Announcements of the Protein Information Resource
Network Request Service
Highlights
1. Submitting Sequence Data to GenBank, EMBL, DDBJ or PIR
2. PIR Network Request Service Command Summary
1. Submitting Sequence Data to GenBank, EMBL, DDBJ or PIR
The National Biomedical Research Foundation Protein Information Resource has a
Network Request Server that, among other things, accepts electronic submission
of sequence data. Sequence data submission policies have been designed by
agreement among the nucleotide and protein sequence databanks. We wish to take
this opportunity to restate for BIONEWS subscribers a few general guidelines on
submission of their sequence data.
Researchers should submit nucleotide sequence data directly to GenBank or EMBL
for assignment of an accession number prior to publication. Derived amino acid
sequence data may also be included at the same time. Amino acid sequence data
submitted in this way to GenBank, EMBL or DDBJ are eventually passed on to PIR,
and need not be submitted separately to PIR. This is done so correct cross-
references can be made between nucleotide and protein sequence accession
numbers.
All other amino acid sequences may be submitted directly to PIR when the
authors permit their public release prior to publication. Sequences submitted
for publication in the journal Protein Science are automatically passed on to
the PIR for assignment of accession numbers prior to publication, and those
authors do not need not to make separate submissions.
Authors are strongly urged to use the sequence submission software package
AUTHORIN to submit their sequence data to the databanks; a free copy (for
either the IBM PC or Macintosh) can be obtained by sending your request and
regular postal mailing address to:
authorin at net.bio.net
Japanese authors who use the NEC 9801 PC should communicate directly with
DDBJ, as these machines use a version of DOS that is significantly different
enough to render the discs unreadable on MS-DOS computers here. The staff at
DDBJ will forward the data to the appropriate databank via electronic mail.
DDBJ may be contacted at:
ddbjsubs at flat.nig.ac.jp
The address for GenBank submissions is:
GenBank Submissions
Mail Stop K710
Los Alamos National Laboratory
Los Alamos, NM 87545
U.S.A.
Telephone: (505) 665-2177
Electronic mail: gb-sub at life.lanl.gov
The address for EMBL submissions is:
EMBL Data Submissions
Postfach 10.2209
D-6900, Heidelburg
Federal Republic of Germany
Telephone (+49) 6221-387-258
Electronic mail: DATASUBS at EMBL-Heidelberg.DE
The address for DDBJ submissions is:
DNA Database of Japan
Center for Genetic Information Research
National Institute of Genetics
111 Yata
Mishima, Shizuoka 411
JAPAN
Telephone (+81) 559-75-3651
Electronic mail: ddbjsubs at flat.nig.ac.jp
The address for PIR submissions is:
PIR Submissions
National Biomedical Research Foundation
3900 Reservoir Road, NW
Washington, DC 20007
U.S.A.
Telephone: (202) 687-2121
Electronic mail: FILESERV at GUNBRF.BITNET, FILESERV at NBRF.Georgetown.EDU
While we would again urge that AUTHORIN be used as the first choice in data
submission tools, the GenBank/EMBL/PIR Data Submission Form can be obtained
either by sending a message consisting of the word DATASUB to
retrieve at net.bio.net
or by sending a message consisting of the words
SEND SUBFORM
to the FILESERV address. This form can be filled in using any text editor,
saved in ASCII (text) format, and mailed electronically or on disk to the
databanks.
Please, do not submit data either by electronic mail or on disk in files that
are formatted for word processing programs. Such files are almost always
unreadable except by systems with the same configuration of computer, operating
system and word-processing program. For files sent by disk, either DOS or Mac
formatted disks can be used but we would prefer receiving regular "double
density" disks rather than "high density" disks.
Additional information about submitting sequence data to PIR can be obtained
by sending the message HELP DEPOSIT to the FILESERV address.
2. PIR Network Request Service Command Summary
The National Biomedical Research Foundation Protein Information Resource
network request service is a full-function fileserver and database query
system. Operating since August 1990 it is capable of handling database
queries, sequence searches and sequence submissions, in addition to
fileserver requests. To use this server, request commands should be sent to
FILESERV at GUNBRF on BITNET or FILESERV at NBRF.Georgetown.EDU on Internet.
