From owner-acedb@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!NETCOM.COM!gothmog From: gothmog@NETCOM.COM (En ring til aa herske) Newsgroups: bionet.software.acedb Subject: unsubscribe acedb Date: 4 Apr 1995 08:14:28 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net unsubscribe acedb From owner-acedb@net.bio.net Mon Apr 03 23:00:00 1995 Path: biosci!GDB.ORG!letovsky From: letovsky@GDB.ORG (Stan Letovsky) Newsgroups: bionet.software.acedb Subject: core dump on reading models Date: 4 Apr 1995 07:31:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Anyone familiar with an acedb3 bug in which the system dumps core on (re)reading models? Any known cause/cure? (The models need not have changed...) Cheers. -Stan From owner-acedb@net.bio.net Wed Apr 05 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: mieg@watson.wustl.edu (Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: printing is ACE3-7 on sun sparc Date: 7 Apr 1995 00:51:19 +0100 Lines: 32 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3m1upn$83j@mserv1.dl.ac.uk> Original-To: john.morris@frodo.mgh.harvard.edu, net@kaa.crbm.cnrs-mop.fr i use print window without problem may be it looks for the definiton of the printers which is possibly forbiden at ncbi so may be we need an environment variable does anyone have a clue ? problem is: m: john.morris@frodo.mgh.harvard.edu (John Morris) Subject: printing is ACE3-7 on sun sparc Hi Jean, I'm trying to work with the ACE3-7b binary on the ncbi server. I like tablemaker, pulled out a sequence table that I couldn't create in 3-0. However, the Print/Mail window comes up blank, and ACE seems to freeze. I can move windows around the screen but nothing that I click on has any effect, nor do the ACE windows refresh. Should I try compiling locally? - John AAtDB From owner-acedb@net.bio.net Thu Apr 06 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!pipex!warwick!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!srk From: srk@handa.sanger.ac.uk (Simon Kelley) Newsgroups: bionet.software.acedb Subject: Re: printing is ACE3-7 on sun sparc Date: 07 Apr 1995 09:21:09 GMT Organization: Sanger Centre, Hinxton Hall, England. Lines: 19 Distribution: bionet Message-ID: References: <3m1upn$83j@mserv1.dl.ac.uk> NNTP-Posting-Host: handa.sanger.ac.uk In-reply-to: mieg@watson.wustl.edu's message of 7 Apr 1995 00:51:19 +0100 I've just re-coded the print window to look for the available printers in /etc/printcap. (We used to use lpc, but that's always in a different place, or not on the path, or blocks or ... or ...) Is there something odd about your /etc/printcap? Or maybe the /etc/printcap code didn't make it into 3_7 and lpc is blocking, the symptoms you describe are typical of what I was seeing in that case. Jean, what version of graphprint.c did you have for 3_7b? Simon. ------------------------------------------------------------------------------- Simon Kelley. srk@sanger.ac.uk work: +44 223 494980 home: +44 223 832411 -- ------------------------------------------------------------------------------- Simon Kelley. srk@sanger.ac.uk work: +44 223 494980 home: +44 223 832411 From owner-acedb@net.bio.net Thu Apr 06 23:00:00 1995 Path: biosci!agate!usenet.ins.cwru.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!newsspool.doit.wisc.edu!decwrl!enews.sgi.com!sgigate.sgi.com!olivea!charnel.ecst.csuchico.edu!nic-nac.CSU.net!cello.gina.calstate.edu!usenet From: Nancy Bosserman Newsgroups: bionet.software.acedb Subject: Stealth.B Date: 7 Apr 1995 19:24:36 GMT Organization: Teacher Lines: 6 Distribution: world Message-ID: <3m43hk$l1c@cello.gina.calstate.edu> NNTP-Posting-Host: 130.150.1.105 X-UserAgent: 1.1 X-XXDate: Fri, 7 Apr 95 19:32:05 GMT Please, anyone who knows any thing about the, "Stealth.B" virus (Aliases:STB. AMSES) write to me at the adress listed above. My 386 has been taken over by this virus. This virus also over wrote Norton Anti Virus. Any information you might have will be appreciated. Shut Down From owner-acedb@net.bio.net Thu Apr 06 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!uunet!rose.uthscsa.edu!bloch.nmr.mgh.harvard.edu!usenet From: John Morris Newsgroups: bionet.software.acedb Subject: Re: printing is ACE3-7 on sun sparc Date: 7 Apr 1995 16:04:54 GMT Organization: Mass General Hospital Lines: 16 Message-ID: <3m3nr6$27n@bloch.nmr.mgh.harvard.edu> References: <3m1upn$83j@mserv1.dl.ac.uk> NNTP-Posting-Host: thale.mgh.harvard.edu srk@handa.sanger.ac.uk (Simon Kelley) wrote: > > > I've just re-coded the print window to look for the available printers > in /etc/printcap. (We used to use lpc, but that's always in a > different place, or not on the path, or blocks or ... or ...) > > Is there something odd about your /etc/printcap? > I will have to look at /etc/printcap (I'm don't anticipate understanding much) In the mean time I've recompiled on my local sparc and printing works fine on one machine, the other, however, produces oversized type. -- like 1/2 page expands to 4 pages. John AAtDB From owner-acedb@net.bio.net Sat Apr 08 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!Norway.EU.net!EU.net!howland.reston.ans.net!news.sprintlink.net!uunet!bloom-beacon.mit.edu!mojo.eng.umd.edu!cs.umd.edu!news.umbc.edu!haven.umd.edu!purdue!yuma!klab3.agsci.colostate.edu!user From: martinf@lamar.colostate.edu (Martin Ferguson) Newsgroups: bionet.software.acedb Subject: Query syntax Date: Fri, 07 Apr 1995 13:17:09 -0600 Organization: Colorado State University Lines: 44 Distribution: world Message-ID: Reply-To: martinf@lamar.colostate.edu NNTP-Posting-Host: klab3.agsci.colostate.edu Greetings all, I have a query language question (using ACEDB v3). How do you identify a specific paper that is listed in one specific keyset which is in a list of keysets? For example, on my system: If you click on "KeySet", you get a window with several keysets listed: 1984 1985 1986 1987 Each of these KeySets is a KeySet which contains data related to that year. For example, if you click on "1984", it has certain loci, journals, paper names, and authors: Est-6 Est-6Mal Gpd-1 Idh-2 Py(2) J. Med. Ent. J. Med. Entomol. Japanese Journal of Genetics Transactions of the American Microbiological Society edwar-1984-38899 <<<<<<< Paper item field-1984-29951 <<<<<<< Paper item oro---1984-63853 <<<<<<< Paper item rowle-1987-36038 <<<<<<< Paper item Oro, G. Powell, J. R. Rowley, W. A. Stollar, V. Sutherland, D. R. So, how do I write a query that will pull out the 4 papers listed? Thanks. /s/ Martin From owner-acedb@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!mrc-lmb.cam.ac.uk!rd From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: ACEDB data update for worm - data only Date: 10 Apr 1995 14:22:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 122 Sender: daemon@net.bio.net Distribution: world Message-ID: <9504102119.AA06431@cele.mrc-lmb.cam.ac.uk> NNTP-Posting-Host: net.bio.net This is a broadcast message to the ACEDB mailing list and related newsgroups. If you are on the mailing list and do not want to be, please send email to rd@sanger.ac.uk. ACEDB data updates 2-15, 2-16, 2-17, 2-18 for C. elegans ======================================================== A set of four new data update files are available for the C. elegans database. Once again they are incremental updates, with new data but no change to the program. This means Sparc users will again have to build the maps by hand after adding the updates (see below). As with the previous release, there are 4 update files because there is a large amount of new data. The total database size is now approximately 140Mbytes. This release is fully up to date with respect to the physical map, the CGC information, and gene/genetic map information prior to that resulting from the recent call for data (which we are working on now). We have also added over 200 Medline references and a significant number of missing Gazette pages. There is also a lot of new genomic sequence information. There will be a further release with at least the worm meeting abstracts and further sequence data three weeks before the worm meeting. Code ==== There is no new code version. You should continue to use your existing version of the binary (2_0). We are close to a version 4 code release (most of the kernel bugs have been fixed), but did not want to wait