More Information on the DPDC
Purpose and objectives
The main purpose of the DPDC is to make diatom data easily available to
paleoecologists, paleoclimatologists, and diatomists interested in global
change. The DPDC is intended primarily for researchers looking for long-term
data related to climate change and other global environmental issues, and for
diatom ecologists who are using methods for inferring environmental
characteristics from diatom data and need more information on ecological
characteristics of taxa. Most data are from studies published in the literature,
but not all. All data are freely available to the public.
Key objectives of the DPDC
- improve diatom paleolimnologist’s ability to infer trends in
characteristics related to global change by providing easy access to a large
amount of data on diatom distributions and ecology
- improve accuracy of ecosystem models by giving modelers easy access to
many data sets of long-term ecological trends inferred from diatom data
- create a DPDC database with an underlying structure compatible with
other paleoclimate-related databases, e.g., the North American Pollen Database
- create a website where users can:
- browse and download data sets so they
can explore them further and use them in their own studies
- search the database for occurrences of
taxa in all samples and view associated ecological information
- include a large number of North and South American diatom
data sets relating to global change
Data contents
As of October 2021, the DPDC includes more than 20 data sets with over 4000
samples, and representing over 700 sites. The main types of data included are
site information, diatom counts, water chemistry and other environmental data, and chronologies.
The DPDC is intended to include a wide range of diatom data sets (Sullivan and Charles
1994). They are not limited by geographic area, but emphasize North and South America.
They can represent any time period, but those of most current interest include Late
Glacial to Holocene, Younger Dryas, Little Ice Age, recent times (measurement records),
and times of rapid environmental change.
Raw diatom counts (actual numbers of valves or cells counted by analysts) are included
in the database. Both raw and percentage counts are provided in response to most
retrievals. The taxon names used in the data sets submitted by the contributors are
linked to a master list of diatom taxa names in the database so that all counts
can be interrelated. This allows retrieval of information about occurrence of
individual taxa among all data sets. There has been no attempt to harmonize taxonomy
among data sets. The taxonomic code system is based on the list developed for the
PIRLA Project (Paleoecological Investigation of Recent Lake Acidification) in the
mid-1980's, and later expanded and modified to the NADED (North American Diatom
Ecological Database) list of names currently used in the Phycology Section at The
Academy of Natural Sciences of Drexel University. DPDC data set contributors have
also added names to the list.
Database structure
Many aspects of the database design are similar to those in the North
American Pollen Database, and other constituent databases within Neotoma.
This is required so that the diatom data can be stored with a structure
such that they can be viewed and analyzed with programs that allow
browsing and visualization of multiple types of paleo data. Key parts of
the database structure were borrowed directly from the PIRLA database
(Paleolimnological Investigation of Lake Acidification), especially
those dealing with diatom data.
The DPDC data are managed at ANSP with Microsoft SQL Server 2014 on a
server running Windows Server 2012 R2. The web application uses
Internet Information Server (IIS 8.5). Older applications using
Active Server Pages (ASP), and Visual Basic 6 are currently non-working.
We do not know if we'll be able to resurrect those or not.
The DPDC is designed to hold many types of information about a project.
The basic data, such as diatom counts, dates, site locations, and physical
and chemical environmental variables are stored in tables, along with
derived or secondary information. There are also tables designed to hold
much of the underlying, supportive information: e.g., taxonomic information,
raw data and techniques concerning dating, worker names and addresses,
textual notes on many fields, etc. The amount of information about a
project that can be entered is limited primarily by the amount investigators
were willing to contribute.
Data availability
All data in the DPDC are available to the public. This is in accordance
with policies of agencies and programs that sponsored the DPDC. Data sets
and results of data searches can be downloaded as tab-delimited ASCII files.
Data downloaded from this website should be cited; following is an example.
Original source publications and investigators should also be cited.
“Data were obtained from the Diatom Paleolimnology Data Cooperative (https://diatom.ansp.org/dpdc/"),
a constituent database of Neotoma Paleoecology database (https://www.neotomadb.org/").
The work of data contributors, data stewards, and the Neotoma and DPDC communities
is gratefully acknowledged.”
