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Relationship type ontology

A brief description of the ontology is found on the ontologies page.

  • Relationship

    • Observation
      • Temporal
        • COOCCUR

          Use as COOCCUR(arg1,arg2,...,argN). The arguments are events that occur together.

        • COEXPRESS

          Use as COEXPRESS(arg1,arg2,...,argN). The arguments (genes) are expressed together.

      • Spatial
        • COPRECIPITATE

          Use as COPRECIPITATE(arg1,arg2,...,argN) where the arguments are proteins. The arguments precipitate as a complex.

        • PRESENCE

          Use as PRESENCE(arg1,arg2). An observation that arg1 is present when arg2 occurs. Experimental setups or the presence in a cell are not included.

        • COLOCALIZE

          Use as COLOCALIZE(arg1,arg2,...,argN). The arguments (proteins) are found in the same place (or move to the same place) at the same time.

        • ABSENCE

          Use as ABSENCE(arg1,arg2). An observation that arg1 is absent when arg2 occurs. Experimental setups or the absence in a cell are not included.

      • COREGULATE

        Use as COREGULATE(arg1,arg2,...,argN). The arguments are coregulated.

      • CORELATE

        Use as CORELATE(arg1,arg2,...,argN). A general, unspecified co-relation between the arguments.

    • PART_OF
      • Collection:Member
        • MEMBER

          Use as MEMBER(arg1,arg2). A member (arg2) belongs to a collection (arg1). For example a protein belongs to a protein family.

      • Object:Component
        • SUBSTRUCTURE

          Use as SUBSTRUCTURE(arg1,arg2). A component (arg2) is a part of a structure other than a complex (arg1). For example a polymer contains many monomers.

        • F-CONTAIN

          Use as F-CONTAIN(arg1,arg2). Like CONTAIN but arg1 is a fusion protein.

        • MUTUALCOMPLEX

          Use as MUTUALCOMPLEX(arg1,arg2,...,argN). Like BIND but the arguments may form several complexes, each complex having a different composition.

        • CONTAIN

          Use as CONTAIN(arg1,arg2). A component (arg2) is a part of a complex (arg1).

    • IS_A
      • Similarity
        • Functional-Similarity
          • FNSIMILAR

            Use as FNSIMILAR(arg1,arg2,...,argN). A functional similarity. The arguments (proteins) have similar functions. Use only if functional similarity cannot be expressed through interactions with other entities.

        • Physical-Similarity
          • STSIMILAR

            Use as STSIMILAR(arg1,arg2,...,argN). A structural similarity. The arguments (proteins) have similar structures. For example two proteins have a domain in common.

          • SQSIMILAR

            Use as SQSIMILAR(arg1,arg2,...,argN). A sequence similarity. The arguments (genes/proteins) have similar sequences.

        • SIMILAR

          Use as SIMILAR(arg1,arg2,...,argN). A general, unspecified similarity between the arguments.

      • Equality
        • ENCODE

          Use as ENCODE(arg1,arg2). A gene (arg1) produces an mRNA or a protein (arg2).

        • EQUAL

          Use as EQUAL(arg1,arg2). Only for aliases.

        • COREFER

          Use as COREFER(arg1,arg2). An anaphoric equality where arg1 is the anaphora and arg2 the referent.

    • Causal
      • Condition
        • PREVENT

          Use as PREVENT(arg1,arg2). The arg1 prevents arg2 from happening. The condition for using this predicate is that arg2 must not have been happening before. See also Full-Stop.

        • CONDITION

          Use as CONDITION(arg1,arg2). The arg1 is required (but is not necessarily sufficient) for the arg2.

        • MUTUALCONDITION

          Use as MUTUALCONDITION(arg1,arg2). Consider as non-directional CONDITION. MUTUALCONDITION(a,b) translates to CONDITION(a,b) CONDITION(b,a).

      • Change
        • Dynamics
          • Start
            • INITIATE

              Use as INITIATE(arg1,arg2) where arg2 is a process. This predicate is used when arg2 has not been happening and is now started by arg1. See also HALT and STIMULATE.

