jjw@rsbs0.anu.oz@ (10/12/90)
Dear Netlanders, I've got a problem. (No flames please!) I am trying to obtain a sequence, the accession number of which is given in a recent paper (PNAS vol 87, pp5397-5401, by Feiler and Jacobs). The paper states that the sequence had been deposited in the GenBank data base and an accesion number was given, X53035. I have tried with no success to obtain the sequence from <retrieve@genbank.bio.net> and from the EMBL server ( I don't have the address at hand but it's worked for me countless times before). Both servers give me back the message that this particular data file can not be found. I've tried to check the veracity of the accesion number by checking the EMBL newauthor index; again no joy. Can anybody out there help me? I would realy like to get hold of this sequence and the inability to get it from the servers using a published accession number is realy bugging me. Many thanks in advance. ******************************************************************************** Jeremy Weinman Plant Microbe Interaction group Research School of Biological Sciences Australian National University Email: jjw@rsbs0.anu.oz Phone: 61 6 2495051 Fax: 61 6 2490754 Snail: PO Box 475, Canberra, ACT 2601, AUSTRALIA ********************************************************************************
elliston@av8tr.UUCP (Keith Elliston) (10/13/90)
In article <1990Oct12.164624.1@rsbs0.anu.oz>, jjw@rsbs0.anu.oz@ writes: > I've got a problem. (No flames please!) I am trying to obtain a > sequence, the accession number of which is given in a recent paper (PNAS > vol 87, pp5397-5401, by Feiler and Jacobs). The paper states that the > sequence had been deposited in the GenBank data base and an accesion number > was given, X53035. I have tried with no success to obtain the sequence from > <retrieve@genbank.bio.net> and from the EMBL server ( I don't have the address I have seen this at least once myself lately. The sequence of the D3 receptor was published in Science a few weeks ago, with an accession number. I tried to get the sequence from the Genbank server, Genbank online, and from the EMBL server. I kept trying, and after about a week it finally showed up at EMBL. I also have noticed that at least Genbank has been known to give out accession numbers without actually having the sequence in hand. Perhaps it is time to standardize things, such that when an accession number is finally granted, the data will be available for accession. This might impede the publication of a paper that needs the accession number before publication, but would stop all this frustrating business of trying to track down the data. just my $0.02 Keith uunet!av8tr!elliston -- =============================================================================== Keith O. Elliston | .signature really under construction.... uunet!av8tr!elliston | ===============================================================================
kristoff@GENBANK.BIO.NET (Dave Kristofferson) (10/13/90)
Dear Jeremy, I can appreicate your frustration, but let me assure you that, even though the author has an accession number, this does not mean that they released the sequence to the public. Even though they may submit data prior to publication, authors often request that data be withheld until the article appears in print (sometimes in a completely different journal than the one that they report to us!). This puts an additional delay into the works because the database staff must still scan the literature, determine that the article has actually appeared and then retrieve and release the data. While we still save on having to annotate the sequence from scratch, a significant amount of time may still go by from the time that data is first sent to GenBank until it appears in the database. Unfortunately this happens with sufficient frequency that we can not handle these kinds of requests routinely without impeding progress on producing the next release of the database. If the paper is out in print there is a very decent chance that it will make it's way into the database in the next few weeks. It is possible that the data may appear at any point, so I would encourage you to try again periodically. If you don't find anything within a month to six weeks, please send us the reference again, but I doubt that you will have to wait that long. In summary, getting an accession number in advance does help get the data into the database more rapidly, but requesting confidentiality introduces another delay. Perhaps we would be happier all around if everyone were willing to release their own data as quickly as they request to see results from others. Sincerely, Dave Kristofferson GenBank Manager kristoff@genbank.bio.net
jjw@rsbs0.anu.oz@ (10/13/90)
