TurtleBase

1
Eco-informatics leveraging bioinformatics skills
to maximize agility in non-computational
environments
John Van Hemert1, Yves Sucaet1, Lyric
Bartholomay2, Anne Bronikowski3, Dan Warner3,
Fredric Janzen3 1) Bioinformatics and
Computational Biology Laboratory, Iowa State
University, Ames, IA USA http//lab.bcb.iastate.
edu, http//eco.bcb.iastate.edu 2) Department of
Entomology, Medical Entomology Laboratory, Iowa
State University, Ames, IA USA 3) Department of
Ecology, Evolution, and Organismal Biology, Iowa
State University, IA USA

• TurtleBase
• Herpetologists in Dr. Fredric Janzen's group have
  been studying nests of painted turtles (Chrysemys
  picta) on a Mississippi River island called the
  Thomson Causeway, in South Potter's Marsh,
  Thomson, Illinois since 1989. They collect a
  large amount of data every season representing at
  least the following entities
• Turtle nests (temperature, location)
• Turtle mothers (tracking code, size)
• Eggs (mass)
• Hatchlings (sex, abnormalities, size)
• Vegetation (southward and westward cover)
• In addition to a consistent and efficient data
  entry
• and download portal, analytical platforms are
• expected to include the following
• Track Nest Temperatures Visualize and download
  temperature data for any group of nests over
  time. Nests can be selected for analysis based
  on complex criteria such as location, vegetation
  cover, date, associated turtle mother(s), or
  number of hatchlings. Individual readings (30
  per day during the 6-week summer season), daily
  averages, as well as daily and seasonal upper and
  lower bounds can be plotted. In addition,
  histograms of nest temperatures for respective
  nests can be dynamically generated for
  temperature distribution analysis.

• Current projects
• MosquitoBase http//www.iowa-mosquito.net
• During the summer months, the ISU Medical
  Entomology Research
• Laboratory monitors mosquito populations and
  mosquito-borne
• disease in the State of Iowa. Data has been
  collected as early as
• 1969, but was never pooled and/or made available
  through a single
• access point.
• A relational database and web interface was
  created and functions
• both for entering observational data, and
  tracking information
• through the years in spatiotemporal terms for
  each mosquito species
• observed.
• The analytical platforms offer the following
  functions
• Analyze Locations see year-over-year or
  week-over-week comparisons for a set of
  locations. Multiple locations can be viewed over
  different counties. Raw data can be downloaded
  for further analysis.
• Analyze species and sex composition custom
  granular view of month-over-month and
  week-over-week comparison of male and female
  individuals. Additionally, femalemale ratios are
  presented for further analysis.
• Matrix builder heatmap representation to
  generate a top-level view on mosquito abundance.
  Different parameters can be selected and compared
  to one another (species, time, location).
• Historical week-by-week comparison side-by-side
  comparison of different parameters. E.g.
  compare all locations in a given county with the
  aggregate distribution for that county.

• Abstract
• The observation that many ecological
  survey-projects have led to massive collections
  of static data suggests the construction of a
  centralized platform for eco-informatics. Much
  ecological and environmental research is
  conducted by accumulating observational data
  across long timeframes. Such projects can
  outlive researchers time, resulting in
  inconsistent data management methods. A software
  development pipeline and platform for
  eco-informatics was developed in which data
  management principles are applied to
  species-centric ecological information. Benefits
  are instantly available in several areas
  consistency, automation, data input, data
  analysis tools, and data retrieval via download.
  In the past year, two databases were completed
  (mosquitoes and baboons) and an additional
  database (turtles) is currently under
  development. All systems are developed using the
  MySQL database system and the PHP scripting
  engine for dynamic web accessibility.
  IowaMosquito.net is a web portal to historical
  mosquito surveillance data. BaboonBase is
  developed for primatologists of the Southwest
  National Primate Research Center to manage and
  analyze baboon pedigree, menstrual, and fecundity
  data. TurtleBase will serve herpetologists
  observing turtles nesting on an island in the
  Mississippi River. We have assisted laboratories
  in many departments to migrate spreadsheet, text
  file, and even notebook based observational data.
  This set of eco-informatics websites can be
  reached at http//eco.bcb.iastate.edu
• Methodology