          • Negative
            • DOWNREGULATE

              Use as DOWNREGULATE(arg1,arg2) where arg2 is a gene (or more specifically gene expression). The arg1 decreases the expression level (i.e. the rate at which the product is produced) of a gene (arg2). See also UPREGULATE and REGULATE.

            • SUPPRESS

              Use as SUPPRESS(arg1,arg2) where arg2 is a process. The arg1 decreases the speed of the process (arg2). See also STIMULATE and CONTROL.

            • INHIBIT

              Use as INHIBIT(arg1,arg2) where arg2 is a protein. The arg1 decreases the activity (e.g. enzymatic activity) of the protein (arg2). See also ACTIVATE, MODULATE, and INACTIVATE.

          • Unspecified
            • REGULATE

              Use as REGULATE(arg1,arg2). A general regulatory relationship where arg2 is a gene expression. See also UPREGULATE and DOWNREGULATE.

            • CONTROL

              Use as CONTROL(arg1,arg2). A general regulatory relationship where arg2 is a process. See also STIMULATE and SUPPRESS.

            • MODULATE

              Use as MODULATE(arg1,arg2). A general regulatory relationship where arg2 is a protein. See also ACTIVATE and INHIBIT.

          • Positive
            • CATALYZE

              Use as CATALYZE(arg1,arg2). The arg1 (an enzyme) catalyzes arg2 (a reaction).

            • UPREGULATE

              Use as UPREGULATE(arg1,arg2) where arg2 is a gene (or more specifically gene expression). The arg1 increases the expression level (i.e. the rate at which the product is produced) of the gene (arg2). See also DOWNREGULATE and REGULATE.

            • STIMULATE

              Use as STIMULATE(arg1,arg2) where arg2 is a process. The arg1 increases the speed of the process (arg2). See also SUPPRESS and CONTROL.

            • MEDIATE

              Use as MEDIATE(arg1,arg2). The arg1 mediates arg2 but does not necessarily regulate it.

            • ACTIVATE

              Use as ACTIVATE(arg1,arg2) where arg2 is a protein. The arg1 increases the activity (e.g. enzymatic activity) of a protein (arg2). See also INHIBIT and MODULATE.

          • Full-Stop
            • HALT

              Use as HALT(arg1,arg2) where arg2 is a process. This predicate is used when arg2 has been happening and is now stopped by arg1. See also INITIATE and SUPPRESS.

            • INACTIVATE

              Use as INACTIVATE(arg1,arg2) where arg2 is a protein or a gene. This predicate is used when a gene expression or protein activity (arg2) is decreased to essentially zero by arg1. This can be considered as an extremely strong downregulation or inhibition. See also DOWNREGULATE and INHIBIT.

        • Physical
          • Modification
            • Removal
              • REMOVE

                Use as REMOVE(arg1,arg2) where arg2 is a protein. A general relationship in which arg1 modifies arg2 by removing a (small) molecule from it. See also ADD.

              • DEPHOSPHORYLATE

                Use as DEPHOSPHORYLATE(arg1,arg2) where arg2 is a protein. A phosphate group is removed from arg2 by arg1. See also PHOSPHORYLATE.

            • Addition
              • ACETYLATE

                Use as ACETYLATE(arg1,arg2) where arg2 is a protein. An acetyl group is added to arg2 by arg1.

              • ADD

                Use as ADD(arg1,arg2) where arg2 is a protein. A general relationship in which arg1 modifies arg2 by adding a (small) molecule to it. See also REMOVE.

              • PHOSPHORYLATE

                Use as PHOSPHORYLATE(arg1,arg2) where arg2 is a protein. A phosphate group is added to arg2 by arg1. See also DEPHOSPHORYLATE.

            • MODIFY

              Use as MODIFY(arg1,arg2). An unspecified modification where arg1 modifies arg2.

          • Break-Down
            • UNBIND

              Use as UNBIND(arg1,arg2). arg1 and arg2 dissociate from each other. See also BIND.

            • CLEAVE

              Use as CLEAVE(arg1,arg2) where arg2 is a a protein or a gene. arg2 is physically cleaved into two by arg1.

