diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..3fb8482 --- /dev/null +++ b/Makefile @@ -0,0 +1,5 @@ +ODK = docker run -m 12g -v $PWD/:/work -w /work --rm -ti obolibrary/odkfull + +start-robot: + $(ODK) robot python + diff --git a/README.md b/README.md new file mode 100644 index 0000000..47cb656 --- /dev/null +++ b/README.md @@ -0,0 +1,69 @@ +# oakx-robot: A robot plugin for OAK + +This is a plugin for [OAK](https://incatools.github.io/ontology-access-kit/) that wraps [ROBOT](robot.obolibrary.org) + +It provides a RobotImplementation (see [implementations](https://incatools.github.io/ontology-access-kit/implementations/index.html) of an OntologyInterface, so far this only implements +a portion of the [ValidatorInterface](https://incatools.github.io/ontology-access-kit/interfaces/validator.html) + +Currently this is more of a demonstrator/proof of concept than a useful tool. For most purposes you will likely want to simply +use robot on the command line tool + +## Selector + +This plugin registers the `robot` scheme + +Use `robot:path/to/ontology.owl` as the [selector](https://incatools.github.io/ontology-access-kit/selectors.html) + +## Initial Setup + +1. Install robot +2. Start robot python + +run: + +``` +robot python & +``` + +## Command Line + +The test folder contains an ontology with a deliberate error: + +```bash +runoak -i robot:tests/input/go-nucleus-unsat.owl validate +``` + +yields: + +|type|severity|subject|instantiates|predicate|object|object_str|source|info +|---|---|---|---|---|---|---|---|---| +|owl:Nothing|ERROR|GO:0031965|None|None|None|None|None|None + + +## Programmatic + +See [tests](tests/) + +```python +from oaklib.selector import get_resource_from_shorthand, discovered_plugins, get_implementation_from_shorthand +from oakx_robot.robot_implementation import RobotImplementation, OWL_NOTHING + +path = 'tests/input/go-nucleus-unsat.owl' +oi = get_implementation_from_shorthand(f'robot:{path}') +if oi.is_coherent(): + print('Congratulations! The ontology is coherent') +else: + print('Reasoner detected usatisfiable classes') + for c in oi.unsatisfiable_classes(): + print(f'Unsatisfiable: {c}') +``` + +## How it works + +See [robot/python](https://robot.obolibrary.org/python) + +## TODO + +- Implement OwlInterface +- Implement more reasoning operations +- Allow selection of different reasoners diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..477c945 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,2697 @@ +[[package]] +name = "aiohttp" +version = "3.8.1" +description = "Async http client/server framework (asyncio)" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +aiosignal = ">=1.1.2" +async-timeout = ">=4.0.0a3,<5.0" +attrs = ">=17.3.0" +charset-normalizer = ">=2.0,<3.0" +frozenlist = ">=1.1.1" +multidict = ">=4.5,<7.0" +yarl = ">=1.0,<2.0" + +[package.extras] +speedups = ["aiodns", "brotli", "cchardet"] + +[[package]] +name = "aiosignal" +version = "1.2.0" +description = "aiosignal: a list of registered asynchronous callbacks" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +frozenlist = ">=1.1.0" + +[[package]] +name = "alabaster" +version = "0.7.12" +description = "A configurable sidebar-enabled Sphinx theme" +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "antlr4-python3-runtime" +version = "4.9.3" +description = "ANTLR 4.9.3 runtime for Python 3.7" +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "appdirs" +version = "1.4.4" +description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "argparse" +version = "1.4.0" +description = "Python command-line parsing library" +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "async-timeout" +version = "4.0.2" +description = "Timeout context manager for asyncio programs" +category = "main" +optional = false +python-versions = ">=3.6" + +[[package]] +name = "atomicwrites" +version = "1.4.0" +description = "Atomic file writes." +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + +[[package]] +name = "attrs" +version = "21.4.0" +description = "Classes Without Boilerplate" +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" + +[package.extras] +dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"] +docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] +tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] +tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"] + +[[package]] +name = "babel" +version = "2.10.1" +description = "Internationalization utilities" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +pytz = ">=2015.7" + +[[package]] +name = "bioregistry" +version = "0.4.115" +description = "Integrated registry of biological databases and nomenclatures" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +click = "*" +more-click = "*" +pydantic = "*" +pystow = ">=0.1.13" +requests = "*" +tqdm = "*" + +[package.extras] +align = ["pyyaml", "beautifulsoup4", "tabulate", "defusedxml"] +charts = ["matplotlib", "matplotlib-venn", "seaborn"] +docs = ["sphinx", "sphinx-rtd-theme", "sphinx-click", "sphinx-autodoc-typehints", "sphinx-automodapi", "autodoc-pydantic"] +export = ["pyyaml", "rdflib", "rdflib-jsonld"] +gha = ["more-itertools"] +health = ["click-default-group", "pandas"] +tests = ["coverage", "pytest", "more-itertools"] +web = ["pyyaml", "rdflib", "rdflib-jsonld", "flask", "flasgger", "bootstrap-flask (<=2.0.0)", "markdown"] + +[[package]] +name = "certifi" +version = "2021.10.8" +description = "Python package for providing Mozilla's CA Bundle." +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "cfgraph" +version = "0.2.1" +description = "rdflib collections flattening graph" +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +rdflib = ">=0.4.2" + +[[package]] +name = "chardet" +version = "4.0.0" +description = "Universal encoding detector for Python 2 and 3" +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" + +[[package]] +name = "charset-normalizer" +version = "2.0.12" +description = "The Real First Universal Charset Detector. 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/dev/null +++ b/pyproject.toml @@ -0,0 +1,17 @@ +[tool.poetry] +name = "oakx-robot" +version = "0.1.0" +description = "" +authors = ["cmungall "] + +[tool.poetry.dependencies] +python = "^3.9" +py4j = "^0.10.9" +oaklib = "^0.1.16" + +[tool.poetry.dev-dependencies] +pytest = "^5.2" + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" diff --git a/src/oakx_robot/__init__.py b/src/oakx_robot/__init__.py new file mode 100644 index 0000000..7fa1e00 --- /dev/null +++ b/src/oakx_robot/__init__.py @@ -0,0 +1,7 @@ +__version__ = '0.1.0' + +from oakx_robot.robot_implementation import RobotImplementation + +schemes = { + 'robot': RobotImplementation +} diff --git a/src/oakx_robot/robot_implementation.py b/src/oakx_robot/robot_implementation.py new file mode 100644 index 0000000..58a14cf --- /dev/null +++ b/src/oakx_robot/robot_implementation.py @@ -0,0 +1,109 @@ +import logging +from abc import ABC +from dataclasses import dataclass +from typing import Any, Iterable, Optional + +import oaklib.datamodels.validation_datamodel as vdm +from oaklib.datamodels.vocabulary import DEFAULT_PREFIX_MAP, OBO_PURL +from oaklib.interfaces import ValidatorInterface +from oaklib.interfaces.basic_ontology_interface import PREFIX_MAP +from oaklib.interfaces.rdf_interface import RdfInterface +from oaklib.types import CURIE, URI +from py4j.java_gateway import JavaGateway + +OWL_NOTHING = 'owl:Nothing' + +# https://robot.obolibrary.org/python +# Not required when running `robot python` from the command line: +# launch_gateway(jarpath='bin/robot.jar', +# classpath='org.obolibrary.robot.PythonOperation', +# port=25333, +# die_on_exit=True) + +gateway = JavaGateway() + + +@dataclass +class RobotImplementation(RdfInterface, ValidatorInterface): + robot_ontology: Any = None + robot_gateway: Any = None + reasoner: Any = None + + def __post_init__(self): + if self.robot_ontology is None: + io_helper = gateway.jvm.org.obolibrary.robot.IOHelper() + path = self.resource.slug + ontology = io_helper.loadOntology(path) + self.robot_ontology = ontology + self.robot_gateway = gateway.jvm.org.obolibrary.robot + rf = gateway.jvm.org.semanticweb.elk.owlapi.ElkReasonerFactory() + self.reasoner = rf.createReasoner(ontology) + + def get_prefix_map(self) -> PREFIX_MAP: + # TODO + # return {'rdfs': str(RDFS)} + return DEFAULT_PREFIX_MAP + + # def store(self, resource: OntologyResource) -> None: + # SparqlBasicImpl.dump(self.engine, resource) + + def curie_to_uri(self, curie: CURIE, strict: bool = False) -> URI: + if curie.startswith('http'): + return curie + pm = self.get_prefix_map() + if ':' in curie: + toks = curie.split(':') + if len(toks) > 2: + logging.warning(f'CURIE should not contain double colons: {toks}') + pfx = toks[0] + local_id = '_'.join(toks[1:]) + else: + pfx, local_id = toks + if pfx in pm: + return f'{pm[pfx]}{local_id}' + else: + return f'http://purl.obolibrary.org/obo/{pfx}_{local_id}' + else: + logging.warning(f'Not a curie: {curie}') + return curie + + def uri_to_curie(self, uri: URI, strict=True) -> Optional[CURIE]: + # TODO: do not hardcode OBO + pm = self.get_prefix_map() + for k, v in pm.items(): + if uri.startswith(v): + return uri.replace(v, f'{k}:') + if uri.startswith(OBO_PURL): + uri = uri.replace(OBO_PURL, "") + return uri.replace('_', ':') + return uri + + def all_entity_curies(self) -> Iterable[CURIE]: + ontology = self.robot_ontology + entities = self.robot_gateway.OntologyHelper.getEntities(ontology).toArray() + for e in entities: + yield self.uri_to_curie(e.getIRI().toString()) + + def is_coherent(self) -> bool: + if len(list(self.unsatisfiable_classes())) > 0: + return False + elif not self.reasoner.isConsistent(): + return False + else: + return True + + def unsatisfiable_classes(self, exclude_nothing=True) -> Iterable[CURIE]: + ontology = self.robot_ontology + reasoner = self.reasoner + for c in ontology.getClassesInSignature().toArray(): + if not reasoner.isSatisfiable(c): + curie = self.uri_to_curie(c.getIRI().toString()) + if curie == OWL_NOTHING and exclude_nothing: + continue + yield curie + + def validate(self, configuration: vdm.ValidationConfiguration = None) -> Iterable[vdm.ValidationResult]: + for c in self.unsatisfiable_classes(): + yield vdm.ValidationResult(subject=c, + type='owl:Nothing', + severity=vdm.SeverityOptions(vdm.SeverityOptions.ERROR)) diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..0739670 --- /dev/null +++ b/tests/__init__.py @@ -0,0 +1,16 @@ +import os +import pprint +from pathlib import Path + +ROOT = os.path.abspath(os.path.dirname(__file__)) +INPUT_DIR = Path(ROOT) / 'input' +OUTPUT_DIR = Path(ROOT) / 'output' + +CHEBI_NUCLEUS = 'CHEBI:33252' +NUCLEUS = 'GO:0005634' +NUCLEAR_ENVELOPE = 'GO:0005635' +THYLAKOID = 'GO:0009579' + + +def output_path(fn: str) -> str: + return str(Path(OUTPUT_DIR) / fn) diff --git a/tests/input/go-nucleus-unsat.owl b/tests/input/go-nucleus-unsat.owl new file mode 100644 index 0000000..db50b91 --- /dev/null +++ b/tests/input/go-nucleus-unsat.owl @@ -0,0 +1,7476 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + a core relation that holds between a part and its whole + BFO:0000050 + external + part_of + part_of + part of + part of + part_of + + + + + + + + + + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + a core relation that holds between a whole and its part + BFO:0000051 + external + has_part + has_part + has part + has part + has_part + + + + + + + + + + + + + + + + + The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. + X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + BFO:0000062 + is preceded by + takes place after + external + preceded_by + preceded_by + preceded by + preceded by + preceded_by + + + + + + + + + + + + + + + + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + BFO:0000063 + external + precedes + precedes + precedes + precedes + + + + + + + + + + + + + + + + + + + b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + BFO:0000066 + external + occurs_in + occurs_in + occurs in + occurs in + + + + + + + + [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + BFO:0000067 + contains_process + contains process + contains process + + + + + + + + + + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + RO:0000052 + inheres_in + inheres in + + + + + + + + + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + RO:0000053 + external + bearer_of + bearer_of + bearer of + bearer of + + + + + + + + + + + a relation between a continuant and a process, in which the continuant is somehow involved in the process + RO:0000056 + external + participates_in + participates_in + participates in + participates in + participates_in + + + + + + + + + + + + + + a relation between a process and a continuant, in which the continuant is somehow involved in the process + RO:0000057 + external + has_participant + has_participant + has participant + has participant + has_participant + + + + + + + + + + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + RO:0000081 + role_of + role of + + + + + + + + + + + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + RO:0000087 + has_role + has role + has role + + + + + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + RO:0002013 + external + has_regulatory_component_activity + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + RO:0002014 + external + has_negative_regulatory_component_activity + has_negative_regulatory_component_activity + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + