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Journal ArticleDOI

Paleobot.org: establishing open-access online reference collections for archaeobotanical research

08 Feb 2011-Vegetation History and Archaeobotany (Springer-Verlag)-Vol. 20, Iss: 3, pp 241-244

TL;DR: The establishment of Paleobot.org is described, an open access online reference collection database for macrobotanical, microbotanical and isotopic data to help standardize and improve the identification of archaeobotanical remains.
Abstract: Difficulty in accessing high quality reference materials has been a limiting factor in the advancement of archaeobotanical research. However, new developments in online open source content management technology and faster downloading capabilities make high quality and low cost dynamic online curation of archaeobotanical reference images increasingly feasible. We describe the establishment of Paleobot.org, an open access online reference collection database for macrobotanical, microbotanical and isotopic data to help standardize and improve the identification of archaeobotanical remains.

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Year:2011
Paleobot.org:establishingopen-accessonlinereferencecollectionsfor
archaeobotanicalresearch
Warinner,C;d’AlpoimGuedes,J;Goode,D
Abstract:Likeotheranalyticaspectsofarchaeology,archaeobotanyhasbeengrowingprogressivelymore
quantitativeinthepastfewdecades.Thismaybeasignoftheproliferationofincreasinglymature
andsophisticatedmethodologiesforanalyzingbotanicaldata,butassociatedwiththesophisticationof
quantitativemethodsistheirinherentopacity:thevalueandapplicabilityofanthropologicalconclusions
drawnfromquantitativearchaeobotanicaldataarenotonlylimitedbytheamountofinformationthat
canbeextractedfromdatabysophisticatedstatisticaltools,butalsobyourabilitytodrawreasonable
anthropological—asopposedtomerelystatistical—conclusions.Eventhewords“classication”and“sig-
nicance”havedierentmeaningsinstatisticsandinanthropology.Inthispaper,Iproposetheuse
ofgraphicalanalysisforarchaeobotanicaldatainadditionto,orinsteadof,typicalstatisticaltoolslike
signicancetests,variablereduction,andclustering.Appliedtodatafromcharredseedassemblagesfrom
theancientNearEast,thevisualrepresentationofquantitativedatahastheadvantageofhandlingsemi-
quantitativedatabetterandbeinginterpretablewithoutrelianceontheparadigmofaformalstatistical
test.
DOI:https://doi.org/10.1007/s00334-011-0282-6
PostedattheZurichOpenRepositoryandArchive,UniversityofZurich
ZORAURL:https://doi.org/10.5167/uzh-58024
JournalArticle
PublishedVersion
Originallypublishedat:
Warinner,C;d’AlpoimGuedes,J;Goode,D(2011).Paleobot.org:establishingopen-accessonlinerefer-
encecollectionsforarchaeobotanicalresearch.VegetationHistoryandArchaeobotany,20(3):241-244.
DOI:https://doi.org/10.1007/s00334-011-0282-6

