to associate to associate is the capability to physically interact with another object. to immobilize is the capability to contain an entity in such a way that it may not move in space. to immobilize to be transported is the disposition to undergo motion. to be transported to serve as a template for DNA synthesis to serve as a template for DNA synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which a DNA molecule may be produced. to serve as a primer for DNA synthesis to serve as a primer for DNA synthesis is the capability of a short nucleic acid to bind to the 5' end of single strand of DNA template and help initiate DNA replication. to infect to infect is the capability to administer a disease-causing organism into some object. to serve as host is the capability to act in a manner that provides hospitality, serves to harbour an organism in or on itself. to serve as a host to regulate to regulate is to control or maintain the rate or speed of an object or process. to modulate to test a hypothesis to test a hypothesis is the capability to evaluate the truth value of a proposition based on gathered evidence. to change the activation energy is to change the amount of energy required to form or break a chemical bond. to change the activation energy to record is the capability to detect and transcribe information in a specified format on some physical medium. http://purl.obolibrary.org/obo/OBI_0000368 to record to be activated is the capability to be modified in such a way that the conformational change leads to an increase in another capability. to be activated to change appearance is the capability to change the visual attributes of an object. to change appearance to be translocated is the capability to be physically displaced from one location to another to be moved to be translocated to be actively interacted with is the capability to be manipulated by some device or agent. to be actively interacted with to interact with is a capabililty that involves another object. to interact with to positively charge is the capability to remove an electron or add a positively charged ion to a chemical entity. to positively charge to observe to observe is the capability to watch attentively. to be electronically modified is the capability of a chemical entity to have electrons added or removed. to be electronically modified to boil is the capability to increase the internal kinetic energy of a material such that it changes state from a solid or liquid to a gas. to boil to be compared is the capability of an object to be examined in order to note the similarities or differences among a set of objects. to be compared to be interacted with to be interacted with is the capability of an object to be target of a physical interaction. to modify conformation of is to affect the spatial arrangement of an entity. to modify conformation of to lose an electron to lose an electron is the capability of a chemical entity to lose an electron. to regulate the rate of formation to regulate the rate of formation is to modify the rate at which an object is formed. to translocate is the capability to displace oneself from one location to another. to translocate to move core disposition A disposition is the tendency of a capability to be exhibited under certain conditions or in response to a certain stimulus (trigger). solubility (to dissolve when put in fluid); fragility (disposition to break when dropped) to be a member of to be a member of is the capability to be considered a part of a collection. to supply energy is the capability to transfer energy from a source to a sink. to supply energy to combine is the capability to modify a set of objects in a way that the object is merged with another object to form a new object or substance. to combine to freeze http://purl.obolibrary.org/obo/OBI_0000375 to freeze is the capability to decrease the internal kinetic energy of a material such that it changes state from a gas or liquid to a solid. A mutual disposition is a disposition that simulataneously invokes another disposition when realized. mutual disposition en Contributors are those that engage in discussions in the context of SIO (in alphabetical order): sivaram arabandi christopher baker joachim baran jerven bolleman matthew brush alison callahan leonid chepelev kevin cohen melanie courtot geraint duck laura furlong elisa kendall tatsuya kushida luke mccarthy jim mccusker jose miguel cruz-toledo chris mungall robert hoehndorf simon jupp jin-dong kim dana klassen thomas luetteke james malone chris mungall david osumi-sutherland tazro ohta nuria queralt stephen reed alexandre riazanov matthias samwald robert stevens mark wilkinson karin verspoor natalia villanueva-rosales Michel Dumontier http://orcid.org/0000-0003-4727-9435 The semanticscience integrated ontology (SIO) provides a simple, integrated ontology (types, relations) for objects, processes and their attributes. This project provides foundational support for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects. website: http://semanticscience.org email: sio-ontology@googlegroups.com mailing list: http://groups.google.com/group/sio-ontology 2010-03-29 free to use,share,modify. modify with attribution [http://creativecommons.org/licenses/by/4.0/]. Semanticscience Integrated Ontology (SIO) http://www.jbiomedsem.com/content/5/1/14 sio http://semanticscience.org/resource/ general class inclusion axioms: 'is part of' some 'physical entity' subClassOf 'is located in' some 'physical entity' role chains: 'has capability' o 'is realized in' -> 'is participant in' http://sio.semanticscience.org 2026-10-12 sio.owl sio-subset-capability.owl capability A capability is a realizable entity whose basis lies in one or more parts or qualities and reflects possibility of an entity to behave in a specified way under certain conditions or in response to a certain stimulus (trigger). capability+ core to contain to contain is the capability to bound or constrain a physical entity in some site. to reduce is the capability to add an electron or an decrease in oxidation state of a chemical entity. to reduce to change energetically is the capability to change the energetic aspects of an object. to change energetically to filter is the capability to retain certain entities based on selected attribute(s) while allowing other entities to pass through. to filter to retrieve the capability to retrieve a (digitial/physical/mental) object from a location. to produce is the capability to create new objects to produce to assemble is the capability to combine entities together into a larger object that persists in time. to assemble to reduce the activation energy to activate to reduce the activation energy is to require a smaller amount of energy in order to form or break a chemical bond. to be covalently modified is the capability of a chemical entity to have bonds added or removed to be covalently modified to demagnify to demagnify is the capability to decrease the appearance of the size of an object. to transport to transport is the capability to displace a material from one location to another. to modify electronically to modify electronically is the capability to change the electronic properties of an object. to consume is the capability to internalize a material entity. to consume to fluoresce to fluoresce is to emit light as a result of absorbing light or other electromagnetic radiation. to extract is the capability to remove certain entities based on selected attribute(s) while allowing other entities to remain. to extract to heat is a capability to increase the internal kinetic energy of a material. to heat to serve as to serve as is the capability to act in a manner corresponding