diff test-data/goslim_generic.obo @ 0:52964064db8a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/goslim_generic.obo	Fri Jan 11 06:18:35 2019 -0500
@@ -0,0 +1,170 @@
+format-version: 1.2
+subsetdef: goantislim_grouping "Grouping classes that can be excluded"
+subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
+subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
+subsetdef: goslim_agr "AGR slim"
+subsetdef: goslim_aspergillus "Aspergillus GO slim"
+subsetdef: goslim_candida "Candida GO slim"
+subsetdef: goslim_chembl "ChEMBL protein targets summary"
+subsetdef: goslim_generic "Generic GO slim"
+subsetdef: goslim_goa "GOA and proteome slim"
+subsetdef: goslim_metagenomics "Metagenomics GO slim"
+subsetdef: goslim_mouse "Mouse GO slim"
+subsetdef: goslim_pir "PIR GO slim"
+subsetdef: goslim_plant "Plant GO slim"
+subsetdef: goslim_pombe "Fission yeast GO slim"
+subsetdef: goslim_synapse "synapse GO slim"
+subsetdef: goslim_virus "Viral GO slim"
+subsetdef: goslim_yeast "Yeast GO slim"
+subsetdef: gosubset_prok "Prokaryotic GO subset"
+subsetdef: mf_needs_review "Catalytic activity terms in need of attention"
+subsetdef: termgenie_unvetted "Terms created by TermGenie that do not follow a template and require additional vetting by editors"
+subsetdef: virus_checked "Viral overhaul terms"
+synonymtypedef: syngo_official_label "label approved by the SynGO project"
+synonymtypedef: systematic_synonym "Systematic synonym" EXACT
+ontology: go/subsets/goslim_generic
+
+[Term]
+id: GO:0003674
+name: molecular_function
+namespace: molecular_function
+alt_id: GO:0005554
+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]
+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.
+subset: goslim_aspergillus
+subset: goslim_candida
+subset: goslim_chembl
+subset: goslim_generic
+subset: goslim_metagenomics
+subset: goslim_pir
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+synonym: "molecular function" EXACT []
+
+[Term]
+id: GO:0005575
+name: cellular_component
+namespace: cellular_component
+alt_id: GO:0008372
+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]
+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.
+subset: goslim_aspergillus
+subset: goslim_candida
+subset: goslim_chembl
+subset: goslim_generic
+subset: goslim_metagenomics
+subset: goslim_pir
+subset: goslim_plant
+subset: goslim_yeast
+subset: gosubset_prok
+synonym: "cell or subcellular entity" EXACT []
+synonym: "cellular component" EXACT []
+synonym: "subcellular entity" RELATED [NIF_Subcellular:nlx_subcell_100315]
+xref: NIF_Subcellular:sao-1337158144
+xref: NIF_Subcellular:sao1337158144
+
+[Term]
+id: GO:0008150
+name: biological_process
+namespace: biological_process
+alt_id: GO:0000004
+alt_id: GO:0007582
+alt_id: GO:0044699
+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]
+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.
+subset: goslim_aspergillus
+subset: goslim_candida
+subset: goslim_chembl
+subset: goslim_generic
+subset: goslim_metagenomics
+subset: goslim_pir
+subset: goslim_plant
+subset: goslim_pombe
+subset: goslim_yeast
+subset: gosubset_prok
+synonym: "biological process" EXACT []
+synonym: "physiological process" EXACT []
+synonym: "single organism process" RELATED []
+synonym: "single-organism process" RELATED []
+xref: Wikipedia:Biological_process
+created_by: janelomax
+creation_date: 2012-09-19T15:05:24Z
+
+[Typedef]
+id: ends_during
+name: ends_during
+namespace: external
+xref: RO:0002093
+
+[Typedef]
+id: happens_during
+name: happens_during
+namespace: external
+xref: RO:0002092
+is_transitive: true
+is_a: ends_during ! ends_during
+
+[Typedef]
+id: has_part
+name: has_part
+namespace: external
+xref: BFO:0000051
+is_transitive: true
+
+[Typedef]
+id: negatively_regulates
+name: negatively regulates
+namespace: external
+xref: RO:0002212
+is_a: regulates ! regulates
+transitive_over: part_of ! part of
+
+[Typedef]
+id: never_in_taxon
+name: never_in_taxon
+namespace: external
+xref: RO:0002161
+expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y" []
+is_metadata_tag: true
+is_class_level: true
+
+[Typedef]
+id: occurs_in
+name: occurs in
+namespace: external
+xref: BFO:0000066
+holds_over_chain: part_of occurs_in
+transitive_over: part_of ! part of
+
+[Typedef]
+id: part_of
+name: part of
+namespace: external
+xref: BFO:0000050
+is_transitive: true
+inverse_of: has_part ! has_part
+
+[Typedef]
+id: positively_regulates
+name: positively regulates
+namespace: external
+xref: RO:0002213
+holds_over_chain: negatively_regulates negatively_regulates
+is_a: regulates ! regulates
+transitive_over: part_of ! part of
+
+[Typedef]
+id: regulates
+name: regulates
+namespace: external
+xref: RO:0002211
+is_transitive: true
+transitive_over: part_of ! part of
+
+[Typedef]
+id: starts_during
+name: starts_during
+namespace: external
+xref: RO:0002091
+