            • DISASSEMBLE

              Use as DISASSEMBLE(arg1,arg2). A general relationship for describing catabolic reactions where arg1 degrades arg2. See also ASSEMBLE.

            • DEPOLYMERIZE

              Use as DEPOLYMERIZE(arg1,arg2). Components (monomers) of arg2 (a polymer) are cleaved/removed from arg2 by arg1. See also POLYMERIZE.

            • DISRUPT

              Use as DISRUPT(arg1,arg2) where arg2 is a complex. This predicate is used when arg1 makes arg2 to dissociate to its components. See also BIND.

          • Assembly
            • ATTACH

              Use as ATTACH(arg1,arg2,...,argN). A general relationship for describing anabolic reactions where the arguments join together to form a new structure.. See also ASSEMBLE.

            • ASSEMBLE

              Use as ASSEMBLE(arg1,arg2). A general relationship for describing anabolic reactions where arg1 synthesises arg2. See also DISASSEMBLE.

            • CROSS-LINK-AP

              Use as CROSS-LINK-AP(arg1,arg2). The arg1 causes the arg2 to cross-link.

            • CROSS-LINK

              Use as CROSS-LINK(arg1,arg2). arg1 and arg2 are proteins and are covalently bound. See also BIND.

            • BIND

              Use as BIND(arg1,arg2,...,argN). Non-covalent binding (i.e. formation of a complex, association) between the arguments. Each argument is present in the same complex but there are not necessarily all pairwise contacts between the arguments. See also CROSS-LINK and DISRUPT.

            • POLYMERIZE

              Use as POLYMERIZE(arg1,arg2). The arg1 joins multiple arg2 (monomers) covalently together to form a chain (a polymer). See also DEPOLYMERIZE.

        • Amount
          • DECREASE

            Use as DECREASE(arg1,arg2). The absolute amount of arg2 is decreased by arg1. See also INCREASE.

          • INCREASE

            Use as INCREASE(arg1,arg2). The absolute amount of arg2 is increased by arg1. See also DECREASE.

        • Location
          • LOCALIZE

            Use as LOCALIZE(arg1,arg2). This predicate is used when arg1 causes the position of arg2 to change. See also LOCALIZE-TO.

          • LOCALIZE-TO

            Use as LOCALIZE-TO(arg1,arg2). This predicate is used when arg1 changes its position to arg2. See also LOCALIZE.

        • AFFECT

          Use as AFFECT(arg1,arg2). A general directional relationship where arg1 causes a change in arg2. See also INTERACT.

        • INTERACT

          Use as INTERACT(arg1,arg2,...,argN). A general non-directional relationship where each argument causes a change in the other arguments . See also AFFECT.

        • MUTUAL-AFFECT

          Use as MUTUAL-AFFECT(arg1,arg2). Consider as non-directional AFFECT. MUTUAL-AFFECT(a,b) translates to AFFECT(a,b) AFFECT(b,a).

      • PARTICIPATE

        Use as PARTICIPATE(arg1,arg2). The arg1 is involved in the arg2 but is not alone sufficient to cause it.

      • CAUSE

        Use as CAUSE(arg1,arg2). A general directional causal relationship. The arg1 is the cause for the arg2.

      • XOR

        Use as XOR(arg1,arg2). The arguments are mutually exclusive.

    • HUMANMADE

      Use as HUMANMADE(arg1,arg2). This predicate is used when the relationship is forced or caused by human intervention. The actual type of the relationship is not stated but is one of the types in this ontology.

    • NOT

      Use as NOT(arg1) where arg1 is a relationship. This predicate is used when a relationship is explicitly stated not to be true.

    • RELATE

      Use as RELATE(arg1,arg2). A general, unspecified, non-directional relationship. This predicate is used when no details of the relationship is known.

    • REL-ENT

      Use as REL-ENT(arg1,arg2). This predicate is used when an unnamed entity (arg1) refers to that of a named entity (arg2). E.g. REL-ENT("activation","sphingomyelinase") means that "activation" is "activation of sphingomyelinase".