stat-ontology@googlegroups.com Orlaith Burke http://creativecommons.org/licenses/by/3.0/ 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. Statistical Method, Design of Experiment, Plots, Statistical Model 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) This Ontology is distributed under a Creative Commons Attribution License Philippe Rocca-Serra (http://orcid.org/0000-0001-9853-5668) Nolan Nichols (http://orcid.org/0000-0003-1099-3328) STATO: the statistical methods ontology Chris Mungall (http://orcid.org/0000-0002-6601-2165) 1.2 http://stato-ontology.org/ 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 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-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 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_0000295 Alan Ruttenberg http://purl.obolibrary.org/obo/OBI_0000295 PERSON:Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000295 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000295 is_specified_input_of http://purl.obolibrary.org/obo/OBI_0000299 has_specified_output http://purl.obolibrary.org/obo/OBI_0000299 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000299 A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/OBI_0000299 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/OBI_0000299 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000299 PERSON: Larry Hunter http://purl.obolibrary.org/obo/OBI_0000299 PERSON: Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000299 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000299 has_specified_output http://purl.obolibrary.org/obo/OBI_0000312 is_specified_output_of http://purl.obolibrary.org/obo/OBI_0000312 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000312 A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/OBI_0000312 Alan Ruttenberg http://purl.obolibrary.org/obo/OBI_0000312 PERSON:Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000312 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000312 is_specified_output_of http://purl.obolibrary.org/obo/OBI_0000314 is_proxy_for http://purl.obolibrary.org/obo/OBI_0000314 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000314 A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be. http://purl.obolibrary.org/obo/OBI_0000314 Alan Ruttenberg http://purl.obolibrary.org/obo/OBI_0000314 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000314 is_proxy_for http://purl.obolibrary.org/obo/OBI_0000319 material to be added role http://purl.obolibrary.org/obo/OBI_0000319 drug added to a buffer contained in a tube; substance injected into an animal; http://purl.obolibrary.org/obo/OBI_0000319 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000319 material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process http://purl.obolibrary.org/obo/OBI_0000319 Role Branch http://purl.obolibrary.org/obo/OBI_0000319 OBI http://purl.obolibrary.org/obo/OBI_0000319 9 March 09 from discussion with PA branch http://purl.obolibrary.org/obo/OBI_0000319 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000319 material to be added role http://purl.obolibrary.org/obo/OBI_0000338 drawing a conclusion based on data http://purl.obolibrary.org/obo/OBI_0000338 Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. http://purl.obolibrary.org/obo/OBI_0000338 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000338 A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion http://purl.obolibrary.org/obo/OBI_0000338 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000338 PERSON: Jennifer Fostel http://purl.obolibrary.org/obo/OBI_0000338 Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000338 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000338 drawing a conclusion based on data http://purl.obolibrary.org/obo/OBI_0000339 planning http://purl.obolibrary.org/obo/OBI_0000339 The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. http://purl.obolibrary.org/obo/OBI_0000339 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000339 a process of creating or modifying a plan specification http://purl.obolibrary.org/obo/OBI_0000339 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. http://purl.obolibrary.org/obo/OBI_0000339 Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000339 Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000339 Plans and Planned Processes Branch http://purl.obolibrary.org/obo/OBI_0000339 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000339 planning http://purl.obolibrary.org/obo/OBI_0000367 light emission function http://purl.obolibrary.org/obo/OBI_0000367 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000367 A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. http://purl.obolibrary.org/obo/OBI_0000367 Bill Bug http://purl.obolibrary.org/obo/OBI_0000367 Daniel Schober http://purl.obolibrary.org/obo/OBI_0000367 Frank Gibson http://purl.obolibrary.org/obo/OBI_0000367 Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000367 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000367 light emission function http://purl.obolibrary.org/obo/OBI_0000370 contain function http://purl.obolibrary.org/obo/OBI_0000370 A syringe, a beaker http://purl.obolibrary.org/obo/OBI_0000370 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000370 A contain function is a function to constrain a material entities location in space http://purl.obolibrary.org/obo/OBI_0000370 Bill Bug http://purl.obolibrary.org/obo/OBI_0000370 Daniel Schober http://purl.obolibrary.org/obo/OBI_0000370 Frank Gibson http://purl.obolibrary.org/obo/OBI_0000370 Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000370 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000370 contain function http://purl.obolibrary.org/obo/OBI_0000371 heat function http://purl.obolibrary.org/obo/OBI_0000371 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000371 A heat function is a function that increases the internal kinetic energy of a material http://purl.obolibrary.org/obo/OBI_0000371 Bill Bug http://purl.obolibrary.org/obo/OBI_0000371 Daniel Schober http://purl.obolibrary.org/obo/OBI_0000371 Frank Gibson http://purl.obolibrary.org/obo/OBI_0000371 Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000371 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000371 heat function http://purl.obolibrary.org/obo/OBI_0000372 material separation function http://purl.obolibrary.org/obo/OBI_0000372 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000372 A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality. http://purl.obolibrary.org/obo/OBI_0000372 Bill Bug http://purl.obolibrary.org/obo/OBI_0000372 Daniel Schober http://purl.obolibrary.org/obo/OBI_0000372 Frank Gibson http://purl.obolibrary.org/obo/OBI_0000372 Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000372 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000372 material separation function http://purl.obolibrary.org/obo/OBI_0000374 excitation function http://purl.obolibrary.org/obo/OBI_0000374 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000374 A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons. http://purl.obolibrary.org/obo/OBI_0000374 Bill Bug http://purl.obolibrary.org/obo/OBI_0000374 Daniel Schober http://purl.obolibrary.org/obo/OBI_0000374 Frank Gibson http://purl.obolibrary.org/obo/OBI_0000374 Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000374 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000374 excitation function http://purl.obolibrary.org/obo/OBI_0000378 filter function http://purl.obolibrary.org/obo/OBI_0000378 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000378 A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through http://purl.obolibrary.org/obo/OBI_0000378 Frank Gibson http://purl.obolibrary.org/obo/OBI_0000378 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000378 filter function http://purl.obolibrary.org/obo/OBI_0000387 cool function http://purl.obolibrary.org/obo/OBI_0000387 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000387 A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material. http://purl.obolibrary.org/obo/OBI_0000387 Daniel Schober http://purl.obolibrary.org/obo/OBI_0000387 Frank Gibson http://purl.obolibrary.org/obo/OBI_0000387 Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000387 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000387 cool function http://purl.obolibrary.org/obo/OBI_0000399 solid support function http://purl.obolibrary.org/obo/OBI_0000399 Taped, glued, pinned, dried or molecularly bonded to a solid support http://purl.obolibrary.org/obo/OBI_0000399 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000399 A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement http://purl.obolibrary.org/obo/OBI_0000399 Daniel Schober http://purl.obolibrary.org/obo/OBI_0000399 Frank Gibson http://purl.obolibrary.org/obo/OBI_0000399 Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000399 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000399 solid support function http://purl.obolibrary.org/obo/OBI_0000401 environment control function http://purl.obolibrary.org/obo/OBI_0000401 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000401 An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature. http://purl.obolibrary.org/obo/OBI_0000401 Bill Bug http://purl.obolibrary.org/obo/OBI_0000401 Daniel Schober http://purl.obolibrary.org/obo/OBI_0000401 Frank Gibson http://purl.obolibrary.org/obo/OBI_0000401 Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000401 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000401 environment control function http://purl.obolibrary.org/obo/OBI_0000403 sort function http://purl.obolibrary.org/obo/OBI_0000403 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000403 A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order. http://purl.obolibrary.org/obo/OBI_0000403 Daniel Schober http://purl.obolibrary.org/obo/OBI_0000403 Frank Gibson http://purl.obolibrary.org/obo/OBI_0000403 Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000403 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000403 sort function http://purl.obolibrary.org/obo/OBI_0000411 cloning vector role http://purl.obolibrary.org/obo/OBI_0000411 http://purl.obolibrary.org/obo/OBI_0000411 pBluescript plays the role of a cloning vector http://purl.obolibrary.org/obo/OBI_0000411 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000411 a vector role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning. http://purl.obolibrary.org/obo/OBI_0000411 PERSON: Helen Parkinson http://purl.obolibrary.org/obo/OBI_0000411 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000411 http://purl.obolibrary.org/obo/OBI_0000411 cloning vector role http://purl.obolibrary.org/obo/OBI_0000416 cloning insert role http://purl.obolibrary.org/obo/OBI_0000416 http://purl.obolibrary.org/obo/IAO_0000121 http://purl.obolibrary.org/obo/OBI_0000416 cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process. http://purl.obolibrary.org/obo/OBI_0000416 Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process" http://purl.obolibrary.org/obo/OBI_0000416 GROUP: Role branch http://purl.obolibrary.org/obo/OBI_0000416 OBII and Wikipedia http://purl.obolibrary.org/obo/OBI_0000416 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000416 cloning insert role http://purl.obolibrary.org/obo/OBI_0000417 achieves_planned_objective http://purl.obolibrary.org/obo/OBI_0000417 A cell sorting process achieves the objective specification 'material separation objective' http://purl.obolibrary.org/obo/OBI_0000417 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000417 This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. http://purl.obolibrary.org/obo/OBI_0000417 BP, AR, PPPB branch http://purl.obolibrary.org/obo/OBI_0000417 PPPB branch derived http://purl.obolibrary.org/obo/OBI_0000417 modified according to email thread from 1/23/09 in accordince with DT and PPPB branch http://purl.obolibrary.org/obo/OBI_0000417 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000417 achieves_planned_objective http://purl.obolibrary.org/obo/OBI_0000423 extract http://purl.obolibrary.org/obo/OBI_0000423 Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 http://purl.obolibrary.org/obo/OBI_0000423 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000423 an extract is a material entity which results from an extraction process http://purl.obolibrary.org/obo/OBI_0000423 PERSON: Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000423 extracted material http://purl.obolibrary.org/obo/OBI_0000423 GROUP: OBI Biomatrial Branch http://purl.obolibrary.org/obo/OBI_0000423 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000423 extract http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay http://purl.obolibrary.org/obo/OBI_0000424 Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858 http://purl.obolibrary.org/obo/OBI_0000424 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000424 An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot http://purl.obolibrary.org/obo/OBI_0000424 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000424 gene expression profiling http://purl.obolibrary.org/obo/OBI_0000424 OBI http://purl.obolibrary.org/obo/OBI_0000424 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling http://purl.obolibrary.org/obo/OBI_0000424 transcription profiling assay http://purl.obolibrary.org/obo/OBI_0000425 averaging objective http://purl.obolibrary.org/obo/OBI_0000425 A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. http://purl.obolibrary.org/obo/OBI_0000425 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000425 An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. http://purl.obolibrary.org/obo/OBI_0000425 Elisabetta Manduchi http://purl.obolibrary.org/obo/OBI_0000425 James Malone http://purl.obolibrary.org/obo/OBI_0000425 PERSON: Elisabetta Manduchi http://purl.obolibrary.org/obo/OBI_0000425 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000425 averaging objective http://purl.obolibrary.org/obo/OBI_0000427 enzyme http://purl.obolibrary.org/obo/OBI_0000427 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0000427 person: Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000427 GROUP:OBI http://purl.obolibrary.org/obo/OBI_0000427 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000427 enzyme http://purl.obolibrary.org/obo/OBI_0000434 adding material objective http://purl.obolibrary.org/obo/OBI_0000434 creating a mouse infected with LCM virus http://purl.obolibrary.org/obo/OBI_0000434 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000434 is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity http://purl.obolibrary.org/obo/OBI_0000434 BP http://purl.obolibrary.org/obo/OBI_0000434 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000434 adding material objective http://purl.obolibrary.org/obo/OBI_0000435 genotyping assay http://purl.obolibrary.org/obo/OBI_0000435 High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 http://purl.obolibrary.org/obo/OBI_0000435 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000435 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000435 genotype profiling, SNP genotyping http://purl.obolibrary.org/obo/OBI_0000435 OBI Biomaterial http://purl.obolibrary.org/obo/OBI_0000435 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000435 SNP analysis http://purl.obolibrary.org/obo/OBI_0000435 genotyping assay http://purl.obolibrary.org/obo/OBI_0000437 analyte measurement objective http://purl.obolibrary.org/obo/OBI_0000437 The objective to measure the concentration of glucose in a blood sample http://purl.obolibrary.org/obo/OBI_0000437 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000437 an assay objective to determine the presence or concentration of an analyte in the evaluant http://purl.obolibrary.org/obo/OBI_0000437 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000437 PPPB branch http://purl.obolibrary.org/obo/OBI_0000437 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000437 analyte measurement objective http://purl.obolibrary.org/obo/OBI_0000441 assay objective http://purl.obolibrary.org/obo/OBI_0000441 the objective to determine the weight of a mouse. http://purl.obolibrary.org/obo/OBI_0000441 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000441 an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) http://purl.obolibrary.org/obo/OBI_0000441 PPPB branch http://purl.obolibrary.org/obo/OBI_0000441 PPPB branch http://purl.obolibrary.org/obo/OBI_0000441 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000441 assay objective http://purl.obolibrary.org/obo/OBI_0000443 analyte assay http://purl.obolibrary.org/obo/OBI_0000443 example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output http://purl.obolibrary.org/obo/OBI_0000443 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000443 An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. http://purl.obolibrary.org/obo/OBI_0000443 2013-09-23: simplify equivalent axiom http://purl.obolibrary.org/obo/OBI_0000443 Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement. http://purl.obolibrary.org/obo/OBI_0000443 PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg http://purl.obolibrary.org/obo/OBI_0000443 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000443 analyte assay http://purl.obolibrary.org/obo/OBI_0000444 target of material addition role http://purl.obolibrary.org/obo/OBI_0000444 peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application. http://purl.obolibrary.org/obo/OBI_0000444 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000444 target of material addition role is a role realized by an entity into which a material is added in a material addition process http://purl.obolibrary.org/obo/OBI_0000444 From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role. http://purl.obolibrary.org/obo/OBI_0000444 GROUP: Role Branch http://purl.obolibrary.org/obo/OBI_0000444 OBI http://purl.obolibrary.org/obo/OBI_0000444 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000444 target of material addition role http://purl.obolibrary.org/obo/OBI_0000451 normalized data set http://purl.obolibrary.org/obo/OBI_0000451 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0000451 A data set that is produced as the output of a normalization data transformation. http://purl.obolibrary.org/obo/OBI_0000451 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0000451 PERSON: Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000451 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000451 normalized data set http://purl.obolibrary.org/obo/OBI_0000453 measure function http://purl.obolibrary.org/obo/OBI_0000453 A glucometer measures blood glucose concentration, the glucometer has a measure function. http://purl.obolibrary.org/obo/OBI_0000453 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000453 Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. http://purl.obolibrary.org/obo/OBI_0000453 PERSON: Daniel Schober http://purl.obolibrary.org/obo/OBI_0000453 PERSON: Helen Parkinson http://purl.obolibrary.org/obo/OBI_0000453 PERSON: Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000453 PERSON:Frank Gibson http://purl.obolibrary.org/obo/OBI_0000453 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000453 measure function http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective http://purl.obolibrary.org/obo/OBI_0000456 The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. http://purl.obolibrary.org/obo/OBI_0000456 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000456 an objective specifiction that creates an specific output object from input materials. http://purl.obolibrary.org/obo/OBI_0000456 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000456 PERSON: Frank Gibson http://purl.obolibrary.org/obo/OBI_0000456 PERSON: Jennifer Fostel http://purl.obolibrary.org/obo/OBI_0000456 PERSON: Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000456 PERSON: Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000456 artifact creation objective http://purl.obolibrary.org/obo/OBI_0000456 GROUP: OBI PlanAndPlannedProcess Branch http://purl.obolibrary.org/obo/OBI_0000456 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective http://purl.obolibrary.org/obo/OBI_0000471 study design execution http://purl.obolibrary.org/obo/OBI_0000471 injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. http://purl.obolibrary.org/obo/OBI_0000471 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000471 a planned process that realizes the concretization of a study design http://purl.obolibrary.org/obo/OBI_0000471 removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. http://purl.obolibrary.org/obo/OBI_0000471 branch derived http://purl.obolibrary.org/obo/OBI_0000471 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. http://purl.obolibrary.org/obo/OBI_0000471 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000471 study design execution http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing http://purl.obolibrary.org/obo/OBI_0000626 Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858 http://purl.obolibrary.org/obo/OBI_0000626 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument. http://purl.obolibrary.org/obo/OBI_0000626 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000626 OBI Branch derived http://purl.obolibrary.org/obo/OBI_0000626 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000626 nucleotide sequencing http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing http://purl.obolibrary.org/obo/OBI_0000639 material separation objective http://purl.obolibrary.org/obo/OBI_0000639 The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. http://purl.obolibrary.org/obo/OBI_0000639 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000639 is an objective to transform a material entity into spatially separated components. http://purl.obolibrary.org/obo/OBI_0000639 PPPB branch http://purl.obolibrary.org/obo/OBI_0000639 PPPB branch http://purl.obolibrary.org/obo/OBI_0000639 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000639 material separation objective http://purl.obolibrary.org/obo/OBI_0000643 has grain http://purl.obolibrary.org/obo/OBI_0000643 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000643 the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. http://purl.obolibrary.org/obo/OBI_0000643 Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form http://purl.obolibrary.org/obo/OBI_0000643 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/OBI_0000643 PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 http://purl.obolibrary.org/obo/OBI_0000643 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000643 has grain http://purl.obolibrary.org/obo/OBI_0000649 data set of features http://purl.obolibrary.org/obo/OBI_0000649 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0000649 A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set. http://purl.obolibrary.org/obo/OBI_0000649 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0000649 PERSON: Monnie McGee http://purl.obolibrary.org/obo/OBI_0000649 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000649 data set of features http://purl.obolibrary.org/obo/OBI_0000650 differential expression analysis data transformation http://purl.obolibrary.org/obo/OBI_0000650 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000650 A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of http://purl.obolibrary.org/obo/OBI_0000650 James Malone http://purl.obolibrary.org/obo/OBI_0000650 Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000650 Monnie McGee http://purl.obolibrary.org/obo/OBI_0000650 WEB: http://purl.obolibrary.org/obo/OBI_0000650 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000650 differential expression analysis data transformation http://purl.obolibrary.org/obo/OBI_0000652 material combination http://purl.obolibrary.org/obo/OBI_0000652 Mixing two fluids. Adding salt into water. Injecting a mouse with PBS. http://purl.obolibrary.org/obo/OBI_0000652 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000652 is a material processing with the objective to combine two or more material entities as input into a single material entity as output. http://purl.obolibrary.org/obo/OBI_0000652 created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. http://purl.obolibrary.org/obo/OBI_0000652 bp http://purl.obolibrary.org/obo/OBI_0000652 bp http://purl.obolibrary.org/obo/OBI_0000652 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000652 material combination http://purl.obolibrary.org/obo/OBI_0000659 specimen collection http://purl.obolibrary.org/obo/OBI_0000659 drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation http://purl.obolibrary.org/obo/OBI_0000659 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000659 A planned process with the objective of collecting a specimen. http://purl.obolibrary.org/obo/OBI_0000659 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_0000659 Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. http://purl.obolibrary.org/obo/OBI_0000659 Philly2013: The specimen_role for the specimen is created during the specimen collection process. http://purl.obolibrary.org/obo/OBI_0000659 Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000659 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession http://purl.obolibrary.org/obo/OBI_0000659 6/9/09: used at workshop http://purl.obolibrary.org/obo/OBI_0000659 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000659 specimen collection http://purl.obolibrary.org/obo/OBI_0000662 error corrected data set http://purl.obolibrary.org/obo/OBI_0000662 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0000662 A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for). http://purl.obolibrary.org/obo/OBI_0000662 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0000662 PERSON: Monnie McGee http://purl.obolibrary.org/obo/OBI_0000662 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000662 error corrected data set http://purl.obolibrary.org/obo/OBI_0000668 error correction data transformation http://purl.obolibrary.org/obo/OBI_0000668 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000668 An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation. http://purl.obolibrary.org/obo/OBI_0000668 James Malone http://purl.obolibrary.org/obo/OBI_0000668 Monnie McGee http://purl.obolibrary.org/obo/OBI_0000668 EDITORS http://purl.obolibrary.org/obo/OBI_0000668 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000668 error correction data transformation http://purl.obolibrary.org/obo/OBI_0000671 sample from organism http://purl.obolibrary.org/obo/OBI_0000671 http://purl.obolibrary.org/obo/IAO_0000002 http://purl.obolibrary.org/obo/OBI_0000671 a material obtained from an organism in order to be a representative of the whole http://purl.obolibrary.org/obo/OBI_0000671 5/29: This is a helper class for now http://purl.obolibrary.org/obo/OBI_0000671 we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. http://purl.obolibrary.org/obo/OBI_0000671 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000671 sample from organism http://purl.obolibrary.org/obo/OBI_0000673 statistical hypothesis test http://purl.obolibrary.org/obo/OBI_0000673 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000673 "A statistical test provides a mechanism for making quantitative decisions about a process or processes". http://purl.obolibrary.org/obo/OBI_0000673 A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test. http://purl.obolibrary.org/obo/OBI_0000673 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/OBI_0000673 James Malone http://purl.obolibrary.org/obo/OBI_0000673 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000673 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0000673 http://www.itl.nist.gov/div898/handbook/prc/section1/prc13.htm http://purl.obolibrary.org/obo/OBI_0000673 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000673 NHST http://purl.obolibrary.org/obo/OBI_0000673 Null Hypothesis Statistical Testing http://purl.obolibrary.org/obo/OBI_0000673 statistical hypothesis testing http://purl.obolibrary.org/obo/OBI_0000673 statistical hypothesis test http://purl.obolibrary.org/obo/OBI_0000674 center value http://purl.obolibrary.org/obo/OBI_0000674 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0000674 A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. http://purl.obolibrary.org/obo/OBI_0000674 PRS and AGB added restriction about 'measure of central tendency' and quartile, june 2013 http://purl.obolibrary.org/obo/OBI_0000674 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/OBI_0000674 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0000674 PERSON: Monnie McGee http://purl.obolibrary.org/obo/OBI_0000674 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000674 median http://purl.obolibrary.org/obo/OBI_0000674 second quartile http://purl.obolibrary.org/obo/OBI_0000674 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000674 second quartile http://purl.obolibrary.org/obo/OBI_0000674 center value http://purl.obolibrary.org/obo/OBI_0000675 statistical hypothesis test objective http://purl.obolibrary.org/obo/OBI_0000675 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000675 is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation http://purl.obolibrary.org/obo/OBI_0000675 James Malone http://purl.obolibrary.org/obo/OBI_0000675 Person:Helen Parkinson http://purl.obolibrary.org/obo/OBI_0000675 hypothesis test objective http://purl.obolibrary.org/obo/OBI_0000675 WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing http://purl.obolibrary.org/obo/OBI_0000675 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000675 statistical hypothesis test objective http://purl.obolibrary.org/obo/OBI_0000678 portioning objective http://purl.obolibrary.org/obo/OBI_0000678 The objective to obtain multiple aliquots of an enzyme preparation. http://purl.obolibrary.org/obo/OBI_0000678 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000678 A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. http://purl.obolibrary.org/obo/OBI_0000678 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000678 portioning objective http://purl.obolibrary.org/obo/OBI_0000679 average value http://purl.obolibrary.org/obo/OBI_0000679 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0000679 A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. http://purl.obolibrary.org/obo/OBI_0000679 PRS and AGB added restriction about 'measure of central tendency', june 2013 http://purl.obolibrary.org/obo/OBI_0000679 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/OBI_0000679 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0000679 PERSON: Monnie McGee http://purl.obolibrary.org/obo/OBI_0000679 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000679 arithmetic mean http://purl.obolibrary.org/obo/OBI_0000679 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000679 http://purl.obolibrary.org/obo/OBI_0000679 average value http://purl.obolibrary.org/obo/OBI_0000681 separation into different composition objective http://purl.obolibrary.org/obo/OBI_0000681 The objective to obtain cells contained in a sample of blood. http://purl.obolibrary.org/obo/OBI_0000681 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000681 A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). http://purl.obolibrary.org/obo/OBI_0000681 We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives http://purl.obolibrary.org/obo/OBI_0000681 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000681 separation into different composition objective http://purl.obolibrary.org/obo/OBI_0000684 specimen collection objective http://purl.obolibrary.org/obo/OBI_0000684 The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. http://purl.obolibrary.org/obo/OBI_0000684 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000684 A objective specification to obtain a material entity for potential use as an input during an investigation. http://purl.obolibrary.org/obo/OBI_0000684 Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000684 Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000684 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000684 specimen collection objective http://purl.obolibrary.org/obo/OBI_0000686 material combination objective http://purl.obolibrary.org/obo/OBI_0000686 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000686 is an objective to obtain an output material that contains several input materials. http://purl.obolibrary.org/obo/OBI_0000686 PPPB branch http://purl.obolibrary.org/obo/OBI_0000686 bp http://purl.obolibrary.org/obo/OBI_0000686 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000686 material combination objective http://purl.obolibrary.org/obo/OBI_0000722 paired-end library http://purl.obolibrary.org/obo/OBI_0000722 PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. http://purl.obolibrary.org/obo/OBI_0000722 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000722 is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs http://purl.obolibrary.org/obo/OBI_0000722 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000722 mate-paired library http://purl.obolibrary.org/obo/OBI_0000722 paired-end tag (PET) library http://purl.obolibrary.org/obo/OBI_0000722 adapted from information provided by Solid web site http://purl.obolibrary.org/obo/OBI_0000722 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000722 paired-end library http://purl.obolibrary.org/obo/OBI_0000731 recombinant vector http://purl.obolibrary.org/obo/OBI_0000731 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000731 A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. http://purl.obolibrary.org/obo/OBI_0000731 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000731 recombinant vector http://purl.obolibrary.org/obo/OBI_0000736 single fragment library http://purl.obolibrary.org/obo/OBI_0000736 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000736 is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs http://purl.obolibrary.org/obo/OBI_0000736 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000736 fragment library http://purl.obolibrary.org/obo/OBI_0000736 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000736 single fragment library http://purl.obolibrary.org/obo/OBI_0000737 cloning vector http://purl.obolibrary.org/obo/OBI_0000737 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000737 A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site. http://purl.obolibrary.org/obo/OBI_0000737 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000737 cloning vector http://purl.obolibrary.org/obo/OBI_0000739 Student's t-test http://purl.obolibrary.org/obo/OBI_0000739 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000739 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000739 Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value. http://purl.obolibrary.org/obo/OBI_0000739 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/OBI_0000739 James Malone http://purl.obolibrary.org/obo/OBI_0000739 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000739 t-test http://purl.obolibrary.org/obo/OBI_0000739 WEB: http://en.wikipedia.org/wiki/T-test http://purl.obolibrary.org/obo/OBI_0000739 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000739 http://purl.obolibrary.org/obo/OBI_0000739 t.test(dependent variable ~ independant variable, data = dataset, var.equal = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html http://purl.obolibrary.org/obo/OBI_0000739 Student's t-test http://purl.obolibrary.org/obo/OBI_0000740 material sample role http://purl.obolibrary.org/obo/OBI_0000740 a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. http://purl.obolibrary.org/obo/OBI_0000740 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0000740 A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. http://purl.obolibrary.org/obo/OBI_0000740 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. http://purl.obolibrary.org/obo/OBI_0000740 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000740 material sample role http://purl.obolibrary.org/obo/OBI_0000744 material sampling process http://purl.obolibrary.org/obo/OBI_0000744 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000744 A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity http://purl.obolibrary.org/obo/OBI_0000744 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000744 material sampling process http://purl.obolibrary.org/obo/OBI_0000747 material sample http://purl.obolibrary.org/obo/OBI_0000747 blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. http://purl.obolibrary.org/obo/OBI_0000747 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000747 A material entity that has the material sample role http://purl.obolibrary.org/obo/OBI_0000747 OBI: workshop http://purl.obolibrary.org/obo/OBI_0000747 sample population http://purl.obolibrary.org/obo/OBI_0000747 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000747 sample http://purl.obolibrary.org/obo/OBI_0000747 material sample http://purl.obolibrary.org/obo/OBI_0000750 study design independent variable http://purl.obolibrary.org/obo/OBI_0000750 In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable. http://purl.obolibrary.org/obo/OBI_0000750 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000750 a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled http://purl.obolibrary.org/obo/OBI_0000750 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. http://purl.obolibrary.org/obo/OBI_0000750 In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling http://purl.obolibrary.org/obo/OBI_0000750 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/OBI_0000750 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000750 PERSON: Chris Stoeckert http://purl.obolibrary.org/obo/OBI_0000750 experimental factor http://purl.obolibrary.org/obo/OBI_0000750 independent variable http://purl.obolibrary.org/obo/OBI_0000750 Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables http://purl.obolibrary.org/obo/OBI_0000750 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 thisdefinition please notify OBI. http://purl.obolibrary.org/obo/OBI_0000750 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000750 study factor http://purl.obolibrary.org/obo/OBI_0000750 explanatory variable http://purl.obolibrary.org/obo/OBI_0000750 factor http://purl.obolibrary.org/obo/OBI_0000750 study design independent variable http://purl.obolibrary.org/obo/OBI_0000751 study design dependent variable http://purl.obolibrary.org/obo/OBI_0000751 In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable. http://purl.obolibrary.org/obo/OBI_0000751 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000751 PRS-AGB: a dependent variable is a variable which assumes only values set by the operator according to a plan and are expected to influence the ranges of values assumed by a response variable aka independent variable. http://purl.obolibrary.org/obo/OBI_0000751 dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies. http://purl.obolibrary.org/obo/OBI_0000751 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. http://purl.obolibrary.org/obo/OBI_0000751 In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling http://purl.obolibrary.org/obo/OBI_0000751 PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/OBI_0000751 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000751 PERSON: Chris Stoeckert http://purl.obolibrary.org/obo/OBI_0000751 dependent variable http://purl.obolibrary.org/obo/OBI_0000751 WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables http://purl.obolibrary.org/obo/OBI_0000751 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 thisdefinition please notify OBI. http://purl.obolibrary.org/obo/OBI_0000751 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000751 response variable