P. & P. (2007).- PalyWeb: A palynomorph database project on the web. In: P. & E. (eds.), Recent Advances in Palynology.- Carnets de Géologie / Notebooks on Geology, Brest, Memoir 2007/01, Abstract 08 (CG2007_M01/08)
Palynology; database;
Internet.
Palynologie ; banque de
données ; Internet.
Since the sixties, palaeopalynology has been experiencing a spectacular growth. Already by the end of 1966,
(in et alii, 1996) had calculated that about 330 new articles on palynology were published each year in more than 200 journals, and about 4200 had already been published. In a paper published during the 90's, and
(1996) made an estimation of the number of palynological papers published each year. Although they
noted that data are incomplete, around 400 new articles are published annually.
Because of this, palynology is a victim of the abundance of published information,
which has created taxonomic chaos in some palynological groups. In addition, numerous palynomorphs have been published invalidly, some with redundant names. Several taxa have been described in publications with a limited distribution
in other countries or in languages not accessible to most palynologists. Therefore, palynologists
were soon convinced that an urgent need existed to create catalogues, or large datasets to manage this mountain of data. The first
of these were in a paper format but it rapidly became clear that the solution to
the management of palynological data is the use of personal computers. The better
known applications for this purpose, like PALYNODATA, DinoSys, etc. are briefly
described in et alii
(1996), but there are other projects: for the Palaeozoic,
Phytopal for acritarchs and Chitinovosp for Chitinozoans.
Originally written for the well-known Wikipedia encyclopaedia,
MediaWiki is free software accessible on the Internet (http://en.wikipedia.org/wiki/), but is now run on other projects of the non-profit Wikimedia Foundation
(http://en.wikipedia.org/wiki/Wikimedia_Foundation/) and many other wikis. The term wiki is a
short form of
"wiki wiki" which means something quick or fast in Hawaiian. On the Internet, a wiki is a website that allows users to add, remove, or edit
content very quickly and easily.
PalyWeb is a new palynomorph database project based on MediaWiki technology. It is a web-based
open-access, free-content palynological database. To our knowledge, it is alone in its mode of data acquisition and management
for palynology. It is also the only one to have as an objective the presentation in one dataset
of all fossilised palynomorph
taxa. Its conception is similar to that of the Wikipedia encyclopaedia, so it can be considered a wiki website. The ease of interaction and operation makes a wiki website an effective tool for collaborative scientific writing. PalyWeb is
designed to be a database compiled collaboratively by volunteers, and allows most articles to be changed by anyone with access to a computer,
a web browser and an Internet connection. However, users must be logged in to avoid
vandalism and inconsistency. PalyWeb is built
with the expectation that over time collaboration among users will improve the
quality of the articles.
The PalyWeb project
is housed on the web server of the University of
Liège. A daily backup is carried out to safeguard all information in the event of failure of the system. Its
Internet address
(URL) is: http://www.palyweb.ulg.ac.be/wiki/. To give
an estimation of the volume of information that the operating system can manage, the Wikipedia website provides some statistics: on May 2006, Wikipedia had 1,122,525 articles. That number excludes redirects, discussion pages, image description pages, user profile pages, templates, help pages, portals, articles without links to other articles, and pages about
Wikipedia. Including these, Wikipedia has 4,154,971 pages. Users have made 53,926,940 edits, an average of 12.98 per page, since July 2002.
At that time Wikipedia had 1,395,387 registered user accounts.
PalyWeb is
designed to accept the descriptions of a maximum number of published palynomorph taxa
available from conventional scientific reviews in accordance with the Botanical and Zoological Nomenclature Codes. PalyWeb has been deliberately limited to pre-Mesozoic palynomorphs, the field of research of the authors. It
was presented to the scientific community officially at the General meeting in Prague
(2006) of the
"Commission International de la Microflore du Paléozoïque" (http://www.cimp.ulg.ac.be/). PalyWeb is not an
online medium for publication. New taxa cannot be presented on its website.
However, concerning a published species there is no limitation in the number of pages
or their length. Text, figures and pictures may be up- and downloaded. Of course, to avoid
long delays, pictures may be compressed. It is forbidden to up-load pictures protected by
copyright. Navigation through pages may be done by clicking on internal links or
by typing keywords in the search engine
(e.g. the name of species, etc.).