RO:0002015 + has_positive_regulatory_component_activity + has positive regulatory component activity + + + + + + + + + RO:0002017 + has_component_activity + has component activity + + + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + RO:0002018 + has_component_process + has component process + + + + + + + + + + RO:0002022 + directly_regulated_by + directly regulated by + + + + + + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + RO:0002023 + directly_negatively_regulated_by + directly negatively regulated by + + + + + + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + RO:0002024 + directly_positively_regulated_by + directly positively regulated by + + + + + + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + RO:0002025 + has_effector_activity + has effector activity + + + + + + + + + + RO:0002086 + ends_after + ends after + + + + + + + + + + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + RO:0002087 + directly preceded by + is directly preceded by + is immediately preceded by + starts_at_end_of + external + immediately_preceded_by + immediately_preceded_by + immediately preceded by + immediately_preceded_by + + + + + + + + + RO:0002090 + external + immediately_precedes + immediately_precedes + immediately precedes + immediately_precedes + + + + + + + + + + + + + + + + + + + + + + + + + A overlaps B if they share some part in common. + x overlaps y if and only if there exists some z such that x has part z and z part of y + RO:0002131 + external + overlaps + overlaps + overlaps + overlaps + + + + + + + + + + S only_in_taxon T iff: S SubClassOf in_taxon only T + U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon. + x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. + RO:0002160 + never_outside_taxon + specific_to + specific_to_taxon + only_in_taxon + only in taxon + only_in_taxon + + + + + + + + + + + + + + + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + RO:0002162 + in_taxon + in taxon + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + RO:0002180 + external + has_component + has_component + has component + has component + has_component + + + + + + + + + + + + + + + + + + + + + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + RO:0002211 + external + regulates + regulates + regulates + regulates + + + + + + + + + + + Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + RO:0002212 + external + negatively_regulates + negatively_regulates + negatively regulates + negatively regulates + + + + + + + + + + + + + + + + Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + RO:0002213 + external + positively_regulates + positively_regulates + positively regulates + positively regulates + + + + + + + + + + + + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + RO:0002215 + external + capable_of + capable_of + capable of + capable of + capable_of + + + + + + + + + + + + + + c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. + RO:0002216 + external + capable_of_part_of + capable_of_part_of + capable of part of + capable of part of + + + + + + + + + + RO:0002222 + temporally_related_to + temporally related to + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + RO:0002233 + external + has_input + has_input + has input + has input + + + + + + + + + + + + + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + RO:0002263 + acts_upstream_of + acts upstream of + + + + + + + + + + + + + c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. + RO:0002264 + affects + acts_upstream_of_or_within + acts upstream of or within + + + + + + + + + + RO:0002304 + external + causally_upstream_of,_positive_effect + causally_upstream_of,_positive_effect + causally upstream of, positive effect + + + + + + + + + + RO:0002305 + external + causally_upstream_of,_negative_effect + causally_upstream_of,_negative_effect + causally upstream of, negative effect + + + + + + + + + + + + + + + + + q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. + RO:0002314 + inheres_in_part_of + inheres in part of + + + + + + + + A relationship that holds via some environmental process + RO:0002320 + evolutionarily_related_to + evolutionarily related to + + + + + + + + A mereological relationship or a topological relationship + RO:0002323 + mereotopologically_related_to + mereotopologically related to + + + + + + + + + + + + + + + + + + RO:0002327 + enables + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + RO:0002328 + functionally_related_to + functionally related to + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + RO:0002329 + part_of_structure_that_is_capable_of + part of structure that is capable of + part of structure that is capable of + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + RO:0002331 + involved_in + involved in + + + + + + + + + + inverse of enables + RO:0002333 + enabled_by + enabled by + + + + + + + + + + + + inverse of regulates + RO:0002334 + external + regulated_by + regulated_by + regulated by + regulated by + + + + + + + + + inverse of negatively regulates + RO:0002335 + external + negatively_regulated_by + negatively_regulated_by + negatively regulated by + negatively regulated by + + + + + + + + + inverse of positively regulates + RO:0002336 + external + positively_regulated_by + positively_regulated_by + positively regulated by + positively regulated by + + + + + + + + + + inverse of has input + RO:0002352 + input_of + input of + + + + + + + + + + + inverse of upstream of + RO:0002404 + external + causally_downstream_of + causally_downstream_of + causally downstream of + causally downstream of + + + + + + + + + + + RO:0002405 + external + immediately_causally_downstream_of + immediately_causally_downstream_of + immediately causally downstream of + immediately causally downstream of + + + + + + + + This relation groups causal relations between material entities and causal relations between processes + RO:0002410 + causally_related_to + causally related to + + + + + + + + + + + p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + RO:0002411 + external + causally_upstream_of + causally_upstream_of + causally upstream of + causally upstream of + + + + + + + + + + p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + RO:0002412 + external + immediately_causally_upstream_of + immediately_causally_upstream_of + immediately causally upstream of + immediately causally upstream of + + + + + + + + + + + p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + RO:0002418 + external + affects + causally_upstream_of_or_within + causally_upstream_of_or_within + causally upstream of or within + + + + + + + + + + inverse of causally upstream of or within + RO:0002427 + external + causally_downstream_of_or_within + causally_downstream_of_or_within + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + RO:0002428 + involved_in_regulation_of + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + RO:0002429 + involved_in_positive_regulation_of + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + RO:0002430 + involved_in_negative_regulation_of + involved in negative regulation of + + + + + + + + + + + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + RO:0002431 + involved_in_or_involved_in_regulation_of + involved in or involved in regulation of + + + + + + + + + + + + + + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + RO:0002432 + enables activity in + is_active_in + is active in + + + + + + + + + + + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + RO:0002434 + in pairwise interaction with + interacts_with + interacts with + + + + + + + + + + An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. + RO:0002436 + molecularly_interacts_with + molecularly interacts with + + + + + + + + + RO:0002447 + phosphorylates + phosphorylates + + + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. + RO:0002448 + molecularly controls + directly_regulates_activity_of + directly regulates activity of + + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + RO:0002449 + molecularly decreases activity of + directly_negatively_regulates_activity_of + directly negatively regulates activity of + + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + RO:0002450 + molecularly increases activity of + directly_positively_regulates_activity_of + directly positively regulates activity of + + + + + + + + + + + + + + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + RO:0002479 + has_part_that_occurs_in + has part that occurs in + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + RO:0002500 + causal_agent_in_process + causal agent in process + + + + + + + + + + + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + RO:0002501 + causal_relation_between_processes + causal relation between processes + + + + + + + + RO:0002502 + depends_on + depends on + + + + + + + + + + + RO:0002506 + causal_relation_between_entities + causal relation between entities + + + + + + + + + + RO:0002559 + causally_influenced_by + causally influenced by + + + + + + + + + + + + + + + + + + + + + The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). + RO:0002566 + causally_influences + causally influences + + + + + + + + + + Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + RO:0002578 + directly_regulates + directly regulates + + + + + + + + + + + + + + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + RO:0002584 + has_part_structure_that_is_capable_of + has part structure that is capable of + + + + + + + + + + + A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. + RO:0002595 + causal_relation_between_material_entity_and_a_process + causal relation between material entity and a process + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + RO:0002596 + capable_of_regulating + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + RO:0002597 + capable_of_negatively_regulating + capable of negatively regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + RO:0002598 + capable_of_positively_regulating + capable of positively regulating + + + + + + + + + Inverse of 'causal agent in process' + RO:0002608 + external + process_has_causal_agent + process_has_causal_agent + process has causal agent + + + + + + + + + + Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + RO:0002629 + directly_positively_regulates + directly positively regulates + + + + + + + + + + Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + RO:0002630 + directly_negatively_regulates + directly negatively regulates + + + + + + + + + p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. + RO:0004007 + external + has_primary_input_or_output + has_primary_input_or_output + has primary input or output + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + RO:0004031 + enables_subfunction + enables subfunction + + + + + + + + + + + + + RO:0004032 + acts_upstream_of_or_within,_positive_effect + acts upstream of or within, positive effect + + + + + + + + + + + + + RO:0004033 + acts_upstream_of_or_within,_negative_effect + acts upstream of or within, negative effect + + + + + + + + + + + + + + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive + RO:0004034 + acts_upstream_of,_positive_effect + acts upstream of, positive effect + + + + + + + + + + + + + + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative + RO:0004035 + acts_upstream_of,_negative_effect + acts upstream of, negative effect + + + + + + + + + RO:0004046 + causally_upstream_of_or_within,_negative_effect + causally upstream of or within, negative effect + + + + + + + + + RO:0004047 + causally_upstream_of_or_within,_positive_effect + causally upstream of or within, positive effect + + + + + + + + + + + The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. + RO:0011002 + regulates_activity_of + regulates activity of + + + + + + + + + + + + + + + + + + + + + + + + + + + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + continuant + + + + + + + + + + + + + + + + + + + + + An entity that has temporal parts and that happens, unfolds or develops through time. + occurrent + + + + + + + + + + + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + independent continuant + + + + + + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + process + + + + + + + + + + + + + + + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable entity + + + + + + + + + + + + + + + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + specifically dependent continuant + + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity + + + + + + + + + anatomical entity + anatomical entity + + + + + + + + + connected anatomical structure + connected anatomical structure + + + + + + + + + + material anatomical entity + material anatomical entity + + + + + + + + + organism or virus or viroid + + + + + + + + + biological entity + + + + + + + + + + electron + + + + + + + + + molecular entity + + + + + + + + + + chemical entity + + + + + + + + + + biological role + + + + + + + + + + + + + + + group + + + + + + + + + nonmetal atom + + + + + + + + + phosphate + + + + + + + + + phosphoric acid derivative + + + + + + + + + + + + + + + phosphorus molecular entity + + + + + + + + + + + + + + + + + phosphorus atom + + + + + + + + + fundamental particle + + + + + + + + + oxoacid derivative + + + + + + + + + + + + + + + + + + + + + atom + + + + + + + + + + + + + + + atomic nucleus + + + + + + + + + + nucleon + + + + + + + + + nutrient + + + + + + + + + pnictogen + + + + + + + + + + + + + + + pnictogen molecular entity + + + + + + + + + main group element atom + + + + + + + + + p-block