Section 2 of 2 - Prev - Next

Plants of the North American Indians. USDA Miscellaneous Publication Number
237.
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/related/
FAQ_updated : May 1995

Database : GrainGenes
Species : Wheat, barley, oats, sugarcane, relatives
Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu
Curator : Gerard R. Lazo, lazo@pw.usda.gov
PI : Olin D. Anderson, oandersn@pw.usda.gov
ACEDB_version : 4_3 (Unix), 4.1b1 (MacAce)
Data_version : 1.7, December 1996
Availability : UNIX and Macintosh versions via anonymous ftp
Availability : Macintosh version on CD-ROM "RiceMac / MacGrainGenes", from
Dr. Baek Hie Nahm, Korea Rice Genome Research Program, Myongji University,
Yongin, Korea.
FTP : probe.nalusda.gov in pub/graingenes
FTP : grain.jouy.inra.fr in pub/database
Gopher : greengenes.cit.cornell.edu
Gopher : grain.jouy.inra.fr
Gopher : probe.nalusda.gov:7002
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/plant/
WWW : http://wheat.pw.usda.gov/
WWW : http://grain.jouy.inra.fr
Data_updated : December 1996
FAQ_updated : December 1996

Database : IGD (Integrated Genomic Database)
Species : Homo sapiens
Subject : Chromosome 21
Availability : September 1994 by ftp, on-line server October 1994
Contact : Otto Ritter, o.ritter@dkfz-heidelberg.de
Contact : Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr
Contact : Nicole Creau-Goldberg, creau@arthur.citi2.fr
Contact : Jean-Maurice Delabar, delabar@arthur.citi2.fr
Description : IGD (Integrated Genomic Database) aims to integrate multiple
public general molecular biology and human genome specific databases into
single logical database with unified interface to existing analysis tools.
From data produced by the 4th International Workshop on Chromosome 21
(Genomics,1993,18,735-744) and from data provided by or taken from the
following databases and data repositories: GDB, OMIM, EMBL, CEPH, Genethon,
UKProbeBank, and RLDB.

Database : IXDB (Integrated X chromosome DataBase)
Species: Homo sapiens
Subject: Chromosome X
Acedb_version : 4.1
Data: The YAC map constructed by the Max-Planck-Institut fuer Molekulare
Genetik in Berlin, with all the attached experimental data necessary to
reconstruct the map. Information on each of 9000 YAC clones mapped to the X
chromosome, and constituting the YAC collection assembled with clone sets
from 14 different laboratories worldwide.
Latest_release:March 1996
Curator: Hugues Roest Crollius, roest@mpimg-berlin-dahlem.mpg.de
Contact: Ulf Leser, leser@mpimg-berlin-dahlem.mpg.de
PI: Hans Lehrach
FTP: ftp.mpimg-berlin-dahlem.mpg.de in directory pub/lehrach/x-map
WWW: http://www.mpimg-berlin-dahlem.mpg.de/~xteam

Database: Leishdb
Species: Leishmania major, L. infantum, L. peruviana, L. donovani and others
PI: Jennie Blackwell
PI: Al Ivens
ACEDB_version: 4.3
Curator: Martin Aslett
Contact: Martin Aslett, aslett@ebi.ac.uk
FTP: ftp.ebi.ac.uk/pub/databases/parasites/Leish
WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html
WWW: http://www.ebi.ac.uk/parasites/leish/leishpage.html (in development)
Data_updated: October 1996
FAQ_updated : November 1996

Database : LIGM-DB
Curator : Veronique Giudicelli
Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell
receptors
PI : Marie-Paule Lefranc
Contact : Veronique Giudicelli, LIGM IGMM UMR CNRS 9942, BP 5051 Rte de
Mende, 34000 Montpellier, giudi@ligm.crbm.cnrs-mop.fr