SHORT COMMUNICATION
Paleobot.org: establishing open-access online reference collections
for archaeobotanical research
Christina Warinner
Jade d’Alpoim Guedes
David Goode
Received: 30 September 2010 / Accepted: 22 January 2011 / Published online: 8 February 2011
Ó Springer-Verlag 2011
Abstract Difficulty in accessing high quality reference
materials has been a limiting factor in the advancem ent of
archaeobotanical research. However, new developments in
online open source content management technology and
faster downloading capabiliti es make high quality and low
cost dynamic online curation of archaeobotanical reference
images increasingly feasible. We describe the establish-
ment of Pa leobot.org, an open access online reference
collection database for macrobotanical, microbotanical and
isotopic data to help standardize and improve the identifi-
cation of archaeobotanical remains.
Keywords Digital reference collection Macrobotanical
remains Phytolith Starch Pollen Archaeobotany
Introduction
The level of confidence with which one is able to make an
accurate taxonomic identification of a given archaeobo-
tanical specimen is closely rel ated to the size and quality of
the available reference collection. As a result, access to a
suitable reference collection is essential for the positive
identification of unknown archaeobo tanical remains. As
archaeobotanists are now working across the globe, the
establishment of large, regionally based reference collec-
tions poses increasing challenges. The identification of
unknowns using herbaria alone can be costly both in terms
of travel and time. In many regions, access to herbaria and
identification guides is poor, and where access does exist,
many institutions discourage repeated sampling of impor-
tant type specimens. Online reference collections can
greatly lower the cost of establishing a relevant compara-
tive collection, while also reducing over-sampling and
redundant destructive analysis of valuable type material.
As an aid to archaeobotanists both in the field and at
their home institutions, high-quality online reference col-
lections can facilitate rapid preliminary identification,
thereby reducing the number of taxa that will need to be
viewed and compared using conventional type collections
in the final stages of taxonomic identification. Open-access
online reference collections also allow individual research-
ers to make available images of specimens collected from
non-traditional sources, including archaeological sites and
modern agricultural fields and markets.
These specimens, which are not typically curated by
herbaria, may have particular relevance for archaeobotan-
ists concerned with morphological changes that accompany
domestication and regional trait selection.
Finally, the development of new fields in microfossil
analysis such as starch grain analysis and phytolith
Communicated by F. Bittmann.
Electronic supplementary material The online version of this
article (doi:
10.1007/s00334-011-0282-6) contains supplementary
material, which is available to authorized users.
C. Warinner (&)
Centre for Evolutionary Medicine, Institute of Anatomy,
University of Zu
¨
rich, Winterthurerstr. 190,
8057 Zu
¨
rich, Switzerland
e-mail: christina.warinner@uzh.ch
J. d’Alpoim Guedes
Department of Anthropology, Harvard University,
11 Divinity Ave, Cambridge, MA 02138, USA
D. Goode
Harvard College, Harvard University, University Hall,
Cambridge, MA 02138, USA
123
Veget Hist Archaeobot (2011) 20:241–244
DOI 10.1007/s00334-011-0282-6

research, have made new demands on the field. Questions
such as variability in starch grain and phytolith morphol-
ogy are currently under investigation, and access to large
online reference collections of modern microfossil images
would greatly facilitate the establishment of robust dia-
gnostic criteria for positive taxo nomic identification.
Demand for online reference collections and forums
In 2010, Dr. Naomi Miller circulated a questionnaire to
archaeobotanists working in the field with the goal of
determining the state of current archaeobotanical research
and identifying areas in need of improvement (Archaeo-
botany Questionnaire
2010). The results were presented at
the 2010 Society for American Archaeology meetings in a
forum entitled, ‘Quantification and presentation: effective
means of presenting plant evidence in Archaeology,’
organized by Christine Hastorf.
One of the major challenges listed by archaeobotanists in
the survey was the lack of identification tools and reference
collection images for both specific regions and overall.
When asked what would facilitate or enhance their own
archaeobotanical research in a practical or intellectual way,
respondents listed the development of online identification
databases as the single most-desired resource. A strong
desire for a website dedicated to the identification of
unknown specimens was also expressed. At present,
archaeobotanists most frequently solicit assistance with
difficult identifications by disseminating images over email
list servers, but email is poorly suited for such purposes and
is ill-equipped to handle large image files and complicated
discussion threads involving multiple individuals. It became
clear that a dedicated online source that could host high
quality images, as well as curate associated metadata such
as field notes, site information, and comments and discus-
sion, would greatly benefit the archaeobotany community.
Current online resources
There are currently a large number of web-based resources
available to archaeobotanists specializing in macro and
microfossil remains (Table 1 ESM). These resources range
from personal research websites of individual analysts to
multi-institution searchable photographic collections of
particular plant parts or types. While these websites offer
many advantages, there are also a number of practical
limitations to currently available archaeobotanical online
resources. First, with respect to submission, most online
resources are closed access. This means that the
images available on a particular website are limited to
those uploaded by the website’s creators.
Aside from Inside Wood, none of the current online
resources allow other individual s to dynamically upload
images from their own reference collections. For individuals
interested in making their own reference collection photo-
graphs available online, it has been necessary for them to
create their own webpage or website, which can be difficult
and time-consuming. Another problem is cost. Although
most websites are free, some online resources, such as
Discover Seeds and the Digital Plant Atlas Project, require
payment for full access to their online collections. For those
wishing to create their own website, the costs of program-
ming, site hosting, and server space rental can be prohibitive.
An alternative is to use freely available, third party websites,
such as Flickr.com, Ning.com, or Wiki Sites, but these free
services also greatly limit website flexibility and control.
Herbaria and botanical gardens are increasingly digi-
tizing their collections, but these digitized images are lar-
gely limited to scans of botanical sheets. With the
exception of the Seed Herbarium Image Project (SHIP), a
Harvard University initiative that provides online images
of seeds housed within the Arnold Arboretum’s North
American collection, high quality images of seeds or other
plant parts which can be useful as identification tools for
palaeoethnobotanists are rarely included in digitized her-
barium records. While scans of botanical sheets can be
helpful for assessing the taxonomic scope of the collection,
they are generally not useful for aiding in the identification
of macro or microfossils.
In terms of scope, several currently available archaeo-
botanical websites have a strong regional focus. This poses
challenges to researchers engaged in cross-regional rese arch
or who work in understudied regions. Additionall y, many
online collections are biased toward common taxa, and
taxonomic coverage is frequently incomplete.
There are also relatively few images of archaeological
plants available on current botanical websites. Taphonomic
processes such as dessication and carbonization can dra-
matically alter the appearance of botanical macro and
microfossils, and reference collection images of archaeolog-
ical specimens that have undergone these processes can
greatly aid with the identification of unknowns. The Digital
Plant Atlas Project published an online Digital Atlas of Eco-
nomic Plants in 2010 (Cappers et al.
2010), and an online
Digital Atlas of Economic Plants in Archaeology is in prep-
aration, but the images will be limited to archaeobotanical
remains excavated from Europe, western Asia and North
Africa, by the Deutsches Archa
¨
ologisches Institut and the
Groningen Institute of Archaeology. Geographical coverage
of other online images of archaeological plant remains is
generally restricted to only a few, mostly Old World, cultural
areas.
One major d rawback of current resources is that there
are very few online forums available for the discussion of
242 Veget Hist Archaeobot (2011) 20:241–244
123