element atom + + + + + + + + + + + + + + + main group molecular entity + + + + + + + + + + + + + + + p-block molecular entity + + + + + + + + + macronutrient + + + + + + + + + + lepton + + + + + + + + + + baryon + + + + + + + + + fermion + + + + + + + + + subatomic particle + + + + + + + + + composite particle + + + + + + + + + hadron + + + + + + + + + nuclear particle + + + + + + + + + + + + + + + polyatomic entity + + + + + + + + + + phosphorus oxoacid derivative + + + + + + + + + phosphorus oxoacids and derivatives + + + + + + + + + heteroatomic molecular entity + + + + + + + + + role + + + + + + + + + physiological role + + + + + + + + + food component + + + + + + + + + + + + + + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + cell + cell + + + + + + + + + + + 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. + GO:0005554 + molecular function + molecular_function + GO:0003674 + + + + + + + + + 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. + molecular_function + + + + + 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 + + + + + + + + + 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. + Wikipedia:Enzyme + enzyme activity + molecular_function + GO:0003824 + + + + + + + catalytic activity + + + + + 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 + + + + + enzyme activity + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Binds to and stops, prevents or reduces the activity of an enzyme. + GO:0048551 + metalloenzyme inhibitor activity + molecular_function + GO:0004857 + enzyme inhibitor activity + + + + + Binds to and stops, prevents or reduces the activity of an enzyme. + GOC:ai + GOC:ebc + + + + + + + + + + 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). + GO:0008372 + NIF_Subcellular:sao1337158144 + cell or subcellular entity + cellular component + cellular_component + subcellular entity + GO:0005575 + + + + + + + + + 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. + cellular_component + + + + + 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:sao1337158144 + + + + + subcellular entity + NIF_Subcellular:nlx_subcell_100315 + + + + + + + + + + + + + + + A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. + https://github.com/geneontology/go-ontology/issues/17776 + Wikipedia:Intracellular + internal to cell + intracellular + protoplasm + cellular_component + nucleocytoplasm + protoplast + GO:0005622 + + + + + + intracellular anatomical structure + + + + + A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. + ISBN:0198506732 + + + + + nucleocytoplasm + GOC:mah + + + + + protoplast + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. + NIF_Subcellular:sao1702920020 + Wikipedia:Cell_nucleus + cell nucleus + horsetail nucleus + cellular_component + GO:0005634 + + + + + + + + + + + + + nucleus + + + + + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. + GOC:go_curators + + + + + horsetail nucleus + GOC:al + GOC:mah + GOC:vw + PMID:15030757 + + + + + + + + + + + + + + + + + + + + + The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). + GO:0005636 + Wikipedia:Nuclear_envelope + cellular_component + GO:0005635 + + + + nuclear envelope + + + + + The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). + ISBN:0198547684 + + + + + + + + + + + + + + + All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. + Wikipedia:Cytoplasm + cellular_component + GO:0005737 + + + + + + + + cytoplasm + + + + + All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. + ISBN:0198547684 + + + + + + + + + + + + + + + A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. + Wikipedia:Vacuole + cellular_component + vacuolar carboxypeptidase Y + GO:0005773 + + + + + + + + + + + + vacuole + + + + + A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. + GOC:mtg_sensu + ISBN:0198506732 + + + + + + + + + + + + + + + The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. + GO:0005904 + juxtamembrane + NIF_Subcellular:sao1663586795 + Wikipedia:Cell_membrane + cell membrane + cellular membrane + cytoplasmic membrane + plasmalemma + bacterial inner membrane + inner endospore membrane + plasma membrane lipid bilayer + cellular_component + GO:0005886 + + + + + + + + + + + plasma membrane + + + + + The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. + ISBN:0716731363 + + + + + cellular membrane + NIF_Subcellular:sao6433132645 + + + + + plasma membrane lipid bilayer + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. + Wikipedia:Cell_cortex + cellular_component + cell periphery + peripheral cytoplasm + GO:0005938 + + + + cell cortex + + + + + The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. + GOC:mah + ISBN:0815316194 + + + + + + + + + + + + + + + + + + + + + + + + + + The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). + phosphorus metabolism + biological_process + GO:0006793 + + phosphorus metabolic process + + + + + The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. + phosphate metabolism + biological_process + phosphate metabolic process + GO:0006796 + phosphate-containing compound metabolic process + + + + + The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + Binds to and increases the activity of an enzyme. + GO:0010577 + metalloenzyme activator activity + molecular_function + GO:0008047 + enzyme activator activity + + + + + Binds to and increases the activity of an enzyme. + GOC:dph + GOC:mah + GOC:tb + + + + + + + + + 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. + jl + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process + biological process + physiological process + biological_process + single organism process + single-organism process + GO:0008150 + + + + + + + + + + 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. + biological_process + + + + + 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 + + + + + + + + + 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. + jl + 2012-10-17T15:46:40Z + GO:0044236 + GO:0044710 + Wikipedia:Metabolism + metabolism + metabolic process resulting in cell growth + metabolism resulting in cell growth + multicellular organism metabolic process + biological_process + single-organism metabolic process + GO:0008152 + + + + + + Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. + metabolic process + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GO:0044252 + down regulation of metabolic process + down-regulation of metabolic process + downregulation of metabolic process + negative regulation of metabolism + negative regulation of organismal metabolism + inhibition of metabolic process + inhibition of organismal metabolic process + negative regulation of multicellular organismal metabolic process + biological_process + GO:0009892 + negative regulation of metabolic process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GO:0044253 + positive regulation of metabolism + up regulation of metabolic process + up-regulation of metabolic process + upregulation of metabolic process + activation of metabolic process + positive regulation of multicellular organismal metabolic process + positive regulation of organismal metabolism + stimulation of metabolic process + stimulation of organismal metabolic process + up-regulation of organismal metabolic process + biological_process + GO:0009893 + positive regulation of metabolic process + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GOC:go_curators + + + + + + + + + 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. + jl + 2012-12-11T16:56:55Z + GO:0008151 + GO:0044763 + GO:0050875 + cell physiology + cellular physiological process + cell growth and/or maintenance + biological_process + single-organism cellular process + GO:0009987 + + cellular process + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + biological_process + GO:0010562 + positive regulation of phosphorus metabolic process + + + + + Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + biological_process + GO:0010563 + negative regulation of phosphorus metabolic process + + + + + Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. + Wikipedia:Endomembrane_system + cellular_component + GO:0012505 + + + + + endomembrane system + + + + + A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. + GOC:lh + + + + + + + + + A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. + 2014-03-06T11:37:54Z + GO:0098589 + GO:0098805 + Wikipedia:Biological_membrane + membrane region + region of membrane + whole membrane + cellular_component + GO:0016020 + + + + + + + + + membrane + + + + + A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. + GOC:dos + GOC:mah + ISBN:0815316194 + + + + + + + + + + + + + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + Reactome:R-HSA-6788855 + Reactome:R-HSA-6788867 + phosphokinase activity + molecular_function + GO:0016301 + + + + + + + Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. + kinase activity + + + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + ISBN:0198506732 + + + + + Reactome:R-HSA-6788855 + FN3KRP phosphorylates PsiAm, RibAm + + + + + Reactome:R-HSA-6788867 + FN3K phosphorylates ketosamines + + + + + + + + + The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. + Wikipedia:Phosphorylation + biological_process + GO:0016310 + + + phosphorylation + + + + + The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. + ISBN:0198506732 + + + + + + + + + Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + EC:2.-.-.- + Reactome:R-HSA-1483089 + Reactome:R-HSA-1483186 + Reactome:R-HSA-5668414 + Reactome:R-HSA-8868783 + molecular_function + GO:0016740 + + + + + + + + + transferase activity + + + + + Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + ISBN:0198506732 + + + + + Reactome:R-HSA-1483089 + PE is converted to PS by PTDSS2 + + + + + Reactome:R-HSA-1483186 + PC is converted to PS by PTDSS1 + + + + + Reactome:R-HSA-5668414 + TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK + + + + + Reactome:R-HSA-8868783 + TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 + + + + + + + + + Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). + EC:2.7.-.- + molecular_function + GO:0016772 + + Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. + transferase activity, transferring phosphorus-containing groups + + + + + Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). + GOC:jl + ISBN:0198506732 + + + + + + + + + + + + + + + + + + + + + + + + + + Modulates the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + molecular_function + GO:0019207 + kinase regulator activity + + + + + Modulates the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Binds to and increases the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + molecular_function + GO:0019209 + kinase activator activity + + + + + Binds to and increases the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Binds to and stops, prevents or reduces the activity of a kinase. + molecular_function + GO:0019210 + kinase inhibitor activity + + + + + Binds to and stops, prevents or reduces the activity of a kinase. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + regulation of phosphate metabolism + biological_process + GO:0019220 + regulation of phosphate metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GO:0044246 + regulation of metabolism + regulation of multicellular organismal metabolic process + regulation of organismal metabolic process + biological_process + GO:0019222 + + regulation of metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GOC:go_curators + + + + + regulation of organismal metabolic process + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. + NIF_Subcellular:sao830981606 + cellular_component + intracellular membrane + GO:0031090 + organelle membrane + + + + + A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. + GOC:dos + GOC:mah + + + + + intracellular membrane + NIF_Subcellular:sao830981606 + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + regulation of cellular metabolism + biological_process + GO:0031323 + regulation of cellular metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + down regulation of cellular metabolic process + down-regulation of cellular metabolic process + downregulation of cellular metabolic process + negative regulation of cellular metabolism + inhibition of cellular metabolic process + biological_process + GO:0031324 + negative regulation of cellular metabolic process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + positive regulation of cellular metabolism + up regulation of cellular metabolic process + up-regulation of cellular metabolic process + upregulation of cellular metabolic process + activation of cellular metabolic process + stimulation of cellular metabolic process + biological_process + GO:0031325 + positive regulation of cellular metabolic process + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. + NIF_Subcellular:sao1687101204 + cellular_component + GO:0031965 + nuclear membrane UNSAT + + + + + Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. + GOC:mah + GOC:pz + + + + + + + + + + + + + + + + + + + + + A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. + cellular_component + GO:0031967 + + organelle envelope + + + + + A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. + GOC:mah + GOC:pz + + + + + + + + + + + + + + + A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. + cellular_component + GO:0031975 + envelope + + + + + A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. + GOC:mah + GOC:pz + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + down regulation of kinase activity + down-regulation of kinase activity + downregulation of kinase activity + inhibition of kinase activity + kinase inhibitor + biological_process + GO:0033673 + negative regulation of kinase activity + + + + + + + + + + + https://github.com/geneontology/go-ontology/issues/13926 + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + up regulation of kinase activity + up-regulation of kinase activity + upregulation of kinase activity + kinase activator + stimulation of kinase activity + biological_process + GO:0033674 + positive regulation of kinase activity + + + + + + + + + + + https://github.com/geneontology/go-ontology/issues/13926 + + + + + Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. + biological_process + GO:0042325 + regulation of phosphorylation + + + + + Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. + GOC:jl + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. + down regulation of phosphorylation + down-regulation of phosphorylation + downregulation of phosphorylation + inhibition of phosphorylation + biological_process + GO:0042326 + negative regulation of phosphorylation + + + + + Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. + GOC:jl + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. + up regulation of phosphorylation + up-regulation of phosphorylation + upregulation of phosphorylation + activation of phosphorylation + stimulation of phosphorylation + biological_process + GO:0042327 + positive regulation of phosphorylation + + + + + Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. + GOC:jl + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the activity of an enzyme. + GO:0048554 + positive regulation of enzyme activity + up regulation of enzyme activity + up-regulation of enzyme activity + upregulation of enzyme activity + activation of enzyme activity + activation of metalloenzyme activity + positive regulation of metalloenzyme activity + stimulation of enzyme activity + stimulation of metalloenzyme activity + up regulation of metalloenzyme activity + up-regulation of metalloenzyme activity + upregulation of metalloenzyme activity + biological_process + GO:0043085 + + positive regulation of catalytic activity + + + + + Any process that activates or increases the activity of an enzyme. + GOC:ebc + GOC:jl + GOC:tb + GOC:vw + + + + + positive regulation of enzyme activity + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops or reduces the activity of an enzyme. + GO:0048553 + down regulation of enzyme activity + down-regulation of enzyme activity + down-regulation of metalloenzyme activity + downregulation of enzyme activity + negative regulation of enzyme activity + down regulation of metalloenzyme activity + downregulation of metalloenzyme activity + inhibition of enzyme activity + inhibition of metalloenzyme activity + negative regulation of metalloenzyme activity + biological_process + GO:0043086 + negative regulation of catalytic activity + + + + + Any process that stops or reduces the activity of an enzyme. + GOC:ebc + GOC:jl + GOC:tb + GOC:vw + + + + + negative regulation of enzyme activity + GOC:tb + + + + + + + + + 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. + NIF_Subcellular:sao1539965131 + Wikipedia:Organelle + cellular_component + GO:0043226 + + + + organelle + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + NIF_Subcellular:sao414196390 + membrane-enclosed organelle + cellular_component + GO:0043227 + membrane-bounded organelle + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + cellular_component + GO:0043229 + + intracellular organelle + + + + + Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + intracellular membrane-enclosed organelle + cellular_component + GO:0043231 + + intracellular membrane-bounded organelle + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + biological_process + GO:0043549 + regulation of kinase activity + + + + + + + + + + + https://github.com/geneontology/go-ontology/issues/13926 + + + + + Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:bf + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + jl + 2009-04-21T04:07:27Z + biological_process + GO:0044092 + negative regulation of molecular function + + + + + Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + GO:jl + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + jl + 2009-04-21T04:11:06Z + biological_process + GO:0044093 + positive regulation of molecular function + + + + + Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + GO:jl + + + + + + + + + + The chemical reactions and pathways by which individual cells transform chemical substances. + cellular metabolism + biological_process + intermediary metabolism + GO:0044237 + cellular metabolic process + + + + + The chemical reactions and pathways by which individual cells transform chemical substances. + GOC:go_curators + + + + + intermediary metabolism + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + down regulation of phosphate metabolic process + down-regulation of phosphate metabolic process + downregulation of phosphate metabolic process + negative regulation of phosphate metabolism + inhibition of phosphate metabolic process + biological_process + GO:0045936 + negative regulation of phosphate metabolic process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + positive regulation of phosphate metabolism + up regulation of phosphate metabolic process + up-regulation of phosphate metabolic process + upregulation of phosphate metabolic process + activation of phosphate metabolic process + stimulation of phosphate metabolic process + biological_process + GO:0045937 + positive regulation of phosphate metabolic process + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GO:0043119 + positive regulation of physiological process + up regulation of biological process + up-regulation of biological process + upregulation of biological process + activation of biological process + stimulation of biological process + biological_process + GO:0048518 + + positive regulation of biological process + + + + + Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GO:0043118 + down regulation of biological process + down-regulation of biological process + downregulation of biological process + negative regulation of physiological process + inhibition of biological process + biological_process + GO:0048519 + + negative regulation of biological process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GO:0051242 + positive regulation of cellular physiological process + up regulation of cellular process + up-regulation of cellular process + upregulation of cellular process + activation of cellular process + stimulation of cellular process + biological_process + GO:0048522 + positive regulation of cellular process + + + + + Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GO:0051243 + down regulation of cellular process + down-regulation of cellular process + downregulation of cellular process + negative regulation of cellular physiological process + inhibition of cellular process + biological_process + GO:0048523 + negative regulation of cellular process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GO:0050791 + regulation of physiological process + biological_process + GO:0050789 + + + + + regulation of biological process + + + + + Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GOC:ai + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the activity of an enzyme. + GO:0048552 + regulation of enzyme activity + regulation of metalloenzyme activity + biological_process + GO:0050790 + + regulation of catalytic activity + + + + + Any process that modulates the activity of an enzyme. + GOC:ai + GOC:ebc + GOC:vw + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GO:0051244 + regulation of cellular physiological process + biological_process + GO:0050794 + regulation of cellular process + + + + + Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are 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 + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + regulation of phosphorus metabolism + biological_process + GO:0051174 + regulation of phosphorus metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + transferase regulator + biological_process + GO:0051338 + + This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. + regulation of transferase activity + + + + + Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + EC:2.-.-.- + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + transferase activator + up regulation of transferase activity + up-regulation of transferase activity + upregulation of transferase activity + activation of transferase activity + stimulation of transferase activity + biological_process + GO:0051347 + + This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. + positive regulation of transferase activity + + + + + Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + down regulation of transferase activity + down-regulation of transferase activity + downregulation of transferase activity + transferase inhibitor + inhibition of transferase activity + biological_process + GO:0051348 + + This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. + negative regulation of transferase activity + + + + + Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + GOC:ai + + + + + + + + + Any process that modulates a measurable attribute of any biological process, quality or function. + regulation + biological_process + GO:0065007 + + + biological regulation + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + regulation of a molecular function + biological_process + GO:0065009 + + + + regulation of molecular function + + + + + Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + GOC:isa_complete + + + + + + + + + The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures. + mah + 2010-10-04T01:51:47Z + cellular_component + GO:0071944 + + cell periphery + + + + + The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + A membrane that is a (regional) part of the plasma membrane. + dos + 2014-03-06T11:55:32Z + region of plasma membrane + cellular_component + GO:0098590 + + Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass. + plasma membrane region + + + + + A membrane that is a (regional) part of the plasma membrane. + GOC:dos + + + + + + + + + + + + + + + + + + + + + + + + + + Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. + cellular_component + GO:0099568 + cytoplasmic region + + + + + Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. + GOC:dos + + + + + + + + + + + + + + + + + + + + + + + + + + + The complete extent of cell cortex that underlies some some region of the plasma membrane. + perimembrane region + cellular_component + GO:0099738 + cell cortex region + + + + + The complete extent of cell cortex that underlies some some region of the plasma membrane. + GOC:dos + + + + + + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + kmv + 2019-08-12T18:01:37Z + cellular_component + GO:0110165 + cellular anatomical entity + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + GOC:kmv + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + all + root + + + + + + + + + + + + + + + + Vira + Viridae + viruses + Viruses + + + + + + + + + + + + + + + + blue-green algae + blue-green bacteria + cyanophytes + Cyanophyceae + Cyanophycota + Cyanophyta + Oxygenic photosynthetic bacteria + Oxyphotobacteria + cyanobacteria + Cyanobacteria + + + + + + + + + + + + + + + biota + cellular organisms + + + + + + + + + + + + + + + Eumycetozoa Zopf, 1884 + Mycetozoa + mycetozoans + Eumycetozoa + + + + + + + + + + + + + + + Terrabacteria group + + + + + + + + + + + + + + + Cyanobacteria/Melainabacteria group + + + + + + + + + + + + + + + + + + + eubacteria + Monera + Procaryotae + Prokaryota + Prokaryotae + bacteria + prokaryote + prokaryotes + Bacteria + + + + + + + + + + + + + + + Dictyosteliaceae + + + + + + + + + + + + + + + Dictyosteliales + + + + + + + + + + + + + + + + + Archaebacteria + Mendosicutes + Metabacteria + Monera + Procaryotae + Prokaryota + Prokaryotae + archaea + prokaryote + prokaryotes + Archaea + + + + + + + + + + + + + + + Evosea + + + + + + + + + + + + + + + + + + Discoba + + + + + + + + + + + + + + + eucaryotes + eukaryotes + Eucarya + Eucaryotae + Eukarya + Eukaryotae + eukaryotes + Eukaryota + + + + + + + + + + + + + + + dictyostelid cellular slime molds + Dictyostelida + Dictyostelids + Dictyosteliida + cellular slime molds + Dictyostelia + + + + + + + + + + + + + + + + + + Chlorophyta/Embryophyta group + chlorophyte/embryophyte group + green plants + Chlorobionta + Chloroplastida + green plants + Viridiplantae + + + + + + + + + + + + + + + + Fungi/Metazoa group + opisthokonts + Opisthokonta + + + + + + + + + + + + + + + + Euglenozoans + Euglenozoa + + + + + + + + + + + + + + + + + Mycota + fungi + Fungi + + + + + + + + + + + + + + + Amoebozoa + + + + + + + + + + + + + + + + Hyalostilbum + Dictyostelium + + + + + + + + + + + + + + + + + + Jennifer I Deegan + 2009-08-10T10:46:43Z + Viridiplantae or Bacteria + + + + + + + + + + + + + + + + + The union of the taxa Viridiplantae and Cyanobacteria. + Jennifer Deegan + 2008-07-16T03:33:38Z + Viridiplantae or Cyanobacteria + + + + + The union of the taxa Viridiplantae and Cyanobacteria. + GOC:mtg_go-taxon + + + + + + + + + + + + + + + + + + jdeegan + 2008-07-24T11:56:07Z + Prokaryota + + + + + + + + + + + + + + + + + + jdeegan + 2008-08-14T10:45:59Z + Viridiplantae or Archaea or Bacteria + + + + + + + + + + + + + + + + + + Jennifer I Deegan + 2009-08-10T10:46:43Z + Viridiplantae or Bacteria or Euglenozoa + + + + + + + + + + + + + + + + + + Jennifer I Deegan + 2009-08-10T10:46:43Z + Viridiplantae or Euglenozoa + + + + + + + + + + + + + + + + + Jennifer Deegan + 2008-07-24T04:15:25Z + Fungi or Bacteria + + + + + + + + + + + + + + + + + + + Jennifer I Deegan + 2009-08-10T10:46:43Z + Viridiplantae or Bacteria or Euglenozoa or Archaea + + + + + + + + + + + + + + + + + Fungi or Dictyostelium + + + + + + + + + + + + + + + + + + Fungi or Bacteria or Archaea + + + + + + + + + + + + + + + + + The unikonts have a triple-gene fusion that is lacking in the bikonts. The three genes that are fused together in the unikonts but not bacteria or bikonts encode enzymes for synthesis of the pyrimidine nucleotides: carbamoyl phosphate synthase, dihydroorotase, aspartate carbamoyltransferase. This must have involved a double fusion, a rare pair of events, supporting the shared ancestry of Opisthokonta and Amoebozoa. + unikonts + Unikonta + + + + + The unikonts have a triple-gene fusion that is lacking in the bikonts. The three genes that are fused together in the unikonts but not bacteria or bikonts encode enzymes for synthesis of the pyrimidine nucleotides: carbamoyl phosphate synthase, dihydroorotase, aspartate carbamoyltransferase. This must have involved a double fusion, a rare pair of events, supporting the shared ancestry of Opisthokonta and Amoebozoa. + http://en.wikipedia.org/wiki/Unikont + + + + + + + + + + + + + + + + + archaea-eukaryota + Archaea or Eukaryota + + + + + + + + + + + + + + + + + cellular organisms or viruses + + + + + + + + + + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + quality + + + + + + + + + A quality which inheres in a continuant. + monadic quality of a continuant + multiply inhering quality of a physical entity + quality of a continuant + quality of a single physical entity + quality of an object + quality of continuant + monadic quality of an object + monadic quality of continuant + physical object quality + + + + + + + + + A monadic quality of continuant that exists at the cellular level of organisation. + cellular quality + + + + + + + + + A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. + nucleate quality + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. + anucleate + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. + binucleate + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. + mononucleate + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. + multinucleate + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. + nucleated + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + example to be eventually removed + + + + + + + + + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + failed exploratory term + + + + + + + + + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + + term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + core + + + + + + + + + placeholder removed + + + + + + + + + terms merged + + + + + + + + + term imported + + + + + + + + + term split + + + + + + + + + universal + + + + + + + + + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + defined class + + + + + + + + + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expression + + + + + + + + + Terms with this status should eventually replaced with a term from another ontology. + to be replaced with external ontology term + + + + + + + + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + requires discussion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/input/go-nucleus.owl b/tests/input/go-nucleus.owl new file mode 100644 index 0000000..984e464 --- /dev/null +++ b/tests/input/go-nucleus.owl @@ -0,0 +1,7475 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + a core relation that holds between a part and its whole + BFO:0000050 + external + part_of + part_of + part of + part of + part_of + + + + + + + + + + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + a core relation that holds between a whole and its part + BFO:0000051 + external + has_part + has_part + has part + has part + has_part + + + + + + + + + + + + + + + + + The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. + X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + BFO:0000062 + is preceded by + takes place after + external + preceded_by + preceded_by + preceded by + preceded by + preceded_by + + + + + + + + + + + + + + + + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + BFO:0000063 + external + precedes + precedes + precedes + precedes + + + + + + + + + + + + + + + + + + + b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + BFO:0000066 + external + occurs_in + occurs_in + occurs in + occurs in + + + + + + + + [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + BFO:0000067 + contains_process + contains process + contains process + + + + + + + + + + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + RO:0000052 + inheres_in + inheres in + + + + + + + + + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + RO:0000053 + external + bearer_of + bearer_of + bearer of + bearer of + + + + + + + + + + + a relation between a continuant and a process, in which the continuant is somehow involved in the process + RO:0000056 + external + participates_in + participates_in + participates in + participates in + participates_in + + + + + + + + + + + + + + a relation between a process and a continuant, in which the continuant is somehow involved in the process + RO:0000057 + external + has_participant + has_participant + has participant + has participant + has_participant + + + + + + + + + + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + RO:0000081 + role_of + role of + + + + + + + + + + + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + RO:0000087 + has_role + has role + has role + + + + + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + RO:0002013 + external + has_regulatory_component_activity + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + RO:0002014 + external + has_negative_regulatory_component_activity + has_negative_regulatory_component_activity + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + RO:0002015 + has_positive_regulatory_component_activity + has positive regulatory component activity + + + + + + + + + RO:0002017 + has_component_activity + has component activity + + + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + RO:0002018 + has_component_process + has component process + + + + + + + + + + RO:0002022 + directly_regulated_by + directly regulated by + + + + + + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + RO:0002023 + directly_negatively_regulated_by + directly negatively regulated by + + + + + + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + RO:0002024 + directly_positively_regulated_by + directly positively regulated by + + + + + + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + RO:0002025 + has_effector_activity + has effector activity + + + + + + + + + + RO:0002086 + ends_after + ends after + + + + + + + + + + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + RO:0002087 + directly preceded by + is directly preceded by + is immediately preceded by + starts_at_end_of + external + immediately_preceded_by + immediately_preceded_by + immediately preceded by + immediately_preceded_by + + + + + + + + + RO:0002090 + external + immediately_precedes + immediately_precedes + immediately precedes + immediately_precedes + + + + + + + + + + + + + + + + + + + + + + + + + A overlaps B if they share some part in common. + x overlaps y if and only if there exists some z such that x has part z and z part of y + RO:0002131 + external + overlaps + overlaps + overlaps + overlaps + + + + + + + + + + S only_in_taxon T iff: S SubClassOf in_taxon only T + U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon. + x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. + RO:0002160 + never_outside_taxon + specific_to + specific_to_taxon + only_in_taxon + only in taxon + only_in_taxon + + + + + + + + + + + + + + + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + RO:0002162 + in_taxon + in taxon + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + RO:0002180 + external + has_component + has_component + has component + has component + has_component + + + + + + + + + + + + + + + + + + + + + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + RO:0002211 + external + regulates + regulates + regulates + regulates + + + + + + + + + + + Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + RO:0002212 + external + negatively_regulates + negatively_regulates + negatively regulates + negatively regulates + + + + + + + + + + + + + + + + Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + RO:0002213 + external + positively_regulates + positively_regulates + positively regulates + positively regulates + + + + + + + + + + + + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + RO:0002215 + external + capable_of + capable_of + capable of + capable of + capable_of + + + + + + + + + + + + + + c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. + RO:0002216 + external + capable_of_part_of + capable_of_part_of + capable of part of + capable of part of + + + + + + + + + + RO:0002222 + temporally_related_to + temporally related to + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + RO:0002233 + external + has_input + has_input + has input + has input + + + + + + + + + + + + + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + RO:0002263 + acts_upstream_of + acts upstream of + + + + + + + + + + + + + c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. + RO:0002264 + affects + acts_upstream_of_or_within + acts upstream of or within + + + + + + + + + + RO:0002304 + external + causally_upstream_of,_positive_effect + causally_upstream_of,_positive_effect + causally upstream of, positive effect + + + + + + + + + + RO:0002305 + external + causally_upstream_of,_negative_effect + causally_upstream_of,_negative_effect + causally upstream of, negative effect + + + + + + + + + + + + + + + + + q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. + RO:0002314 + inheres_in_part_of + inheres in part of + + + + + + + + A relationship that holds via some environmental process + RO:0002320 + evolutionarily_related_to + evolutionarily related to + + + + + + + + A mereological relationship or a topological relationship + RO:0002323 + mereotopologically_related_to + mereotopologically related to + + + + + + + + + + + + + + + + + + RO:0002327 + enables + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + RO:0002328 + functionally_related_to + functionally related to + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + RO:0002329 + part_of_structure_that_is_capable_of + part of structure that is capable of + part of structure that is capable of + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + RO:0002331 + involved_in + involved in + + + + + + + + + + inverse of enables + RO:0002333 + enabled_by + enabled by + + + + + + + + + + + + inverse of regulates + RO:0002334 + external + regulated_by + regulated_by + regulated by + regulated by + + + + + + + + + inverse of negatively regulates + RO:0002335 + external + negatively_regulated_by + negatively_regulated_by + negatively regulated by + negatively regulated by + + + + + + + + + inverse of positively regulates + RO:0002336 + external + positively_regulated_by + positively_regulated_by + positively regulated by + positively regulated by + + + + + + + + + + inverse of has input + RO:0002352 + input_of + input of + + + + + + + + + + + inverse of upstream of + RO:0002404 + external + causally_downstream_of + causally_downstream_of + causally downstream of + causally downstream of + + + + + + + + + + + RO:0002405 + external + immediately_causally_downstream_of + immediately_causally_downstream_of + immediately causally downstream of + immediately causally downstream of + + + + + + + + This relation groups causal relations between material entities and causal relations between processes + RO:0002410 + causally_related_to + causally related to + + + + + + + + + + + p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + RO:0002411 + external + causally_upstream_of + causally_upstream_of + causally upstream of + causally upstream of + + + + + + + + + + p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + RO:0002412 + external + immediately_causally_upstream_of + immediately_causally_upstream_of + immediately causally upstream of + immediately causally upstream of + + + + + + + + + + + p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + RO:0002418 + external + affects + causally_upstream_of_or_within + causally_upstream_of_or_within + causally upstream of or within + + + + + + + + + + inverse of causally upstream of or within + RO:0002427 + external + causally_downstream_of_or_within + causally_downstream_of_or_within + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + RO:0002428 + involved_in_regulation_of + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + RO:0002429 + involved_in_positive_regulation_of + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + RO:0002430 + involved_in_negative_regulation_of + involved in negative regulation of + + + + + + + + + + + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + RO:0002431 + involved_in_or_involved_in_regulation_of + involved in or involved in regulation of + + + + + + + + + + + + + + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + RO:0002432 + enables activity in + is_active_in + is active in + + + + + + + + + + + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + RO:0002434 + in pairwise interaction with + interacts_with + interacts with + + + + + + + + + + An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. + RO:0002436 + molecularly_interacts_with + molecularly interacts with + + + + + + + + + RO:0002447 + phosphorylates + phosphorylates + + + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. + RO:0002448 + molecularly controls + directly_regulates_activity_of + directly regulates activity of + + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + RO:0002449 + molecularly decreases activity of + directly_negatively_regulates_activity_of + directly negatively regulates activity of + + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + RO:0002450 + molecularly increases activity of + directly_positively_regulates_activity_of + directly positively regulates activity of + + + + + + + + + + + + + + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + RO:0002479 + has_part_that_occurs_in + has part that occurs in + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + RO:0002500 + causal_agent_in_process + causal agent in process + + + + + + + + + + + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + RO:0002501 + causal_relation_between_processes + causal relation between processes + + + + + + + + RO:0002502 + depends_on + depends on + + + + + + + + + + + RO:0002506 + causal_relation_between_entities + causal relation between entities + + + + + + + + + + RO:0002559 + causally_influenced_by + causally influenced by + + + + + + + + + + + + + + + + + + + + + The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). + RO:0002566 + causally_influences + causally influences + + + + + + + + + + Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + RO:0002578 + directly_regulates + directly regulates + + + + + + + + + + + + + + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + RO:0002584 + has_part_structure_that_is_capable_of + has part structure that is capable of + + + + + + + + + + + A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. + RO:0002595 + causal_relation_between_material_entity_and_a_process + causal relation between material entity and a process + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + RO:0002596 + capable_of_regulating + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + RO:0002597 + capable_of_negatively_regulating + capable of negatively regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + RO:0002598 + capable_of_positively_regulating + capable of positively regulating + + + + + + + + + Inverse of 'causal agent in process' + RO:0002608 + external + process_has_causal_agent + process_has_causal_agent + process has causal agent + + + + + + + + + + Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + RO:0002629 + directly_positively_regulates + directly positively regulates + + + + + + + + + + Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + RO:0002630 + directly_negatively_regulates + directly negatively regulates + + + + + + + + + p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. + RO:0004007 + external + has_primary_input_or_output + has_primary_input_or_output + has primary input or output + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + RO:0004031 + enables_subfunction + enables subfunction + + + + + + + + + + + + + RO:0004032 + acts_upstream_of_or_within,_positive_effect + acts upstream of or within, positive effect + + + + + + + + + + + + + RO:0004033 + acts_upstream_of_or_within,_negative_effect + acts upstream of or within, negative effect + + + + + + + + + + + + + + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive + RO:0004034 + acts_upstream_of,_positive_effect + acts upstream of, positive effect + + + + + + + + + + + + + + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative + RO:0004035 + acts_upstream_of,_negative_effect + acts upstream of, negative effect + + + + + + + + + RO:0004046 + causally_upstream_of_or_within,_negative_effect + causally upstream of or within, negative effect + + + + + + + + + RO:0004047 + causally_upstream_of_or_within,_positive_effect + causally upstream of or within, positive effect + + + + + + + + + + + The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. + RO:0011002 + regulates_activity_of + regulates activity of + + + + + + + + + + + + + + + + + + + + + + + + + + + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + continuant + + + + + + + + + + + + + + + + + + + + + An entity that has temporal parts and that happens, unfolds or develops through time. + occurrent + + + + + + + + + + + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + independent continuant + + + + + + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + process + + + + + + + + + + + + + + + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable entity + + + + + + + + + + + + + + + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + specifically dependent continuant + + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity + + + + + + + + + anatomical entity + anatomical entity + + + + + + + + + connected anatomical structure + connected anatomical structure + + + + + + + + + + material anatomical entity + material anatomical entity + + + + + + + + + organism or virus or viroid + + + + + + + + + biological entity + + + + + + + + + + electron + + + + + + + + + molecular entity + + + + + + + + + + chemical entity + + + + + + + + + + biological role + + + + + + + + + + + + + + + group + + + + + + + + + nonmetal atom + + + + + + + + + phosphate + + + + + + + + + phosphoric acid derivative + + + + + + + + + + + + + + + phosphorus molecular entity + + + + + + + + + + + + + + + + + phosphorus atom + + + + + + + + + fundamental particle + + + + + + + + + oxoacid derivative + + + + + + + + + + + + + + + + + + + + + atom + + + + + + + + + + + + + + + atomic nucleus + + + + + + + + + + nucleon + + + + + + + + + nutrient + + + + + + + + + pnictogen + + + + + + + + + + + + + + + pnictogen molecular entity + + + + + + + + + main group element atom + + + + + + + + + p-block element atom + + + + + + + + + + + + + + + main group molecular entity + + + + + + + + + + + + + + + p-block molecular entity + + + + + + + + + macronutrient + + + + + + + + + + lepton + + + + + + + + + + baryon + + + + + + + + + fermion + + + + + + + + + subatomic particle + + + + + + + + + composite particle + + + + + + + + + hadron + + + + + + + + + nuclear particle + + + + + + + + + + + + + + + polyatomic entity + + + + + + + + + + phosphorus oxoacid derivative + + + + + + + + + phosphorus oxoacids and derivatives + + + + + + + + + heteroatomic molecular entity + + + + + + + + + role + + + + + + + + + physiological role + + + + + + + + + food component + + + + + + + + + + + + + + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + cell + cell + + + + + + + + + + + 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. + GO:0005554 + molecular function + molecular_function + GO:0003674 + + + + + + + + + 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. + molecular_function + + + + + 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 + + + + + + + + + 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. + Wikipedia:Enzyme + enzyme activity + molecular_function + GO:0003824 + + + + + + + catalytic activity + + + + + 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 + + + + + enzyme activity + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Binds to and stops, prevents or reduces the activity of an enzyme. + GO:0048551 + metalloenzyme inhibitor activity + molecular_function + GO:0004857 + enzyme inhibitor activity + + + + + Binds to and stops, prevents or reduces the activity of an enzyme. + GOC:ai + GOC:ebc + + + + + + + + + + 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). + GO:0008372 + NIF_Subcellular:sao1337158144 + cell or subcellular entity + cellular component + cellular_component + subcellular entity + GO:0005575 + + + + + + + + + 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. + cellular_component + + + + + 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:sao1337158144 + + + + + subcellular entity + NIF_Subcellular:nlx_subcell_100315 + + + + + + + + + + + + + + + A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. + https://github.com/geneontology/go-ontology/issues/17776 + Wikipedia:Intracellular + internal to cell + intracellular + protoplasm + cellular_component + nucleocytoplasm + protoplast + GO:0005622 + + + + + + intracellular anatomical structure + + + + + A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. + ISBN:0198506732 + + + + + nucleocytoplasm + GOC:mah + + + + + protoplast + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. + NIF_Subcellular:sao1702920020 + Wikipedia:Cell_nucleus + cell nucleus + horsetail nucleus + cellular_component + GO:0005634 + + + + + + + + + + + + + nucleus + + + + + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. + GOC:go_curators + + + + + horsetail nucleus + GOC:al + GOC:mah + GOC:vw + PMID:15030757 + + + + + + + + + + + + + + + + + + + + + The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). + GO:0005636 + Wikipedia:Nuclear_envelope + cellular_component + GO:0005635 + + + + nuclear envelope + + + + + The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). + ISBN:0198547684 + + + + + + + + + + + + + + + All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. + Wikipedia:Cytoplasm + cellular_component + GO:0005737 + + + + + + + + cytoplasm + + + + + All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. + ISBN:0198547684 + + + + + + + + + + + + + + + A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. + Wikipedia:Vacuole + cellular_component + vacuolar carboxypeptidase Y + GO:0005773 + + + + + + + + + + + + vacuole + + + + + A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. + GOC:mtg_sensu + ISBN:0198506732 + + + + + + + + + + + + + + + The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. + GO:0005904 + juxtamembrane + NIF_Subcellular:sao1663586795 + Wikipedia:Cell_membrane + cell membrane + cellular membrane + cytoplasmic membrane + plasmalemma + bacterial inner membrane + inner endospore membrane + plasma membrane lipid bilayer + cellular_component + GO:0005886 + + + + + + + + + + + plasma membrane + + + + + The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. + ISBN:0716731363 + + + + + cellular membrane + NIF_Subcellular:sao6433132645 + + + + + plasma membrane lipid bilayer + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. + Wikipedia:Cell_cortex + cellular_component + cell periphery + peripheral cytoplasm + GO:0005938 + + + + cell cortex + + + + + The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. + GOC:mah + ISBN:0815316194 + + + + + + + + + + + + + + + + + + + + + + + + + + The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). + phosphorus metabolism + biological_process + GO:0006793 + + phosphorus metabolic process + + + + + The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. + phosphate metabolism + biological_process + phosphate metabolic process + GO:0006796 + phosphate-containing compound metabolic process + + + + + The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + Binds to and increases the activity of an enzyme. + GO:0010577 + metalloenzyme activator activity + molecular_function + GO:0008047 + enzyme activator activity + + + + + Binds to and increases the activity of an enzyme. + GOC:dph + GOC:mah + GOC:tb + + + + + + + + + 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. + jl + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process + biological process + physiological process + biological_process + single organism process + single-organism process + GO:0008150 + + + + + + + + + + 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. + biological_process + + + + + 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 + + + + + + + + + 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. + jl + 2012-10-17T15:46:40Z + GO:0044236 + GO:0044710 + Wikipedia:Metabolism + metabolism + metabolic process resulting in cell growth + metabolism resulting in cell growth + multicellular organism metabolic process + biological_process + single-organism metabolic process + GO:0008152 + + + + + + Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. + metabolic process + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GO:0044252 + down regulation of metabolic process + down-regulation of metabolic process + downregulation of metabolic process + negative regulation of metabolism + negative regulation of organismal metabolism + inhibition of metabolic process + inhibition of organismal metabolic process + negative regulation of multicellular organismal metabolic process + biological_process + GO:0009892 + negative regulation of metabolic process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GO:0044253 + positive regulation of metabolism + up regulation of metabolic process + up-regulation of metabolic process + upregulation of metabolic process + activation of metabolic process + positive regulation of multicellular organismal metabolic process + positive regulation of organismal metabolism + stimulation of metabolic process + stimulation of organismal metabolic process + up-regulation