Database : MaizeDB
Species : Zea mays L. ssp. mays and related species
Content : Maps, raw map data, loci, probes, genetic stocks, variations,
mutant images, agronomic traits, gene products, QTL, bibliography, colleague
addresses; hardlinks to sequence and germplasm databases.
Latest_release : Oct 1996
Acedb_version : 4.1
Curator : Mary Polacco, maryp@teosinte.agron.missouri
PI : Ed Coe, Jr., ed@teosinte.agron.missouri.edu
Systems : Denis Hancock, dhancock@teosinte.agron.missouri.edu
FTP : probe.nalusda.gov/pub/maizedb/macedist961001.tar.gz
WWW : http://www.agron.missouri.edu
WEBACE : http://probe.nalusda.gov:8300/
Contact : db_request@teosinte.agron.missouri.edu
Comment : Data are periodically extracted into ACEDB format from Sybase
Comment : Genera software used to maintain the Sybase database and its
gateways, except for ACEDB
Comment : ACEDB releases are announced on the MAIZE bulletin board;
http://www.bio.net/hypermail/MAIZE/
Comment : WEBACE records are hardlinked to the Sybase server where data are
curated
Funding : USDA ARS Plant Genome Research Program
FAQ_updated : Mar 7, 1997

Database : Mendel (plant wide gene names)
Species : wide range of plant species
Subject : standardized designations for sequenced genes
Comment : The purpose is to provide a common system of nomenclature for
substantially similar genes across the plant kingdom. Mendel is maintained
by the Commission on Plant Gene Nomenclature.
ACEDB_version : 4.0
Curator : Carl Price, price@mbcl.rutgers.edu
Curator : Ellen Reardon, reardon@mbcl.rutgers.edu
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/related/
FAQ_updated : July 1995

Database : Millet Genes
Species : Pennisetum glaucum (Pearl Millet)
ACEDB_version : 4.3
Curator : Matt Couchman, Matthew.Couchman@bbsrc.ac.uk
PI : Katrien Devos, Katrien.Devos@bbsrc.ac.uk
FTP: ftp://jiio5.jic.bbsrc.ac.uk/pub/millet
WWW : http://synteny.nott.ac.uk/millet.html
WWW : http://jiio5.jic.bbsrc.ac.uk:8000/index.shtml
WWW : http://probe.nalusda.gov:8300/plant/
FAQ_updated : March 1997

DataBase : Mousedb
Species : Mus Musculus
Species : Homo Sapiens
ACEDB_version : 3.0 with extensions to define and display cytogenetic data.
Description : Mouse genome data from the published literature, including
mouse genes with phenotypic effects, chromosome anomalies, imprinted regions
and man-mouse homologies with associated pathological disorders. The maps
are consensus ones. They use data, such as the HIS and anomaly data, to show
alignments between the genetic and cytogenetic maps.
Curator : Rachael Selley, rselley@har-rbu.mrc.ac.uk
PI : Mary Lyon
PI : Jo Peters
Availability : Mousedb is available publicly from the UK HGMP Resource
Centre's computing service via the INTERNET. For user id. please contact
Administration, HGMP Resource Centre, Hinxton Hall, Cambridgeshire CB10 1RQ,
UK.
Tel: (+44) 1223 494520 Fax: (+44) 1223 494510
Contact : Rachael Selley, MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11
ORD
FAQ_updated : July 1995

Database : MPNADB (Medicinal Plants of Native America)
Species : Over 2,100 plant species
Curator : Daniel E. Moerman, dmoerman@umich.edu
Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov - ACEDB version

Comment : MPNADB is based on a two-volume book of the same name published in
1986 by the Museum of Anthropology of the University of Michigan. MPNADB was
first developed at the University of Michigan in DBase II.
ACEDB_version : 4.0
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/related/
FAQ_updated : June 1995

Database : MsqDB
Species : Interspecies Mosquito database
ACEDB_version : 4.3
WWW : http://klab.agsci.colostate.edu/
Curator : Dennis Knudson, dknudson@lamar.colostate.edu
Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu
Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu
Contact : aaedbmgr@klab.agsci.colostate.edu
Data_updated : regularly
FAQ_updated : April 1997

Database : MycDB
Species : Mycobacteria
Comment : MycDB is a collation of data on the mycobacteria, causative agents
of tuberculosis and leprosy. It is centered on the mapping and sequencing
projects under way in M.leprae and M.tuberculosis.
Curator : Staffan Bergh, staffan@biochem.kth.se
Curator : Stewart Cole, stcole@pasteur.fr
ACEDB_version : 4.3
Data_version : 4-22 (December 1996)
FTP : www.biochem.kth.se (130.237.52.64) in pub/MycDB
FTP : ftp.pasteur.fr (157.99.64.12) in pub/MycDB
FTP : bioinformatics.weizmann.ac.il (132.76.55.12) in
pub/databases/acedb/mycdb
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://www.biochem.kth.se/MycDB.html
WWW : http://probe.nalusda.gov:8300/other/
FAQ_updated : December 1996