even longer to make this data available. That has not turned out to be a good strategy! ****** IMPORTANT ****** There is a bug in version 2_0 of the code that causes the program to crash ("bus error" or "segmentation violation") in some versions of the binary (particularly sparc) at the very end of reading the updates. This does not lose any data. It does remove the precalculation of the genetic and physical maps, which should speed up their display. You can do this precalculation by hand as follows: After adding the update, as the administrator (the person who installed ACEDB) Select "Write Access" from the main menu Select "Align Maps" from the main menu Press the "Make pMaps" button to make the physical maps Press the "Make gMaps" button to make the genetic maps Select "Save" from the main menu. ************************** Macintosh version ================= There will be a new macace self-extracting archive containing this data, ready in approximately a week from now (Frank is away just now). It will be announced separately on the celegans and acedb newsgroups, and to the macace mailing list (contact Frank Eeckman if you wish to be added to this: eeckman@genome.lbl.gov). Instructions for obtaining updates/the whole thing ================================================== All the files are available in the following public access accounts (anonymous ftp sites) accessible over internet: ncbi.nlm.nih.gov (130.14.20.1) in the USA, in repository/acedb/ace2 cele.mrc-lmb.cam.ac.uk (131.11.84.1) in England, in pub/acedb/ace2 lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/acedb/ace2 In each case, log in as user "anonymous" and give a user identifier as password. Remember to transfer the files in BINARY mode by typing the word "binary" at the start of your ftp session. Many thanks to NCBI for letting us share in their excellent resource. Example: ftp ncbi.nlm.nih.gov login: anonymous password 'your email address' cd repository/acedb/ace2 binary mget * get README y/n answer yes etc .. .. quit If installing for the first time -------------------------------- Get all the update.2-n.tar.Z and read the files README and NOTES before proceeding further. If updating an existing system ------------------------------ Just get the update.2-n.tar.Z files that you are missing, plus INSTALL. Always get a copy of the INSTALL script. Move it and the .tar.Z files into the home directory in which you are installing ACEDB. Type "source INSTALL". Start acedb (normally by typing "acedb") and choose "Add Update File" from the menu (right button), and press "All updates" with the left mouse button. If you have a problem making the program work, look at the section on problems in NOTES, and if that fails to help, let us know. ****************************************************************** Please send any comments, especially about anything you think is wrong to one of us: Richard Durbin (rd@sanger.ac.uk) Sylvia Martinelli (sylvia@sanger.ac.uk) -------------------- end of message -------------------- From owner-acedb@net.bio.net Sun Apr 09 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!math.ohio-state.edu!uwm.edu!lll-winken.llnl.gov!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 10 Apr 1995 18:40:55 GMT Organization: Dendrome, A genome database for forest trees Lines: 1063 Approved: news-answers-request@MIT.Edu Message-ID: <3mbu3n$o10@overload.lbl.gov> Reply-To: acedbfaq@s27w007.pswfs.gov NNTP-Posting-Host: s27w007.pswfs.gov Summary: Frequently Asked Questions about finding and getting started with the database system ACEDB. ACEDB is used to collect information regarding the molecular biology of the genome. Xref: biosci bionet.software.acedb:564 news.answers:36143 Archive-name: acedb-faq Last-modified: 4/10/95 Version: 1.20 ACEDB FAQ ********* Frequently Asked Questions about ACEDB ====================================== o Q0 : What is ACEDB? o ++++++++++++++++++++ o Q1 : What is the current version of ACEDB? o +++++++++++++++++++++++++++++++++++++++++++ o Q2 : What hardware/software do I need to run ACEDB? o ++++++++++++++++++++++++++++++++++++++++++++++++++++ o Q3 : Where can I get ACEDB? o ++++++++++++++++++++++++++++ o Q4 : What ACEDB databases exist? o +++++++++++++++++++++++++++++++++ o Q5 : What written documentation exists for ACEDB? o ++++++++++++++++++++++++++++++++++++++++++++++++++ o Q6 : !Where can I find further information about ACEDB? o ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ o Q7 : How should ACEDB be cited? o ++++++++++++++++++++++++++++++++ o Q8 : Is ACEDB object-oriented? o +++++++++++++++++++++++++++++++ o Q9 : What's all this about Gopher, WAIS, FTP, WWW, URL, ... o ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ o Q10 : How can I get on/off the ACEDB announcements mailing list? o +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ o Q11 : When and where is the next ACEDB Workshop? o +++++++++++++++++++++++++++++++++++++++++++++++++ o Q411 : Who prepared this document & where is the current version? o ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Questions marked with '+' are new, those with '!' have substantially changed answers. Q0: What is ACEDB? ================== A0: ACEDB is an acronym for A Caenorhabditis elegans Database. It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. This document is concerned primarily with the latter meaning. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species [Q4 gives contact information]. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning circa 1990. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available [See Q3]. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups including Lawrence Berkeley Laboratory and the Integrated Genomic Database (IGD) project headed by Otto Ritter. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage -missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions Q1: What is the current version of ACEDB? ========================================= A1: === (This answer refers to the software not the C. elegans data.) Most production sites are using 3.0 (or 2.0) binaries. The most recent beta source code distribution (1/95) is test.source.3.6a.tar.gz. A Macintosh version is available as version 2.0b4. To retrieve the software see Q3. To be kept informed of new releases see Q10. Return to List of Questions Q2: What hardware/software do I need to run ACEDB? ================================================== A2: === The software is available as source code, so you may be able to get it working on any machine, with effort. It is also available in binary (pre-compiled) format for a variety of machines. To retrieve the software see Q3. o Unix and X11: o Sun/SunOS 4.x o Sun/Solaris o DEC DECstation3100, 5100 etc. o DEC Alpha/OSF-1 o Silicon Graphics Iris series o PC 386/486 with Linux (free Unix) [note from Jeff Bryer, jbryer@darwin.mbb.sfu.ca] I just installed up Linux yesterday and today spent the many hours to compile in the C. elegans data for ACEDB v2.0 So to save other people the trouble of doing the same the entire package ACEDB for Linux 2-10 is available on trog.mbb.sfu.ca in /pub/acedb as linux.2_10.tar.Z The data was compiled in on a 486DX-33 with 16MBs of RAM running Linux 1.1.18 (Slackware 2.0.0 distribution) and a 32MB swap device (and it chugged away for a couple hours chewing up all 16MBs and half the swap space). File size is about 73MBs uncompressed, 26MBs compressed. This is based on the ACEDB v2.0 port for Linux that Ken Clark (ken@darwin.mbb.sfu.ca) did. o There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM R6000, Convex. You may have to contact the developer responsible for the port to make these real. o NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu o MSDOS/Windows/NT: o A port to NT is rumored to be in the works. o Macintosh: o [Contributed by Frank Eeckman] Macace is distributed as a self-extracting archive that contains the application, the wspec files, and a fully up to date database. macace 3.0 is available with an updated 21bdb database. Please send all questions/bug reports to eeckman@llnl.gov A native powerPC version is available as well. Macace needs a macintosh with > 16 MBytes of RAM, and a decent color monitor is preferred. System 7 or greater is required. For the multimedia extensions Quicktime 1.0 is