Mercurial > repos > iuc > goenrichment
changeset 0:52964064db8a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
| author | iuc |
|---|---|
| date | Fri, 11 Jan 2019 06:18:35 -0500 |
| parents | |
| children | 5ace5c7d1a86 |
| files | goenrichment.xml test-data/MF_result.txt test-data/annotations.tab test-data/go.obo test-data/goslim_generic.obo test-data/population.txt test-data/slim_annotations.tab test-data/study.txt |
| diffstat | 8 files changed, 2097 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/goenrichment.xml Fri Jan 11 06:18:35 2019 -0500 @@ -0,0 +1,151 @@ +<tool id="goenrichment" name="GOEnrichment" version="2.0.1"> + <description>performs GO enrichment analysis of a set of gene products</description> + <requirements> + <requirement type="package" version="2.0.1">goenrichment</requirement> + </requirements> + <command detect_errors="exit_code">goenrichment +--go '${go}' +--annotation '${annotation}' +--study '${study}' +#if str($population) != 'None' +--population '${population}' +#end if +--correction ${correction} +$summarize +$singletons +$relations +--graph_format $graph +--cut_off $cutoff +--mf_result '${mf_result}' +--bp_result '${bp_result}' +--cc_result '${cc_result}' +--mf_graph '${mf_graph}' +--bp_graph '${bp_graph}' +--cc_graph '${cc_graph}' + </command> + <inputs> + <param name="go" type="data" format="obo,owl" label="Gene Ontology File" help="Gene Ontology file in OBO or OWL format (see http://geneontology.org/page/download-ontology)"/> + <param name="annotation" type="data" format="tabular,txt" label="Gene Product Annotation File" help="Tabular file containing annotations from gene products to GO terms (in GAF or BLAST2GO format, or a simple two-column table)"/> + <param name="study" type="data" format="txt" label="Study Set File" help="File containing the gene products corresponding to the study set (one per line)"/> + <param name="population" type="data" format="txt" optional="true" label="Population Set File (Optional)" help="File containing the gene products corresponding to the population set (one per line). If no file is submitted, the population set will be the set of all gene products listed in the annotation file."/> + <param name="correction" type="select" label="Multiple Test Correction" help="The multiple test correction method to use (Benjamini-Hochberg is recommended)."> + <option value="Benjamini-Hochberg" selected="true"/> + <option value="SDA"/> + <option value="Bonferroni-Holm"/> + <option value="Sidak"/> + <option value="Bonferroni"/> + </param> + <param name="cutoff" type="select" label="P-Value Cut-Off" help="The corrected p-value (or q-value) cut-off to apply for the graph output."> + <option value="1.0"/> + <option value="0.1"/> + <option value="0.05"/> + <option value="0.01" selected="true"/> + </param> + <param name="graph" type="select" label="Output Graph Format" help="The format of the output graphs (png, svg, or tabular for importing into cytoscape)."> + <option value="png" selected="true"/> + <option value="svg"/> + <option value="tabular"/> + </param> + <param name="summarize" type="boolean" checked="true" truevalue="--summarize_output" falsevalue="" label="Summarize Output" help="Whether to produce a summarized list of GO terms or the full list of those that are statistically significant"/> + <param name="singletons" type="boolean" checked="true" truevalue="--ignore_singletons" falsevalue="" label="Exclude Singletons" help="Whether to exclude GO terms that are annotated to a single gene product in the study set"/> + <param name="relations" type="boolean" checked="false" truevalue="--use_all_relations" falsevalue="" label="Use All Relations" help="Whether to infer annotations through 'part_of' and other non-hierarchical relationships, or only through 'is_a' relations"/> + </inputs> + <outputs> + <data name="mf_result" format="tabular" label="MF Result File"/> + <data name="bp_result" format="tabular" label="BP Result File"/> + <data name="cc_result" format="tabular" label="CC Result File"/> + <data name="mf_graph" format="png" label="MF Graph File"> + <change_format> + <when input="graph" value="svg" format="svg"/> + <when input="graph" value="tabular" format="tabular"/> + </change_format> + </data> + <data name="bp_graph" format="png" label="BP Graph File"> + <change_format> + <when input="graph" value="svg" format="svg"/> + <when input="graph" value="tabular" format="tabular"/> + </change_format> + </data> + <data name="cc_graph" format="png" label="CC Graph File"> + <change_format> + <when input="graph" value="svg" format="svg"/> + <when input="graph" value="tabular" format="tabular"/> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="go" ftype="obo" value="go.obo"/> + <param name="annotation" ftype="txt" value="annotations.tab"/> + <param name="study" ftype="txt" value="study.txt"/> + <param name="summarize" value="false"/> + <output name="mf_result" ftype="tabular" file="MF_result.txt" lines_diff="0"/> + </test> + <test> + <param name="go" ftype="obo" value="go.obo"/> + <param name="annotation" ftype="txt" value="annotations.tab"/> + <param name="study" ftype="txt" value="study.txt"/> + <param name="population" ftype="txt" value="population.txt"/> + <param name="summarize" value="false"/> + <output name="mf_result" ftype="tabular" file="MF_result.txt" lines_diff="0"/> + </test> + </tests> + <help> +.. class:: infomark + +GOEnrichment is a Java application that can be used to analyze gene product sets (e.g., from