From wallinc@ncbi.nlm.nih.gov Tue May 22 09:13:41 2007 Return-Path: X-Original-To: gene-announce@reba.ncbi.nlm.nih.gov Delivered-To: gene-announce@reba.ncbi.nlm.nih.gov Received: from mail2.ncbi.nlm.nih.gov (mail2.ncbi.nlm.nih.gov [130.14.29.42]) by reba.ncbi.nlm.nih.gov (Postfix) with ESMTP id B97453D9D for ; Tue, 22 May 2007 09:13:41 -0400 (EDT) Received: by mail2.ncbi.nlm.nih.gov (Postfix) id AA50B76C2A2; Tue, 22 May 2007 09:13:41 -0400 (EDT) Delivered-To: gene-announce@mailgw.ncbi.nlm.nih.gov Received: from NIHCESSMTP3.hub.nih.gov (nihcessmtp3.hub.nih.gov [128.231.90.117]) by mail2.ncbi.nlm.nih.gov (Postfix) with ESMTP id 6CFBB76C2CE for ; Tue, 22 May 2007 09:13:41 -0400 (EDT) Received: from NIHCESMLBX8.nih.gov ([156.40.71.208]) by NIHCESSMTP3.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.1830); Tue, 22 May 2007 09:13:41 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Date: Tue, 22 May 2007 09:13:40 -0400 Message-ID: <7F40ACD22B0A23448C4E8755E5875FE707CEF5AE@NIHCESMLBX8.nih.gov> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Change to the gene2go ftp file Thread-Index: AceccwPugRsfeNaiQumcSYEP9zTDYA== To: X-OriginalArrivalTime: 22 May 2007 13:13:41.0288 (UTC) FILETIME=[046EA280:01C79C73] From: gene-announce@ncbi.nlm.nih.gov Subject: [Gene-announce] Change to the gene2go ftp file X-BeenThere: gene-announce@ncbi.nlm.nih.gov X-Mailman-Version: 2.1.3 Precedence: list List-Id: Announcing changes in Entrez Gene List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 22 May 2007 13:13:41 -0000 This week there will be a change to the gene2go ftp file. When a field has no data value, it will be represented with a hyphen. This will be consistent with other gene ftp files. The README file in the Entrez Gene ftp site has been updated to document this change. See: ftp://ftp.ncbi.nlm.nih.gov/gene/README From maglott@ncbi.nlm.nih.gov Mon Jun 11 15:55:12 2007 Return-Path: X-Original-To: gene-announce@reba.ncbi.nlm.nih.gov Delivered-To: gene-announce@reba.ncbi.nlm.nih.gov Received: from mail2.ncbi.nlm.nih.gov (mail2.ncbi.nlm.nih.gov [130.14.29.42]) by reba.ncbi.nlm.nih.gov (Postfix) with ESMTP id BB7413D9B for ; Mon, 11 Jun 2007 15:55:12 -0400 (EDT) Received: by mail2.ncbi.nlm.nih.gov (Postfix) id 94FFA76C07C; Mon, 11 Jun 2007 15:55:12 -0400 (EDT) Delivered-To: gene-announce@mailgw.ncbi.nlm.nih.gov Received: from NIHCESSMTP3.hub.nih.gov (nihcessmtp3.hub.nih.gov [128.231.90.117]) by mail2.ncbi.nlm.nih.gov (Postfix) with ESMTP id 89A8F76C070 for ; Mon, 11 Jun 2007 15:55:12 -0400 (EDT) Received: from NIHCESMLBX8.nih.gov ([156.40.71.208]) by NIHCESSMTP3.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.1830); Mon, 11 Jun 2007 15:55:12 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Date: Mon, 11 Jun 2007 15:55:11 -0400 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: A new method to construct URLs to Entrez Gene (and other NCBI databases) Thread-Index: AcesYmt/JG6/b1ThQiyxTLHGq70j/w== To: X-OriginalArrivalTime: 11 Jun 2007 19:55:12.0371 (UTC) FILETIME=[6C192C30:01C7AC62] From: gene-announce@ncbi.nlm.nih.gov Subject: [Gene-announce] A new method to construct URLs to Entrez Gene (and other NCBI databases) X-BeenThere: gene-announce@ncbi.nlm.nih.gov X-Mailman-Version: 2.1.3 Precedence: list List-Id: Announcing changes in Entrez Gene List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 11 Jun 2007 19:55:12 -0000 NCBI now supports a more simplified and memorable method to construct URLs to an Entrez database. Documentation is provided here: http://view.ncbi.nlm.nih.gov=20 For Gene, this means that instead of constructing a URL like http://www.ncbi.nlm.nih.gov/sites/entrez?db=3Dgene&cmd=3Dretrieve&dopt=3D= full_ report&list_uids=3D1 or=20 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=3Dgene&cmd=3Dretrieve&do= pt=3D default&list_uids=3D1 to retrieve a specific record,=20 you can instead use http://view.ncbi.nlm.nih.gov/gene/1 Note that a search function is also supported, which can facilitate searching by gene symbols. http://view.ncbi.nlm.nih.gov/gene/search/ttn From maglott@ncbi.nlm.nih.gov Sat Aug 4 14:01:11 2007 Return-Path: X-Original-To: gene-announce@reba.ncbi.nlm.nih.gov Delivered-To: gene-announce@reba.ncbi.nlm.nih.gov Received: from mail1.ncbi.nlm.nih.gov (mail1.ncbi.nlm.nih.gov [130.14.29.41]) by reba.ncbi.nlm.nih.gov (Postfix) with ESMTP id CDB1E3D9B for ; Sat, 4 Aug 2007 14:01:11 -0400 (EDT) Received: by mail1.ncbi.nlm.nih.gov (Postfix) id 778E2167572; Sat, 4 Aug 2007 14:01:07 -0400 (EDT) Delivered-To: gene-announce@mailgw.ncbi.nlm.nih.gov Received: from NIHCESSMTP2.hub.nih.gov (nihcessmtp2.hub.nih.gov [128.231.90.116]) by mail1.ncbi.nlm.nih.gov (Postfix) with ESMTP id 8D57B167603; Sat, 4 Aug 2007 14:00:48 -0400 (EDT) Received: from NIHCESMLBX8.nih.gov ([156.40.71.208]) by NIHCESSMTP2.