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From: gabbyreeves <gab...@us...> - 2008-06-24 15:59:25
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Date: Tuesday June 24, 2008 @ 8:32 Author: gabbyreeves http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/controlledVocab/biosapiens Update of /cvsroot/psidev/psi/mi/controlledVocab/biosapiens In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29192 Modified Files: biosapiens_lite.obo Log Message: addition of non positional terms taxonomy, organism_species, protein_name and positional term polypeptide_conserved_motif |
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From: Lukasz S. <luk...@us...> - 2008-06-22 06:58:17
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Date: Saturday June 21, 2008 @ 8:03 Author: lukasz99 http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/rel25/src Update of /cvsroot/psidev/psi/mi/rel25/src In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv21085/mi/rel25/src Modified Files: MIF254.xsd Log Message: minorVersion set to 4 |
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From: luisa m. <lui...@us...> - 2008-06-18 14:51:57
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Date: Wednesday June 18, 2008 @ 7:51 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/rel25/data Update of /cvsroot/psidev/psi/mi/rel25/data In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12116/mi/rel25/data Modified Files: psi-mi25.obo Log Message: MInor fixing: existing terms added to the drugable subset. |
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From: luisa m. <lui...@us...> - 2008-06-18 10:41:27
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Date: Wednesday June 18, 2008 @ 3:41 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/rel25/data Update of /cvsroot/psidev/psi/mi/rel25/data In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14725/mi/rel25/data Modified Files: psi-mi25.obo Log Message: MInor fixing: removed unimod reference on MI:0832 |
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From: luisa m. <lui...@us...> - 2008-06-18 10:18:38
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Date: Wednesday June 18, 2008 @ 3:18 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/rel25/data Update of /cvsroot/psidev/psi/mi/rel25/data In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv6142/mi/rel25/data Modified Files: psi-mi25.obo Log Message: MInor fixing: addition of existing terms to the drugable subset, addition of short labels synonyms. |
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From: gabbyreeves <gab...@us...> - 2008-06-05 12:51:18
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Date: Thursday June 5, 2008 @ 5:24 Author: gabbyreeves http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/controlledVocab/biosapiens Update of /cvsroot/psidev/psi/mi/controlledVocab/biosapiens In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20660 Modified Files: biosapiens_lite.obo Log Message: update mapping uniprot to ontology terms in synonyms and dbx_refs |
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From: gabbyreeves <gab...@us...> - 2008-06-05 12:51:09
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Date: Thursday June 5, 2008 @ 5:24 Author: gabbyreeves http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/controlledVocab/biosapiens Update of /cvsroot/psidev/psi/mi/controlledVocab/biosapiens In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20678 Modified Files: biosapiens_lite.xml Log Message: update mapping uniprot to ontology terms in synonyms and dbx_refs |
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From: gabbyreeves <gab...@us...> - 2008-06-05 12:31:21
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Date: Thursday June 5, 2008 @ 5:14 Author: gabbyreeves http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/controlledVocab/biosapiens Update of /cvsroot/psidev/psi/mi/controlledVocab/biosapiens In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16913 Modified Files: biosapiens.obo Log Message: update mapping uniprot to ontology terms in synonyms and dbx_refs |
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From: gabbyreeves <gab...@us...> - 2008-05-29 13:41:28
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Date: Thursday May 29, 2008 @ 6:41 Author: gabbyreeves http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/controlledVocab/biosapiens Update of /cvsroot/psidev/psi/mi/controlledVocab/biosapiens In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4792 Modified Files: mapping_table_uniprot_ontology.csv Log Message: Addition of non positional terms relating to uniprot cc_topics and uniprot keywords. |
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From: gabbyreeves <gab...@us...> - 2008-05-29 13:40:56
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Date: Thursday May 29, 2008 @ 6:41 Author: gabbyreeves http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/controlledVocab/biosapiens Update of /cvsroot/psidev/psi/mi/controlledVocab/biosapiens In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4417 Modified Files: biosapiens_lite.xml Log Message: Addition of non positional terms relating to uniprot cc_topics and uniprot keywords. |
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From: gabbyreeves <gab...@us...> - 2008-05-29 13:40:44
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Date: Thursday May 29, 2008 @ 6:40 Author: gabbyreeves http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/controlledVocab/biosapiens Update of /cvsroot/psidev/psi/mi/controlledVocab/biosapiens In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4404 Modified Files: biosapiens_lite.obo Log Message: Addition of non positional terms relating to uniprot cc_topics and uniprot keywords. |
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From: gabbyreeves <gab...@us...> - 2008-05-29 13:40:33
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Date: Thursday May 29, 2008 @ 6:40 Author: gabbyreeves http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/controlledVocab/biosapiens Update of /cvsroot/psidev/psi/mi/controlledVocab/biosapiens In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4388 Modified Files: biosapiens.obo Log Message: Addition of non positional terms relating to uniprot cc_topics and uniprot keywords. |
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From: luisa m. <lui...@us...> - 2008-05-29 10:27:01
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Date: Thursday May 29, 2008 @ 3:26 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/rel25/data Update of /cvsroot/psidev/psi/mi/rel25/data In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29689/mi/rel25/data Modified Files: psi-mi25.obo Log Message: Minor fixing on MI:2127 |
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From: luisa m. <lui...@us...> - 2008-05-27 17:41:36
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Date: Tuesday May 27, 2008 @ 10:41 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/rel25/data Update of /cvsroot/psidev/psi/mi/rel25/data In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10761/mi/rel25/data Modified Files: psi-mi25.obo Log Message: Minor fixing on synonyms of MI:2046 and definition of MI:0867 |