required. Please add your name to our mailing list by sending email to eeckman@llnl.gov. It is our belief that for cost savings a powerPC mac will beat the advertised linux-intel combination. Macace is fully compatible with xace, but includes some multimedia extensions (picture and movie support) not found in the unix versions. o ACEDB for The NEC EWS4800 is available via anonymous ftp at ftp.nec.co.jp (192.135.93.2) in /pub/packages/acedb/ace2. Contact Tohru Sano Fundamental Research Laboratories NEC Corporation Tsukuba, 305, JAPAN, e-mail: sano@exp.cl.nec.co.jp, FAX: +81-298-56-6136, VOICE: +81-298-50-1507 (Here at the Institute of Forest Genetics we run ACEDB on a Sun Microsystems SPARCstation II, and users can interact using Macintoshes and PC-clones by using X11 implementations for the personal computers and a LAN. --bks) X11 fonts note: ACEDB uses fonts listed in the xfonts.wrm file. If you install new fonts on your machine be sure to run bldfamily(1) so that they are available. Return to List of Questions Q3: Where can I get ACEDB? ========================== A3: === The standard ACEDB source and binaries are available in the following public access accounts (anonymous ftp sites) accessible via Internet: o lirmm.lirmm.fr in pub/acedb o cele.mrc-lmb.cam.ac.uk in pub/acedb o ncbi.nlm.nih.gov in repository/acedb o bioinformatics.weizmann.ac.il in pub/databases/acedb. MacAce is available from: o genome.lbl.gov in pub/macace o cele.mrc-lmb.cam.ac.uk in pub/acedb/macace Linux; ACEDB version 2.0 for Linux 2-10: o trog.mbb.sfu.ca /pub/acedb as linux.2_10.tar.Z ACEDB for The NEC EWS4800: o ftp.nec.co.jp in /pub/packages/acedb/ace2. Return to List of Questions Q4: What ACEDB databases exist? =============================== A4: === In alphabetic order by Database name ------------------------------------ [Curators, please submit changes as new paragraphs] o Database : AaeDB o Species : Aedes aegypti o Last_update : December 1994 o ACEDB_version : 3.0 o WWW : http://klab.agsci.colostate.edu/index.html o PI : Dennis Knudson, dknudson@lamar.colostate.edu o Curator : Martin Ferguson, martinf@lamar.colostate.edu o Curator : Dave Severson, dave@aedes.vetsci.wisc.edu o Contact : aaedbmgr@klab.agsci.colostate.edu o Database : AAnDB-1.0 o Species : Aspergillus nidulans o PI : Leland Ellis o Last_update : February 1994 o ACEDB_version : 3.0 o Contact : leland@stralight.tamu.edu o URL: http://keck.tamu.edu/ibt.html o Comment : defunct, See AGsDB o Database : AAtDB o Species : Arabidopsis thaliana o Current version : 3-4 o Last_update : November 1994 o Curator : John Morris o Contact : curator@frodo.mgh.harvard.edu o Availability : ftp weeds.mgh.harvard.edu/aatdb/aatdb.3x o Availability : Macintosh version in /aatdb/MacAAtDB directory o URL : gopher://weeds.mgh.harvard.edu/ o URL : http://weeds.mgh.harvard.edu:80/index.html o URL : http://probe.nalusda.gov:8300/ o Database : ABtDB-1.0 o Species : Bovine, Bos taurus o ACEDB_version : 3.0 extended o PI : Leland Ellis o Last_update : February 1994 o Contact : leland@stralight.tamu.edu o URL : http://keck.tamu.edu/ibt.html o Comment : defunct, See AGsDB o Database : AboutDB o Curator : Staffan Bergh o PI : Staffan Bergh o Subject : ACEDB itself (Is this meta-meta-metadata) o ACEDB 3.0 o Contact : staffan@biochem.kth.se o URL : http://kiev.physchem.kth.se/AboutDB.html o Database : ACeDB o Species : Caenorhabditis elegans o Current version: 2-10 o Curator : Jean Thierry-Mieg o Curator : Richard Durbin o Contact : rd@mrc-lmb.cam.ac.uk o Contact : mieg@kaa.crbm.cnrs-mop.fr o Last_update : May 1994 o DataBase : AceMap o Species : Homo sapiens (Mus musculus under development) o Focus : Physical mapping of human chromsome X and 21 o ACEDB_version : 3.0 o Curator : Hugues Roest Crollius o PI : Hans Lehrach o Availability : beta release of the X chr. data/models by anonymous ftp to ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap. Get the README file in the directory above. o Contact : hrc@gea.lif.icnet.uk (Hugues Roest Crollius) ICRF, Lincoln's Inn Fields London, UK. o Last_update : August 94 o Database : AGsDB A Genus species Database o Species : Aspergillus nidulans o Species : Neurospora crassa o Species : cow w/ human anchor loci o Species : cotton (demo) o Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast o PI : Leland Ellis o Curator : Leland Ellis o Last_update : March 1994 o ACeDB_version : 3.0 (beta still), with extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe) yeast); interacting loci via defined Interactions for each locus o Models : as of 3.13.94 o Data : as of 3.13.94 o Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. o WWW : WWW-AGsDB is an interface of AGsDB with the World-Wide Web, and utilizes the WWW-ACeDB Server (nph-acedb3) of Guy Ducoux (ducoux@moulon.inra.fr). o URL : http://keck.tamu.edu/ibt.html o Contact : leland@straylight.tamu.edu o Database : Alfagenes o Species : Medicago sativa (Alfalfa, Lucerne) o Availability : Under development o Curator : D. Z. Skinner o Contact : dzolek@ksu.ksu.edu o Telephone : (913) 532-7247 o Database : BeanGenes o Species : Phaseolus and Vigna species o PI : Phillip E. McCLean o Email : mcclean@beangenes.cws.ndsu.nodak.edu o WWW : http://probe.nalusda.gov:8300 o Gopher: probe.nalusda.gov o Database : ChlamyDB o Species : Chlamydomonas o PI : Elizabeth Harris o Contact : chlamy@acpub.duke.edu o Availability : ChlamyDB 1.0, using ACEDB 3.0, is now on WWW and gopher (probe.nalusda.gov). Complete version using ACECB 3.0 now available by ftp from probe.nalusda.gov in the pub/chlamydirectory. A Macintosh version is avaliable in ftp://ftp.duke.edu/pub/chlamy/MacChalmy o URL : http://probe.nalusda.gov:8300 o Last_update : 25 Oct, 1994 o Database : CottonDB o Species : Gossypium hirsutum (cotton) and related species o PI : Russell J. Kohel, USDA-ARS, Southern Crops Research Laboratory, Route 5, Box 805, College Station, Texas 77845 o Curator : Gerard R. Lazo o Curator : Sridhar Madhavan o Last_update : January, 1995 (version 95.1) o ACEDB_version : 3.0 o Contact : lazo@tam2000.tamu.edu (Gerard R. Lazo) o Contact : rjk0339@zeus.tamu.edu (Russell J. Kohel) o URL : http://probe.nalusda.gov:8000/index.html o Data_submission_form : http://algodon.tamu.edu o Phone : 409-260-9311 o Fax : 409-260-9333 o Database : CSNDB o Focus : Cell Signalling Molecules and Interactions o Contact : Takako Igarashi National Insitute of Health Sciences Division of Chem-Bio Informatics Setagaya-ku, Tokyo, Japan 158 taka@nihs.go.jp o Database : EcoDB o Species : E. coli o PI : Staffan Bergh o Contact : staffan@biochem.kth.se o Availability : Proposed o Last_update : Aug. 1994 o Database : 11DB o Species : Homo sapiens o Focus : Physical mapping of chromosome 11 o Availability : under development o Curator : Benedict Arnold o PI : Peter Little o Contact : Benedict Arnold Dept. Biochemistry, Imperial College, London, SW7 2AZ b.arnold@ic.ac.uk o Database : The Encyclopaedia of the Drosophila Genome. o Acronym : (none) o Species : Drosophilidae (primarily D. melanogaster) o Availability : MacFly/FlyDB-based distribution by ftp and CD-ROM due early 1995 o Developer : Suzanna Lewis o Contact : suzi@fly2.berkeley.edu o Developer : Cyrus Harmon o Contact : sly@fly2.berkeley.edu o Developer : Edward Welbourne o Contact : eddy@gen.cam.ac.uk o Curation : Data is provided by the collaborating organisations: o Collaborator : The FlyBase Consortium, flybase@morgan.harvard.edu o Collaborator : The Berkeley Drosophila Genome Project o URL : gopher://fly.bio.indiana.edu:70+/11/Flybase o Database : Flydb o Species : Drosophila melanogaster o Curator : Suzanna Lewis o Contact : suzi@fly2.berkeley.edu o Database : GrainGenes o Species : Wheat, barley, oats, relatives o Availability : Anonymous ftp from probe.nalusda.gov:pub/grains o Availability : Gopher greengenes.cit.cornell.edu port 70 o Availability : Gopher probe.nalusda.gov port 7002 o Curator : David E. Matthews o PI : Olin D. Anderson o Contact : matthews@greengenes.cit.cornell.edu o Contact : oandersn@wheat.usda.gov o URL : gopher://greengenes.cit.cornell.edu/1/ o Data_version : 1.3 o Released : 12 Jan 1994 o Based_on : acedb.1-10 o Availability : See following WWW URL o URL : http://probe.nalusda.gov:8300 o Last_update : Feb. 1994 o Database : human.c17 o Species : Homo sapiens o