stat-ontology@googlegroups.com 1.3 http://creativecommons.org/licenses/by/3.0/ Orlaith Burke Statistical Method, Design of Experiment, Plots, Statistical Model STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots. Camille Maumet (http://orcid.org/0000-0002-6290-553X) Alejandra Gonzalez-Beltran (http://orcid.org/0000-0003-3499-8262) https://github.com/ISA-tools/stato/issues Thomas Nichols (http://orcid.org/0000-0002-4516-5103) Philippe Rocca-Serra (http://orcid.org/0000-0001-9853-5668) Nolan Nichols (http://orcid.org/0000-0003-1099-3328) STATO: the statistical methods ontology This Ontology is distributed under a Creative Commons Attribution License Chris Mungall (http://orcid.org/0000-0002-6601-2165) http://stato-ontology.org/ 0 true true true true This statement can actually be inferred from 'plan specification', because 'independent variable specification' is a subclass of 'is part of' some 'plan specification' true true true true true true true 0 5 true true true -1 1 2 1 0 0 true true true true 0 0 true true 0 0 http://purl.obolibrary.org/obo/BFO_0000001 entity http://purl.obolibrary.org/obo/BFO_0000001 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000001 entity http://purl.obolibrary.org/obo/BFO_0000002 continuant http://purl.obolibrary.org/obo/BFO_0000002 a heart http://purl.obolibrary.org/obo/BFO_0000002 a person http://purl.obolibrary.org/obo/BFO_0000002 a symphony orchestra http://purl.obolibrary.org/obo/BFO_0000002 the color of a tomato http://purl.obolibrary.org/obo/BFO_0000002 the disposition of blood to coagulate http://purl.obolibrary.org/obo/BFO_0000002 the lawn and atmosphere in front of our building http://purl.obolibrary.org/obo/BFO_0000002 the mass of a cloud http://purl.obolibrary.org/obo/BFO_0000002 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/BFO_0000002 endurant http://purl.obolibrary.org/obo/BFO_0000002 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000002 continuant http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000003 a surgical operation as processual context for a nosocomical infection http://purl.obolibrary.org/obo/BFO_0000003 the life of an organism http://purl.obolibrary.org/obo/BFO_0000003 the most interesting part of Van Gogh's life http://purl.obolibrary.org/obo/BFO_0000003 the spatiotemporal context occupied by a process of cellular meiosis http://purl.obolibrary.org/obo/BFO_0000003 the spatiotemporal region occupied by the development of a cancer tumor http://purl.obolibrary.org/obo/BFO_0000003 An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants. http://purl.obolibrary.org/obo/BFO_0000003 perdurant http://purl.obolibrary.org/obo/BFO_0000003 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000004 a chair http://purl.obolibrary.org/obo/BFO_0000004 a heart http://purl.obolibrary.org/obo/BFO_0000004 a leg http://purl.obolibrary.org/obo/BFO_0000004 a person http://purl.obolibrary.org/obo/BFO_0000004 a symphony orchestra http://purl.obolibrary.org/obo/BFO_0000004 an organism http://purl.obolibrary.org/obo/BFO_0000004 the bottom right portion of a human torso http://purl.obolibrary.org/obo/BFO_0000004 the lawn and atmosphere in front of our building http://purl.obolibrary.org/obo/BFO_0000004 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/BFO_0000004 substantial entity http://purl.obolibrary.org/obo/BFO_0000004 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000005 dependent continuant http://purl.obolibrary.org/obo/BFO_0000005 A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. http://purl.obolibrary.org/obo/BFO_0000005 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000005 dependent continuant http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000006 parts of the sum total of all space in the universe http://purl.obolibrary.org/obo/BFO_0000006 the sum total of all space in the universe http://purl.obolibrary.org/obo/BFO_0000006 A continuant that is neither bearer of quality entities nor inheres in any other entities. http://purl.obolibrary.org/obo/BFO_0000006 All instances of continuant [snap:Continuant] are spatial entities, that is, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself. http://purl.obolibrary.org/obo/BFO_0000006 An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe, a designated individual, which is thus itself a spatial region [snap:SpatialRegion]. http://purl.obolibrary.org/obo/BFO_0000006 Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO, the class site [snap:Site] allows for a so-called relational view of space, that is to say, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities, they are nevertheless spatial entities. http://purl.obolibrary.org/obo/BFO_0000006 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000007 process http://purl.obolibrary.org/obo/BFO_0000007 the life of an organism http://purl.obolibrary.org/obo/BFO_0000007 the process of cell-division http://purl.obolibrary.org/obo/BFO_0000007 the process of sleeping http://purl.obolibrary.org/obo/BFO_0000007 A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities. http://purl.obolibrary.org/obo/BFO_0000007 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000007 process http://purl.obolibrary.org/obo/BFO_0000009 two dimensional region http://purl.obolibrary.org/obo/BFO_0000009 the surface of a cube-shaped part of space http://purl.obolibrary.org/obo/BFO_0000009 the surface of a rectilinear planar figure-shaped part of space http://purl.obolibrary.org/obo/BFO_0000009 the surface of a sphere-shaped part of space http://purl.obolibrary.org/obo/BFO_0000009 A spatial region with two dimensions. http://purl.obolibrary.org/obo/BFO_0000009 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000009 two dimensional region http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000016 the disposition of a patient with a weakened immune system to contract disease http://purl.obolibrary.org/obo/BFO_0000016 the disposition of a vase to brake if dropped http://purl.obolibrary.org/obo/BFO_0000016 the disposition of blood to coagulate http://purl.obolibrary.org/obo/BFO_0000016 the disposition of metal to conduct electricity http://purl.obolibrary.org/obo/BFO_0000016 the disposition of vegetables to decay when not refrigerated http://purl.obolibrary.org/obo/BFO_0000016 A realizable entity that essentially causes a specific process or transformation in the object in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object has the disposition D to (transform, initiate a process) R under conditions C. http://purl.obolibrary.org/obo/BFO_0000016 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000017 the disposition of blood to coagulate http://purl.obolibrary.org/obo/BFO_0000017 the disposition of metal to conduct electricity http://purl.obolibrary.org/obo/BFO_0000017 the function of the reproductive organs http://purl.obolibrary.org/obo/BFO_0000017 the role of being a doctor http://purl.obolibrary.org/obo/BFO_0000017 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. http://purl.obolibrary.org/obo/BFO_0000017 If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized. http://purl.obolibrary.org/obo/BFO_0000017 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000018 zero dimensional region http://purl.obolibrary.org/obo/BFO_0000018 a point http://purl.obolibrary.org/obo/BFO_0000018 A spatial region with no dimensions. http://purl.obolibrary.org/obo/BFO_0000018 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000018 zero dimensional region http://purl.obolibrary.org/obo/BFO_0000019 quality http://purl.obolibrary.org/obo/BFO_0000019 the ambient temperature of air http://purl.obolibrary.org/obo/BFO_0000019 the circumference of a waist http://purl.obolibrary.org/obo/BFO_0000019 the color of a tomato http://purl.obolibrary.org/obo/BFO_0000019 the mass of a piece of gold http://purl.obolibrary.org/obo/BFO_0000019 the shape of a nose http://purl.obolibrary.org/obo/BFO_0000019 the weight of a chimpanzee http://purl.obolibrary.org/obo/BFO_0000019 A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property). http://purl.obolibrary.org/obo/BFO_0000019 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000019 quality http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/BFO_0000020 the color of a tomato http://purl.obolibrary.org/obo/BFO_0000020 the disposition of fish to decay http://purl.obolibrary.org/obo/BFO_0000020 the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc. http://purl.obolibrary.org/obo/BFO_0000020 the liquidity of blood http://purl.obolibrary.org/obo/BFO_0000020 the mass of a cloud http://purl.obolibrary.org/obo/BFO_0000020 the role of being a doctor http://purl.obolibrary.org/obo/BFO_0000020 the smell of mozzarella http://purl.obolibrary.org/obo/BFO_0000020 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/BFO_0000020 mode http://purl.obolibrary.org/obo/BFO_0000020 property http://purl.obolibrary.org/obo/BFO_0000020 trope http://purl.obolibrary.org/obo/BFO_0000020 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/BFO_0000023 role http://purl.obolibrary.org/obo/BFO_0000023 the role of a biological grandfather as legal guardian in the context of a system of laws http://purl.obolibrary.org/obo/BFO_0000023 the role of a chemical compound in an experiment http://purl.obolibrary.org/obo/BFO_0000023 the role of a patient relative as defined by a hospital administrative form http://purl.obolibrary.org/obo/BFO_0000023 the role of a person as a surgeon http://purl.obolibrary.org/obo/BFO_0000023 the role of a student in a university http://purl.obolibrary.org/obo/BFO_0000023 the role of a woman as a legal mother in the context of system of laws http://purl.obolibrary.org/obo/BFO_0000023 the role of ingested matter in digestion http://purl.obolibrary.org/obo/BFO_0000023 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. http://purl.obolibrary.org/obo/BFO_0000023 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000023 role http://purl.obolibrary.org/obo/BFO_0000026 one dimensional region http://purl.obolibrary.org/obo/BFO_0000026 an edge of a cube-shaped part of space http://purl.obolibrary.org/obo/BFO_0000026 the part of space that is a line stretching from one end of absolute space to the other http://purl.obolibrary.org/obo/BFO_0000026 A spatial region with one dimension. http://purl.obolibrary.org/obo/BFO_0000026 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000026 one dimensional region http://purl.obolibrary.org/obo/BFO_0000028 three dimensional region http://purl.obolibrary.org/obo/BFO_0000028 a cube-shaped part of space http://purl.obolibrary.org/obo/BFO_0000028 a sphere-shaped part of space http://purl.obolibrary.org/obo/BFO_0000028 A spatial region with three dimensions. http://purl.obolibrary.org/obo/BFO_0000028 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000028 three dimensional region