microarray or RNAseq experiments) for enriched GO terms. + +----- + +.. class:: infomark + +GOEnrichment requires: + +- A Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/download-ontology). +- A tabular annotation file in GAF (http://geneontology.org/page/download-annotations) format, BLAST2GO format, or a simple two-column table (e.g. from BioMart) with gene product ids in the first column and GO terms in the second one. +- A list of gene products comprising the study set (a flat text file with one gene product per line). +- Optionally, a list of gene products comprising the population set (if none is submitted, the population set will be the set of gene products listed in the annotation file). + +----- + +.. class:: infomark + +GOEnrichment produces a tabular result file and a graph file for each GO type (MF - Molecular Function, BP - Biological Process and CC - Cellular Component): + +- The result file is a tabular list of all GO terms present in the study set and their respective p-values. +- The graph file can be either a png image, an svg image, or a text file for importing into cytoscape (together with the result file). + +----- + +.. class:: infomark + +The graph is colored by p-value: terms with p-value above cut-off appear in white; and the color gets darker as the p-value decreases + +.. image:: https://github.com/DanFaria/GOEnrichment/raw/master/Scale.png + :width: 600 + :height: 315 + +(see the scale at https://github.com/DanFaria/GOEnrichment/blob/master/Scale.png). In addition to the name of each GO term, the graph +shows its frequency in the study set. Dashed edges indicate that one or more intermediate terms were ommited from the graph. + +----- + +.. class:: warningmark + +Gene products listed in either the study or population set files that are not present in the annotation file will be ignored. + </help> + + <citations> + <citation type="bibtex"> +@misc{githubgoenrichment, + author = {Faria, Daniel}, + year = {2017}, + title = {GOEnrichment}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/DanFaria/GOEnrichment}, +} + </citation> + </citations> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MF_result.txt Fri Jan 11 06:18:35 2019 -0500 @@ -0,0 +1,5 @@ +GO Term Study # Study Freq. Pop. Freq. p-value q-value name gene products +GO:0005488 7 35% 7.0% 4.84E-6 1.94E-5 binding fake13,fake12,fake11,fake10,fake8,fake9,fake14 +GO:0016209 7 35% 7.0% 4.84E-6 1.94E-5 antioxidant activity fake4,fake3,fake2,fake1,fake7,fake6,fake5 +GO:0038024 6 30% 10% 3.93E-3 5.24E-3 cargo receptor activity fake20,fake19,fake18,fake17,fake16,fake15 +GO:0003674 20 100% 100% 1.0 1.0 molecular_function fake13,fake12,fake11,fake10,fake20,fake8,fake7,fake6,fake19,fake5,fake18,fake17,fake16,fake15,fake9,fake14,fake4,fake3,fake2,fake1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations.tab Fri Jan 11 06:18:35 2019 -0500 @@ -0,0 +1,300 @@ +fake1 GO:0007610 +fake2 GO:0007610 +fake3 GO:0007610 +fake4 GO:0007610 +fake5 GO:0022610 +fake6 GO:0022610 +fake7 GO:0022610 +fake8 GO:0022610 +fake9 GO:0044848 +fake10 GO:0044848 +fake11 GO:0044848 +fake12 GO:0044848 +fake13 GO:0065007 +fake14 GO:0065007 +fake15 GO:0065007 +fake16 GO:0009758 +fake17 GO:0009758 +fake18 GO:0009758 +fake19 GO:0015976 +fake20 GO:0015976 +fake21 GO:0015976 +fake22 GO:0015976 +fake23 GO:0098743 +fake24 GO:0001906 +fake25 GO:0008283 +fake26 GO:0071840 +fake27 GO:0009987 +fake28 GO:0098754 +fake29 GO:0032502 +fake30 GO:0040007 +fake31 GO:0002376 +fake32 GO:0051179 +fake33 GO:0040011 +fake34 GO:0008152 +fake35 GO:0051704 +fake36 GO:0032501 +fake37 GO:0019740 +fake38 GO:0006794 +fake39 GO:0043473 +fake40 GO:0000003 +fake41 GO:0022414 +fake42 GO:0050896 +fake43 GO:0048511 +fake44 GO:0023052 +fake45 GO:0006791 +fake46 GO:0098743 +fake47 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GO:0016209 +fake6 GO:0016209 +fake7 GO:0016209 +fake8 GO:0005488 +fake9 GO:0005488 +fake10 GO:0005488 +fake11 GO:0005488 +fake12 GO:0005488 +fake13 GO:0005488 +fake14 GO:0005488 +fake15 GO:0038024 +fake16 GO:0038024 +fake17 GO:0038024 +fake18 GO:0038024 +fake19 GO:0038024 +fake20 GO:0038024 +fake21 GO:0038024 +fake22 GO:0038024 +fake23 GO:0038024 +fake24 GO:0038024 +fake25 GO:0003824 +fake26 GO:0003824 +fake27 GO:0003824 +fake28 GO:0003824 +fake29 GO:0003824 +fake30 GO:0003824 +fake31 GO:0003824 +fake32 GO:0104005 +fake33 GO:0104005 +fake34 GO:0104005 +fake35 GO:0104005 +fake36 GO:0104005 +fake37 GO:0104005 +fake38 GO:0140104 +fake39 GO:0140104 +fake40 GO:0140104 +fake41 GO:0140104 +fake42 GO:0140104 +fake43 GO:0140104 +fake44 GO:0098772 +fake45 GO:0098772 +fake46 GO:0098772 +fake47 GO:0098772 +fake48 GO:0098772 +fake49 GO:0098772 +fake50 GO:0060089 +fake51 GO:0060089 +fake52 GO:0060089 +fake53 GO:0060089 +fake54 GO:0060089 +fake55 GO:0060089 +fake56 GO:0045735 +fake57 GO:0045735 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/go.obo Fri Jan 11 06:18:35 2019 -0500 @@ -0,0 +1,1050 @@ +format-version: 1.2 +data-version: releases/2018-04-30 +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 +default-namespace: gene_ontology +remark: cvs version: $Revision: 38972$ +remark: Includes Ontology(OntologyID(Anonymous-35)) [Axioms: 230 Logical Axioms: 228] +remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/go/never_in_taxon.owl>))) [Axioms: 18 Logical Axioms: 0] +ontology: go +property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/licenses/by/4.0/ + +[Term] +id: GO:0000003 +name: reproduction +namespace: biological_process +alt_id: GO:0019952 +alt_id: GO:0050876 +def: "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [GOC:go_curators, GOC:isa_complete, GOC:jl, ISBN:0198506732] +subset: goslim_agr +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "reproductive physiological process" EXACT [] +xref: Wikipedia:Reproduction +is_a: GO:0008150 ! biological_process +disjoint_from: GO:0044848 ! biological phase + +[Term] +id: GO:0001906 +name: cell killing +namespace: biological_process +def: "Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions." [GOC:add] +subset: goslim_pir +subset: gosubset_prok +synonym: "necrosis" RELATED [] +is_a: GO:0008150 ! biological_process +disjoint_from: GO:0044848 ! biological phase + +[Term] +id: GO:0002376 +name: immune system process +namespace: biological_process +def: "Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05] +comment: Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). This term was added by GO_REF:0000022. +subset: goslim_agr +subset: goslim_chembl +subset: goslim_generic +subset: goslim_mouse +subset: goslim_pir +xref: Wikipedia:Immune_system +is_a: GO:0008150 ! biological_process +disjoint_from: GO:0044848 ! biological phase + +[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:0003824 +name: catalytic activity +namespace: molecular_function +def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [GOC:vw, ISBN:0198506732] +subset: goslim_chembl +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb] +xref: Wikipedia:Enzyme +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0005198 +name: structural molecule activity +namespace: molecular_function +def: "The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell." [GOC:mah, GOC:vw] +subset: goslim_agr +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0005215 +name: transporter activity +namespace: molecular_function +alt_id: GO:0005478 +def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells." [GOC:ai, GOC:dgf] +comment: Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules. +subset: goslim_agr +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_metagenomics +subset: goslim_mouse +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "carrier" RELATED [] +xref: Reactome:REACT_6315 "Virion-associated M2 protein mediated ion infusion, Homo sapiens" +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0005488 +name: binding +namespace: molecular_function +def: "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732] +comment: Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. +subset: gocheck_do_not_manually_annotate +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "ligand" NARROW [] +xref: Wikipedia:Binding_(molecular) +is_a: GO:0003674 ! molecular_function + +[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:0005576 +name: extracellular region +namespace: cellular_component +def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:go_curators] +comment: Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'. +subset: goslim_agr +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_mouse +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +synonym: "extracellular" EXACT [] +xref: Wikipedia:Extracellular +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0005623 +name: cell +namespace: cellular_component +def: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:go_curators] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_plant +subset: gosubset_prok +xref: NIF_Subcellular:sao1813327414 +xref: Wikipedia:Cell_(biology) +is_a: GO:0005575 ! cellular_component +property_value: IAO:0000589 "cell and encapsulating structures" xsd:string + +[Term] +id: GO:0006791 +name: sulfur utilization +namespace: biological_process +def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary sulfur sources and then activates genes to scavenge the last traces of the primary sulfur source and to transport and metabolize alternate sulfur sources. The utilization process begins when the cell or organism detects sulfur levels, includes the activation of genes whose products detect, transport or metabolize sulfur-containing compounds, and ends when the sulfur is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mlg] +subset: gosubset_prok +synonym: "sulphur utilization" EXACT [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0006794 +name: phosphorus utilization +namespace: biological_process +def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary phosphorus source and then activates genes to scavenge the last traces of the primary phosphorus source and to transport and metabolize alternative phosphorus sources. The utilization process begins when the cell or organism detects phosphorus levels, includes the phosphorus-containing substances, and ends when phosphorus is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mlg] +subset: gosubset_prok +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0007610 +name: behavior +namespace: biological_process +alt_id: GO:0044708 +def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] +comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). +subset: gocheck_do_not_manually_annotate +subset: goslim_agr +subset: goslim_plant +subset: gosubset_prok +synonym: "behavioral response to stimulus" EXACT [] +synonym: "behaviour" EXACT [] +synonym: "behavioural response to stimulus" EXACT [] +synonym: "single-organism behavior" RELATED [] +xref: Wikipedia:Behavior +is_a: GO:0008150 ! biological_process +disjoint_from: GO:0032502 ! developmental process +created_by: janelomax +creation_date: 2012-09-20T14:06:08Z + +[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 + +[Term] +id: GO:0008152 +name: metabolic process +namespace: biological_process +alt_id: GO:0044236 +alt_id: GO:0044710 +def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] +comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. +subset: gocheck_do_not_manually_annotate +subset: goslim_chembl +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "metabolic process resulting in cell growth" NARROW [] +synonym: "metabolism" EXACT [] +synonym: "metabolism resulting in cell growth" NARROW [] +synonym: "multicellular organism metabolic process" NARROW [] +synonym: "single-organism metabolic process" RELATED [] +xref: Wikipedia:Metabolism +is_a: GO:0008150 ! biological_process +disjoint_from: GO:0044848 ! biological phase +created_by: janelomax +creation_date: 2012-10-17T15:46:40Z + +[Term] +id: GO:0008283 +name: cell proliferation +namespace: biological_process +def: "The multiplication or reproduction of cells, resulting in the expansion of a cell population." [GOC:mah, GOC:mb] +comment: This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms. +subset: goslim_agr +subset: goslim_chembl +subset: goslim_generic +subset: goslim_mouse +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0009295 +name: nucleoid +namespace: cellular_component +def: "The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined." [GOC:bm, GOC:ma, ISBN:3540076689] +subset: gosubset_prok +xref: Wikipedia:Nucleoid +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0009758 +name: carbohydrate utilization +namespace: biological_process +alt_id: GO:0007587 +def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary carbohydrate sources,usually glucose, and then activates genes to scavenge the last traces of the primary carbohydrate source and to transport and metabolize alternate carbohydrate sources. The utilization process begins when the cell or organism detects carbohydrate levels, includes the activation of genes whose products detect, transport or metabolize carbohydrates, and ends when the carbohydrate is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mcc2, GOC:mlg] +synonym: "sugar utilization" NARROW [GOC:mcc2] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0009987 +name: cellular process +namespace: biological_process +alt_id: GO:0008151 +alt_id: GO:0044763 +alt_id: GO:0050875 +def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "cell growth and/or maintenance" NARROW [] +synonym: "cell physiology" EXACT [] +synonym: "cellular physiological process" EXACT [] +synonym: "single-organism cellular process" RELATED [] +is_a: GO:0008150 ! biological_process +disjoint_from: GO:0044848 ! biological phase +created_by: janelomax +creation_date: 2012-12-11T16:56:55Z + +[Term] +id: GO:0015976 +name: carbon utilization +namespace: biological_process +alt_id: GO:0015978 +def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary carbon sources and then activates genes to scavenge the last traces of the primary carbon source and to transport and metabolize alternative carbon sources such as carbon dioxide or carbonic acid. The utilization process begins when the cell or organism detects carbon levels, includes the activation of genes whose products detect, transport or metabolize carbon-containing substances, and ends when carbon is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mlg] +subset: goslim_chembl +subset: goslim_pir +subset: gosubset_prok +synonym: "carbon utilization by utilization of organic compounds" EXACT [GOC:mah] +synonym: "heterotrophy" EXACT [] +xref: Wikipedia:Heterotroph +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0016020 +name: membrane +namespace: cellular_component +def: "A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_yeast +subset: gosubset_prok +xref: Wikipedia:Biological_membrane +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0016209 +name: antioxidant activity +namespace: molecular_function +def: "Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage." [ISBN:0198506732] +subset: goslim_metagenomics +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0019012 +name: virion +namespace: cellular_component +def: "The complete fully infectious extracellular virus particle." [ISBN:0781718325] +subset: goslim_chembl +subset: goslim_metagenomics +subset: goslim_pir +synonym: "complete virus particle" EXACT [] +xref: Wikipedia:Virus +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0019740 +name: nitrogen utilization +namespace: biological_process +def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary nitrogen source, usually ammonia, and then activates genes to scavenge the last traces of the primary nitrogen source and to transport and metabolize alternative nitrogen sources. The utilization process begins when the cell or organism detects nitrogen levels, includes the activation of genes whose products detect, transport or metabolize nitrogen-containing substances, and ends when nitrogen is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mlg] +subset: gosubset_prok +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0022414 +name: reproductive process +namespace: biological_process +alt_id: GO:0044702 +def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete] +subset: gosubset_prok +synonym: "single organism reproductive process" RELATED [] +is_a: GO:0008150 ! biological_process +intersection_of: GO:0008150 ! biological_process +intersection_of: part_of GO:0000003 ! reproduction +disjoint_from: GO:0044848 ! biological phase +relationship: part_of GO:0000003 ! reproduction +created_by: janelomax +creation_date: 2012-09-19T15:56:06Z + +[Term] +id: GO:0022610 +name: biological adhesion +namespace: biological_process +def: "The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions." [GOC:isa_complete] +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0008150 ! biological_process +disjoint_from: GO:0044848 ! biological phase + +[Term] +id: GO:0023052 +name: signaling +namespace: biological_process +alt_id: GO:0023046 +alt_id: GO:0044700 +def: "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling] +comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. +subset: goslim_agr +subset: goslim_mouse +subset: goslim_pombe +subset: goslim_yeast +synonym: "biological signaling" EXACT [] +synonym: "signaling process" EXACT [] +synonym: "signalling" EXACT [] +synonym: "signalling process" RELATED [GOC:mah] +synonym: "single organism signaling" RELATED [] +is_a: GO:0008150 ! biological_process +disjoint_from: GO:0044848 ! biological phase +created_by: janelomax +creation_date: 2010-02-16T09:30:50Z + +[Term] +id: GO:0030054 +name: cell junction +namespace: cellular_component +def: "A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix." [GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732] +subset: goslim_agr +xref: Wikipedia:Cell_junction +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0031386 +name: protein tag +namespace: molecular_function +def: "A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation." [GOC:dos, GOC:go_curators, PMID:19028679, PMID:20054389, PMID:6305978] +comment: Use this term to annotate conjugated tags, not for conjugating enzymes. At the time of writing, all known gene products with this activity are ubiquitin-like, either based on overall sequence similarity or the presence of common motifs and structures. +subset: goslim_pir +synonym: "covalent modifier" RELATED [GOC:vw] +synonym: "protein tagging activity" RELATED [] +synonym: "ubiquitin" RELATED [] +synonym: "ubiquitin-like protein modifier" EXACT [] +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0031974 +name: membrane-enclosed lumen +namespace: cellular_component +def: "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen." [GOC:add, GOC:mah] +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0032501 +name: multicellular organismal process +namespace: biological_process +alt_id: GO:0044707 +alt_id: GO:0050874 +def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] +subset: goslim_pir +synonym: "organismal physiological process" EXACT [] +synonym: "single-multicellular organism process" RELATED [] +is_a: GO:0008150 ! biological_process +disjoint_from: GO:0044848 ! biological phase +created_by: janelomax +creation_date: 2012-09-19T16:07:47Z + +[Term] +id: GO:0032502 +name: developmental process +namespace: biological_process +alt_id: GO:0044767 +def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] +subset: goslim_agr +subset: goslim_aspergillus +subset: goslim_pir +subset: gosubset_prok +synonym: "development" NARROW [] +synonym: "single-organism developmental process" RELATED [] +is_a: GO:0008150 ! biological_process +disjoint_from: GO:0044848 ! biological phase +created_by: janelomax +creation_date: 2012-12-19T12:21:31Z + +[Term] +id: GO:0032991 +name: protein-containing complex +namespace: cellular_component +alt_id: GO:0043234 +def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." [GOC:dos, GOC:mah] +comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. +subset: goslim_agr +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +synonym: "macromolecular complex" EXACT [] +synonym: "macromolecule complex" EXACT [] +synonym: "protein complex" NARROW [] +synonym: "protein containing complex" EXACT [] +synonym: "protein-protein complex" NARROW [] +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0038024 +name: cargo receptor activity +namespace: molecular_function +def: "Combining selectively with an extracellular substance and delivering the substance into the cell via endocytosis." [GOC:bf, GOC:signaling, PMID:15239958] +comment: Note that this term and its child terms are intended for receptors that bind to and internalize molecules by receptor-mediated endocytosis. For receptors that are coupled to a signal transduction pathway, consider instead the term 'signaling receptor activity ; GO:0038023' and its children. +synonym: "endocytic receptor activity" EXACT [GOC:signaling, ISBN:0123645387, PMID:12671190] +synonym: "receptor activity" BROAD [] +synonym: "receptor activity involved in ligand uptake" EXACT [PMID:12671190] +synonym: "receptor activity involved in receptor-mediated endocytosis" EXACT [GOC:bf] +synonym: "transport receptor activity" BROAD [GOC:signaling] +is_a: GO:0003674 ! molecular_function +created_by: rfoulger +creation_date: 2011-08-01T02:50:45Z + +[Term] +id: GO:0040007 +name: growth +namespace: biological_process +alt_id: GO:0048590 +def: "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC:bf, GOC:ma] +comment: See also the biological process term 'cell growth ; GO:0016049'. +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "growth pattern" RELATED [] +synonym: "non-developmental growth" RELATED [GOC:mah] +is_a: GO:0008150 ! biological_process +disjoint_from: GO:0044848 ! biological