Availability : the database is under development o Contact : lsprilus@weizmann.weizmann.ac.il o Focus : mapping & sequencing of Human Chromosome 17 o Based_on: acedb.3-0 o Last_update : Jan. 1994 o Database : IGD - the Integrated Genomic Database o Species : Homo sapiens (later mouse and other mammalian species) o Availability : September 1994 by ftp, on-line server October 1994 o Contact : Otto Ritter [ o.ritter@dkfz-heidelberg.de ] o Curator : tba o Description : IGD - the 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. o Database : LIGM-DB o Curator : Veronique Giudicelli o Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors o PI : Marie_paule Lefranc o Contact : Veronique Giudicelli LIGM IGMM UMR CNRS 9942 BP 5051 Rte de Mende 34000 Montpellier giudi@ligm.crbm.cnrs-mop.fr o Database : Maize o Species : Zea mays L. ssp. mays o Focus : Maize genome o Acedb_version : 1.9 o FTP : probe.nalusda.gov, pub directory; anonymous ftp o Comment : Maize is an acedb front end for the Maize Genome Database, MaizeDB, a SYBASE database. o Comment : MaizeDB is updated daily and has WWW connectivity to external databases: GenBank (loci, alleles and probes), SwissProt (gene products) and the E. coli Stock Center (loci). o Data : Major data categories: 4522 mapped loci (located to chromosome or better) including 684 mapped genes and 1423 mapped probed sites (gene candidates); 982 probes; 1850 map scores; 1533 gel patterns (Probe/Enzyme/Stock); 4231 stocks; 5105 Variations (alleles, DNA polymorphisms, rearrangements, etc); 465 phenotypes; 223 traits; 547 gene products; 5314 bibliographic references; 1979 persons with addresses. o Gopher : host = teosinte.agron.missouri.edu, port = 70 o Telnet : telnet teosinte.agron.missouri.edu login as guest, use password 'corncob' o HTTP : http://teosinte.agron.missouri/top.html o HTTP : http://probe.nalusda.gov:8000/acedbs/index.html via PGD, the Plant Genome Database o Comment : Genera is a software toolkit for creating and extracting data from Sybase databases; used to create MaizeDB and Worldwide Web connectivity. o HTTP : Genera Info http://cgsc.biology.yale.edu/genera.html o Funding : MaizeDB USDA/ARS to E. Coe o Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn o Curator/PI : Ed Coe ed@teosinte.agron.missouri.edu o Curator : Pat Byrne byrne@teosinte.agron.missouri.edu o Curator : Georgia Davis gdavis@teosinte.agron.missouri.edu o Curator : Mary Polacco maryp@teosinte.agron.missouri.edu o Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu o Curator : Christiane Fauron FAURON@GENE1.med.utah.edu o Curator : Carolyn Wetzel cmwetzel@iastate.edu o Curator : Steve Rodermel S1SRR@ISUVAX.IASTATE.EDU o Design : Stan Letovsky letovsky-stan@CS.YALE.EDU o Design : Mary Berlyn mary@fetalpig.biology.yale.edu o Systems Manager : Denis Hancock dhancock@teosinte.agron.missouri.edu o Contact : db_request@teosinte.agron.missouri.edu o Last_update : 25 April 1994 o Database : MycDB o Species : Mycobacteria o 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. o PI : Staffan Bergh o PI : Stewart Cole o PI : Doug Smith o Curator : Staffan Bergh o Contact : staffan@biochem.kth.se o Last_update : Apr. 1994 o WWW : http://kiev.physchem.kth.se/MycDB.html o ftp : ftp.pasteur.fr (157.99.64.12) in pub/MycDB o ftp : kiev.physchem.kth.se (130.237.52.64) in pub/MycDB o ftp : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/mycdb o Database : PomBase o Curator : Sean Walsh o Curator : Marie-Adele Rajendream o PI : Bart Barrell o Species : Schizosaccharomyces pombe o Contact : svw@sanger.ac.uk o Contact : barrell@sanger.ac.uk o Comment : Not yet available for distribution o DataBase : Mousedb o Species : Musculus Musculus o Species : Homo Sapiens o ACEDB_version : 3.0 with extensions to define and display cytogenetic data. o 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. o Curator : Michelle Kirby o Curator : Rachael Selley o PI : Mary Lyon o PI : Jo Peters o 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 For other information contact Michelle Kirby. o Contact : kirbym@har-rbu.mrc.ac.uk (or mkirby@hgmp.mrc.ac.uk) rselley@har-rbu.mrc.ac.uk MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD o Last_update : February 1995 o Database : RiceGenes o Species : Rice (O. sativa) o Availability : Anonymous ftp from probe.nalusda.gov:pub/rice o Availability : Gopher nightshade.cit.cornell.edu port 70 o Availability : Gopher probe.nalusda.gov port 7007 o Curator : Edie Paul o PI : Susah McCouch o Contact : epaul@nightshade.cit.cornell.edu o ACEDB_version : 3.0 o Last_update : May 1994 o Database : SacchDB o Species : Saccharomyces cerevisiae o Focus : Budding (common baker's) Yeast Genome o ACEDB_version : UNIX 2.0, MacAce 2.0b4 o FTP : genome-ftp.stanford.edu in /pub/SacchDB o FTP : ncbi.nlm.nih.gov in /repository/SacchDB o 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. o Gopher : host = genome-gopher.stanford.edu, port = 70 o HTTP : http://genome-www.stanford.edu/ o Funding : National Center for Human Genome Research, NIH o PI : David Botstein, botstein@genome.stanford.edu o Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu o Curator : Selena Dwight, dwight@genome.stanford.edu o Curator : Cathy Ball, ball@genome.stanford.edu o Curator : Rita Schmidt, bleb@genome.stanford.edu o Programmer : Karen Davis, karen@genome.stanford.edu o Sys. Admin : Mark Schroeder, mark@genome.stanford.edu o Contact : yeast-curator@genome.stanford.edu o Data_Submission : yeast-curator@genome.stanford.edu o Last_update : 2 February 1995 o Database : SolGenes o Coverage: Solanaceae - tomato, potato, pepper o Availability : Anonymous ftp from probe.nalusda.gov:pub/solgenes o Availability : Gopher nightshade.cit.cornell.edu port 71 o Availability : Gopher probe.nalusda.gov port 7006 o Curator : Clare Nelson o PI : Steve Tanksley o Contact : cnelson@nightshade.cit.cornell.edu o Release : ACEDB 3.0 o Last_update : May 1994 o Database : SorghumDB o Species : Sorghum bicolor (L.) Moench o PI : Keith F. Schertz USDA-ARS Dept. of Soil & Crop Sciences Texas A&M University College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 E_mail : schertz@tamvm1.tamu.edu o Curator : Najeeb U. Siddiqui Southern Crop Improvement Facility Crop Biotechnology Center Texas A&M University College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 E_mail : nus6389@tamsun.tamu.edu o Last_update : July 1994 o ACEDB_version : 3.0 o Availability : Under Development o Database : SoyBase o Species : Soybeans o Curator : Lisa Lorenzen o PI : Randy Shoemaker o Contact : lorenzen@mendel.agron.iastate.edu o Phone : 515-294-0421 o Fax : 515-294-2299 o Last_update : Sept. 1993 o Gopher : probe.nalusda.gov port 7005 o Database : Sybace o Species : Homo sapiens o Creator : Detlef Wolf o Comment : Custom software --ACEDB front-end to SYBASE data o Contact : D.Wolf@dfkz-heidelberg.de o See_also : IGD o Database : Syndb o Species : Homo sapiens, Mus musculus o Focus : STS content mapping & directed sequencing of Human Chromosomes 21,5 with Mouse for syntenic comparison o Availability : by request, via ftp, world-wide-web o Based_on : acedb v3.3 plus moulon server o URL: ftp://genome.lbl.gov/pub/acedb/syndb.tar.Z o URL: http://genome.lbl.gov/Genome/acepage.html o Curator : Donn F. Davy o Contact : DFDavy@lbl.gov o Contact : aggarwal@genome.lbl.gov o Focus : STS content mapping & directed sequencing of Human Chromosomes 21 and 5, with Mouse data for syntenic comparison o PI : Michael Palazzolo o PI : Chris Martin o PI : Jan-Fang Cheng o Last_update : Oct. 1994 o Database : TreeGenes o Species : Forest trees o ACEDB_version : 3.0 o Curator : Bradley K. Sherman o PI : David B. Neale o Contact : Dendrome@s27w007.pswfs.gov o Contact : bks@s27w007.pswfs.gov o Contact : dbn@s27w007.pswfs.gov o Last_update : March 1994 o Gopher: s27w007.pswfs.gov o WWW: http://s27w007.pswfs.gov/ o FTP: probe.nalusda.gov in /pub/trees o Database : 21Bdb o Species : Homo sapiens o Focus : STS content mapping & sequencing of Human Chromosome 21 o Availability : by request, via ftp, world-wide-web o Based_on : acedb.1-10 plus moulon server o URL: ftp://genome.lbl.gov/pub/21Bdb-v1.1.tar.Z o URL: http://genome.lbl.gov/Genome/acepage.html o Curator : Donn F. Davy o Contact : DFDavy@lbl.gov o Contact : aggarwal@genome.lbl.gov o Focus : STS content