http://purl.obolibrary.org/obo/OBI_0000751 study design dependent variable http://purl.obolibrary.org/obo/OBI_0000789 survival rate http://purl.obolibrary.org/obo/OBI_0000789 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000789 A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring. http://purl.obolibrary.org/obo/OBI_0000789 Oliver He http://purl.obolibrary.org/obo/OBI_0000789 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000789 survival rate http://purl.obolibrary.org/obo/OBI_0000791 multiple testing correction objective http://purl.obolibrary.org/obo/OBI_0000791 Application of the Bonferroni correction http://purl.obolibrary.org/obo/OBI_0000791 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000791 A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously http://purl.obolibrary.org/obo/OBI_0000791 multiple comparison correction objective http://purl.obolibrary.org/obo/OBI_0000791 http://en.wikipedia.org/wiki/Multiple_Testing_Correction http://purl.obolibrary.org/obo/OBI_0000791 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000791 multiple testing correction objective http://purl.obolibrary.org/obo/OBI_0000806 material maintenance objective http://purl.obolibrary.org/obo/OBI_0000806 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000806 An objective specification maintains some or all of the qualities of a material over time. http://purl.obolibrary.org/obo/OBI_0000806 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000806 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000806 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000806 material maintenance objective http://purl.obolibrary.org/obo/OBI_0000811 primary structure of DNA macromolecule http://purl.obolibrary.org/obo/OBI_0000811 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000811 a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. http://purl.obolibrary.org/obo/OBI_0000811 placeholder for SO http://purl.obolibrary.org/obo/OBI_0000811 BP et al http://purl.obolibrary.org/obo/OBI_0000811 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000811 primary structure of DNA macromolecule http://purl.obolibrary.org/obo/OBI_0000832 measurement device http://purl.obolibrary.org/obo/OBI_0000832 A ruler, a microarray scanner, a Geiger counter. http://purl.obolibrary.org/obo/OBI_0000832 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000832 A device in which a measure function inheres. http://purl.obolibrary.org/obo/OBI_0000832 GROUP:OBI Philly workshop http://purl.obolibrary.org/obo/OBI_0000832 OBI http://purl.obolibrary.org/obo/OBI_0000832 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000832 measurement device http://purl.obolibrary.org/obo/OBI_0000838 material maintenance http://purl.obolibrary.org/obo/OBI_0000838 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000838 a process with that achieves the objective to maintain some or all of the characteristics of an input material over time http://purl.obolibrary.org/obo/OBI_0000838 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000838 material maintenance http://purl.obolibrary.org/obo/OBI_0000846 is member of organization http://purl.obolibrary.org/obo/OBI_0000846 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000846 Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. http://purl.obolibrary.org/obo/OBI_0000846 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population http://purl.obolibrary.org/obo/OBI_0000846 JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. http://purl.obolibrary.org/obo/OBI_0000846 Person:Alan Ruttenberg http://purl.obolibrary.org/obo/OBI_0000846 Person:Helen Parkinson http://purl.obolibrary.org/obo/OBI_0000846 Person:Alan Ruttenberg http://purl.obolibrary.org/obo/OBI_0000846 Person:Helen Parkinson http://purl.obolibrary.org/obo/OBI_0000846 2009/09/28 Alan Ruttenberg. Fucoidan-use-case http://purl.obolibrary.org/obo/OBI_0000846 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000846 is member of organization http://purl.obolibrary.org/obo/OBI_0000861 Likelihood-ratio test http://purl.obolibrary.org/obo/OBI_0000861 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000861 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000861 Likelihood-ratio test is a statistical test which evaluates the goodness-of-fit between two models and whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one) http://purl.obolibrary.org/obo/OBI_0000861 date: March 2013 AGB and PRS provide formal definition expressed the test in terms of output and input, specifying the nature of the variables, the purpose of the test and the distribution used. http://purl.obolibrary.org/obo/OBI_0000861 Alejandra Gonzales-Beltran http://purl.obolibrary.org/obo/OBI_0000861 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000861 Tina Boussard http://purl.obolibrary.org/obo/OBI_0000861 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000861 lrtest() http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/lmtest/html/lrtest.html http://purl.obolibrary.org/obo/OBI_0000861 Likelihood-ratio test http://purl.obolibrary.org/obo/OBI_0000889 survival curve http://purl.obolibrary.org/obo/OBI_0000889 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000889 A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. http://purl.obolibrary.org/obo/OBI_0000889 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/OBI_0000889 PERSON:Chris Stoeckert http://purl.obolibrary.org/obo/OBI_0000889 PERSON:James Malone http://purl.obolibrary.org/obo/OBI_0000889 PERSON:Melanie Courtot http://purl.obolibrary.org/obo/OBI_0000889 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0000889 WEB: http://www.graphpad.com/www/book/survive.htm http://purl.obolibrary.org/obo/OBI_0000889 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000889 survival curve http://purl.obolibrary.org/obo/OBI_0000916 flow cytometry assay http://purl.obolibrary.org/obo/OBI_0000916 Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody. http://purl.obolibrary.org/obo/OBI_0000916 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000916 An assay that uses a flow cytometer to detect fluorescence in individual particles that flow by a laser in solution. http://purl.obolibrary.org/obo/OBI_0000916 http://purl.obolibrary.org/obo/OBI_0000916 PERSON:Randi Vita, Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000916 http://purl.obolibrary.org/obo/OBI_0000916 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000916 flow cytometry http://purl.obolibrary.org/obo/OBI_0000916 FACS http://purl.obolibrary.org/obo/OBI_0000916 flow cytometry assay http://purl.obolibrary.org/obo/OBI_0000924 labeled specimen http://purl.obolibrary.org/obo/OBI_0000924 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000924 A specimen that has been modified in order to be able to detect it in future experiments http://purl.obolibrary.org/obo/OBI_0000924 added during call 3/1/2010 http://purl.obolibrary.org/obo/OBI_0000924 OBI group http://purl.obolibrary.org/obo/OBI_0000924 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000924 labeled specimen http://purl.obolibrary.org/obo/OBI_0000931 study intervention http://purl.obolibrary.org/obo/OBI_0000931 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000931 the part of the execution of an intervention design study which is varied between two or more subjects in the study http://purl.obolibrary.org/obo/OBI_0000931 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000931 GROUP: OBI http://purl.obolibrary.org/obo/OBI_0000931 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000931 study intervention http://purl.obolibrary.org/obo/OBI_0000932 material separation device http://purl.obolibrary.org/obo/OBI_0000932 flow cytometer http://purl.obolibrary.org/obo/OBI_0000932 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000932 A device with a separation function realized in a planed process http://purl.obolibrary.org/obo/OBI_0000932 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000932 material separation device http://purl.obolibrary.org/obo/OBI_0000938 categorical measurement datum http://purl.obolibrary.org/obo/OBI_0000938 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000938 A measurement datum that is reported on a categorical scale http://purl.obolibrary.org/obo/OBI_0000938 Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000938 nominal mesurement datum http://purl.obolibrary.org/obo/OBI_0000938 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000938 categorical measurement datum http://purl.obolibrary.org/obo/OBI_0000953 processed specimen http://purl.obolibrary.org/obo/OBI_0000953 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000953 A specimen that has been intentionally physically modified. http://purl.obolibrary.org/obo/OBI_0000953 Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000953 Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000953 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000953 A tissue sample that has been sliced and stained for a histology study. http://purl.obolibrary.org/obo/OBI_0000953 processed specimen http://purl.obolibrary.org/obo/OBI_0000963 categorical label http://purl.obolibrary.org/obo/OBI_0000963 The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. http://purl.obolibrary.org/obo/OBI_0000963 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000963 A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. http://purl.obolibrary.org/obo/OBI_0000963 Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000963 Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000963 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000963 categorical label http://purl.obolibrary.org/obo/OBI_0000964 in live cell assay http://purl.obolibrary.org/obo/OBI_0000964 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000964 An assay in which a measurement is made by observing entities located in a live cell. http://purl.obolibrary.org/obo/OBI_0000964 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000964 in live cell assay http://purl.obolibrary.org/obo/OBI_0000967 container http://purl.obolibrary.org/obo/OBI_0000967 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000967 A device that can be used to restrict the location of material entities over time http://purl.obolibrary.org/obo/OBI_0000967 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) http://purl.obolibrary.org/obo/OBI_0000967 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000967 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000967 container http://purl.obolibrary.org/obo/OBI_0000968 device http://purl.obolibrary.org/obo/OBI_0000968 A voltmeter is a measurement device which is intended to perform some measure function. http://purl.obolibrary.org/obo/OBI_0000968 An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. http://purl.obolibrary.org/obo/OBI_0000968 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0000968 A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. http://purl.obolibrary.org/obo/OBI_0000968 PERSON: Helen Parkinson http://purl.obolibrary.org/obo/OBI_0000968 instrument http://purl.obolibrary.org/obo/OBI_0000968 OBI development call 2012-12-17. http://purl.obolibrary.org/obo/OBI_0000968 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000968 device http://purl.obolibrary.org/obo/OBI_0000973 sequence data http://purl.obolibrary.org/obo/OBI_0000973 example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. http://purl.obolibrary.org/obo/OBI_0000973 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0000973 Person:Chris Stoeckert http://purl.obolibrary.org/obo/OBI_0000973 GROUP: OBI http://purl.obolibrary.org/obo/OBI_0000973 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000973 sequence data http://purl.obolibrary.org/obo/OBI_0000984 dose http://purl.obolibrary.org/obo/OBI_0000984 An organism has been injected 1ml of vaccine http://purl.obolibrary.org/obo/OBI_0000984 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0000984 A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. http://purl.obolibrary.org/obo/OBI_0000984 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0000984 dose http://purl.obolibrary.org/obo/OBI_0001010 nucleic acid extract http://purl.obolibrary.org/obo/OBI_0001010 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001010 An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. http://purl.obolibrary.org/obo/OBI_0001010 PERSON: Jie Zheng http://purl.obolibrary.org/obo/OBI_0001010 UPenn Group http://purl.obolibrary.org/obo/OBI_0001010 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001010 nucleic acid extract http://purl.obolibrary.org/obo/OBI_0001032 light emission device http://purl.obolibrary.org/obo/OBI_0001032 A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) http://purl.obolibrary.org/obo/OBI_0001032 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001032 a device which has a function to emit light. http://purl.obolibrary.org/obo/OBI_0001032 Person:Helen Parkinson http://purl.obolibrary.org/obo/OBI_0001032 OBI http://purl.obolibrary.org/obo/OBI_0001032 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001032 light emission device http://purl.obolibrary.org/obo/OBI_0001034 environmental control device http://purl.obolibrary.org/obo/OBI_0001034 A growth chamber is an environmental control device. http://purl.obolibrary.org/obo/OBI_0001034 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001034 An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity. http://purl.obolibrary.org/obo/OBI_0001034 Helen Parkinson http://purl.obolibrary.org/obo/OBI_0001034 OBI http://purl.obolibrary.org/obo/OBI_0001034 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001034 environmental control device http://purl.obolibrary.org/obo/OBI_0001143 labeled nucleic acid extract http://purl.obolibrary.org/obo/OBI_0001143 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001143 a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. http://purl.obolibrary.org/obo/OBI_0001143 Person: Jie Zheng http://purl.obolibrary.org/obo/OBI_0001143 labeled extract http://purl.obolibrary.org/obo/OBI_0001143 MO_221 labeledExtract http://purl.obolibrary.org/obo/OBI_0001143 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001143 labeled extract http://purl.obolibrary.org/obo/OBI_0001143 labeled nucleic acid extract http://purl.obolibrary.org/obo/OBI_0001172 dose response curve http://purl.obolibrary.org/obo/OBI_0001172 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001172 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0001172 A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve. http://purl.obolibrary.org/obo/OBI_0001172 Bjoern Peters; Randi Vita http://purl.obolibrary.org/obo/OBI_0001172 Philippe Rocca-Serra, Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/OBI_0001172 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001172 dose response curve http://purl.obolibrary.org/obo/OBI_0001225 genetic population background information http://purl.obolibrary.org/obo/OBI_0001225 genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information http://purl.obolibrary.org/obo/OBI_0001225 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001225 a genetic characteristics information which is a part of genotype information that identifies the population of organisms http://purl.obolibrary.org/obo/OBI_0001225 proposed and discussed on San Diego OBI workshop, March 2011 http://purl.obolibrary.org/obo/OBI_0001225 Group: OBI group http://purl.obolibrary.org/obo/OBI_0001225 Group: OBI group http://purl.obolibrary.org/obo/OBI_0001225 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001225 genetic population background information http://purl.obolibrary.org/obo/OBI_0001265 FWER adjusted p-value http://purl.obolibrary.org/obo/OBI_0001265 http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html http://purl.obolibrary.org/obo/OBI_0001265 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0001265 A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests http://purl.obolibrary.org/obo/OBI_0001265 Addition of restriction 'output of null hypothesis testing' and specified output by AGB and PRS while working on STATO http://purl.obolibrary.org/obo/OBI_0001265 PERS:Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0001265 adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate) http://purl.obolibrary.org/obo/OBI_0001265 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001265 Family-wise type I error rate http://purl.obolibrary.org/obo/OBI_0001265 FWER adjusted p-value http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay http://purl.obolibrary.org/obo/OBI_0001271 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001271 An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance http://purl.obolibrary.org/obo/OBI_0001271 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0001271 transcription profiling by high throughput sequencing http://purl.obolibrary.org/obo/OBI_0001271 EFO_0002770 transcription profiling by high throughput sequencing http://purl.obolibrary.org/obo/OBI_0001271 JZ: should be inferred as 'DNA sequencing'. Will check in the future. http://purl.obolibrary.org/obo/OBI_0001271 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001271 RNA-seq assay http://purl.obolibrary.org/obo/OBI_0001305 genotype information http://purl.obolibrary.org/obo/OBI_0001305 Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information http://purl.obolibrary.org/obo/OBI_0001305 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001305 a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc. http://purl.obolibrary.org/obo/OBI_0001305 discussed on San Diego OBI workshop, March 2011 http://purl.obolibrary.org/obo/OBI_0001305 Group: OBI group http://purl.obolibrary.org/obo/OBI_0001305 Group: OBI group http://purl.obolibrary.org/obo/OBI_0001305 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001305 genotype information http://purl.obolibrary.org/obo/OBI_0001331 transcription profiling identification objective http://purl.obolibrary.org/obo/OBI_0001331 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001331 A molecular feature identification objective that aims to characterize the abundance of transcripts http://purl.obolibrary.org/obo/OBI_0001331 Person: Chris Stoeckert, Jie Zheng http://purl.obolibrary.org/obo/OBI_0001331 Group: Penn Group http://purl.obolibrary.org/obo/OBI_0001331 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001331 transcription profiling identification objective http://purl.obolibrary.org/obo/OBI_0001352 allele information http://purl.obolibrary.org/obo/OBI_0001352 genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information http://purl.obolibrary.org/obo/OBI_0001352 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001352 a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition. http://purl.obolibrary.org/obo/OBI_0001352 discussed on San Diego OBI workshop, March 2011 http://purl.obolibrary.org/obo/OBI_0001352 Person: Chris Stoeckert, Jie Zheng http://purl.obolibrary.org/obo/OBI_0001352 MO_58 Allele http://purl.obolibrary.org/obo/OBI_0001352 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001352 allele information http://purl.obolibrary.org/obo/OBI_0001364 genetic alteration information http://purl.obolibrary.org/obo/OBI_0001364 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001364 a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc. http://purl.obolibrary.org/obo/OBI_0001364 proposed and discussed on San Diego OBI workshop, March 2011 http://purl.obolibrary.org/obo/OBI_0001364 Group: OBI group http://purl.obolibrary.org/obo/OBI_0001364 Group: OBI group http://purl.obolibrary.org/obo/OBI_0001364 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001364 genetic alteration information http://purl.obolibrary.org/obo/OBI_0001404 genetic characteristics information http://purl.obolibrary.org/obo/OBI_0001404 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001404 a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. http://purl.obolibrary.org/obo/OBI_0001404 Person: Chris Stoeckert, Jie Zheng http://purl.obolibrary.org/obo/OBI_0001404 MO_66 IndividualGeneticCharacteristics http://purl.obolibrary.org/obo/OBI_0001404 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001404 genetic characteristics information http://purl.obolibrary.org/obo/OBI_0001442 q-value http://purl.obolibrary.org/obo/OBI_0001442 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0001442 Addition of restriction 'output of null hypothesis testing' by AGB and PRS while working on STATO http://purl.obolibrary.org/obo/OBI_0001442 PERS:Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0001442 FDR adjusted p-value http://purl.obolibrary.org/obo/OBI_0001442 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001442 q-value http://purl.obolibrary.org/obo/OBI_0001444 genotyping design http://purl.obolibrary.org/obo/OBI_0001444 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001444 A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs. http://purl.obolibrary.org/obo/OBI_0001444 Person: Chris Stoeckert, Jie Zheng http://purl.obolibrary.org/obo/OBI_0001444 MO_560 genotyping_design http://purl.obolibrary.org/obo/OBI_0001444 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001444 http://purl.obolibrary.org/obo/OBI_0001444 genotyping design http://purl.obolibrary.org/obo/OBI_0001479 tissue specimen http://purl.obolibrary.org/obo/OBI_0001479 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0001479 A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). http://purl.obolibrary.org/obo/OBI_0001479 PERSON: Chris Stoeckert, Jie Zheng http://purl.obolibrary.org/obo/OBI_0001479 MO_954 organism_part http://purl.obolibrary.org/obo/OBI_0001479 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001479 tissue specimen http://purl.obolibrary.org/obo/OBI_0001554 rate measurement datum http://purl.obolibrary.org/obo/OBI_0001554 The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time. http://purl.obolibrary.org/obo/OBI_0001554 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001554 A scalar measurement datum that represents the number of events occuring over a time interval http://purl.obolibrary.org/obo/OBI_0001554 PERSON: Bjoern Peters, Randi Vita http://purl.obolibrary.org/obo/OBI_0001554 IEDB http://purl.obolibrary.org/obo/OBI_0001554 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001554 rate measurement datum http://purl.obolibrary.org/obo/OBI_0001573 DNA sequence data http://purl.obolibrary.org/obo/OBI_0001573 The part of a FASTA file that contains the letters ACTGGGAA http://purl.obolibrary.org/obo/OBI_0001573 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001573 A sequence data item that is about the primary structure of DNA http://purl.obolibrary.org/obo/OBI_0001573 OBI call; Bjoern Peters http://purl.obolibrary.org/obo/OBI_0001573 OBI call; Melanie Courtout http://purl.obolibrary.org/obo/OBI_0001573 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there. http://purl.obolibrary.org/obo/OBI_0001573 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001573 DNA sequence data http://purl.obolibrary.org/obo/OBI_0001755 selection criterion http://purl.obolibrary.org/obo/OBI_0001755 rats should be aged between 6 and 8 weeks and weight between 180-250grams http://purl.obolibrary.org/obo/OBI_0001755 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0001755 A directive information entity which defines and states a principle of standard by which selection process may take place. http://purl.obolibrary.org/obo/OBI_0001755 Person: Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0001755 selection rule http://purl.obolibrary.org/obo/OBI_0001755 OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/ http://purl.obolibrary.org/obo/OBI_0001755 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001755 selection criterion http://purl.obolibrary.org/obo/OBI_0001834 drawing a conclusion http://purl.obolibrary.org/obo/OBI_0001834 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0001834 A planned process in which new information is inferred from existing information. http://purl.obolibrary.org/obo/OBI_0001834 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001834 drawing a conclusion http://purl.obolibrary.org/obo/OBI_0001847 ISA alternative term http://purl.obolibrary.org/obo/OBI_0001847 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0001847 An alternative term used by the ISA tools project (http://isa-tools.org). http://purl.obolibrary.org/obo/OBI_0001847 Person: Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/OBI_0001847 Person: Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0001847 ISA tools project (http://isa-tools.org) http://purl.obolibrary.org/obo/OBI_0001847 ISA alternative term http://purl.obolibrary.org/obo/OBI_0001865 assay array http://purl.obolibrary.org/obo/OBI_0001865 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001865 A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. http://purl.obolibrary.org/obo/OBI_0001865 PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg http://purl.obolibrary.org/obo/OBI_0001865 Penn Group http://purl.obolibrary.org/obo/OBI_0001865 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001865 assay array http://purl.obolibrary.org/obo/OBI_0001909 conclusion based on data http://purl.obolibrary.org/obo/OBI_0001909 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0001909 An information content entity that is inferred from data. http://purl.obolibrary.org/obo/OBI_0001909 In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. http://purl.obolibrary.org/obo/OBI_0001909 Group:2013 Philly Workshop group http://purl.obolibrary.org/obo/OBI_0001909 Group:2013 Philly Workshop group http://purl.obolibrary.org/obo/OBI_0001909 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001909 conclusion based on data http://purl.obolibrary.org/obo/OBI_0001912 cell freezing medium http://purl.obolibrary.org/obo/OBI_0001912 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001912 A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. http://purl.obolibrary.org/obo/OBI_0001912 PERSON: Matthew Brush http://purl.obolibrary.org/obo/OBI_0001912 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001912 cell freezing medium http://purl.obolibrary.org/obo/OBI_0001927 specifies value of http://purl.obolibrary.org/obo/OBI_0001927 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0001927 A relation between a value specification and an entity which the specification is about. http://purl.obolibrary.org/obo/OBI_0001927 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001927 specifies value of http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification http://purl.obolibrary.org/obo/OBI_0001930 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0001930 A value specification that is specifies one category out of a fixed number of nominal categories http://purl.obolibrary.org/obo/OBI_0001930 PERSON:Bjoern Peters http://purl.obolibrary.org/obo/OBI_0001930 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification http://purl.obolibrary.org/obo/OBI_0001931 scalar value specification http://purl.obolibrary.org/obo/OBI_0001931 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0001931 A value specification that consists of two parts: a numeral and a unit label http://purl.obolibrary.org/obo/OBI_0001931 PERSON:Bjoern Peters http://purl.obolibrary.org/obo/OBI_0001931 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001931 scalar value specification http://purl.obolibrary.org/obo/OBI_0001933 value specification http://purl.obolibrary.org/obo/OBI_0001933 The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. http://purl.obolibrary.org/obo/OBI_0001933 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0001933 An information content entity that specifies a value within a classification scheme or on a quantitative scale. http://purl.obolibrary.org/obo/OBI_0001933 This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. http://purl.obolibrary.org/obo/OBI_0001933 PERSON:Bjoern Peters http://purl.obolibrary.org/obo/OBI_0001933 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001933 value specification http://purl.obolibrary.org/obo/OBI_0001936 molecular-labeled material http://purl.obolibrary.org/obo/OBI_0001936 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0001936 a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay http://purl.obolibrary.org/obo/OBI_0001936 PERSON:Matthew Brush http://purl.obolibrary.org/obo/OBI_0001936 OBI developer call, 3-12-12 http://purl.obolibrary.org/obo/OBI_0001936 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001936 molecular-labeled material http://purl.obolibrary.org/obo/OBI_0001937 has specified value http://purl.obolibrary.org/obo/OBI_0001937 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001937 A relation between a value specification and a number that quantifies it. http://purl.obolibrary.org/obo/OBI_0001937 A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. http://purl.obolibrary.org/obo/OBI_0001937 PERSON: James A. Overton http://purl.obolibrary.org/obo/OBI_0001937 OBI http://purl.obolibrary.org/obo/OBI_0001937 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001937 has specified value http://purl.obolibrary.org/obo/OBI_0001938 has value specification http://purl.obolibrary.org/obo/OBI_0001938 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0001938 A relation between an information content entity and a value specification that specifies its value. http://purl.obolibrary.org/obo/OBI_0001938 PERSON: James A. Overton http://purl.obolibrary.org/obo/OBI_0001938 OBI http://purl.obolibrary.org/obo/OBI_0001938 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0001938 has value specification http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/OBI_0100026 animal http://purl.obolibrary.org/obo/OBI_0100026 fungus http://purl.obolibrary.org/obo/OBI_0100026 plant http://purl.obolibrary.org/obo/OBI_0100026 virus http://purl.obolibrary.org/obo/OBI_0100026 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0100026 A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. http://purl.obolibrary.org/obo/OBI_0100026 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') http://purl.obolibrary.org/obo/OBI_0100026 GROUP: OBI Biomaterial Branch http://purl.obolibrary.org/obo/OBI_0100026 WEB: http://en.wikipedia.org/wiki/Organism http://purl.obolibrary.org/obo/OBI_0100026 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/OBI_0100051 specimen http://purl.obolibrary.org/obo/OBI_0100051 Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. http://purl.obolibrary.org/obo/OBI_0100051 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0100051 A material entity that has the specimen role. http://purl.obolibrary.org/obo/OBI_0100051 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_0100051 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0100051 PERSON: Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0100051 GROUP: OBI Biomaterial Branch http://purl.obolibrary.org/obo/OBI_0100051 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0100051 specimen http://purl.obolibrary.org/obo/OBI_0100060 cultured cell population http://purl.obolibrary.org/obo/OBI_0100060 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0100060 A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. http://purl.obolibrary.org/obo/OBI_0100060 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. http://purl.obolibrary.org/obo/OBI_0100060 PERSON:Matthew Brush http://purl.obolibrary.org/obo/OBI_0100060 cell culture sample http://purl.obolibrary.org/obo/OBI_0100060 PERSON:Matthew Brush http://purl.obolibrary.org/obo/OBI_0100060 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0100060 The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. http://purl.obolibrary.org/obo/OBI_0100060 cultured cell population http://purl.obolibrary.org/obo/OBI_0100064 screening library http://purl.obolibrary.org/obo/OBI_0100064 PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library] http://purl.obolibrary.org/obo/OBI_0100064 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0100064 a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process? http://purl.obolibrary.org/obo/OBI_0100064 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_0100064 GROUP: IEDB http://purl.obolibrary.org/obo/OBI_0100064 7/13/09: Need to clarify if this meets reagent role definition http://purl.obolibrary.org/obo/OBI_0100064 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0100064 screening library http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://purl.obolibrary.org/obo/OBI_0200000 The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. http://purl.obolibrary.org/obo/OBI_0200000 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0200000 A planned process that produces output data from input data. http://purl.obolibrary.org/obo/OBI_0200000 Elisabetta Manduchi http://purl.obolibrary.org/obo/OBI_0200000 Helen Parkinson http://purl.obolibrary.org/obo/OBI_0200000 James Malone http://purl.obolibrary.org/obo/OBI_0200000 Melanie Courtot http://purl.obolibrary.org/obo/OBI_0200000 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0200000 Richard Scheuermann http://purl.obolibrary.org/obo/OBI_0200000 Ryan Brinkman http://purl.obolibrary.org/obo/OBI_0200000 Tina Hernandez-Boussard http://purl.obolibrary.org/obo/OBI_0200000 data analysis http://purl.obolibrary.org/obo/OBI_0200000 data processing http://purl.obolibrary.org/obo/OBI_0200000 Branch editors http://purl.obolibrary.org/obo/OBI_0200000 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://purl.obolibrary.org/obo/OBI_0200031 differential expression analysis objective http://purl.obolibrary.org/obo/OBI_0200031 Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software http://purl.obolibrary.org/obo/OBI_0200031 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0200031 A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions. http://purl.obolibrary.org/obo/OBI_0200031 Elisabetta Manduchi http://purl.obolibrary.org/obo/OBI_0200031 PERSON: Elisabetta Manduchi http://purl.obolibrary.org/obo/OBI_0200031 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200031 differential expression analysis objective http://purl.obolibrary.org/obo/OBI_0200036 Benjamini and Hochberg false discovery rate correction method http://purl.obolibrary.org/obo/OBI_0200036 Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate) http://purl.obolibrary.org/obo/OBI_0200036 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0200036 A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate http://purl.obolibrary.org/obo/OBI_0200036 Helen Parkinson http://purl.obolibrary.org/obo/OBI_0200036 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0200036 Helen Parkinson http://purl.obolibrary.org/obo/OBI_0200036 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200036 Benjamini and Hochberg false discovery rate correction method http://purl.obolibrary.org/obo/OBI_0200049 Benjamini and Yekutieli false discovery rate correction method http://purl.obolibrary.org/obo/OBI_0200049 The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli) http://purl.obolibrary.org/obo/OBI_0200049 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0200049 A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate http://purl.obolibrary.org/obo/OBI_0200049 Helen Parkinson http://purl.obolibrary.org/obo/OBI_0200049 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0200049 Helen Parkinson http://purl.obolibrary.org/obo/OBI_0200049 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200049 Benjamini and Yekutieli false discovery rate correction method http://purl.obolibrary.org/obo/OBI_0200066 Holm-Bonferroni family-wise error rate correction method http://purl.obolibrary.org/obo/OBI_0200066 t-tests were used with the type I error adjusted for multiple comparisons, Holm's correction (HOLM 1979), and false discovery rate, http://www.genetics.org/cgi/content/full/172/2/1179 http://purl.obolibrary.org/obo/OBI_0200066 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0200066 a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction http://purl.obolibrary.org/obo/OBI_0200066 Person:Helen Parkinson http://purl.obolibrary.org/obo/OBI_0200066 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0200066 WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method http://purl.obolibrary.org/obo/OBI_0200066 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200066 Bonferroni adjustment method http://purl.obolibrary.org/obo/OBI_0200066 Holm-Bonferroni family-wise error rate correction method http://purl.obolibrary.org/obo/OBI_0200073 family wise error rate correction method http://purl.obolibrary.org/obo/OBI_0200073 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0200073 A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive. http://purl.obolibrary.org/obo/OBI_0200073 Monnie McGee http://purl.obolibrary.org/obo/OBI_0200073 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0200073 FWER correction http://purl.obolibrary.org/obo/OBI_0200073 Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 http://purl.obolibrary.org/obo/OBI_0200073 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200073 family wise error rate correction method http://purl.obolibrary.org/obo/OBI_0200078 descriptive statistical calculation objective http://purl.obolibrary.org/obo/OBI_0200078 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0200078 A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. http://purl.obolibrary.org/obo/OBI_0200078 Elisabetta Manduchi http://purl.obolibrary.org/obo/OBI_0200078 James Malone http://purl.obolibrary.org/obo/OBI_0200078 Melanie Courtot http://purl.obolibrary.org/obo/OBI_0200078 Monnie McGee http://purl.obolibrary.org/obo/OBI_0200078 PERSON: Elisabetta Manduchi http://purl.obolibrary.org/obo/OBI_0200078 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200078 PERSON: Melanie Courtot http://purl.obolibrary.org/obo/OBI_0200078 PERSON: Monnie McGee http://purl.obolibrary.org/obo/OBI_0200078 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200078 descriptive statistical calculation objective http://purl.obolibrary.org/obo/OBI_0200083 survival analysis objective http://purl.obolibrary.org/obo/OBI_0200083 Kaplan meier data transformation http://purl.obolibrary.org/obo/OBI_0200083 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0200083 A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables http://purl.obolibrary.org/obo/OBI_0200083 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200083 PERSON: Tina Boussard http://purl.obolibrary.org/obo/OBI_0200083 survival analysis http://purl.obolibrary.org/obo/OBI_0200083 http://en.wikipedia.org/wiki/Survival_analysis http://purl.obolibrary.org/obo/OBI_0200083 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200083 survival analysis objective http://purl.obolibrary.org/obo/OBI_0200089 multiple testing correction method http://purl.obolibrary.org/obo/OBI_0200089 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0200089 A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate http://purl.obolibrary.org/obo/OBI_0200089 Monnie McGee http://purl.obolibrary.org/obo/OBI_0200089 multiple testing procedure http://purl.obolibrary.org/obo/OBI_0200089 PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10. http://purl.obolibrary.org/obo/OBI_0200089 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200089 multiple testing correction method http://purl.obolibrary.org/obo/OBI_0200094 logarithmic transformation http://purl.obolibrary.org/obo/OBI_0200094 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0200094 A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm. http://purl.obolibrary.org/obo/OBI_0200094 Elisabetta Manduchi http://purl.obolibrary.org/obo/OBI_0200094 WEB: http://en.wikipedia.org/wiki/Logarithm