Summary: What data sets are available?

Don Gilbert gilbertd at bio.indiana.edu
Thu Jun 24 09:07:25 EST 1993


My question: What data sets are/will be soon available for use
with ACeDB software?


Currently available:

acedb for C.elegans, ftp/gopher to ncbi.nlm.nih.gov:/repository/aatdb 
aatdb for Arabidopsis, ftp/gopher to ncbi.nlm.nih.gov:/repository/acedb  
mycdb for Mycobacterium, ftp/gopher to ftp.pasteur.fr:/pub/MycDB
graingenes for Triticeae, gopher to greengenes.cit.cornell.edu for info


Plans:

 
> From: Mike Cherry <CHERRY at Frodo.MGH.Harvard.EDU>
> 
> Besides worms and weeds I believe the only other publically released
> ACEDB db is MycDB by Staffan Bergh (staffan at pasteur.fr) of the Pasteur
> Institute on mycobacterium.  There was an announcement a couple months
> ago in bionet.announce. MycDB is available via anonymous ftp from
> ftp.pasteur.fr or via Gopher from ftp.pasteur.fr.
> 
> There are many others in the works. I shouldn't publically list all
> that I have heard about, each group should make their own
> announcements. But generally almost every genomic database you can
> think of is looking into using ACEDB as a method of distribution. Plus
> there are >10 other species databases from the plant and animal
> kingdoms that are developing an ACEDB database.


> From: bks at s27w007.pswfs.gov (Bradley K. Sherman)
>
> We will be making APtDB (A Pinus taeda Database) available soon.
> This will have all of our data for the construction of a 
> loblolly pine genetic map as well as a cross-index to a
> complete set of online autorads.
> 
> p.s. by soon, I mean maybe September/October


> From: Lisa Lorenzen <lorenzen at mendel.agron.iastate.edu>
> 
> The USDA-ARS is currently funding three ACE-type databases, Soybean, Wheat/small grains, and Forest Crops. I am currently working on the
> soybean database, and can only say that it will be 'released' someday.
> The USDA is putting together a public database, called PGD, which is a
> relational database encompassing 'all' crop species.  The initial
> species involved in this are maize, soybean, wheat, forest trees, and 
> arabidopsis.


> From: reisner at angis.su.OZ.AU (Alex Reisner)
> 
> 	we run four 'acedb' types  ACeDB and AAtDB of course and
> GranGenes (David Mathews, cornell (mostly wheat and barley) MycDB
> for Mycobacteria  from the Pasteur.  I know of no others though am told
> Michael Ashburner is working on Dros., as is possibly a US group.


> From: glh at bio5.acpub.duke.edu (Geoff Hughes)
> > 
> Currently, there are only the Arabidopsis(AAtDB) and ACeDB data sets available,
> as far as I know, but there are at least ten projects that are in the making;
> I am working on one of them. To get an idea of what's to come, take a look at
> ACeDB's latest release and look at the file tags.wrm in the wspec directory;
> this is where registered developers tag number allotments can be seen- I think
> Drosophila, human genome, and mice are among the databases being developed, and
> I am currently designing a new database from AAtDB for Chlamydomonas.
> 


--
Don Gilbert                                     gilbert at bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405




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