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bioftp gopher searches now available

doelz at urz.unibas.ch doelz at urz.unibas.ch
Thu Feb 27 14:52:03 EST 1992


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. 




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