http://purl.obolibrary.org/obo/OBI_0200094 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200094 logarithmic transformation http://purl.obolibrary.org/obo/OBI_0200102 regression analysis method http://purl.obolibrary.org/obo/OBI_0200102 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0200102 Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data. http://purl.obolibrary.org/obo/OBI_0200102 Date:2013-11-15 Person: AGB,PRS Adding restrictions, specifying model + parameter estimation process change of label from 'regression analysis method' to 'regression analysis' http://purl.obolibrary.org/obo/OBI_0200102 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/OBI_0200102 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0200102 Tina Hernandez-Boussard http://purl.obolibrary.org/obo/OBI_0200102 BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048 http://purl.obolibrary.org/obo/OBI_0200102 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200102 regression analysis method http://purl.obolibrary.org/obo/OBI_0200111 data visualization http://purl.obolibrary.org/obo/OBI_0200111 Generation of a heatmap from a microarray dataset http://purl.obolibrary.org/obo/OBI_0200111 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0200111 An planned process that creates images, diagrams or animations from the input data. http://purl.obolibrary.org/obo/OBI_0200111 Elisabetta Manduchi http://purl.obolibrary.org/obo/OBI_0200111 James Malone http://purl.obolibrary.org/obo/OBI_0200111 Melanie Courtot http://purl.obolibrary.org/obo/OBI_0200111 Tina Boussard http://purl.obolibrary.org/obo/OBI_0200111 data encoding as image http://purl.obolibrary.org/obo/OBI_0200111 visualization http://purl.obolibrary.org/obo/OBI_0200111 PERSON: Elisabetta Manduchi http://purl.obolibrary.org/obo/OBI_0200111 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200111 PERSON: Melanie Courtot http://purl.obolibrary.org/obo/OBI_0200111 PERSON: Tina Boussard http://purl.obolibrary.org/obo/OBI_0200111 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200111 data visualization http://purl.obolibrary.org/obo/OBI_0200117 mode calculation http://purl.obolibrary.org/obo/OBI_0200117 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0200117 A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data. http://purl.obolibrary.org/obo/OBI_0200117 James Malone http://purl.obolibrary.org/obo/OBI_0200117 Monnie McGee http://purl.obolibrary.org/obo/OBI_0200117 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200117 PERSON: Monnie McGee http://purl.obolibrary.org/obo/OBI_0200117 From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) http://purl.obolibrary.org/obo/OBI_0200117 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200117 mode calculation http://purl.obolibrary.org/obo/OBI_0200119 median calculation http://purl.obolibrary.org/obo/OBI_0200119 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0200119 A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values. http://purl.obolibrary.org/obo/OBI_0200119 James Malone http://purl.obolibrary.org/obo/OBI_0200119 Monnie McGee http://purl.obolibrary.org/obo/OBI_0200119 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200119 PERSON: Monnie McGee http://purl.obolibrary.org/obo/OBI_0200119 From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) http://purl.obolibrary.org/obo/OBI_0200119 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200119 median calculation http://purl.obolibrary.org/obo/OBI_0200163 false discovery rate correction method http://purl.obolibrary.org/obo/OBI_0200163 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0200163 The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. . http://purl.obolibrary.org/obo/OBI_0200163 Monnie McGee http://purl.obolibrary.org/obo/OBI_0200163 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0200163 FDR correction method http://purl.obolibrary.org/obo/OBI_0200163 Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate http://purl.obolibrary.org/obo/OBI_0200163 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200163 false discovery rate correction method http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective http://purl.obolibrary.org/obo/OBI_0200166 normalize objective http://purl.obolibrary.org/obo/OBI_0200166 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0200166 An objective specification to transformation input data into output data http://purl.obolibrary.org/obo/OBI_0200166 Modified definition in 2013 Philly OBI workshop http://purl.obolibrary.org/obo/OBI_0200166 James Malone http://purl.obolibrary.org/obo/OBI_0200166 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200166 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective http://purl.obolibrary.org/obo/OBI_0200167 data normalization objective http://purl.obolibrary.org/obo/OBI_0200167 Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. http://purl.obolibrary.org/obo/OBI_0200167 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0200167 Elisabetta Manduchi http://purl.obolibrary.org/obo/OBI_0200167 Helen Parkinson http://purl.obolibrary.org/obo/OBI_0200167 James Malone http://purl.obolibrary.org/obo/OBI_0200167 PERSON: Elisabetta Manduchi http://purl.obolibrary.org/obo/OBI_0200167 PERSON: Helen Parkinson http://purl.obolibrary.org/obo/OBI_0200167 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200167 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200167 data normalization objective http://purl.obolibrary.org/obo/OBI_0200168 correction objective http://purl.obolibrary.org/obo/OBI_0200168 Type I error correction http://purl.obolibrary.org/obo/OBI_0200168 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0200168 A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself http://purl.obolibrary.org/obo/OBI_0200168 James Malone http://purl.obolibrary.org/obo/OBI_0200168 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200168 PERSON: Melanie Courtot http://purl.obolibrary.org/obo/OBI_0200168 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200168 correction objective http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation http://purl.obolibrary.org/obo/OBI_0200169 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0200169 A normalization data transformation is a data transformation that has objective normalization. http://purl.obolibrary.org/obo/OBI_0200169 James Malone http://purl.obolibrary.org/obo/OBI_0200169 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200169 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation http://purl.obolibrary.org/obo/OBI_0200170 averaging data transformation http://purl.obolibrary.org/obo/OBI_0200170 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0200170 An averaging data transformation is a data transformation that has objective averaging. http://purl.obolibrary.org/obo/OBI_0200170 James Malone http://purl.obolibrary.org/obo/OBI_0200170 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200170 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200170 averaging data transformation http://purl.obolibrary.org/obo/OBI_0200176 Fisher's exact test http://purl.obolibrary.org/obo/OBI_0200176 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0200176 Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests. http://purl.obolibrary.org/obo/OBI_0200176 James Malone http://purl.obolibrary.org/obo/OBI_0200176 WEB:http://mathworld.wolfram.com/FishersExactTest.html http://purl.obolibrary.org/obo/OBI_0200176 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200176 Fisher's exact test http://purl.obolibrary.org/obo/OBI_0200177 center calculation objective http://purl.obolibrary.org/obo/OBI_0200177 A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average. http://purl.obolibrary.org/obo/OBI_0200177 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0200177 A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. http://purl.obolibrary.org/obo/OBI_0200177 James Malone http://purl.obolibrary.org/obo/OBI_0200177 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200177 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200177 center calculation objective http://purl.obolibrary.org/obo/OBI_0200181 center calculation data transformation http://purl.obolibrary.org/obo/OBI_0200181 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0200181 A center calculation data transformation is a data transformation that has objective of center calculation. http://purl.obolibrary.org/obo/OBI_0200181 James Malone http://purl.obolibrary.org/obo/OBI_0200181 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200181 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200181 center calculation data transformation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation http://purl.obolibrary.org/obo/OBI_0200184 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0200184 A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. http://purl.obolibrary.org/obo/OBI_0200184 James Malone http://purl.obolibrary.org/obo/OBI_0200184 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200184 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation http://purl.obolibrary.org/obo/OBI_0200186 error correction objective http://purl.obolibrary.org/obo/OBI_0200186 Application of a multiple testing correction method http://purl.obolibrary.org/obo/OBI_0200186 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0200186 An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. http://purl.obolibrary.org/obo/OBI_0200186 James Malone, Helen Parkinson http://purl.obolibrary.org/obo/OBI_0200186 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200186 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200186 error correction objective http://purl.obolibrary.org/obo/OBI_0200191 gene list visualization http://purl.obolibrary.org/obo/OBI_0200191 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0200191 Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type. http://purl.obolibrary.org/obo/OBI_0200191 James Malone http://purl.obolibrary.org/obo/OBI_0200191 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200191 gene list visualization http://purl.obolibrary.org/obo/OBI_0200194 survival analysis data transformation http://purl.obolibrary.org/obo/OBI_0200194 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0200194 A data transformation which has the objective of performing survival analysis. http://purl.obolibrary.org/obo/OBI_0200194 James Malone http://purl.obolibrary.org/obo/OBI_0200194 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200194 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200194 survival analysis data transformation http://purl.obolibrary.org/obo/OBI_0200200 chi square test http://purl.obolibrary.org/obo/OBI_0200200 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0200200 The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough. http://purl.obolibrary.org/obo/OBI_0200200 negociation with OBI hence definition and definition source are missing from this class http://purl.obolibrary.org/obo/OBI_0200200 PERSON: James Malone http://purl.obolibrary.org/obo/OBI_0200200 PERSON: Tina Boussard http://purl.obolibrary.org/obo/OBI_0200200 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200200 chi square test http://purl.obolibrary.org/obo/OBI_0200201 ANOVA http://purl.obolibrary.org/obo/OBI_0200201 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0200201 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0200201 ANalysis Of VAriance (ANOVA) is a data transformation in which a statistical test is performed to evaluate the null hypothesis that the means computed over the different groups as specified by the investigator do not differ. The test compares an F-statistics (a ratio of means) to an F-distribution and produces a p-value, used to reject or accept the null hypothesis given a false positive rate. The test assumes normality and equivariance of the data. http://purl.obolibrary.org/obo/OBI_0200201 AGB and PRS augmented the class with formal definitions as part of STATO extension http://purl.obolibrary.org/obo/OBI_0200201 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/OBI_0200201 James Malone http://purl.obolibrary.org/obo/OBI_0200201 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0200201 Analysis of Variance http://purl.obolibrary.org/obo/OBI_0200201 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0200201 http://purl.obolibrary.org/obo/OBI_0200201 stat.anova() http://purl.obolibrary.org/obo/OBI_0200201 ANOVA http://purl.obolibrary.org/obo/OBI_0300311 observation design http://purl.obolibrary.org/obo/OBI_0300311 PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. http://purl.obolibrary.org/obo/OBI_0300311 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0300311 observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. http://purl.obolibrary.org/obo/OBI_0300311 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0300311 OBI branch derived http://purl.obolibrary.org/obo/OBI_0300311 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0300311 observation design http://purl.obolibrary.org/obo/OBI_0302884 extraction http://purl.obolibrary.org/obo/OBI_0302884 nucleic acid extraction using phenol chloroform http://purl.obolibrary.org/obo/OBI_0302884 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0302884 A material separation in which a desired component of an input material is separated from the remainder http://purl.obolibrary.org/obo/OBI_0302884 Person:Bjoern Peters http://purl.obolibrary.org/obo/OBI_0302884 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0302884 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0302884 extraction http://purl.obolibrary.org/obo/OBI_0302900 group randomization http://purl.obolibrary.org/obo/OBI_0302900 PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6. http://purl.obolibrary.org/obo/OBI_0302900 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0302900 A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up. http://purl.obolibrary.org/obo/OBI_0302900 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0302900 adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization] http://purl.obolibrary.org/obo/OBI_0302900 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0302900 group randomization http://purl.obolibrary.org/obo/OBI_0302903 nucleic acid hybridization http://purl.obolibrary.org/obo/OBI_0302903 PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27. http://purl.obolibrary.org/obo/OBI_0302903 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0302903 a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity. http://purl.obolibrary.org/obo/OBI_0302903 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0302903 adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization] http://purl.obolibrary.org/obo/OBI_0302903 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0302903 hybridization assay http://purl.obolibrary.org/obo/OBI_0302903 nucleic acid hybridization http://purl.obolibrary.org/obo/OBI_0400043 flow cell http://purl.obolibrary.org/obo/OBI_0400043 Biofilm Flow Cell http://purl.obolibrary.org/obo/OBI_0400043 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0400043 Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell. http://purl.obolibrary.org/obo/OBI_0400043 Person:John Quinn http://purl.obolibrary.org/obo/OBI_0400043 flow_cell http://purl.obolibrary.org/obo/OBI_0400043 http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm http://purl.obolibrary.org/obo/OBI_0400043 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0400043 flow cell http://purl.obolibrary.org/obo/OBI_0400044 flow cytometer http://purl.obolibrary.org/obo/OBI_0400044 FACS Calibur http://purl.obolibrary.org/obo/OBI_0400044 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0400044 A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium. http://purl.obolibrary.org/obo/OBI_0400044 John Quinn http://purl.obolibrary.org/obo/OBI_0400044 http://en.wikipedia.org/wiki/Flow_cytometer http://purl.obolibrary.org/obo/OBI_0400044 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0400044 flow cytometer http://purl.obolibrary.org/obo/OBI_0400065 light source http://purl.obolibrary.org/obo/OBI_0400065 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0400065 A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. http://purl.obolibrary.org/obo/OBI_0400065 Elizabeth M. Goralczyk http://purl.obolibrary.org/obo/OBI_0400065 John Quinn http://purl.obolibrary.org/obo/OBI_0400065 Olga Tchuvatkina http://purl.obolibrary.org/obo/OBI_0400065 Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 http://purl.obolibrary.org/obo/OBI_0400065 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0400065 light source http://purl.obolibrary.org/obo/OBI_0400078 obscuration bar http://purl.obolibrary.org/obo/OBI_0400078 obscuration bar in a flow cytometer http://purl.obolibrary.org/obo/OBI_0400078 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0400078 An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device. http://purl.obolibrary.org/obo/OBI_0400078 Daniel Schober http://purl.obolibrary.org/obo/OBI_0400078 Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249 http://purl.obolibrary.org/obo/OBI_0400078 John Quinn http://purl.obolibrary.org/obo/OBI_0400078 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0400078 obscuration bar http://purl.obolibrary.org/obo/OBI_0400079 optical filter http://purl.obolibrary.org/obo/OBI_0400079 720 LP filter, 580/30 BP filter http://purl.obolibrary.org/obo/OBI_0400079 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0400079 An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length. http://purl.obolibrary.org/obo/OBI_0400079 John Quinn http://purl.obolibrary.org/obo/OBI_0400079 http://en.wikipedia.org/wiki/Optical_filter http://purl.obolibrary.org/obo/OBI_0400079 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0400079 optical filter http://purl.obolibrary.org/obo/OBI_0400082 photodetector http://purl.obolibrary.org/obo/OBI_0400082 A photomultiplier tube, a photo diode http://purl.obolibrary.org/obo/OBI_0400082 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0400082 A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye. http://purl.obolibrary.org/obo/OBI_0400082 John Quinn http://purl.obolibrary.org/obo/OBI_0400082 http://einstein.stanford.edu/content/glossary/glossary.html http://purl.obolibrary.org/obo/OBI_0400082 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0400082 photodetector http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer http://purl.obolibrary.org/obo/OBI_0400103 ABI 377 DNA Sequencer, ABI 310 DNA Sequencer http://purl.obolibrary.org/obo/OBI_0400103 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0400103 A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. http://purl.obolibrary.org/obo/OBI_0400103 Trish Whetzel http://purl.obolibrary.org/obo/OBI_0400103 MO http://purl.obolibrary.org/obo/OBI_0400103 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0400103 DNA sequencer http://purl.obolibrary.org/obo/OBI_0400110 hybridization chamber http://purl.obolibrary.org/obo/OBI_0400110 Glass Array Hybridization Cassette http://purl.obolibrary.org/obo/OBI_0400110 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0400110 A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide. http://purl.obolibrary.org/obo/OBI_0400110 Trish Whetzel http://purl.obolibrary.org/obo/OBI_0400110 MO_563 hybridization_chamber http://purl.obolibrary.org/obo/OBI_0400110 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0400110 hybridization chamber http://purl.obolibrary.org/obo/OBI_0400137 cytometer http://purl.obolibrary.org/obo/OBI_0400137 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0400137 A cytometer is an instrument for counting and measuring cells. http://purl.obolibrary.org/obo/OBI_0400137 Melanie Courtot http://purl.obolibrary.org/obo/OBI_0400137 http://medical.merriam-webster.com/medical/cytometer http://purl.obolibrary.org/obo/OBI_0400137 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0400137 cytometer http://purl.obolibrary.org/obo/OBI_0400147 microarray http://purl.obolibrary.org/obo/OBI_0400147 An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays. http://purl.obolibrary.org/obo/OBI_0400147 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0400147 A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position. http://purl.obolibrary.org/obo/OBI_0400147 Daniel Schober http://purl.obolibrary.org/obo/OBI_0400147 PERSON: Chris Stoeckert http://purl.obolibrary.org/obo/OBI_0400147 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0400147 microarray http://purl.obolibrary.org/obo/OBI_0400148 DNA microarray http://purl.obolibrary.org/obo/OBI_0400148 Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115 http://purl.obolibrary.org/obo/OBI_0400148 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0400148 A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample. http://purl.obolibrary.org/obo/OBI_0400148 PERSON: Daniel Schober http://purl.obolibrary.org/obo/OBI_0400148 PERSON: Frank Gibson http://purl.obolibrary.org/obo/OBI_0400148 DNA Chip http://purl.obolibrary.org/obo/OBI_0400148 DNA-array http://purl.obolibrary.org/obo/OBI_0400148 Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03 http://purl.obolibrary.org/obo/OBI_0400148 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0400148 DNA microarray http://purl.obolibrary.org/obo/OBI_0400153 droplet sorter http://purl.obolibrary.org/obo/OBI_0400153 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/OBI_0400153 OBI Instrument branch http://purl.obolibrary.org/obo/OBI_0400153 OBI Instrument branch http://purl.obolibrary.org/obo/OBI_0400153 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0400153 droplet sorter http://purl.obolibrary.org/obo/OBI_0500000 study design http://purl.obolibrary.org/obo/OBI_0500000 a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. http://purl.obolibrary.org/obo/OBI_0500000 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0500000 A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. http://purl.obolibrary.org/obo/OBI_0500000 Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. http://purl.obolibrary.org/obo/OBI_0500000 PERSON: Chris Stoeckert http://purl.obolibrary.org/obo/OBI_0500000 experimental design http://purl.obolibrary.org/obo/OBI_0500000 rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. http://purl.obolibrary.org/obo/OBI_0500000 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0500000 http://purl.obolibrary.org/obo/OBI_0500000 study design http://purl.obolibrary.org/obo/OBI_0500002 repeated measure design http://purl.obolibrary.org/obo/OBI_0500002 PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations. http://purl.obolibrary.org/obo/OBI_0500002 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0500002 a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs http://purl.obolibrary.org/obo/OBI_0500002 PlanAndPlannedProcess Branch http://purl.obolibrary.org/obo/OBI_0500002 http://www.holah.karoo.net/experimentaldesigns.htm http://purl.obolibrary.org/obo/OBI_0500002 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0500002 http://purl.obolibrary.org/obo/OBI_0500002 repeated measure design http://purl.obolibrary.org/obo/OBI_0500003 cross over design http://purl.obolibrary.org/obo/OBI_0500003 PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity. http://purl.obolibrary.org/obo/OBI_0500003 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0500003 a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control http://purl.obolibrary.org/obo/OBI_0500003 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0500003 (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html) http://purl.obolibrary.org/obo/OBI_0500003 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0500003 http://purl.obolibrary.org/obo/OBI_0500003 cross over design http://purl.obolibrary.org/obo/OBI_0500005 matched pairs design http://purl.obolibrary.org/obo/OBI_0500005 PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs. http://purl.obolibrary.org/obo/OBI_0500005 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0500005 A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment. http://purl.obolibrary.org/obo/OBI_0500005 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0500005 http://www.holah.karoo.net/experimentaldesigns.htm http://purl.obolibrary.org/obo/OBI_0500005 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0500005 http://purl.obolibrary.org/obo/OBI_0500005 matched pairs design http://purl.obolibrary.org/obo/OBI_0500006 parallel group design http://purl.obolibrary.org/obo/OBI_0500006 PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR. http://purl.obolibrary.org/obo/OBI_0500006 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0500006 A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment http://purl.obolibrary.org/obo/OBI_0500006 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0500006 independent measure design http://purl.obolibrary.org/obo/OBI_0500006 http://www.holah.karoo.net/experimentaldesigns.htm http://purl.obolibrary.org/obo/OBI_0500006 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0500006 parallel group design http://purl.obolibrary.org/obo/OBI_0500007 randomized complete block design http://purl.obolibrary.org/obo/OBI_0500007 http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd)) http://purl.obolibrary.org/obo/OBI_0500007 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0500007 A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups. http://purl.obolibrary.org/obo/OBI_0500007 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0500007 http://www.tufts.edu/~gdallal/ranblock.htm http://purl.obolibrary.org/obo/OBI_0500007 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0500007 http://purl.obolibrary.org/obo/OBI_0500007 randomized complete block design http://purl.obolibrary.org/obo/OBI_0500011 latin square design http://purl.obolibrary.org/obo/OBI_0500011 PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. http://purl.obolibrary.org/obo/OBI_0500011 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0500011 Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables). The 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once. http://purl.obolibrary.org/obo/OBI_0500011 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0500011 Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and http://purl.obolibrary.org/obo/OBI_0500011 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0500011 http://purl.obolibrary.org/obo/OBI_0500011 latin square design http://purl.obolibrary.org/obo/OBI_0500012 graeco latin square design http://purl.obolibrary.org/obo/OBI_0500012 PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes. http://purl.obolibrary.org/obo/OBI_0500012 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0500012 graeco-latin square design is a block design which declares 3 blocking variables (aka nuisance variables) in addition to the treatment variable http://purl.obolibrary.org/obo/OBI_0500012 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0500012 Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and http://purl.obolibrary.org/obo/OBI_0500012 only 2 articles in pubmed ->probably irrelevant http://purl.obolibrary.org/obo/OBI_0500012 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0500012 http://purl.obolibrary.org/obo/OBI_0500012 Euler square design http://purl.obolibrary.org/obo/OBI_0500012 orthogonal latin squares design http://purl.obolibrary.org/obo/OBI_0500012 graeco latin square design http://purl.obolibrary.org/obo/OBI_0500013 hyper graeco latin square design http://purl.obolibrary.org/obo/OBI_0500013 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0500013 hyper graeco-latin square design is a block design which declares 4 blocking variables (aka nuisance variables) in addition to the treatment variable http://purl.obolibrary.org/obo/OBI_0500013 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0500013 Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and http://purl.obolibrary.org/obo/OBI_0500013 no example found in pubmed->not in use in the community http://purl.obolibrary.org/obo/OBI_0500013 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0500013 http://purl.obolibrary.org/obo/OBI_0500013 hyper graeco latin square design http://purl.obolibrary.org/obo/OBI_0500014 factorial design http://purl.obolibrary.org/obo/OBI_0500014 PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. http://purl.obolibrary.org/obo/OBI_0500014 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0500014 factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable. http://purl.obolibrary.org/obo/OBI_0500014 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0500014 http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment) http://purl.obolibrary.org/obo/OBI_0500014 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0500014 http://purl.obolibrary.org/obo/OBI_0500014 factorial design http://purl.obolibrary.org/obo/OBI_0500015 2x2 factorial design http://purl.obolibrary.org/obo/OBI_0500015 PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed. http://purl.obolibrary.org/obo/OBI_0500015 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0500015 a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors http://purl.obolibrary.org/obo/OBI_0500015 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0500015 PMID: 17561240 http://purl.obolibrary.org/obo/OBI_0500015 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0500015 http://purl.obolibrary.org/obo/OBI_0500015 2x2 factorial design http://purl.obolibrary.org/obo/OBI_0500016 fractional factorial design http://purl.obolibrary.org/obo/OBI_0500016 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0500016 A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run http://purl.obolibrary.org/obo/OBI_0500016 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0500016 http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control http://purl.obolibrary.org/obo/OBI_0500016 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0500016 fractional factorial design http://purl.obolibrary.org/obo/OBI_0500017 dye swap design http://purl.obolibrary.org/obo/OBI_0500017 PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. http://purl.obolibrary.org/obo/OBI_0500017 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0500017 An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip http://purl.obolibrary.org/obo/OBI_0500017 Philippe Rocca-Serra on behalf of MO http://purl.obolibrary.org/obo/OBI_0500017 MO_858 http://purl.obolibrary.org/obo/OBI_0500017 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0500017 http://purl.obolibrary.org/obo/OBI_0500017 dye swap design http://purl.obolibrary.org/obo/OBI_0500020 time series design http://purl.obolibrary.org/obo/OBI_0500020 PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources. http://purl.obolibrary.org/obo/OBI_0500020 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0500020 Groups of assays that are related as part of a time series. http://purl.obolibrary.org/obo/OBI_0500020 PRS-AGB adding formal restriction on independent variable specification about time (march 2013) and making time series design class a defined class. http://purl.obolibrary.org/obo/OBI_0500020 Philippe Rocca-Serra on behalf of MO http://purl.obolibrary.org/obo/OBI_0500020 MO_887 http://purl.obolibrary.org/obo/OBI_0500020 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0500020 http://purl.obolibrary.org/obo/OBI_0500020 time series design http://purl.obolibrary.org/obo/OBI_0600005 collecting specimen from organism http://purl.obolibrary.org/obo/OBI_0600005 taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient http://purl.obolibrary.org/obo/OBI_0600005 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0600005 a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation http://purl.obolibrary.org/obo/OBI_0600005 PERSON:Bjoern Peters http://purl.obolibrary.org/obo/OBI_0600005 IEDB http://purl.obolibrary.org/obo/OBI_0600005 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0600005 collecting specimen from organism http://purl.obolibrary.org/obo/OBI_0600014 material component separation http://purl.obolibrary.org/obo/OBI_0600014 Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification http://purl.obolibrary.org/obo/OBI_0600014 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0600014 a material processing in which components of an input material become segregated in space http://purl.obolibrary.org/obo/OBI_0600014 Bjoern Peters http://purl.obolibrary.org/obo/OBI_0600014 IEDB http://purl.obolibrary.org/obo/OBI_0600014 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0600014 material component separation http://purl.obolibrary.org/obo/OBI_0600015 group assignment http://purl.obolibrary.org/obo/OBI_0600015 Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation http://purl.obolibrary.org/obo/OBI_0600015 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_0600015 group assignment is a process which has an organism as specified input and during which a role is assigned http://purl.obolibrary.org/obo/OBI_0600015 Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_0600015 cohort assignment http://purl.obolibrary.org/obo/OBI_0600015 study assignment http://purl.obolibrary.org/obo/OBI_0600015 OBI Plan http://purl.obolibrary.org/obo/OBI_0600015 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0600015 group assignment http://purl.obolibrary.org/obo/OBI_0600024 maintaining cell culture http://purl.obolibrary.org/obo/OBI_0600024 When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture http://purl.obolibrary.org/obo/OBI_0600024 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0600024 a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing http://purl.obolibrary.org/obo/OBI_0600024 PlanAndPlannedProcess Branch http://purl.obolibrary.org/obo/OBI_0600024 OBI branch derived http://purl.obolibrary.org/obo/OBI_0600024 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0600024 maintaining cell culture http://purl.obolibrary.org/obo/OBI_0600036 establishing cell culture http://purl.obolibrary.org/obo/OBI_0600036 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0600036 a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). http://purl.obolibrary.org/obo/OBI_0600036 PERSON:Matthew Brush http://purl.obolibrary.org/obo/OBI_0600036 PERSON:Matthew Brush http://purl.obolibrary.org/obo/OBI_0600036 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0600036 A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. http://purl.obolibrary.org/obo/OBI_0600036 establishing cell culture http://purl.obolibrary.org/obo/OBI_0600038 addition of molecular label http://purl.obolibrary.org/obo/OBI_0600038 The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+. http://purl.obolibrary.org/obo/OBI_0600038 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0600038 a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay http://purl.obolibrary.org/obo/OBI_0600038 PERSON:Matthew Brush http://purl.obolibrary.org/obo/OBI_0600038 labeling http://purl.obolibrary.org/obo/OBI_0600038 OBI developer call, 3-12-12 http://purl.obolibrary.org/obo/OBI_0600038 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0600038 addition of molecular label http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay http://purl.obolibrary.org/obo/OBI_0600047 The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template http://purl.obolibrary.org/obo/OBI_0600047 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0600047 the use of a chemical or biochemical means to infer the sequence of a biomaterial http://purl.obolibrary.org/obo/OBI_0600047 has_output should be sequence of input; we don't have sequence well defined yet http://purl.obolibrary.org/obo/OBI_0600047 PlanAndPlannedProcess Branch http://purl.obolibrary.org/obo/OBI_0600047 OBI branch derived http://purl.obolibrary.org/obo/OBI_0600047 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay http://purl.obolibrary.org/obo/OBI_0600064 recombinant vector cloning http://purl.obolibrary.org/obo/OBI_0600064 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_0600064 a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material http://purl.obolibrary.org/obo/OBI_0600064 pa_branch (Alan, Randi, Kevin, Jay, Bjoern) http://purl.obolibrary.org/obo/OBI_0600064 molecular cloning http://purl.obolibrary.org/obo/OBI_0600064 OBI branch derived http://purl.obolibrary.org/obo/OBI_0600064 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0600064 recombinant vector cloning http://purl.obolibrary.org/obo/OBI_0666667 nucleic acid extraction http://purl.obolibrary.org/obo/OBI_0666667 Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet. http://purl.obolibrary.org/obo/OBI_0666667 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/OBI_0666667 a material separation to recover the nucleic acid fraction of an input material http://purl.obolibrary.org/obo/OBI_0666667 PlanAndPlannedProcess Branch http://purl.obolibrary.org/obo/OBI_0666667 OBI branch derived http://purl.obolibrary.org/obo/OBI_0666667 requested by Helen Parkinson for MO. Could be defined class http://purl.obolibrary.org/obo/OBI_0666667 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_0666667 nucleic acid extraction http://purl.obolibrary.org/obo/OBI_1000029 phage display library http://purl.obolibrary.org/obo/OBI_1000029 PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides] http://purl.obolibrary.org/obo/OBI_1000029 http://purl.obolibrary.org/obo/IAO_0000120 http://purl.obolibrary.org/obo/OBI_1000029 a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified. http://purl.obolibrary.org/obo/OBI_1000029 PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_1000029 PERSON: Philippe Rocca-Serra http://purl.obolibrary.org/obo/OBI_1000029 display library http://purl.obolibrary.org/obo/OBI_1000029 WEB: http://www.immuneepitope.org/home.do http://purl.obolibrary.org/obo/OBI_1000029 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_1000029 phage display library http://purl.obolibrary.org/obo/OBI_1110108 material to be added http://purl.obolibrary.org/obo/OBI_1110108 A mixture of peptides that is being added into a cell culture. http://purl.obolibrary.org/obo/OBI_1110108 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_1110108 a material that is added to another one in a material combination process http://purl.obolibrary.org/obo/OBI_1110108 10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export http://purl.obolibrary.org/obo/OBI_1110108 2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes http://purl.obolibrary.org/obo/OBI_1110108 IEDB http://purl.obolibrary.org/obo/OBI_1110108 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_1110108 material to be added http://purl.obolibrary.org/obo/OBI_1110109 target of material addition http://purl.obolibrary.org/obo/OBI_1110109 A cell culture into which a mixture of peptides is being added. http://purl.obolibrary.org/obo/OBI_1110109 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_1110109 A material entity into which another is being added in a material combinatino process http://purl.obolibrary.org/obo/OBI_1110109 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export. http://purl.obolibrary.org/obo/OBI_1110109 IEDB http://purl.obolibrary.org/obo/OBI_1110109 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OBI_1110109 target of material addition http://purl.obolibrary.org/obo/OBI_9991118 IEDB alternative term http://purl.obolibrary.org/obo/OBI_9991118 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/OBI_9991118 An alternative term used by the IEDB. http://purl.obolibrary.org/obo/OBI_9991118 PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters http://purl.obolibrary.org/obo/OBI_9991118 IEDB http://purl.obolibrary.org/obo/OBI_9991118 IEDB alternative term http://purl.obolibrary.org/obo/OGMS_0000023 