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.1830); Sat, 4 Aug 2007 14:00:47 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Date: Sat, 4 Aug 2007 14:00:46 -0400 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: WARNING: recent error in calculating protein names Thread-Index: AcfWwWGzkLeao5RgQJ+8yDOVMErZww== To: , X-OriginalArrivalTime: 04 Aug 2007 18:00:47.0671 (UTC) FILETIME=[62B99470:01C7D6C1] Cc: From: gene-announce@ncbi.nlm.nih.gov Subject: [Gene-announce] WARNING: recent error in calculating protein names X-BeenThere: gene-announce@ncbi.nlm.nih.gov X-Mailman-Version: 2.1.3 Precedence: list List-Id: Announcing changes in Entrez Gene List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 04 Aug 2007 18:01:11 -0000 Beginning mid July, 2007, an error was introduced in the method of = calculating protein names associated with RefSeq mRNAs of some = eukaryotic animals. This affected both records in Gene and some RefSeqs = released after RefSeq Release 24, =20 The consequence was that about 900 records were calculated to have a = protein name of 'alpha-defensin 11' =20 This error was identified August 3, and the bug has been removed. =20 The corrected data should be available from our public sites by Monday, = August 6, 2007. =20 We regret the error and any inconvenience it may have caused. =20 -RefSeq and Gene staff =20 From maglott@ncbi.nlm.nih.gov Wed Oct 3 10:30:44 2007 Return-Path: X-Original-To: gene-announce@reba.ncbi.nlm.nih.gov Delivered-To: gene-announce@reba.ncbi.nlm.nih.gov Received: from mail2.ncbi.nlm.nih.gov (mail2.be-md.ncbi.nlm.nih.gov [130.14.29.42]) by reba.ncbi.nlm.nih.gov (Postfix) with ESMTP id B787F3D9B for ; Wed, 3 Oct 2007 10:30:44 -0400 (EDT) Received: by mail2.ncbi.nlm.nih.gov (Postfix) id B4E8E1880A6; Wed, 3 Oct 2007 10:30:44 -0400 (EDT) Delivered-To: gene-announce@ncbi.nlm.nih.gov Received: from NIHCESSMTP2.hub.nih.gov (nihcessmtp2.hub.nih.gov [128.231.90.116]) by mail2.ncbi.nlm.nih.gov (Postfix) with ESMTP id AC7A918807F for ; Wed, 3 Oct 2007 10:30:44 -0400 (EDT) Received: from NIHCESMLBX8.nih.gov ([156.40.71.208]) by NIHCESSMTP2.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.1830); Wed, 3 Oct 2007 10:30:44 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C805C9.FB26FF25" Date: Wed, 3 Oct 2007 10:30:43 -0400 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: NCBI's implementation of the new UniProtKB/RefSeq collaboration thread-index: AcgFAejUHDexJBODQsunRo9q7DzU1AAArqFAAAoRklAAAX8ZsAABCfngAABfDPAAABCoIAACfR5eAB148bAAAkrZsAABP1DAAACqA9A= To: X-OriginalArrivalTime: 03 Oct 2007 14:30:44.0384 (UTC) FILETIME=[FB5D9A00:01C805C9] From: gene-announce@ncbi.nlm.nih.gov Subject: [Gene-announce] NCBI's implementation of the new UniProtKB/RefSeq collaboration X-BeenThere: gene-announce@ncbi.nlm.nih.gov X-Mailman-Version: 2.1.3 Precedence: list List-Id: Announcing changes in Entrez Gene List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 03 Oct 2007 14:30:44 -0000 This is a multi-part message in MIME format. ------_=_NextPart_001_01C805C9.FB26FF25 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit > Announcing the availability of RefSeq-UniProtKB cross-link data > > In collaboration with UniProtKB (http://www.pir.uniprot.org/) , the RefSeq group is now reporting explicit cross-references to Swiss-Prot and TrEMBL proteins that correspond to a RefSeq protein. These correspondences are being calculated by the UniProtKB group, and will be updated every three weeks to correspond to UniProt's release cycle. The data are being made available from several sites within NCBI: > > > 1. The full report from Entrez Gene, in the Reference Sequences section. > > For an example, go to the Full Report page for the sevenless gene of Drosophila melanogaster (http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=DetailsSearch&Term=32039%5Buid%5D) and click on the Reference Sequences section in the table of contents on the right. You will see > > > mRNA and Protein(s) > NM_078559.2> →> NP_511114.2 sevenless CG18085-PA [Drosophila melanogaster] > UniProtKB/Swiss-Prot P13368 <--- new data > > 2. Links in NCBI's Protein database > > Explicit links between corresponding RefSeq and Swiss-Prot proteins are now provided within the NCBI Protein database. These links are available in the ‘Links’ menu located at the upper right of the protein display page. The link names are: > > Protein (RefSeq): provides a link from a Swiss-Prot record the corresponding RefSeq record > Protein (UniProtKB): provides a link to the equivalent Swiss-Prot record > > 3. Filter choices in NCBI's Protein database > > protein protein refseq2uniprot find RefSeq protein records with a link to a UniProtKB protein in NCBI's protein database > protein protein uniprot2refseq find UniProtKB protein records with a link to a RefSeq protein in NCBI's protein database > > 4. ftp sites > > A new file was added to the gene and refseq ftp sites to report the relationship between NCBI Reference Sequence protein accessions and UniProtKB protein accessions. The new gene_refseq_uniprotkb_collab.gz file specifies the corresponding pairs of NCBI and UniProtKB protein accessions. > > ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_refseq_uniprotkb_collab.gz > or > ftp://ftp.ncbi.nlm.nih.gov/refseq/uniprotkb/gene_refseq_uniprotkb_collab.gz > > The README file on the gene and refseq ftp sites has been updated to document this addition. See: > > ftp://ftp.ncbi.nlm.nih.gov/gene/README > ftp://ftp.ncbi.nlm.nih.gov/refseq/README > > 5. the ASN.1 in Entrez Gene > > New implementation of a gene-commentary: > > Each cross-reference will be reported in a gene-commentary of type other. Note: more than one cross-reference per RefSeq protein record is possible. > > type other, > source { > { > src { > db "UniProtKB/Swiss-Prot", > tag str "P23760" > }, > anchor "P23760" > } > { > src { > db "UniProtKB/TrEMBL", > tag str "O23760" > }, > anchor "O23760" > } > > > > ------_=_NextPart_001_01C805C9.FB26FF25 Content-Type: text/html; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit NCBI's implementation of the new UniProtKB/RefSeq collaboration