Database : OMIA (Online Mendelian Inheritance in Animals)
Species : wide range of animal species
Subject : gene and phene (familial trait or phenotype) information
Comment : MIA is modeled after Victor McKusick's Mendelian Inheritance in
Man (MIM) database and was developed at the University of Sydney, Australia,
in Advanced Revelation.
Curator : Frank Nicholas, frankn@doolittle.vetsci.su.oz.au
ACEDB_version : 4.0
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/animal/
WWW : http://morgan.angis.su.oz.au/BIRX/phenes_form.html
FAQ_updated : September 1995

Database : PhytochemDB (Plant Chemicals)
Species : wide range of plant species
Subject : Consists primarily of plant chemical data, including quantity,
taxonomic occurrence, and chemical activity.
Comment : Converted to ACEDB from the original SQL database.
ACEDB_version : 4.0
Data_version : July 1994
Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov
Curator : James A. Duke, ngrljd@ars-grin.gov
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/related/
FAQ_updated : June 1995

Database : PomBase
Curator : Sean Walsh, svw@sanger.ac.uk
Curator : Marie-Adele Rajendream
PI : Bart Barrell, barrell@sanger.ac.uk
Species : Schizosaccharomyces pombe
ACEDB_version : 4.1
FTP : ftp.sanger.ac.uk in pub/PomBase
FAQ_updated : September 1995

Database : PVP (Plant Variety Protection)
Species : Glycine max (soybeans)
Subject : Data about plant varieties that have been granted a Certificate of
Protection by the Plant Variety Protection Office.
Curator : Stephen M. Beckstrom-Sternberg, sbeckstr@nalusda.gov - ACEDB
version
ACEDB_version : 4.0
Contact: The Plant Variety Protection Office, Room. 500, National
Agriculture Library, 10301 Baltimore Blvd., Beltsville, Maryland 20705
Telephone : 301-504-5518
Fax : 301-504-5291
Email : Jeff Strachan, strachan@locus.nalusda.gov
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/related/
FAQ_updated : June 1995

Database : Receptor Database
Species : all
Curator : Kotoko Nakata, nakata@nihs.go.jp
Co-Curator : Takako Igarashi, taka@nihs.go.jp
Co-Curator : Tsuguchika Kaminuma, kaminuma@nihs.go.jp
Contact : Kotoko Nakata, nakata@nihs.go.jp
ACeDB_version : 4.1
WWW : http://impact.nihs.go.jp/RDB.html
Data_updated : regularly
FAQ_updated : October 1997

Database : RiceGenes
Species : Oryza sativa
Curator : Edie Paul, epaul@nightshade.cit.cornell.edu
PI : Susan McCouch
ACEDB_version : 4.1
FTP : probe.nalusda.gov in pub/ricegenes
Gopher : nightshade.cit.cornell.edu
Gopher : probe.nalusda.gov:7007
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/plant/
FAQ_updated : November 1996

Database : SacchDB
Species : Saccharomyces cerevisiae
Subject : Budding (common baker's) Yeast Genome
ACEDB_version : UNIX 4.3, MacAce 4.0b4
Data_version : 4.6
Data : All Saccharomyces genes contained in the Registry of Gene Names.
Results of the completed chromosomal sequencing projects have been
integrated into the database. Physical Maps based on DNA sequencing
projects, hybridization to the Olson/Riles prime filter grids, and
restriction mapping. For the completely sequenced chromosomes the Olson
prime clones have been re-mapped (on the computer) to the DNA sequence.
Saccharomyces DNA sequences contained within GenBank are incorporated.
Literature references, most including abstracts, for the information
contained within the database. Gene protein product information obtained
from the YPD database (Garrels and Latter, CSHL) and the literature. Genetic
Maps including the underlying two point tetrad data. Including all tetrad
data reported in previous additions of the Mortimer Yeast Maps.
FTP : genome-ftp.stanford.edu in pub/yeast/SacchDB
FTP : ncbi.nlm.nih.gov in repository/SacchDB
WWW : http://genome-www.stanford.edu/
Funding : National Center for Human Genome Research, NIH
PI : David Botstein, botstein@genome.stanford.edu
Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu
Curator : Selena Dwight, dwight@genome.stanford.edu
Curator : Cathy Ball, ball@genome.stanford.edu
Curator : Caroline Adler, adler@genome.stanford.edu
Curator : Yankai Jia, jia@genome.stanford.edu
Programmer : Gail Juvik, gjuvik@genome.stanford.edu
Programmer : Shuai Weng, shuai@genome.stanford.edu
Sys. Admin : Mark Schroeder, mark@genome.stanford.edu
Contact : yeast-curator@genome.stanford.edu
Data_Submission : yeast-curator@genome.stanford.edu
FAQ_updated : September 1996