At the moment, the database is organized in three sections: the main
one hosts the descriptions of taxa previously published in scientific reviews, the second
concerns unpublished taxa left in open nomenclature for which information from the PalyWeb community is requested, and the third is
devoted to enigmatic
palynomorphs. The second and third are actually discussion forums, not a part of
the database. Of course, this structure is tentative, and can be debated and easily modified.
Such flexibility is one of the advantages of a wiki-type website. Each page (article) is articulated around four main components. The first is the
"page" itself (Fig. 1 
) with a title,
a name at the top of the screen. The second component is obtained by selecting the heading "to modify" (edit page), where
upon the page can be changed immediately, without restrictions. A third component is the heading "discussion", where PalyWeb
users can exchange their ideas on the contents of the pages. The last component is the
"history" of pages
(Fig. 2 ). All former versions of the pages are stored with the user names,
the authors of its modifications. Each previous version can be restored (a very useful tool as this
procedure prevents mistakes and allows the evolution of the page content to be followed
in accordance with modifications made by various contributors).
The general architecture of the website is illustrated on
Figure 3
using as an example the organization of a page concerning the cryptospore genus Tetrahedraletes. The words
in blue are internal links to existing pages. The words are in red when a link has been created but the page
to be linked does not yet exist. All words useful for indicating relationships
within the database can be converted into links to other PalyWeb pages (external links are also possible). Most of the connexions
in the example link to taxonomic pages, but is possible to link to pages of other
subjects, for example, pages with bibliographic references, personal pages,
etc. Each page can be classed in several categories. This is a very important tool, not only
as an aid to navigation through the website, but also to organize pages in relation to
several discrete criteria. It is particularly interesting to group taxa by morphological characteristics, by stratigraphic levels
(Fig. 4 ), by geographic distribution and so on. Categories make this
possible for the application groups pages automatically and alphabetically by
the several criteria. One page can be assigned to several different categories.
Categories can be created or modified like a conventional page. However, the
great flexibility of a database of this kind could generate problems. To avoid inconsistency, it is important
that syntactical rules be established for naming the internal links. For example,
in PalyWeb, "cryptospore" and "cryptospores" are
discrete pages. Therefore, it is necessary to be strict in the way one contributes to the database.
The advantages of such a database are numerous. The whole palynological community has free access to the website and everybody is allowed to improve or to
add to its contents. The free distribution, constant updates, diverse and detailed coverage, by numerous professional palynologists
guaranties the high quality of data. The database is accessible by any computer with an
Internet connexion (Windows, Mac, Linux). Common web browsers are adequate for work with the database
(Internet Explorer,
Firefox, etc.). Therefore, it is not necessary to buy new software and to keep it up to date. The database is accessible
from wherever you are. To work with a colleague in a foreign country, a copy of the database
in your computer is not needed and there is no problem of cross-platform incompatibility. Information introduced into the database is immediately available to all.
Unlike other databases, it is not necessary to wait until the database is considered
complete before it becomes accessible. In addition, as new palynological data are available
continually, databases may be constantly and immediately upgraded. Wait for the new version of a database
(usually obsolete in a short time) is eliminated. There is no limitation on size
or contents (except the capacity of the disk on which the information is stored). The content of the database is highly flexible and
it was concepted to facilitate discussion. The website was not conceived and
built by a pugnacious individual or a small group; it is the result of the worldwide collaboration of the whole palynological community.
Meetings for the exchange of information are no longer necessary, and in any
event, were commonly restricted in number to those with travel subsidies.
J. & D.C. (1996).- Chapter 1. Introduction. In: J. & D.C. (eds.), Palynology: Principles and applications.- American Association of Stratigraphic Palynologists Foundation, Salt Lake City, n° 1, p. 1-10.
J.K., O.K., T.S. & K.M. (1996).- Chapter 24. Personal computers in palynology. In: J. & D.C. (Eds.), Palynology: Principles and applications.- American Association of Stratigraphic Palynologists Foundation, Salt Lake City, n° 1, p. 961-984.
Click on thumbnail to enlarge the image.
Figure 1: Example of a PalyWeb page containing the description of the Tetrahedraletes genus. Bleu words inside of the descriptive text are links to other pages (bibliographic references or genus description pages).
Click on thumbnail to enlarge the image.
Figure 2: Example of an historic page with the date and the author of the modifications.
Click on thumbnail to enlarge the image.
Figure 3: General architecture of PalyWeb based on the example of the Tetrahedraletes cryptospore genus.
Click on thumbnail to enlarge the image.
Figure 4: Example of a category page based on the example of Llandovery cryptospores already introduced in the PalyWeb database.