    Announcing the availability of RefSeq-UniProtKB cross-link data

            In collaboration with UniProtKB  (http://www.pir.uniprot.org/) ,  the RefSeq group is now  reporting explicit cross-references to Swiss-Prot and  TrEMBL proteins  that correspond to a RefSeq protein. These correspondences are being calculated by the UniProtKB group, and will be updated every three weeks to correspond to UniProt's release cycle. The data are being made available  from several sites within NCBI:

            
            1.   The  full report from Entrez Gene, in the Reference Sequences section.

               For an example, go to the Full Report page for the sevenless gene of  Drosophila melanogaster  (http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=DetailsSearch&Term=32039%5Buid%5D) and click on the Reference Sequences section in the table of contents on the right.  You will see


                  mRNA and Protein(s)
                  NM_078559.2→NP_511114.2 sevenless CG18085-PA [Drosophila melanogaster]
                 UniProtKB/Swiss-Prot  P13368    <--- new data

             2. Links in NCBI's  Protein database

                Explicit links between corresponding RefSeq and Swiss-Prot proteins are now provided within  the NCBI Protein database.  These links are available in the ‘Links’ menu located at the upper right of the protein display page.  The link names are:

                  Protein (RefSeq):          provides a link from a Swiss-Prot record the corresponding RefSeq record
                  Protein (UniProtKB):       provides a link to the equivalent Swiss-Prot record

             3. Filter choices in NCBI's  Protein database

                    protein protein refseq2uniprot    find RefSeq protein records with a link to a UniProtKB protein in NCBI's protein database
                        protein protein uniprot2refseq    find UniProtKB protein records with a link to a RefSeq protein in NCBI's protein database

            4. ftp sites

                    A new file was added to the gene and refseq ftp sites to report the relationship between NCBI Reference Sequence protein accessions and UniProtKB protein accessions.  The new gene_refseq_uniprotkb_collab.gz file specifies the corresponding pairs of NCBI and UniProtKB protein accessions.