phenotype http://purl.obolibrary.org/obo/OGMS_0000023 A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. http://purl.obolibrary.org/obo/OGMS_0000023 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/OGMS_0000023 http://purl.obolibrary.org/obo/ogms.owl http://purl.obolibrary.org/obo/OGMS_0000023 phenotype http://purl.obolibrary.org/obo/PR_000000001 protein http://purl.obolibrary.org/obo/PR_000000001 antithrombin III is a protein http://purl.obolibrary.org/obo/PR_000000001 An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA. http://purl.obolibrary.org/obo/PR_000000001 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/PR_000000001 http://purl.obolibrary.org/obo/pr.owl http://purl.obolibrary.org/obo/PR_000000001 protein http://purl.obolibrary.org/obo/REO_0000171 molecular label role http://purl.obolibrary.org/obo/REO_0000171 a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. http://purl.obolibrary.org/obo/REO_0000171 MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role) http://purl.obolibrary.org/obo/REO_0000171 molecular tracer role http://purl.obolibrary.org/obo/REO_0000171 OBI developer call, 3-12-12 http://purl.obolibrary.org/obo/REO_0000171 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/REO_0000171 http://purl.obolibrary.org/obo/reo.owl http://purl.obolibrary.org/obo/REO_0000171 molecular label role http://purl.obolibrary.org/obo/REO_0000280 molecular label http://purl.obolibrary.org/obo/REO_0000280 a molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay http://purl.obolibrary.org/obo/REO_0000280 molecular tracer http://purl.obolibrary.org/obo/REO_0000280 OBI developer call, 3-12-12 http://purl.obolibrary.org/obo/REO_0000280 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/REO_0000280 http://purl.obolibrary.org/obo/reo.owl http://purl.obolibrary.org/obo/REO_0000280 molecular label http://purl.obolibrary.org/obo/RO_0001000 derives from http://purl.obolibrary.org/obo/RO_0001000 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/RO_0001000 http://purl.obolibrary.org/obo/ro.owl http://purl.obolibrary.org/obo/RO_0001000 derives from http://purl.obolibrary.org/obo/SO_0000001 region http://purl.obolibrary.org/obo/SO_0000001 A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. http://purl.obolibrary.org/obo/SO_0000001 primary structure of sequence macromolecule http://purl.obolibrary.org/obo/SO_0000001 sequence http://purl.obolibrary.org/obo/SO_0000001 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/SO_0000001 http://purl.obolibrary.org/obo/so.owl http://purl.obolibrary.org/obo/SO_0000001 region http://purl.obolibrary.org/obo/STATO_0000001 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000001 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000001 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000001 declares http://purl.obolibrary.org/obo/STATO_0000002 digital images may be stored as electronic file in TIFF format on mass memory storage devices http://purl.obolibrary.org/obo/STATO_0000002 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000002 an electronic file is an information content entity which conforms to a specification or format and which is meant to hold data and information in digital form, accessible to software agents http://purl.obolibrary.org/obo/STATO_0000002 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000002 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000002 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000002 STATO http://purl.obolibrary.org/obo/STATO_0000002 digital file http://purl.obolibrary.org/obo/STATO_0000003 a balanced design is a an experimental design where all experimental group have the an equal number of subject observations http://purl.obolibrary.org/obo/STATO_0000003 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000003 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000003 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000003 STATO http://purl.obolibrary.org/obo/STATO_0000003 http://purl.obolibrary.org/obo/STATO_0000003 balanced design http://purl.obolibrary.org/obo/STATO_0000004 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000004 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000004 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000004 is declared by http://purl.obolibrary.org/obo/STATO_0000005 a single factor design is a study design which declares exactly 1 independent variable http://purl.obolibrary.org/obo/STATO_0000005 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000005 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000005 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000005 STATO http://purl.obolibrary.org/obo/STATO_0000005 http://purl.obolibrary.org/obo/STATO_0000005 single factor design http://purl.obolibrary.org/obo/STATO_0000006 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000006 x-axis is a cartesian coordinate axis which is orthogonal to the y-axis and the z-axis http://purl.obolibrary.org/obo/STATO_0000006 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000006 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000006 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000006 STATO http://purl.obolibrary.org/obo/STATO_0000006 x-axis http://purl.obolibrary.org/obo/STATO_0000007 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000007 an axis is a line graph used as reference line for the measurement of coordinates. http://purl.obolibrary.org/obo/STATO_0000007 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000007 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000007 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000007 http://www.oxforddictionaries.com/definition/english/axis http://purl.obolibrary.org/obo/STATO_0000007 axis http://purl.obolibrary.org/obo/STATO_0000008 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000008 y-axis is a cartesian coordinate axis which is orthogonal to the x-axis and the z-axis http://purl.obolibrary.org/obo/STATO_0000008 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000008 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000008 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000008 STATO http://purl.obolibrary.org/obo/STATO_0000008 y-axis http://purl.obolibrary.org/obo/STATO_0000009 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000009 A Cartesian coordinate system is a coordinate system that specifies each point uniquely in a plane by a pair of numerical coordinates, which are the signed distances from the point to two fixed perpendicular directed lines, measured in the same unit of length. http://purl.obolibrary.org/obo/STATO_0000009 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000009 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000009 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000009 http://en.wikipedia.org/wiki/Cartesian_coordinate_system http://purl.obolibrary.org/obo/STATO_0000009 http://purl.obolibrary.org/obo/STATO_0000009 cartesian coordinate system http://purl.obolibrary.org/obo/STATO_0000010 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000010 In geometry, a coordinate system is a system which uses one or more numbers, or coordinates, to uniquely determine the position of a point or other geometric element on a manifold such as Euclidean space. http://purl.obolibrary.org/obo/STATO_0000010 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000010 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000010 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000010 http://en.wikipedia.org/wiki/Coordinate_system http://purl.obolibrary.org/obo/STATO_0000010 http://purl.obolibrary.org/obo/STATO_0000010 coordinate system http://purl.obolibrary.org/obo/STATO_0000011 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000011 a cartesian axis is one of 3 the axis in a cartesian coordinate system defining a referential in 3 dimensions. each of the axis is orthogonal to the other 2 http://purl.obolibrary.org/obo/STATO_0000011 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000011 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000011 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000011 rectangular coordinate axis http://purl.obolibrary.org/obo/STATO_0000011 adapted from Wolfram Alpha: https://www.wolframalpha.com/input/?i=cartesian+coordinates&lk=4&num=6&lk=4&num=6 http://purl.obolibrary.org/obo/STATO_0000011 cartesian coordinate axis http://purl.obolibrary.org/obo/STATO_0000012 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000012 z-axis is a cartesian coordinate axis which is orthogonal to the x-axis and the y-axis http://purl.obolibrary.org/obo/STATO_0000012 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000012 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000012 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000012 STATO http://purl.obolibrary.org/obo/STATO_0000012 z-axis http://purl.obolibrary.org/obo/STATO_0000013 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000013 a 2 dimensional cartesian coordinate system is a cartesian coordinate system which defines 2 orthogonal one dimensional axes and which may be used to describe a 2 dimensional spatial region http://purl.obolibrary.org/obo/STATO_0000013 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000013 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000013 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000013 http://purl.obolibrary.org/obo/STATO_0000013 two dimensional cartesian coordinate system http://purl.obolibrary.org/obo/STATO_0000014 http://purl.obolibrary.org/obo/IAO_0000226 http://purl.obolibrary.org/obo/STATO_0000014 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000014 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000014 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000014 http://purl.obolibrary.org/obo/STATO_0000014 spherical coordinate system http://purl.obolibrary.org/obo/STATO_0000015 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/STATO_0000015 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000015 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000015 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000015 http://purl.obolibrary.org/obo/STATO_0000015 cylindrical coordinate system http://purl.obolibrary.org/obo/STATO_0000016 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000016 In mathematics, the polar coordinate system is a two-dimensional coordinate system in which each point on a plane is determined by a distance from a fixed point and an angle from a fixed direction. http://purl.obolibrary.org/obo/STATO_0000016 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000016 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000016 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000016 http://en.wikipedia.org/wiki/Polar_coordinate_system http://purl.obolibrary.org/obo/STATO_0000016 http://purl.obolibrary.org/obo/STATO_0000016 polar coordinate system http://purl.obolibrary.org/obo/STATO_0000017 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000017 Wilks' lambda distribution (named for Samuel S. Wilks), is a probability distribution used in multivariate hypothesis testing, especially with regard to the likelihood-ratio test and Multivariate analysis of variance. It is a multivariate generalization of the univariate F-distribution, and generalizes the F-distribution in the same way that the Hotelling's T-squared distribution generalizes Student's t-distribution. http://purl.obolibrary.org/obo/STATO_0000017 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000017 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000017 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000017 wikipedia: last accessed: 2013-09-11 http://en.wikipedia.org/wiki/Wilks%27_lambda_distribution http://purl.obolibrary.org/obo/STATO_0000017 Wilk's lambda distribution http://purl.obolibrary.org/obo/STATO_0000018 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000018 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000018 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000018 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000018 three dimensional cartesian spatial coordinage origin http://purl.obolibrary.org/obo/STATO_0000019 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000019 normal distribution hypothesis is a goodness of fit hypothesis stating that the distribution computed from the sample population fits a normal distribution http://purl.obolibrary.org/obo/STATO_0000019 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000019 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000019 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000019 STATO http://purl.obolibrary.org/obo/STATO_0000019 normal distribution hypothesis http://purl.obolibrary.org/obo/STATO_0000020 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000020 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000020 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000020 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000020 two dimensional cartesian spatial coordinate origin http://purl.obolibrary.org/obo/STATO_0000021 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000021 a confidence interval which covers 90% of the sampling distribution, meaning that there is a 90% risk of false positive (type I error) http://purl.obolibrary.org/obo/STATO_0000021 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000021 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000021 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000021 STATO http://purl.obolibrary.org/obo/STATO_0000021 http://purl.obolibrary.org/obo/STATO_0000021 90% confidence interval http://purl.obolibrary.org/obo/STATO_0000022 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000022 a three dimensional cartesian coordinate system is a cartesian coordinate system which defines 3 orthogonal one dimensional axis and which may be used to describe a 3 dimensional spatial region http://purl.obolibrary.org/obo/STATO_0000022 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000022 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000022 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000022 http://purl.obolibrary.org/obo/STATO_0000022 one dimensional cartesian coordinate system http://purl.obolibrary.org/obo/STATO_0000023 http://www.stat.duke.edu/courses/Spring98/sta110c/qtable.html http://purl.obolibrary.org/obo/STATO_0000023 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000023 The studentized range (q) distribution is a probability distribution used by the Tukey Honestly Significant Difference test. The distribution of the statistic [x̄(k)- x̄(1)]/(s/√n) where random samples of size n have been taken from k independent and identically distributed normal populations, with x̄(1) and x̄(k) being, respectively, the smallest and largest of the k sample means, and s2 being the pooled estimate of the common variance. This statistic is particularly used in multiple comparison tests. http://purl.obolibrary.org/obo/STATO_0000023 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000023 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000023 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000023 q distribution http://purl.obolibrary.org/obo/STATO_0000023 A Dictionary of Statistics (2 rev ed.), OUP. ISBN-13: 9780199541454 http://www.oxfordreference.com/view/10.1093/acref/9780199541454.001.0001/acref-9780199541454-e-1588 http://purl.obolibrary.org/obo/STATO_0000023 http://purl.obolibrary.org/obo/STATO_0000023 http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Tukey.html http://purl.obolibrary.org/obo/STATO_0000023 studentized range distribution http://purl.obolibrary.org/obo/STATO_0000024 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000024 a three dimensional cartesian coordinate system is a cartesian coordinate system which defines 3 orthogonal one dimensional axes and which may be used to describe a 3 dimensional spatial region http://purl.obolibrary.org/obo/STATO_0000024 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000024 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000024 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000024 http://purl.obolibrary.org/obo/STATO_0000024 three dimensional cartesian coordinate system http://purl.obolibrary.org/obo/STATO_0000025 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000025 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000025 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000025 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000025 one dimensional cartesian spatial coordinate origin http://purl.obolibrary.org/obo/STATO_0000026 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000026 placeholder, more work needed http://purl.obolibrary.org/obo/STATO_0000026 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000026 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000026 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000026 cartesian spatial coordinate origin http://purl.obolibrary.org/obo/STATO_0000027 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000027 linkage between 2 categorical variable test is a statistical test which evaluates if there is an association between a predictor variable assuming discrete values and a response variable also assuming discrete values http://purl.obolibrary.org/obo/STATO_0000027 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000027 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000027 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000027 test of association http://purl.obolibrary.org/obo/STATO_0000027 STATO http://purl.obolibrary.org/obo/STATO_0000027 test of independence http://purl.obolibrary.org/obo/STATO_0000027 test of independence between variables http://purl.obolibrary.org/obo/STATO_0000027 test of association between categorical variables http://purl.obolibrary.org/obo/STATO_0000028 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000028 measure of variation or statistical dispersion is a data item which describes how much a theoritical distribution or dataset is spread. http://purl.obolibrary.org/obo/STATO_0000028 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000028 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000028 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000028 STATO http://purl.obolibrary.org/obo/STATO_0000028 measure of dispersion http://purl.obolibrary.org/obo/STATO_0000028 measure of variation http://purl.obolibrary.org/obo/STATO_0000028 measure of variation http://purl.obolibrary.org/obo/STATO_0000029 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000029 a measure of central tendency is a data item which attempts to describe a set of data by identifying the value of its centre. http://purl.obolibrary.org/obo/STATO_0000029 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000029 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000029 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000029 measure of central tendency http://purl.obolibrary.org/obo/STATO_0000029 measure of central tendency http://purl.obolibrary.org/obo/STATO_0000030 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000030 Chi-squared statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Chi-Squared distribution. http://purl.obolibrary.org/obo/STATO_0000030 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000030 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000030 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000030 STATO http://purl.obolibrary.org/obo/STATO_0000030 Chi-Squared statistic http://purl.obolibrary.org/obo/STATO_0000031 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000031 binary classification (or binomial classification) is a data transformation which aims to cast members of a set into 2 disjoint groups depending on whether the element have a given property/feature or not. http://purl.obolibrary.org/obo/STATO_0000031 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000031 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000031 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000031 adapted from wikipedia: http://en.wikipedia.org/wiki/Binary_classifier last accessed: 2013-11-21 http://purl.obolibrary.org/obo/STATO_0000031 binomial classification http://purl.obolibrary.org/obo/STATO_0000031 binary classification http://purl.obolibrary.org/obo/STATO_0000032 an alternative term used for STATO statistical ontology and ISA team http://purl.obolibrary.org/obo/STATO_0000032 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000032 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000032 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000032 STATO alternative term http://purl.obolibrary.org/obo/STATO_0000033 The mode is a data item which corresponds to the most frequently occurring number in a set of numbers. http://purl.obolibrary.org/obo/STATO_0000033 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000033 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000033 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000033 http://www.sagepub.com/upm-data/47775_ch_3.pdf http://purl.obolibrary.org/obo/STATO_0000033 mode http://purl.obolibrary.org/obo/STATO_0000033 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000033 mode http://purl.obolibrary.org/obo/STATO_0000034 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000034 a model parameter is a data item which is part of a model and which is meant to characterize an theoritecal or unknown population. a model parameter may be estimated by considering the properties of samples presumably taken from the theoritecal population http://purl.obolibrary.org/obo/STATO_0000034 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000034 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000034 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000034 STATO http://purl.obolibrary.org/obo/STATO_0000034 model parameter http://purl.obolibrary.org/obo/STATO_0000035 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000035 the range is a measure of variation which describes the difference between the lowest score and the highest score in a set of numbers (a data set) http://purl.obolibrary.org/obo/STATO_0000035 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000035 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000035 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000035 http://www.sagepub.com/upm-data/47775_ch_3.pdf http://purl.obolibrary.org/obo/STATO_0000035 http://purl.obolibrary.org/obo/STATO_0000035 range(..., na.rm = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/base/html/range.html http://purl.obolibrary.org/obo/STATO_0000035 range http://purl.obolibrary.org/obo/STATO_0000036 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000036 Outliers are deviant scores that have been legitimately gathered and are not due to equipment failures. http://purl.obolibrary.org/obo/STATO_0000036 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000036 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000036 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000036 http://www.sagepub.com/upm-data/47775_ch_3.pdf http://purl.obolibrary.org/obo/STATO_0000036 outlier http://purl.obolibrary.org/obo/STATO_0000037 http://stats.stackexchange.com/questions/50623/r-calculating-mean-and-standard-error-of-mean-for-factors-with-lm-vs-direct http://purl.obolibrary.org/obo/STATO_0000037 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000037 The standard error of the mean (SEM) is data item denoting the the standard deviation of the sample-mean's estimate of a population mean. It is calculated by dividing the sample standard deviation (i.e., the sample-based estimate of the standard deviation of the population) by the square root of n , the size (number of observations) of the sample. http://purl.obolibrary.org/obo/STATO_0000037 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000037 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000037 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000037 SEM http://purl.obolibrary.org/obo/STATO_0000037 http://purl.obolibrary.org/obo/STATO_0000037 adapted from wikipedia (https://en.wikipedia.org/wiki/Standard_error) http://purl.obolibrary.org/obo/STATO_0000037 http://purl.obolibrary.org/obo/STATO_0000037 standard error of the mean http://purl.obolibrary.org/obo/STATO_0000038 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000038 a set of 2 subjects which result from a pairing process which assigns subject to a set based on a pairing rule/criteria http://purl.obolibrary.org/obo/STATO_0000038 possibly submit to 'Population and Community Ontology' http://purl.obolibrary.org/obo/STATO_0000038 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000038 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000038 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000038 STATO http://purl.obolibrary.org/obo/STATO_0000038 http://purl.obolibrary.org/obo/STATO_0000038 matched pair of subjects http://purl.obolibrary.org/obo/STATO_0000039 http://purl.obolibrary.org/obo/STATO_0000039 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000039 a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data. http://purl.obolibrary.org/obo/STATO_0000039 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000039 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000039 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000039 STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic). http://purl.obolibrary.org/obo/STATO_0000039 statistic http://purl.obolibrary.org/obo/STATO_0000039 statistic http://purl.obolibrary.org/obo/STATO_0000040 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000040 an MA plot is a scatter plot of the log intensity ratios M = log_2(T/R) versus the average log intensities A = log_2(T*T)/2, where T and R represent the signal intensities in the test and reference channels respectively. http://purl.obolibrary.org/obo/STATO_0000040 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000040 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000040 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000040 M vs A plot http://purl.obolibrary.org/obo/STATO_0000040 http://www.stat.berkeley.edu/users/terry/zarray/Software/SMAcode/html/plot.mva.html http://purl.obolibrary.org/obo/STATO_0000040 MA plot http://purl.obolibrary.org/obo/STATO_0000040 plot.mva() http://purl.obolibrary.org/obo/STATO_0000040 MA plot http://purl.obolibrary.org/obo/STATO_0000041 a R command syntax or link to a R documentation in support of Statistical Ontology Classes or Data Transformations http://purl.obolibrary.org/obo/STATO_0000041 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000041 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000041 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000041 R command http://purl.obolibrary.org/obo/STATO_0000042 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000042 The Anderson–Darling test is a statistical test of whether a given sample of data is drawn from a given probability distribution. http://purl.obolibrary.org/obo/STATO_0000042 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000042 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000042 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000042 http://en.wikipedia.org/wiki/Anderson_Darling_test http://purl.obolibrary.org/obo/STATO_0000042 http://purl.obolibrary.org/obo/STATO_0000042 ad.test(x) function, where x is a numeric vector http://purl.obolibrary.org/obo/STATO_0000042 Anderson-Darling test http://purl.obolibrary.org/obo/STATO_0000044 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000044 one-way anova is an analysis of variance where the different groups being compared are associated with the factor levels of only one independent variable. The null hypothesis is an absence of difference between the means calculated for each of the groups. The test assumes normality and equivariance of the data. http://purl.obolibrary.org/obo/STATO_0000044 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000044 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000044 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000044 one factor ANOVA http://purl.obolibrary.org/obo/STATO_0000044 STATO http://purl.obolibrary.org/obo/STATO_0000044 http://purl.obolibrary.org/obo/STATO_0000044 http://statland.org/R/R/R1way.htm http://purl.obolibrary.org/obo/STATO_0000044 one-way ANOVA http://purl.obolibrary.org/obo/STATO_0000045 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000045 two-way anova is an analysis of variance where the different groups being compared are associated the factor levels of exatly 2 independent variables. The null hypothesis is an absence of difference between the means calculated for each of the groups. The test assumes normality and equivariance of the data. http://purl.obolibrary.org/obo/STATO_0000045 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000045 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000045 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000045 two factor ANOVA http://purl.obolibrary.org/obo/STATO_0000045 STATO http://purl.obolibrary.org/obo/STATO_0000045 http://purl.obolibrary.org/obo/STATO_0000045 http://courses.statistics.com/software/R/Rtwoway.htm http://purl.obolibrary.org/obo/STATO_0000045 two-way ANOVA http://purl.obolibrary.org/obo/STATO_0000046 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000046 a block design is a kind of study design which declares a blocking variable (also known as nuisance variable) in order to account for a known source of variation and reduce its impact on the acquisition of the signal http://purl.obolibrary.org/obo/STATO_0000046 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000046 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000046 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000046 adapted from several sources including Wikipedia http://purl.obolibrary.org/obo/STATO_0000046 http://purl.obolibrary.org/obo/STATO_0000046 block design http://purl.obolibrary.org/obo/STATO_0000047 a count of 4 resulting from counting limbs in humans http://purl.obolibrary.org/obo/STATO_0000047 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000047 a count is a data item denoted by an integer and represented the number of instances or occurences of an entity http://purl.obolibrary.org/obo/STATO_0000047 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000047 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000047 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000047 STATO http://purl.obolibrary.org/obo/STATO_0000047 http://purl.obolibrary.org/obo/STATO_0000047 count http://purl.obolibrary.org/obo/STATO_0000048 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000048 Multi-way anova is an analysis of variance where the difference groups being compared are associated to the factor levels of more than 2 independent variables. The null hypothesis is an absence of difference between the means calculated for each of the groups. The test assumes normality and equivariance of the data. http://purl.obolibrary.org/obo/STATO_0000048 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000048 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000048 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000048 STATO http://purl.obolibrary.org/obo/STATO_0000048 http://purl.obolibrary.org/obo/STATO_0000048 multiway ANOVA http://purl.obolibrary.org/obo/STATO_0000049 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581961/ http://purl.obolibrary.org/obo/STATO_0000049 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000049 Hardy-Weinberg equilibrium hypothesis is a good of fit hypothesis which states that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences (non-random mating, mutation, selection, genetic drift, gene flow and meiotic drive). http://purl.obolibrary.org/obo/STATO_0000049 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000049 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000049 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000049 STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Hardy–Weinberg_principle) http://purl.obolibrary.org/obo/STATO_0000049 http://purl.obolibrary.org/obo/STATO_0000049 Hardy-Weinberg equilibrium hypothesis http://purl.obolibrary.org/obo/STATO_0000050 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000050 signal to noise ratio is a measurement datum comparing the amount of meaningful, useful or interesting data (the signal) to the amount of irrelevant or false data (the noise). Depending on the field and domain of application, different variables will be used to determinate a 'signal to noise ratio'. In statistics, the definition of signal to noise ratio is the ratio of the mean of a measurement to its standard deviation. It thus corresponds to the inverse of the coefficient of variation http://purl.obolibrary.org/obo/STATO_0000050 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000050 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000050 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000050 adapted from Wikipedia: http://en.wikipedia.org/wiki/Signal-to-noise_ratio#Alternative_definition last accessed: 2013-10-18 http://purl.obolibrary.org/obo/STATO_0000050 S/N http://purl.obolibrary.org/obo/STATO_0000050 SNR http://purl.obolibrary.org/obo/STATO_0000050 signal to noise ratio http://purl.obolibrary.org/obo/STATO_0000051 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000051 Poisson distribution is a probability distribution used to model the number of events occurring within a given time interval. It is defined by a real number (λ) and an integer k representing the number of events and a function. The expected value of a Poisson-distributed random variable is equal to λ and so is its variance. http://purl.obolibrary.org/obo/STATO_0000051 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000051 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000051 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000051 http://purl.obolibrary.org/obo/STATO_0000051 dpois(x, lambda, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Poisson.html http://purl.obolibrary.org/obo/STATO_0000051 NIST: http://www.itl.nist.gov/div898/handbook/eda/section3/eda366j.htm http://purl.obolibrary.org/obo/STATO_0000051 Poisson distribution http://purl.obolibrary.org/obo/STATO_0000052 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000052 Z-test is a statistical test which evaluate the null hypothesis that the means of 2 populations are equal and returns a p-value. http://purl.obolibrary.org/obo/STATO_0000052 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000052 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000052 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000052 http://reference.wolfram.com/mathematica/ref/ZTest.html http://purl.obolibrary.org/obo/STATO_0000052 http://purl.obolibrary.org/obo/STATO_0000052 simple.z.test(x, sigma, conf.level=0.95) http://www.inside-r.org/packages/cran/UsingR/docs/simple.z.test http://purl.obolibrary.org/obo/STATO_0000052 Z-test http://purl.obolibrary.org/obo/STATO_0000053 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000053 a false positive rate is a data item which accounts for the proportion of incorrect rejection of a true null hypothesis. http://purl.obolibrary.org/obo/STATO_0000053 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000053 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000053 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000053 PRS,AGB adapted from wikipedia and wolfram alpha http://purl.obolibrary.org/obo/STATO_0000053 significance level http://purl.obolibrary.org/obo/STATO_0000053 type I error rate http://purl.obolibrary.org/obo/STATO_0000053 α http://purl.obolibrary.org/obo/STATO_0000053 false positive rate http://purl.obolibrary.org/obo/STATO_0000054 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000054 homoskedasticity is a null hypothesis stating that all variances under consideration are homogenous http://purl.obolibrary.org/obo/STATO_0000054 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000054 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000054 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000054 equality of variance http://purl.obolibrary.org/obo/STATO_0000054 STATO http://purl.obolibrary.org/obo/STATO_0000054 http://purl.obolibrary.org/obo/STATO_0000054 homoskedasticity hypothesis http://purl.obolibrary.org/obo/STATO_0000055 http://www.ncbi.nlm.nih.gov/assembly/model/ chrX:35,000,000-36,000,000. http://purl.obolibrary.org/obo/STATO_0000055 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000055 chromosome coordinate system is a genomic coordinate which uses chromosome of a particular assembly build process to define start and end positions. This coordinate system is unstable and will change with each new genome sequence assembly build. http://purl.obolibrary.org/obo/STATO_0000055 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000055 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000055 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000055 http://purl.obolibrary.org/obo/STATO_0000055 chromosome coordinate system http://purl.obolibrary.org/obo/STATO_0000056 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000056 a null hypothesis which states that no linkage exists between 2 categorical variables http://purl.obolibrary.org/obo/STATO_0000056 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000056 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000056 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000056 STATO http://purl.obolibrary.org/obo/STATO_0000056 no relationship between the variables http://purl.obolibrary.org/obo/STATO_0000056 variables are independent http://purl.obolibrary.org/obo/STATO_0000056 absence of association hypothesis http://purl.obolibrary.org/obo/STATO_0000057 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000057 A null hypothesis is a statistical hypothesis that is tested for possible rejection under the assumption that it is true (usually that observations are the result of chance). The concept was introduced by R. A. Fisher. The hypothesis contrary to the null hypothesis, usually that the observations are the result of a real effect, is known as the alternative hypothesis.