For the past 18 months, some of the labs involved in the WHO
Schistosoma Genome Initiative's gene discovery effort have been using a
standardised nomenclature for naming cDNA clones and the expressed
sequence tag (EST) sequences derived from them.
At a recent meeting of the WHO Genome Network, it was decided to
revise this nomenclature so that the designation could be used
as a file name under the DOS operating system (ie. limiting it to 8+3
letters long). Below is the proposed new nomenclature.
clone = ABCCCCCC.DE
EST derived from clone ABCCCCCC.DE = ABCCCCCC.DEF
(UPPER CASE throughout) where:
A=species
(M=mansoni, J=japonicum, other species to be added as required)
B=stage
(A=adult, E=egg, L=miracidium (larvae), S=sporocyst, C=cercaria, L=lung, M=
male adult, F=female adult, others to be added as required)
CCCCCC=unique clone identifier
(freeform 6 characters (must use all 6))
D=laboratory
(A=Ain Shams University, Cairo; M=Federal University of
Minas Gerias, Belo Horizonte; N=Natural History Museum, London; P=
Institute Pasteur, Lille; Q=Queensland Institute for Medical Research,
Brisbane; R=Centro de Pesquisas Rene Rachou, Belo Horizonte; T=Theodor
Bilharz Research Institute, Cairo; others to be added as required)
E=unique library identifier
(to be asigned by the designating lab to distinguish between multiple
libraries from the same life cycle stage)
F=primer used to generate the EST
(3=T3, 7=T7, F=M13 forward, R=M13 reverse, S=SK, K=KS, others to be added
as required)
Please mail comments and suggestions concerning this proposed new
designation to the newsgroup for discussion.
(Note to the EST producing Labs. Once we have decided on the final
designation, NCBI have confirmed that they are happy to update the existing
schisto ESTs on DBEST to reflect this new designation. All that they
require is to be told how the old clone/EST names need to be altered to
reflect the new designation and they will write data parsing scripts to do
the updating automatically so that all the schisto records will have the
same type of designation. I will arrange this for all the submitting labs.)
DAJ
David A. Johnston
Executive Secretary to the WHO Schistosoma Genome Network,
Researcher, Biomedical Parasitology Division,
Dept of Zoology,
The Natural History Museum,
Cromwell Road,
South Kensington,
London SW7 5BD,
England
tel 0171 9389297 (from outside UK: 44 171 9389297)
fax 0171 9388754 (from outside UK: 44 171 9388754)
email daj at nhm.ac.uk