                            ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_refseq_uniprotkb_collab.gz
             or
                            ftp://ftp.ncbi.nlm.nih.gov/refseq/uniprotkb/gene_refseq_uniprotkb_collab.gz

    The README file on the gene and refseq ftp sites has been updated to document this addition. See:

                            ftp://ftp.ncbi.nlm.nih.gov/gene/README
                            ftp://ftp.ncbi.nlm.nih.gov/refseq/README

            5. the ASN.1 in Entrez Gene
            
              New implementation of a gene-commentary:

         Each cross-reference will be reported in a gene-commentary of type other. Note: more than one cross-reference per RefSeq protein record is possible.

                              type other,
                              source {
                                 {
                                  src {
                                      db "UniProtKB/Swiss-Prot",
                                      tag str "P23760"
                                 },
                                  anchor "P23760"
                                 }
                                 {
                                  src {
                                      db "UniProtKB/TrEMBL",
                                      tag str "O23760"
                                 },
                                 anchor "O23760"
                                }
                            

            

------_=_NextPart_001_01C805C9.FB26FF25-- From wallinc@ncbi.nlm.nih.gov Tue Dec 11 10:05:03 2007 Return-Path: X-Original-To: gene-announce@reba.ncbi.nlm.nih.gov Delivered-To: gene-announce@reba.ncbi.nlm.nih.gov Received: from mail2.ncbi.nlm.nih.gov (mail2.be-md.ncbi.nlm.nih.gov [130.14.26.42]) by reba.ncbi.nlm.nih.gov (Postfix) with ESMTP id 148DE3D9B for ; Tue, 11 Dec 2007 10:05:03 -0500 (EST) Received: by mail2.ncbi.nlm.nih.gov (Postfix) id E92851880B8; Tue, 11 Dec 2007 10:05:02 -0500 (EST) Delivered-To: gene-announce@ncbi.nlm.nih.gov Received: from NIHCESSMTP2.hub.nih.gov (nihcessmtp2.hub.nih.gov [128.231.90.116]) by mail2.ncbi.nlm.nih.gov (Postfix) with ESMTP id DC7421880B7 for ; Tue, 11 Dec 2007 10:05:02 -0500 (EST) Received: from NIHCESMLBX8.nih.gov ([156.40.71.208]) by NIHCESSMTP2.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.1830); Tue, 11 Dec 2007 10:05:01 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Date: Tue, 11 Dec 2007 10:05:00 -0500 Message-ID: <7F40ACD22B0A23448C4E8755E5875FE70514B722@NIHCESMLBX8.nih.gov> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Change to Conserved Domains display Thread-Index: Acg8BzOIZS63zuEEQZ+0NIXcMG/JVg== To: X-OriginalArrivalTime: 11 Dec 2007 15:05:02.0162 (UTC) FILETIME=[34665B20:01C83C07] From: gene-announce@ncbi.nlm.nih.gov Subject: [Gene-announce] Change to Conserved Domains display X-BeenThere: gene-announce@ncbi.nlm.nih.gov X-Mailman-Version: 2.1.3 Precedence: list List-Id: Announcing changes in Entrez Gene List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 11 Dec 2007 15:05:03 -0000 The Conserved Domains summary section of the Full Report view in Entrez = Gene has been showing a combination of locations and sublocations within = CDD hit intervals. For clarity and simplicity, the sublocations have = been removed from the display, leaving the location range or ranges for = the regions. This change is effective Monday, December 10, 2007. From wallinc@ncbi.nlm.nih.gov Wed Dec 19 09:00:52 2007 Return-Path: X-Original-To: gene-announce@reba.ncbi.nlm.nih.gov Delivered-To: gene-announce@reba.ncbi.nlm.nih.gov Received: from mail1.ncbi.nlm.nih.gov (mail1.be-md.ncbi.nlm.nih.gov [130.14.26.41]) by reba.ncbi.nlm.nih.gov (Postfix) with ESMTP id D5EBF3D9B for ; Wed, 19 Dec 2007 09:00:52 -0500 (EST) Received: by mail1.ncbi.nlm.nih.gov (Postfix) id CDFB1A80A0; Wed, 19 Dec 2007 09:00:52 -0500 (EST) Delivered-To: gene-announce@ncbi.nlm.nih.gov Received: from NIHCESSMTP.hub.nih.gov (nihcessmtp.hub.nih.gov [128.231.90.115]) by mail1.ncbi.nlm.nih.gov (Postfix) with ESMTP id C4606A8098 for ; Wed, 19 Dec 2007 09:00:52 -0500 (EST) Received: from NIHCESMLBX8.nih.gov ([156.40.71.208]) by NIHCESSMTP.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.1830); Wed, 19 Dec 2007 09:00:52 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Date: Wed, 19 Dec 2007 09:00:51 -0500 Message-ID: <7F40ACD22B0A23448C4E8755E5875FE70F0046B9@NIHCESMLBX8.nih.gov> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: ASN file for corn added to Entrez Gene ftp site Thread-Index: AchCR5CU6T8AdfEISEOiNJHrhIxVSQ== To: X-OriginalArrivalTime: 19 Dec 2007 14:00:52.0365 (UTC) FILETIME=[910BF3D0:01C84247] From: gene-announce@ncbi.nlm.nih.gov Subject: [Gene-announce] ASN file for corn added to Entrez Gene ftp site X-BeenThere: gene-announce@ncbi.nlm.nih.gov X-Mailman-Version: 2.1.3 Precedence: list List-Id: Announcing changes in Entrez Gene List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 19 Dec 2007 14:00:52 -0000 The ASN file Zea_mays.ags.gz has been added to the Entrez Gene ftp site. It can be found in the directory at: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN_BINARY/Plants Documentation of the data on the ftp site can be found at: ftp://ftp.ncbi.nlm.nih.gov/gene/README From maglott@ncbi.nlm.nih.gov Wed Dec 19 21:32:14 2007 Return-Path: X-Original-To: gene-announce@reba.ncbi.nlm.nih.gov Delivered-To: gene-announce@reba.ncbi.nlm.nih.gov Received: from mail1.ncbi.nlm.nih.gov (mail1.be-md.ncbi.nlm.nih.gov [130.14.26.41]) by reba.ncbi.nlm.nih.gov (Postfix) with ESMTP id 92F843D9B for ; Wed, 19 Dec 2007 21:32:14 -0500 (EST) Received: by mail1.ncbi.nlm.nih.gov (Postfix) id 8A964A8098; Wed, 19 Dec 2007 21:32:14 -0500 (EST) Delivered-To: gene-announce@ncbi.nlm.nih.gov Received: from NIHCESSMTP2.hub.nih.gov (nihcessmtp2.hub.nih.gov [128.231.90.116]) by mail1.ncbi.nlm.nih.gov (Postfix) with ESMTP id 7A18DA8080 for ; Wed, 19 Dec 2007 21:32:14 -0500 (EST) Received: from NIHCESMLBX8.nih.gov ([156.40.71.208]) by NIHCESSMTP2.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.1830); Wed, 19 Dec 2007 21:32:14 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Date: Wed, 19 Dec 2007 21:32:13 -0500 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Reporting of EST sequences from Entrez Gene Thread-Index: AchCsIe5zGsSKiZfQX6nO3D/bF2U9w== To: X-OriginalArrivalTime: 20 Dec 2007 02:32:14.0339 (UTC) FILETIME=[87FF4530:01C842B0] From: gene-announce@ncbi.nlm.nih.gov Subject: [Gene-announce] Reporting of EST sequences from Entrez Gene X-BeenThere: gene-announce@ncbi.nlm.nih.gov X-Mailman-Version: 2.1.3 Precedence: list List-Id: Announcing changes in Entrez Gene List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 20 Dec 2007 02:32:14 -0000 As you probably know, Entrez Gene reports a subset of the ESTs that are = gene-specific. It is not the function of Entrez Gene to duplicate = UniGene in reporting all gene-specific transcripts, so Gene will soon = restrict the ESTs it iincludes in reports from the web or on the ftp = site. =20 =20 Beginning next week, Entrez Gene will report an EST as related to a = GeneID only in the following cases: =20 1. The EST was used explicitly to construct a RefSeq RNA record = (NM_123456 or NM_123456789). Rationale: Entrez Gene reports all sequences, including ESTs, that = are source sequences for a RefSeq.=20 2. One or more ESTs defines the Gene, and there is no curated RefSeq = yet. Rationale: Until there is a RefSeq cDNA, ESTs will be reported to = help define the transcription unit.=20 3. One or more ESTs are reported by an external annotation group as = related to a gene and that annotation is retained in the RefSeq record. =20 =20 In other words, UniGene should be used to identify all transcripts = specific to a gene rather than the gene2accession reports Entrez Gene = provides. =20 As a consequence of this new policy, when a RefSeq RNA record is = established for the first time, EST accessions that were previously = reported in gene2accession will be removed from the report. We want to = make it clear that removal of a sequence from the gene2accession report = should not be interpreted to mean that the sequence is not valid for the = gene. =20 -Entrez Gene staff From maglott@ncbi.nlm.nih.gov Wed Jan 9 17:54:09 2008 Return-Path: X-Original-To: gene-announce@reba.ncbi.nlm.nih.gov Delivered-To: gene-announce@reba.ncbi.nlm.nih.gov Received: from mail2.ncbi.nlm.nih.gov (mail2.be-md.ncbi.nlm.nih.gov [130.14.26.42]) by reba.ncbi.nlm.nih.gov (Postfix) with ESMTP id 4D8473D9B for ; Wed, 9 Jan 2008 17:54:09 -0500 (EST) Received: by mail2.ncbi.nlm.nih.gov (Postfix) id 45A8B1880B1; Wed, 9 Jan 2008 17:54:09 -0500 (EST) Delivered-To: gene-announce@ncbi.nlm.nih.gov Received: from NIHCESSMTP3.hub.nih.gov (nihcessmtp3.hub.nih.gov [128.231.90.117]) by mail2.ncbi.nlm.nih.gov (Postfix) with ESMTP id 34C7818807F for ; Wed, 9 Jan 2008 17:54:09 -0500 (EST) Received: from NIHCESMLBX8.nih.gov ([156.40.71.208]) by NIHCESSMTP3.