to some role. to examine to examine is the capability to make detailed observation. to describe is the capabilty to communicate facts about an entity. to describe to serve as a template for RNA synthesis to serve as a template for RNA synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which an RNA molecule may be produced. to disassemble to disassemble is to physically separate the parts of an object. to investigate is the capability to uncover facts. to investigate to magnify is the capability to increase the appearance of the size of an object. to magnify to breathe is the capability to inhale and exhale air into the body during respiration. to breathe to conformationally inhibit to conformationally inhibit is to modify the conformation of an entity in such a way that it functionally is reduced or inhibited. to serve as a template for molecular synthesis to serve as a template for molecular synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which another molecule may be produced. to characterize is the capability to classify the attributes or features of an entity against a reference classification. to characterize to maintain information the capability to maintain information such that it can be retrieved in the future. to be inhibited is the capability to be modified in such a way that the conformational change leads to an decrease in another capability. to be inhibited to modify is the capability to change some entity. to modify to disassociate is to cease or break association with some thing. to disassociate to ionize is the capability to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. to ionize to interact and to be interacted with to interact and to be interacted with is a mutual disposition of interacting objects. to modify oxidation state of to modify the oxidation state of is to change the number of electrons of a molecule, atom or ion. to change appearance is the capability to change the material composition of an object. to change materially to conformationally activate to conformationally activate is to modify the conformation of an entity in such a way that it becomes activated or functional. to identify is the capability to determine the identity of something. to identify to luminesce is to emit light through cold body radiation to luminesce to decrease the rate of formation to decrease the rate of formation is to regulate the rate of formation in a manner that decreases this rate relative to a reference process. to encode information the capability to encode information in a different representation to be combined to be combined is the capability to be modified in a way that the object is merged with another object to form a new object or substance. to actively interact with to actively interact with is the capability to interact with another entity in a way that requires physical contact. to inhibit to increase the activation energy is to require a larger amount of energy in order to form or break a chemical bond. to increase the activation energy the ability to reverse an encoding operation to decode information to be a part of to be a part of is the capability to be assembled into a larger structure that persists in time. to be cleaved to be cleaved is the capability to be modified in a way that splits one part of the object from the other. to gain a covalent bond is the capability of a chemical entity to have bonds added. to gain a covalent bond to oxidize is the capability to remove an electron or an increase in oxidation state of a chemical entity. to oxidize to be examined is the capability of an object to be observed in a detailed manner. to be examined to remove a covalent bond is the capability to covalently modify a chemical entity by removing a covalent bond. to remove a covalent bond to cleave to cleave is to split or sever an object along a natural line or grain. to emit to emit is the capability to release some physical entity (light, pollution, etc). A function is a capability that satisfies some agentive objective, or (evolutionary) optimization. function core dysfunction dysfunction is a capability to act in a manner that is abnormal or opposite to the object's typical function. to be observed is the capability of an object to be perceived. to be observed to inject is the capability to administer a substance into some object through its external barrier. to inject to lose a covalent bond to lose a covalent bond is the capability of a chemical entity to have bonds removed. to bind to is the capability to physically interact with another object through a set of non-covalent interactions. to bind to to ingest is the capability to take into the body by the mouth for digestion or absorption. to ingest to excite to excite is the capability to supply energy to a materila by bombarding it with energetic particles (e.g., photons). to negatively charge to negatively charge is the capability to add an electron or negatively charged ion to a chemical entity. to provide to provide is the capability to make available some object to another that requires it. to increase the rate of formation to increase the rate of formation is to regulate the rate of formation in a manner that increases this rate relative to a reference process. to measure to measure is the capability to obtain information about some entity by examining its attributes in relation to some reference metric. to gain an electron to gain an electron is the capability of a chemical entity to receive an electron. to separate to separate is the capability to i) distinguish some entities based on some attribute(s) and ii) subsequently physically displace them. to cause disease is the capability to materially change a biological object in that it functions abnormally. to cause disease to change spatially to change spatially is the capability to affect the physical movement of some entity. to be recorded to be recorded is the capability of an object to be observed in such a way that information about it can be transcribed in a specified format on some physical medium. to be conformationally changed is the capability to be modified in such a way that the object's conformation is changed. to be conformationally changed to be modified to be modified is the capability to be actively interacted with in such a way that it leads to a physical reconfiguration. to serve as a template for protein synthesis to serve as a template for protein synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which a protein may be produced. to add a covalent bond is the capability to covalently modify a chemical entity by adding a covalent bond. to add a covalent bond to reduce energy to reduce energy is the capability to remove energy from a source. to supply electricity to supply electricity is the capability to transfer electricity from a source to a sink. to covalently modify is to materially change a molecule by adding or removing covalent bonds between atoms. to covalently modify to passively interact with is the capability to interact with another entity in a way that does not require physical contact. to passively interact with to compare to compare is the capability to examine in order to note the similarities or differences among a set of objects. to distort to distort is the capability to change the appearance of an entity by some transformation. to store is the capability to place an object into a medium in which it can be retrieved in the future. to store http://purl.obolibrary.org/obo/OBI_0000387 to cool is the capability to decrease the internal kinetic energy of a material. to cool to be passively interacted with is the capability of an object to be observed. to be passively interacted with