WMBORMON@hlerul52.bitnet (04/11/89)
The organization of a BIO-JOURNALS newsgroup is an excellent idea, but it will of real help only if the various journal contents will be organized in the same format. As of now, there are as many formats as there are journals who are willing to participate in this project. You can't have software for each of them individually. But otherwise, a laudable initiative. Hans van Ormondt Sylvius Laboratory Leiden, NL. WMBORMOND@HLERUL52.BITNET
Kristofferson@BIONET-20.BIO.NET (David Kristofferson) (04/11/89)
The organization of a BIO-JOURNALS newsgroup is an excellent idea, but it will of real help only if the various journal contents will be organized in the same format. As of now, there are as many formats as there are journals who are willing to participate in this project. You can't have software for each of them individually. But otherwise, a laudable initiative. Hans van Ormondt Sylvius Laboratory Leiden, NL. WMBORMOND@HLERUL52.BITNET ---------------------------------------------------------------------- Thanks a lot for taking the time to comment. Actually we are taking steps to standardize on a format (a subset of Medline). The last few postings from J. Virol., Mol. Cell. Biol. and CABIOS are converging. The publishers have been very cooperative to date, but I can not force anyone to conform to a standard if it is economically unfeasible for them. We will do our best in this area, but it seems that it is better to get the data at least for on-line browsing than not at all if format is a sticking point. Sincerely, Dave Kristofferson BIONET Resource Manager kristofferson@bionet-20.bio.net -------
elliston@rob.UUCP ( Keith Elliston) (04/13/89)
In article <8904111128.AA22235@net.bio.net>, WMBORMON@hlerul52.bitnet writes: > The organization of a BIO-JOURNALS newsgroup is an excellent idea, > but it will of real help only if the various journal contents will > be organized in the same format. As of now, there are as many formats > as there are journals who are willing to participate in this project. > You can't have software for each of them individually. > But otherwise, a laudable initiative. This is a very good point. What format are we going to adopt for these contents? I think that my favorite is the EMBL-like form, where each line of each entry is preceded by a 2 letter field identifier. It is rather primitive but it allows everyone to easily write a little parser to convert it to whatever format they are using. In fact, someone could volunteer to write a little for this type of conversion. Another point... what should we request as far as info included in the toc's? I suggest that we try to get the journals to include the abstracts if at all possible. That would make searching them a whole lot easier. I think that this wouldnt be a whole lot of extra work for the contributors, as they must have this stuff stored electronically anyway. > > Hans van Ormondt > Sylvius Laboratory > Leiden, NL. > WMBORMOND@HLERUL52.BITNET -Keith Elliston =============================================================================== Keith O. Elliston | Usenet: uunet!rob!elliston Senior Information Scientist | Arpanet: rob!elliston@uunet.uu.net Merck Sharp & Dohme Res. Lab. | Bitnet: elliston%rob.uucp@psuvax1 Rahway, NJ 07065 U.S.A. | -or- elliston@biovax =============================================================================== Disclaimer: I can have no OFFICIAL comments about anything........ ===============================================================================
kristoff@NET.BIO.NET (David Kristofferson) (04/13/89)
Keith, By now you have probably seen my follow-up message to Dr. van Ormondt which states that we are going with a Medline format. I have yet to find a publisher that can easily give out the abstracts. All have claimed that this involves much more expense on their part than they currently care to pay to separate this material out. The fact that the abstracts aren't here yet does not mean that we haven't tried to get them. -- Sincerely, Dave Kristofferson BIONET Resource Manager kristoff@net.bio.net or kristofferson@bionet-20.bio.net
elliston@rob.UUCP ( Keith Elliston) (04/14/89)
In article <Apr.12.20.00.23.1989.14858@NET.BIO.NET>, kristoff@NET.BIO.NET (David Kristofferson) writes: > By now you have probably seen my follow-up message to Dr. van Ormondt > which states that we are going with a Medline format. I have yet to Dave: Can we have the actual MEDLINE format posted, so that some of us...(me) can work on our programs that read the various formats and parse them for our databases? I have a Hypercard stack (that interfaces ORACLE) that I use for that purpose, and it currently uses the EMBL type format, and the BRS format. If you could post the MEDLINE format, I could modify it to do that, and then post that stack to the net for those who might want to use it. Thanks... > > Dave Kristofferson > BIONET Resource Manager > > kristoff@net.bio.net > or kristofferson@bionet-20.bio.net -Keith =============================================================================== Keith O. Elliston | Usenet: uunet!rob!elliston Senior Information Scientist | Arpanet: rob!elliston@uunet.uu.net Merck Sharp & Dohme Res. Lab. | Bitnet: elliston%rob.uucp@psuvax1 Rahway, NJ 07065 U.S.A. | -or- elliston@biovax =============================================================================== Disclaimer: I can have no OFFICIAL comments about anything........ ===============================================================================
kristoff@NET.BIO.NET (David Kristofferson) (04/15/89)
Keith, I was going to post a request for somebody to do just that as soon as the BIO-JOURNAL newsgroup was functional. We will be happy to put any such utilities into our anonymous FTP directory. In fact, both versions (Medline and EMBL) would probably be of interest to people since I know that Amos Bairoch's sequence analysis reference database is in EMBL format. I would also encourage anyone else who creates similar software to contribute it for the FTP software since I am sure that people are probably using a variety of reference database software out there. I hope that the BIO-JOURNALS bulletin board will be functional this next week. I am still waiting to hear back from some of the other BIOSCI nodes on this. In a nutshell, the references are divided into three fields in the current format. The authors are the first field and this line is preceeded by an AU identifier followed by a space, then the names. Next is the title field identified by TI then a space. Finally is the reference itself identified by an SO. Continuation lines for any field are simply indented three spaces. We don't have total conformity to this between all of our submittors yet but will make the necessary changes. For example, right now CABIOS is terminating their references with a blank line and the ASM journals are using a //. ASM is also using three spaces after the identifiers instead of one. I have had on my list of projects a note to resolve these differences and this will be done soon. -- Sincerely, Dave Kristofferson BIONET Resource Manager kristoff@net.bio.net or kristofferson@bionet-20.bio.net