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.1830); Wed, 9 Jan 2008 17:54:08 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Date: Wed, 9 Jan 2008 17:53:19 -0500 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Recent modifications in Entrez Gene Thread-Index: AchTEm2SWFHzG0d3RmmOi+qHqm0Rgw== To: X-OriginalArrivalTime: 09 Jan 2008 22:54:08.0769 (UTC) FILETIME=[8B107F10:01C85312] From: gene-announce@ncbi.nlm.nih.gov Subject: [Gene-announce] Recent modifications in Entrez Gene X-BeenThere: gene-announce@ncbi.nlm.nih.gov X-Mailman-Version: 2.1.3 Precedence: list List-Id: Announcing changes in Entrez Gene List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 09 Jan 2008 22:54:09 -0000 Entrez Gene is announcing several recent changes. 1. Opportunity to test NCBI's new sequence viewer. Entrez Gene's full report web display option is now providing links to a new graphical sequence viewer.=20 A. In the section entitled=20 Genomic regions, transcripts, and products, click on the link named "Try our new Sequence Viewer" The sequence being displayed corresponds to the sequence retrieved by clicking on the genomic RefSeq labeling the top of the gene diagram. B. In the section entitled 'Reference Sequences',=20 click on the link named 'Sequence Viewer (beta) ' The sequence displayed corresponds to the sequence retrieved by clicking on either the GenBank or FASTA links. C. Please note the help documentation for sviewer is available here, http://www.ncbi.nlm.nih.gov/projects/sviewer/help/ and from the ? link in the upper right corner. 2. More consistent population of prot.desc. This value used to be omitted from records in some taxa; the value corresponds to the desc given to the RefSeq protein. 3. Refinement of the terms indexed under the field 'domainname'. Previously this included any text provided by the Conserved Domain Database; now it is limited to the names and identifiers of the domain.] 4. Addition of RefSeqs and links to MaizeGDB for cDNAs and proteins for corn. Please be aware that this collaboration is in its early stages; we expect more links for maize genes to be added in the next few months. 5. Restricted reporting of gene-related ESTs as related sequences and in the gene2accession file on gene's ftp site. Entrez Gene does not generate a comprehensive report of gene-specific ESTs; this is the function of UniGene. Gene will continue to report ESTs as valid for a gene in the related sequences section and in the gene2accession file ONLY in the following situations: a. There is no public RefSeq RNA for the gene, so the only defining RNA sequence is indeed EST-based b. The sequence of the EST was used to construct the RefSeq. Gene will report all accessions used to generate a RefSeq RNA as a related sequence. c. The EST was used to define a probe for GENSAT. If you have any questions or comments, please contact info@ncbi.nlm.nih.gov or submit the form at http://www.ncbi.nlm.nih.gov/RefSeq/update.cgi. From maglott@ncbi.nlm.nih.gov Wed Jan 16 17:50:28 2008 Return-Path: X-Original-To: gene-announce@reba.ncbi.nlm.nih.gov Delivered-To: gene-announce@reba.ncbi.nlm.nih.gov Received: from mail2.ncbi.nlm.nih.gov (mail2.be-md.ncbi.nlm.nih.gov [130.14.26.42]) by reba.ncbi.nlm.nih.gov (Postfix) with ESMTP id 623C33D9B for ; Wed, 16 Jan 2008 17:50:28 -0500 (EST) Received: by mail2.ncbi.nlm.nih.gov (Postfix) id 5A5291880B1; Wed, 16 Jan 2008 17:50:28 -0500 (EST) Delivered-To: gene-announce@ncbi.nlm.nih.gov Received: from NIHCESSMTP2.hub.nih.gov (nihcessmtp2.hub.nih.gov [128.231.90.116]) by mail2.ncbi.nlm.nih.gov (Postfix) with ESMTP id 501F218807F for ; Wed, 16 Jan 2008 17:50:28 -0500 (EST) Received: from NIHCESMLBX8.nih.gov ([156.40.71.208]) by NIHCESSMTP2.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.1830); Wed, 16 Jan 2008 17:50:27 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Date: Wed, 16 Jan 2008 17:50:26 -0500 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: updating names and removing HomoloGene-specific Gene commentaries Thread-Index: AchYki9jjHApX7GET8q+vpGA1wjRUg== To: X-OriginalArrivalTime: 16 Jan 2008 22:50:27.0320 (UTC) FILETIME=[2FF64F80:01C85892] From: gene-announce@ncbi.nlm.nih.gov Subject: [Gene-announce] updating names and removing HomoloGene-specific Gene commentaries X-BeenThere: gene-announce@ncbi.nlm.nih.gov X-Mailman-Version: 2.1.3 Precedence: list List-Id: Announcing changes in Entrez Gene List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 16 Jan 2008 22:50:28 -0000 Entrez Gene is announcing several recent changes. 1. Updates to names of some vertebrate genes 2. Removal of gene commentaries with outdated links to HomoloGene 1. Updates to names of some vertebrate genes Entrez Gene is in the process of renaming a subset of genes from vertebrate species without nomenclature committees. These genes are being renamed according to the standards outlined by the HUGO Gene Nomenclature Committee (HGNC): http://www.genenames.org/guidelines.html#5.%20Homologies%20with%20other% 20species For the case of C#orf# genes, the symbol will be created as documented by HGNC and the human symbol will be retained as an alias. The full name will match the full name assigned to the human ortholog, with the word ' ortholog' appended. The suggestion by HGNC for the full name will not be used, because Entrez Gene tries to avoid including species names as part of a gene name, unless such a full name is official for the gene. Names are being updated gradually. Modification to names of bovine genes should be public in a few days. 2. Removal of gene commentaries with outdated links to HomoloGene Some records in Entrez Gene included a comment reporting an outdated URL to HomoloGene (below). If you have been using this comment to identify GeneIDs processed by HomoloGene, please use instead HomoloGene's ftp site, since this commentary in Entrez Gene will be discontinued completely.=20 ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/ ftp://ftp.ncbi.nih.gov/pub/HomoloGene/README =20 When browsing a record or set of records in Gene, you can always find the corresponding records in HomoloGene by selecting HomoloGene Links from the Display menu, or by clicking on the named HomoloGene link. We regret any inconvenience removing this text may cause, but believe you will find HomoloGene's ftp site easy to use. type comment, source { { src { db "HomoloGene", tag str "71950" }, anchor "HomoloGene", url "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=3D 71950[loc]&TAXID=3D10090" } } 254 HomoloGene 71950 HomoloGene =20 http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi? TEXT=3D71950[loc]&TAXID=3D10090 -------------------------------------------------- If you have any questions or comments, please contact=20 info@ncbi.nlm.nih.gov=20 or submit the form at http://www.ncbi.nlm.nih.gov/RefSeq/update.cgi. From maglott@ncbi.nlm.nih.gov Mon Mar 10 15:12:32 2008 Return-Path: X-Original-To: gene-announce@reba.ncbi.nlm.nih.gov Delivered-To: gene-announce@reba.ncbi.nlm.nih.gov Received: from mail2.ncbi.nlm.nih.gov (mail2.be-md.ncbi.nlm.nih.gov [130.14.26.42]) by reba.ncbi.nlm.nih.gov (Postfix) with ESMTP id 11BB13D9B for ; Mon, 10 Mar 2008 15:12:32 -0400 (EDT) Received: by mail2.ncbi.nlm.nih.gov (Postfix) id 092371880B4; Mon, 10 Mar 2008 15:12:32 -0400 (EDT) Delivered-To: gene-announce@ncbi.nlm.nih.gov Received: from NIHCESSMTP.hub.nih.gov (nihcessmtp.hub.nih.gov [128.231.90.115]) by mail2.ncbi.nlm.nih.gov (Postfix) with ESMTP id F2ADB1880B1 for ; Mon, 10 Mar 2008 15:12:31 -0400 (EDT) Received: from NIHCESMLBX15.nih.gov ([156.40.71.215]) by NIHCESSMTP.