unidentified archaeological botanical remains. Although
many researchers currently use listservs to discuss uniden-
tified plant remains, there are no websites that allow indi-
vidual researchers to upload images of unknowns and
solicit assistance with iden tification.
Finally, current online resources for archaeobotanical
research are heavily biased toward macrobotanical remains.
There are few online resources available for researchers
engaged in the identification of phytoliths and starch
microfossils, and there are currently no online databases of
plant isotopic data.
Paleobot.org
In order to address the diverse online needs of the ar-
chaeobotany community, we have develop ed Paleobot.org ,
a collaborative, open-access website that allows individual
researchers to share refere nce collection images and data,
as well as images of unidentified remains, using a free
online platform. The goal of Paleobot.org is to bring
together a large academic community of archaeobotanists
to share data, information, and expertise for the common
purpose of improving the identification of archaeobotanica l
specimens. As with other online resources, the goal of
Paleobot.org is not to duplicate the function of a herbar-
ium, reference collection specimens, or slides. Rather, the
aim of the website is to assist researchers with preliminary
identifications, which can then be confirmed with the use of
reference collections, literature, or the assistance of a
specialist. In other words, Paleobot.org is not a replace-
ment for reference collections or plan t taxonomists, but
rather a way to use them more effectively. Paleobot.org
was officially launched on July 1, 2010, and the site can be
accessed at http://www.paleobot.org. Paleobot.org is dis-
tinguished by a number of user-friendly features that facil-
itate scholarly communication and collaborative research,
including: open-access viewing and submission, the sup-
port of multiple data types, an unidentified forum, assis-
tance with copyright retention, and the ability to create
personal research profiles.
Open access: submission and viewing
Open access submission has proven to be a powerful tool for
the rapid development of new research and the dissemination
of data to both professionals and the public. Examples of
successful open access web-databases in the field of biology
include GenBank (Benson et al.
2008) and Florida State
University’s Morphbank (
2010), and the websites Bone-
commons and Zooarchaeology.ning.com offer open-access
platforms for individuals engaged in zooarchaeological
research (Morris
2009). Current non-open access botanical
websites often contain data from either a regional herbarium
or an individual’s regionally specific collection. Individuals
working in areas, for which taxa from two different regions
must be consult ed, such as the Eurasian steppes, must
attempt to access reference collections from widely disparate
sources. When such websites contain data from archaeo-
logical sites, they are also limited in regional scope and
focus. Open access submission is important for allowing data
from otherwise underrepresented regions to be accessible to
the scholarly community. In addition, open access submis-
sion will allow individuals who otherwise would not have the
means to develop a website to place their collection online.
Data types
Archaeobotanists work with a wide variety of macro and
microbotanical remains and require access to large refer-
ence collections to be able to effectively and accurately
identify specimens. Paleo bot.org curates images of the
most commonly analyzed types of macro- and microbo-
tanical remains, including macrobotanical remains, pollen,
phytoliths and starches, to facilitate this process. In addi-
tion to image files, C, N, O, and H isotopi c data may also
be uploaded. A planned members-only portion of the web-
site will soon allow scholars to share additional documents
and information, including identification guides. We
anticipate that Paleobot.org will play an important rol e in
the development of identification procedures for newer
fields such as phytolith research and starch grain analysis.
In particular, little is under stood of intra species/genus/
family variation in starch due to a lack of access to large
numbers of reference collection images. We hope that by
making large numbers of images available online a better
understanding of intra taxa variation will be achieved.
Unidentified forum
All archaeobotanists, at one time or another, encounter a
specimen that eludes identification. Paleobot.org provides
an unidentified forum where researchers can upload images
of unidentified specimens and solicit advice from fellow
archaeobotanists. Comments and discussion threads are
curated with the image for easy reference and may later serve
as an archived source of information for similar specimens.
Intellectual property
We acknowledge that reference collections take consider-
able time and effort to construct. For an open-access online
Veget Hist Archaeobot (2011) 20:241–244 243
123