http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant http://purl.obolibrary.org/obo/BFO_0000031 a certain PDF file that exists in different and in several hard drives http://purl.obolibrary.org/obo/BFO_0000031 A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. http://purl.obolibrary.org/obo/BFO_0000031 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant http://purl.obolibrary.org/obo/BFO_0000034 function http://purl.obolibrary.org/obo/BFO_0000034 the digestive function of the stomach to nutriate the body http://purl.obolibrary.org/obo/BFO_0000034 the function of a birth canal to enable transport http://purl.obolibrary.org/obo/BFO_0000034 the function of a computer program to compute mathematical equations http://purl.obolibrary.org/obo/BFO_0000034 the function of a hammer to drive in nails http://purl.obolibrary.org/obo/BFO_0000034 the function of a judge in a court of law http://purl.obolibrary.org/obo/BFO_0000034 the function of an automobile to provide transportation http://purl.obolibrary.org/obo/BFO_0000034 the function of reproduction in the transmission of genetic material http://purl.obolibrary.org/obo/BFO_0000034 the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc. http://purl.obolibrary.org/obo/BFO_0000034 A realizable entity the manifestation of which is an essentially end-directed activity of a continuant entity in virtue of that continuant entity being a specific kind of entity in the kind or kinds of contexts that it is made for. http://purl.obolibrary.org/obo/BFO_0000034 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000034 function http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000040 An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. http://purl.obolibrary.org/obo/BFO_0000040 Examples: collection of random bacteria, a chair, dorsal surface of the body http://purl.obolibrary.org/obo/BFO_0000040 Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000050 is part of http://purl.obolibrary.org/obo/BFO_0000050 There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else http://purl.obolibrary.org/obo/BFO_0000050 part of http://purl.obolibrary.org/obo/BFO_0000050 part_of http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000050 is part of http://purl.obolibrary.org/obo/BFO_0000051 has part http://purl.obolibrary.org/obo/BFO_0000051 has_part http://purl.obolibrary.org/obo/BFO_0000051 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000051 has part http://purl.obolibrary.org/obo/BFO_0000052 inheres in http://purl.obolibrary.org/obo/BFO_0000052 inheres_in http://purl.obolibrary.org/obo/BFO_0000052 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000052 inheres in http://purl.obolibrary.org/obo/BFO_0000053 is bearer of http://purl.obolibrary.org/obo/BFO_0000053 bearer of http://purl.obolibrary.org/obo/BFO_0000053 bearer_of http://purl.obolibrary.org/obo/BFO_0000053 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000053 is bearer of http://purl.obolibrary.org/obo/BFO_0000054 is realized by http://purl.obolibrary.org/obo/BFO_0000054 realized by http://purl.obolibrary.org/obo/BFO_0000054 realized_by http://purl.obolibrary.org/obo/BFO_0000054 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000054 is realized by http://purl.obolibrary.org/obo/BFO_0000055 realizes http://purl.obolibrary.org/obo/BFO_0000055 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000055 realizes http://purl.obolibrary.org/obo/BFO_0000056 participates in http://purl.obolibrary.org/obo/BFO_0000056 participates_in http://purl.obolibrary.org/obo/BFO_0000056 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000056 participates in http://purl.obolibrary.org/obo/BFO_0000057 has participant http://purl.obolibrary.org/obo/BFO_0000057 has_participant http://purl.obolibrary.org/obo/BFO_0000057 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000057 has participant http://purl.obolibrary.org/obo/BFO_0000058 is concretized as http://purl.obolibrary.org/obo/BFO_0000058 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000058 is concretized as http://purl.obolibrary.org/obo/BFO_0000059 concretizes http://purl.obolibrary.org/obo/BFO_0000059 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000059 concretizes http://purl.obolibrary.org/obo/BFO_0000062 is preceded by http://purl.obolibrary.org/obo/BFO_0000062 preceded by http://purl.obolibrary.org/obo/BFO_0000062 preceded_by http://purl.obolibrary.org/obo/BFO_0000062 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000062 is preceded by http://purl.obolibrary.org/obo/BFO_0000063 precedes http://purl.obolibrary.org/obo/BFO_0000063 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000063 precedes http://purl.obolibrary.org/obo/BFO_0000070 s depends on http://purl.obolibrary.org/obo/BFO_0000070 s_depends_on http://purl.obolibrary.org/obo/BFO_0000070 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000070 s depends on http://purl.obolibrary.org/obo/BFO_0000079 is function of http://purl.obolibrary.org/obo/BFO_0000079 function of http://purl.obolibrary.org/obo/BFO_0000079 function_of http://purl.obolibrary.org/obo/BFO_0000079 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000079 is function of http://purl.obolibrary.org/obo/BFO_0000081 is role of http://purl.obolibrary.org/obo/BFO_0000081 role of http://purl.obolibrary.org/obo/BFO_0000081 role_of http://purl.obolibrary.org/obo/BFO_0000081 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000081 is role of http://purl.obolibrary.org/obo/BFO_0000082 is located in http://purl.obolibrary.org/obo/BFO_0000082 located in http://purl.obolibrary.org/obo/BFO_0000082 located_in http://purl.obolibrary.org/obo/BFO_0000082 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000082 is located in http://purl.obolibrary.org/obo/BFO_0000085 has function http://purl.obolibrary.org/obo/BFO_0000085 has_function http://purl.obolibrary.org/obo/BFO_0000085 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000085 has function http://purl.obolibrary.org/obo/BFO_0000086 has quality http://purl.obolibrary.org/obo/BFO_0000086 has_quality http://purl.obolibrary.org/obo/BFO_0000086 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000086 has quality http://purl.obolibrary.org/obo/BFO_0000087 has role http://purl.obolibrary.org/obo/BFO_0000087 has_role http://purl.obolibrary.org/obo/BFO_0000087 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/BFO_0000087 has role http://purl.obolibrary.org/obo/CARO_0001008 gross anatomical part http://purl.obolibrary.org/obo/CARO_0001008 Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. http://purl.obolibrary.org/obo/CARO_0001008 http://purl.obolibrary.org/obo/caro.owl http://purl.obolibrary.org/obo/CARO_0001008 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/CARO_0001008 gross anatomical part http://purl.obolibrary.org/obo/CHEBI_16670 peptide http://purl.obolibrary.org/obo/CHEBI_16670 Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. http://purl.obolibrary.org/obo/CHEBI_16670 http://purl.obolibrary.org/obo/chebi.owl http://purl.obolibrary.org/obo/CHEBI_16670 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/CHEBI_16670 peptide http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acid http://purl.obolibrary.org/obo/CHEBI_16991 High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. http://purl.obolibrary.org/obo/CHEBI_16991 http://purl.obolibrary.org/obo/chebi.owl http://purl.obolibrary.org/obo/CHEBI_16991 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acid http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/CHEBI_23367 Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. http://purl.obolibrary.org/obo/CHEBI_23367 We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well http://purl.obolibrary.org/obo/CHEBI_23367 http://purl.obolibrary.org/obo/chebi.owl http://purl.obolibrary.org/obo/CHEBI_23367 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/CHEBI_33250 atom http://purl.obolibrary.org/obo/CHEBI_33250 A chemical entity constituting the smallest component of an element having the chemical properties of the element. http://purl.obolibrary.org/obo/CHEBI_33250 http://purl.obolibrary.org/obo/chebi.owl http://purl.obolibrary.org/obo/CHEBI_33250 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/CHEBI_33250 atom http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696 A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. http://purl.obolibrary.org/obo/CHEBI_33696 http://purl.obolibrary.org/obo/chebi.owl http://purl.obolibrary.org/obo/CHEBI_33696 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid http://purl.obolibrary.org/obo/CHEBI_33697 ribonucleic acid http://purl.obolibrary.org/obo/CHEBI_33697 High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. http://purl.obolibrary.org/obo/CHEBI_33697 http://purl.obolibrary.org/obo/chebi.owl http://purl.obolibrary.org/obo/CHEBI_33697 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/CHEBI_33697 ribonucleic acid http://purl.obolibrary.org/obo/CHEBI_33839 macromolecule http://purl.obolibrary.org/obo/CHEBI_33839 A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. http://purl.obolibrary.org/obo/CHEBI_33839 polymer http://purl.obolibrary.org/obo/CHEBI_33839 http://purl.obolibrary.org/obo/chebi.owl http://purl.obolibrary.org/obo/CHEBI_33839 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/CHEBI_33839 macromolecule http://purl.obolibrary.org/obo/CL_0000000 cell http://purl.obolibrary.org/obo/CL_0000000 PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." http://purl.obolibrary.org/obo/CL_0000000 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. http://purl.obolibrary.org/obo/CL_0000000 http://purl.obolibrary.org/obo/cl.owl http://purl.obolibrary.org/obo/CL_0000000 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/CL_0000000 cell http://purl.obolibrary.org/obo/CL_0000010 cultured cell http://purl.obolibrary.org/obo/CL_0000010 A cell in vitro that is or has been maintained or propagated as part of a cell culture. http://purl.obolibrary.org/obo/CL_0000010 http://purl.obolibrary.org/obo/cl.owl http://purl.obolibrary.org/obo/CL_0000010 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/CL_0000010 cultured cell http://purl.obolibrary.org/obo/CL_0000578 experimentally modified cell in vitro http://purl.obolibrary.org/obo/CL_0000578 A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. http://purl.obolibrary.org/obo/CL_0000578 http://purl.obolibrary.org/obo/cl.owl http://purl.obolibrary.org/obo/CL_0000578 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/CL_0000578 experimentally modified cell in vitro http://purl.obolibrary.org/obo/GO_0003674 molecular_function http://purl.obolibrary.org/obo/GO_0003674 Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. http://purl.obolibrary.org/obo/GO_0003674 http://purl.obolibrary.org/obo/go.owl http://purl.obolibrary.org/obo/GO_0003674 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/GO_0003674 