- Launching of GeminiNet 2000
-
At The Danforth Plant Science Center
Dear colleagues,
In 1995, we set-up a network for information about geminiviruses entitled GeminiNet and
it ran until 1999, the date of ILTAB's move from San Diego to St. Louis at the newly created Donald Danforth Plant Science Center. It took us some time to
get the hardware and the personnel to get GeminiNet running again, but it is now operational.
The principle is the same as in the past, but we improved the
appearance of the website and developed the GeminiDb 2000. You will find the
following on the Gemini website:
- some basic information on the taxonomy of
geminiviruses, composition of the Geminiviridae ICTV Study-Group, current ICTV Description in the ICTV VIIth Report, list of
geminiviruses, phylogenetic trees, alignments and matrices, pairwise comparison distributions, genome organization…
- the GeminiNet, where you can register, update your information, and of course
send messages to everybody
- the GeminiDb 2000, a database of information on each geminivirus that will grow
with your participation!
The GeminiNet is self explanatory and does not require any
special software. Jjust follow the instructions. In the future we will improve it in such way that
you will be able to upload and download documents, allowing everyone to post proposals about
geminiviruses. For now we will use it as a messaging system.
All the geminivirus names have been changed to
those in the proposal entitled: "Revised Proposal for Naming Geminiviruses"
(published in
the Archives of Virology and presented in the webpage under the headline of "Nomenclature" and subheadline of "Naming
Geminiviruses."
We are aware that the proposal is not perfect and will not satisfy everyone, but we are confident that it is much better and clearer than the previous system. A direct correlation can be made between the name and the taxonomic status of the
virus. If you want to be convinced, look at the tree made with these names under "Quantitative Taxonomy, Phylogeny" and enlarge one of the branches of the tree!
The GeminiDatabase 2000 is a real database, meaning that we have the flexibility to enrich it further with text information, numbers, and pictures. Currently it is filled with nomenclature, taxonomy, and sequences, but as soon as this first phase is fully operational I
intend to invite volunteers to contribute by adding descriptions and pictures for their preferred
virus(es). The unit of the database
is a virus name, representing an isolate, a strain, or a species. We have about 56 fields covering past and present nomenclature, taxonomic status, GeneBank accession
number(s), genome organization features (beginning and ending of each ORF), and the nucleotide and peptide sequences of full genomes and independent
ORFs. In addition, we have about 800 references on geminiviruses that will be in the database and also presented as an alphabetical list of references,
arranged by the name of the first author. There is a search engine to search the database and retrieve the information available, whatever the type of information is, including images.
Currently, you can access the database only via the phylogenetic tree, but very soon we will have
the search engine running, allowing you to retrieve all sorts of information,
including images.
What will the GeminiDb be tomorrow?
That depends on what you will contribute to it. The current system is a very flexible database and we will upgrade to Oracle in
the near future. Currently, the only limitation is the time that we can dedicate to collecting information and to
storing it properly. Every geminivirologist can contribute to GeminiDb by providing information on one virus or a set of viruses; this information could be field data, losses, geographical distribution, epidemiological data, resistance, serological information, or simply pictures of symptoms. We will post all the pictures we have at
ILTAB, but
these only encompass the cassava geminiviruses and some tomato and cotton
geminiviruses. So, any person interested
in either organizing and stimulating the collection of specific information about
geminiviruses or interested in providing, individually, information about a specific virus is
welcome. Please contact me and we will work on it. Technically we have very
few constraints as we can store huge amounts of information in alphanumerical or image formats. Images are stored as Jpeg, Pict or Gif images at 200 dpi with a size of 5" x 7.5", allowing
the making of slides or prints with a good quality. A short caption and an author are stored with each image. Images are shown as stamps or low resolution images to allow a reasonable speed
for viewing.
GeminiNet could become a
valuable research and documentary tool. In the process of writing papers about geminivirus taxonomy and phylogeny, I
created a database of thousands of sequences which took countless hours of work.
I have provided the information so that it can be useful to others. Similarly, it is always difficult to have, on a short-term
basis, information about the distribution and importance of diseases. Having
this available in the GeminiDb would be extremely useful. There is a lot of information that is difficult to publish,
such as the pairwise distribution comparison for every single ORF or genome organization
data. All of this can be posted on the GeminiNet, and you can refer to it when you publish
by providing the webpage address. I hope to stimulate some of you to
contribute and enrich
GeminiDb 2000, so that it will become a unique
tool.
Regards to all,
Dr. Claude Fauquet
Director of ILTAB
iltab@danforthcenter.org
http://www.danforthcenter.org/iltab
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