Mercurial > repos > proteore > proteore_id_converter

comparison README.rst @ 19:9d758344d36e draft

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planemo upload commit 339ab77a83db03409c8001324f10b36ff5b13a39-dirty
author proteore
date Wed, 19 Jun 2019 04:38:12 -0400
parents 5252bbcfbdd7
children
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18:5252bbcfbdd7 19:9d758344d36e
61 61
62 .. class:: warningmark 62 .. class:: warningmark
63 63
64 Nextprot and OMIM are only available for Human. 64 Nextprot and OMIM are only available for Human.
65 65
66 .. class:: warningmark
67
68 For Uniprot-AC, only Uniprot-AC reviewed are considered here, except for releases before 27-05-2019 where all uniprot-AC (at the time) are considered.
69
66 This tool converts human IDs using file built from: 70 This tool converts human IDs using file built from:
67 71
68 * HUMAN_9606_idmapping_selected.tab (Uniprot 23/10/2018) 72 * Current release of Uniprot, for idmapping_selected.tab and idmapping.dat for Human, Mouse and Rat: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism
69 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ 73 * All previous release of uniprot can be found here: ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases/
70 74 * **nextprot_ac_list_all.txt (Nextprot released on 13/02/2019 - current)**: ftp://ftp.nextprot.org/pub/current_release/ac_lists/
71 * HUMAN_9606_idmapping.dat (Uniprot 23/10/18) 75 * All previous release of **nextprot_ac_list_all.txt** can be foud here: ftp://ftp.nextprot.org/pub/previous_releases/
72 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ 76 * `Human uniprot-AC entries reviewed (05/06/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606+AND+created:[20120720%20TO%2020190605]&format=list>`_.
73 77 * `Mouse uniprot-AC entries reviewed (05/06/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10090+AND+created:[20120720%20TO%2020190605]&format=list>`_.
74 * Human uniprot-AC entries reviewed : https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606&format=list 78 * `Rat uniprot-AC entries reviewed (05/06/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10116+AND+created:[20120720%20TO%2020190605]&format=list>`_.
75 79 * `Human uniprot-AC entries reviewed (08/05/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606+AND+created:[20120720%20TO%2020190508]&format=list>`_.
76 80 * `Mouse uniprot-AC entries reviewed (08/05/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10090+AND+created:[20120720%20TO%2020190508]&format=list>`_.
77 * nextprot_ac_list_all.txt (Nextprot released on 10/10/2018) 81 * `Rat uniprot-AC entries reviewed (08/05/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10116+AND+created:[20120720%20TO%2020190508]&format=list>`_.
78 Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/ 82 * `Human uniprot-AC entries reviewed (10/10/2018) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606+AND+created:[20120720%20TO%2020181010]&format=list>`_.
79 83 * `Mouse uniprot-AC entries reviewed (10/10/2018) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10090+AND+created:[20120720%20TO%2020181010]&format=list>`_.
80 * MOUSE_10090_idmapping_selected.tab (Uniprot 23/10/2018) 84 * `Rat uniprot-AC entries reviewed (10/10/2018) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10116+AND+created:[20120720%20TO%2020181010]&format=list>`_.
81 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
82
83 * MOUSE_10090_idmapping.dat (Uniprot 23/10/18)
84 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
85
86 * Mouse uniprot-AC entries reviewed : https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10090&format=list
87
88
89 * RAT_10116_idmapping.dat (Uniprot 23/10/18)
90 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
91
92 * RAT_10116_idmapping_selected.tab (Uniprot 23/10/18)
93 Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
94
95 * Rat uniprot-AC entries reviewed : https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10116&format=list