[wolfram alpha] http://purl.obolibrary.org/obo/STATO_0000057 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000057 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000057 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000057 http://mathworld.wolfram.com/NullHypothesis.html http://purl.obolibrary.org/obo/STATO_0000057 http://purl.obolibrary.org/obo/STATO_0000057 null hypothesis http://purl.obolibrary.org/obo/STATO_0000058 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000058 goodness of fit hypothesis is a null hypothesis stating that the distribution computed from the sample population fits a theoretical distribution or that a dataset can be correctly explained by a model http://purl.obolibrary.org/obo/STATO_0000058 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000058 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000058 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000058 STATO http://purl.obolibrary.org/obo/STATO_0000058 http://purl.obolibrary.org/obo/STATO_0000058 goodness of fit hypothesis http://purl.obolibrary.org/obo/STATO_0000059 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000059 the Student's t distribution is a continuous probability distribution which arises when estimating the mean of a normally distributed population in situations where the sample size is small and population standard deviation is unknown. http://purl.obolibrary.org/obo/STATO_0000059 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000059 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000059 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000059 STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Student's_t-distribution) http://purl.obolibrary.org/obo/STATO_0000059 t distribution http://purl.obolibrary.org/obo/STATO_0000059 dt(x, df, ncp, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/TDist.html http://purl.obolibrary.org/obo/STATO_0000059 Student's t distribution http://purl.obolibrary.org/obo/STATO_0000060 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000060 hypergeometric distribution is a probability distribution that describes the probability of k successes in n draws from a finite population of size N containing K successes without replacement http://purl.obolibrary.org/obo/STATO_0000060 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000060 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000060 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000060 http://en.wikipedia.org/wiki/Hypergeometric_distribution http://purl.obolibrary.org/obo/STATO_0000060 http://purl.obolibrary.org/obo/STATO_0000060 dhyper(x, m, n, k, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Hypergeometric.html http://purl.obolibrary.org/obo/STATO_0000060 hypergeometric distribution http://purl.obolibrary.org/obo/STATO_0000061 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000061 is a null hypothesis stating that there are no differences observed between group of subjects http://purl.obolibrary.org/obo/STATO_0000061 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000061 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000061 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000061 STATO http://purl.obolibrary.org/obo/STATO_0000061 http://purl.obolibrary.org/obo/STATO_0000061 absence of between group difference hypothesis http://purl.obolibrary.org/obo/STATO_0000062 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000062 is a null hypothesis stating that there are no difference observed across a series of measurements made one same subject. http://purl.obolibrary.org/obo/STATO_0000062 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000062 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000062 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000062 STATO http://purl.obolibrary.org/obo/STATO_0000062 http://purl.obolibrary.org/obo/STATO_0000062 absence of within subject difference hypothesis http://purl.obolibrary.org/obo/STATO_0000063 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000063 genomic coordinate datum is a data item which denotes a genomic position expressed using a genomic coordinate system http://purl.obolibrary.org/obo/STATO_0000063 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000063 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000063 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000063 STATO http://purl.obolibrary.org/obo/STATO_0000063 http://purl.obolibrary.org/obo/STATO_0000063 genomic coordinate datum http://purl.obolibrary.org/obo/STATO_0000064 http://left.subtree.org/2012/04/13/counting-the-number-of-reads-in-a-bam-file/ http://purl.obolibrary.org/obo/STATO_0000064 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000064 sequence read count is a data item determining how many sequence reads generated by a DNA sequencing assay for a given stretch of DNA can counted http://purl.obolibrary.org/obo/STATO_0000064 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000064 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000064 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000064 AGB-PRS, STATO http://purl.obolibrary.org/obo/STATO_0000064 http://purl.obolibrary.org/obo/STATO_0000064 sequence read count http://purl.obolibrary.org/obo/STATO_0000065 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000065 In statistics, a statement that can be tested.[wolfram alpha] http://purl.obolibrary.org/obo/STATO_0000065 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000065 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000065 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000065 STATO http://purl.obolibrary.org/obo/STATO_0000065 http://mathworld.wolfram.com/Hypothesis.html http://purl.obolibrary.org/obo/STATO_0000065 http://purl.obolibrary.org/obo/STATO_0000065 hypothesis http://purl.obolibrary.org/obo/STATO_0000066 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000066 Cleveland dot plot is a dot plot which plots points that each belong to one of several categories. They are an alternative to bar charts or pie charts, and look somewhat like a horizontal bar chart where the bars are replaced by a dots at the values associated with each category. Compared to (vertical) bar charts and pie charts, Cleveland argues that dot plots allow more accurate interpretation of the graph by readers by making the labels easier to read, reducing non-data ink (or graph clutter) and supporting table look-up.which http://purl.obolibrary.org/obo/STATO_0000066 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000066 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000066 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000066 adapted from Wikipedia: http://en.wikipedia.org/wiki/Dot_plot_(statistics) and Cleveland, William S. (1993). Visualizing Data. Hobart Press. ISBN 0-9634884-0-6. hdl:2027/mdp.39015026891187. http://purl.obolibrary.org/obo/STATO_0000066 http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/dotchart.html dotchart(x, labels = NULL, groups = NULL, gdata = NULL, cex = par("cex"), pch = 21, gpch = 21, bg = par("bg"), color = par("fg"), gcolor = par("fg"), lcolor = "gray", xlim = range(x[is.finite(x)]), main = NULL, xlab = NULL, ylab = NULL, ...) http://purl.obolibrary.org/obo/STATO_0000066 Cleveland dot plot http://purl.obolibrary.org/obo/STATO_0000067 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000067 a continuousprobability distribution is a probability distribution which is defined by a probability density function http://purl.obolibrary.org/obo/STATO_0000067 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000067 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000067 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000067 adapted from Wikipedia http://en.wikipedia.org/wiki/Probability_distribution#Continuous_probability_distribution last accessed: 14/01/2014 http://purl.obolibrary.org/obo/STATO_0000067 http://purl.obolibrary.org/obo/STATO_0000067 continuous probability distribution http://purl.obolibrary.org/obo/STATO_0000068 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000068 Skewness is a data item indicating of the degree of asymmetry of a distribution. http://purl.obolibrary.org/obo/STATO_0000068 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000068 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000068 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000068 http://mathworld.wolfram.com/Skewness.html http://purl.obolibrary.org/obo/STATO_0000068 http://purl.obolibrary.org/obo/STATO_0000068 skewness(x, na.rm = FALSE, type = 3) http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/e1071/html/skewness.html http://purl.obolibrary.org/obo/STATO_0000068 skewness http://purl.obolibrary.org/obo/STATO_0000069 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000069 The number degree of freedom is a count evaluating the number of values in a calculation that can vary. In statistics, the number of degrees of freedom ν is equal to N-1 in the case of the direct measurement of a quantity estimated by the arithmetic mean of N independent observations. http://purl.obolibrary.org/obo/STATO_0000069 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000069 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000069 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000069 http://stats.stackexchange.com/questions/16921/how-to-understand-degrees-of-freedom http://purl.obolibrary.org/obo/STATO_0000069 http://www.optique-ingenieur.org/en/courses/OPI_ang_M07_C01/co/Contenu_07.html http://purl.obolibrary.org/obo/STATO_0000069 the rank of the quadratic form (mathematical definition) http://purl.obolibrary.org/obo/STATO_0000069 http://purl.obolibrary.org/obo/STATO_0000069 number of degrees of freedom http://purl.obolibrary.org/obo/STATO_0000070 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000070 Yate's corrected Chi-Squared test is a statistical test which is used to test the association/linkage/independence of 2 dichotomous variables while introducing a correction for using the continous Chi-squared distribution for the test. To reduce the error in approximation, Frank Yates, an English statistician, suggested a correction for continuity that adjusts the formula for Pearson's chi-squared test by subtracting 0.5 from the difference between each observed value and its expected value in a 2 × 2 contingency table. This reduces the chi-squared value obtained and thus increases its p-value. http://purl.obolibrary.org/obo/STATO_0000070 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000070 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000070 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000070 STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Yates's_correction_for_continuity) polled in June 2013 http://purl.obolibrary.org/obo/STATO_0000070 Yate's correction for continuity http://purl.obolibrary.org/obo/STATO_0000070 chisq.test(x, y = NULL, correct = TRUE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html http://purl.obolibrary.org/obo/STATO_0000070 Yate's corrected Chi-Squared test http://purl.obolibrary.org/obo/STATO_0000071 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000071 reaction rate is a measurement datum which represents the speed of a chemical reaction turning reactive species into product species of event (i.e the number of such conversions)s occuring over a time interval http://purl.obolibrary.org/obo/STATO_0000071 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000071 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000071 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000071 STATO http://purl.obolibrary.org/obo/STATO_0000071 reaction rate http://purl.obolibrary.org/obo/STATO_0000072 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000072 substrate concentration is a scalar measurement datum which denotes the amount of molecular entity involved in an enzymatic reaction (or catalytic chemical reaction) and whose role in that reaction is as substrate. http://purl.obolibrary.org/obo/STATO_0000072 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000072 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000072 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000072 STATO http://purl.obolibrary.org/obo/STATO_0000072 substrate concentration http://purl.obolibrary.org/obo/STATO_0000073 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000073 Fisher's exact test is a statistical test used to determine if there are nonrandom associations between two categorical variables. http://purl.obolibrary.org/obo/STATO_0000073 duplicate with OBI_0200176. so either MIREOT and add metadata and axioms or move from OBI http://purl.obolibrary.org/obo/STATO_0000073 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000073 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000073 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000073 http://mathworld.wolfram.com/FishersExactTest.html http://purl.obolibrary.org/obo/STATO_0000073 http://purl.obolibrary.org/obo/STATO_0000073 fisher.test(x) function, where x is a matrix http://purl.obolibrary.org/obo/STATO_0000073 Fisher's exact test http://purl.obolibrary.org/obo/STATO_0000074 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000074 Cochran-Mantel-Haenzel test for repeated tests of independence is a statitiscal test which allows the comparison of two groups on a dichotomous/categorical response. It is used when the effect of the explanatory variable on the response variable is influenced by covariates that can be controlled. It is often used in observational studies where random assignment of subjects to different treatments cannot be controlled, but influencing covariates can. The null hypothesis is that the two nominal variables that are tested within each repetition are independent of each other. So there are 3 variables to consider: two categorical variables to be tested for independence of each other, and the third variable identifies the repeats. http://purl.obolibrary.org/obo/STATO_0000074 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000074 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000074 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000074 CHM test http://purl.obolibrary.org/obo/STATO_0000074 STATO adapted from wikipedia (http://en.wikipedia.org/wiki/Cochran–Mantel–Haenszel_statistics) and from the Handbook of Biological Statistics (http://udel.edu/~mcdonald/statcmh.html) http://purl.obolibrary.org/obo/STATO_0000074 http://purl.obolibrary.org/obo/STATO_0000074 cmh.test(x,y,z) http://purl.obolibrary.org/obo/STATO_0000074 Cochran-Mantel-Haenzel test for repeated tests of independence http://purl.obolibrary.org/obo/STATO_0000075 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000075 a rarefaction curve is a graph used for estimating species richness in ecology studies http://purl.obolibrary.org/obo/STATO_0000075 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000075 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000075 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000075 STATO http://purl.obolibrary.org/obo/STATO_0000075 http://purl.obolibrary.org/obo/STATO_0000075 >library(vegan) >rarefaction(x, subsample=5, plot=TRUE, color=TRUE, error=FALSE, legend=TRUE, symbol) http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/vegan/html/vegan-package.html http://purl.obolibrary.org/obo/STATO_0000075 rarefaction curve http://purl.obolibrary.org/obo/STATO_0000076 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000076 The Mann-Whitney U-test is a null hypothesis statistical testing procedure which allows two groups (or conditions or treatments) to be compared without making the assumption that values are normally distributed. The Mann-Whitney test is the non-parametric equivalent of the t-test for independent samples http://purl.obolibrary.org/obo/STATO_0000076 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000076 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000076 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000076 U test http://purl.obolibrary.org/obo/STATO_0000076 Wilcoxon rank-sum test http://purl.obolibrary.org/obo/STATO_0000076 rank-sum test for the comparison of two samples http://purl.obolibrary.org/obo/STATO_0000076 adapted from http://udel.edu/~mcdonald/statkruskalwallis.html and from http://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U last accessed [2014-03-04] http://purl.obolibrary.org/obo/STATO_0000076 Wilcoxon Rank-Sum test http://purl.obolibrary.org/obo/STATO_0000076 wilcox.test(dependent variable ~ independant variable, data = dataset) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/wilcox.test.html http://purl.obolibrary.org/obo/STATO_0000076 Mann-Whitney U-test http://purl.obolibrary.org/obo/STATO_0000077 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000077 Shapiro-Wilk test is a goodness of fit test which evaluates the null hypothesis that the sample is drawn from a population following a normal distribution http://purl.obolibrary.org/obo/STATO_0000077 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000077 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000077 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000077 S-W test http://purl.obolibrary.org/obo/STATO_0000077 STATO, adapted from wikipedia (https://en.wikipedia.org/wiki/Shapiro–Wilk_test) http://purl.obolibrary.org/obo/STATO_0000077 http://purl.obolibrary.org/obo/STATO_0000077 shapiro.test(x) function, where x is a numeric vector https://stat.ethz.ch/R-manual/R-devel/library/stats/html/shapiro.test.html http://purl.obolibrary.org/obo/STATO_0000077 Shapiro-Wilk test http://purl.obolibrary.org/obo/STATO_0000078 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000078 Levene's test is a null hypothesis statistical test which evaluates the null hypothesis of equality of variance in several populations. http://purl.obolibrary.org/obo/STATO_0000078 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000078 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000078 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000078 http://en.wikipedia.org/wiki/Levene_test http://purl.obolibrary.org/obo/STATO_0000078 http://purl.obolibrary.org/obo/STATO_0000078 levene.test(x) function, where x is a numeric vector http://purl.obolibrary.org/obo/STATO_0000078 Levene's test http://purl.obolibrary.org/obo/STATO_0000079 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000079 Bartlett's test (see Snedecor and Cochran, 1989) is used to test if k samples are from populations with equal variances. Equal variances across samples is called homoscedasticity or homogeneity of variances. Some statistical tests, for example the analysis of variance, assume that variances are equal across groups or samples. The Bartlett test can be used to verify that assumption. Bartlett's test is sensitive to departures from normality. That is, if the samples come from non-normal distributions, then Bartlett's test may simply be testing for non-normality. Levene's test and the Brown–Forsythe test are alternatives to the Bartlett test that are less sensitive to departures from normality. http://purl.obolibrary.org/obo/STATO_0000079 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000079 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000079 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000079 http://en.wikipedia.org/wiki/Bartlett_test http://purl.obolibrary.org/obo/STATO_0000079 http://purl.obolibrary.org/obo/STATO_0000079 bartlett.test(x) function, where x is a numeric vector http://purl.obolibrary.org/obo/STATO_0000079 Barlett's test http://purl.obolibrary.org/obo/STATO_0000080 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000080 the Brown Forsythe test is a statistical test which evaluates if the variance of different groups are equal. It relies on computing the median rather than the mean, as used in the Levene's test for homoschedacity. This test maybe used to, for instance, ensure that the conditions of applications of ANOVA are met. http://purl.obolibrary.org/obo/STATO_0000080 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000080 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000080 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000080 adapted from Wikipedia and Brown, M. B., and A. B. Forsythe. 1974a. The small sample behavior of some statistics which test the equality of several means. Technometrics, 16, 129-132. http://purl.obolibrary.org/obo/STATO_0000080 http://purl.obolibrary.org/obo/STATO_0000080 http://www.statmethods.net/stats/anovaAssumptions.html The hovPlot( ) function in the HH package provides a graphic test of homogeneity of variances based on Brown-Forsyth. In the following example, y is numeric and G is a grouping factor. Note that G must be of type factor. # Homogeneity of Variance Plot library(HH) hov(y~G, data=mydata) hovPlot(y~G,data=mydata) http://purl.obolibrary.org/obo/STATO_0000080 Brown Forsythe test http://purl.obolibrary.org/obo/STATO_0000081 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000081 Pearson's Chi-Squared test is a statistical null hypothesis test which is used to either evaluate goodness of fit of dataset to a Chi-Squared distribution or used to test independence of 2 categorical variables (ie absence of association between those variables). http://purl.obolibrary.org/obo/STATO_0000081 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000081 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000081 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000081 Chi2 test for independence http://purl.obolibrary.org/obo/STATO_0000081 adapted from: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html and http://en.wikipedia.org/wiki/Pearson's_chi-squared_test http://purl.obolibrary.org/obo/STATO_0000081 http://purl.obolibrary.org/obo/STATO_0000081 http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html chisq.test(x, y = NULL, correct = TRUE, p = rep(1/length(x), length(x)), rescale.p = FALSE, simulate.p.value = FALSE, B = 2000) http://purl.obolibrary.org/obo/STATO_0000081 http://www.inside-r.org/packages/cran/nortest/docs/pearson.test pearson.test(x) function, where x is a numeric vector http://purl.obolibrary.org/obo/STATO_0000081 Pearson's Chi square test of independence between categorical variables http://purl.obolibrary.org/obo/STATO_0000082 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000082 a fixed effect model is a statistical model which represents the observed quantities in terms of explanatory variables that are treated as if the quantities were non-random. http://purl.obolibrary.org/obo/STATO_0000082 PRS: this is a stub and more work is needed to reconcile conflicting definitions http://purl.obolibrary.org/obo/STATO_0000082 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000082 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000082 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000082 adapted from wikipedia: http://en.wikipedia.org/wiki/Fixed_effects_model http://purl.obolibrary.org/obo/STATO_0000082 http://purl.obolibrary.org/obo/STATO_0000082 fixed effects model http://purl.obolibrary.org/obo/STATO_0000083 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000083 Kolmogorov-Smirnov test is a goodness of fit test which evaluates the null hypothesis that a sample is drawn from a population that follows a specific continuous probability distribution. http://purl.obolibrary.org/obo/STATO_0000083 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000083 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000083 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000083 K-S test http://purl.obolibrary.org/obo/STATO_0000083 STATO, adapted from wikipedia (https://en.wikipedia.org/wiki/Kolmogorov–Smirnov_test) http://purl.obolibrary.org/obo/STATO_0000083 http://www.itl.nist.gov/div898/handbook/eda/section3/eda35g.htm http://purl.obolibrary.org/obo/STATO_0000083 http://purl.obolibrary.org/obo/STATO_0000083 ks.test(dataset, distribution) http://purl.obolibrary.org/obo/STATO_0000083 Kolmogorov-Smirnov test http://purl.obolibrary.org/obo/STATO_0000084 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000084 multinomial logistic regression model is a model which attempts to explain data distribution associated with *polychotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is probit function. http://purl.obolibrary.org/obo/STATO_0000084 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000084 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000084 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000084 STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Multinomial_probit) polled in June 2013 http://purl.obolibrary.org/obo/STATO_0000084 http://purl.obolibrary.org/obo/STATO_0000084 http://cran.r-project.org/web/packages/mlogit/vignettes/mlogit.pdf http://purl.obolibrary.org/obo/STATO_0000084 multinomial probit regression for analysis of polychotomous dependent variable http://purl.obolibrary.org/obo/STATO_0000085 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/ http://purl.obolibrary.org/obo/STATO_0000085 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000085 effect size estimate is a data item about the direction and strength of the consequences of a causative agent as explored by statistical methods. Those methods produce estimates of the effect size, e.g. confidence interval http://purl.obolibrary.org/obo/STATO_0000085 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000085 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000085 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000085 AGB,PRS http://purl.obolibrary.org/obo/STATO_0000085 effect size http://purl.obolibrary.org/obo/STATO_0000085 effect size estimate http://purl.obolibrary.org/obo/STATO_0000086 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000086 an F-test is a statistical test which evaluates that the computed test statistics follows an F-distribution under the null hypothesis. The F-test is sensitive to departure from normality. F-test arise when decomposing the variability in a data set in terms of sum of squares. http://purl.obolibrary.org/obo/STATO_0000086 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000086 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000086 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000086 STATO http://purl.obolibrary.org/obo/STATO_0000086 http://purl.obolibrary.org/obo/STATO_0000086 F-test http://purl.obolibrary.org/obo/STATO_0000087 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000087 a polychotomous variable is a categorical variable which is defined to have minimally 2 categories or possible values http://purl.obolibrary.org/obo/STATO_0000087 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000087 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000087 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000087 STATO http://purl.obolibrary.org/obo/STATO_0000087 http://udel.edu/~mcdonald/statvartypes.html http://purl.obolibrary.org/obo/STATO_0000087 http://purl.obolibrary.org/obo/STATO_0000087 polychotomous variable http://purl.obolibrary.org/obo/STATO_0000088 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000088 statistical sample size is a count evaluating the number of individual experimental units http://purl.obolibrary.org/obo/STATO_0000088 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000088 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000088 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000088 AGB-PRS http://purl.obolibrary.org/obo/STATO_0000088 http://purl.obolibrary.org/obo/STATO_0000088 statistical sample size http://purl.obolibrary.org/obo/STATO_0000088 study group population size http://purl.obolibrary.org/obo/STATO_0000089 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000089 a case-control study design is a observation study design which assess the risk of particular outcome (a trait or a disease) associated with an event (either an exposure or endogenous factor). A case-control study design therefore declares an exposure variable which is dichotomous in nature (exposed/non-exposed) and an outcome variable, which is also dichotomous (case or control), thus giving the name to the design. During the execution of the design, a case control study defines a population and counts the events to determine their frequency. http://purl.obolibrary.org/obo/STATO_0000089 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000089 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000089 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000089 STATO, adapted from: http://www.drcath.net/toolkit/casecontrol.html http://purl.obolibrary.org/obo/STATO_0000089 http://purl.obolibrary.org/obo/STATO_0000089 case-control study design http://purl.obolibrary.org/obo/STATO_0000090 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000090 a dichotomous variable is a categorical variable which is defined to have only 2 categories or possible values http://purl.obolibrary.org/obo/STATO_0000090 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000090 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000090 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000090 AGB-PRS http://purl.obolibrary.org/obo/STATO_0000090 http://udel.edu/~mcdonald/statvartypes.html http://purl.obolibrary.org/obo/STATO_0000090 http://purl.obolibrary.org/obo/STATO_0000090 'has part' exactly 1 ('categorical measurement datum' and ('has category label' exactly 2 'categorical label')) http://purl.obolibrary.org/obo/STATO_0000090 dichotomous variable http://purl.obolibrary.org/obo/STATO_0000091 Genome wide association study is a kind of study whose objective is to detect association between genetic markers (SNP or otherwise) accross the genome and a trait which may be a disease or another phenotype (e.g. trait of agronomic relevance in animal or plant studies). Genome wide association study compare the allele frequencies in 2 populations, one free of the trait used as control, the other one showing the trait use as 'case'. GWAS studies implement case-control design http://purl.obolibrary.org/obo/STATO_0000091 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000091 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000091 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000091 AGB, PRS http://purl.obolibrary.org/obo/STATO_0000091 http://purl.obolibrary.org/obo/STATO_0000091 GWAS study http://purl.obolibrary.org/obo/STATO_0000091 whole genome association study http://purl.obolibrary.org/obo/STATO_0000091 genome-wide association study http://purl.obolibrary.org/obo/STATO_0000092 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000092 The Wilcoxon signed rank test is a statistical test which tests the null hypothesis that the median difference between pairs of observations is zero. This is the non-parametric analogue to the paired t-test, and should be used if the distribution of differences between pairs may be non-normally distributed. The procedure involves a ranking hence the name. The absolute value of the differences between observations are ranked from smallest to largest, with the smallest difference getting a rank of 1, then next larger difference getting a rank of 2, etc. Ties are given average ranks. The ranks of all differences in one direction are summed, and the ranks of all differences in the other direction are summed. The smaller of these two sums is the test statistic, W (sometimes symbolized Ts). Unlike most test statistics, smaller values of W are less likely under the null hypothesis. http://purl.obolibrary.org/obo/STATO_0000092 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000092 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000092 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000092 http://udel.edu/~mcdonald/statsignedrank.html http://purl.obolibrary.org/obo/STATO_0000092 http://purl.obolibrary.org/obo/STATO_0000092 signrank() http://purl.obolibrary.org/obo/STATO_0000092 Wilcoxon signed rank test http://purl.obolibrary.org/obo/STATO_0000093 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/STATO_0000093 http://purl.obolibrary.org/obo/STATO_0000093 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000093 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000093 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000093 http://purl.obolibrary.org/obo/STATO_0000093 date http://purl.obolibrary.org/obo/STATO_0000094 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000094 The Kruskal–Wallis test is a null hypothesis statistical testing objective which allows multiple (n>=2) groups (or conditions or treatments) to be compared, without making the assumption that values are normally distributed. The Kruskal–Wallis test is the non-parametric equivalent of the independent samples ANOVA The Kruskal–Wallis test is most commonly used when there is one nominal variable and one measurement variable, and the measurement variable does not meet the normality assumption of an anova. http://purl.obolibrary.org/obo/STATO_0000094 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000094 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000094 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000094 H test http://purl.obolibrary.org/obo/STATO_0000094 rank-sum test for the comparison of multiple (more than 2) samples http://purl.obolibrary.org/obo/STATO_0000094 http://udel.edu/~mcdonald/statkruskalwallis.html http://purl.obolibrary.org/obo/STATO_0000094 http://purl.obolibrary.org/obo/STATO_0000094 kruskal.test() http://stat.ethz.ch/R-manual/R-patched/library/stats/html/kruskal.test.html http://purl.obolibrary.org/obo/STATO_0000094 Kruskal Wallis test http://purl.obolibrary.org/obo/STATO_0000095 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000095 paired t-test is a statistical test which is specifically designed to analysis differences between paired observations in the case of studies realizing repeated measures design with only 2 repeated measurements per subject (before and after treatment for example) http://purl.obolibrary.org/obo/STATO_0000095 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000095 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000095 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000095 http://udel.edu/~mcdonald/statpaired.html http://purl.obolibrary.org/obo/STATO_0000095 http://udel.edu/~mcdonald/statsignedrank.html http://purl.obolibrary.org/obo/STATO_0000095 t-test for dependent means http://purl.obolibrary.org/obo/STATO_0000095 t-test for repeated measures http://purl.obolibrary.org/obo/STATO_0000095 http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html t.test(dependent variable ~ independant variable, data = dataset, var.equal = FALSE, paired= TRUE) http://purl.obolibrary.org/obo/STATO_0000095 paired t-test http://purl.obolibrary.org/obo/STATO_0000096 stratification is a planned process which executes a stratification rule using as input a population and assign it member to mutually exclusive subpopulation based on the values defined by the stratification rule http://purl.obolibrary.org/obo/STATO_0000096 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000096 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000096 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000096 PRS+AGB adapted from wikipedia: http://en.wikipedia.org/wiki/Stratified_sampling polled on June 7th,2013 http://purl.obolibrary.org/obo/STATO_0000096 stratifying population http://purl.obolibrary.org/obo/STATO_0000096 population stratification prior to sampling http://purl.obolibrary.org/obo/STATO_0000097 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000097 stastical test power analysis is a data transformation which aims to determine the size of a statistical sample required to reach a desired significance level given a particular statistical test http://purl.obolibrary.org/obo/STATO_0000097 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000097 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000097 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000097 http://www.statmethods.net/stats/power.html http://purl.obolibrary.org/obo/STATO_0000097 http://purl.obolibrary.org/obo/STATO_0000097 http://www.statmethods.net/stats/power.html http://purl.obolibrary.org/obo/STATO_0000097 statistical test power analysis http://purl.obolibrary.org/obo/STATO_0000098 http://arxiv.org/pdf/1007.1094.pdf http://purl.obolibrary.org/obo/STATO_0000098 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000098 Hotelling's T2 test is a statistical test which is a generalization of Student's T-test to a assess if the means of a set of variables remains unchanged when studying 2 populations. It is a type of multivariate analysis http://purl.obolibrary.org/obo/STATO_0000098 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000098 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000098 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000098 STATO http://purl.obolibrary.org/obo/STATO_0000098 http://purl.obolibrary.org/obo/STATO_0000098 http://svitsrv25.epfl.ch/R-doc/library/rrcov/html/T2.test.html http://purl.obolibrary.org/obo/STATO_0000098 two sample Hotelling T2 test http://purl.obolibrary.org/obo/STATO_0000099 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000099 a random effect(s) model, also called a variance components model, is a kind of hierarchical linear model. It assumes that the dataset being analysed consists of a hierarchy of different populations whose differences relate to that hierarchy. http://purl.obolibrary.org/obo/STATO_0000099 PRS: this is a stub and more work is needed to reconcile conflicting definitions http://purl.obolibrary.org/obo/STATO_0000099 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000099 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000099 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000099 variance components model http://purl.obolibrary.org/obo/STATO_0000099 adapted from wikipedia: http://en.wikipedia.org/wiki/Random_effects_model#Qualitative_description http://purl.obolibrary.org/obo/STATO_0000099 http://purl.obolibrary.org/obo/STATO_0000099 random effects model http://purl.obolibrary.org/obo/STATO_0000100 standardized mean difference is data item computed by forming the difference between two means, divided by an estimate of the within-group standard deviation. It is used to provide an estimatation of the effect size between two treatments when the predictor (independent variable) is categorical and the response(dependent) variable is continuous http://purl.obolibrary.org/obo/STATO_0000100 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000100 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000100 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000100 SMD http://purl.obolibrary.org/obo/STATO_0000100 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000100 adapted from "Effect size, confidence interval and statistical significance: a practical guide for biologists" Nakagawa and Cuthill DOI: 10.1111/j.1469-185X.2007.00027.x http://purl.obolibrary.org/obo/STATO_0000100 adapted from http://htaglossary.net/standardised+mean+difference+(SMD) http://purl.obolibrary.org/obo/STATO_0000100 Cohen's d statistic http://purl.obolibrary.org/obo/STATO_0000100 standardized mean difference http://purl.obolibrary.org/obo/STATO_0000101 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000101 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000101 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000101 has numerator http://purl.obolibrary.org/obo/STATO_0000102 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000102 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000102 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000102 executes http://purl.obolibrary.org/obo/STATO_0000103 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000103 the multinomial distribution is a probability distribution which gives the probability of any particular combination of numbers of successes for various categories defined in the context of n independent trials each of which leads to a success for exactly one of k categories, with each category having a given fixed success probability. http://purl.obolibrary.org/obo/STATO_0000103 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000103 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000103 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000103 adapted from http://mathworld.wolfram.com/MultinomialDistribution.html and http://en.wikipedia.org/wiki/Multinomial_distribution http://purl.obolibrary.org/obo/STATO_0000103 dmultinom(x, size = NULL, prob, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Multinom.html http://purl.obolibrary.org/obo/STATO_0000103 multinomial distribution http://purl.obolibrary.org/obo/STATO_0000104 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000104 A z-score (also known as z-value, standard score, or normal score) is a measure of the divergence of an individual experimental result from the most probable result, the mean. Z is expressed in terms of the number of standard deviations from the mean value. http://purl.obolibrary.org/obo/STATO_0000104 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000104 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000104 