mapping & sequencing of Human Chromosome 21 o PI : Michael Palazzolo o PI : Chris Martin o PI : Jan-Fang Cheng o Last_update : Apr. 1994 o Database : 22ace o Species : Homo sapiens o Curator : Ian Dunham o Focus : Physical mapping of chromosome 22 o PI : Ian Dunham o Contact : Ian Dunham Sanger Centre Hinxton Hall, Cambs. UK. id1@sanger.ac.uk o Database : VoxPop o Species : Populus spp. o Availability : contact curator o Curator : Carl G. Riches o PI : Reinhard F. Stettler o Contact : cgr@poplar1.cfr.washington.edu o Contact : STETTLER@coyote.cfr.washington.edu o Gopher : poplar1.crf.washington.edu o Last_update : Sept. 1993 o Database : Xace o Species : Homo sapiens o Curator : Gareth Maslen o Focus : Physical mapping of chromosome X o PI : David Bentley o Contact : Gareth Maslen Sanger Centre Hinxton Hall, Cambs. UK. glm@sanger.ac.uk o Database : ? o Species : Homo sapiens o Focus : Physical mapping of human chromosome 6. o Curator : Ioannis Ragoussis o Availability : Unknown o Contact : Guy's hospital o Database : ? o PI : Scott Chasalow o Species : Potato o Contact : Scottish Crop Institute, Dundee o Last_update : Sept. 1993 o Database : ? o PI : George Murphy o PI : David Flanders o Species : Arabidopsis thaliana o Contact : John Innes Center, Norwich, England o Last_update : Sept. 1993 o Database : ? o Species : Homo Sapiens o Focus : Physical and linkage mapping of chromosome 8 o Availability : o Curator : Stephen Wood o PI : Stephen Wood o Contact : Stephen Wood Dept. Medical Genetics University of B. C. Vancouver, B. C. Canada swood@unixg.ubc.cq Return to List of Questions Q5: What written documentation exists for ACEDB? ================================================ A5: === From Sam Cartinhour: The ACEDB Documentation Server is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. Eventually we hope to offer all kinds of documentation, from reprints to (technical) gossip. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The documentation server is listed on the home page for the Agricultural Genome World Wide Web Server at http://probe.nalusda.gov:8000 . Primary documents from the developers are: o acedb -- A C. elegans Database: I. Users' Guide. o acedb -- A C. elegans Database: II. Installation Guide. o acedb -- A C. elegans Database: III. Configuration Guide. o Syntactic Definitions for the ACEDB Data Base Manager --Jean Thierry-Mieg and Richard Durbin (1991-) Get By anonymous ftp from ncbi.nlm.nih.gov in repository/acedb: ftp://ncbi.nlm.nih.gov/respository/acedb/doc*tar.Z and ftp://weeds.mgh.harvard.edu/acedb_doc The files are in tex (Jean Thierry-Mieg suggests latex xxx.tex; dvi2ps xxx.dvi > xxx.ps; lpr xxx.ps) and PostScript. Japanese language guides: _Japanese ACEDB Guide Ver.1.2._ _ACEDB ver.2 for NEC engineering workstation EWS4800 series_ are available in PostScript via anonymous ftp at ftp.nec.co.jp as /pub/packages/acedb/acemanjp.1_2.ps.Z . You will find interesting documents in the wdoc subdirectory of the ACEDB distribution. The Australian National Genomic Information Service has prepared good documentation of the C. elegans version as Angisturte.ps and angistute.hqx available by anonymous ftp at ncbi.hih.gov in repository/acedb/ace2. Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992) AAtDB, An Arabidopsis thaliana Database. Plant Molecular Biology Reporter 10 (4): 308-309,409-410 Tutorial manual for AAtDB: Cartinhour, S., Cherry, J.M., and Goodman, H.M. (1992) An Introduction to ACeDB: For AAtDB, An Arabidopsis thaliana Database. Massachusetts General Hospital. (Available on request in printed form from the AAtDB curator). A description of ACEDB: Cherry, J.M. and Cartinhour, S.W. (1994) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press, pages 347-356. [text is available through ftp or gopher from weeds.mgh.harvard.edu] Another description of ACEDB for physical mapping projects: Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. Academic Press, pages 111-158. [text is available through ftp or gopher from weeds.mgh.harvard.edu] Return to List of Questions Q6: Where can I find further information about ACEDB? ===================================================== A6: === The Developers' Archive +++++++++++++++++++++++ Mike Cherry maintains an archive of tools that may be useful in curating ACEDB databases. It can be reached by anonymous ftp at URL ftp://weeds.mgh.harvard.edu/acedb_dev/ or via gopher at gopher://genome-gopher.stanford.edu:70/11/ftp If you have a contribution place it in ftp://weeds.mgh.harvard.edu/acedb_dev/incoming/ and send a message to Mike (cherry@genome.stanford.edu). The Biosci conference bionet.software.acedb +++++++++++++++++++++++++++++++++++++++++++ There is a USENET/Biosci conference titled bionet.software.acedb created expressly for discussion of ACEDB. The best way to interact with the Biosci conferences is via a newsreader like rn, trn, tin or a WWW browser. Consult your system administrator for more information. If you do not have access to the Biosci conferences via a newsreader (e.g. rn, trn, tin) you can participate in the conference by electronic mail. To subscribe to the e-mail version of the conference send email to biosci-server@net.bio.net (UK, European readers use biosci@uk.ac.daresbury or biosci.daresbury.ac.uk) with no subject line and only the message subscribe ACEDB-SOFT in the body. To unsubscribe send the message unsubscribe ACEDB-SOFT to the same address. This is an automated service. Your e-mail address will be taken from the header of the message that you send. If you then send mail to acedb@net.bio.net the mail will be distributed to all subscribers and to the electronic conference. o All of the articles in biosci.software.acedb are archived by Biosci at gopher://gopher.bio.net/1/ACEDB o Mike Cherry makes it possible to search past articles in biosci.software.acedb using WAIS at gopher://genome-gopher.stanford.edu:80/77/.index/acedb-biosci . And more ++++++++ The AAtDB, Soybase, GrainGenes, Mace, and TreeGenes [see Q4] databases regularly submit data to the Plant Genome Database at the National Agricultural Library (NAL). Nal makes this data available via the WWW using an http server with URL: http://probe.nalusda.gov:8000/index.html You will also find a selection of models.wrm files (schemata) for the various databases here. You will want to get a "mosaic client" to examine this. AboutDB is a stab at an integrated info and project tracking database for the 'Greater ACEDB Community'. It was conceived and implemented by Staffan Bergh (staffan@biochem.kth.se), the 'coordinator', during the ace94 workshop in Montpellier, based on an earlier effort by John McCarthy. The aim is to collect information on all aspects of ACEDB use as a database manager. Currently it contains information on Databases implemented in ACEDB, Colleagues in the community, some Tools for >curators of ACEDB databases and some of the information on 'magic tags' collected during the ace94 workshop. AboutDB can be reached at URL: http://kiev.physchem.kth.se/AboutDB.html Other URL's that readers with mosaic clients might want to examine are: o http://moulon.inra.fr/acedb/acedb.html for C. elegans data o http://kiev.physchem.kth.se/MycDB.html for Mycobacterium data o http://moulon.inra.fr:8001/acedb/igd.html for an integrated genome database. For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html and en francais http://moulon.inra.fr/acedb_conf.html The Genome Computing Group, Lawrence Berkeley Laboratory, has an anonymous ftp service at machine genome.lbl.gov which contains: o flydb - LBL's Drosophila Acedb-style database o 21bdb - LBL's Human Chromosome 21 Acedb-style database o querdb - LBL's query-language extensions to Acedb o metadata - LBL's compendium of Acedb database schema variants o macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version o There is also a repository of contributed software for data conversions and the like. [From Otto Ritter] IGD - the Integrated Genomic Database - is an international project of DKFZ, Heidelberg (Germany), CNRS, Montpellier (France), ICRF, London (UK), LBL, Berkeley (USA), and MRC, London/Cambridge, (UK). IGD is an extensible object-oriented distributed information management system with one global schema, physical data integration at the back-end, and local data management