molecular_function http://purl.obolibrary.org/obo/GO_0003824 catalytic activity http://purl.obolibrary.org/obo/GO_0003824 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. http://purl.obolibrary.org/obo/GO_0003824 http://purl.obolibrary.org/obo/go.owl http://purl.obolibrary.org/obo/GO_0003824 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/GO_0003824 catalytic activity http://purl.obolibrary.org/obo/GO_0008150 biological_process http://purl.obolibrary.org/obo/GO_0008150 Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/go.owl http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/GO_0008150 biological_process http://purl.obolibrary.org/obo/GO_0010467 gene expression http://purl.obolibrary.org/obo/GO_0010467 The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. http://purl.obolibrary.org/obo/GO_0010467 http://purl.obolibrary.org/obo/go.owl http://purl.obolibrary.org/obo/GO_0010467 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/GO_0010467 gene expression http://purl.obolibrary.org/obo/GO_0043234 protein complex http://purl.obolibrary.org/obo/GO_0043234 A ribosome is a protein complex http://purl.obolibrary.org/obo/GO_0043234 Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules. http://purl.obolibrary.org/obo/GO_0043234 http://purl.obolibrary.org/obo/go.owl http://purl.obolibrary.org/obo/GO_0043234 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/GO_0043234 protein complex http://purl.obolibrary.org/obo/IAO_0000001 conditional specification http://purl.obolibrary.org/obo/IAO_0000001 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/IAO_0000001 a directive information entity that specifies what should happen if the trigger condition is fulfilled http://purl.obolibrary.org/obo/IAO_0000001 PlanAndPlannedProcess Branch http://purl.obolibrary.org/obo/IAO_0000001 OBI branch derived http://purl.obolibrary.org/obo/IAO_0000001 OBI_0000349 http://purl.obolibrary.org/obo/IAO_0000001 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000001 conditional specification http://purl.obolibrary.org/obo/IAO_0000002 example to be eventually removed http://purl.obolibrary.org/obo/IAO_0000002 example to be eventually removed http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/IAO_0000003 Examples of measurement unit labels are liters, inches, weight per volume. http://purl.obolibrary.org/obo/IAO_0000003 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000003 A data item label that denotes a unit of measure. http://purl.obolibrary.org/obo/IAO_0000003 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. http://purl.obolibrary.org/obo/IAO_0000003 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000003 PERSON: Melanie Courtot http://purl.obolibrary.org/obo/IAO_0000003 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/IAO_0000005 objective specification http://purl.obolibrary.org/obo/IAO_0000005 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000005 a directive information entity that describes an intended process endpoint. http://purl.obolibrary.org/obo/IAO_0000005 Answers the question, why did you do this experiment? http://purl.obolibrary.org/obo/IAO_0000005 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000005 PERSON: Barry Smith http://purl.obolibrary.org/obo/IAO_0000005 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/IAO_0000005 PERSON: Jennifer Fostel http://purl.obolibrary.org/obo/IAO_0000005 OBI Plan and Planned Process/Roles Branch http://purl.obolibrary.org/obo/IAO_0000005 OBI_0000217 http://purl.obolibrary.org/obo/IAO_0000005 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000005 objective specification http://purl.obolibrary.org/obo/IAO_0000007 action specification http://purl.obolibrary.org/obo/IAO_0000007 Pour the contents of flask 1 into flask 2 http://purl.obolibrary.org/obo/IAO_0000007 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000007 a directive information entity that describes an action the bearer will take http://purl.obolibrary.org/obo/IAO_0000007 Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000007 OBI Plan and Planned Process branch http://purl.obolibrary.org/obo/IAO_0000007 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000007 action specification http://purl.obolibrary.org/obo/IAO_0000009 data item label http://purl.obolibrary.org/obo/IAO_0000009 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000009 An information content entity that is part of some data item and is used to partially define the denotation of that data item. http://purl.obolibrary.org/obo/IAO_0000009 http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n http://purl.obolibrary.org/obo/IAO_0000009 GROUP: IAO http://purl.obolibrary.org/obo/IAO_0000009 datum label http://purl.obolibrary.org/obo/IAO_0000009 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000009 data item label http://purl.obolibrary.org/obo/IAO_0000015 information carrier http://purl.obolibrary.org/obo/IAO_0000015 In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. http://purl.obolibrary.org/obo/IAO_0000015 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000015 A quality of an information bearer that imparts the information content http://purl.obolibrary.org/obo/IAO_0000015 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. http://purl.obolibrary.org/obo/IAO_0000015 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000015 Smith, Ceusters, Ruttenberg, 2000 years of philosophy http://purl.obolibrary.org/obo/IAO_0000015 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000015 information carrier http://purl.obolibrary.org/obo/IAO_0000027 data item http://purl.obolibrary.org/obo/IAO_0000027 Data items include counts of things, analyte concentrations, and statistical summaries. http://purl.obolibrary.org/obo/IAO_0000027 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000027 An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method that reliably tends to produce (approximately) truthful statements. http://purl.obolibrary.org/obo/IAO_0000027 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. http://purl.obolibrary.org/obo/IAO_0000027 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. http://purl.obolibrary.org/obo/IAO_0000027 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. http://purl.obolibrary.org/obo/IAO_0000027 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000027 PERSON: Chris Stoeckert http://purl.obolibrary.org/obo/IAO_0000027 PERSON: Jonathan Rees http://purl.obolibrary.org/obo/IAO_0000027 data http://purl.obolibrary.org/obo/IAO_0000027 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000027 data item http://purl.obolibrary.org/obo/IAO_0000028 symbol http://purl.obolibrary.org/obo/IAO_0000028 A written proper name such as “OBI”; a serial number such as “12324X”; a stop sign. http://purl.obolibrary.org/obo/IAO_0000028 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000028 An information content entity that is a mark or character used as a conventional representation of another entity. http://purl.obolibrary.org/obo/IAO_0000028 20091104, MC: this needs work and will most probably change http://purl.obolibrary.org/obo/IAO_0000028 PERSON: Jonathan Rees http://purl.obolibrary.org/obo/IAO_0000028 based on Oxford English Dictionary http://purl.obolibrary.org/obo/IAO_0000028 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000028 symbol http://purl.obolibrary.org/obo/IAO_0000030 information content entity http://purl.obolibrary.org/obo/IAO_0000030 Examples of information content entites include journal articles, data, graphical layouts, and graphs. http://purl.obolibrary.org/obo/IAO_0000030 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000030 an information content entity is an entity that is generically dependent on some material entity and stands in relation of aboutness to some entity http://purl.obolibrary.org/obo/IAO_0000030 PERSON: Chris Stoeckert http://purl.obolibrary.org/obo/IAO_0000030 OBI_0000142 http://purl.obolibrary.org/obo/IAO_0000030 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000030 information content entity http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum http://purl.obolibrary.org/obo/IAO_0000032 10 feet. 3 ml. http://purl.obolibrary.org/obo/IAO_0000032 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/IAO_0000032 a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. http://purl.obolibrary.org/obo/IAO_0000032 Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. http://purl.obolibrary.org/obo/IAO_0000032 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000032 PERSON: Melanie Courtot http://purl.obolibrary.org/obo/IAO_0000032 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum http://purl.obolibrary.org/obo/IAO_0000033 directive information entity http://purl.obolibrary.org/obo/IAO_0000033 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000033 An information content entity whose concretizations indicate to their bearer how to realize them in a process. http://purl.obolibrary.org/obo/IAO_0000033 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO http://purl.obolibrary.org/obo/IAO_0000033 Philly2013 - AR: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. http://purl.obolibrary.org/obo/IAO_0000033 Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan http://purl.obolibrary.org/obo/IAO_0000033 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000033 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/IAO_0000033 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000033 directive information entity http://purl.obolibrary.org/obo/IAO_0000037 dot plot http://purl.obolibrary.org/obo/IAO_0000037 Dot plot of SSC-H and FSC-H. http://purl.obolibrary.org/obo/IAO_0000037 http://purl.obolibrary.org/obo/IAO_0000002 http://purl.obolibrary.org/obo/IAO_0000037 A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. http://purl.obolibrary.org/obo/IAO_0000037 person:Allyson Lister http://purl.obolibrary.org/obo/IAO_0000037 person:Chris Stoeckert http://purl.obolibrary.org/obo/IAO_0000037 OBI_0000123 http://purl.obolibrary.org/obo/IAO_0000037 group:OBI http://purl.obolibrary.org/obo/IAO_0000037 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000037 dot plot http://purl.obolibrary.org/obo/IAO_0000038 graph http://purl.obolibrary.org/obo/IAO_0000038 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/IAO_0000038 A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. http://purl.obolibrary.org/obo/IAO_0000038 PERSON: Lawrence Hunter http://purl.obolibrary.org/obo/IAO_0000038 person:Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000038 person:Allyson Lister http://purl.obolibrary.org/obo/IAO_0000038 OBI_0000240 http://purl.obolibrary.org/obo/IAO_0000038 group:OBI http://purl.obolibrary.org/obo/IAO_0000038 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000038 graph