phase + +[Term] +id: GO:0040011 +name: locomotion +namespace: biological_process +def: "Self-propelled movement of a cell or organism from one location to another." [GOC:dgh] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0008150 ! biological_process +disjoint_from: GO:0044848 ! biological phase + +[Term] +id: GO:0043226 +name: organelle +namespace: cellular_component +def: "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane." [GOC:go_curators] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +xref: NIF_Subcellular:sao1539965131 +xref: Wikipedia:Organelle +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0043473 +name: pigmentation +namespace: biological_process +def: "The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells." [GOC:jl] +subset: goslim_chembl +subset: goslim_generic +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0044215 +name: other organism +namespace: cellular_component +def: "A secondary organism with which the first organism is interacting." [GOC:jl] +comment: We plan to obsolete this branch of GO and replace its usage in annotation with a system for multi-organism annotation. +is_a: GO:0005575 ! cellular_component +created_by: jane +creation_date: 2009-11-12T01:04:58Z + +[Term] +id: GO:0044217 +name: other organism part +namespace: cellular_component +def: "Any constituent part of a secondary organism with which the first organism is interacting." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0044215 ! other organism +relationship: part_of GO:0044215 ! other organism +created_by: jane +creation_date: 2009-11-12T01:18:21Z + +[Term] +id: GO:0044421 +name: extracellular region part +namespace: cellular_component +def: "Any constituent part of the extracellular region, the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers constituent parts of the host cell environment outside an intracellular parasite." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: goantislim_grouping +subset: gocheck_do_not_annotate +subset: gosubset_prok +synonym: "extracellular structure" RELATED [NIF_Subcellular:sao9117790637] +xref: NIF_Subcellular:sao9117790637 +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005576 ! extracellular region +relationship: part_of GO:0005576 ! extracellular region + +[Term] +id: GO:0044422 +name: organelle part +namespace: cellular_component +def: "Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: goantislim_grouping +subset: gocheck_do_not_annotate +subset: gosubset_prok +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0043226 ! organelle +relationship: part_of GO:0043226 ! organelle + +[Term] +id: GO:0044423 +name: virion part +namespace: cellular_component +def: "Any constituent part of a virion, a complete fully infectious extracellular virus particle." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: goantislim_grouping +subset: gocheck_do_not_annotate +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0019012 ! virion +relationship: part_of GO:0019012 ! virion + +[Term] +id: GO:0044425 +name: membrane part +namespace: cellular_component +def: "Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: goantislim_grouping +subset: gocheck_do_not_annotate +subset: gosubset_prok +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0016020 ! membrane +relationship: part_of GO:0016020 ! membrane + +[Term] +id: GO:0044456 +name: synapse part +namespace: cellular_component +def: "Any constituent part of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: goantislim_grouping +subset: gocheck_do_not_annotate +synonym: "synaptic component" RELATED [NIF_Subcellular:sao1784069613] +xref: NIF_Subcellular:sao1784069613 +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0045202 ! synapse +relationship: part_of GO:0045202 ! synapse + +[Term] +id: GO:0044464 +name: cell part +namespace: cellular_component +def: "Any constituent part of a cell, the basic structural and functional unit of all organisms." [GOC:jl] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: goantislim_grouping +subset: gocheck_do_not_annotate +subset: goslim_pir +subset: gosubset_prok +synonym: "cellular subcomponent" EXACT [NIF_Subcellular:sao628508602] +synonym: "protoplast" RELATED [GOC:mah] +xref: NIF_Subcellular:sao628508602 +is_a: GO:0005575 ! cellular_component +intersection_of: GO:0005575 ! cellular_component +intersection_of: part_of GO:0005623 ! cell +relationship: part_of GO:0005623 ! cell + +[Term] +id: GO:0044848 +name: biological phase +namespace: biological_process +def: "A distinct period or stage in a biological process or cycle." [GOC:jl] +comment: Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase. +subset: gocheck_do_not_manually_annotate +is_a: GO:0008150 ! biological_process +disjoint_from: GO:0048511 ! rhythmic process +disjoint_from: GO:0050896 ! response to stimulus +disjoint_from: GO:0051179 ! localization +disjoint_from: GO:0051704 ! multi-organism process +disjoint_from: GO:0071840 ! cellular component organization or biogenesis +disjoint_from: GO:0098743 ! cell aggregation +created_by: janelomax +creation_date: 2014-07-16T13:12:40Z + +[Term] +id: GO:0045182 +name: translation regulator activity +namespace: molecular_function +def: "Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome." [GOC:ai] +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_pir +subset: goslim_plant +subset: gosubset_prok +synonym: "translation factor activity" EXACT [] +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0045202 +name: synapse +namespace: cellular_component +def: "The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane." [ISBN:0198506732] +subset: goslim_agr +subset: goslim_mouse +subset: goslim_pir +subset: goslim_synapse +synonym: "electrotonic synapse" RELATED [NIF_Subcellular:sao1311109124] +synonym: "mixed synapse" NARROW [NIF_Subcellular:sao1506103497] +synonym: "synaptic junction" EXACT [] +xref: NIF_Subcellular:sao914572699 +xref: Wikipedia:Chemical_synapse +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0045735 +name: nutrient reservoir activity +namespace: molecular_function +def: "Functions in the storage of nutritious substrates." [GOC:ai] +comment: Note that this term can be used in place of the obsolete terms 'storage protein ; GO:0005187' and 'storage protein of fat body (sensu Insecta) ; GO:0008041'. +subset: goslim_pir +subset: gosubset_prok +synonym: "storage protein" RELATED [] +synonym: "storage protein of fat body" RELATED [] +synonym: "yolk protein" RELATED [] +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0048511 +name: rhythmic process +namespace: biological_process +def: "Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism." [GOC:jid] +subset: goslim_pir +subset: gosubset_prok +synonym: "rhythm" RELATED [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0050896 +name: response to stimulus +namespace: biological_process +alt_id: GO:0051869 +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_manually_annotate +subset: goslim_agr +subset: goslim_mouse +subset: goslim_pir +subset: gosubset_prok +synonym: "physiological response to stimulus" EXACT [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0051179 +name: localization +namespace: biological_process +alt_id: GO:1902578 +def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation." [GOC:ai, GOC:dos] +subset: goslim_pir +subset: gosubset_prok +synonym: "establishment and maintenance of cellular component location" NARROW [] +synonym: "establishment and maintenance of localization" EXACT [] +synonym: "establishment and maintenance of position" EXACT [] +synonym: "establishment and maintenance of substance location" NARROW [] +synonym: "establishment and maintenance of substrate location" NARROW [] +synonym: "localisation" EXACT [GOC:mah] +synonym: "single organism localization" RELATED [GOC:TermGenie] +synonym: "single-organism localization" RELATED [] +is_a: GO:0008150 ! biological_process +created_by: jl +creation_date: 2013-12-18T13:51:04Z + +[Term] +id: GO:0051704 +name: multi-organism process +namespace: biological_process +alt_id: GO:0051706 +def: "A biological process which involves another organism of the same or different species." [GOC:jl] +subset: goslim_pir +subset: gosubset_prok +synonym: "interaction between organisms" EXACT [] +synonym: "physiological interaction between organisms" EXACT [] +synonym: "physiological interaction with other organism" EXACT [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0055044 +name: symplast +namespace: cellular_component +def: "The interconnected cell membranes and intracellular regions of a plant. The interconnections occur via the plasmodesmata." [GOC:mtg_sensu] +subset: goslim_pir +xref: Wikipedia:Symplast +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0060089 +name: molecular transducer activity +namespace: molecular_function +def: "A compound molecular function in which an effector function is controlled by one or more regulatory components." [GOC:dos, GOC:pdt] +subset: gocheck_do_not_manually_annotate +subset: goslim_pir +subset: gosubset_prok +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0065007 +name: biological regulation +namespace: biological_process +def: "Any process that modulates a measurable attribute of any biological process, quality or function." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw] +subset: gocheck_do_not_annotate +subset: goslim_pir +subset: gosubset_prok +synonym: "regulation" BROAD [] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0071840 +name: cellular component organization or biogenesis +namespace: biological_process +alt_id: GO:0071841 +def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] +subset: goslim_metagenomics +synonym: "cellular component organisation or biogenesis" EXACT [GOC:mah] +synonym: "cellular component organisation or biogenesis at cellular level" EXACT [GOC:mah] +synonym: "cellular component organization or biogenesis at cellular level" EXACT [] +is_a: GO:0008150 ! biological_process +created_by: midori +creation_date: 2010-09-10T01:39:16Z + +[Term] +id: GO:0090729 +name: toxin activity +namespace: molecular_function +alt_id: GO:0050827 +def: "Interacting selectively with one or more biological molecules in another organism (the \"target\" organism), initiating pathogenesis (leading to an abnormal, generally detrimental state) in the target organism. The activity should refer to an evolved function of the active gene product, i.e. one that was selected for. Examples include the activity of botulinum toxin, and snake venom." [GOC:pt] +synonym: "toxin receptor binding" EXACT [] +xref: Wikipedia:Toxin +is_a: GO:0003674 ! molecular_function +created_by: tanyaberardini +creation_date: 2016-12-19T15:23:27Z + +[Term] +id: GO:0097423 +name: mitochondrion-associated adherens complex +namespace: cellular_component +def: "An organelle arrangement comprised of the following elements: a mitochondrion positioned near the presynaptic membrane; an