rdonis@crcvms.unl.edu (03/16/91)
-Message-Text-Follows- To the Genbank managers and keepers: My thanks for the fantastic work you are doing in keeping this great resource alive. Of course there are always little things to pick on. Here is one: PNAS 88:1711 (March 1991) carries an article on hepatitis C virus nucleotide sequences. Accession number: M58406 I did "retrieve@genbank..." and the reply was "no matches on m58406" meaning the sequence is not available to the rest of us as yet. This is probably the consequence of the "release after publication date" clause in the sequence submission form. OK, fine... but it is frustrating for the rest of us to just keep trying to see when the *GENBANK* folks realize that maybe its time to make the sequence available. How many PhDs does it take to come up with a solution to this? My 2 pennies: I suggest all the Scientific Journal publishers send Genbank E-mails like this: Nucleic Acids Research; vol 56, number 2. Date: 2-15-91 Accessions to Genbank M1234 M5678 Accessions to EMBL etc, etc.... Then Genbank folks would perhaps automate moving the accessions included in the E-mails from the private to the public GB directory Next we have to figure out how to get the Presses to do their part, and send the info to GB. Any ideas? Ruben Donis University of Nebraska-Lincoln Rdonis@crcvms.unl.edu 402/472-6063
kristoff@GENBANK.BIO.NET (Dave Kristofferson) (03/19/91)
> To the Genbank managers and keepers: > > My thanks for the fantastic work you are doing in keeping this great > resource alive. Of course there are always little things to pick on. Thanks (I hope 8-)! > Here is one: > > PNAS 88:1711 (March 1991) carries an article on hepatitis C virus > nucleotide sequences. Accession number: M58406 > > I did "retrieve@genbank..." and the reply was "no matches on m58406" > meaning the sequence is not available to the rest of us as yet. > > This is probably the consequence of the "release after publication date" > clause in the sequence submission form. OK, fine... > but it is frustrating for the rest of us to just keep trying to > see when the *GENBANK* folks realize that maybe its time to make the > sequence available. > > How many PhDs does it take to come up with a solution to this? Paul Gilna would normally have issued his usual prompt response to this, but I just found out that he is en route to a meeting in DC. So as not to leave you feeling ignored, I will make a couple of small points now and Paul may fill in any gaps later. When people ask that data be held for publication it is obviously the case that the GenBank staff must get the journals, locate articles with sequence data, confirm that the data is in-house and then release it (kind of defeats author entry to some extent, doesn't it). You have obviously received your March issue of PNAS, but I can't say for certain whether or not the same issue has arrived at Los Alamos. Given the above possibility, it will not uncommonly be the case that those who receive a journal and promptly sit down at their terminal will be disappointed not to find the data up on the server, particularly if they happen to be one of the first groups to receive the issue (does PNAS mail issues out alphabetically by subscriber, by zip code, by ????). We currently ask those who notice that data cited in the literature is not available on the server to send the reference to update@genome.lanl.gov, and LANL will release the data as soon as publication can be confirmed (often within a day). Of course, we would all like to reach the point of having data appear concurrently with its hard copy publication. Having a Ph.D. unfortunately is not all it takes to solve this problem. It requires a lot of coordination between quite a few journals and the databases. Paul has been working on this for quite some time, so please don't feel that we are totally clueless here. > My 2 pennies: > I suggest all the Scientific Journal publishers send Genbank E-mails > like this: > Nucleic Acids Research; vol 56, number 2. Date: 2-15-91 > Accessions to Genbank M1234 > M5678 > Accessions to EMBL etc, etc.... > > Then Genbank folks would perhaps automate moving the accessions included > in the E-mails from the private to the public GB directory I would not be surprised if LANL would be elated to receive such contributions. > Next we have to figure out how to get the Presses to do their part, and > send the info to GB. Any ideas? Hmm ... this should be easy, shouldn't it 8-)? Unfortunately this creates even more work for sometimes overworked journal staff people and it is not always clear to the journals what benefit they derive by taking this on. Perhaps Paul will have some success stories to tell you about. Paul is getting the advance postings of journal TOCS from BIO-JOURNALS and has found these to be of some use in finding data before hardcopy publication. This gives the journals a small incentive because BIO-JOURNALS is a form of "advertising" for them to some extent. However it doesn't solve the problem completely because quite often sequences are submitted to more than one journal before they appear in print. The concept that LANL has pushed is one of making a database submission a recognized publication in the academic community, thus allowing the database to release data soon after submission. This idea also may not meet with everyone's cooperation undoubtedly, but I have yet to see a way out of this morass unless people simply agree to allow the databases to release data after a certain specified time. Even here patent rights and other issues can be compromised, so you can see that the situation is not as simple as it might seem at first glance. Please be assured that we are making best efforts to get the data to the community as quickly as possible, but confidentiality issues will continue to be responsible for much of the remaining delays. Sincerely, Dave Kristofferson GenBank Manager kristoff@genbank.bio.net