at the front-end. It supports local schema evolution and local data integration, and has a potential for truly virtual "on-the-fly" integration (federation) of its resource databases. Beside data integration, IGD provides graphical user interface, client/server communication, and seamless interface to a growing number of tools for structure, sequence, genetic, physical and comparative mapping analysis. ACEDB is the IGD main software component for data management. As a database, IGD integrates and references genome related data from public sources. As an analysis tool, IGD provides uniform interface to existing programs and program packages for tructure and sequence analysis, genetic and physical map construction and analysis, etc. In addition to the major human and mouse databases already planned SWISS-PROT/PIR, PDB, GDB, OMIM, CitDB, CEPH, CHLC, CEPH-Genethon, Genbase, UK DNA ProbeBank, RLDB2, CAD, MGD, MouseBackcross DB), crossreferences will be maintained to dataabases established around specific model organisms (C.elegans, D. melanogaster, S. cerevisiae, pombe etc.). Refs: o 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). o 2/ Ritter,O., Kocab,P., Senger,M., Wolf,D., and Suhai,S.: Prototype Implementation of the Integrated Genomic Database, Computers and Biomedical Research, 27, 97-115 (1994) Computer staff for the UC Berkeley Drosophila physical mapping project the LBL Human Chromosome 21 project, and the LBL plant genome projects meet regularly to coordinate their ACEDB extension and development efforts, along with Frank Eeckman, who is working on the Macintosh version of ACEDB (for further information, contact jlmccarthy@lbl.gov). They also keep in close touch (via email, personal visits, etc.) with their counterparts in Cambridge (Richard Durbin et al), Montpellier Jean Thierry-Mieg et al), and the Interated Genome Database project in Heidelburg (Otto Ritter, Detlef Wolf et al). Return to List of Questions Q7: How should ACEDB be cited? ============================== A7: === From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit available via anonymous ftp. Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions Q8: Is ACEDB object-oriented? ============================= A8: === From the ACEDB User's Guide: A major current vogue in computer languages and database design is for ``object-oriented'' systems. It's also a source of lots of argument. We are just trying to build a good system, and don't want to get caught in the crossfire, but we do talk about organising our data into objects and classes. We have undoubtedly been influenced by many of the ideas going around, but it isn't likely our system would be regarded as kosher by the object- oriented community. In particular there is no class hierarchy, nor inheritance, and it is written in a modular but non-ideological way in straight C. However display and disk storage methods are class dependent. In some ways the class hierarchy is replaced by our system of models and trees, which seems to be rather unusual. We think it is very natural for the representation of biological information, where for some members of a class a lot might be known about some aspect, but for most only a little is known. The advantages of our sytem over a relational database, such as Oracle or Sybase, is our ability to refine our descriptions without rebuilding the database and the possibility of organising the storage of data on disk according to their class, i.e. we store in a very different way the tree-objects and the long stretches of DNA sequence. Return to List of Questions Q9: What's all this about Gopher, WAIS, FTP, WWW, URL, ... ========================================================== A9: === These terms all refer to Internet protocols. An excellent introduction to the Internet is: _The Whole Internet User's Guide & Catalog_, by Ed Krol, O'Reilly & Associates, 1992. Or ask your system administrator to provide you with a gopher client or mosaic client and begin navigating on your own. URL is a Universal Resource Locator on the World-Wide Web (WWW). There are many free Internet browsers available that allow you to use an Internet connection and a URL to access services. Mosaic may be the most popular and it is available for Mac, PC or Unix via anonymous ftp from ftp.ncsa.uiuc.edu. Return to List of Questions Q10: How can I get on/off the ACEDB announcements mailing list? =============================================================== A10: To get on or off the mailing list send mail to rd@mrc-lmb.cam.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. New releases of the software are announced to this list and very little else. The BIOSCI newsgroup bionet.software.acedb [See Q6 for details] is on the mailing list. Return to List of Questions Q11: When and where is the Next ACEDB Workshop? =============================================== A11: ==== The 1995 ACEDB Conference and Workshop will be held May 14-27, 1995, at the Isis Oasis, a small retreat center in Geyserville, about 80 miles north of SanFrancisco in Sonoma County, California. We will have exclusive use of the entire retreat center, including the theater (for workstations and primary sessions), dining room, lodge, and other residential facilities. For more information send email to ace95@genome.lbl.gov or vist URL http://genome.lbl.gov/ace95.html on the WWW. If you would like to see some pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers, there are online collections: o by Mike Cherry at http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ; o by John Morris at http://weeds.mgh.harvard.edu/ace94/ace94.image.html ; o and by Brad Sherman at ftp://s27w007.pswfs.gov/ACEDB/ace94pix.html Return to List of Questions Q411:Who prepared this document & where is the current version? =============================================================== A411: (Note to international readers: 411 is the phone number for information in the USA.) This document will be 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 latest text version of the ACEDB FAQ should be available via anonymous ftp at machine net.bio.net as file pub/BIOSCI/ACEDB/ACEDB.FAQ or at 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. There is an HyperText Markup Language (HTML) version of this document available on the World Wide Web: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html and http://s27w007.pswfs.gov/Homepage/acedbfaq.html 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 Major contributions in getting this FAQ off the ground were made by John McCarthy and Mike Cherry. Other contributors include: o Lisa Lorenzen o David Matthews o Edie Paul o Donn Davy o Eric De Mund o Sam Cartinhour Please cite as: Sherman,B.K., ACEDB Genome Database Software FAQ, ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq, http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993,1994,1995 approx. 50K bytes. To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov Bradley K. Sherman Dendrome Project Institute of Forest Genetics P.O. Box 245, Berkeley, CA, 94701 Phone: 510-559-6437 Fax: 510-559-6440 The Dendrome Project and TreeGenes are funded by the USDA ARS Plant Genome Research Program. Return to List of Questions End of ACEDB FAQ --bks From owner-acedb@net.bio.net Tue Apr 11 23:00:00 1995 Path: biosci!informatik.uni-stuttgart.de!Baumann From: Baumann@informatik.uni-stuttgart.de (Joachim Baumann) Newsgroups: bionet.software.acedb Subject: Post Scriptum: Announcement: TextConvert Date: 12 Apr 1995 07:35:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <199504121435.QAA16274@chronos.informatik.uni-stuttgart.de> NNTP-Posting-Host: net.bio.net I forgot to give the path on the ftp-server ftp://ftp.informatik.uni-stuttgart.de/pub/DART Best Wishes, Joachim _______________________________________________________________________________ Snail: Joachim Baumann, | Universitaet Stuttgart, IPVR, | Phone: (+49 | 0 ) 711/7816-218 Breitwiesenstr. 