comparison test-data/goslim_generic.obo @ 0:294de027cb5d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
author iuc
date Fri, 11 Jan 2019 06:18:00 -0500
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-1:000000000000 0:294de027cb5d
1 format-version: 1.2
2 subsetdef: goantislim_grouping "Grouping classes that can be excluded"
3 subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
4 subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
5 subsetdef: goslim_agr "AGR slim"
6 subsetdef: goslim_aspergillus "Aspergillus GO slim"
7 subsetdef: goslim_candida "Candida GO slim"
8 subsetdef: goslim_chembl "ChEMBL protein targets summary"
9 subsetdef: goslim_generic "Generic GO slim"
10 subsetdef: goslim_goa "GOA and proteome slim"
11 subsetdef: goslim_metagenomics "Metagenomics GO slim"
12 subsetdef: goslim_mouse "Mouse GO slim"
13 subsetdef: goslim_pir "PIR GO slim"
14 subsetdef: goslim_plant "Plant GO slim"
15 subsetdef: goslim_pombe "Fission yeast GO slim"
16 subsetdef: goslim_synapse "synapse GO slim"
17 subsetdef: goslim_virus "Viral GO slim"
18 subsetdef: goslim_yeast "Yeast GO slim"
19 subsetdef: gosubset_prok "Prokaryotic GO subset"
20 subsetdef: mf_needs_review "Catalytic activity terms in need of attention"
21 subsetdef: termgenie_unvetted "Terms created by TermGenie that do not follow a template and require additional vetting by editors"
22 subsetdef: virus_checked "Viral overhaul terms"
23 synonymtypedef: syngo_official_label "label approved by the SynGO project"
24 synonymtypedef: systematic_synonym "Systematic synonym" EXACT
25 ontology: go/subsets/goslim_generic
26
27 [Term]
28 id: GO:0003674
29 name: molecular_function
30 namespace: molecular_function
31 alt_id: GO:0005554
32 def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process." [GOC:pdt]
33 comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
34 subset: goslim_aspergillus
35 subset: goslim_candida
36 subset: goslim_chembl
37 subset: goslim_generic
38 subset: goslim_metagenomics
39 subset: goslim_pir
40 subset: goslim_plant
41 subset: goslim_yeast
42 subset: gosubset_prok
43 synonym: "molecular function" EXACT []
44
45 [Term]
46 id: GO:0005575
47 name: cellular_component
48 namespace: cellular_component
49 alt_id: GO:0008372
50 def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome)." [GOC:pdt, NIF_Subcellular:sao-1337158144]
51 comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this.
52 subset: goslim_aspergillus
53 subset: goslim_candida
54 subset: goslim_chembl
55 subset: goslim_generic
56 subset: goslim_metagenomics
57 subset: goslim_pir
58 subset: goslim_plant
59 subset: goslim_yeast
60 subset: gosubset_prok
61 synonym: "cell or subcellular entity" EXACT []
62 synonym: "cellular component" EXACT []
63 synonym: "subcellular entity" RELATED [NIF_Subcellular:nlx_subcell_100315]
64 xref: NIF_Subcellular:sao-1337158144
65 xref: NIF_Subcellular:sao1337158144
66
67 [Term]
68 id: GO:0008150
69 name: biological_process
70 namespace: biological_process
71 alt_id: GO:0000004
72 alt_id: GO:0007582
73 alt_id: GO:0044699
74 def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt]
75 comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this.
76 subset: goslim_aspergillus
77 subset: goslim_candida
78 subset: goslim_chembl
79 subset: goslim_generic
80 subset: goslim_metagenomics
81 subset: goslim_pir
82 subset: goslim_plant
83 subset: goslim_pombe
84 subset: goslim_yeast
85 subset: gosubset_prok
86 synonym: "biological process" EXACT []
87 synonym: "physiological process" EXACT []
88 synonym: "single organism process" RELATED []
89 synonym: "single-organism process" RELATED []
90 xref: Wikipedia:Biological_process
91 created_by: janelomax
92 creation_date: 2012-09-19T15:05:24Z
93
94 [Typedef]
95 id: ends_during
96 name: ends_during
97 namespace: external
98 xref: RO:0002093
99
100 [Typedef]
101 id: happens_during
102 name: happens_during
103 namespace: external
104 xref: RO:0002092
105 is_transitive: true
106 is_a: ends_during ! ends_during
107
108 [Typedef]
109 id: has_part
110 name: has_part
111 namespace: external
112 xref: BFO:0000051
113 is_transitive: true
114
115 [Typedef]
116 id: negatively_regulates
117 name: negatively regulates
118 namespace: external
119 xref: RO:0002212
120 is_a: regulates ! regulates
121 transitive_over: part_of ! part of
122
123 [Typedef]
124 id: never_in_taxon
125 name: never_in_taxon
126 namespace: external
127 xref: RO:0002161
128 expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y" []
129 is_metadata_tag: true
130 is_class_level: true
131
132 [Typedef]
133 id: occurs_in
134 name: occurs in
135 namespace: external
136 xref: BFO:0000066
137 holds_over_chain: part_of occurs_in
138 transitive_over: part_of ! part of
139
140 [Typedef]
141 id: part_of
142 name: part of
143 namespace: external
144 xref: BFO:0000050
145 is_transitive: true
146 inverse_of: has_part ! has_part
147
148 [Typedef]
149 id: positively_regulates
150 name: positively regulates
151 namespace: external
152 xref: RO:0002213
153 holds_over_chain: negatively_regulates negatively_regulates
154 is_a: regulates ! regulates
155 transitive_over: part_of ! part of
156
157 [Typedef]
158 id: regulates
159 name: regulates
160 namespace: external
161 xref: RO:0002211
162 is_transitive: true
163 transitive_over: part_of ! part of
164
165 [Typedef]
166 id: starts_during
167 name: starts_during
168 namespace: external
169 xref: RO:0002091
170