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.3959); Mon, 10 Mar 2008 15:12:32 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Date: Mon, 10 Mar 2008 15:12:31 -0400 Message-ID: <7B6F170840CA6C4DA63EE0C8A7BB43EC13B42B@NIHCESMLBX15.nih.gov> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Finding genes by position thread-index: AciC4rBaE97+AoWLRQaA3ZHy941mYw== To: X-OriginalArrivalTime: 10 Mar 2008 19:12:32.0309 (UTC) FILETIME=[B0F47650:01C882E2] From: gene-announce@ncbi.nlm.nih.gov Subject: [Gene-announce] Finding genes by position X-BeenThere: gene-announce@ncbi.nlm.nih.gov X-Mailman-Version: 2.1.3 Precedence: list List-Id: Announcing changes in Entrez Gene List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 10 Mar 2008 19:12:32 -0000 Entrez Gene is announcing a new function on the Limits page. The Limits page, accessed by clicking on Limits in the Query bar, now has a function to facilitate retrieving Gene records by chromosomal location. =20 The section supporting this function is titled: Limit by Chromosomal Region.=20 =20 You must first select the organism against which you want to do a search. A scrollable menu is provided, but you can jump to the region of interest by beginning to type a trivial name or the binomial (e.g. human, Homo sapiens, rat, Rattus norvegicus). For example, if you want to find genes on mouse chromosome 5, you do not have to scroll all the way down to Mus musculus, but can type Mus and then scroll to find and select Mus musculus. =20 When you have selected a species, a new menu is offered with the chromosomes appropriate to the species. For most genomes represented in Gene, the only choice will the mitochondrion or a plastid. For Drosophila melanogaster, the choices are the arms for chromosomes 2 and 3 rather than the complete chromosome. =20 After selecting the chromosome (or arm) you can enter the integers representing the lower and upper boundaries between which you want to find genes. These values will be used as additional query elements.=20 For example, if you wanted to identify all zinc finger genes on human chromosome 19 between 40,000,000 and 50,000,000 bp, you could follow these steps: --enter the words zinc finger in the query box --click on the limits tab --start typing Homo sapiens in the organism box and select Homo sapiens --the chromosome selection menu will appear --select 19 --enter 40000000 in the From box (no punctuation) --enter 50000000 in the To box (no punctuation) --press go Your result should look like this: http://tinyurl.com/yt9afn and is equivalent to entering this in Gene's query box: zinc finger[All Fields] AND (NC_000019[nucl_accn] AND 40000000[CHRPOS]:50000000[CHRPOS]) Please note "Limits: human Chr.19 From 40000000 to 50000000" is displayed in yellow on the results page, and will remain set until you remove the check in the Limits tab or return to the Limits pages to refine your query. -------------------------------------------------- If you have any questions or comments, please contact=20 info@ncbi.nlm.nih.gov=20 or submit the form at http://www.ncbi.nlm.nih.gov/RefSeq/update.cgi. From wallinc@ncbi.nlm.nih.gov Tue Mar 18 14:33:12 2008 Return-Path: X-Original-To: gene-announce@reba.ncbi.nlm.nih.gov Delivered-To: gene-announce@reba.ncbi.nlm.nih.gov Received: from mail2.ncbi.nlm.nih.gov (mail2.be-md.ncbi.nlm.nih.gov [130.14.26.42]) by reba.ncbi.nlm.nih.gov (Postfix) with ESMTP id A67AE3D9B for ; Tue, 18 Mar 2008 14:33:12 -0400 (EDT) Received: by mail2.ncbi.nlm.nih.gov (Postfix) id 9F08418807F; Tue, 18 Mar 2008 14:33:12 -0400 (EDT) Delivered-To: gene-announce@ncbi.nlm.nih.gov Received: from NIHCESSMTP3.hub.nih.gov (nihcessmtp3.hub.nih.gov [128.231.90.117]) by mail2.ncbi.nlm.nih.gov (Postfix) with ESMTP id 92CF118800A for ; Tue, 18 Mar 2008 14:33:12 -0400 (EDT) Received: from NIHCESMLBX15.nih.gov ([156.40.71.215]) by NIHCESSMTP3.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.1830); Tue, 18 Mar 2008 14:33:09 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C88926.70B76074" Date: Tue, 18 Mar 2008 14:32:36 -0400 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Enhancements to Entrez Gene thread-index: AciJJnBk914jiLjHSoCfL+tKP9fiJg== To: X-OriginalArrivalTime: 18 Mar 2008 18:33:09.0942 (UTC) FILETIME=[842DDD60:01C88926] From: gene-announce@ncbi.nlm.nih.gov Subject: [Gene-announce] Enhancements to Entrez Gene X-BeenThere: gene-announce@ncbi.nlm.nih.gov X-Mailman-Version: 2.1.3 Precedence: list List-Id: Announcing changes in Entrez Gene List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 18 Mar 2008 18:33:12 -0000 This is a multi-part message in MIME format. ------_=_NextPart_001_01C88926.70B76074 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Entrez Gene is announcing several changes: =20 1. Adding a "sort by" function so search results can be reordered 2. Gene FTP site updated with subset gene_info files 3. Gene FTP file Plasmodium_falciparum to be moved, and All_Protozoa file to be added =20 =20 1. New "sort by" function =20 An option has been added to the gray query bar to allow you to re-sort the results of your query. The options currently are: =20 Sort by Relevance Sort by Gene Weight Sort by Gene Symbol =20 We hope these functions facilitate finding records of most interest in a result set. If there are other methods by which you think results should be ordered, please contact us at: =20 info@ncbi.nlm.nih.gov=20 =20 or submit the form at =20 http://www.ncbi.nlm.nih.gov/RefSeq/update.cgi =20 =20 Sort by Relevance (the current default) --------------------------------------- =20 Relevance is calculated from Gene's assessment of what fields are the most important by which to find search results. For example, Gene assigns more value to results if they match a term in the 'Gene Name' (symbol) field than to a match in free text such as the RefSeq or GeneRIF summary. Thus if your query is the single term 'cat', then records with symbols of 'cat' will be sorted ahead of records with the term cat only elsewhere in the record. =20 Sort by Gene Weight ------------------- =20 Gene Weight is calculated from multiple lines of evidence geared toward evaluating how well a gene has been characterized. These lines include: =20 (1) Informative Gene-PubMed links. Informativeness is inversely proportional to the number of Genes connected to a PubMed record. =20 (2) Informative symbols or full names. A gene with a LOC+GeneID is weighted less, for example, than a gene with the symbol 'ABCA1'.=20 A gene with a description that starts with the word 'hypothetical' is weighted less than one with a description that starts with 'cystic=20 fibrosis'. =20 (3) Inclusion in HomoloGene or Protein Clusters. Genes (or their products) that are known to be conserved are weighted more highly. =20 (4) Inclusion in OMIM or Books. =20 Sort by Gene Symbol ------------------- =20 This sort orders records by the preferred symbol assigned to the gene. =20 =20 =20 2. Gene FTP site updated with subset gene_info files =20 Entrez Gene is announcing the addition of subset gene_info files to our FTP site. These files have been added in a new GENE_INFO subdirectory beneath the=20 DATA directory. This directory and all its subdirectories contain extractions from Entrez Gene in the same format as the gene_info FTP file. Each file contains a subset of data for the species or taxonomic group indicated by the file name.=20 =20 If you are interested in a limited number of taxa, we hope that these subdivisions will make it easier to process data of interest. =20 The content and directory structure of the GENE_INFO directory mirror the content and structure of the ASN_BINARY directory. The file names in this directory are qualified to distinguish them from the binary ASN.1 files. For example, the gene_info subset file for human is found in: =20 DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz =20 The comprehensive gene_info.gz file will continue to be updated in its original location in the DATA directory.=20 =20 =20 =20 3. Gene FTP file Plasmodium_falciparum to be moved, and All_Protozoa file to be added =20 The Plasmodium_falciparum.ags.gz file will be moved to a new Protozoa directory, to more accurately reflect its taxonomic lineage. It will no longer reside in the Invertebrates directory. =20 The new Protozoa directory will also be home to a new file, All_Protozoa.ags.gz. =20 =20 ------_=_NextPart_001_01C88926.70B76074 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Entrez Gene is announcing several = changes:

