From owner-embldatabank@net.bio.net Fri Sep 02 23:00:00 1994 Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.genome-program,bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!spool.mu.edu!darwin.sura.net!fconvx.ncifcrf.gov!fcsparc6!toms From: toms@fcsparc6.ncifcrf.gov (Tom Schneider) Subject: Re: BCM Sequence Annotation Web Server Message-ID: Sender: usenet@ncifcrf.gov (C News) Nntp-Posting-Host: fcsparc6.ncifcrf.gov Organization: Frederick Cancer Research and Development Center References: <1994Aug31.142529.4040@emba.uvm.edu> Date: Fri, 2 Sep 1994 23:59:29 GMT Lines: 46 Xref: biosci bionet.molbio.genbank:1737 bionet.molbio.embldatabank:362 bionet.molbio.genome-program:925 bionet.molbio.proteins:2587 In article rsmith@dot.bcm.tmc.edu (Randall Smith) writes: | : Announcing a new WWW Server: The BCM Sequence Annotation Server | : URL: http://dot.imgen.bcm.tmc.edu:9331/seq-annot/home.html This idea has both good and bad points and I think that they should be considered extremely carefully. First, the idea that individual researchers should be able to update a database directly is wonderful. If everybody were to do that to the data they are experts on, GenBank would quickly become a clean database. However, there are several problems: 1. Corruption of the data either intentionally or inadvertently. The authors already are aware of this possibility. 2. Inconsistency between researchers. The NCBI attempts to make entries uniform by certain standards, but individual researchers cannot know what these are in detail. The only solutions I see are to force the kinds of annotations to follow certain forms or to pass all the changes to experts for editing. The trouble with passing the data to experts is that the number of experts has to grow exponentially along with the growth of the database. Maybe we just have to accept that to avoid a worse mess! 2. Do the data flow into GenBank? There is no indication that it will. This means that if GenBank makes a correction it won't go into this database and vice versa. Since the data are not maintained in one place, it is duplicated and will eventually become inconsistent. Who should or will a researcher believe? A randomly annotated database or the "official" one? How will inconsistencies be resolved? I see this as an experiment. Once the experiment has been shown to work reasonably well, all the data should be passed to NCBI for careful processing along with all new data. That is, the server should be run by NCBI or closely in conjunction with them. For my reasoning behind this posting, see the philosophy paper available from: http://fconvx.ncifcrf.gov:2001/~toms/onlinepapers.html Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov From owner-embldatabank@net.bio.net Sun Sep 11 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!Germany.EU.net!news.dfn.de!urmel.informatik.rwth-aachen.de!news.rhrz.uni-bonn.de!usenet From: allera@mailer.meb.uni-bonn.de Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.genome-program,bionet.molbio.proteins Subject: Re: BCM Sequence Annotation Web Server Date: 12 Sep 1994 15:49:53 GMT Organization: Klin.Biochemie/MEB Lines: 47 Message-ID: <351tb1$3k2@news.rhrz.uni-bonn.de> NNTP-Posting-Host: allera.meb.uni-bonn.de X-Newsreader: Xref: biosci bionet.molbio.genbank:1742 bionet.molbio.embldatabank:363 bionet.molbio.genome-program:935 bionet.molbio.proteins:2653 In article toms@fcsparc6.ncifcrf.gov (Tom Schneider) writes: >In article rsmith@dot.bcm.tmc.edu >(Randall Smith) writes: > >| : Announcing a new WWW Server: The BCM Sequence Annotation Server >| : URL: http://dot.imgen.bcm.tmc.edu:9331/seq-annot/home.html > >This idea has both good and bad points and I think that they should be >considered extremely carefully. > >First, the idea that individual researchers should be able to update a database >directly is wonderful. If everybody were to do that to the data they are >experts on, GenBank would quickly become a clean database. > >However, there are several problems: > >1. Corruption of the data either intentionally