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000104 https://controls.engin.umich.edu/wiki/index.php/Basic_statistics:_mean,_median,_average,_standard_deviation,_z-scores,_and_p-value#Z-Scores http://purl.obolibrary.org/obo/STATO_0000104 normal score http://purl.obolibrary.org/obo/STATO_0000104 standard score http://purl.obolibrary.org/obo/STATO_0000104 z-score http://purl.obolibrary.org/obo/STATO_0000105 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000105 log signal intensity ratio is a data item which corresponding the logarithmitic base 2 of the ratio between 2 signal intensity, each corresponding to a condition. http://purl.obolibrary.org/obo/STATO_0000105 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000105 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000105 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000105 adapted from wikipedia: http://en.wikipedia.org/wiki/MA_plot last accessed: 2014-03-13 http://purl.obolibrary.org/obo/STATO_0000105 M-value http://purl.obolibrary.org/obo/STATO_0000105 http://purl.obolibrary.org/obo/STATO_0000105 log signal intensity ratio http://purl.obolibrary.org/obo/STATO_0000106 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000106 probit regression model is a model which attempts to explain data distribution associated with *dichotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is the probit function aka the quantile function, i.e., the inverse cumulative distribution function (CDF), associated with the standard normal distribution. http://purl.obolibrary.org/obo/STATO_0000106 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000106 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000106 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000106 STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Probit_model) polled in June 2013 http://purl.obolibrary.org/obo/STATO_0000106 http://purl.obolibrary.org/obo/STATO_0000106 probit regression for analysis of polychotomous dependent variable http://purl.obolibrary.org/obo/STATO_0000107 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000107 a statistical model is an information content entity which is a formalization of relationships between variables in the form of mathematical equations. A statistical model describes how one or more random variables are related to one or more other variables. The model is statistical as the variables are not deterministically but stochastically related. http://purl.obolibrary.org/obo/STATO_0000107 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000107 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000107 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000107 adapted from Wikipedia: http://en.wikipedia.org/wiki/Statistical_model last accessed: 14/01/2014 http://purl.obolibrary.org/obo/STATO_0000107 statistical model http://purl.obolibrary.org/obo/STATO_0000107 statistical model http://purl.obolibrary.org/obo/STATO_0000108 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000108 linear regression model is a model which attempts to explain data distribution associated with response/dependent variable in terms of values assumed by the independent variable uses a linear function or linear combination of the regression parameters and the predictor/independent variable(s). linear regression modeling makes a number of assumptions, which includes homoskedasticity (constance of variance) http://purl.obolibrary.org/obo/STATO_0000108 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000108 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000108 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000108 STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Linear_regression) polled in June 2013 http://purl.obolibrary.org/obo/STATO_0000108 http://purl.obolibrary.org/obo/STATO_0000108 linear regression for analysis of continuous dependent variable http://purl.obolibrary.org/obo/STATO_0000109 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000109 multinomial logistic regression model is a model which attempts to explain data distribution associated with *polychotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is logistic function. http://purl.obolibrary.org/obo/STATO_0000109 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000109 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000109 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000109 STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Multinomial_logistic_regression) polled in June 2013 http://purl.obolibrary.org/obo/STATO_0000109 http://purl.obolibrary.org/obo/STATO_0000109 http://cran.r-project.org/web/packages/mlogit/vignettes/mlogit.pdf http://purl.obolibrary.org/obo/STATO_0000109 multinomial logistic regression for analysis of dichotomous dependent variable http://purl.obolibrary.org/obo/STATO_0000110 This is the inverse of 'specifies value of' and it is intended to say things such as 'compound' 'assumes values specified by' 'independent variable specification' http://purl.obolibrary.org/obo/STATO_0000110 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000110 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000110 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000110 assumes values specified by http://purl.obolibrary.org/obo/STATO_0000111 a sequence read is a DNA sequence data which is generated by a DNA sequencer http://purl.obolibrary.org/obo/STATO_0000111 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000111 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000111 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000111 sequence read http://purl.obolibrary.org/obo/STATO_0000112 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000112 a Funnel plot is a scatter plot of treatment effect versus a measure of study size and aims to provide a visual aid to detecting bias or systematic heterogeneity. A symmetric inverted funnel shape arises from a ‘well-behaved’ data set, in which publication bias is unlikely. An asymmetric funnel indicates a relationship between treatment effect and study size. Known caveats: If high precision studies really are different from low precision studies with respect to effect size (e.g., due to different populations examined) a funnel plot may give a wrong impression of publication bias. The appearance of the funnel plot can change quite dramatically depending on the scale on the y-axis — whether it is the inverse square error or the trial size. Funnel plot was introduced by Light and Palmer in 1984. http://purl.obolibrary.org/obo/STATO_0000112 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000112 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000112 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000112 adapted from Wikipedia: http://en.wikipedia.org/wiki/Funnel_plot http://purl.obolibrary.org/obo/STATO_0000112 Funnel plot http://purl.obolibrary.org/obo/STATO_0000113 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000113 variance is a data item about a random variable or probability distribution. it is equivalent to the square of the standard deviation. It is one of several descriptors of a probability distribution, describing how far the numbers lie from the mean (expected value).The variance is the second moment of a distribution. http://purl.obolibrary.org/obo/STATO_0000113 Alejandra Gonzalez-Belran http://purl.obolibrary.org/obo/STATO_0000113 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000113 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000113 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000113 σ2 http://purl.obolibrary.org/obo/STATO_0000113 http://purl.obolibrary.org/obo/STATO_0000113 var(x, y = NULL, na.rm = FALSE, use) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cor.html http://purl.obolibrary.org/obo/STATO_0000113 variance http://purl.obolibrary.org/obo/STATO_0000114 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000114 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000114 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000114 is member of http://purl.obolibrary.org/obo/STATO_0000115 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000115 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000115 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000115 has member http://purl.obolibrary.org/obo/STATO_0000116 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000116 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000116 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000116 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000116 assess stastistical evidence http://purl.obolibrary.org/obo/STATO_0000116 assess statistical evidence http://purl.obolibrary.org/obo/STATO_0000117 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000117 a discrete probability distribution is a probability distribution which is defined by a probability mass function where the random variable can only assume a finite number of values or infinitely countable values http://purl.obolibrary.org/obo/STATO_0000117 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000117 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000117 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000117 adapted from Wikipedia http://en.wikipedia.org/wiki/Probability_distribution#Discrete_probability_distribution last accessed: 14/01/2014 http://purl.obolibrary.org/obo/STATO_0000117 discrete probability distribution http://purl.obolibrary.org/obo/STATO_0000118 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000118 ranking is a data transformation which turns a non-ordinal variable into a Ordinal variable by sorting the values of the input variable and replacing their value by their position in the sorting result http://purl.obolibrary.org/obo/STATO_0000118 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000118 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000118 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000118 STATO http://purl.obolibrary.org/obo/STATO_0000118 http://purl.obolibrary.org/obo/STATO_0000118 ranking http://purl.obolibrary.org/obo/STATO_0000119 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000119 model parameter estimation is a data transformation that finds parameter values (the model parameter estimates) most compatible with the data as judged by the model. http://purl.obolibrary.org/obo/STATO_0000119 textual definition modified following contributiong by Thomas Nichols: https://github.com/ISA-tools/stato/issues/18 http://purl.obolibrary.org/obo/STATO_0000119 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000119 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000119 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000119 http://purl.obolibrary.org/obo/STATO_0000119 model parameter estimation http://purl.obolibrary.org/obo/STATO_0000120 http://www.r-bloggers.com/boxplots-beyond-iv-beanplots/ http://purl.obolibrary.org/obo/STATO_0000120 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000120 beanplot is a plot in which (one or) multiple batches ("beans") are shown. Each bean consists of a density trace, which is mirrored to form a polygon shape. Next to that, a one-dimensional scatter plot shows all the individual measurements, like in a stripchart. The name beanplot stems from green beans. The density shape can be seen as the pod of a green bean, while the scatter plot shows the seeds inside the pod. http://purl.obolibrary.org/obo/STATO_0000120 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000120 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000120 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000120 http://www.jstatsoft.org/v28/c01/paper http://purl.obolibrary.org/obo/STATO_0000120 http://cran.r-project.org/web/packages/beanplot/index.html http://purl.obolibrary.org/obo/STATO_0000120 bean plot http://purl.obolibrary.org/obo/STATO_0000121 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000121 the objective of a data transformation to evaluate a null hypothesis of absence of linkage between variables. http://purl.obolibrary.org/obo/STATO_0000121 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000121 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000121 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000121 STATO http://purl.obolibrary.org/obo/STATO_0000121 http://purl.obolibrary.org/obo/STATO_0000121 association between categorical variables testing objective http://purl.obolibrary.org/obo/STATO_0000122 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000122 a pedigree chart is a graph which plots parent child relations http://purl.obolibrary.org/obo/STATO_0000122 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000122 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000122 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000122 STATO adapted from wikipedia (https://en.wikipedia.org/wiki/Pedigree_chart) http://purl.obolibrary.org/obo/STATO_0000122 family tree http://purl.obolibrary.org/obo/STATO_0000122 plot.pedigree {kinship} http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/kinship/html/plot.pedigree.html http://purl.obolibrary.org/obo/STATO_0000122 pedigree chart http://purl.obolibrary.org/obo/STATO_0000123 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000123 r2 is a correlation coefficient which is computed over the frequency of 2 dichotomous variable and is used as a measure of Linkage Disequilibrium and as input data item to the creation of an LD plot http://purl.obolibrary.org/obo/STATO_0000123 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000123 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000123 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000123 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2580747/ http://purl.obolibrary.org/obo/STATO_0000123 r2 http://purl.obolibrary.org/obo/STATO_0000123 r2 http://purl.obolibrary.org/obo/STATO_0000124 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000124 a stratification rule/criteria is a criteria used to determine population strata so that a stratification process implementing the rule can result in any member of the total population being assigned to one and only one stratum http://purl.obolibrary.org/obo/STATO_0000124 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000124 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000124 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000124 STATO http://purl.obolibrary.org/obo/STATO_0000124 adapted from wikipedia: http://en.wikipedia.org/wiki/Stratified_sampling polled on June 7th,2013 http://purl.obolibrary.org/obo/STATO_0000124 http://purl.obolibrary.org/obo/STATO_0000124 stratification rule http://purl.obolibrary.org/obo/STATO_0000125 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000125 The dot plot as a representation of a distribution consists of group of data points plotted on a simple scale. Dot plots are used for continuous, quantitative, univariate data. Data points may be labelled if there are few of them. http://purl.obolibrary.org/obo/STATO_0000125 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000125 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000125 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000125 adapted from Wikipedia: Wilkinson, Leland (1999). "Dot plots". The American Statistician (American Statistical Association) 53 (3): 276–281. doi:10.2307/2686111 http://purl.obolibrary.org/obo/STATO_0000125 http://purl.obolibrary.org/obo/STATO_0000125 Wilkinson dot plot http://purl.obolibrary.org/obo/STATO_0000126 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000126 volcano plot is a kind of scatter plot which graphs the negative log of the p-value (significance) on the y-axis versus log2 of fold-change between 2 conditions on the x-axis. It is a popular method for visualizing differential occurence of variables between 2 conditions. http://purl.obolibrary.org/obo/STATO_0000126 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000126 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000126 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000126 http://en.wikipedia.org/wiki/Volcano_plot_(statistics) http://purl.obolibrary.org/obo/STATO_0000126 volcanoplot(fit, coef=1, highlight=0, names=fit$genes$ID, ...) http://rss.acs.unt.edu/Rdoc/library/limma/html/volcanoplot.html http://purl.obolibrary.org/obo/STATO_0000126 volcano plot http://purl.obolibrary.org/obo/STATO_0000127 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/ http://purl.obolibrary.org/obo/STATO_0000127 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000127 a confidence interval which covers 99% of the sampling distribution, meaning that there is a 1% risk of false positive (type I error) http://purl.obolibrary.org/obo/STATO_0000127 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000127 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000127 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000127 confidence interval at 1% of type I error rate http://purl.obolibrary.org/obo/STATO_0000127 STATO http://purl.obolibrary.org/obo/STATO_0000127 http://purl.obolibrary.org/obo/STATO_0000127 99% confidence interval http://purl.obolibrary.org/obo/STATO_0000128 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000128 Altman Box and Whisker plot is a variation of Tukey Box and Whisker plot which use the criteria of Altman to create the 'whisker' of the plot. http://purl.obolibrary.org/obo/STATO_0000128 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000128 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000128 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000128 Altman, D.G. Practical Statistics for Medical Research (Chapman and Hall, 1991). http://purl.obolibrary.org/obo/STATO_0000128 Altman box and whisker plot http://purl.obolibrary.org/obo/STATO_0000129 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000129 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000129 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000129 has value http://purl.obolibrary.org/obo/STATO_0000130 http://www.biomedcentral.com/1471-2288/11/58#B9 http://purl.obolibrary.org/obo/STATO_0000130 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000130 the Breslow-Day test is a statistical test which evaluates if the odds ratios are homogenous across N 2x2 contingency tables, for instance several 2x2 contingency tables associated with different strata of a stratified population when evaluating the relationship between exposure and outcome or associated with the different samples coming from several centres in a multicentric study in clinical trial context. http://purl.obolibrary.org/obo/STATO_0000130 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000130 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000130 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000130 adapted from wikipedia: http://en.wikipedia.org/wiki/Odds_ratio#Statistical_inference polled on June 8th,2013 http://purl.obolibrary.org/obo/STATO_0000130 Breslow-Day test http://purl.obolibrary.org/obo/STATO_0000130 http://www.math.montana.edu/~jimrc/classes/stat524/Rcode/breslowday.test.r http://purl.obolibrary.org/obo/STATO_0000130 Breslow-Day test for homogeneity of odds ratio http://purl.obolibrary.org/obo/STATO_0000131 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000131 a sphericity test is a null hypothesis statistical testing procedure which posits a null hypothesis of equality of the variances of the differences between levels of the repeated measures factor http://purl.obolibrary.org/obo/STATO_0000131 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000131 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000131 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000131 STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Sphericity#Sphericity_in_statistics) http://purl.obolibrary.org/obo/STATO_0000131 test of data sphericity http://purl.obolibrary.org/obo/STATO_0000131 sphericity test http://purl.obolibrary.org/obo/STATO_0000132 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000132 Hotelling T squared distribution is a probability distribution used in multivariate hypothesis testing, which is a univariate distribution proportional to the F-distribution and arises importantly as the distribution of a set of statistics which are natural generalizations of the statistics underlying Student's t-distribution. In particular, the distribution arises in multivariate statistics in undertaking tests of the differences between the (multivariate) means of different populations, where tests for univariate problems would make use of a t-test. The distribution is named for Harold Hotelling, who developed it[1] as a generalization of Student's t-distribution. This distribution is commonly used to describe the sample Mahalanobis distance between two populations. http://purl.obolibrary.org/obo/STATO_0000132 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000132 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000132 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000132 adapted from Wikipedia "http://en.wikipedia.org/wiki/Hotelling's_T-squared_distribution" last polled: 2013-11-09 http://purl.obolibrary.org/obo/STATO_0000132 Hotelling T2 distribution http://purl.obolibrary.org/obo/STATO_0000133 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000133 a post-hoc analysis is a statistical test carried out following an analysis of variance which ruled out the null hypothesis of absence of difference between group which allows identifying which groups differ. http://purl.obolibrary.org/obo/STATO_0000133 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000133 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000133 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000133 a posteriori test http://purl.obolibrary.org/obo/STATO_0000133 adapted from wikipedia: http://en.wikipedia.org/wiki/Post-hoc_analysis last accessed: 2013-11-15 http://purl.obolibrary.org/obo/STATO_0000133 post-hoc analysis http://purl.obolibrary.org/obo/STATO_0000134 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000134 specificity is a measurement datum qualifying a binary classification test and is computed by substracting the false positive rate to the integral numeral 1 http://purl.obolibrary.org/obo/STATO_0000134 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000134 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000134 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000134 specificity http://purl.obolibrary.org/obo/STATO_0000134 http://purl.obolibrary.org/obo/STATO_0000134 true negative rate http://purl.obolibrary.org/obo/STATO_0000135 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789971/ http://purl.obolibrary.org/obo/STATO_0000135 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000135 strictly standardized mean difference (SSMS) is a standardized mean difference which corresponds to the ratio of mean to the standard deviation of the difference between two groups. SSMD directly measures the magnitude of difference between two groups. SSMD is widely used in High Content Screen for hit selection and quality control. When the data is preprocessed using log-transformation as normally done in HTS experiments, SSMD is the mean of log fold change divided by the standard deviation of log fold change with respect to a negative reference. In other words, SSMD is the average fold change (on the log scale) penalized by the variability of fold change (on the log scale). For quality control, one index for the quality of an HTS assay is the magnitude of difference between a positive control and a negative reference in an assay plate. For hit selection, the size of effects of a compound (i.e., a small molecule or an siRNA) is represented by the magnitude of difference between the compound and a negative reference. SSMD directly measures the magnitude of difference between two groups. Therefore, SSMD can be used for both quality control and hit selection in HTS experiments. http://purl.obolibrary.org/obo/STATO_0000135 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000135 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000135 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000135 http://en.wikipedia.org/wiki/SSMD http://purl.obolibrary.org/obo/STATO_0000135 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789971/ http://purl.obolibrary.org/obo/STATO_0000135 http://purl.obolibrary.org/obo/STATO_0000135 strictly standardized mean difference http://purl.obolibrary.org/obo/STATO_0000136 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000136 Tarone's test for homogeneity of odds ratio is a statistical test which evaluates the null hypothesis that odds ratio are homogeneous http://purl.obolibrary.org/obo/STATO_0000136 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000136 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000136 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000136 > library("metafor") > calcTaronesTest <- function(mylist,referencerow=2) http://a-little-book-of-r-for-biomedical-statistics.readthedocs.org/en/latest/src/biomedicalstats.html#calculating-the-mantel-haenszel-odds-ratio-when-there-is-a-stratifying-variable http://purl.obolibrary.org/obo/STATO_0000136 Tarone's test for homogeneity of odds ratio http://purl.obolibrary.org/obo/STATO_0000137 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000137 an homoskedasticity test is a statistical test aiming at evaluate if the variances from several random samples are similar http://purl.obolibrary.org/obo/STATO_0000137 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000137 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000137 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000137 STATO http://purl.obolibrary.org/obo/STATO_0000137 equivariance test http://purl.obolibrary.org/obo/STATO_0000137 homoskedasticity test http://purl.obolibrary.org/obo/STATO_0000138 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000138 a 2x2 contingency table is a contingency table build for 2 dichotomous variables (i.e. 2 categorical variables, each with only 2 possible outcomes). It is the simplest of contingency tables http://purl.obolibrary.org/obo/STATO_0000138 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000138 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000138 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000138 STATO http://purl.obolibrary.org/obo/STATO_0000138 2x2 contingency table http://purl.obolibrary.org/obo/STATO_0000138 xtabs(formula = ~., data = parent.frame(), subset, sparse = FALSE, na.action, exclude = c(NA, NaN), drop.unused.levels = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/xtabs.html flat contingency tables: ftable(x, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/ftable.html http://purl.obolibrary.org/obo/STATO_0000138 2 by 2 contingency table http://purl.obolibrary.org/obo/STATO_0000139 pairing patients by age, pairing animals by body weight range http://purl.obolibrary.org/obo/STATO_0000139 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000139 a subject pairing is a planned process which executes a pairing rule and results in the creation of sets of 2 subjects meeting the pairing criteria http://purl.obolibrary.org/obo/STATO_0000139 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000139 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000139 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000139 STATO http://purl.obolibrary.org/obo/STATO_0000139 http://purl.obolibrary.org/obo/STATO_0000139 subject pairing http://purl.obolibrary.org/obo/STATO_0000140 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000140 a contigency table is a data item which displays the (multivariate) frequency distribution of the possible values of categorical variables. The first row of the table corresponds to categories of one categorical variable, the first column of the table corresponds to categories of the other categorical variable, the cells corresponding to each combination of categories is filled with the observed occurences in the sample being considered. The table also contains marginal total (marginal sums) and grand total of the occurences The term contingency table was first used by Karl Pearson in "On the Theory of Contingency and Its Relation to Association and Normal Correlation", part of the Drapers' Company Research Memoirs Biometric Series I published in 1904. http://purl.obolibrary.org/obo/STATO_0000140 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000140 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000140 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000140 STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Contingency_table) http://purl.obolibrary.org/obo/STATO_0000140 http://purl.obolibrary.org/obo/STATO_0000140 xtabs(formula = ~., data = parent.frame(), subset, sparse = FALSE, na.action, exclude = c(NA, NaN), drop.unused.levels = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/xtabs.html flat contingency tables: ftable(x, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/ftable.html http://purl.obolibrary.org/obo/STATO_0000140 contingency table http://purl.obolibrary.org/obo/STATO_0000141 acute toxicity study is an investigation which use interventions organized according to a factorial design and a parallel group design to observe the effect of use of high dose xenobiotics in animal models or cellular models http://purl.obolibrary.org/obo/STATO_0000141 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000141 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000141 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000141 acute toxicity study http://purl.obolibrary.org/obo/STATO_0000141 acute toxicity study http://purl.obolibrary.org/obo/STATO_0000142 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000142 The correlation coefficient of two variables in a data sample is their covariance divided by the product of their individual standard deviations. It is a normalized measurement of how the two are linearly related. http://purl.obolibrary.org/obo/STATO_0000142 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000142 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000142 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000142 STATO http://purl.obolibrary.org/obo/STATO_0000142 r http://purl.obolibrary.org/obo/STATO_0000142 r statistics http://purl.obolibrary.org/obo/STATO_0000142 correlation coefficient http://purl.obolibrary.org/obo/STATO_0000143 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000143 a Bayesian model selection is a data transformation which is based on Bayesian statistics to compute Bayes factor in order to evaluate which model best explains data. http://purl.obolibrary.org/obo/STATO_0000143 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000143 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000143 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000143 adapted from wikipedia http://purl.obolibrary.org/obo/STATO_0000143 Bayesian model selection http://purl.obolibrary.org/obo/STATO_0000144 for example , model parameter estimates could be produced using regression analysis (used in a model estimation process) , which attempts to express the response variable in terms of function of predictor variable and model parameters. http://purl.obolibrary.org/obo/STATO_0000144 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000144 a model parameter estimate is a data item which results from a model parameter estimation process and which provides a numerical value is about a model parameter. http://purl.obolibrary.org/obo/STATO_0000144 textual definition modified following contributiong by Thomas Nichols: https://github.com/ISA-tools/stato/issues/18 http://purl.obolibrary.org/obo/STATO_0000144 Alejandra Gonzalez Beltran http://purl.obolibrary.org/obo/STATO_0000144 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000144 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000144 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000144 STATO http://purl.obolibrary.org/obo/STATO_0000144 model parameter estimate http://purl.obolibrary.org/obo/STATO_0000145 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000145 the geometric distribution is a negative binomial distribution where r is 1. It is useful for modeling the runs of consecutive successes (or failures) in repeated independent trials of a system. The geometric distribution models the number of successes before one failure in an independent succession of tests where each test results in success or failure. The geometric distribution with prob = p has density p(x) = p (1-p)^x for x = 0, 1, 2, …, 0 < p ≤ 1. If an element of x is not integer, the result of dgeom is zero, with a warning. The quantile is defined as the smallest value x such that F(x) ≥ p, where F is the distribution function. http://purl.obolibrary.org/obo/STATO_0000145 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000145 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000145 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000145 http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Geometric.html http://purl.obolibrary.org/obo/STATO_0000145 http://www.mathworks.co.uk/help/stats/geometric-distribution.html http://purl.obolibrary.org/obo/STATO_0000145 http://purl.obolibrary.org/obo/STATO_0000145 dgeom(x, prob, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Geometric.html http://purl.obolibrary.org/obo/STATO_0000145 geometric distribution http://purl.obolibrary.org/obo/STATO_0000146 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000146 a null hypothesis stating that there are differences observed between group of subjects http://purl.obolibrary.org/obo/STATO_0000146 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000146 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000146 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000146 STATO http://purl.obolibrary.org/obo/STATO_0000146 presence of between group difference hypothesis http://purl.obolibrary.org/obo/STATO_0000147 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000147 Linkage Disequilibrium plot is a graph which represents pairwise linkage disequilibrium measures between SNP as a heatmap http://purl.obolibrary.org/obo/STATO_0000147 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000147 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000147 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000147 STATO, adapted from R documentation (http://cran.r-project.org/web/packages/LDheatmap/index.html) http://purl.obolibrary.org/obo/STATO_0000147 LD plot http://purl.obolibrary.org/obo/STATO_0000147 Linkage Disequilibrium plot http://purl.obolibrary.org/obo/STATO_0000147 http://purl.obolibrary.org/obo/STATO_0000147 LD plot http://purl.obolibrary.org/obo/STATO_0000148 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000148 The Cochran-Armitage test is a statistical test used in categorical data analysis when the aim is to assess for the presence of an association between a dichotomous variable (variable with two categories) and a polychotomous variable (a variable with k categories). The two-level variable represents the response, and the other represents an explanatory variable with ordered levels. The null hypothesis is the hypothesis of no trend, which means that the binomial proportion is the same for all levels of the explanatory variable For example, doses of a treatment can be ordered as 'low', 'medium', and 'high', and we may suspect that the treatment benefit cannot become smaller as the dose increases. The trend test is often used as a genotype-based test for case-control genetic association studies. http://purl.obolibrary.org/obo/STATO_0000148 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000148 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000148 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000148 CATT http://purl.obolibrary.org/obo/STATO_0000148 http://en.wikipedia.org/wiki/Cochran%E2%80%93Armitage_test_for_trend http://purl.obolibrary.org/obo/STATO_0000148 http://purl.obolibrary.org/obo/STATO_0000148 http://purl.obolibrary.org/obo/STATO_0000148 Cochran-Armitage test for trend http://purl.obolibrary.org/obo/STATO_0000149 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000149 binomial logistic regression model is a model which attempts to explain data distribution associated with *dichotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is logistic function. http://purl.obolibrary.org/obo/STATO_0000149 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000149 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000149 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000149 STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Logistic_regression) polled in June 2013 http://purl.obolibrary.org/obo/STATO_0000149 http://purl.obolibrary.org/obo/STATO_0000149 binomial logistic regression for analysis of dichotomous dependent variable http://purl.obolibrary.org/obo/STATO_0000150 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000150 a minimum value is a data item which denotes the smallest value found in a dataset or resulting from a calculation. http://purl.obolibrary.org/obo/STATO_0000150 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000150 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000150 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000150 STATO http://purl.obolibrary.org/obo/STATO_0000150 minimum value http://purl.obolibrary.org/obo/STATO_0000151 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000151 maximum value is a data item which denotes the largest value found in a dataset or resulting from a calculation. http://purl.obolibrary.org/obo/STATO_0000151 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000151 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000151 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000151 STATO http://purl.obolibrary.org/obo/STATO_0000151 maximum value http://purl.obolibrary.org/obo/STATO_0000152 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000152 a quartile is a quantile which splits data into sections accrued of 25% of data, so the first quartile delineates 25% of the data, the second quartile delineates 50% of the data and the third quartile, 75 % of the data http://purl.obolibrary.org/obo/STATO_0000152 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000152 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000152 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000152 STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Quartile) http://purl.obolibrary.org/obo/STATO_0000152 http://purl.obolibrary.org/obo/STATO_0000152 quartile http://purl.obolibrary.org/obo/STATO_0000153 http://arxiv.org/pdf/1007.1094.pdf http://purl.obolibrary.org/obo/STATO_0000153 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000153 Hotelling's T2 test is a statistical test which is a generalization of Student's T-test to a assess if the means of a set of variables remains unchanged when studying 2 populations. It is a type of multivariate analysis http://purl.obolibrary.org/obo/STATO_0000153 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000153 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000153 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000153 STATO http://purl.obolibrary.org/obo/STATO_0000153 http://purl.obolibrary.org/obo/STATO_0000153 http://svitsrv25.epfl.ch/R-doc/library/rrcov/html/T2.test.html http://purl.obolibrary.org/obo/STATO_0000153 one sample Hotelling T2 test http://purl.obolibrary.org/obo/STATO_0000154 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000154 a violin plot is a plot combining the features of box plot and kernel density plot. The violin plot is therefore similar to box plot but it incorporated in the