20-22, | Fax: (+49 | 0 ) 711/7816-424 70565 Stuttgart, Germany | EMail: joachim.baumann@informatik.uni-stuttgart.de(.sol_3.milky-way.universe) PGP: finger baumann@orgel.informatik.uni-stuttgart.de From owner-acedb@net.bio.net Tue Apr 11 23:00:00 1995 Path: biosci!informatik.uni-stuttgart.de!Baumann From: Baumann@informatik.uni-stuttgart.de (Joachim Baumann) Newsgroups: bionet.software.acedb Subject: Announcement: TextConvert Date: 12 Apr 1995 07:21:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: <199504121416.QAA15943@chronos.informatik.uni-stuttgart.de> NNTP-Posting-Host: net.bio.net Hi all, Richard Sanger suggested, that I send the following announcement to this group as well as to the IGD Developer's mailing list. I hope it is of some interest. :-) Announcing TextConvert ---------------------- TextConvert is a tool to ease the conversion of data in flat file libraries to ACEDB format. It takes as input a description file in a format that resembles the format of AWK-scripts, reads a data stream and produces another data stream according to patterns and attached code, so called actions, in a given description file. The patterns can be formed according to Perl's regular expressions, and the actions are formulated as Perl source code enriched with additional commands to ease the conversion of text-based data. The additional commands support the ACEDB format. In fact, the program is written in Perl, and builds a program from the description file. This program is then evaluated. The additional commands support input, output, an object stack and decoding of 2-Bit coded data. Included are 23 pages of documentation including a tutorial, and in case this doesn't help, the author is reachable via EMail :-) The address is: joachim.baumann@informatik.uni-stuttgart.de The program can be ftp'ed from ftp.informatik.uni-stuttgart.de Best Wishes, Joachim PS: This work has been funded by the DKFZ (The German Cancer Research Centre), and is part of the IGD development under the CEU contract GENE-CT93-0003. _______________________________________________________________________________ Snail: Joachim Baumann, | Universitaet Stuttgart, IPVR, | Phone: (+49 | 0 ) 711/7816-218 Breitwiesenstr. 20-22, | Fax: (+49 | 0 ) 711/7816-424 70565 Stuttgart, Germany | EMail: joachim.baumann@informatik.uni-stuttgart.de(.sol_3.milky-way.universe) PGP: finger baumann@orgel.informatik.uni-stuttgart.de From owner-acedb@net.bio.net Wed Apr 12 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!Germany.EU.net!Dortmund.Germany.EU.net!nntp.gmd.de!news.rwth-aachen.de!news.rhrz.uni-bonn.de!news.uni-stuttgart.de!news.belwue.de!news.belwue.de!News.Uni-Marburg.DE!pc2011.Humangenetik.Humanmedizin.Uni-Marburg.DE!otto From: otto@pc2011.humangenetik.humanmedizin.uni-marburg.de (Michael Otto) Newsgroups: bionet.software.acedb Subject: data entering tools Date: Thu, 13 Apr 1995 07:43:16 GMT Organization: Humangenetik Marburg Lines: 15 Message-ID: NNTP-Posting-Host: pc2011.humangenetik.humanmedizin.uni-marburg.de Keywords: data tools We plan to setup a local database for Human chromosome 7 based on ACEDB/IGD. Is there a community of groups with similar activities for other chromosomes in the internet ?. We found a number of addresses. Is there a exchange of usefull tools for data entering between this groups ? We would be very grateful if you could help us setting up our own database. thanks in advance Michael Otto From owner-acedb@net.bio.net Sun Apr 16 23:00:00 1995 Path: biosci!TEOSINTE.AGRON.MISSOURI.EDU!maryp From: maryp@TEOSINTE.AGRON.MISSOURI.EDU (Mary Polacco) Newsgroups: bionet.software.acedb Subject: ACEDB FAQ re SYBASE Date: 17 Apr 1995 11:19:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <199504171816.NAA06943@teosinte.agron.missouri.edu> NNTP-Posting-Host: net.bio.net ACEDB FAQ Q&A #8, paragraph 3 starts: "The advantages of our system[ACeDB] over a relational database, such as Oracle or Sybase, is our ability to refine our descriptions without rebuilding the database..." This is not necessarily true, at least when Genera is used to build the database. For the past few years, I have been associated with curating MaizeDB, a Sybase database. We often refine descriptions without rebuilding the entire database. New Sybase tables, or new columns to existing SYBASE tables are able to be queried by both the APT and WWW query forms, updatable by our on-site systems analyst using Stan Letovsky's software, Genera. The process of updating query forms takes lots less time (minutes) than the decision-making (hours to weeks) involved in deciding how the data should be represented. -Mary Polacco --NAA06895.798142078/teosinte.agron.missouri.edu-- ----- End Included Message ----- From owner-acedb@net.bio.net Sun Apr 16 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!usenet.ins.cwru.edu!lerc.nasa.gov!purdue!yuma!klab3.agsci.colostate.edu!user From: martinf@lamar.colostate.edu (Martin Ferguson) Newsgroups: bionet.software.acedb Subject: Does GRID display work in 3.7b? Date: Mon, 17 Apr 1995 13:29:19 -0600 Organization: Colorado State University Lines: 6 Distribution: world Message-ID: NNTP-Posting-Host: klab3.agsci.colostate.edu Greetings all, Does the clone_grid display work in version 3.7b? When I click on a grid name, I get the "Show as text" type window. Thanks. /s/ Martin From owner-acedb@net.bio.net Wed Apr 19 23:00:00 1995 Path: biosci!rutgers!oitnews.harvard.edu!bloch.nmr.mgh.harvard.edu!usenet From: John Morris Newsgroups: bionet.software.acedb Subject: [Q] Help on muliple pmap prints? Date: 20 Apr 1995 13:14:57 GMT Organization: Mass General Hospital Lines: 17 Message-ID: <3n5moi$ke5@bloch.nmr.mgh.harvard.edu> NNTP-Posting-Host: thale.mgh.harvard.edu Greetings, I'm interested in printing out about a chromosome's worth of physical maps. Does anyone have a suggestion on how this could be automated? Could 'Expect' be trained to make the proper button clicks? Alternatively, does anyone know of a simple drawing package that I could feed line coordinates to, and produce a post-script file? Suggestions welcome, John Morris AAtDB Project john.morris@frodo.mgh.harvard.edu From owner-acedb@net.bio.net Fri Apr 21 23:00:00 1995 Path: biosci!agate!dog.ee.lbl.gov!news.cs.utah.edu!cc.usu.edu!slip25 Newsgroups: bionet.software.acedb Subject: test-disregard Message-ID: <1995Apr22.014504.48256@cc.usu.edu> From: sl5dl@cc.usu.edu (omonj) Date: Sat, 22 Apr 95 04:35:26 GMT Distribution: world Organization: usu Nntp-Posting-Host: slip25.nb1.usu.edu X-Newsreader: News Xpress Version 1.0 Beta #2.1 Lines: 1 this is a test From owner-acedb@net.bio.net Sun Apr 23 23:00:00 1995 Path: biosci!bcm!news.msfc.nasa.gov!cs.utk.edu!cssun.mathcs.emory.edu!hobbes.cc.uga.edu!dogwood.botany.uga.edu!pbrunk From: pbrunk@dogwood.botany.uga.edu (Paul Brunk) Newsgroups: bionet.software.acedb Subject: acedb 3.7 Date: 24 Apr 1995 19:29:47 GMT Organization: University of Georgia, Athens Lines: 24 Message-ID: <3ngu7b$3ft@hobbes.cc.uga.edu> NNTP-Posting-Host: dogwood.botany.uga.edu X-Newsreader: Tin 1.1 PL4 Hi all: I downloaded the acedb 3.7 source from ncbi.nlm.nih.gov and compiled it (gcc, Solaris 2.4) without any unusual errors. When I first run it I get a messout Type of Locus does not check in B object "Gene" Type of Locus does not check in B object "Other_Locus" Type of Clone does not check in B object "Expression" and 4 more such errors, then Missing or unrecognised Class #Class# after FIND then Less than 3 visible classes. Any ideas? Thanks. -- Paul Brunk, ancillary staff University of Georgia Botany Department pbrunk@dogwood.botany.uga.edu From owner-acedb@net.bio.net Sun Apr 23 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: Author order Date: 24 Apr 1995 22:06:39 +0100 Lines: 41 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3nh3sv$5d8@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk > We're running version 3.0 on a SUN. I've noticed that after several days > of use, our database has changed the order of Author's names inside of > Paper objects. Have others experienced this? Has it been addressed in > later versions? I doubt the order is changing. The order in a column is determined by the order in which items are entered. If they are there already then they are not reentered. People have had problems with Author order before, for the following reason. If you XREF from Author to ?Paper, e.g. your models contain something like ?Author Address ... Paper ?Paper XREF Author // <1> ?Paper Reference Title ?Text Author ?Author XREF Paper // <2> then if you add Author objects before the Paper objects, the Paper object will be created by the XREF <1>, and the author list in position <2> in the paper object