http://purl.obolibrary.org/obo/IAO_0000039 has measurement unit label http://purl.obolibrary.org/obo/IAO_0000039 A relation between a value specification and its unit of measurement. http://purl.obolibrary.org/obo/IAO_0000039 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000039 has measurement unit label http://purl.obolibrary.org/obo/IAO_0000055 rule http://purl.obolibrary.org/obo/IAO_0000055 example to be added http://purl.obolibrary.org/obo/IAO_0000055 http://purl.obolibrary.org/obo/IAO_0000124 http://purl.obolibrary.org/obo/IAO_0000055 a rule is an executable which guides, defines, restricts actions http://purl.obolibrary.org/obo/IAO_0000055 MSI http://purl.obolibrary.org/obo/IAO_0000055 PRS http://purl.obolibrary.org/obo/IAO_0000055 OBI_0500021 http://purl.obolibrary.org/obo/IAO_0000055 PRS http://purl.obolibrary.org/obo/IAO_0000055 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000055 rule http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://purl.obolibrary.org/obo/IAO_0000064 PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. http://purl.obolibrary.org/obo/IAO_0000064 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000064 A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. http://purl.obolibrary.org/obo/IAO_0000064 Philippe Rocca-Serra http://purl.obolibrary.org/obo/IAO_0000064 PlanAndPlannedProcess Branch http://purl.obolibrary.org/obo/IAO_0000064 OBI_0000270 http://purl.obolibrary.org/obo/IAO_0000064 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) http://purl.obolibrary.org/obo/IAO_0000064 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://purl.obolibrary.org/obo/IAO_0000078 curation status specification http://purl.obolibrary.org/obo/IAO_0000078 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/IAO_0000078 The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. http://purl.obolibrary.org/obo/IAO_0000078 Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) http://purl.obolibrary.org/obo/IAO_0000078 PERSON:Bill Bug http://purl.obolibrary.org/obo/IAO_0000078 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> http://purl.obolibrary.org/obo/IAO_0000078 OBI_0000266 http://purl.obolibrary.org/obo/IAO_0000078 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000078 curation status specification http://purl.obolibrary.org/obo/IAO_0000088 report http://purl.obolibrary.org/obo/IAO_0000088 journal article, patent application, grant progress report, case report (not patient record) http://purl.obolibrary.org/obo/IAO_0000088 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000088 An information content entity assembled by an author for the purpose of providing information for an audience, and that is meant to provide an accurate account of something that happened. http://purl.obolibrary.org/obo/IAO_0000088 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. http://purl.obolibrary.org/obo/IAO_0000088 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. http://purl.obolibrary.org/obo/IAO_0000088 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion http://purl.obolibrary.org/obo/IAO_0000088 disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification http://purl.obolibrary.org/obo/IAO_0000088 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000088 PERSON: Melanie Courtot http://purl.obolibrary.org/obo/IAO_0000088 PERSON:Chris Stoeckert http://purl.obolibrary.org/obo/IAO_0000088 GROUP: OBI http://purl.obolibrary.org/obo/IAO_0000088 OBI_0000099 http://purl.obolibrary.org/obo/IAO_0000088 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000088 report http://purl.obolibrary.org/obo/IAO_0000100 data set http://purl.obolibrary.org/obo/IAO_0000100 Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). http://purl.obolibrary.org/obo/IAO_0000100 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000100 A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. http://purl.obolibrary.org/obo/IAO_0000100 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type http://purl.obolibrary.org/obo/IAO_0000100 person:Allyson Lister http://purl.obolibrary.org/obo/IAO_0000100 person:Chris Stoeckert http://purl.obolibrary.org/obo/IAO_0000100 OBI_0000042 http://purl.obolibrary.org/obo/IAO_0000100 group:OBI http://purl.obolibrary.org/obo/IAO_0000100 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000100 data set http://purl.obolibrary.org/obo/IAO_0000101 image http://purl.obolibrary.org/obo/IAO_0000101 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000101 An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. http://purl.obolibrary.org/obo/IAO_0000101 person:Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000101 person:Allyson http://purl.obolibrary.org/obo/IAO_0000101 person:Chris Stoeckert http://purl.obolibrary.org/obo/IAO_0000101 OBI_0000030 http://purl.obolibrary.org/obo/IAO_0000101 group:OBI http://purl.obolibrary.org/obo/IAO_0000101 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000101 image http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part is a data item about a part of an ontology, for example a term http://purl.obolibrary.org/obo/IAO_0000102 Person:Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000102 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part http://purl.obolibrary.org/obo/IAO_0000104 plan specification http://purl.obolibrary.org/obo/IAO_0000104 To lose weight, go running daily for at least 30 minutes. To isolate plasma from blood, centrifuge tubes at 1100-1300 rpm for 15 minutes. http://purl.obolibrary.org/obo/IAO_0000104 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000104 a directive information entity that, when concretized, is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. http://purl.obolibrary.org/obo/IAO_0000104 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. http://purl.obolibrary.org/obo/IAO_0000104 Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved http://purl.obolibrary.org/obo/IAO_0000104 Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000104 OBI Plan and Planned Process branch http://purl.obolibrary.org/obo/IAO_0000104 OBI_0000344 http://purl.obolibrary.org/obo/IAO_0000104 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000104 plan specification http://purl.obolibrary.org/obo/IAO_0000109 measurement data item http://purl.obolibrary.org/obo/IAO_0000109 Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. http://purl.obolibrary.org/obo/IAO_0000109 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000109 A data item that is a recording of the output of an assay. http://purl.obolibrary.org/obo/IAO_0000109 2/2/2009 is_specified_output of some assay? http://purl.obolibrary.org/obo/IAO_0000109 person:Chris Stoeckert http://purl.obolibrary.org/obo/IAO_0000109 measurement datum http://purl.obolibrary.org/obo/IAO_0000109 OBI_0000305 http://purl.obolibrary.org/obo/IAO_0000109 group:OBI http://purl.obolibrary.org/obo/IAO_0000109 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000109 measurement data item http://purl.obolibrary.org/obo/IAO_0000111 editor preferred label http://purl.obolibrary.org/obo/IAO_0000111 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000111 The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) http://purl.obolibrary.org/obo/IAO_0000111 PERSON:Daniel Schober http://purl.obolibrary.org/obo/IAO_0000111 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> http://purl.obolibrary.org/obo/IAO_0000111 editor preferred label http://purl.obolibrary.org/obo/IAO_0000111 editor preferred term http://purl.obolibrary.org/obo/IAO_0000111 editor preferred term http://purl.obolibrary.org/obo/IAO_0000112 example of usage http://purl.obolibrary.org/obo/IAO_0000112 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000112 A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not http://purl.obolibrary.org/obo/IAO_0000112 PERSON:Daniel Schober http://purl.obolibrary.org/obo/IAO_0000112 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> http://purl.obolibrary.org/obo/IAO_0000112 example of usage http://purl.obolibrary.org/obo/IAO_0000114 has curation status http://purl.obolibrary.org/obo/IAO_0000114 PERSON:Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000114 PERSON:Bill Bug http://purl.obolibrary.org/obo/IAO_0000114 PERSON:Melanie Courtot http://purl.obolibrary.org/obo/IAO_0000114 OBI_0000281 http://purl.obolibrary.org/obo/IAO_0000114 has curation status http://purl.obolibrary.org/obo/IAO_0000115 definition http://purl.obolibrary.org/obo/IAO_0000115 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000115 The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. http://purl.obolibrary.org/obo/IAO_0000115 The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. http://purl.obolibrary.org/obo/IAO_0000115 PERSON:Daniel Schober http://purl.obolibrary.org/obo/IAO_0000115 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> http://purl.obolibrary.org/obo/IAO_0000115 definition http://purl.obolibrary.org/obo/IAO_0000115 definition http://purl.obolibrary.org/obo/IAO_0000115 definition http://purl.obolibrary.org/obo/IAO_0000115 textual definition http://purl.obolibrary.org/obo/IAO_0000116 editor note http://purl.obolibrary.org/obo/IAO_0000116 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000116 An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. http://purl.obolibrary.org/obo/IAO_0000116 PERSON:Daniel Schober http://purl.obolibrary.org/obo/IAO_0000116 GROUP:OBI:<http://purl.obfoundry.org/obo/obi> http://purl.obolibrary.org/obo/IAO_0000116 editor note http://purl.obolibrary.org/obo/IAO_0000117 term editor http://purl.obolibrary.org/obo/IAO_0000117 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000117 Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people http://purl.obolibrary.org/obo/IAO_0000117 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. http://purl.obolibrary.org/obo/IAO_0000117 PERSON:Daniel Schober http://purl.obolibrary.org/obo/IAO_0000117 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> http://purl.obolibrary.org/obo/IAO_0000117 term editor http://purl.obolibrary.org/obo/IAO_0000118 alternative term http://purl.obolibrary.org/obo/IAO_0000118 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/IAO_0000118 An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) http://purl.obolibrary.org/obo/IAO_0000118 PERSON:Daniel Schober http://purl.obolibrary.org/obo/IAO_0000118 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> http://purl.obolibrary.org/obo/IAO_0000118 alternative term http://purl.obolibrary.org/obo/IAO_0000119 definition source http://purl.obolibrary.org/obo/IAO_0000119 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000119 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 http://purl.obolibrary.org/obo/IAO_0000119 PERSON:Daniel Schober http://purl.obolibrary.org/obo/IAO_0000119 Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w