display the probability density of the data at different values. Typically violin plots will include a marker for the median of the data and a box indicating the interquartile range, as in standard box plots. http://purl.obolibrary.org/obo/STATO_0000154 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000154 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000154 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000154 http://en.wikipedia.org/wiki/Violin_plot and Hintze, J. L. and R. D. Nelson (1998). Violin plots: a box plot-density trace synergism. The American Statistician, 52(2):181-4. http://purl.obolibrary.org/obo/STATO_0000154 http://www.inside-r.org/packages/cran/vioplot/docs/vioplot vioplot( x, ..., range=1.5, h, ylim, names, horizontal=FALSE, col="magenta", border="black", lty=1, lwd=1, rectCol="black", colMed="white", pchMed=19, at, add=FALSE, wex=1, drawRect=TRUE) http://purl.obolibrary.org/obo/STATO_0000154 violin plot http://purl.obolibrary.org/obo/STATO_0000155 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000155 meta-analysis is a data transformation which uses the effect size estimates from several independent quantitative scientific studies addressing the same question in order to assess finding consistency. http://purl.obolibrary.org/obo/STATO_0000155 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000155 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000155 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000155 adapted from wikipedia: http://en.wikipedia.org/wiki/Metaanalysis last accessed: 2013-11-15 http://purl.obolibrary.org/obo/STATO_0000155 meta analysis http://purl.obolibrary.org/obo/STATO_0000156 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000156 the Scheffe test is a data transformation which evaluates all possible contrasts and adjusting the levels significance by accounting for multiple comparison. The test is therefore conservative. Confidence intervals can be constructed for the corresponding linear regression. It was developped by American statistician Henry Scheffe in 1959. http://purl.obolibrary.org/obo/STATO_0000156 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000156 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000156 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000156 STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Scheffé's_method) http://purl.obolibrary.org/obo/STATO_0000156 http://purl.obolibrary.org/obo/STATO_0000156 http://www.inside-r.org/packages/cran/agricolae/docs/scheffe.test http://purl.obolibrary.org/obo/STATO_0000156 Scheffe test http://purl.obolibrary.org/obo/STATO_0000157 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000157 the LSD test is a statistical test for multiple comparisons of treatments by means of least significant difference following an ANOVA analysis http://purl.obolibrary.org/obo/STATO_0000157 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000157 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000157 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000157 R http://purl.obolibrary.org/obo/STATO_0000157 LSD test http://purl.obolibrary.org/obo/STATO_0000157 http://rss.acs.unt.edu/Rdoc/library/agricolae/html/LSD.test.html http://purl.obolibrary.org/obo/STATO_0000157 Least significance different test http://purl.obolibrary.org/obo/STATO_0000158 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000158 a null hypothesis which states that a linkage exists between 2 categorical variables http://purl.obolibrary.org/obo/STATO_0000158 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000158 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000158 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000158 STATO http://purl.obolibrary.org/obo/STATO_0000158 presence of association hypothesis http://purl.obolibrary.org/obo/STATO_0000159 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000159 Stacked bar chart is a bar which is used to compare overall quantities across items while showing the contribution of category to the total amount. Stacked bar chart can be used for highlighting the total as they visually aggregate all of the categories in a group while indicating a part to whole relationship. The downside is that it becomes harder to compare the sizes of the individual categories. http://purl.obolibrary.org/obo/STATO_0000159 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000159 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000159 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000159 adapter from http://www2.le.ac.uk/offices/ld/resources/numeracy/bar-charts and http://blog.visual.ly/how-groups-stack-up-when-to-use-grouped-vs-stacked-column-charts/ [last accessed: 2014-03-04] http://purl.obolibrary.org/obo/STATO_0000159 barplot(height....) set argument " beside = FALSE " http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/barplot.html http://purl.obolibrary.org/obo/STATO_0000159 stacked bar chart http://purl.obolibrary.org/obo/STATO_0000160 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000160 The exponential distribution (a.k.a. negative exponential distribution) is the probability distribution that describes the time between events in a Poisson process, i.e. a process in which events occur continuously and independently at a constant average rate. It is the continuous analogue of the geometric distribution, and it has the key property of being memoryless. http://purl.obolibrary.org/obo/STATO_0000160 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000160 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000160 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000160 http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Exponential.html dexp(x, rate = 1, log = FALSE) pexp(q, rate = 1, lower.tail = TRUE, log.p = FALSE) qexp(p, rate = 1, lower.tail = TRUE, log.p = FALSE) rexp(n, rate = 1) http://purl.obolibrary.org/obo/STATO_0000160 exponential distribution http://purl.obolibrary.org/obo/STATO_0000161 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000161 variable distribution is data item which denotes the spatial resolution of data point making up a variable. variable distribution may be compared to a known probability distribution using goodness of fit test or plotting a quantile-quantile plot for visual assessment of the fit. http://purl.obolibrary.org/obo/STATO_0000161 TODO: Probably need to drop it http://purl.obolibrary.org/obo/STATO_0000161 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000161 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000161 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000161 STATO http://purl.obolibrary.org/obo/STATO_0000161 data distribution http://purl.obolibrary.org/obo/STATO_0000161 data distribution http://purl.obolibrary.org/obo/STATO_0000162 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000162 the role played by an entity part of study group as defined by an experimental design and realized in a data analysis and data interpretation http://purl.obolibrary.org/obo/STATO_0000162 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000162 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000162 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000162 experimental unit role http://purl.obolibrary.org/obo/STATO_0000163 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000163 trimmed mean or truncated mean is a measure of central tendency which involves the calculation of the mean after discarding given parts of a probability distribution or sample at the high and low end, and typically discarding an equal amount of both http://purl.obolibrary.org/obo/STATO_0000163 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000163 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000163 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000163 adapted from wikipedia [last accessed 2014-03-04] http://en.wikipedia.org/wiki/Truncated_mean http://purl.obolibrary.org/obo/STATO_0000163 truncated mean http://purl.obolibrary.org/obo/STATO_0000163 trimmed mean http://purl.obolibrary.org/obo/STATO_0000164 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000164 The interquartile range is a data item which corresponds to the difference between the upper quartile (3rd quartile) and lower quartile (1st quartile). The interquartile range contains the second quartile or median. The interquartile range is a data item providing a measure of data dispersion http://purl.obolibrary.org/obo/STATO_0000164 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000164 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000164 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000164 STATO adapted from wikipedia, wolfram alpha and oxford dictionary of statistics http://purl.obolibrary.org/obo/STATO_0000164 IQR(x, na.rm = FALSE, type = 7) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/IQR.html http://purl.obolibrary.org/obo/STATO_0000164 inter quartile range http://purl.obolibrary.org/obo/STATO_0000165 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000165 a pie chart is a graph in which a circular graph is divided into sector illustrating numerical proportion, meaning that the arc length of each sector (and consequently its central angle and area), is proportional to the quantity it represents. http://purl.obolibrary.org/obo/STATO_0000165 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000165 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000165 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000165 adapted from Wikipedia, last accessed [2014-03-05] http://en.wikipedia.org/wiki/Pie_chart http://purl.obolibrary.org/obo/STATO_0000165 pie(x, labels = names(x), edges = 200, radius = 0.8, clockwise = FALSE, init.angle = if(clockwise) 90 else 0, density = NULL, angle = 45, col = NULL, border = NULL, lty = NULL, main = NULL, ...) https://stat.ethz.ch/R-manual/R-devel/library/graphics/html/pie.html http://purl.obolibrary.org/obo/STATO_0000165 pie chart http://purl.obolibrary.org/obo/STATO_0000166 A bar chart is appropriate to represent counts of data. http://purl.obolibrary.org/obo/STATO_0000166 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000166 the bart chart is a graph resulting from plotting rectangular bars with lengths proportional to the values that they represent. http://purl.obolibrary.org/obo/STATO_0000166 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000166 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000166 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000166 adapted from wikipedia (http://en.wikipedia.org/wiki/Bar_chart) polled in June 2013 http://purl.obolibrary.org/obo/STATO_0000166 bar plot http://purl.obolibrary.org/obo/STATO_0000166 barplot(height, ...) http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/barplot.html http://purl.obolibrary.org/obo/STATO_0000166 bar chart http://purl.obolibrary.org/obo/STATO_0000167 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000167 the first quartile is a quartile which splits the lower 25 % of the data http://purl.obolibrary.org/obo/STATO_0000167 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000167 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000167 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000167 STATO http://purl.obolibrary.org/obo/STATO_0000167 first quartile http://purl.obolibrary.org/obo/STATO_0000168 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000168 a real time quantitative pcr plot is a line graph which plots the signal fluorescence intensity as a function of the number of PCR cycle http://purl.obolibrary.org/obo/STATO_0000168 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000168 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000168 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000168 real time quantitative pcr plot http://purl.obolibrary.org/obo/STATO_0000169 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000169 Fold change is a number describing how much a quantity changes going from an initial to a final value or one condition to another condition http://purl.obolibrary.org/obo/STATO_0000169 30/04/2014 - removed restriction: 'is about' exactly 2 'study group population' - need more discussion for the relationship of fold change to study group populations for particular examples. http://purl.obolibrary.org/obo/STATO_0000169 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000169 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000169 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000169 http://en.wikipedia.org/wiki/Fold_change http://purl.obolibrary.org/obo/STATO_0000169 http://purl.obolibrary.org/obo/STATO_0000169 fold change http://purl.obolibrary.org/obo/STATO_0000170 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000170 the first quartile is a quartile which splits the 75 % of the data http://purl.obolibrary.org/obo/STATO_0000170 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000170 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000170 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000170 STATO http://purl.obolibrary.org/obo/STATO_0000170 http://purl.obolibrary.org/obo/STATO_0000170 third quartile http://purl.obolibrary.org/obo/STATO_0000171 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000171 Spear Box and Whisker plot is a variation of Tukey Box and Whisker plot which use the criteria of Spear to create the 'whisker' of the plot. http://purl.obolibrary.org/obo/STATO_0000171 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000171 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000171 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000171 Spear, M.E. Charting Statistics (McGraw-Hill, 1952) http://purl.obolibrary.org/obo/STATO_0000171 Spear box and whisker plot http://purl.obolibrary.org/obo/STATO_0000172 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000172 expected fragments per kilobase of transcript per million fragments mapped is a metric used to report transcript expression event as generated by RNA-Seq using paired-end library. The calculated value results from 2 types of normalization, one to take into account the difference in reads counts associated with transcript length (at equal abundance, longer transcripts will have more reads than shorter transcripts) , (hence the 'per kilobase of transcript') and the other one to take into account different sequencing depth during distinct sequencing runs (hence the 'per millions mapped fragment'. The metric is specifically produced by cufflink software. http://purl.obolibrary.org/obo/STATO_0000172 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000172 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000172 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000172 FPKM http://purl.obolibrary.org/obo/STATO_0000172 adapted from: http://seqanswers.com/forums/showthread.php?t=3254 and from http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html http://purl.obolibrary.org/obo/STATO_0000172 fragments per kilobase of transcript per million fragments mapped http://purl.obolibrary.org/obo/STATO_0000173 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000173 homogeneity testing objective is the objective of a data transformation to test a null hypothesis that two or more sub-groups of a population share the same distribution of a single categorical variable. For example, do people of different countries have the same proportion of smokers to non-smokers http://purl.obolibrary.org/obo/STATO_0000173 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000173 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000173 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000173 STATO http://purl.obolibrary.org/obo/STATO_0000173 http://purl.obolibrary.org/obo/STATO_0000173 homogeneity test objective http://purl.obolibrary.org/obo/STATO_0000174 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000174 A forest plot is a graph designed to illustrate the relative strength of treatment effects in multiple quantitative scientific studies addressing the same question. http://purl.obolibrary.org/obo/STATO_0000174 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000174 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000174 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000174 http://en.wikipedia.org/wiki/Forest_plot http://purl.obolibrary.org/obo/STATO_0000174 http://purl.obolibrary.org/obo/STATO_0000174 metaplot(mn, se, nn=NULL, labels=NULL, conf.level=0.95, xlab="Odds ratio", ylab="Study Reference",xlim=NULL, summn=NULL, sumse=NULL, sumnn=NULL, summlabel="Summary", logeffect=FALSE, lwd=2, boxsize=1, zero=as.numeric(logeffect), colors=meta.colors(), xaxt="s", logticks=TRUE, ...) http://rss.acs.unt.edu/Rdoc/library/rmeta/html/metaplot.html http://purl.obolibrary.org/obo/STATO_0000174 Forest plot http://purl.obolibrary.org/obo/STATO_0000175 http://stat.ethz.ch/R-manual/R-patched/library/stats/html/confint.html http://purl.obolibrary.org/obo/STATO_0000175 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000175 confidence interval calculation is a data transformation which determines a confidence interval for a given statistical parameter http://purl.obolibrary.org/obo/STATO_0000175 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000175 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000175 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000175 STATO http://purl.obolibrary.org/obo/STATO_0000175 http://purl.obolibrary.org/obo/STATO_0000175 confidence interval calculation http://purl.obolibrary.org/obo/STATO_0000176 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000176 t-statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Student's t distribution. http://purl.obolibrary.org/obo/STATO_0000176 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000176 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000176 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000176 STATO http://purl.obolibrary.org/obo/STATO_0000176 http://purl.obolibrary.org/obo/STATO_0000176 t-statistic http://purl.obolibrary.org/obo/STATO_0000177 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000177 the beta distribution is a continuous probability distributions defined on the interval [0, 1] parametrized by two positive shape parameters, denoted by α and β, that appear as exponents of the random variable and control the shape of the distribution http://purl.obolibrary.org/obo/STATO_0000177 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000177 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000177 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000177 adapted from Wikipedia: http://en.wikipedia.org/wiki/Beta_distribution http://purl.obolibrary.org/obo/STATO_0000177 http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Beta.html dbeta(x, shape1, shape2, ncp = 0, log = FALSE) pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE) qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE) rbeta(n, shape1, shape2, ncp = 0) http://purl.obolibrary.org/obo/STATO_0000177 beta distribution http://purl.obolibrary.org/obo/STATO_0000178 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000178 Kurtosis is a data item which denotes the degree of peakedness of a distribution. It is defined as a normalized form of the fourth central moment of a distribution. http://purl.obolibrary.org/obo/STATO_0000178 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000178 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000178 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000178 http://mathworld.wolfram.com/Kurtosis.html http://purl.obolibrary.org/obo/STATO_0000178 http://purl.obolibrary.org/obo/STATO_0000178 kurtosis http://purl.obolibrary.org/obo/STATO_0000179 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000179 ANCOVA or analysis of covariance is a data transformation which evaluates if population means of a dependent variable are equal across levels of a categorical independent variables while controlling for the effects of other continuous variable s, known as covariates. Therefore, when performing ANCOVA, we are adjusting the dependent variable means to what they would be if all groups were equal on the covariates. It augments the ANOVA model with one or more additional quantitative variables, called covariates, which are related to the response variable. The covariates are included to reduce the variance in the error terms and provide more precise measurement of the treatment effects. ANCOVA is used to test the main and interaction effects of the factors, while controlling for the effects of the covariate http://purl.obolibrary.org/obo/STATO_0000179 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000179 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000179 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000179 adapted from wikipedia http://purl.obolibrary.org/obo/STATO_0000179 http://purl.obolibrary.org/obo/STATO_0000179 ANCOVA http://purl.obolibrary.org/obo/STATO_0000180 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000180 standard normal distribution is a normal distribution with variance = 1 and mean=0 http://purl.obolibrary.org/obo/STATO_0000180 we need to formally set value for mean and variance http://purl.obolibrary.org/obo/STATO_0000180 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000180 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000180 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000180 http://purl.obolibrary.org/obo/STATO_0000180 dnorm(x, mean = 0, sd = 1, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Normal.html http://purl.obolibrary.org/obo/STATO_0000180 standard normal distribution http://purl.obolibrary.org/obo/STATO_0000181 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000181 Hardy-Weinberg equilibrium test is a statistical test which aims to evaluate if a population's proportion of allele is stable or not. It is used as means of quality control to evaluate possibility of genotyping error or population structure. http://purl.obolibrary.org/obo/STATO_0000181 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000181 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000181 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000181 STATO: adapted from wikipedia (http://en.wikipedia.org/wiki/Hardy–Weinberg_principle) http://purl.obolibrary.org/obo/STATO_0000181 http://purl.obolibrary.org/obo/STATO_0000181 > library(HardyWeinberg) > x <- c(298,489,213) > HW.test <- HWChisq(x,verbose=TRUE) http://cran.r-project.org/web/packages/HardyWeinberg/index.html http://purl.obolibrary.org/obo/STATO_0000181 Hardy-Weinberg equilibrium testing http://purl.obolibrary.org/obo/STATO_0000182 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000182 Odds ratio is a ratio that measures effect size, that is the strength of association between 2 dichotomous variables, one describing an exposure and one describing an outcome. It represents the odds that an outcome will occur given a particular exposure, compared to the odds of the outcome occurring in the absence of that exposure ( the probability of the event occuring divided by the probability of an event not occurring). The odds ratio is a ratio of describing the strength of association or non-independence between two binary data values by forming the ratio of the odds for the first group and the odds for the second group. Odds ratio are used when one wants to compare the odds of something occurring to two different groups. http://purl.obolibrary.org/obo/STATO_0000182 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000182 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000182 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000182 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938757/ http://www.stats.org/stories/2008/odds_ratios_april4_2008.html http://purl.obolibrary.org/obo/STATO_0000182 OR http://purl.obolibrary.org/obo/STATO_0000182 odds ratio http://purl.obolibrary.org/obo/STATO_0000183 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000183 sphericity testing objective is a statistical objective of a data transformation which aims to test a null hypothesis of sphericity holds. http://purl.obolibrary.org/obo/STATO_0000183 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000183 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000183 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000183 STATO http://purl.obolibrary.org/obo/STATO_0000183 sphericity testing objective http://purl.obolibrary.org/obo/STATO_0000183 sphericity testing objective http://purl.obolibrary.org/obo/STATO_0000184 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000184 A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s. http://purl.obolibrary.org/obo/STATO_0000184 review formal definition as both numerator and denominator should be of the same type, not just some data item http://purl.obolibrary.org/obo/STATO_0000184 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000184 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000184 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000184 adapted from Wolfram Alpha: https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig76g7 http://purl.obolibrary.org/obo/STATO_0000184 ratio http://purl.obolibrary.org/obo/STATO_0000185 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000185 a 2 by n contingency table is a contingency table built for one dichotomous variable (a categorical variable with only 2 outcomes) and one polychotomous variable (a polychomotomous variable with at least 2 outcomes) http://purl.obolibrary.org/obo/STATO_0000185 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000185 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000185 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000185 STATO http://purl.obolibrary.org/obo/STATO_0000185 http://purl.obolibrary.org/obo/STATO_0000185 xtabs(formula = ~., data = parent.frame(), subset, sparse = FALSE, na.action, exclude = c(NA, NaN), drop.unused.levels = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/xtabs.html flat contingency tables: ftable(x, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/ftable.html http://purl.obolibrary.org/obo/STATO_0000185 2 by n contingency table http://purl.obolibrary.org/obo/STATO_0000186 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000186 Lineweaver-Burk plot is a graph which is the graphical representation of the Lineweaver–Burk equation of enzyme kinetics, described by Hans Lineweaver and Dean Burk in 1934. The plot provides a useful graphical method for analysis of the Michaelis–Menten equation. It was widely used to determine important terms in enzymology and enzyme kinetics as the x-intercept of the graph represents −1/Km and the y-intercept of such a graph is equivalent to the inverse of Vmax http://purl.obolibrary.org/obo/STATO_0000186 TODO: create 'inverse function' and replace 'data transformation' in the assertions http://purl.obolibrary.org/obo/STATO_0000186 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000186 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000186 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000186 double reciprocal plot http://purl.obolibrary.org/obo/STATO_0000186 Lineweaver-Burk plot http://purl.obolibrary.org/obo/STATO_0000187 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000187 Tukey Honestly Significant Difference (HSD) test is a statistical test used following an ANOVA test yielding a statistically significant p-value in order to determine which means are different, to a given level of significance. The Tukey HSD test relies on the q-distribution. The procedure is conservative, meaning that if sample sizes (the sizes of different study groups) are equal, the risk of a Type I error is exactly α, and if sample sizes are unequal it’s less than α. http://purl.obolibrary.org/obo/STATO_0000187 IMPORTANT: Do Not to confuse the Tukey HSD test with Tukey Mean Difference Test (Bland-Altman test) http://purl.obolibrary.org/obo/STATO_0000187 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000187 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000187 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000187 http://www.tc3.edu/instruct/sbrown/stat/anova1.htm#ANOVAprereq http://purl.obolibrary.org/obo/STATO_0000187 Tukey's honestly significant difference http://purl.obolibrary.org/obo/STATO_0000187 http://stat.ethz.ch/R-manual/R-patched/library/stats/html/TukeyHSD.html http://purl.obolibrary.org/obo/STATO_0000187 Tukey HSD for Post-Hoc Analysis http://purl.obolibrary.org/obo/STATO_0000188 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000188 average log signal intensity is a data time which corresponds to the sum of 2 distinct logarithm base 2 transformed signal intensity, each corresponding to a distinct condition of signal acquisition, divided by 2. http://purl.obolibrary.org/obo/STATO_0000188 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000188 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000188 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000188 adapted from wikipedia: http://en.wikipedia.org/wiki/MA_plot last accessed: 2014-03-13 http://purl.obolibrary.org/obo/STATO_0000188 A-value http://purl.obolibrary.org/obo/STATO_0000188 average log signal intensity http://purl.obolibrary.org/obo/STATO_0000189 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000189 A mixed model is a statistical model containing both fixed effects and random effects http://purl.obolibrary.org/obo/STATO_0000189 PRS: this is a stub and more work is needed to reconcile conflicting definitions http://purl.obolibrary.org/obo/STATO_0000189 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000189 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000189 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000189 adapted from wikipedia http://purl.obolibrary.org/obo/STATO_0000189 http://purl.obolibrary.org/obo/STATO_0000189 mixed model http://purl.obolibrary.org/obo/STATO_0000190 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000190 Threshold cycle (or Ct or Cq) is a count which is defined as the fractional PCR cycle number at which the reporter fluorescence is greater than the threshold in the context of the RT-qPCR assay. The Ct is a basic principle of real time PCR and is an essential component in producing accurate and reproducible data. http://purl.obolibrary.org/obo/STATO_0000190 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000190 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000190 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000190 Cq http://purl.obolibrary.org/obo/STATO_0000190 Ct http://purl.obolibrary.org/obo/STATO_0000190 http://www.ncbi.nlm.nih.gov/genome/probe/doc/TechQPCR.shtml http://purl.obolibrary.org/obo/STATO_0000190 threshold cycle http://purl.obolibrary.org/obo/STATO_0000191 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000191 a goodness of fit statistical test is a statistical test which aim to evaluate if a sample distribution can be considered equivalent to a theoretical distribution used as input http://purl.obolibrary.org/obo/STATO_0000191 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000191 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000191 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000191 http://purl.obolibrary.org/obo/STATO_0000191 goodness of fit statistical test http://purl.obolibrary.org/obo/STATO_0000192 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000192 a cartesian product is a data transformation which operates on a n Sets to produce a set of all possible ordered n-tuples where each element of the tuple comes from a Set http://purl.obolibrary.org/obo/STATO_0000192 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000192 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000192 PERSON: Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000192 adapted from math wolfram (http://mathworld.wolfram.com/CartesianProduct.html) http://purl.obolibrary.org/obo/STATO_0000192 http://purl.obolibrary.org/obo/STATO_0000192 cartesian product http://purl.obolibrary.org/obo/STATO_0000193 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000193 is a population whose individual members realize (may be expressed as) a combination of inclusion rule values specifications or resulting from a sampling process (e.g. recruitment followed by randomization to group) on which a number of measurements will be carried out, which may be used as input to statistical tests and statistical inference. http://purl.obolibrary.org/obo/STATO_0000193 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000193 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000193 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000193 STATO http://purl.obolibrary.org/obo/STATO_0000193 statistical sample http://purl.obolibrary.org/obo/STATO_0000193 study group population http://purl.obolibrary.org/obo/STATO_0000194 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000194 self explanatory http://purl.obolibrary.org/obo/STATO_0000194 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000194 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000194 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000194 http://purl.obolibrary.org/obo/STATO_0000194 cartesian product 2 sets http://purl.obolibrary.org/obo/STATO_0000195 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000195 A non-negative integer defining how many combination of factor levels (or treatments in the statistical sense) are to be used in a study. http://purl.obolibrary.org/obo/STATO_0000195 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000195 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000195 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000195 STATO http://purl.obolibrary.org/obo/STATO_0000195 http://purl.obolibrary.org/obo/STATO_0000195 number of factor level combinations http://purl.obolibrary.org/obo/STATO_0000196 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/ http://purl.obolibrary.org/obo/STATO_0000196 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000196 A confidence interval is a data item which defines an range of values in which a measurement or trial falls corresponding to a given probability. http://purl.obolibrary.org/obo/STATO_0000196 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000196 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000196 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000196 http://mathworld.wolfram.com/ConfidenceInterval.html http://purl.obolibrary.org/obo/STATO_0000196 http://purl.obolibrary.org/obo/STATO_0000196 confidence interval http://purl.obolibrary.org/obo/STATO_0000197 http://purl.obolibrary.org/obo/STATO_0000197 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000197 a genomic coordinate system is a coordinate system to describe position of sequence on a genomic scaffold (assembly of chromosome, contig....) http://purl.obolibrary.org/obo/STATO_0000197 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000197 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000197 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000197 ensembl, ucsc http://purl.obolibrary.org/obo/STATO_0000197 http://purl.obolibrary.org/obo/STATO_0000197 genomic coordinate system http://purl.obolibrary.org/obo/STATO_0000198 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000198 a statistical test which makes no assumption about the underlying data distribution http://purl.obolibrary.org/obo/STATO_0000198 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000198 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000198 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000198 STATO http://purl.obolibrary.org/obo/STATO_0000198 non-parametric test http://purl.obolibrary.org/obo/STATO_0000199 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000199 the Mauchly's test for sphericity is a statistical test which evaluates if the variance of the differences between all combinations of the groups are equal, a property known as 'sphericity' in the context of repeated measures. It is used for instance prior to repeated measure ANOVA. The test works by assessing if a Wishart-distributed covariance matrix (or transformation thereof) is proportional to a given matrix. http://purl.obolibrary.org/obo/STATO_0000199 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000199 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000199 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000199 AGB-PRS, adapted from wikipedia (http://en.wikipedia.org/wiki/Mauchly's_sphericity_test) polled on june,10th, 2013 and from R manual: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/mauchly.test.html http://purl.obolibrary.org/obo/STATO_0000199 Mauchly's test for sphericity http://purl.obolibrary.org/obo/STATO_0000199 mauchly.test(object, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/mauchly.test.html http://purl.obolibrary.org/obo/STATO_0000199 Mauchly's test for sphericity http://purl.obolibrary.org/obo/STATO_0000200 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000200 the statistical test power is data item which is about a statistical test and is obtained by subtracting the false negative rate (type II error rate) to 1. The power of a statistical test is the probability that it will correctly lead to the rejection of a false null hypothesis (Greene 2000). The statistical power is the ability of a test to detect an effect, if the effect actually exists (High 2000). http://purl.obolibrary.org/obo/STATO_0000200 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000200 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000200 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000200 adapted from wikipedia (http://en.wikipedia.org/wiki/Statistical_power), polled June 10th, 2013 http://purl.obolibrary.org/obo/STATO_0000200 http://purl.obolibrary.org/obo/STATO_0000200 statistical test power http://purl.obolibrary.org/obo/STATO_0000201 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000201 Spearman's rank correlation coefficient is a correlation coefficient which is a nonparametric measure of statistical dependence between two ranked variables. It assesses how well the relationship between two variables can be described using a monotonic function. If there are no repeated data values, a perfect Spearman correlation of +1 or −1 occurs when each of the variables is a perfect monotone function of the other. Spearman's coefficient may be used when the conditions for computing Pearson's correlation are not met (e.g linearity, normality of the 2 continuous variables) but may require a ranking transformation of the variables http://purl.obolibrary.org/obo/STATO_0000201 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000201 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000201 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000201 Spearman's rho http://purl.obolibrary.org/obo/STATO_0000201 http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient http://purl.obolibrary.org/obo/STATO_0000201 http://purl.obolibrary.org/obo/STATO_0000201 cor(x, y = NULL, use = "everything",method = c("spearman")) http://purl.obolibrary.org/obo/STATO_0000201 Spearman's rank correlation coefficient http://purl.obolibrary.org/obo/STATO_0000202 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000202 within subject comparison statistical test is a kind of statistical test which evaluates if a change occurs within one experimental unit over time following a treatment or an event http://purl.obolibrary.org/obo/STATO_0000202 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000202 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000202 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000202 STATO http://purl.obolibrary.org/obo/STATO_0000202 http://purl.obolibrary.org/obo/STATO_0000202 