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From: luisa m. <lui...@us...> - 2008-05-16 14:29:00
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Date: Friday May 16, 2008 @ 7:28 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/rel25/data Update of /cvsroot/psidev/psi/mi/rel25/data In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv28315/mi/rel25/data Modified Files: psi-mi25.obo Log Message: error fixing MI:02013 obsolete as redundant with MI:0730, short label editing on MI:0717 and MI:0852. |
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From: luisa m. <lui...@us...> - 2008-05-16 14:14:13
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Date: Friday May 16, 2008 @ 7:14 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/rel25/data Update of /cvsroot/psidev/psi/mi/rel25/data In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv21845/mi/rel25/data Modified Files: psi-mi25.obo Log Message: error fixing on the Xref of MI:0911 and MI:0853, and xrefs on drug dataset replace 'pubmed' by 'PMID:' |
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From: luisa m. <lui...@us...> - 2008-05-16 14:09:11
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Date: Friday May 16, 2008 @ 7:08 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/rel25/data Update of /cvsroot/psidev/psi/mi/rel25/data In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19741/mi/rel25/data Modified Files: psi-mi25.obo Log Message: error fixing on the Xref of MI:0911 and MI:0853 |
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From: luisa m. <lui...@us...> - 2008-05-13 12:23:13
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Date: Tuesday May 13, 2008 @ 5:23 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/rel25/data Update of /cvsroot/psidev/psi/mi/rel25/data In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15746/mi/rel25/data Modified Files: LASTAC psi-mi25.obo Log Message: - format has been upgraded from OBO1.0 to OBO1.2 format - taking advantage of the 1.2 format, two synonym types as been created 'short label' and 'alternate name' (see definitions in the header) - terms can now belong to different subsets also defined in the header one being the 'usual' PSI-MI (called PSI-MI slim) and a new set of terms dedicated to drug-target interactions (called Drugable) - !!!!warning!!!! Note one term (heavily used) term has been obsoleted MI:0218 physical interaction, it is now replaced by two terms with more fine grained meaning: association (or affinity complex) and physical association (more functional complex). For bulk remapping a possible criteria can be: whatever physical interaction that has among its participants a bait should become 'association' MI:0914 the others can become 'physical association' MI:0915. Two hybrid interactions are an expection and can be 'physical association' MI:0915. I have just released the obo file for PSI-MI activities covering the following tracker issues: 1945124 AlphaScreen 1941929 udape url of pirsf 1935512 AU1 tag 1931436 experimental prep, new exp role heat shock prot 1893514 lexa vp16 1893511 This should be lexa b42 complementation 1887958 Ribonuclease 1881298 interaction detection: mass spectrometry 1748485 crosslinkers as PTM 1710745 association/physical/direct I also added other terms from informal requests I received and was dicussed during the PSI meeting : - addition of databases MBIDB, matrixdb, iRefIndex - addition of polysaccaride as interactor type - addition of 103 terms dedicated to drugs |
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From: David G. <dav...@us...> - 2008-05-07 20:48:36
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Date: Wednesday May 7, 2008 @ 11:56 Author: davidgloriam http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/controlledVocab/proteomeBinder Update of /cvsroot/psidev/psi/mi/controlledVocab/proteomeBinder In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv13502 Modified Files: psi-par.obo Log Message: psi-par.obo |
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From: David G. <dav...@us...> - 2008-04-25 17:47:27
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Date: Friday April 25, 2008 @ 10:47 Author: davidgloriam http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/controlledVocab/proteomeBinder Update of /cvsroot/psidev/psi/mi/controlledVocab/proteomeBinder In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24580 Modified Files: psi-par.obo Log Message: psi-par.obo |
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From: gabbyreeves <gab...@us...> - 2008-04-25 15:51:26
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Date: Friday April 25, 2008 @ 8:51 Author: gabbyreeves http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/controlledVocab/biosapiens Update of /cvsroot/psidev/psi/mi/controlledVocab/biosapiens In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12918 Modified Files: biosapiens_lite.xml Log Message: change protein_ligand_contact to ligand_contact. add DNA_contact |
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From: gabbyreeves <gab...@us...> - 2008-04-25 15:36:00
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Date: Friday April 25, 2008 @ 8:36 Author: gabbyreeves http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/controlledVocab/biosapiens Update of /cvsroot/psidev/psi/mi/controlledVocab/biosapiens In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9383 Modified Files: biosapiens_lite.obo Log Message: change protein_ligand_contact to ligand_contact. add DNA_contact |
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From: gabbyreeves <gab...@us...> - 2008-04-25 15:31:39
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Date: Friday April 25, 2008 @ 8:31 Author: gabbyreeves http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/controlledVocab/biosapiens Update of /cvsroot/psidev/psi/mi/controlledVocab/biosapiens In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv6548 Modified Files: biosapiens.obo Log Message: change protein_ligand_contact to ligand_contact. add DNA_contact |
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From: David G. <dav...@us...> - 2008-04-16 15:15:09
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Date: Wednesday April 16, 2008 @ 8:15 Author: davidgloriam http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/controlledVocab/proteomeBinder Update of /cvsroot/psidev/psi/mi/controlledVocab/proteomeBinder In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv5732 Modified Files: psi-par.obo Log Message: |
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From: David G. <dav...@us...> - 2008-04-16 14:32:35
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Date: Wednesday April 16, 2008 @ 7:23 Author: davidgloriam http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/mi/controlledVocab/proteomeBinder Update of /cvsroot/psidev/psi/mi/controlledVocab/proteomeBinder In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv18255 Added Files: psi-par.obo Removed Files: protein-binder.obo Log Message: |