electron-dense mitochondrial plaque adjacent to the outer mitochondrial membrane that faces the presynaptic membrane; filament-like elements appearing to link the mitochondrial plaque to a cell-cell junction region (sometimes termed punctum adherens); tubular or vesicular-appearing membrane (also called vesicular chain) interposed among the filaments. Mitochondrion-associated adherens complexes were initially described in the dorsal horn of the spinal cord. They are found in calyces and other large terminals of the auditory brainstem, and in a variety of mammalian species including humans." [NIF_Subcellular:sao1933817066, PMID:20089910] +synonym: "MAC" RELATED [] +synonym: "mitochondrial adhaerens complex" EXACT [] +xref: NIF_Subcellular:sao1933817066 +is_a: GO:0005575 ! cellular_component +created_by: paola +creation_date: 2012-11-07T13:38:50Z + +[Term] +id: GO:0098743 +name: cell aggregation +namespace: biological_process +def: "The clustering together and adhesion of initially separate cells to form an aggregate. Examples include the clustering of unicellular organisms or blood cells in suspension and the condensation of mesenchymal cells during cartilage formation." [GOC:dos] +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0098754 +name: detoxification +namespace: biological_process +def: "Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance." [GOC:dos] +subset: goslim_pombe +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0098772 +name: molecular function regulator +namespace: molecular_function +def: "A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators." [GOC:dos, GOC:pt] +is_a: GO:0003674 ! molecular_function +relationship: regulates GO:0003674 ! molecular_function + +[Term] +id: GO:0099080 +name: supramolecular complex +namespace: cellular_component +def: "A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber." [GOC:dos] +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0104005 +name: hijacked molecular function +namespace: molecular_function +def: "A function that was not selected for in the evolution of an organism, but arises from co-option by another organism, e.g. a human protein used as a virus receptor." [GOC:pdt] +is_a: GO:0003674 ! molecular_function +created_by: dos +creation_date: 2017-08-04T02:12:09Z + +[Term] +id: GO:0140104 +name: molecular carrier activity +namespace: molecular_function +def: "Directly binding to a specific ion or molecule and delivering it either to an acceptor molecule or to a specific location." [GOC:pdt] +comment: https://github.com/geneontology/go-ontology/issues/14221 +subset: gocheck_do_not_annotate +is_a: GO:0003674 ! molecular_function +created_by: pg +creation_date: 2017-09-19T13:10:18Z + +[Term] +id: GO:0140110 +name: transcription regulator activity +namespace: molecular_function +def: "A molecular function that controls the rate, timing and/or magnitude of transcription of genetic information. The function of transcriptional regulators is to modulate gene expression at the transcription step so that they are expressed in the right cell at the right time and in the right amount throughout the life of the cell and the organism." [GOC:pg, GOC:txnOH-2018, Wikipedia:Transcription_factor] +comment: https://github.com/geneontology/go-ontology/issues/13588 +subset: gocheck_do_not_annotate +is_a: GO:0003674 ! molecular_function +created_by: pg +creation_date: 2017-10-18T07:05:44Z + +[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 +
--- /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 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/population.txt Fri Jan 11 06:18:35 2019 -0500 @@ -0,0 +1,100 @@ +fake1 +fake2 +fake3 +fake4 +fake5 +fake6 +fake7 +fake8 +fake9 +fake10 +fake11 +fake12 +fake13 +fake14 +fake15 +fake16 +fake17 +fake18 +fake19 +fake20 +fake21 +fake22 +fake23 +fake24 +fake25 +fake26 +fake27 +fake28 +fake29 +fake30 +fake31 +fake32 +fake33 +fake34 +fake35 +fake36 +fake37 +fake38 +fake39 +fake40 +fake41 +fake42 +fake43 +fake44 +fake45 +fake46 +fake47 +fake48 +fake49 +fake50 +fake51 +fake52 +fake53 +fake54 +fake55 +fake56 +fake57 +fake58 +fake59 +fake60 +fake61 +fake62 +fake63 +fake64 +fake65 +fake66 +fake67 +fake68 +fake69 +fake70 +fake71 +fake72 +fake73 +fake74 +fake75 +fake76 +fake77 +fake78 +fake79 +fake80 +fake81 +fake82 +fake83 +fake84 +fake85 +fake86 +fake87 +fake88 +fake89 +fake90 +fake91 +fake92 +fake93 +fake94 +fake95 +fake96 +fake97 +fake98 +fake99 +fake100
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/slim_annotations.tab Fri Jan 11 06:18:35 2019 -0500 @@ -0,0 +1,301 @@ +Gene GOSlim Term +fake46 GO:0003674 +fake46 GO:0005575 +fake46 GO:0008150 +fake45 GO:0003674 +fake45 GO:0005575 +fake45 GO:0008150 +fake44 GO:0003674 +fake44 GO:0005575 +fake44 GO:0008150 +fake43 GO:0003674 +fake43 GO:0005575 +fake43 GO:0008150 +fake42 GO:0003674 +fake42 GO:0005575 +fake42 GO:0008150 +fake41 GO:0003674 +fake41 GO:0005575 +fake41 GO:0008150 +fake40 GO:0003674 +fake40 GO:0005575 +fake40 GO:0008150 +fake49 GO:0003674 +fake49 GO:0005575 +fake49 GO:0008150 +fake48 GO:0003674 +fake48 GO:0005575 +fake48 GO:0008150 +fake47 GO:0003674 +fake47 GO:0005575 +fake47 GO:0008150 +fake57 GO:0003674 +fake57 GO:0005575 +fake57 GO:0008150 +fake56 GO:0003674 +fake56 GO:0005575 +fake56 GO:0008150 +fake55 GO:0003674 +fake55 GO:0005575 +fake55 GO:0008150 +fake54 GO:0003674 +fake54 GO:0005575 +fake54 GO:0008150 +fake53 GO:0003674 +fake53 GO:0005575 +fake53 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