or inadvertently. The authors >already are aware of this possibility. > >2. Inconsistency between researchers. The NCBI attempts to make entries >uniform by certain standards, but individual researchers cannot know what these >are in detail. The only solutions I see are to force the kinds of annotations >to follow certain forms or to pass all the changes to experts for editing. The >trouble with passing the data to experts is that the number of experts has to >grow exponentially along with the growth of the database. Maybe we just have >to accept that to avoid a worse mess! > >2. Do the data flow into GenBank? There is no indication that it will. This >means that if GenBank makes a correction it won't go into this database and >vice versa. Since the data are not maintained in one place, it is duplicated >and will eventually become inconsistent. Who should or will a researcher >believe? A randomly annotated database or the "official" one? How will >inconsistencies be resolved? > >I see this as an experiment. Once the experiment has been shown to work >reasonably well, all the data should be passed to NCBI for careful processing >along with all new data. That is, the server should be run by NCBI or closely >in conjunction with them. > >For my reasoning behind this posting, see the philosophy paper available from: >http://fconvx.ncifcrf.gov:2001/~toms/onlinepapers.html > > Tom Schneider > National Cancer Institute > Laboratory of Mathematical Biology > Frederick, Maryland 21702-1201 > toms@ncifcrf.gov From owner-embldatabank@net.bio.net Mon Sep 19 23:00:00 1994 Newsgroups: bionet.molbio.embldatabank,embnet.general Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!stoehr From: stoehr@ebi.ac.uk Subject: EMBL Data Library moves to the EBI Message-ID: <1994Sep19.200721@ebi.ac.uk> Lines: 30 Sender: news@ebi.ac.uk (Mr news) Organization: European BioInformatics Institute Date: Mon, 19 Sep 1994 19:07:21 GMT IMPORTANT ANNOUNCEMENT! IMPORTANT ANNOUNCEMENT! EFFECTIVE SEPTEMBER 1, 1994, ALL ACTIVITIES AND SERVICES OF THE EMBL DATA LIBRARY HAVE BEEN MOVED TO THE EUROPEAN BIOINFORMATICS INSTITUTE (EBI). The European Bioinformatics Institute is a new EMBL Outstation, located at Hinxton Hall, near Cambridge, UK. The database services of the EBI are the continuation of the EMBL Data Library activities. During the time of this transition, mechanisms will be in place to ensure that correspondence and queries sent to the old EMBL addresses will be forwarded to the EBI. How To Contact the European Bioinformatics Institute (after 1-SEP-1994) Network: Datalib@EBI.AC.UK (for general enquiries) Datasubs@EBI.AC.UK (for data submissions) Update@EBI.AC.UK (for corrections to nucleotide entries) Postal address: European Bioinformatics Institute, Hinxton Hall, Hinxton, Cambridge CB10 1RQ, UK. Telephone: +44 (0) 1223 494400 Telefax: +44 (0) 1223 494468 From owner-embldatabank@net.bio.net Tue Sep 20 23:00:00 1994 Path: biosci!biosci!not-for-mail From: "Nikolai I. Baev" Newsgroups: bionet.general,bionet.molec-model,bionet.molbio.proteins,bionet.molbio.genbank,bionet.molbio.embldatabank Subject: Lost "motif" e-mail server Date: 21 Sep 1994 09:57:00 -0700 Organization: McGill University Lines: 19 Sender: kristoff@net.bio.net Distribution: world Message-ID: <21SEP94.12198965.0075@VM1.MCGILL.CA> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.general:11239 bionet.molec-model:109 bionet.molbio.proteins:2712 bionet.molbio.genbank:1751 bionet.molbio.embldatabank:365 Dear netters..I lost, unfortunately, the e-mail address of an important protein "motif" server. The request format was as follows: TYPE Protein TARGET Prosite TARGET PDB COMMENT xxxxxxxxxxxxxxxxxxxxxxxxxx SEQ XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX END The databases searched by that server were PDB, SwissProt, Genome Sequence Database (GSDB-LANL), and Prosite. Could you please help me to identify that server and its e-mail address. Thanks in advance. Nikolai I. Baev, M.D. Montreal Neurological Institute Montreal, PQ, Canada mdnb@musica.mcgill.ca