 

1. Adding a "sort by" function so search results can = be reordered

2. Gene FTP site updated with subset gene_info = files

3. Gene FTP file Plasmodium_falciparum to be moved, and = All_Protozoa file to be added

 

 

1. New "sort by" function

 

An option has been added to the gray query bar to allow you to = re-sort the results of your query.  The options currently = are:

 

    Sort by = Relevance

    Sort by Gene = Weight

    Sort by Gene = Symbol

 

We hope these functions facilitate finding records of most = interest in a result set.  If there are other methods by which you think = results should be ordered, please contact us at:

 

    info@ncbi.nlm.nih.gov =

 

    or submit the form = at

 

    http://www.ncbi.nl= m.nih.gov/RefSeq/update.cgi

 

 

Sort by Relevance (the current = default)

---------------------------------------<= /p>

        =

Relevance is calculated from Gene's assessment of what fields = are the most important by which to find search results.  For example, Gene = assigns more value to results if they match a term in the 'Gene Name' (symbol) = field than to a match in free text such as the RefSeq or GeneRIF summary. =  Thus if your query is the single term 'cat', then records with symbols of = 'cat' will be sorted ahead of records with the term cat only elsewhere in the = record.

 

Sort by Gene Weight

-------------------

 

Gene Weight is calculated from multiple lines of evidence geared = toward evaluating how well a gene has been characterized.  These lines include: 

 

    (1) Informative Gene-PubMed links.  Informativeness is inversely proportional to the number of Genes = connected to a PubMed record.

 

    (2) Informative symbols or full names.  = A gene with a LOC+GeneID is weighted less, for example, than a gene with the = symbol 'ABCA1'.

        A gene with a = description that starts with the word 'hypothetical' is weighted less than one with = a description that starts with 'cystic

        = fibrosis'.

 

    (3) Inclusion in HomoloGene or Protein Clusters.  Genes (or their products) that are known to be conserved = are weighted more highly.

 

    (4) Inclusion in OMIM or = Books.

 

Sort by Gene Symbol

-------------------

 

This sort orders records by the preferred symbol assigned to the = gene.

 

 

 

2. Gene FTP site updated with subset gene_info = files

 

Entrez Gene is announcing the addition of subset gene_info files = to our FTP site.  These files have been added in a new GENE_INFO = subdirectory beneath the

DATA directory.  This directory and all its subdirectories = contain extractions from Entrez Gene in the same format as the gene_info FTP file.  Each file contains a subset of data for the species or = taxonomic group indicated by the file name.

 

If you are interested in a limited number of taxa, we hope that = these subdivisions will make it easier to process data of = interest.

 

The content and directory structure of the GENE_INFO directory = mirror the content and structure of the ASN_BINARY directory.  The file = names in this directory are qualified to distinguish them from the binary ASN.1 files.  For example, the gene_info subset file for human is found = in:

 

    = DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz

 

The comprehensive gene_info.gz file will continue to be updated = in its original location in the DATA directory.

 

 

 

3. Gene FTP file Plasmodium_falciparum to be moved, and = All_Protozoa file to be added

 

The Plasmodium_falciparum.ags.gz file will be moved to a new = Protozoa directory, to more accurately reflect its taxonomic lineage.  It = will no longer reside in the Invertebrates = directory.

 

The new Protozoa directory will also be home to a new file, All_Protozoa.ags.gz.

 

 

------_=_NextPart_001_01C88926.70B76074-- From maglott@ncbi.nlm.nih.gov Tue Apr 1 17:49:39 2008 Return-Path: X-Original-To: gene-announce@reba.ncbi.nlm.nih.gov Delivered-To: gene-announce@reba.ncbi.nlm.nih.gov Received: from mail2.ncbi.nlm.nih.gov (mail2.be-md.ncbi.nlm.nih.gov [130.14.26.42]) by reba.ncbi.nlm.nih.gov (Postfix) with ESMTP id 85ECF3D9B for ; Tue, 1 Apr 2008 17:49:39 -0400 (EDT) Received: by mail2.ncbi.nlm.nih.gov (Postfix) id 7C1E51880AB; Tue, 1 Apr 2008 17:49:39 -0400 (EDT) Delivered-To: gene-announce@ncbi.nlm.nih.gov Received: from NIHCESSMTP2.hub.nih.gov (nihcessmtp2.hub.nih.gov [128.231.90.116]) by mail2.ncbi.nlm.nih.gov (Postfix) with ESMTP id 6F59118807F for ; Tue, 1 Apr 2008 17:49:39 -0400 (EDT) Received: from NIHCESMLBX15.nih.gov ([156.40.71.215]) by NIHCESSMTP2.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.1830); Tue, 1 Apr 2008 17:49:39 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Date: Tue, 1 Apr 2008 17:49:38 -0400 Message-ID: <7B6F170840CA6C4DA63EE0C8A7BB43EC646B07@NIHCESMLBX15.nih.gov> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Announcing: Collaboration with HuGE Navigator thread-index: AciUQkiAMxvNMItqQLWw8j/ExUOEUQ== To: X-OriginalArrivalTime: 01 Apr 2008 21:49:39.0474 (UTC) FILETIME=[49122F20:01C89442] From: gene-announce@ncbi.nlm.nih.gov Subject: [Gene-announce] Announcing: Collaboration with HuGE Navigator X-BeenThere: gene-announce@ncbi.nlm.nih.gov X-Mailman-Version: 2.1.3 Precedence: list List-Id: Announcing changes in Entrez Gene List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 01 Apr 2008 21:49:39 -0000 Entrez Gene and HuGE Navigator initiated a collaboration in March. HuGE Navigator, which is an integrated knowledge base of genetic associations and human genome epidemiology, is supplying Entrez Gene with the PubMed identifiers for citations HuGE Navigator staff curated for human genes. These links between GeneIDs and PubMed ids are assigned subcategories, which are converted into text displayed as a GeneRIF. >From Entrez Gene, you can retrieve genes included in this collaboration by using the search terms HuGE Navigator (http://view.ncbi.nlm.nih.gov/gene/huge+navigator) GeneRIFs from this collaboration are indicated by appending "(HuGE Navigator)". Examples: Observational study of gene-disease association, gene-gene interaction, and gene-environment interaction. (HuGE Navigator) Meta-analysis of gene-disease association. (HuGE Navigator) A link to HuGE Navigator has also been added to the menu at the right side of the full report page. From HuGE Navigator, there is a link back to Entrez Gene. -Gene and HuGE Navigator staff From maglott@ncbi.nlm.nih.gov Fri Jun 6 13:37:02 2008 Return-Path: X-Original-To: gene-announce@reba.ncbi.nlm.nih.gov Delivered-To: gene-announce@reba.ncbi.nlm.nih.gov Received: from mail2.ncbi.nlm.nih.gov (mail2.be-md.ncbi.nlm.nih.gov [130.14.26.42]) by reba.ncbi.nlm.nih.gov (Postfix) with ESMTP id 5B2A13D9B for ; Fri, 6 Jun 2008 13:37:02 -0400 (EDT) Received: by mail2.ncbi.nlm.nih.gov (Postfix) id 54B191880B9; Fri, 6 Jun 2008 13:37:02 -0400 (EDT) Delivered-To: gene-announce@ncbi.nlm.nih.gov Received: from nihxway4out.hub.nih.gov (nihxway4out.hub.nih.gov [128.231.90.112]) by mail2.ncbi.nlm.nih.gov (Postfix) with ESMTP id 4BA5618807F for ; Fri, 6 Jun 2008 13:37:02 -0400 (EDT) X-IronPortListener: Outbound_SMTP Received: from nihcessmtp.hub.nih.gov ([128.231.90.115]) by nihxway4out.hub.nih.gov with ESMTP; 06 Jun 2008 13:37:02 -0400 Received: from NIHCESMLBX15.nih.gov ([156.40.71.215]) by NIHCESSMTP.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.3959); Fri, 6 Jun 2008 13:36:58 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C8C7FB.EBB27589" Date: Fri, 6 Jun 2008 13:36:58 -0400 Message-ID: <7B6F170840CA6C4DA63EE0C8A7BB43EC0122414A@NIHCESMLBX15.nih.gov> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Entrez Gene removes links to GDB Thread-Index: AcjH++trs5Sf9ng/SxqyCEc0iW7qiQ== To: X-OriginalArrivalTime: 06 Jun 2008 17:36:58.0761 (UTC) FILETIME=[EBD87790:01C8C7FB] Cc: From: gene-announce@ncbi.nlm.nih.gov Subject: [Gene-announce] Entrez Gene removes links to GDB X-BeenThere: gene-announce@ncbi.nlm.nih.gov X-Mailman-Version: 2.1.3 Precedence: list List-Id: Announcing changes in Entrez Gene List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 06 Jun 2008 17:37:02 -0000 This is a multi-part message in MIME format. ------_=_NextPart_001_01C8C7FB.EBB27589 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Because RTI International is no longer hosting GDB... =20 The GDB Human Genome Data Base was first established in 1991 as a central international repository of human genetic mapping and related data, with funding from United States Department of Energy and National Institutes of Health. Hosted originally at the Johns Hopkins University School of Medicine and later moved to the University of Toronto affiliated Hospital for Sick Children, GDB has received international funding as well as philanthropic support. RTI International of Research Triangle Park, North Carolina began hosting GDB in November 2003.=20 Because interest in GDB data resources has diminished over the years, RTI International will discontinue hosting GDB effective May 31, 2008. If you have any comments, please contact help@gdb.org. After May 31, 2008, please contact Mr. Philip S. Roberts, Associate General Counsel at Johns Hopkins University at philroberts@jhu.edu for any GDB related questions. =20 ...Entrez Gene will remove all links to www.gdb.org. GDB identifiers will be retained in the records, however, to support searching. --Gene Staff =20 ------_=_NextPart_001_01C8C7FB.EBB27589 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Because  RTI International is no longer = hosting GDB…

