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comparison README.rst @ 15:b50d913ec067 draft

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planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b
author proteore
date Tue, 18 Dec 2018 09:57:21 -0500
parents 659f1248f535
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14:659f1248f535 15:b50d913ec067
1 Wrapper for ID Converter tool 1 Wrapper for ID Converter tool
2 ============================= 2 =============================
3 3
4 **Authors** 4 **Authors**
5 5
6 T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 6 David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
7 7
8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform 8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
9 9
10 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 10 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
11 11
49 49
50 * Ensembl transcript ID (e.g. ENST00000353703; ENST00000372839) 50 * Ensembl transcript ID (e.g. ENST00000353703; ENST00000372839)
51 51
52 * Ensembl protein ID (e.g. ENSP00000300161; ENSP00000361930) 52 * Ensembl protein ID (e.g. ENSP00000300161; ENSP00000361930)
53 53
54 * BioGrid (e.g. 113361)
55
56 * STRING (e.g. 9606.ENSP00000300161)
57
58 * KEGG gene id (e.g. hsa:7529)
59
60 .. class:: warningmark
61
62 Nextprot and OMIM are only available for Human.
63
54 This tool converts human IDs using file built from: 64 This tool converts human IDs using file built from:
55 65
56 * HUMAN_9606_idmapping_selected.tab 66 * HUMAN_9606_idmapping_selected.tab (Uniprot 23/10/2018)
57 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ 67 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
58 68
59 * nextprot_ac_list_all.txt 69 * HUMAN_9606_idmapping.dat (Uniprot 23/10/18)
70 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
71
72 * nextprot_ac_list_all.txt (Nextprot released on 10/10/2018)
60 Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/ 73 Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/
74
75 * MOUSE_10090_idmapping_selected.tab (Uniprot 23/10/2018)
76 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
77
78 * MOUSE_10090_idmapping.dat (Uniprot 23/10/18)
79 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
80
81 * RAT_10116_idmapping.dat (Uniprot 23/10/18)
82 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
83
84 * RAT_10116_idmapping_selected.tab (Uniprot 23/10/18)
85 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/