From usenet.ucs.indiana.edu!sol.ctr.columbia.edu!zaphod.mps.ohio-state.edu!saimiri.primate.wisc.edu!ames!agate!biosci!NBRF.GEORGETOWN.EDU!POSTMASTER Wed Dec 2 13:27:07 EST 1992 Article: 102 of bionet.molbio.proteins Path: usenet.ucs.indiana.edu!sol.ctr.columbia.edu!zaphod.mps.ohio-state.edu!saimiri.primate.wisc.edu!ames!agate!biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Announcements of the Protein Information Resource Message-ID: <01GRUA9XSD4M94DW7D@NBRF.Georgetown.Edu> Date: 2 Dec 92 16:53:52 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 226 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@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@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@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@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@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@GUNBRF.BITNET, FILESERV@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@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@GUNBRF on BITNET or FILESERV@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@GUNBRF on BITNET, POSTMASTER@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@GUNBRF.BITNET POSTMASTER@NBRF.Georgetown.Edu