History
Participants at a NOAA funded Workshop on Feasibility of a Paleolimnology Data Co-op,
held at the Academy of Natural Sciences in Philadelphia in May, 1993, recommended
creation of a paleolimnology data cooperative (Sullivan and Charles 1994). Based
partly on this recommendation, the NOAA Paleoclimatology Program funded a proposal
(beginning June 1995) to form the Diatom Paleolimnology Data Cooperative (DPDC).
The proposal was submitted by Donald F. Charles of the Academy, P. Roger Sweets of
the University of Louisville, and Timothy J. Sullivan of E&S Environmental Chemistry
of Corvallis, OR. The National Science Foundation’s Earth System History program
funded further development of the database from 1998 to 2002 and again from 2004 - 2008.
Further development of the DPDC database stopped in 2010 when data entry shifted to
the Neotoma paleoecology database (Williams et al. 2018). The DPDC is now a constituent
database in Neotoma, and is supported by Neotoma grants from the National Science
Foundation, Division of Earth Sciences, Geoinformatics Program (2016 - 2020, 2020 - 2023).
The first developer to work on the database was Kellie B. Vaché, of E&S
Environmental Chemistry. He designed and developed the first version of
the database in 1996. Beginning in 1998, Patrick Cotter (Phycology Section,
Patrick Center, ANSP) took over responsibility for the database, made some
revisions in database structure, wrote many queries, and developed the
initial website application. In January 2001, Kathleen Sprouffske ( ANSP
PCER Phycology Section) became the DPDC database administrator and application
developer. She made additional modifications to the database design, updated
the web application, wrote a DPDC data entry application, and developed an
application to automatically upload data from the application to the SQL server
database. Chamira Ratnayaka (ANSP PCER Phycology Section) participated in
the application development efforts during the Spring and Summer of 2002
and Kai Snyder (E&S Environmental Chemistry) provided valuable feedback on
the data entry application.
Acknowledgements
John Keltner at the World Data Center for Paleoclimatology in Boulder,
Colorado provided considerable assistance with many aspects of DPDC
database design. Sherilyn Fritz, John Smol, and Platt Bradbury served
as advisors to the project, reviewing the database and website at various
stages and making helpful comments. Roger Sweets placed an announcement
of the DPDC on the Diatom Home Page
at Indiana University, contacted several people about making contributions, and acquired several data
sets. Diane Winter (ANSP PCER Phycology Section) reformatted files and
prepared several data sets for entry to the DPDC. She also provided many
valuable comments on design of the data entry application, the application
instruction manual, and the data entry process in general. Mihaela Enache
and Sonja Hausmann also helped acquire and enter several datasets. Pat
Palmer has ably maintained the DPDC database and website for the past
several years; Patrick Boylan provided much valuable assistance with
data management.
Reference
Sullivan, T.J. and D.F. Charles. 1994. The feasibility and utility of a
paleolimnology/paleoclimate data cooperative for North America. Journal of
Paleolimnology 10: 265-273. DOI: 10.1007/BF00684036
Williams, J.W., E.C. Grimm, J. Blois, D.F. Charles, E. Davis, S.J. Goring, R.W. Graham, A.J.
Smith, M. Anderson, J. Arroyo-Cabrales, A.C. Ashworth, J.L. Betancourt, B.W. Bills,
R.K. Booth, P. Buckland, B.B. Curry, T. Giesecke, S.T. Jackson, C. Latorre, J. Nichols,
T. Purdum, R.E. Roth, M. Stryker, H. Takahara. 2018. The Neotoma Paleoecology
Database, a multiproxy, international, community-curated data resource. Quaternary
Research 2017: 1-22. DOI: 10.1017/qua.2017.105
Related Websites
The
European Diatom
Database Initiative
(EDDI) is a web-accessible database of diatom training sets and transfer
functions similar in many ways to the DPDC, but covering many regions in Europe,
and parts of Africa and Asia. The EDDI website has applications that allow users
to apply transfer functions to their sediment core data online. Transfer
functions are primarily for inferring environmental conditions related to
surface water acidification, eutrophication and climate change.
The Diatom
Home Page is a major resource for those interested in diatoms and related
algae. It has links to many other diatom-related sites.