Database: SchistoDB
Species: Schistosoma mansoni (plus other schistosomes)
PI: David Johnston
ACEDB_version: 4.3
Curator: Martin Aslett
Contact: Martin Aslett, aslett@ebi.ac.uk
FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/Schisto/
WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html
Data_updated: In development
FAQ_updated : November 1996

Database : SolGenes
Subject : Solanaceae - tomato, potato, pepper
Curator : Sam Beer, sbeer@nightshade.cit.cornell.edu
PI : none currently
Release : ACEDB 4.3
FTP : probe.nalusda.gov in pub/solgenes
Gopher : nightshade.cit.cornell.edu:71
Gopher : probe.nalusda.gov:7006
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/plant/
Data_updated : May 1997
FAQ_updated : May 1997

Database : SorghumDB
Species : Sorghum bicolor (L.) Moench
PI : Keith F. Schertz, schertz@tamvm1.tamu.edu
USDA-ARS, Dept. of Soil & Crop Sciences, Texas A&M University, College
Station, TX 77843-2474
Phone : (409) 260-9252
FAX : (409) 845-0456
Curator : Najeeb U. Siddiqui, nus6389@tam2000.tamu.edu
Southern Crop Improvement Facility, Crop Biotechnology Center, Texas A&M
University, College Station, TX 77843-2123
Phone : (409) 862-1523
FAX : (409) 862-4790
ACEDB_version : 3.0
Data_version : 2.0
FTP : probe.nalusda.gov in pub/sorghumdb
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/plant/
FAQ_updated : September 1995

Database : SoyBase
Species : Glycine max (Soybeans) and related species
PI : Randy Shoemaker, rcsshoe@iastate.edu
Curator : David Grant, dgrant@iastate.edu
Assistant_curator : Marica Imsamde, mimsande@iastate.edu
Contact : David Grant, dgrant@iastate.edu
ACEDB-Version : 3.7
FTP : probe.nalusda.gov in pub/soybase
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/plant/
WWW : http://macgrant.agron.iastate.edu
FAQ_updated : October 1995

Database : Syndb
Species : Homo sapiens, Mus musculus
Subject : STS content mapping & directed sequencing of Human Chromosomes
21,5 with Mouse for syntenic comparison
ACEDB_version : acedb v3.3 plus moulon server
FTP : genome.lbl.gov in pub/acedb/
WWW : http://genome.lbl.gov/Genome/acepage.html
Curator : Donn F. Davy, DFDavy@lbl.gov
Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov
PI : Michael Palazzolo
PI : Chris Martin
PI : Jan-Fang Cheng, jcheng@genome.lbl.gov
FAQ_updated : October 1994

Database: ToxoDB
Species: Toxoplasma gondii
PI: David Sibley
PI: David Roos
PI: Jim Ajioka
ACEDB_version: 4.3
Curator: Martin Aslett
Contact: Martin Aslett, aslett@ebi.ac.uk
FTP: ftp.ebi.ac.uk/pub/databases/parasites/Toxo/
WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html
WWW: http://www.ebi.ac.uk/parasites/toxo/toxpage.html
Data_updated: October 1996
FAQ_updated: November 1996

Database : TreeGenes
Species : Forest trees
ACEDB_version : 4.3
Curator : Bradley K. Sherman, bks@s27w007.pswfs.gov
PI : David B. Neale, dbn@s27w007.pswfs.gov
Contact : Dendrome@s27w007.pswfs.gov
FTP : probe.nalusda.gov in /pub/treegenes
Gopher : s27w007.pswfs.gov/
Gopher : probe.nalusda.gov:7508/
Gopher : probe.nalusda.gov:7000/11/genome.databases/
WWW : http://probe.nalusda.gov:8300/plant/
WWW : http://s27w007.pswfs.gov/
FAQ_updated : May 1996

