Christine Johnson lead) Workflow tours:

    1:15 - 1:50 Fossil Invertebrates

    2:00 - 2:35 Invertebrate Zoology/Entomology

    2:45 - 3:15 Ornithology


    4

    May 16


    Lecture:(Kim Watson)

    • What is georeferencing? Georeferencing tools and approaches (stand alone and on-line)

    • Managing locality data and collection events

    • Capturing geographical information in the field

    • Tools for data visualization

    Lab: (Kim Watson) Georeference a series of specimens using GeoLocate and Google tools

    Suggested Reading:

    Chapman, A.D. and J. Wieczorek (eds). 2006. Guide to Best Practices for Georeferencing (http://herpnet.org/herpnet/documents/biogeomancerguide.pdf)

    Wieczorek, J., D. Bloom, H. Constable, J. Fang, M. Koo, C. Spencer, and K. Yamamoto. Version: 2012-10-08. Georeferencing Quick Reference Guide (http://manisnet.org/GeoreferencingQuickReferenceGuide.pdf)


    5

    May 17



    Lecture: (NYBG Staff) Field trip to see workflows at NYBG

    • Tour of NYBG herbarium facilities

    • Overview of processing collections from field to herbarium

    • Digitization workflow and data entry presentations



    Lab:

    Imaging Lab tour, workflow demonstration and specimen imaging by students

    Field trip into NYBG forest for specimen collecting demonstration


    6

    May 20


    Lecture: (Steve Thurston & Mike Bevans) Best practices in specimen imaging (tools, rationales, image repositories)

    Lab: (Steve Thurston & Mike Bevans) Demonstration of Microptics system and Photoshop tools and techniques by Steve Thurston; tour of Microscopic Imaging Facility; Description of plant specimen imaging techniques by Mike Bevans

    7

    May 21


    Lecture: (Katja Seltmann)

    • Introduction to the Internet and discussion of AEC installation process
    • Mastering the basics of SQL (Structured Query Language)
    • Semantic Web and data linking
    • Introduction to different kinds of databases, semantic web practices, and future tools

    Lab: (Katja Seltmann)  Practical exercises in writing, reading and inserting records into the Arthropod Easy Capture MySQL database; discussion groups on how to extend the existing database to fit individual research needs (how to relate your data to existing data structures). MySQL tutorial exercises (Day 7)


    Suggested Reading:

    Deans, A.R., Yoder, M.J. and Balhoff, J.P. Time to change how we describe biodiversity. Trends in Ecology and Evolution, February 2012, Vol. 27, No. 2

    (http://www.planta.cn/forum/files_planta/opiniontime_to_change_how_we_describe_biodiversity_976.pdf)

    Penev et al. Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples. Zookeys. 2010; (50): 1–16. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088020/)

    8

    May 22


    Lecture: (Christine Johnson)

    • Statistical and ecological software; how to analyze data from a specimen database
    • Check and fix exported database data in Excel using pivot tables
    • How to produce usable reports from Arthropod Easy Capture

    Lab: (Katja Seltmann) Import data using various programs which may including: CartoDB, Discover Life, Gephi, Lifemapper, SimpleMappr, R, PC-Ord

    9

    May 23



    Lecture: (Toby Schuh & Rob Naczi)

    • Online data to publication (current standards)

    • Developing a data management plan and incorporation of plan into grant proposals

    • Management of taxonomic names (issues and solutions)

    • Future directions in biodiversity informatics

    Lab: Independent work and presentation preparation

    10

    May 24

    Student presentations. 10-minute demonstrations of student research using the database to produce a product

     

     


    About the Course:

    Title:  Specimen-level informatics and its relationship to collections-based research

     

    Goals:   Train students in best practices for specimen-level data management from the field to preserved collections and how these can facilitate addressing research questions

     

    Learning Objectives:       Gain familiarity with the tools used in specimen data capture

                                               Learn how these tools may serve as a valuable adjunct to student research

                                                Gain familiarity with the relevant literature on specimen databasing

               Engage in actual application of the software tools using data derived from student research

                                                         

    Student Qualifications:  Advanced undergraduate or graduate student involved in specimen-based research


    Dates: May 13-24, 2013


    Daily Schedule: Lecture: 9:00-12:00; Break: 12:00-1:00; “Lab” time: 1:00-3:00 (exception is the first day, which will run to 5:00pm)


    How to Apply:

    Submit 1) a one-page CV; 2) a one-paragraph (300 word maximum) description of your current or planned research and how this course would benefit your research; and 3) a statement of your financial needs by March 15, 2013 to amnhspecimendata@gmail.com.

     

    Eligibility: Must be enrolled in a degree program at a U.S. institution at the advanced undergraduate or graduate level.

     

    Class size is limited to 20 students.  Students will receive a Certificate of Completion from the Richard Gilder Graduate School. Students are required to bring their own laptops and will be asked to install Arthropod Easy Capture, a MySQL, PhP application, prior to arrival. Technical support will be provided for installation. Housing will be provided for students from outside the New York City metropolitan area.

     

    Contact: amnhspecimendata@gmail.com

    Images by Matthew A. Bertone






    Commitment and Products:  Daily attendance for 10 days over two weeks; a short presentation at the end of the two-week session demonstrating the use of course tools and methods in own research.


    Literature and References: 

                Blagoderov, V. and V.S. Smith (eds.).  2012.  No specimen left behind: Mass digitization of natural history collections.  ZooKeys (special issue):  267 pp.

                Journal articles and WWW resources as appropriate

     

    Grading:  Pass/Fail (no letter grade)

     

    Evaluation Basis:  Students will be evaluated on participation in class exercises and discussions, attendance and a short presentation on how they applied specimen database tools to their research


    Faculty:

                      Randall Schuh, TTD-TCN PI (AMNH)

                      Christine Johnson, TTD-TCN co-PI (AMNH)

                      Katja Seltmann, TTD-TCN Project Manager (AMNH)

                      Rob Naczi, PI (NYBG)

                      Melissa Tulig, TTD-TCN co-PI (NYBG)

                      Kim Watson, TTD-TCN Project Manager (NYBG)

                      Steve Thurston, Imaging Specialist (AMNH)

                      Mike Bevins, Information Manager (NYBG)

    Images provided by New York Botanical Garden