will be determined by the order in which the Author objects are read in, not the order of authors in the Paper object. This was a problem with the very early models used by the C. elegans database, and hence unfortunately propagated around the world. The solution is to remove XREF <1>, so the models look like: ?Author Address ... Paper ?Paper ?Paper Reference Title ?Text Author ?Author XREF Paper Now the authors in the Paper object will only be added when the Paper object is read, and will be in the order specified there. I hope this is both clear, and also the cause of the reported problem. Richard From owner-acedb@net.bio.net Sun Apr 23 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!mojo.eng.umd.edu!cs.umd.edu!news.umbc.edu!haven.umd.edu!purdue!yuma!klab3.agsci.colostate.edu!user From: martinf@lamar.colostate.edu (Martin Ferguson) Newsgroups: bionet.software.acedb Subject: Bug? Re-ordering of Author names in Paper objects. Date: Mon, 24 Apr 1995 12:10:18 -0600 Organization: Colorado State University Lines: 12 Message-ID: NNTP-Posting-Host: klab3.agsci.colostate.edu Keywords: world Greetings all, My apologies if this has been mentioned before... We're running version 3.0 on a SUN. I've noticed that after several days of use, our database has changed the order of Author's names inside of Paper objects. Have others experienced this? Has it been addressed in later versions? Thanks. /s/ Martin From owner-acedb@net.bio.net Mon Apr 24 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!news-feed-1.peachnet.edu!hobbes.cc.uga.edu!dogwood.botany.uga.edu!pbrunk From: pbrunk@dogwood.botany.uga.edu (Paul Brunk) Newsgroups: bionet.software.acedb Subject: Re: acedb 3.7 Date: 25 Apr 1995 19:50:09 GMT Organization: University of Georgia, Athens Lines: 13 Message-ID: <3njjph$bvp@hobbes.cc.uga.edu> NNTP-Posting-Host: dogwood.botany.uga.edu X-Newsreader: Tin 1.1 PL4 Hi all: I asked about some errors in starting up a freshly compiled acedb 3.7. Richard Durbin and Jean Thierry-Mieg both kindly responded, wondering what versioned database I was trying to load. I wasn't trying to load any. I just compiled and started it up (database directory was either empty or nonexistent). -- Paul Brunk, ancillary staff University of Georgia Botany Department pbrunk@dogwood.botany.uga.edu From owner-acedb@net.bio.net Tue Apr 25 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!stern.fokus.gmd.de!nntp.gmd.de!dearn!barilvm!vms.huji.ac.il!wisipc.weizmann.ac.il!ug.eds.com!goel Newsgroups: bionet.software.acedb Subject: PRESS RELEASE - STEREOMETRIX CORP. Message-ID: <1995Apr25.234038.4040@wisipc.weizmann.ac.il> From: goel@ug.eds.com Date: Tue, 25 Apr 1995 23:40:38 GMT Reply-To: goel@ug.eds.com Sender: goel@ug.eds.com (Anurag Goel) Organization: Weizmann Institute of Science, Computation Center. Lines: 85 STEREOMETRIX CORPORATION --------> Computer Aided Diagnosis for Medical Imaging 675 N. 1st Street Suite 700 San Jose, CA 95112 Ph: (408)975-7660 FAX (408)975-7679 PRESS RELEASE Media Contact: Bob Chapman BREAKTHROUGH IN COMPUTER-AIDED BREAST CANCER DIAGNOSIS TECHNOLOGY Accuracy 95% With False Indications Reduced to Negligible Level San Jose, April 26, 1995 - Stereometrix Corporation is in the final stage of completing technology for early and accurate detection of breast cancer. A recent breakthrough has resulted in a significant improvement in system performance. False positive indications (like false alarms) have now been reduced to near zero. False positives occur in both manual and computerized x-ray reading from borderline cases and film artifacts. Dr. K.C. Saxena, Ph.D., Stereometrix's founder and developer of the technology, states that the updated Mammogram Viewstation 5000 computer-aided-diagnosis system will be ready for clinical trials in the near future. The company is presently Alpha testing the new software which incorporates the breakthrough technology. This recent development makes the system much more suitable for breast cancer mass screening programs to combat this deadly disease. Dr. Saxena, a well known photogrammetrist and mathematician, said that the technology he developed over the past several years has been derived from a combination of sciences including mathematics, statistics, image processing and photogrammetry. The keys to success are the novel mathematical algorithms and filters which are able to highlight, extract and classify small features of clinical interest hidden or obliterated by other soft tissues, blood vessels and densities present in mammogram x-rays. The classification algorithms are derived from the criteria used by noted radiologists. They are able to distinguish potential malignancies from benign features and reject film artifacts and characteristics which resemble masses. Some computerized mammographic interpretation techniques being investigated have the possibility of losing elements of vital breast cancer information on the x-ray. Dr. Saxena believes that such methods will not be able to reliably detect or classify small size or early stage cancers. Stereometrix rejected simplistic approaches early in its research and has concentrated on developing a technology in which very obscure and small cancer-like features can be detected. This has resulted in a system whose detection and location accuracy significantly exceeds that achieved by other workers in this field. In addition, the system and its user interface have been designed for efficient integration into the clinical environment. In preliminary testing, the ViewStation 5000's patented software technology demonstrated a 95% accuracy rate in detecting pathologically confirmed (biopsied) potentially malignant microcalcifications and masses on more than 400 mammograms. Detection accuracies for manual (visual) reading of the x-rays typically range from 70% - 90%. The system is also capable of detecting very small features - thus aiding earlier detection of breast cancer. The new breakthrough discovery's reduction of false positives to an insignificant level may also help reduce the number of unnecessary biopsies. Breast cancer kills 46,000 American women every year and costs the U.S. health care system $3.8 billion annually. Increased diagnostic accuracy is expected to ultimately save lives and reduce medical costs. Located in San Jose, California, Stereometrix Corporation develops advanced image analysis technology software. Its present focus in medical applications is to deliver increased diagnostic accuracy and improved patient outcomes. # # # ============================================================================== Any e-mail enquiries resulting from this posting will be forwarded to Stereometrix Corp. by this individual without any obligations to either party. ============================================================================== From owner-acedb@net.bio.net Sat Apr 29 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!reuter.cse.ogi.edu!coho.cse.ogi.edu!benning From: benning@coho.cse.ogi.edu (Paul Benninghoff) Newsgroups: bionet.software.acedb Subject: Documentation on AceDB (esp file format) Date: 30 Apr 1995 23:07:24 GMT Organization: Oregon Grad. Inst. Computer Science and Eng., Beaverton Lines: 14 Distribution: world Message-ID: <3o157c$ha2@reuter.cse.ogi.edu> NNTP-Posting-Host: coho.cse.ogi.edu Hi, I'm looking for some documentation on AceDB. I've tried the Web site: http://moulon.inra.fr/acedb/acedb.html But there's little of no documentation there. Of particular interest is the file format used by AceDB. Thanks in advance, pb From owner-acedb@net.bio.net Sat Apr 29 23:00:00 1995 Path: biosci!GENOME.STANFORD.EDU!cherry From: cherry@GENOME.STANFORD.EDU (Mike Cherry) Newsgroups: bionet.software.acedb Subject: Re: Documentation on AceDB (esp file format) Date: 30 Apr 1995 16:53:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <199504302353.QAA08887@stout.Stanford.EDU> References: <3o157c$ha2@reuter.cse.ogi.edu> NNTP-Posting-Host: net.bio.net > I'm looking for some documentation on AceDB. I've tried the Web site: > > http://moulon.inra.fr/acedb/acedb.html > > But there's little of no documentation there. > > Of particular interest is the file format used by AceDB. pb, Try: http://probe.nalusda.gov:8000/acedocs/index.html You'll want to check out the "Syntactic Definitions" link. Mike