The server recognizes the following commands sent either in a mail message,
or (if the sender is on BITNET) in a command message or a file:
Command Action
------- -----------------------------------------------
ACCESSION list entry codes and titles by accession number
AND combine QUERY commands with Boolean AND
AUTHOR list entry codes and titles by author
BASES list accessible databases
CROSS list PIR entry codes and titles corresponding to
a particular nucleic sequence database entry
DEPOSIT deposit entry for database submission
END DEPOSIT terminate deposit entry
FEATURE list entry codes and titles by feature table entry
GENE list entry codes and titles for a gene name
GET return entry by entry code
HELP return HELP instructions
HOST list entry codes and titles by host species
INDEX list SENDable files
JOURNAL list entry codes and titles by journal citation
KEYWORD list entry codes and titles by keyword
MEMBER list alignments containing entry code as a member
NOT combine QUERY commands with Boolean NOT
OR combine QUERY commands with Boolean OR
QUERY begin collecting QUERY commands
END QUERY terminate collecting commands and execute QUERY
QUIT ignore the remaining text (E-mail signature blocks)
RETURN change return address for gateway mail
SEARCH search for matching sequences by FASTA procedure
END SEARCH terminate sequence for searching
SEND send file
SPECIES list entry codes and titles by species
SUGGEST leave suggestion or correction for PIR staff
END SUGGEST terminate suggestion text
SUPERFAMILY list entry codes and titles by superfamily name
TAXONOMY report taxonomy for scientific or common name
TITLE list entry codes and titles by title
USE set databases, dates or formats to use in limited searches
Multiple commands can be sent with one command on each line of a mail message
or file. Commands should NOT be sent on the Subject line of a mail message.
Receipt of command messages and files will be acknowledged immediately. Mail
messages will be acknowledged by return mail.
For help in using any of the commands, send a request of the form
HELP topic
for example
HELP SEARCH
In addition to the commands, help instructions are also available on the
following topics:
Custom_Services
Databases
FTP
Gateway_Access
Help_en_Espanol
Help_en_francais
Hints
IBM-VM_BITNET
On-Line_Access
PIR_Distribution
VAX-VMS_BITNET
Because of network gateway communication protocols, there are limitations on
requests sent through gateways. Users not on BITNET or INTERNET who access the
server through local or network gateways should read and carefully follow these
instructions before sending requests. Only mail message requests (not command
messages or files) can be sent through gateways. Because addresses posted on
gateway mail do not always work for the return, before you send requests
through network gateways it is strongly recommended that you first contact
John S. Garavelli (POSTMAST at GUNBRF on BITNET, POSTMASTER at NBRF.Georgetown.EDU on
Internet). We will confirm a return address for you and may instruct you to
use the RETURN command to ensure that your request output will reach you. It
is not usually necessary to do this if you are on BITNET or INTERNET, unless
your system employs a local remailer or your mail program applies a
nonstandard return address (for example a personal name on the FROM: line).
The BITNET network and the network gateways impose strict limits on file size.
Poorly posed database queries may result in output so extensive that it could
not be returned by network mail. Therefore, an output limit of 1000 lines for
each command and 3000 lines for each request is imposed by the PIR server.
The DEPOSIT and QUERY commands, and the SEARCH and SUGGEST commands (in their
multiline form) must be followed by their respective END commands after the
text appearing on the intervening lines. The DEPOSIT command requires, and the
SEARCH command optionally uses, parameters that appear on the same line as the
command. Because these four commands are so complex, users should obtain and
carefully read the help instructions before attempting to use them.
The databases available through the PIR Network Server and their abbreviations
for code specification are as follows:
Abbreviation Database Update Schedule
PIR1 PIR Annotated and Classified Entries quarterly
PIR2 PIR Preliminary Entries approximately monthly
PIR3 PIR Unverified Entries weekly
ALN PIR Alignment Entries semiannually
NRL_3D Brookhaven Data Bank Sequences quarterly
PATCHX MIPS PIR-Supplementary Database quarterly
N NBRF Nucleic
GB GenBank (TM) as received
GBSUP GenBank (TM) as received
GBNEW GenBank (TM) New Entries weekly
EMBL EMBL as received
EMBLSUP EMBL as received
In the FASTA output of the SEARCH command the abbreviation for PATCHX is
shortened to PATX and NRL_3D is shortened to NR3D; the longer abbreviation
should be used to retrieve an entry with the GET command. Not all commands
work with all databases; please read the information returned by the command
HELP DATABASES.
------------------------------------------------------------------------
Dr. John S. Garavelli
Database Coordinator
Protein Information Resource
National Biomedical Research Foundation
Washington, DC 20007
POSTMASTER at GUNBRF.BITNETPOSTMASTER at NBRF.Georgetown.Edu