database to be successful, it is essential that contributors
are properly credited for their reference collection images.
Paleobot.org takes a number of measures to ensure that the
authors of these images are given proper citation and
acknowledgment for their work. First, all users retain
copyright over the personal research images that they
upload to the site. This differs from some other sites where
the hosting institution, for example a university, controls
the copyright of any posted material. Clear copyright and
fair use guidelines are posted on the website, and in order
to ensure that images placed on Paleobot.org cannot be
used in presentations or publications without proper image
credit, we employ software that auto matically embeds
copyright information on all images uploaded to the site.
Under the terms of fair use, users agree to allow individuals
to u se content and images from Paleobot.org for their own
identification purposes and in non-commercial scholarly
and educational materials without special permission as
long as they include proper photo credit and citation.
Personal research profile
Contributors of images to the website also gain exposure
through the creation of a personal research profile on our
Contributors page. Although anyone may search the online
collections, contributo rs to the website are required to
create a personal research profile before they submit ima-
ges to the website. Following the creation of a profile, each
contributor’s photograph, institutional affiliation, contact
email address, research website links, and research inter-
ests will be featured on the contributors tab of the website.
We anticipate that this page will serve as a hub for con-
necting researchers around the world.
How Paleobot.org works
Paleobot.org is deployed using PHP as the backend pro-
cessing language which creates the pages displayed to the
user, and MySQL for the database which provides and stores
the updatable content. The site is created using the Drupal
framework, an open source software suite that manages most
basic content submission and user authentication. Coupled
with other open source extensions to this fra mework, termed
modules, many useful behaviours such as location handling,
image uploading and content searching can be implemented.
Using various extensions, this framework was customized to
work as desired for this site. The user-submitted data is
stored with meta-data for each specimen as one entity, to
which various observations can be attached, such as mac-
robotanical or phytolith photographs. This allows for varied
types of data to be stored within a unified, easily searchable
format, and for scientists to subsequently add additional data
that is correctly associated with the same specimen.
Conclusions
Paleobot.org is a new, collaborative online resource aimed
at facilitating archaeobotanical research. Paleobot.org
provides free, open-access hosting of reference collection
images and data provided by contributing researchers, as
well as a dynamic foru m for the discussion of unidentified
archaeobotanical remains. The goal of Paleobot.org is to
bring together the archaeobotany community to share data,
information, and expertise for the common purpose of
improving the identification of archaeobotanical speci-
mens. We invite fellow researchers to submit their refer-
ence collections, archaeobotanical and unidentified
photographs and data to Paleobot.org and to participate in
our uniquely collaborative archaeobotanical web-database.
References
Archaeobotany questionnaire (2010) University of Pennsylvania
School of Arts and Sciences.
http://www.sas.upenn.edu/
*nmiller0/AbotQ.pdf
. Accessed September 27, 2010
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL
(2008) GenBank. Nucleic Acids Res 36:D25–D30
Cappers RTJ, Neef R, Bekker RM (2010) Digital atlas of economic
plants, vols 1–3. Barkhuis, Eelde
Morphbank (2010) Florida State University, Department of Scientific
Computing,
http://www.morphbank.net. Accessed September
25, 2010
Morris J (2009) Zoobook: a zooarchaeology social network. Interna-
tional Council for Archaeozoology Newsletter 10:2
244 Veget Hist Archaeobot (2011) 20:241–244
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