of organismal metabolic process + biological_process + GO:0009893 + positive regulation of metabolic process + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GOC:go_curators + + + + + + + + + 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. + jl + 2012-12-11T16:56:55Z + GO:0008151 + GO:0044763 + GO:0050875 + cell physiology + cellular physiological process + cell growth and/or maintenance + biological_process + single-organism cellular process + GO:0009987 + + cellular process + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + biological_process + GO:0010562 + positive regulation of phosphorus metabolic process + + + + + Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + biological_process + GO:0010563 + negative regulation of phosphorus metabolic process + + + + + Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. + Wikipedia:Endomembrane_system + cellular_component + GO:0012505 + + + + + endomembrane system + + + + + A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. + GOC:lh + + + + + + + + + A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. + 2014-03-06T11:37:54Z + GO:0098589 + GO:0098805 + Wikipedia:Biological_membrane + membrane region + region of membrane + whole membrane + cellular_component + GO:0016020 + + + + + + + + + membrane + + + + + A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. + GOC:dos + GOC:mah + ISBN:0815316194 + + + + + + + + + + + + + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + Reactome:R-HSA-6788855 + Reactome:R-HSA-6788867 + phosphokinase activity + molecular_function + GO:0016301 + + + + + + + Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. + kinase activity + + + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + ISBN:0198506732 + + + + + Reactome:R-HSA-6788855 + FN3KRP phosphorylates PsiAm, RibAm + + + + + Reactome:R-HSA-6788867 + FN3K phosphorylates ketosamines + + + + + + + + + The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. + Wikipedia:Phosphorylation + biological_process + GO:0016310 + + + phosphorylation + + + + + The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. + ISBN:0198506732 + + + + + + + + + Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + EC:2.-.-.- + Reactome:R-HSA-1483089 + Reactome:R-HSA-1483186 + Reactome:R-HSA-5668414 + Reactome:R-HSA-8868783 + molecular_function + GO:0016740 + + + + + + + + + transferase activity + + + + + Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + ISBN:0198506732 + + + + + Reactome:R-HSA-1483089 + PE is converted to PS by PTDSS2 + + + + + Reactome:R-HSA-1483186 + PC is converted to PS by PTDSS1 + + + + + Reactome:R-HSA-5668414 + TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK + + + + + Reactome:R-HSA-8868783 + TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 + + + + + + + + + Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). + EC:2.7.-.- + molecular_function + GO:0016772 + + Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. + transferase activity, transferring phosphorus-containing groups + + + + + Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). + GOC:jl + ISBN:0198506732 + + + + + + + + + + + + + + + + + + + + + + + + + + Modulates the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + molecular_function + GO:0019207 + kinase regulator activity + + + + + Modulates the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Binds to and increases the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + molecular_function + GO:0019209 + kinase activator activity + + + + + Binds to and increases the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Binds to and stops, prevents or reduces the activity of a kinase. + molecular_function + GO:0019210 + kinase inhibitor activity + + + + + Binds to and stops, prevents or reduces the activity of a kinase. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + regulation of phosphate metabolism + biological_process + GO:0019220 + regulation of phosphate metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GO:0044246 + regulation of metabolism + regulation of multicellular organismal metabolic process + regulation of organismal metabolic process + biological_process + GO:0019222 + + regulation of metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GOC:go_curators + + + + + regulation of organismal metabolic process + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. + NIF_Subcellular:sao830981606 + cellular_component + intracellular membrane + GO:0031090 + organelle membrane + + + + + A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. + GOC:dos + GOC:mah + + + + + intracellular membrane + NIF_Subcellular:sao830981606 + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + regulation of cellular metabolism + biological_process + GO:0031323 + regulation of cellular metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + down regulation of cellular metabolic process + down-regulation of cellular metabolic process + downregulation of cellular metabolic process + negative regulation of cellular metabolism + inhibition of cellular metabolic process + biological_process + GO:0031324 + negative regulation of cellular metabolic process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + positive regulation of cellular metabolism + up regulation of cellular metabolic process + up-regulation of cellular metabolic process + upregulation of cellular metabolic process + activation of cellular metabolic process + stimulation of cellular metabolic process + biological_process + GO:0031325 + positive regulation of cellular metabolic process + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. + NIF_Subcellular:sao1687101204 + cellular_component + GO:0031965 + nuclear membrane + + + + + Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. + GOC:mah + GOC:pz + + + + + + + + + + + + + + + + + + + + + A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. + cellular_component + GO:0031967 + + organelle envelope + + + + + A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. + GOC:mah + GOC:pz + + + + + + + + + + + + + + + A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. + cellular_component + GO:0031975 + envelope + + + + + A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. + GOC:mah + GOC:pz + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + down regulation of kinase activity + down-regulation of kinase activity + downregulation of kinase activity + inhibition of kinase activity + kinase inhibitor + biological_process + GO:0033673 + negative regulation of kinase activity + + + + + + + + + + + https://github.com/geneontology/go-ontology/issues/13926 + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + up regulation of kinase activity + up-regulation of kinase activity + upregulation of kinase activity + kinase activator + stimulation of kinase activity + biological_process + GO:0033674 + positive regulation of kinase activity + + + + + + + + + + + https://github.com/geneontology/go-ontology/issues/13926 + + + + + Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. + biological_process + GO:0042325 + regulation of phosphorylation + + + + + Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. + GOC:jl + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. + down regulation of phosphorylation + down-regulation of phosphorylation + downregulation of phosphorylation + inhibition of phosphorylation + biological_process + GO:0042326 + negative regulation of phosphorylation + + + + + Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. + GOC:jl + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. + up regulation of phosphorylation + up-regulation of phosphorylation + upregulation of phosphorylation + activation of phosphorylation + stimulation of phosphorylation + biological_process + GO:0042327 + positive regulation of phosphorylation + + + + + Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. + GOC:jl + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the activity of an enzyme. + GO:0048554 + positive regulation of enzyme activity + up regulation of enzyme activity + up-regulation of enzyme activity + upregulation of enzyme activity + activation of enzyme activity + activation of metalloenzyme activity + positive regulation of metalloenzyme activity + stimulation of enzyme activity + stimulation of metalloenzyme activity + up regulation of metalloenzyme activity + up-regulation of metalloenzyme activity + upregulation of metalloenzyme activity + biological_process + GO:0043085 + + positive regulation of catalytic activity + + + + + Any process that activates or increases the activity of an enzyme. + GOC:ebc + GOC:jl + GOC:tb + GOC:vw + + + + + positive regulation of enzyme activity + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops or reduces the activity of an enzyme. + GO:0048553 + down regulation of enzyme activity + down-regulation of enzyme activity + down-regulation of metalloenzyme activity + downregulation of enzyme activity + negative regulation of enzyme activity + down regulation of metalloenzyme activity + downregulation of metalloenzyme activity + inhibition of enzyme activity + inhibition of metalloenzyme activity + negative regulation of metalloenzyme activity + biological_process + GO:0043086 + negative regulation of catalytic activity + + + + + Any process that stops or reduces the activity of an enzyme. + GOC:ebc + GOC:jl + GOC:tb + GOC:vw + + + + + negative regulation of enzyme activity + GOC:tb + + + + + + + + + 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. + NIF_Subcellular:sao1539965131 + Wikipedia:Organelle + cellular_component + GO:0043226 + + + + organelle + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + NIF_Subcellular:sao414196390 + membrane-enclosed organelle + cellular_component + GO:0043227 + membrane-bounded organelle + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + cellular_component + GO:0043229 + + intracellular organelle + + + + + Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + intracellular membrane-enclosed organelle + cellular_component + GO:0043231 + + intracellular membrane-bounded organelle + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + biological_process + GO:0043549 + regulation of kinase activity + + + + + + + + + + + https://github.com/geneontology/go-ontology/issues/13926 + + + + + Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:bf + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + jl + 2009-04-21T04:07:27Z + biological_process + GO:0044092 + negative regulation of molecular function + + + + + Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + GO:jl + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + jl + 2009-04-21T04:11:06Z + biological_process + GO:0044093 + positive regulation of molecular function + + + + + Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + GO:jl + + + + + + + + + + The chemical reactions and pathways by which individual cells transform chemical substances. + cellular metabolism + biological_process + intermediary metabolism + GO:0044237 + cellular metabolic process + + + + + The chemical reactions and pathways by which individual cells transform chemical substances. + GOC:go_curators + + + + + intermediary metabolism + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + down regulation of phosphate metabolic process + down-regulation of phosphate metabolic process + downregulation of phosphate metabolic process + negative regulation of phosphate metabolism + inhibition of phosphate metabolic process + biological_process + GO:0045936 + negative regulation of phosphate metabolic process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + positive regulation of phosphate metabolism + up regulation of phosphate metabolic process + up-regulation of phosphate metabolic process + upregulation of phosphate metabolic process + activation of phosphate metabolic process + stimulation of phosphate metabolic process + biological_process + GO:0045937 + positive regulation of phosphate metabolic process + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GO:0043119 + positive regulation of physiological process + up regulation of biological process + up-regulation of biological process + upregulation of biological process + activation of biological process + stimulation of biological process + biological_process + GO:0048518 + + positive regulation of biological process + + + + + Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GO:0043118 + down regulation of biological process + down-regulation of biological process + downregulation of biological process + negative regulation of physiological process + inhibition of biological process + biological_process + GO:0048519 + + negative regulation of biological process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GO:0051242 + positive regulation of cellular physiological process + up regulation of cellular process + up-regulation of cellular process + upregulation of cellular process + activation of cellular process + stimulation of cellular process + biological_process + GO:0048522 + positive regulation of cellular process + + + + + Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GO:0051243 + down regulation of cellular process + down-regulation of cellular process + downregulation of cellular process + negative regulation of cellular physiological process + inhibition of cellular process + biological_process + GO:0048523 + negative regulation of cellular process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GO:0050791 + regulation of physiological process + biological_process + GO:0050789 + + + + + regulation of biological process + + + + + Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GOC:ai + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the activity of an enzyme. + GO:0048552 + regulation of enzyme activity + regulation of metalloenzyme activity + biological_process + GO:0050790 + + regulation of catalytic activity + + + + + Any process that modulates the activity of an enzyme. + GOC:ai + GOC:ebc + GOC:vw + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GO:0051244 + regulation of cellular physiological process + biological_process + GO:0050794 + regulation of cellular process + + + + + Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are 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 + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + regulation of phosphorus metabolism + biological_process + GO:0051174 + regulation of phosphorus metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + transferase regulator + biological_process + GO:0051338 + + This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. + regulation of transferase activity + + + + + Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + EC:2.