<From: Dave Kristofferson <kristoff@genbank.bio.net> <. <In-Reply-To: Your message of 12 Oct 90 16:46:24 GMT <To: genbank-bb@genbank.bio.net, jjw@rsbs0.anu.oz.au <. <I can appreicate your frustration, but let me assure you that, even <though the author has an accession number, this does not mean that <they released the sequence to the public. Even though they may submit <. <to annotate the sequence from scratch, a significant amount of time <may still go by from the time that data is first sent to GenBank until <it appears in the database. <. <the database in the next few weeks. It is possible that the data may <appear at any point, so I would encourage you to try again <periodically. If you don't find anything within a month to six weeks, <please send us the reference again, but I doubt that you will have to <wait that long. Thanks for the reply. I understand the situation now. Only one comment, though: The PNAS paper the accession number appeared in was July 1990. It's now mid-October. If that's the usual sort of wait, then I guess I'll just have to chant a few mantras and wait it out, but two and a half months seems a bit longer than the few weeks <Elliston@av8tr.UUCP> mentioned for the appearance of the D3 receptor sequence from an accession no. published in Science. Anyhow, I'll just keep sending to the servers and hope that sooner rather than later something bounces back. Thanks again for the info, Cheers ******************************************************************************** Jeremy Weinman Plant Microbe Interaction group Research School of Biological Sciences Australian National University Email: jjw@rsbs0.anu.oz Phone: 61 6 2495051 Fax: 61 6 2490754 Snail: PO Box 475, Canberra, ACT 2601, AUSTRALIA ********************************************************************************
rak@sun1.ruf.uni-freiburg.de (Bodo Rak) (10/14/90)
jjw@rsbs0.anu.oz@ writes: >I've got a problem. (No flames please!) I am trying to obtain a >sequence, the accession number of which is given in a recent paper (PNAS >vol 87, pp5397-5401, by Feiler and Jacobs). The paper states that the >sequence had been deposited in the GenBank data base and an accesion number >was given, X53035. I have tried with no success to obtain the sequence from ><retrieve@genbank.bio.net> and from the EMBL server - deleted - >newauthor index; again no joy. Can anybody out there help me? I would realy >like to get hold of this sequence and the inability to get it from the >servers using a published accession number is realy bugging me. A few days ago I had the same problem with two sequences that had been published in September and July, respectively and found a fast and efficient solution: I sent a short note to DATALIB@EMBL.BITNET, in which I explained my problem. A few hours later both sequences were available from the EMBL file server. I could imagine that we all could support the people at EMBL and GENBANK who must be trying hard to find out which of the submitted sequences have indeed finally made it to a publication by giving them this kind of feedback. Regards, Bodo Rak ******************************************************** Dept. of Genetics University D-7800 Freiburg - FRG RAK@RUF.UNI-FREIBURG.DBP.DE ********************************************************
pgil%histone@LANL.GOV (Paul Gilna) (10/15/90)
Frequently, an author will request that the sequence be held confidential until publication. This means that although we have the sequence in hand we cannot release the data until we "spot" the appeareance of these data in a journal, at which point we are free to release them. With every submission of this ilk, we strongly encourage authors to inform us of the impending date of publication so that we can have the data out in time, but few respond in this manner. To someone who spots an accession number that cannot be retrieved, I would request that you do us all a service and inform GenBank directly (mail to genbank%life@lanl.gov); we can get the annotated data out and on the servers within 24 hours as soon as we know that the data have been published. There is no doubt in my mind that the necessity of holding onto data seriously hampers our ability to have those data on-line, at the time of publication. We in fact have pondered a great deal over just this topic and are working on a number of solutions that hopefully should lead the way in the whole issue of timely release of data. In the interim (and indeed beyond) I would reiterate my request to the community to help us out. Paul Gilna GenBank, Los Alamos.
kristoff@genbank.bio.net (David Kristofferson) (10/16/90)
Jeremy Weinman writes: > Thanks for the reply. I understand the situation now. Only one comment, though: > The PNAS paper the accession number appeared in was July 1990. It's now > mid-October. If that's the usual sort of wait, then I guess I'll just have > to chant a few mantras and wait it out. This delay is definitely outside of our target window, so thank you for notifying us. Paul Gilna at GenBank LANL also replies: > To someone who spots an accession number that cannot be retrieved, I > would request that you do us all a service and inform GenBank directly > (mail to genbank%life@lanl.gov); we can get the annotated data out and > on the servers within 24 hours as soon as we know that the data have > been published. My thanks to Paul for stating LANL's policy here. I just talked to him on the phone however, and Paul emphasized that the above applies to annotated data waiting in the release queue until appearance of the publication. For those who might want to get a jump on the gun, please be aware that GenBank cannot hunt down and release data in advance to people who request the sequence of some particular gene that they may know is in press. The above policy applies only to data that we can verify is published, so everyone will benefit to the maximum if requests for the release of data that are not available on the servers follow these guidelines. -- Sincerely, Dave Kristofferson GenBank Manager kristoff@genbank.bio.net