editor preferred term example of usage has curation status definition editor note term editor alternative term definition source curator note imported from OBO foundry unique label elucidation temporal interpretation in_subset bearer of this apple is bearer of this red color this vase is bearer of this fragility 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 A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of http://purl.obolibrary.org/obo/ro/releases/2020-02-26/ro.owl bearer of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function http://purl.obolibrary.org/obo/ro/releases/2020-02-26/ro.owl has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality http://purl.obolibrary.org/obo/ro/releases/2020-02-26/ro.owl has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role http://purl.obolibrary.org/obo/ro/releases/2020-02-26/ro.owl has role contains http://purl.obolibrary.org/obo/ro/releases/2020-02-26/ro.owl contains 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. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl regulates (processual) false regulates ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl contributes to inverse of enables Chris Mungall http://purl.obolibrary.org/obo/ro/releases/2020-02-26/ro.owl enabled by a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall http://purl.obolibrary.org/obo/ro/releases/2020-02-26/ro.owl attached to (anatomical structure to anatomical structure) attached to Chris Mungall directly negatively regulates http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl directly inhibits (process to process) directly inhibits This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. http://purl.obolibrary.org/obo/ro/releases/2020-02-26/ro.owl causally related to c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl involved in regulation of Chris Mungall http://purl.obolibrary.org/obo/ro/releases/2020-02-26/ro.owl participates in a biotic-biotic interaction with a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel http://purl.obolibrary.org/obo/ro/releases/2020-02-26/ro.owl Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces 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. http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl continuant An entity that has temporal parts and that happens, unfolds or develops through time. http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl 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. http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl independent continuant An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl process http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl quality 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. http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl specifically dependent continuant http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl biological entity http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl biological_process http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl interspecies interaction between organisms http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl response to stimulus http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl multi-organism process http://purl.obolibrary.org/obo/ro/releases/2020-07-21/ro.owl multi-organism behavior a biofilm development stage where sections of the biofilm break off from the colony. This may due to external factors or internal signalling The external bulk fluid (also known as bulk phase and bulk liquid), is the external liquid that acts as a transportaion system for external biological and chemicals to and from the biofilm Flow rate is the amount of volume of fluid flowing through an area each second. In the context of the biofilm, it can be used to estimate the influx of nutriends and microorganisms to and from the biofilm. The internal bulk fluid (also known as bulk phase and bulk liquid), is the internal liquid that acts as a transportaion system within the biofilm to transport chemicals and organisms Shear force is unaligned forces pushing one object in one direction. In the context of the biofilm, it refers to the force that may cause the expansion of biofilm or aid in dispersal. A biofilm development stage where the cells interact and attach to neighbouring cells through specialized molecules of the cell surface adhesins Adhesins are components or appendages of a microorganisms that exist on the surface of the cell that facilitate the adhesion to other cells or to surfaces aeration Aeration is the force that brings airborne microorganisms and chemicals such as oxygen to the biofilm antibiotic_resistance Antibiotic resistance is a quality of a microorganism to tolerate or resistant to the effects of antimicrobial medication antimicrobial_resistance Antimicrobial resistance is a quality of a organism to tolerate or resistant to the effects of harmful microbes. attachment A biofilm development stage where planktnic or airborne bacteria adhere to a biotic or abiotic surface. autoaggregation Autoaggregation is the process of the formation of bacterial clumps. The process is observed to aid in the formation of biofilms on solid material or particles within a liquid medium autoinducers Autoinducers are signaling molecules by organisms in response to changes in cell-population density. biofilm_development_stage An stage within the life cycle of a biofilm biofilm_formation Biofilm formation is the process of forming a biofilm biological_object_property A property a biological entity may inherit biomass Biomass is the total mass of an organism or colony in a give narea or volume biosurfactants Biosurfactants are chemical molecules produced by organisms to maintain chennels between biofilm structures and aid in the dispersal of cells from biofilms. carbon cell_charge cell_density The density of the population of the cell in a given area or volume chemical_entity chemical_uptake Chemical uptake the process of absorbing and adsorbing nutrients to the biofilm coaggregation Coaggregation is a process by which bateria become attached to one another via specific molecules detachment Detachment is the process of biofilm disperse to form new colonies dissolved_oxygen environmental_property A property of the external environment of the biofilm extracellular_polymeric_substances Extracellular polumeric substances (EPS) are biopolymers that forms a matrix that are embedded with biofilm microorganisms. fibrinogen Fibrinogens are proteins that aid in the binding of microorganisms to surfaces which promotes biofilm formation gas gene_expression Gene expression is the process by which information from a gene is used to synthesis a functional gene product growth_rate Growth rate is the quality of the rate of growth of microorganisms in a biofilm hibernation_promoting_factor Hibernation promoting factors are chemical substances that promotes subpopulations of the biofilm to remain dormant and protect the subpopulation from ribosomal loss. Typically these subpopulations are highly tolerant to antibiotics. hydrophilicity Hydrophilicity is the quality of having a tendency to mix, dissolve or be wetted by water hydrophobicity Hydrophilicity is the quality of having a tendency to repel water, more specifically, the lack of attraction of water. iron liquid maturation_I A biofilm development stage where cell division and recruiment of new bacteria allows bacterial population to increase. Formation of biofilm structures are formed. maturation_II A biofilm development stage where the microbial diversity increases while the rate of cell division decreases. monolayer_microcolony A biofilm development stage where a single layer of bacteria has formed into a matrix of a microcolony nitrogen nutrient_level organism_uptake Organism uptake the process of microorganisms to enter the biofilm organisms An individual animal, plant, or single-celled life form pH permeability Permeability is a quality of material or organism that allows liquid ot gasses to pass through. In the context of the biofilm, it could refered to the permeability of the biofilm or the permeability of the membrane of a specific individual cell persister Persisters are cells that are produced by biofilms to remain dormant and are highly recalcitrant phase_of_matters phosphorus physical_object_property A property in which a physical object may inherit potassium quorem_sensing Quorem sensing is the process by which microorganisms communicate with each other through signaling molecules to regulate gene expression quorum_quenching Quorum quenching is the process by which quorem sensing communication is inhibited ribosome_modulation_factor Ribosome modulation factors are chemical substances that converts active ribosomes into inactive ribosomes to aid in the protection of dormant subpopulations of biofilms. These work along hibernation promoting factors to protect the subpopulation of biofilms that are highly tolerant to antibiotics. solid surface_substrate Surface substrate is the spatial location of where a biofilm may form survival_factors Survival factors are factors that increase survivability of the biofilm temperature trace_minerals virulence_factors Virulence factors are chemical substances produced by the biofilm to increase the long-term survivability of the biofilm. vitamins first order logic expression