http://purl.obolibrary.org/obo/IAO_0000119 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> http://purl.obolibrary.org/obo/IAO_0000119 definition source http://purl.obolibrary.org/obo/IAO_0000120 metadata complete http://purl.obolibrary.org/obo/IAO_0000120 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. http://purl.obolibrary.org/obo/IAO_0000120 metadata complete http://purl.obolibrary.org/obo/IAO_0000121 organizational term http://purl.obolibrary.org/obo/IAO_0000121 term created to ease viewing/sort terms for development purpose, and will not be included in a release http://purl.obolibrary.org/obo/IAO_0000121 PERSON:Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000121 organizational term http://purl.obolibrary.org/obo/IAO_0000122 ready for release http://purl.obolibrary.org/obo/IAO_0000122 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." http://purl.obolibrary.org/obo/IAO_0000122 ready for release http://purl.obolibrary.org/obo/IAO_0000123 metadata incomplete http://purl.obolibrary.org/obo/IAO_0000123 Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. http://purl.obolibrary.org/obo/IAO_0000123 metadata incomplete http://purl.obolibrary.org/obo/IAO_0000124 uncurated http://purl.obolibrary.org/obo/IAO_0000124 Nothing done yet beyond assigning a unique class ID and proposing a preferred term. http://purl.obolibrary.org/obo/IAO_0000124 uncurated http://purl.obolibrary.org/obo/IAO_0000125 pending final vetting http://purl.obolibrary.org/obo/IAO_0000125 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. http://purl.obolibrary.org/obo/IAO_0000125 pending final vetting http://purl.obolibrary.org/obo/IAO_0000129 version number http://purl.obolibrary.org/obo/IAO_0000129 http://purl.obolibrary.org/obo/IAO_0000124 http://purl.obolibrary.org/obo/IAO_0000129 A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. http://purl.obolibrary.org/obo/IAO_0000129 Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version http://purl.obolibrary.org/obo/IAO_0000129 GROUP: IAO http://purl.obolibrary.org/obo/IAO_0000129 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000129 version number http://purl.obolibrary.org/obo/IAO_0000136 is about http://purl.obolibrary.org/obo/IAO_0000136 This document is about information artifacts and their representations http://purl.obolibrary.org/obo/IAO_0000136 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/IAO_0000136 is_about is a (currently) primitive relation that relates an information artifact to an entity. http://purl.obolibrary.org/obo/IAO_0000136 person:Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000136 Smith, Ceusters, Ruttenberg, 2000 years of philosophy http://purl.obolibrary.org/obo/IAO_0000136 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000136 is about http://purl.obolibrary.org/obo/IAO_0000144 conclusion textual entity http://purl.obolibrary.org/obo/IAO_0000144 that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 http://purl.obolibrary.org/obo/IAO_0000144 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/IAO_0000144 A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. http://purl.obolibrary.org/obo/IAO_0000144 2009/09/28 Alan Ruttenberg. Fucoidan-use-case http://purl.obolibrary.org/obo/IAO_0000144 2009/10/23 Alan Ruttenberg: We need to work on the definition still http://purl.obolibrary.org/obo/IAO_0000144 Person:Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000144 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000144 conclusion textual entity http://purl.obolibrary.org/obo/IAO_0000178 material information bearer http://purl.obolibrary.org/obo/IAO_0000178 A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. Additional examples: a hard drive, a brain. http://purl.obolibrary.org/obo/IAO_0000178 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000178 A material entity in which a concretization of an information content entity inheres. http://purl.obolibrary.org/obo/IAO_0000178 GROUP: IAO http://purl.obolibrary.org/obo/IAO_0000178 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000178 material information bearer http://purl.obolibrary.org/obo/IAO_0000184 scatter plot http://purl.obolibrary.org/obo/IAO_0000184 Comparison of gene expression values in two samples can be displayed in a scatter plot http://purl.obolibrary.org/obo/IAO_0000184 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000184 A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. http://purl.obolibrary.org/obo/IAO_0000184 PERSON:Chris Stoeckert http://purl.obolibrary.org/obo/IAO_0000184 PERSON:James Malone http://purl.obolibrary.org/obo/IAO_0000184 PERSON:Melanie Courtot http://purl.obolibrary.org/obo/IAO_0000184 scattergraph http://purl.obolibrary.org/obo/IAO_0000184 WEB: http://en.wikipedia.org/wiki/Scatterplot http://purl.obolibrary.org/obo/IAO_0000184 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000184 scatter plot http://purl.obolibrary.org/obo/IAO_0000219 denotes http://purl.obolibrary.org/obo/IAO_0000219 A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. http://purl.obolibrary.org/obo/IAO_0000219 denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically http://purl.obolibrary.org/obo/IAO_0000219 person:Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000219 Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan http://purl.obolibrary.org/obo/IAO_0000219 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000219 http://purl.obolibrary.org/obo/IAO_0000219 denotes http://purl.obolibrary.org/obo/IAO_0000232 curator note http://purl.obolibrary.org/obo/IAO_0000232 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000232 An administrative note of use for a curator but of no use for a user http://purl.obolibrary.org/obo/IAO_0000232 PERSON:Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000232 curator note http://purl.obolibrary.org/obo/IAO_0000300 textual entity http://purl.obolibrary.org/obo/IAO_0000300 Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities http://purl.obolibrary.org/obo/IAO_0000300 A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. http://purl.obolibrary.org/obo/IAO_0000300 AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. http://purl.obolibrary.org/obo/IAO_0000300 MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. http://purl.obolibrary.org/obo/IAO_0000300 PERSON: Lawrence Hunter http://purl.obolibrary.org/obo/IAO_0000300 text http://purl.obolibrary.org/obo/IAO_0000300 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000300 textual entity http://purl.obolibrary.org/obo/IAO_0000306 table http://purl.obolibrary.org/obo/IAO_0000306 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/IAO_0000306 A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions http://purl.obolibrary.org/obo/IAO_0000306 PERSON: Lawrence Hunter http://purl.obolibrary.org/obo/IAO_0000306 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000306 table http://purl.obolibrary.org/obo/IAO_0000308 figure http://purl.obolibrary.org/obo/IAO_0000308 Any picture, diagram or table http://purl.obolibrary.org/obo/IAO_0000308 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/IAO_0000308 An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. http://purl.obolibrary.org/obo/IAO_0000308 PERSON: Lawrence Hunter http://purl.obolibrary.org/obo/IAO_0000308 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000308 figure http://purl.obolibrary.org/obo/IAO_0000309 diagram http://purl.obolibrary.org/obo/IAO_0000309 A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. http://purl.obolibrary.org/obo/IAO_0000309 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/IAO_0000309 A figure that expresses one or more propositions http://purl.obolibrary.org/obo/IAO_0000309 PERSON: Lawrence Hunter http://purl.obolibrary.org/obo/IAO_0000309 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000309 diagram http://purl.obolibrary.org/obo/IAO_0000400 cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000400 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/IAO_0000400 A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude http://purl.obolibrary.org/obo/IAO_0000400 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 http://purl.obolibrary.org/obo/IAO_0000400 Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000400 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000400 cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000400 http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 http://purl.obolibrary.org/obo/IAO_0000401 one dimensional cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000401 http://purl.obolibrary.org/obo/IAO_0000124 http://purl.obolibrary.org/obo/IAO_0000401 Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000401 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000401 A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region http://purl.obolibrary.org/obo/IAO_0000401 one dimensional cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000402 two dimensional cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000402 http://purl.obolibrary.org/obo/IAO_0000124 http://purl.obolibrary.org/obo/IAO_0000402 Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000402 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000402 A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region http://purl.obolibrary.org/obo/IAO_0000402 two dimensional cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000404 has x coordinate value http://purl.obolibrary.org/obo/IAO_0000404 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000404 has x coordinate value http://purl.obolibrary.org/obo/IAO_0000406 has y coordinate value http://purl.obolibrary.org/obo/IAO_0000406 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000406 has y coordinate value http://purl.obolibrary.org/obo/IAO_0000407 has coordinate unit label http://purl.obolibrary.org/obo/IAO_0000407 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000407 relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point http://purl.obolibrary.org/obo/IAO_0000407 has coordinate unit label http://purl.obolibrary.org/obo/IAO_0000412 imported from http://purl.obolibrary.org/obo/IAO_0000412 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/IAO_0000412 For external terms/classes, the ontology from which the term was imported http://purl.obolibrary.org/obo/IAO_0000412 PERSON:Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000412 PERSON:Melanie Courtot http://purl.obolibrary.org/obo/IAO_0000412 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> http://purl.obolibrary.org/obo/IAO_0000412 imported from http://purl.obolibrary.org/obo/IAO_0000413 is duration of http://purl.obolibrary.org/obo/IAO_0000413 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/IAO_0000413 relates a process to a time-measurement-datum that represents the duration of the process