[Taxacom] Field Biologist Data Gathering Tools

Richard Pyle deepreef at bishopmuseum.org
Mon Mar 26 03:28:44 CDT 2007

Dear Colleagues:

For various reasons, I'm interested to learn what tools those of you who
spend time in the field collecting biological specimens, images, or
observations use to manage the associated data while still in the field.

For example, on my own field projects, the typical pattern is to go into the
field, collect a bunch of specimens, prepare and photograph those specimens
while they are still fresh, take a tissue sample for later biochemical
analysis, and then curate the specimens for transfer back to the Museum for
long-term preservation.  Also, during the collecting activities I will make
observations and/or photographs and/or videotape sequences of organisms
in-situ, often involving individual organisms that are not themselves
collected and preserved as specimens.  I would record a bunch of data for
each "collecting event" (Place description, GPS coordinates, depth and other
environmental parameters, date, collectors, etc.), a bunch of data for
individual specimens or groups of specimens (counts, size measurements,
tentative identifications, color remarks, etc.), a bunch of data relating to
photographs taken of specimens (f-stop, shutter speed, photographer,
lighting details, etc.), a bunch of other data relating to in-situ photos
and videos, and some comments about observations of uncollected organisms
seen during the collecting station.

The traditional data management scheme would be to create field numbers or
station numbers for collected material and collecting events, and then write
little numbered tags to keep with the specimens and tissues samples to
associate them back to some sort of hand-written data sheets or journal logs
that store the collecting event details.

Once the material is returned to the Museum, the hand-written notes and tags
and other information are typically transcribed to whatever computer
database software the Museum uses to manage its collecting data. Ultimately,
these Museum computer records are then exposed to the internet so they can
be found via search protocols such as DiGIR and made visible through portals
such as the GBIF portal.

Being a person who wears both a field biologist/collector's hat, and a
computer database developer's hat, I naturally have been working on ways to
capture all of this information pertaining to specimens, photos and videos,
and observations into my laptop computer while in the field.  The goal has
been twofold:  first, to more effectively and efficiently capture the data
while it is still fresh in mind (i.e., the same day as the specimens are
collected, photographs and videos taken, and observations made); and 2) to
streamline the process of transferring the data to the Museum database
systems, after the expedition is over.

At a pair of workshops for CReefs (www.creefs.org) last year, we discussed
the need for a robust set of tools for field biologists to use to capture
and organize the broad spectrum of data that marine-related collectors and
survey researchers use during expeditions.  The idea would be to have a very
modular set of tools so that researchers could select the specific sets of
tools for the kinds of data they manage (e.g., a specimen module, a tissue
sample module, an image module, a video module, an audio recording module,
an dynamic/interactive identification tool module, a mapping module, a
bibliographic module, and so on), and design these modules so they are
customizable, and conform with existing standards (TDWG).  That way, efforts
like CReefs could support a wide variety of researchers on their field
projects, allowing each researcher to gather and manage his/her own field
data and take it away after the expedition, while still allowing the data
records to be monitored over time, as new species identifications are made,
and so on, and as data are uploaded to broader initiatives like OBIS, etc.

The key to making the software successful is to make it more powerful, more
enabling, and easier to use for the field biologist than simply entering
data into an Excel Spreadsheet (the de facto standard employed by many field

I could go on and on about the systems we've been developing for this
purpose, and the ideas we've had for how they might work, and such -- but
the real reason for this email is to solicit feedback from Taxacomers who
find themselves in the field gathering biodiversity-relevant data.

So...after the lengthy contextual introduction above, my questions are:

1) What system of data management do you use in the field?  Trusty
pen-and-paper, leaving the digitization process until after the expedition?
An Excel spreadsheet?  A custom database you or your colleagues developed
yourself? Commercially available software designed specifically for this
purpose? Something else?

2) On the topic of commercially-available software designed for this
purpose, I am aware of at least two such applications for general-purpose
  - AditSite Wildlife Recording System
  - RECORDER (http://www.recordersoftware.org/) 
There are a number of other specialty software for birdwatchers,
lepidopterists, etc., some of which are listed here:
http://www.bgbm.fu-berlin.de/tdwg/acc/Software.htm.  Also, the Moorea
Barcode of Life project developed some software for this purpose, and there
are other specific-case initiatives like our own.

Does anyone have experience using any of these packages (or better yet,
anyone here involved with their development)?  Any general thoughts on their
functionality and usefulness?

3) Do you or your colleagues see a need/value for such software, assuming it
was made in a generic way (not specific to any taxon group or environment),
was compliant with TDWG standards, was robust, modular, and customizable
(and, of course, open-source).

The main impetus for sending out this lengthy email is that a number of us
who work in marine environments do have needs for such a suite of software
tools, that we feel are not currently met by existing applications, and that
would be superior to continuing our own personalized approaches to this
particular segment of biodiversity data management. Julian Caley and I are
considering requesting financial support for a workshop associated with the
Ocean Biodiversity Informatics (OBI) Conference in Halifax, in early October
of this year.

Any responses (either on or off the list) would be much appreciated!


P.S. I depart April 2 for a month of field work (i.e., gathering data
relating to specimens, photos, videos, and observations....), so I won't be
able to respond to any feedback sent to me after that date, until early May.

Richard L. Pyle, PhD
Database Coordinator for Natural Sciences
  and Associate Zoologist in Ichthyology
Department of Natural Sciences, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at bishopmuseum.org

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