-.-.- + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + transferase activator + up regulation of transferase activity + up-regulation of transferase activity + upregulation of transferase activity + activation of transferase activity + stimulation of transferase activity + biological_process + GO:0051347 + + This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. + positive regulation of transferase activity + + + + + Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + down regulation of transferase activity + down-regulation of transferase activity + downregulation of transferase activity + transferase inhibitor + inhibition of transferase activity + biological_process + GO:0051348 + + This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. + negative regulation of transferase activity + + + + + Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + GOC:ai + + + + + + + + + Any process that modulates a measurable attribute of any biological process, quality or function. + regulation + biological_process + GO:0065007 + + + biological regulation + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + regulation of a molecular function + biological_process + GO:0065009 + + + + regulation of molecular function + + + + + Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + GOC:isa_complete + + + + + + + + + The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures. + mah + 2010-10-04T01:51:47Z + cellular_component + GO:0071944 + + cell periphery + + + + + The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + A membrane that is a (regional) part of the plasma membrane. + dos + 2014-03-06T11:55:32Z + region of plasma membrane + cellular_component + GO:0098590 + + Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass. + plasma membrane region + + + + + A membrane that is a (regional) part of the plasma membrane. + GOC:dos + + + + + + + + + + + + + + + + + + + + + + + + + + Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. + cellular_component + GO:0099568 + cytoplasmic region + + + + + Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. + GOC:dos + + + + + + + + + + + + + + + + + + + + + + + + + + + The complete extent of cell cortex that underlies some some region of the plasma membrane. + perimembrane region + cellular_component + GO:0099738 + cell cortex region + + + + + The complete extent of cell cortex that underlies some some region of the plasma membrane. + GOC:dos + + + + + + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + kmv + 2019-08-12T18:01:37Z + cellular_component + GO:0110165 + cellular anatomical entity + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + GOC:kmv + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + all + root + + + + + + + + + + + + + + + + Vira + Viridae + viruses + Viruses + + + + + + + + + + + + + + + + blue-green algae + blue-green bacteria + cyanophytes + Cyanophyceae + Cyanophycota + Cyanophyta + Oxygenic photosynthetic bacteria + Oxyphotobacteria + cyanobacteria + Cyanobacteria + + + + + + + + + + + + + + + biota + cellular organisms + + + + + + + + + + + + + + + Eumycetozoa Zopf, 1884 + Mycetozoa + mycetozoans + Eumycetozoa + + + + + + + + + + + + + + + Terrabacteria group + + + + + + + + + + + + + + + Cyanobacteria/Melainabacteria group + + + + + + + + + + + + + + + + + + + eubacteria + Monera + Procaryotae + Prokaryota + Prokaryotae + bacteria + prokaryote + prokaryotes + Bacteria + + + + + + + + + + + + + + + Dictyosteliaceae + + + + + + + + + + + + + + + Dictyosteliales + + + + + + + + + + + + + + + + + Archaebacteria + Mendosicutes + Metabacteria + Monera + Procaryotae + Prokaryota + Prokaryotae + archaea + prokaryote + prokaryotes + Archaea + + + + + + + + + + + + + + + Evosea + + + + + + + + + + + + + + + + + + Discoba + + + + + + + + + + + + + + + eucaryotes + eukaryotes + Eucarya + Eucaryotae + Eukarya + Eukaryotae + eukaryotes + Eukaryota + + + + + + + + + + + + + + + dictyostelid cellular slime molds + Dictyostelida + Dictyostelids + Dictyosteliida + cellular slime molds + Dictyostelia + + + + + + + + + + + + + + + + + + Chlorophyta/Embryophyta group + chlorophyte/embryophyte group + green plants + Chlorobionta + Chloroplastida + green plants + Viridiplantae + + + + + + + + + + + + + + + + Fungi/Metazoa group + opisthokonts + Opisthokonta + + + + + + + + + + + + + + + + Euglenozoans + Euglenozoa + + + + + + + + + + + + + + + + + Mycota + fungi + Fungi + + + + + + + + + + + + + + + Amoebozoa + + + + + + + + + + + + + + + + Hyalostilbum + Dictyostelium + + + + + + + + + + + + + + + + + + Jennifer I Deegan + 2009-08-10T10:46:43Z + Viridiplantae or Bacteria + + + + + + + + + + + + + + + + + The union of the taxa Viridiplantae and Cyanobacteria. + Jennifer Deegan + 2008-07-16T03:33:38Z + Viridiplantae or Cyanobacteria + + + + + The union of the taxa Viridiplantae and Cyanobacteria. + GOC:mtg_go-taxon + + + + + + + + + + + + + + + + + + jdeegan + 2008-07-24T11:56:07Z + Prokaryota + + + + + + + + + + + + + + + + + + jdeegan + 2008-08-14T10:45:59Z + Viridiplantae or Archaea or Bacteria + + + + + + + + + + + + + + + + + + Jennifer I Deegan + 2009-08-10T10:46:43Z + Viridiplantae or Bacteria or Euglenozoa + + + + + + + + + + + + + + + + + + Jennifer I Deegan + 2009-08-10T10:46:43Z + Viridiplantae or Euglenozoa + + + + + + + + + + + + + + + + + Jennifer Deegan + 2008-07-24T04:15:25Z + Fungi or Bacteria + + + + + + + + + + + + + + + + + + + Jennifer I Deegan + 2009-08-10T10:46:43Z + Viridiplantae or Bacteria or Euglenozoa or Archaea + + + + + + + + + + + + + + + + + Fungi or Dictyostelium + + + + + + + + + + + + + + + + + + Fungi or Bacteria or Archaea + + + + + + + + + + + + + + + + + The unikonts have a triple-gene fusion that is lacking in the bikonts. The three genes that are fused together in the unikonts but not bacteria or bikonts encode enzymes for synthesis of the pyrimidine nucleotides: carbamoyl phosphate synthase, dihydroorotase, aspartate carbamoyltransferase. This must have involved a double fusion, a rare pair of events, supporting the shared ancestry of Opisthokonta and Amoebozoa. + unikonts + Unikonta + + + + + The unikonts have a triple-gene fusion that is lacking in the bikonts. The three genes that are fused together in the unikonts but not bacteria or bikonts encode enzymes for synthesis of the pyrimidine nucleotides: carbamoyl phosphate synthase, dihydroorotase, aspartate carbamoyltransferase. This must have involved a double fusion, a rare pair of events, supporting the shared ancestry of Opisthokonta and Amoebozoa. + http://en.wikipedia.org/wiki/Unikont + + + + + + + + + + + + + + + + + archaea-eukaryota + Archaea or Eukaryota + + + + + + + + + + + + + + + + + cellular organisms or viruses + + + + + + + + + + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + quality + + + + + + + + + A quality which inheres in a continuant. + monadic quality of a continuant + multiply inhering quality of a physical entity + quality of a continuant + quality of a single physical entity + quality of an object + quality of continuant + monadic quality of an object + monadic quality of continuant + physical object quality + + + + + + + + + A monadic quality of continuant that exists at the cellular level of organisation. + cellular quality + + + + + + + + + A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. + nucleate quality + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. + anucleate + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. + binucleate + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. + mononucleate + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. + multinucleate + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. + nucleated + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + example to be eventually removed + + + + + + + + + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + failed exploratory term + + + + + + + + + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + + term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + core + + + + + + + + + placeholder removed + + + + + + + + + terms merged + + + + + + + + + term imported + + + + + + + + + term split + + + + + + + + + universal + + + + + + + + + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + defined class + + + + + + + + + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expression + + + + + + + + + Terms with this status should eventually replaced with a term from another ontology. + to be replaced with external ontology term + + + + + + + + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + requires discussion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/test_cli.py b/tests/test_cli.py new file mode 100644 index 0000000..6f8be6d --- /dev/null +++ b/tests/test_cli.py @@ -0,0 +1,49 @@ +import unittest + +from click.testing import CliRunner +from oaklib.selector import get_resource_from_shorthand, discovered_plugins, get_implementation_from_shorthand +from oakx_robot.robot_implementation import RobotImplementation, OWL_NOTHING +from oaklib.cli import search, main + +from tests import NUCLEUS + +TEST_OWL = 'tests/input/go-nucleus.owl' +TEST_UNSAT_OWL = 'tests/input/go-nucleus-unsat.owl' + +class TestCommandLineInterface(unittest.TestCase): + + def setUp(self) -> None: + runner = CliRunner(mix_stderr=False) + self.runner = runner + + def test_main_help(self): + result = self.runner.invoke(main, ['--help']) + out = result.stdout + err = result.stderr + self.assertIn('search', out) + self.assertIn('subset', out) + self.assertIn('validate', out) + self.assertEqual(0, result.exit_code) + + def test_main_ontology_is_satisfiable(self): + """ + Test main ontology is coherent + """ + result = self.runner.invoke(main, ['-i', f'robot:{TEST_OWL}', 'validate']) + out = result.stdout + err = result.stderr + #self.assertIn('search', out) + #self.assertIn('subset', out) + #self.assertIn('validate', out) + self.assertEqual(0, result.exit_code) + self.assertNotIn('ERROR', out) + + def test_unsatisfiable(self): + """ + Test main ontology is coherent + """ + result = self.runner.invoke(main, ['-i', f'robot:{TEST_UNSAT_OWL}', 'validate']) + out = result.stdout + err = result.stderr + self.assertEqual(0, result.exit_code) + self.assertIn('ERROR', out) diff --git a/tests/test_oakx_robot.py b/tests/test_oakx_robot.py new file mode 100644 index 0000000..4a942a6 --- /dev/null +++ b/tests/test_oakx_robot.py @@ -0,0 +1,53 @@ +import unittest + +from oaklib.selector import get_resource_from_shorthand, discovered_plugins, get_implementation_from_shorthand +from oakx_robot.robot_implementation import RobotImplementation, OWL_NOTHING + +from tests import NUCLEUS + +TEST_OWL = 'tests/input/go-nucleus.owl' +TEST_UNSAT_OWL = 'tests/input/go-nucleus-unsat.owl' + +class TestSqlDatabaseImplementation(unittest.TestCase): + + def setUp(self) -> None: + self.oi = get_implementation_from_shorthand(f'robot:{TEST_OWL}') + self.unsat_oi = get_implementation_from_shorthand(f'robot:{TEST_UNSAT_OWL}') + + def test_plugin(self): + plugins = discovered_plugins + self.assertIn('oakx_robot', plugins) + slug = f'robot:{TEST_OWL}' + r = get_resource_from_shorthand(slug) + self.assertEqual(r.implementation_class, RobotImplementation) + + def test_all_entities(self): + """ + Test basic functionality + """ + curies = list(self.oi.all_entity_curies()) + self.assertIn(NUCLEUS, curies) + + def test_main_ontology_is_satisfiable(self): + """ + Test main ontology is coherent + """ + assert self.oi.is_coherent() + unsats = list(self.oi.unsatisfiable_classes(exclude_nothing=False)) + self.assertEqual(1, len(unsats)) + self.assertCountEqual([OWL_NOTHING], unsats) + unsats = list(self.oi.unsatisfiable_classes()) + self.assertEqual([], unsats) + results = list(self.oi.validate()) + self.assertEqual([], results) + + def test_find_unsatisfiable_classes(self): + unsat_oi = self.unsat_oi + assert not unsat_oi.is_coherent() + unsats = list(unsat_oi.unsatisfiable_classes(exclude_nothing=True)) + self.assertEqual(1, len(unsats)) + self.assertCountEqual(['GO:0031965'], unsats) + results = list(unsat_oi.validate()) + self.assertEqual(1, len(results)) + result = results[0] + self.assertEqual('ERROR', str(result.severity))