http://purl.obolibrary.org/obo/IAO_0000413 Person:Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000413 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000413 is duration of http://purl.obolibrary.org/obo/IAO_0000414 mass measurement datum http://purl.obolibrary.org/obo/IAO_0000414 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/IAO_0000414 A scalar measurement datum that is the result of measurement of mass quality http://purl.obolibrary.org/obo/IAO_0000414 2009/09/28 Alan Ruttenberg. Fucoidan-use-case http://purl.obolibrary.org/obo/IAO_0000414 Person:Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000414 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000414 mass measurement datum http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum http://purl.obolibrary.org/obo/IAO_0000416 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/IAO_0000416 A scalar measurement datum that is the result of measuring a temporal interval http://purl.obolibrary.org/obo/IAO_0000416 2009/09/28 Alan Ruttenberg. Fucoidan-use-case http://purl.obolibrary.org/obo/IAO_0000416 Person:Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000416 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum http://purl.obolibrary.org/obo/IAO_0000423 to be replaced with external ontology term http://purl.obolibrary.org/obo/IAO_0000423 Terms with this status should eventually replaced with a term from another ontology. http://purl.obolibrary.org/obo/IAO_0000423 Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000423 group:OBI http://purl.obolibrary.org/obo/IAO_0000423 to be replaced with external ontology term http://purl.obolibrary.org/obo/IAO_0000428 requires discussion http://purl.obolibrary.org/obo/IAO_0000428 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. http://purl.obolibrary.org/obo/IAO_0000428 Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000428 group:OBI http://purl.obolibrary.org/obo/IAO_0000428 requires discussion http://purl.obolibrary.org/obo/IAO_0000572 documenting http://purl.obolibrary.org/obo/IAO_0000572 Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. Copying the readout from an instrument into a spreadsheet. http://purl.obolibrary.org/obo/IAO_0000572 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000572 a planned process in which input information is used to create or add to a report http://purl.obolibrary.org/obo/IAO_0000572 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape http://purl.obolibrary.org/obo/IAO_0000572 Bjoern Peters http://purl.obolibrary.org/obo/IAO_0000572 wikipedia http://en.wikipedia.org/wiki/Documenting http://purl.obolibrary.org/obo/IAO_0000572 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000572 documenting http://purl.obolibrary.org/obo/IAO_0000573 line graph http://purl.obolibrary.org/obo/IAO_0000573 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000573 PERSON:Chris Stoeckert http://purl.obolibrary.org/obo/IAO_0000573 PERSON:Melanie Courtot http://purl.obolibrary.org/obo/IAO_0000573 line chart http://purl.obolibrary.org/obo/IAO_0000573 GROUP:OBI http://purl.obolibrary.org/obo/IAO_0000573 WEB: http://en.wikipedia.org/wiki/Line_chart http://purl.obolibrary.org/obo/IAO_0000573 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000573 line graph http://purl.obolibrary.org/obo/IAO_0000577 CRID http://purl.obolibrary.org/obo/IAO_0000577 PubMed identifier “PMID:12345” http://purl.obolibrary.org/obo/IAO_0000577 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000577 A symbol that is sufficient to look up information about the corresponding entity from its CRID (centrally registered identifier) registry. http://purl.obolibrary.org/obo/IAO_0000577 IAO call, 20101124: 12345 is not a CRID symbol. To be a CRID symbol you need to have some information about the registry within which the CRID is recorded. http://purl.obolibrary.org/obo/IAO_0000577 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000577 PERSON: Bill Hogan http://purl.obolibrary.org/obo/IAO_0000577 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/IAO_0000577 PERSON: Melanie Courtot http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier http://purl.obolibrary.org/obo/IAO_0000577 Original proposal from Bjoern, discussions at IAO calls http://purl.obolibrary.org/obo/IAO_0000577 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000577 CRID http://purl.obolibrary.org/obo/IAO_0000578 centrally registered identifier http://purl.obolibrary.org/obo/IAO_0000578 Entries in a Column of which the header is "Pubmed ID" http://purl.obolibrary.org/obo/IAO_0000578 PMID:12345 http://purl.obolibrary.org/obo/IAO_0000578 The following URL: "http://www.ncbi.nlm.nih.gov/pubmed/19918065" http://purl.obolibrary.org/obo/IAO_0000578 The following sentence contains a CRID: "The article with Pubmed ID: 19918065". http://purl.obolibrary.org/obo/IAO_0000578 An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs. http://purl.obolibrary.org/obo/IAO_0000578 Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. http://purl.obolibrary.org/obo/IAO_0000578 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000578 PERSON: Bill Hogan http://purl.obolibrary.org/obo/IAO_0000578 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/IAO_0000578 PERSON: Melanie Courtot http://purl.obolibrary.org/obo/IAO_0000578 Centrally Registered IDentifier (CRID) http://purl.obolibrary.org/obo/IAO_0000578 Original proposal from Bjoern, discussions at IAO calls http://purl.obolibrary.org/obo/IAO_0000578 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000578 centrally registered identifier http://purl.obolibrary.org/obo/IAO_0000579 CRID registry http://purl.obolibrary.org/obo/IAO_0000579 PubMed and GenBank both have CRID registries as parts of their database systems. http://purl.obolibrary.org/obo/IAO_0000579 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/IAO_0000579 A data set that consists of CRIDs (centrally registered identifier) and additional information about their corresponding entities, that were recorded in the dataset through an assigning a centrally registered identifier process. http://purl.obolibrary.org/obo/IAO_0000579 IAO call, 20101124: PubMed registry is an instance of CRID registry http://purl.obolibrary.org/obo/IAO_0000579 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000579 PERSON: Bill Hogan http://purl.obolibrary.org/obo/IAO_0000579 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/IAO_0000579 PERSON: Melanie Courtot http://purl.obolibrary.org/obo/IAO_0000579 centrally registered identifier registry http://purl.obolibrary.org/obo/IAO_0000579 Original proposal from Bjoern, discussions at IAO calls http://purl.obolibrary.org/obo/IAO_0000579 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000579 CRID registry http://purl.obolibrary.org/obo/IAO_0000581 has time stamp http://purl.obolibrary.org/obo/IAO_0000581 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/IAO_0000581 relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken http://purl.obolibrary.org/obo/IAO_0000581 Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000581 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000581 has time stamp http://purl.obolibrary.org/obo/IAO_0000582 time stamped measurement datum http://purl.obolibrary.org/obo/IAO_0000582 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/IAO_0000582 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000582 time stamped measurement datum http://purl.obolibrary.org/obo/IAO_0000583 has measurement datum http://purl.obolibrary.org/obo/IAO_0000583 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/IAO_0000583 relates a time stamped measurement datum to the measurement datum that was measured http://purl.obolibrary.org/obo/IAO_0000583 Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000583 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000583 has measurement datum http://purl.obolibrary.org/obo/IAO_0000584 time sampled measurement data set http://purl.obolibrary.org/obo/IAO_0000584 pmid:20604925 - time-lapse live cell microscopy http://purl.obolibrary.org/obo/IAO_0000584 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/IAO_0000584 A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. http://purl.obolibrary.org/obo/IAO_0000584 Alan Ruttenberg http://purl.obolibrary.org/obo/IAO_0000584 experimental time series http://purl.obolibrary.org/obo/IAO_0000584 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/IAO_0000584 time sampled measurement data set http://purl.obolibrary.org/obo/NCBITaxon_10239 Viruses http://purl.obolibrary.org/obo/NCBITaxon_10239 http://purl.obolibrary.org/obo/ncbitaxon.owl http://purl.obolibrary.org/obo/NCBITaxon_10239 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/NCBITaxon_10239 Viruses http://purl.obolibrary.org/obo/NCBITaxon_117571 Euteleostomi http://purl.obolibrary.org/obo/NCBITaxon_117571 bony vertebrates http://purl.obolibrary.org/obo/NCBITaxon_117571 http://purl.obolibrary.org/obo/ncbitaxon.owl http://purl.obolibrary.org/obo/NCBITaxon_117571 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/NCBITaxon_117571 Euteleostomi http://purl.obolibrary.org/obo/NCBITaxon_2 Bacteria http://purl.obolibrary.org/obo/NCBITaxon_2 eubacteria http://purl.obolibrary.org/obo/NCBITaxon_2 http://purl.obolibrary.org/obo/ncbitaxon.owl http://purl.obolibrary.org/obo/NCBITaxon_2 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/NCBITaxon_2 Bacteria http://purl.obolibrary.org/obo/NCBITaxon_2157 Archaea http://purl.obolibrary.org/obo/NCBITaxon_2157 http://purl.obolibrary.org/obo/ncbitaxon.owl http://purl.obolibrary.org/obo/NCBITaxon_2157 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/NCBITaxon_2157 Archaea http://purl.obolibrary.org/obo/NCBITaxon_2759 Eukaryota http://purl.obolibrary.org/obo/NCBITaxon_2759 eucaryotes http://purl.obolibrary.org/obo/NCBITaxon_2759 eukaryotes http://purl.obolibrary.org/obo/NCBITaxon_2759 http://purl.obolibrary.org/obo/ncbitaxon.owl http://purl.obolibrary.org/obo/NCBITaxon_2759 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/NCBITaxon_2759 Eukaryota http://purl.obolibrary.org/obo/NCBITaxon_314146 Euarchontoglires http://purl.obolibrary.org/obo/NCBITaxon_314146 http://purl.obolibrary.org/obo/ncbitaxon.owl http://purl.obolibrary.org/obo/NCBITaxon_314146 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/NCBITaxon_314146 Euarchontoglires http://purl.obolibrary.org/obo/NCBITaxon_32523 Tetrapoda http://purl.obolibrary.org/obo/NCBITaxon_32523 tetrapods http://purl.obolibrary.org/obo/NCBITaxon_32523 http://purl.obolibrary.org/obo/ncbitaxon.owl http://purl.obolibrary.org/obo/NCBITaxon_32523 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/NCBITaxon_32523 Tetrapoda http://purl.obolibrary.org/obo/NCBITaxon_32524 Amniota http://purl.obolibrary.org/obo/NCBITaxon_32524 amniotes http://purl.obolibrary.org/obo/NCBITaxon_32524 