Database: Trypbase
Species: Trypanosoma brucei
PI: Sara Melville
ACEDB_version: 4.3
Curator: Howard Cobb
Curator: Martin Aslett
Contact: Sara Melville, sm160@mole.bio.cam.ac.uk
Contact: Martin Aslett, aslett@ebi.ac.uk
FTP: ftp.ebi.ac.uk/pub/databases/parasites/brucei
WWW: http://parsun1.path.cam.ac.uk/newtryp/toppage.htm
WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html
Data_updated: October 1996
FAQ_updated: November 1996

Database : 21Bdb
Species : Homo sapiens
Subject : STS content mapping and sequencing of Human Chromosome 21
ACEDB_version : acedb.1-10 plus moulon server
Curator : Donn F. Davy, DFDavy@lbl.gov
Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov
PI : Michael Palazzolo
PI : Chris Martin
PI : Jan-Fang Cheng, jcheng@genome.lbl.gov
FTP : ftp://genome.lbl.gov in pub/acedb/
WWW : http://genome.lbl.gov/Genome/acepage.html
FAQ_updated : April 1994

Database : 11Db
Species : Homo sapiens
Subject : Physical and Genetic mapping of Human Chromosome 11 Description :
11Db attempts to show as full a picture as possible of the genetic and
physical maps of Human Chromosome 11. It has two new displays, one which
attempts to integrate as much of the mapping data as possible using minimal
intervals, and one which displays YAC Contigs downloaded from SEGMAP
datafiles.
Contact : Benedict Arnold (b.arnold@bc.ic.ac.uk)
PI : Peter Little (p.little@bc.ic.ac.uk)
ACEDB_version : based on 4_1 with added map displays.
ACEDB_version : based on 3_6 with added map displays.
Data version : 1.0
Last Update : December 1995
WWW : http://chr11.bc.ic.ac.uk
FTP : ftp.cc.ic.ac.uk
Description : 11Db attempts to show as full a picture as possible of the
genetic and physical maps of Human Chromosome 11. It has two new displays,
one which attempts to integrate as much of the mapping data as possible
using minimal intervals, and one which displays YAC Contigs downloaded from
SEGMAP datafiles.

Database : 22ace
Species : Homo sapiens
Subject : Physical map of human chromosome 22, genomic sequencing and more
ACEDB_version : 4.1
Curator : Ian Dunham, id1@sanger.ac.uk
Curator : Gareth Maslen, glm@sanger.ac.uk
PI : Ian Dunham
FTP : ftp.sanger.ac.uk in pub/human/chr22/physical_map/
WWW : http://www.sanger.ac.uk/hum22/
FAQ_updated : August 1995

Database : VoxPop
Species : Populus species
Curator : Carl G. Riches, cgr@poplar1.cfr.washington.edu
PI : Reinhard F. Stettler, STETTLER@coyote.cfr.washington.edu
ACEDB_version : 1.9
FTP : poplar1.cfr.washington.edu in /pub/
Gopher : poplar1.crf.washington.edu

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Q12:Who prepared this document & where is the current version?

A12:

This document is posted monthly to the BIOSCI newsgroup
bionet.software.acedb and to USENET conference news.answers. It is intended
to be used as an index to ACEDB databases and to information about the
database software.

The WWW version of this document is at:
http://probe.nalusda.gov:8000/acedocs/acedbfaq.html

A text version is available via anonymous ftp at machine rtfm.mit.edu as
pub/usenet/news.answers/acedb-faq. If you only have electronic mail, the FAQ
can be retrieved from mail-server@rtfm.mit.edu.

Curators of ACEDB databases should take note of Question 4 and keep me
apprised of changes.

Errors of commission or omission are unintentional. If I have forgotten to
give you credit please let me know. Please send comments and corrections to:
acedbfaq@s27w007.pswfs.gov

This FAQ was created and maintained from 1993 - 1996 by Bradley K. Sherman.
Major contributions in getting it off the ground were made by Mike Cherry,
John McCarthy, and Doug Bigwood. Other contributors include:

   * Lisa Lorenzen
   * David Matthews
   * Edie Paul
   * Donn Davy
   * Eric De Mund
   * Sam Cartinhour

It is currently maintained by Dave Matthews.

Please cite as:
Matthews, D.E., and B.K. Sherman, ACEDB Genome Database Software FAQ,
ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq,
http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993-1997, approx. 70K
bytes.

To add or modify information in this document, please send mail to:
acedbfaq@s27w007.pswfs.gov

The GrainGenes Project is funded by the USDA ARS Plant Genome Research
Program.

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