As Don stated earlier,
>New biology file formats for WAIS and Gopher include:
>> | genbank /* GenBank flatfile format */
> | embl /* EMBL flatfile format */
> | prositedoc /* Prosite protein doc format */
> | prositedat /* Prosite protein dat format */
> | biojournal /* Bio journal TOC on bionet.journals */
I have further added
| ecoli /* E.Coli flatfile format */
| enzyme /* Amos ' ENZYME flatfile format */
| flybase_ref /* Reference file format of FLYBASE */
| flybase_loci/* Locus format of FLYBASE */
| flybase_ab /* abrerrations file format of FLYBASE */
and I modified the embl format to incorporate the DR field.
Details see below.
>The IUBio gopher hole now includes searching of the current
>full NCBI-Genbank release, and more recent Genbank + EMBL updates;
>searching of the current Prosite protein pattern database;
>searching of Bio Journal tables of contents; searching of a compendium
>of molecular biology materials & methods protocols. As well
>there is access thru Gopher to Drosophila data archives and the IUBio
>software and data ftp archive.
On bioftp gopher, there is now searching for
E.Coli database
EMBL CD-ROM release
ENZYME database
FLYBASE
XEMBL (new since last EMBL release)
XXEMBL (updates since last EMBL release)
SWISS-PROT
PROSITE
pointers go to Don's gopher for
Redbook
GENBANK
Don was wise enough to state
>This gopher is still experimental -- the computer and disk space
>may be required for other projects in the future.
That applies for me as well.
The following is the short description of formats I have added:
/* flybase_loci Flat-file format:
entry; item item
item item
item item item
***/
/* flybase_ref Flat-file format:
entry reference
reference
reference
***/
/* flybase_ab Flat-file format:
entry
item item item
***/
/* enzyme Flat-file format:
ID Identification (Begins each entry; 1 per entry)
DE Description (official name) (>=1 per entry)
AN Alternate name(s) (>=0 per entry)
CA Catalytic activity (>=0 per entry)
CF Cofactor(s) (>=0 per entry)
CC Comments (>=0 per entry)
DI Disease(s) associated with the enzyme (>=0 per entry)
DR Cross-references to SWISS-PROT (>=0 per entry)
*****/
/* ecoli Flat-file format:
ML - map location (begins each entry; 1 per entry)
GS - gene symbol or name (1 per entry)
AC - accession number (1 per entry)
CC - comments (>=1 per entry)
EM - EMBL entry name (1 per entry)
GB - GenBank entry name (1 per entry)
RL - reference location (1 per entry)
***/
My biogopher is homed at
#
###################################
#
Name=bioftp EMBnet Switzerland (experimental)
Type=1
Port=70
Path=
Host=bioftp.unibas.ch
#
###################################
Enjoy!
************************************************************************
Dr. Reinhard Doelz * EAN doelz at urz.unibas.ch
Biocomputing * DECNET 20579::48130::doelz
Biozentrum der Universitaet * X25 psi%022846211142::embnet
Klingelbergstrasse 70 * FAX x41 61 261- 6760
CH 4056 Basel * TEL x41 61 267- 2076 or 2247
************************************************************************
PS:
All the databases mentioned are to be cited properly in publications.
The corresponding description sheet is in each of the directories.