http://purl.obolibrary.org/obo/ncbitaxon.owl http://purl.obolibrary.org/obo/NCBITaxon_32524 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/NCBITaxon_32524 Amniota http://purl.obolibrary.org/obo/NCBITaxon_33154 Opisthokonta http://purl.obolibrary.org/obo/NCBITaxon_33154 http://purl.obolibrary.org/obo/ncbitaxon.owl http://purl.obolibrary.org/obo/NCBITaxon_33154 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/NCBITaxon_33154 Opisthokonta http://purl.obolibrary.org/obo/NCBITaxon_33213 Bilateria http://purl.obolibrary.org/obo/NCBITaxon_33213 http://purl.obolibrary.org/obo/ncbitaxon.owl http://purl.obolibrary.org/obo/NCBITaxon_33213 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/NCBITaxon_33213 Bilateria http://purl.obolibrary.org/obo/NCBITaxon_40674 Mammalia http://purl.obolibrary.org/obo/NCBITaxon_40674 mammals http://purl.obolibrary.org/obo/NCBITaxon_40674 http://purl.obolibrary.org/obo/ncbitaxon.owl http://purl.obolibrary.org/obo/NCBITaxon_40674 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/NCBITaxon_40674 Mammalia http://purl.obolibrary.org/obo/NCBITaxon_7742 Vertebrata <Metazoa> http://purl.obolibrary.org/obo/NCBITaxon_7742 Vertebrata http://purl.obolibrary.org/obo/NCBITaxon_7742 vertebrates http://purl.obolibrary.org/obo/NCBITaxon_7742 http://purl.obolibrary.org/obo/ncbitaxon.owl http://purl.obolibrary.org/obo/NCBITaxon_7742 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/NCBITaxon_7742 Vertebrata <Metazoa> http://purl.obolibrary.org/obo/NCBITaxon_9606 Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 human http://purl.obolibrary.org/obo/NCBITaxon_9606 human being http://purl.obolibrary.org/obo/NCBITaxon_9606 man http://purl.obolibrary.org/obo/NCBITaxon_9606 http://purl.obolibrary.org/obo/ncbitaxon.owl http://purl.obolibrary.org/obo/NCBITaxon_9606 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/NCBITaxon_9606 Homo sapiens http://purl.obolibrary.org/obo/OBI_0000010 fluorescent reporter intensity http://purl.obolibrary.org/obo/OBI_0000010 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0000010 A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter. http://purl.obolibrary.org/obo/OBI_0000010 person:Chris Stoeckert http://purl.obolibrary.org/obo/OBI_0000010 group:OBI http://purl.obolibrary.org/obo/OBI_0000010 From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem. http://purl.obolibrary.org/obo/OBI_0000010 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000010 fluorescent reporter intensity http://purl.obolibrary.org/obo/OBI_0000011 planned process http://purl.obolibrary.org/obo/OBI_0000011 Injecting mice with a vaccine in order to test its efficacy http://purl.obolibrary.org/obo/OBI_0000011 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000011 A processual entity that realizes a plan which is the concretization of a plan specification. http://purl.obolibrary.org/obo/OBI_0000011 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) http://purl.obolibrary.org/obo/OBI_0000011 Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000011 branch derived http://purl.obolibrary.org/obo/OBI_0000011 6/11/9: Edited at workshop. Used to include: is initiated by an agent http://purl.obolibrary.org/obo/OBI_0000011 This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) http://purl.obolibrary.org/obo/OBI_0000011 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000011 planned process http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective http://purl.obolibrary.org/obo/OBI_0000015 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000015 Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature. http://purl.obolibrary.org/obo/OBI_0000015 Jennifer Fostel http://purl.obolibrary.org/obo/OBI_0000015 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective http://purl.obolibrary.org/obo/OBI_0000047 processed material http://purl.obolibrary.org/obo/OBI_0000047 Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples http://purl.obolibrary.org/obo/OBI_0000047 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000047 Is a material entity that is created or changed during material processing. http://purl.obolibrary.org/obo/OBI_0000047 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/OBI_0000047 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000047 processed material http://purl.obolibrary.org/obo/OBI_0000066 investigation http://purl.obolibrary.org/obo/OBI_0000066 Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation http://purl.obolibrary.org/obo/OBI_0000066 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000066 a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). http://purl.obolibrary.org/obo/OBI_0000066 Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000066 OBI branch derived http://purl.obolibrary.org/obo/OBI_0000066 Could add specific objective specification http://purl.obolibrary.org/obo/OBI_0000066 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000066 study http://purl.obolibrary.org/obo/OBI_0000066 investigation http://purl.obolibrary.org/obo/OBI_0000067 evaluant role http://purl.obolibrary.org/obo/OBI_0000067 When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source. http://purl.obolibrary.org/obo/OBI_0000067 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000067 a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role http://purl.obolibrary.org/obo/OBI_0000067 Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) http://purl.obolibrary.org/obo/OBI_0000067 examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") http://purl.obolibrary.org/obo/OBI_0000067 GROUP: Role Branch http://purl.obolibrary.org/obo/OBI_0000067 OBI http://purl.obolibrary.org/obo/OBI_0000067 Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. http://purl.obolibrary.org/obo/OBI_0000067 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000067 evaluant role http://purl.obolibrary.org/obo/OBI_0000070 assay http://purl.obolibrary.org/obo/OBI_0000070 Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. http://purl.obolibrary.org/obo/OBI_0000070 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000070 A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. http://purl.obolibrary.org/obo/OBI_0000070 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. http://purl.obolibrary.org/obo/OBI_0000070 PlanAndPlannedProcess Branch http://purl.obolibrary.org/obo/OBI_0000070 measuring http://purl.obolibrary.org/obo/OBI_0000070 scientific observation http://purl.obolibrary.org/obo/OBI_0000070 OBI branch derived http://purl.obolibrary.org/obo/OBI_0000070 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000070 study assay http://purl.obolibrary.org/obo/OBI_0000070 any method http://purl.obolibrary.org/obo/OBI_0000070 assay http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value http://purl.obolibrary.org/obo/OBI_0000071 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0000071 A data item which is used to indicate the degree of uncertainty about a measurement. http://purl.obolibrary.org/obo/OBI_0000071 person:Chris Stoeckert http://purl.obolibrary.org/obo/OBI_0000071 group:OBI http://purl.obolibrary.org/obo/OBI_0000071 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value http://purl.obolibrary.org/obo/OBI_0000079 culture medium http://purl.obolibrary.org/obo/OBI_0000079 A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 http://purl.obolibrary.org/obo/OBI_0000079 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000079 a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. http://purl.obolibrary.org/obo/OBI_0000079 Person: Jennifer Fostel, Jie Zheng http://purl.obolibrary.org/obo/OBI_0000079 OBI http://purl.obolibrary.org/obo/OBI_0000079 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000079 culture medium http://purl.obolibrary.org/obo/OBI_0000086 reagent role http://purl.obolibrary.org/obo/OBI_0000086 Buffer, dye, a catalyst, a solvating agent. http://purl.obolibrary.org/obo/OBI_0000086 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000086 A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. http://purl.obolibrary.org/obo/OBI_0000086 PERSON:Matthew Brush http://purl.obolibrary.org/obo/OBI_0000086 reagent http://purl.obolibrary.org/obo/OBI_0000086 PERSON:Matthew Brush http://purl.obolibrary.org/obo/OBI_0000086 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000086 reagent role http://purl.obolibrary.org/obo/OBI_0000094 material processing http://purl.obolibrary.org/obo/OBI_0000094 A cell lysis, production of a cloning vector, creating a buffer. http://purl.obolibrary.org/obo/OBI_0000094 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000094 A planned process which results in physical changes in a specified input material http://purl.obolibrary.org/obo/OBI_0000094 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000094 PERSON: Frank Gibson http://purl.obolibrary.org/obo/OBI_0000094 PERSON: Jennifer Fostel http://purl.obolibrary.org/obo/OBI_0000094 PERSON: Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000094 PERSON: Philippe Rocca Serra http://purl.obolibrary.org/obo/OBI_0000094 material transformation http://purl.obolibrary.org/obo/OBI_0000094 OBI branch derived http://purl.obolibrary.org/obo/OBI_0000094 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000094 material processing http://purl.obolibrary.org/obo/OBI_0000097 participant under investigation role http://purl.obolibrary.org/obo/OBI_0000097 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000097 A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. http://purl.obolibrary.org/obo/OBI_0000097 A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation. http://purl.obolibrary.org/obo/OBI_0000097 GROUP: Role Branch http://purl.obolibrary.org/obo/OBI_0000097 OBI http://purl.obolibrary.org/obo/OBI_0000097 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000097 participant under investigation role http://purl.obolibrary.org/obo/OBI_0000109 biological vector role http://purl.obolibrary.org/obo/OBI_0000109 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria. http://purl.obolibrary.org/obo/OBI_0000109 Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280 http://purl.obolibrary.org/obo/OBI_0000109 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000109 a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission. http://purl.obolibrary.org/obo/OBI_0000109 Feb 20, 2009. The material transmitted can be genetic information (as in cloning vector) or a pathogen (as in a disease vector) http://purl.obolibrary.org/obo/OBI_0000109 GROUP: Role Branch http://purl.obolibrary.org/obo/OBI_0000109 OBI and Wikipedia http://purl.obolibrary.org/obo/OBI_0000109 6/12/2009 Alan made this a material to be added role, because it was, and because this speeded up reasoning http://purl.obolibrary.org/obo/OBI_0000109 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000109 biological vector role