 

The GDB Human Genome Data Base was first established in = 1991 as a central international repository of human genetic mapping and related = data, with funding from United States Department of Energy and National = Institutes of Health. Hosted originally at the Johns Hopkins University School of = Medicine and later moved to the University of Toronto affiliated Hospital for = Sick Children, GDB has received international funding as well as = philanthropic support. RTI International of Research Triangle Park, North Carolina = began hosting GDB in November 2003.

B= ecause interest in GDB data resources has diminished over the years, RTI = International will discontinue hosting GDB effective May 31, 2008. If you have any = comments, please contact help@gdb.org. After = May 31, 2008, please contact Mr. Philip S. Roberts, Associate General Counsel at = Johns Hopkins University at philroberts@jhu.edu for any GDB related questions.

<= o:p> 

&= #8230;Entrez Gene will remove all links to www.gdb.org.  GDB identifiers will be retained in the records, however, to support = searching.

-= -Gene Staff

 

------_=_NextPart_001_01C8C7FB.EBB27589-- From wallinc@ncbi.nlm.nih.gov Mon Jul 21 08:44:05 2008 Return-Path: X-Original-To: gene-announce@reba.ncbi.nlm.nih.gov Delivered-To: gene-announce@reba.ncbi.nlm.nih.gov Received: from mail1.ncbi.nlm.nih.gov (mail1.be-md.ncbi.nlm.nih.gov [130.14.26.41]) by reba.ncbi.nlm.nih.gov (Postfix) with ESMTP id 295A33D9B for ; Mon, 21 Jul 2008 08:44:05 -0400 (EDT) Received: by mail1.ncbi.nlm.nih.gov (Postfix) id 1D0E4A80AF; Mon, 21 Jul 2008 08:44:05 -0400 (EDT) Delivered-To: gene-announce@ncbi.nlm.nih.gov Received: from nihxwayout.hub.nih.gov (nihxwayout.hub.nih.gov [128.231.90.109]) by mail1.ncbi.nlm.nih.gov (Postfix) with ESMTP id 10F16A80AE for ; Mon, 21 Jul 2008 08:44:05 -0400 (EDT) X-IronPortListener: Outbound_SMTP Received: from nihcessmtp3.hub.nih.gov ([128.231.90.117]) by nihxwayout.hub.nih.gov with ESMTP; 21 Jul 2008 08:44:05 -0400 Received: from NIHCESMLBX15.nih.gov ([156.40.71.215]) by NIHCESSMTP3.hub.nih.gov with Microsoft SMTPSVC(6.0.3790.1830); Mon, 21 Jul 2008 08:44:04 -0400 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable X-MimeOLE: Produced By Microsoft Exchange V6.5 Date: Mon, 21 Jul 2008 08:44:04 -0400 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Enhancements to Entrez Gene Thread-Index: AcjrL3V6bh/tv3cFTWCjFObIb+/Gjg== To: X-OriginalArrivalTime: 21 Jul 2008 12:44:04.0851 (UTC) FILETIME=[75915C30:01C8EB2F] From: gene-announce@ncbi.nlm.nih.gov Subject: [Gene-announce] Enhancements to Entrez Gene X-BeenThere: gene-announce@ncbi.nlm.nih.gov X-Mailman-Version: 2.1.3 Precedence: list List-Id: Announcing changes in Entrez Gene List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 21 Jul 2008 12:44:05 -0000 Entrez Gene is announcing several changes to facilitate searching: 1. Index field [Exon count] 2. Index field [Gene length] 3. hiv1interactions property 1. Index field [Exon count] This field contains the number of distinct, non-overlapping RefSeq exons annotated for all RNA products of a gene interval, based on annotation in this priority: reference assembly first, alternate assembly second. This field can be queried by either a single integer value or a range. For example, to retrieve all human records with one exon, use: human[orgn] AND 1[exoncount]=20 To retrieve all records with a range of exons: 10:20[exoncount] The aliases for this field are [XC] and [NUMEXONS]. 2. Index field [Gene length] This field contains the gene length based on annotation in this priority: reference assembly first, alternate assembly second. If there are multiple placements, only on non-reference assemblies, then the longest value on non-reference assemblies is used. This field can be queried by either a single integer value or a range. For example, to retrieve all records with a gene span less than or equal to 5kb, use: 1:5000[genelength] The aliases for this field are [GL] and [GENELEN]. 3. hiv1interactions property This property is set for all genes with curated HIV-1:human protein interaction data.=20 Example of usage: hiv1interactions[prop] =20 See also http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/index.html