http://purl.obolibrary.org/obo/OBI_0000112 specimen role http://purl.obolibrary.org/obo/OBI_0000112 liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. http://purl.obolibrary.org/obo/OBI_0000112 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000112 a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation http://purl.obolibrary.org/obo/OBI_0000112 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. http://purl.obolibrary.org/obo/OBI_0000112 Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. http://purl.obolibrary.org/obo/OBI_0000112 GROUP: Role Branch http://purl.obolibrary.org/obo/OBI_0000112 OBI http://purl.obolibrary.org/obo/OBI_0000112 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000112 specimen role http://purl.obolibrary.org/obo/OBI_0000113 sequence feature identification objective http://purl.obolibrary.org/obo/OBI_0000113 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000113 Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide. http://purl.obolibrary.org/obo/OBI_0000113 Jennifer Fostel http://purl.obolibrary.org/obo/OBI_0000113 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000113 sequence feature identification objective http://purl.obolibrary.org/obo/OBI_0000115 intervention design http://purl.obolibrary.org/obo/OBI_0000115 PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. http://purl.obolibrary.org/obo/OBI_0000115 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0000115 An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. http://purl.obolibrary.org/obo/OBI_0000115 Philppe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000115 OBI branch derived http://purl.obolibrary.org/obo/OBI_0000115 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000115 intervention design http://purl.obolibrary.org/obo/OBI_0000118 gene list http://purl.obolibrary.org/obo/OBI_0000118 Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis. http://purl.obolibrary.org/obo/OBI_0000118 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0000118 A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis. http://purl.obolibrary.org/obo/OBI_0000118 person:Chris Stoeckert http://purl.obolibrary.org/obo/OBI_0000118 group:OBI http://purl.obolibrary.org/obo/OBI_0000118 kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object. http://purl.obolibrary.org/obo/OBI_0000118 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000118 gene list http://purl.obolibrary.org/obo/OBI_0000124 is_supported_by_data http://purl.obolibrary.org/obo/OBI_0000124 The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. http://purl.obolibrary.org/obo/OBI_0000124 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000124 The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process http://purl.obolibrary.org/obo/OBI_0000124 OBI http://purl.obolibrary.org/obo/OBI_0000124 OBI http://purl.obolibrary.org/obo/OBI_0000124 Philly 2011 workshop http://purl.obolibrary.org/obo/OBI_0000124 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000124 is_supported_by_data http://purl.obolibrary.org/obo/OBI_0000131 molecular feature identification objective http://purl.obolibrary.org/obo/OBI_0000131 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000131 Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications. http://purl.obolibrary.org/obo/OBI_0000131 Jennifer Fostel http://purl.obolibrary.org/obo/OBI_0000131 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000131 molecular feature identification objective http://purl.obolibrary.org/obo/OBI_0000164 cDNA library http://purl.obolibrary.org/obo/OBI_0000164 PMID:6110205. collection of cDNA derived from mouse splenocytes. http://purl.obolibrary.org/obo/OBI_0000164 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000164 PERSON: Luisa Montecchi http://purl.obolibrary.org/obo/OBI_0000164 PERSON: Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000164 GROUP: PSI http://purl.obolibrary.org/obo/OBI_0000164 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000164 cDNA library http://purl.obolibrary.org/obo/OBI_0000175 p-value http://purl.obolibrary.org/obo/OBI_0000175 http://purl.obolibrary.org/obo/IAO_0000121 http://purl.obolibrary.org/obo/OBI_0000175 A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. http://purl.obolibrary.org/obo/OBI_0000175 Addition of restriction 'output of null hypothesis testing' by AGB and PRS while working on STATO http://purl.obolibrary.org/obo/OBI_0000175 May be outside the scope of OBI long term, is needed so is retained http://purl.obolibrary.org/obo/OBI_0000175 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/OBI_0000175 PERSON:Chris Stoeckert http://purl.obolibrary.org/obo/OBI_0000175 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000175 WEB: http://en.wikipedia.org/wiki/P-value http://purl.obolibrary.org/obo/OBI_0000175 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000175 http://purl.obolibrary.org/obo/OBI_0000175 p http://purl.obolibrary.org/obo/OBI_0000175 p-value http://purl.obolibrary.org/obo/OBI_0000181 population http://purl.obolibrary.org/obo/OBI_0000181 PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. http://purl.obolibrary.org/obo/OBI_0000181 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0000181 a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area http://purl.obolibrary.org/obo/OBI_0000181 PERSON: Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000181 adapted from Oxford English Dictionnary http://purl.obolibrary.org/obo/OBI_0000181 rem1: collection somehow always involve a selection process http://purl.obolibrary.org/obo/OBI_0000181 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000181 population http://purl.obolibrary.org/obo/OBI_0000185 imaging assay http://purl.obolibrary.org/obo/OBI_0000185 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0000185 An imaging assay is an assay to produce a picture of an entity. definition_source: OBI. http://purl.obolibrary.org/obo/OBI_0000185 PlanAndPlannedProcess Branch http://purl.obolibrary.org/obo/OBI_0000185 OBI branch derived http://purl.obolibrary.org/obo/OBI_0000185 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000185 imaging assay http://purl.obolibrary.org/obo/OBI_0000245 organization http://purl.obolibrary.org/obo/OBI_0000245 PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. http://purl.obolibrary.org/obo/OBI_0000245 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000245 An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. http://purl.obolibrary.org/obo/OBI_0000245 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/OBI_0000245 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000245 PERSON: Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000245 PERSON: Susanna Sansone http://purl.obolibrary.org/obo/OBI_0000245 GROUP: OBI http://purl.obolibrary.org/obo/OBI_0000245 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000245 organization http://purl.obolibrary.org/obo/OBI_0000250 dye role http://purl.obolibrary.org/obo/OBI_0000250 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000250 A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest. http://purl.obolibrary.org/obo/OBI_0000250 Jennifer Fostel http://purl.obolibrary.org/obo/OBI_0000250 dye http://purl.obolibrary.org/obo/OBI_0000250 A substance used to color materials www.answers.com/topic/dye 19feb09 http://purl.obolibrary.org/obo/OBI_0000250 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000250 dye role http://purl.obolibrary.org/obo/OBI_0000272 protocol http://purl.obolibrary.org/obo/OBI_0000272 PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. http://purl.obolibrary.org/obo/OBI_0000272 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000272 A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. http://purl.obolibrary.org/obo/OBI_0000272 PlanAndPlannedProcess Branch http://purl.obolibrary.org/obo/OBI_0000272 OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) http://purl.obolibrary.org/obo/OBI_0000272 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000272 study protocol http://purl.obolibrary.org/obo/OBI_0000272 protocol http://purl.obolibrary.org/obo/OBI_0000274 adding a material entity into a target http://purl.obolibrary.org/obo/OBI_0000274 Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water. http://purl.obolibrary.org/obo/OBI_0000274 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000274 is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'. http://purl.obolibrary.org/obo/OBI_0000274 Class was renamed from 'administering substance', as this is commonly used only for additions into organisms. http://purl.obolibrary.org/obo/OBI_0000274 BP http://purl.obolibrary.org/obo/OBI_0000274 branch derived http://purl.obolibrary.org/obo/OBI_0000274 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000274 adding a material entity into a target http://purl.obolibrary.org/obo/OBI_0000275 analyte role http://purl.obolibrary.org/obo/OBI_0000275 Glucose in blood (measured in an assay to determine the concentration of glucose). http://purl.obolibrary.org/obo/OBI_0000275 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000275 A role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role http://purl.obolibrary.org/obo/OBI_0000275 interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role http://purl.obolibrary.org/obo/OBI_0000275 pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested. http://purl.obolibrary.org/obo/OBI_0000275 qualities such as weight, color are not assayed but measured, so they do not fall into this category. http://purl.obolibrary.org/obo/OBI_0000275 GROUP: Role Branch http://purl.obolibrary.org/obo/OBI_0000275 OBI http://purl.obolibrary.org/obo/OBI_0000275 Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. http://purl.obolibrary.org/obo/OBI_0000275 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000275 analyte role http://purl.obolibrary.org/obo/OBI_0000293 has_specified_input http://purl.obolibrary.org/obo/OBI_0000293 see is_input_of example_of_usage http://purl.obolibrary.org/obo/OBI_0000293 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000293 A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/OBI_0000293 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. http://purl.obolibrary.org/obo/OBI_0000293 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/OBI_0000293 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000293 PERSON: Larry Hunter http://purl.obolibrary.org/obo/OBI_0000293 PERSON: Melanie Coutot http://purl.obolibrary.org/obo/OBI_0000293 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000293 has_specified_input http://purl.obolibrary.org/obo/OBI_0000295 is_specified_input_of http://purl.obolibrary.org/obo/OBI_0000295 some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay http://purl.obolibrary.org/obo/OBI_0000295 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000295