within subject comparison statistical test http://purl.obolibrary.org/obo/STATO_0000203 http://purl.obolibrary.org/obo/STATO_0000203 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000203 a cohort is a study group population where the members are human beings which meet inclusion criteria and undergo a longitudinal design http://purl.obolibrary.org/obo/STATO_0000203 possibly submit to 'Population and Community Ontology' http://purl.obolibrary.org/obo/STATO_0000203 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000203 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000203 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000203 STATO http://purl.obolibrary.org/obo/STATO_0000203 http://purl.obolibrary.org/obo/STATO_0000203 cohort http://purl.obolibrary.org/obo/STATO_0000204 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000204 the F-distribution is a continuous probability distribution which arises in the testing of whether two observed samples have the same variance. http://purl.obolibrary.org/obo/STATO_0000204 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000204 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000204 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000204 Fisher distribution http://purl.obolibrary.org/obo/STATO_0000204 Snedecor Fisher distribution http://purl.obolibrary.org/obo/STATO_0000204 http://mathworld.wolfram.com/F-Distribution.html http://purl.obolibrary.org/obo/STATO_0000204 http://purl.obolibrary.org/obo/STATO_0000204 df(x, df1, df2, ncp, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Fdist.html http://purl.obolibrary.org/obo/STATO_0000204 F-distribution http://purl.obolibrary.org/obo/STATO_0000205 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000205 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000205 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000205 is denoted by http://purl.obolibrary.org/obo/STATO_0000206 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000206 RPKM is a kind of count which numbers the sequence reads found per kilobase of transcript reported to million of sequence reads. RPKM is a metric generated by ERANGE software tool as reported by Mortazi et al, in 2008. The metric has been enhanced and replaced by FPKM to better take into account splice variant. FKPM uses a statistical model to perform the computation. http://purl.obolibrary.org/obo/STATO_0000206 Alejandra Gonzalez Beltran http://purl.obolibrary.org/obo/STATO_0000206 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000206 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000206 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000206 RPKM http://purl.obolibrary.org/obo/STATO_0000206 http://www.nature.com/nmeth/journal/v5/n7/full/nmeth.1226.html http://purl.obolibrary.org/obo/STATO_0000206 reads per kilobase of transcript per million fragments mapped http://purl.obolibrary.org/obo/STATO_0000207 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000207 a planned process which etablishes and states the different hypothesis to be evaluated during a null hypothesis statistical test http://purl.obolibrary.org/obo/STATO_0000207 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000207 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000207 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000207 STATO http://purl.obolibrary.org/obo/STATO_0000207 specifying null and alternate hypothesis http://purl.obolibrary.org/obo/STATO_0000208 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000208 alternative hypothesis is an hyopthesis defined in a statistical which is the opposite of the null hypothesis http://purl.obolibrary.org/obo/STATO_0000208 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000208 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000208 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000208 STATO http://purl.obolibrary.org/obo/STATO_0000208 http://purl.obolibrary.org/obo/STATO_0000208 alternate hypothesis http://purl.obolibrary.org/obo/STATO_0000209 PMID:12892658 "Two formulas for computation of the area under the curve represent measures of total hormone concentration versus time-dependent change." http://purl.obolibrary.org/obo/STATO_0000209 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000209 area under curve is a measurement datum which corresponds to the surface define by the x-axis and bound by the line graph represented in a 2 dimensional plot resulting from an integration or integrative calculus. The interpretation of this measurement datum depends on the variables plotted in the graph http://purl.obolibrary.org/obo/STATO_0000209 PRS: submit 'integral calculus' as a kind of data transformation in OBI:DT branch http://purl.obolibrary.org/obo/STATO_0000209 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000209 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000209 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000209 area under curve http://purl.obolibrary.org/obo/STATO_0000210 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000210 is a data item formed by dividing the fluorescence intensity obtained in one channel to that obtained in the other channel, typically the case when considering 2-color microarray data when imaging is done for Cy3 and Cy5 dyes. http://purl.obolibrary.org/obo/STATO_0000210 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000210 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000210 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000210 STATO http://purl.obolibrary.org/obo/STATO_0000210 channel1/channel2 fluorescence intensity ratio http://purl.obolibrary.org/obo/STATO_0000210 channel1/channel2 fluorescence intensity ratio http://purl.obolibrary.org/obo/STATO_0000211 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000211 odds ratio homogeneity hypothesis is a null hypothesis stating that all odds ratio are homogenous, that is remain within the same range http://purl.obolibrary.org/obo/STATO_0000211 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000211 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000211 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000211 STATO http://purl.obolibrary.org/obo/STATO_0000211 odds ratio homogeneity hypothesis http://purl.obolibrary.org/obo/STATO_0000211 odds ratio homogeneity hypothesis http://purl.obolibrary.org/obo/STATO_0000212 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000212 a tetrachoric correlation coefficient is a polychoric correlation coefficient for 2 dichotomous variables used as proxy for correlation between 2 continuous latent variables. http://purl.obolibrary.org/obo/STATO_0000212 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000212 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000212 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000212 adapted from: http://www.rasch.org/rmt/rmt193c.htm and http://en.wikipedia.org/wiki/Polychoric_correlation http://purl.obolibrary.org/obo/STATO_0000212 tetrachoric correlation coefficient http://purl.obolibrary.org/obo/STATO_0000213 http://purl.obolibrary.org/obo/STATO_0000213 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000213 discretization as a processing converting a continuous variable into a polychotomous variable by concretizing a set of discretization rules http://purl.obolibrary.org/obo/STATO_0000213 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000213 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000213 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000213 AGB,PRS adapted from wikipedia (http://en.wikipedia.org/wiki/Discretization) http://purl.obolibrary.org/obo/STATO_0000213 http://purl.obolibrary.org/obo/STATO_0000213 http://cran.r-project.org/web/packages/discretization/index.html http://purl.obolibrary.org/obo/STATO_0000213 continuous variable discretization http://purl.obolibrary.org/obo/STATO_0000214 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/ http://purl.obolibrary.org/obo/STATO_0000214 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000214 a confidence interval which covers 50% of the sampling distribution, meaning that there is a 50% risk of false positive (type I error) http://purl.obolibrary.org/obo/STATO_0000214 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000214 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000214 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000214 confidence interval at 10% of type I error rate http://purl.obolibrary.org/obo/STATO_0000214 STATO http://purl.obolibrary.org/obo/STATO_0000214 http://purl.obolibrary.org/obo/STATO_0000214 50% confidence interval http://purl.obolibrary.org/obo/STATO_0000215 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000215 probit regression model is a model which attempts to explain data distribution associated with *ordinal* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is the ordered probit function. http://purl.obolibrary.org/obo/STATO_0000215 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000215 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000215 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000215 STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Probit_model) polled in June 2013 http://purl.obolibrary.org/obo/STATO_0000215 http://purl.obolibrary.org/obo/STATO_0000215 http://purl.obolibrary.org/obo/STATO_0000215 ordered probit regression for analysis of ordinal dependent variable http://purl.obolibrary.org/obo/STATO_0000216 http://purl.obolibrary.org/obo/STATO_0000216 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000216 a stratum population is a population resulting from a population stratification prior to sampling process which aims to produce homogenous subpopulations from an heterogeneous population by applying one or more stratification criteria http://purl.obolibrary.org/obo/STATO_0000216 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000216 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000216 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000216 STATO http://purl.obolibrary.org/obo/STATO_0000216 http://purl.obolibrary.org/obo/STATO_0000216 stratum population http://purl.obolibrary.org/obo/STATO_0000217 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000217 a null hypothesis which states that a given matrix is proportional to a Wishart-distributed covariance matrix http://purl.obolibrary.org/obo/STATO_0000217 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000217 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000217 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000217 STATO http://purl.obolibrary.org/obo/STATO_0000217 hypothesis of sphericity http://purl.obolibrary.org/obo/STATO_0000217 sphericity hypothesis http://purl.obolibrary.org/obo/STATO_0000218 http://purl.obolibrary.org/obo/STATO_0000218 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000218 Model fitting is a data transformation process which evaluates if a model appropriately represents a dataset. A model fitting process tests the goodness of fit of the model to the data http://purl.obolibrary.org/obo/STATO_0000218 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000218 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000218 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000218 model fitting http://purl.obolibrary.org/obo/STATO_0000219 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000219 a real time pcr standard curve is a line graph which plots the fluorescence intensity signal as a function of the concentration of a sample used as reference and used to determine relative abundance of test samples http://purl.obolibrary.org/obo/STATO_0000219 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000219 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000219 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000219 adapted from: http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/General_Information/qpcr_technical_guide.pdf and http://www.lifetechnologies.com/uk/en/home/life-science/pcr/real-time-pcr/qpcr-education/absolute-vs-relative-quantification-for-qpcr.html http://purl.obolibrary.org/obo/STATO_0000219 RT-PCR standard curve http://purl.obolibrary.org/obo/STATO_0000220 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000220 the false negative rate is a data item which denotes the proportion of missed detection of elements known to be meeting the detection criteria http://purl.obolibrary.org/obo/STATO_0000220 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000220 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000220 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000220 STATO, adapted from http://purl.obolibrary.org/obo/STATO_0000220 type II error rate http://purl.obolibrary.org/obo/STATO_0000220 β http://purl.obolibrary.org/obo/STATO_0000220 false negative rate http://purl.obolibrary.org/obo/STATO_0000221 http://purl.obolibrary.org/obo/STATO_0000221 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000221 a random variable (or aleatory variable or stochastic variable) in probability and statistics, is a variable whose value is subject to variations due to chance (i.e. randomness, in a mathematical sense) http://purl.obolibrary.org/obo/STATO_0000221 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000221 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000221 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000221 aleatory variable http://purl.obolibrary.org/obo/STATO_0000221 stochastic variable http://purl.obolibrary.org/obo/STATO_0000221 wikipedia: http://en.wikipedia.org/wiki/Random_variable http://purl.obolibrary.org/obo/STATO_0000221 random variable http://purl.obolibrary.org/obo/STATO_0000222 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000222 graeco-latin square design is_a study design which allows in its simpler form controlling 3 levels of nuisance variables (also known as blocking variables). The 3 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once. http://purl.obolibrary.org/obo/STATO_0000222 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000222 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000222 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000222 http://purl.obolibrary.org/obo/STATO_0000222 graeco-latin square design http://purl.obolibrary.org/obo/STATO_0000223 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000223 group assignment based on blocking variable specification is a kind of group assignment process which takes into account the levels assumed by a blocking variable to allocate subjects or experimental units to a treatment group http://purl.obolibrary.org/obo/STATO_0000223 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000223 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000223 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000223 STATO http://purl.obolibrary.org/obo/STATO_0000223 group assignment based on blocking variable specification http://purl.obolibrary.org/obo/STATO_0000224 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000224 A testing objective to ensure that the sample used in a statistical test actually follows a normal distribution. http://purl.obolibrary.org/obo/STATO_0000224 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000224 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000224 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000224 STATO http://purl.obolibrary.org/obo/STATO_0000224 http://purl.obolibrary.org/obo/STATO_0000224 goodness of fit testing objective http://purl.obolibrary.org/obo/STATO_0000225 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000225 A probability distribution is a information content entity specifies the probability of the value of a random variable. For a discrete random variable, a mathematical formula that gives the probability of each value of the variable. For a continuous random variable, a curve described by a mathematical formula which specifies, by way of areas under the curve, the probability that the variable falls within a particular interval. http://purl.obolibrary.org/obo/STATO_0000225 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000225 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000225 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000225 probability distribution http://purl.obolibrary.org/obo/STATO_0000226 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000226 It is a testing objective to ensure the variances of the different groups used in a statistical test are similar (i.e. not too different). http://purl.obolibrary.org/obo/STATO_0000226 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000226 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000226 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000226 homoschedacity testing objective http://purl.obolibrary.org/obo/STATO_0000226 STATO http://purl.obolibrary.org/obo/STATO_0000226 http://purl.obolibrary.org/obo/STATO_0000226 equal variance testing objective http://purl.obolibrary.org/obo/STATO_0000227 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000227 a normal distribution is a continuous probability distribution described by a probability distribution function described here: http://mathworld.wolfram.com/NormalDistribution.html http://purl.obolibrary.org/obo/STATO_0000227 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000227 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000227 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000227 Gaussian distribution http://purl.obolibrary.org/obo/STATO_0000227 http://mathworld.wolfram.com/NormalDistribution.html http://purl.obolibrary.org/obo/STATO_0000227 http://purl.obolibrary.org/obo/STATO_0000227 normal distribution http://purl.obolibrary.org/obo/STATO_0000228 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000228 ordinal variable is a categorical variable where the discrete possible values are ordered or correspond to an implicit ranking http://purl.obolibrary.org/obo/STATO_0000228 Alejandra Gonzalez-Beltan http://purl.obolibrary.org/obo/STATO_0000228 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000228 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000228 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000228 ranked variable http://purl.obolibrary.org/obo/STATO_0000228 http://udel.edu/~mcdonald/statvartypes.html http://purl.obolibrary.org/obo/STATO_0000228 http://purl.obolibrary.org/obo/STATO_0000228 ordinal variable http://purl.obolibrary.org/obo/STATO_0000229 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000229 Chi-square probability distribution with k degrees of freedom is a theoretical probability distribution which corresponds to the distribution of a sum of the squares of k independent standard normal random variables. http://purl.obolibrary.org/obo/STATO_0000229 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000229 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000229 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000229 http://purl.obolibrary.org/obo/STATO_0000229 dchisq(x, df, ncp = 0, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Chisquare.html http://purl.obolibrary.org/obo/STATO_0000229 Chi-square probability distribution http://purl.obolibrary.org/obo/STATO_0000230 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000230 the expected value (or expectation, mathematical expectation, EV, mean, or the first moment) of a random variable is a data item which corresponds to the weighted average of all possible values that this random variable can take on. The weights used in computing this average correspond to the probabilities in case of a discrete random variable, or densities in case of a continuous random variable. From a rigorous theoretical standpoint, the expected value is the integral of the random variable with respect to its probability measure. http://purl.obolibrary.org/obo/STATO_0000230 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000230 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000230 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000230 first moment http://purl.obolibrary.org/obo/STATO_0000230 mean http://purl.obolibrary.org/obo/STATO_0000230 μ http://purl.obolibrary.org/obo/STATO_0000230 http://en.wikipedia.org/wiki/Expected_value http://purl.obolibrary.org/obo/STATO_0000230 http://purl.obolibrary.org/obo/STATO_0000230 expected value http://purl.obolibrary.org/obo/STATO_0000231 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/ http://purl.obolibrary.org/obo/STATO_0000231 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000231 a confidence interval which covers 95% of the sampling distribution, meaning that there is a 5% risk of false positive (type I error). If the number of observations made is large enough, the sampling distribution can be assumed to be normal, which entails that 95% of the sampling distributions falls within roughly2 (1.96) standard deviations from the mean. http://purl.obolibrary.org/obo/STATO_0000231 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000231 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000231 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000231 confidence interval at 5% of type I error rate http://purl.obolibrary.org/obo/STATO_0000231 STATO http://purl.obolibrary.org/obo/STATO_0000231 http://purl.obolibrary.org/obo/STATO_0000231 95% confidence interval http://purl.obolibrary.org/obo/STATO_0000232 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000232 number of PCR cycle is a count which enumerates how many iterations of 'annealing, renaturation, amplification,' rounds (or cycles) are performed during a polymerase chain reaction (PCR) or an assay relying on PCR. http://purl.obolibrary.org/obo/STATO_0000232 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000232 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000232 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000232 adapted from various sources including: http://www.ncbi.nlm.nih.gov/genome/probe/doc/TechQPCR.shtml http://purl.obolibrary.org/obo/STATO_0000232 number of PCR cycle http://purl.obolibrary.org/obo/STATO_0000233 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000233 sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1 http://purl.obolibrary.org/obo/STATO_0000233 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000233 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000233 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000233 recall http://purl.obolibrary.org/obo/STATO_0000233 sensitivity http://purl.obolibrary.org/obo/STATO_0000233 adapted from: http://en.wikipedia.org/wiki/Sensitivity_and_specificity and http://mathworld.wolfram.com/Sensitivity.html http://purl.obolibrary.org/obo/STATO_0000233 http://purl.obolibrary.org/obo/STATO_0000233 true positive rate http://purl.obolibrary.org/obo/STATO_0000234 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000234 a residual is a data item which is the output of an error estimate or model fitting process and which is an observable estimate of the unobservable error http://purl.obolibrary.org/obo/STATO_0000234 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000234 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000234 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000234 residual http://purl.obolibrary.org/obo/STATO_0000235 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/STATO_0000235 A genetic association study is a kind of study whose objective is to detect associations between phenotypes, between a phenotype and a genetic polymorphism or between two genetic polymorphisms. http://purl.obolibrary.org/obo/STATO_0000235 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000235 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000235 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000235 http://en.wikipedia.org/wiki/Genetic_association http://purl.obolibrary.org/obo/STATO_0000235 genetic association study http://purl.obolibrary.org/obo/STATO_0000236 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000236 the coefficient of variation is a normalized measure fo dispersion of a probability distribution of frequency distribution. http://purl.obolibrary.org/obo/STATO_0000236 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000236 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000236 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000236 http://en.wikipedia.org/wiki/Coefficient_of_variation last accessed: 2013-10-18 http://purl.obolibrary.org/obo/STATO_0000236 coefficient of variation http://purl.obolibrary.org/obo/STATO_0000237 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000237 The standard deviation of a random variable, statistical population, data set, or probability distribution is a measure of variation which correspond to the average distance from the mean of the data set to any given point of that dataset. It also corresponds to the square root of its variance. http://purl.obolibrary.org/obo/STATO_0000237 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000237 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000237 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000237 σ http://purl.obolibrary.org/obo/STATO_0000237 http://en.wikipedia.org/wiki/Standard_deviation http://purl.obolibrary.org/obo/STATO_0000237 http://purl.obolibrary.org/obo/STATO_0000237 sd(x, na.rm = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/sd.html http://purl.obolibrary.org/obo/STATO_0000237 standard deviation http://purl.obolibrary.org/obo/STATO_0000238 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000238 high content screening is a kind of investigation which uses a standardized cellular assays to test the effect of substances (RNAi or small molecules) held in libraries on a cellular phenotype. it relies on microscopy imaging and or flow-cytometry, robotic handling to ensure fast and high-throughput. http://purl.obolibrary.org/obo/STATO_0000238 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000238 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000238 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000238 high throughput screening http://purl.obolibrary.org/obo/STATO_0000238 adapted from: http://en.wikipedia.org/wiki/High-content_screening http://purl.obolibrary.org/obo/STATO_0000238 http://purl.obolibrary.org/obo/STATO_0000238 high-content screening http://purl.obolibrary.org/obo/STATO_0000239 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000239 high throughput screening is a kind of investigation which uses a standardized assays (cell based, enzymatic or chemometric) to test the effect of substances (RNAi or small molecules) held in libraries on a very specific and measureable outcome (e.g fluorence intensity). it relies on robotic handling to ensure fast and high-throughput in assay performance, data acquisition and hit selection. http://purl.obolibrary.org/obo/STATO_0000239 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000239 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000239 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000239 AGB,PRS http://purl.obolibrary.org/obo/STATO_0000239 http://purl.obolibrary.org/obo/STATO_0000239 high throughput screening http://purl.obolibrary.org/obo/STATO_0000240 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000240 Kendall's correlation coefficient is a correlation coefficient between 2 ordinal variables (natively or following a ranking procedure) and may be used when the conditions for computing Pearson's correlation are not met (e.g linearity, normality of the 2 continuous variables) http://purl.obolibrary.org/obo/STATO_0000240 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000240 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000240 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000240 Kendall rank correlation coefficient http://purl.obolibrary.org/obo/STATO_0000240 Kendall's tau (τ) coefficient http://purl.obolibrary.org/obo/STATO_0000240 STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Kendall_tau_rank_correlation_coefficient), polled in june 2013 and from: http://stamash.org/pearsons-correlation-coefficient/ http://stamash.org/kendalls-tau-correlation/ http://purl.obolibrary.org/obo/STATO_0000240 http://purl.obolibrary.org/obo/STATO_0000240 cor(x, y = NULL, use = "everything",method = c("kendall")) http://purl.obolibrary.org/obo/STATO_0000240 Kendall's correlation coefficient http://purl.obolibrary.org/obo/STATO_0000241 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000241 Q-Q plot or quantile-quantile plot is the output of a graphical method for comparing two probability distributions by plotting their quantiles against each other http://purl.obolibrary.org/obo/STATO_0000241 PRS,AGB: need to add the notion of quantile http://purl.obolibrary.org/obo/STATO_0000241 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000241 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000241 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000241 STATO http://purl.obolibrary.org/obo/STATO_0000241 quantile-quantile plot http://purl.obolibrary.org/obo/STATO_0000241 qqplot(x, y, plot.it = TRUE, xlab = deparse(substitute(x)), ylab = deparse(substitute(y)), ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/qqnorm.html http://purl.obolibrary.org/obo/STATO_0000241 Q-Q plot http://purl.obolibrary.org/obo/STATO_0000242 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000242 statistical error is an data item denoting the amount by which an observation differs from the expected value, being based on the whole statistical population from which the statistical unit was chosen randomly http://purl.obolibrary.org/obo/STATO_0000242 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000242 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000242 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000242 adapted from wikipedia: http://en.wikipedia.org/wiki/Errors_and_residuals_in_statistics last accessed: 18-11-2013 http://purl.obolibrary.org/obo/STATO_0000242 disturbance http://purl.obolibrary.org/obo/STATO_0000242 statistical error http://purl.obolibrary.org/obo/STATO_0000243 A box and whisker plot is appropriate to represent the characteristics oc a distribution. http://purl.obolibrary.org/obo/STATO_0000243 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000243 a box plot is a graph which plots datasets relying on their quartiles and the interquartile range to create the box and the whiskers http://purl.obolibrary.org/obo/STATO_0000243 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000243 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000243 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000243 Tukey box and whisker plot http://purl.obolibrary.org/obo/STATO_0000243 box plot http://purl.obolibrary.org/obo/STATO_0000243 Tukey, J. W. "Box-and-Whisker Plots." §2C in Exploratory Data Analysis. Reading, MA: Addison-Wesley, pp. 39-43, 1977. http://purl.obolibrary.org/obo/STATO_0000243 boxplot http://purl.obolibrary.org/obo/STATO_0000243 boxplot(x, ...) http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/boxplot.html http://purl.obolibrary.org/obo/STATO_0000243 box and whisker plot http://purl.obolibrary.org/obo/STATO_0000244 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000244 (Rn +) − (Rn −), where Rn + = (emission intensity of reporter dye)/(emission intensity of passive reference dye) in PCR with template and Rn − = (emission intensity of reporter dye)/(emission intensity of passive reference dye) in PCR without template or early cycles of a real-time reaction. Ct = threshold cycle, i.e., cycle at which a statistically significant increase in ΔRn is first detected http://purl.obolibrary.org/obo/STATO_0000244 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000244 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000244 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000244 http://jcm.asm.org/content/38/7/2516.figures-only http://purl.obolibrary.org/obo/STATO_0000244 ΔRn http://purl.obolibrary.org/obo/STATO_0000245 Relative risk is a measurement datum which denotes the risk of an 'event' relative to an 'exposure'. Relative risk is calculated by forming the ratio of the probability of the event occurring in the exposed group versus a the probability of this event occurring in the non-exposed group. http://purl.obolibrary.org/obo/STATO_0000245 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000245 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000245 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000245 risk ratio http://purl.obolibrary.org/obo/STATO_0000245 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000245 http://purl.obolibrary.org/obo/STATO_0000245 relative risk http://purl.obolibrary.org/obo/STATO_0000246 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000246 Woolf's test is a statistical test which evaluates the null hypothesis that odds ratio are the same accross all strata of population under investigation http://purl.obolibrary.org/obo/STATO_0000246 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000246 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000246 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000246 http://people.umass.edu/biep640w/pdf/4.%20%20Categorical%20Data%20Analysis%202012.pdf http://purl.obolibrary.org/obo/STATO_0000246 http://purl.obolibrary.org/obo/STATO_0000246 woolf_test(x) where x is 2 x 2 x k contingency table http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/vcd/html/woolf_test.html http://purl.obolibrary.org/obo/STATO_0000246 Woolf's test http://purl.obolibrary.org/obo/STATO_0000247 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000247 odds ratio homogeneity test is a statistical test which aims to evaluate that null the hypothesis of consistency odds ratio accross different strata of population is true or not http://purl.obolibrary.org/obo/STATO_0000247 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000247 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000247 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000247 STATO http://purl.obolibrary.org/obo/STATO_0000247 http://purl.obolibrary.org/obo/STATO_0000247 odds ratio homogeneity test http://purl.obolibrary.org/obo/STATO_0000248 https://onlinecourses.science.psu.edu/stat503/node/19 Often in medical studies, the blocking factor used is the type of institution. This provides a very useful blocking factor, hopefully removing institutionally related factors such as size of the institution, types of populations served, hospitals versus clinics, etc., that would influence the overall results of the experiment. http://purl.obolibrary.org/obo/STATO_0000248 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000248 a blocking variable is a independent variable which is used in a blocking process part of an experiment with the purpose of maximizing the signal coming from the main variable. http://purl.obolibrary.org/obo/STATO_0000248 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000248 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000248 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000248 nuisance variable http://purl.obolibrary.org/obo/STATO_0000248 https://onlinecourses.science.psu.edu/stat503/node/18 http://purl.obolibrary.org/obo/STATO_0000248 http://purl.obolibrary.org/obo/STATO_0000248 blocking variable http://purl.obolibrary.org/obo/STATO_0000249 a DNA microarray hybridization is an assay relying on nucleic acid hybridization , which uses a DNA microarray device and a nucleic acid as input. It precedes a data acquisition process http://purl.obolibrary.org/obo/STATO_0000249 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000249 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000249 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000249 DNA microarray hybridization http://purl.obolibrary.org/obo/STATO_0000250 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/STATO_0000250 group comparison objective is a data transformation objective which aims to determine if 2 or more study group differ with respect to the signal of a response variable http://purl.obolibrary.org/obo/STATO_0000250 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000250 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000250 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000250 STATO http://purl.obolibrary.org/obo/STATO_0000250 group comparison objective http://purl.obolibrary.org/obo/STATO_0000251 "Time to solve an anagram problem" is continuous since it could take 2 minutes, 2.13 minutes etc. to finish a problem http://purl.obolibrary.org/obo/STATO_0000251 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000251 A continuous variable is one for which, within the limits the variable ranges, any value is possible. http://purl.obolibrary.org/obo/STATO_0000251 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000251 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000251 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000251 http://davidmlane.com/hyperstat/A97418.html http://purl.obolibrary.org/obo/STATO_0000251 http://udel.edu/~mcdonald/statvartypes.html http://purl.obolibrary.org/obo/STATO_0000251 http://purl.obolibrary.org/obo/STATO_0000251 continuous variable http://purl.obolibrary.org/obo/STATO_0000252 http://purl.obolibrary.org/obo/STATO_0000252 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000252 a categorical variable is a variable which that can only assume a finite number of value and cast observation in a small number of categories http://purl.obolibrary.org/obo/STATO_0000252 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000252 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000252 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000252 discrete variable http://purl.obolibrary.org/obo/STATO_0000252 nominal variable http://purl.obolibrary.org/obo/STATO_0000252 qualitative factor http://purl.obolibrary.org/obo/STATO_0000252 http://udel.edu/~mcdonald/statvartypes.html http://purl.obolibrary.org/obo/STATO_0000252 http://purl.obolibrary.org/obo/STATO_0000252 https://onlinecourses.science.psu.edu/stat503/node/7 http://purl.obolibrary.org/obo/STATO_0000252 categorical variable http://purl.obolibrary.org/obo/STATO_0000253 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000253 the objective of a data transformation to test a null hypothesis of absence of difference within subject holds. http://purl.obolibrary.org/obo/STATO_0000253 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000253 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000253 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000253 STATO http://purl.obolibrary.org/obo/STATO_0000253 http://purl.obolibrary.org/obo/STATO_0000253 within subject comparison objective http://purl.obolibrary.org/obo/STATO_0000254 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000254 The allele frequency is a data item which denotes the incidence of a gene variant in a population. It is calculated as a ratio, by dividing the number of copies of a particular allele by the number of copies of all alleles at the genetic place (locus) in a population. http://purl.obolibrary.org/obo/STATO_0000254 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000254 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000254 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000254 http://www.nature.com/scitable/definition/allele-frequency-298 http://purl.obolibrary.org/obo/STATO_0000254 http://purl.obolibrary.org/obo/STATO_0000254 allele frequency http://purl.obolibrary.org/obo/STATO_0000255 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000255 the objective of a data transformation to test a null hypothesis of absence of difference withing subject holds. http://purl.obolibrary.org/obo/STATO_0000255 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000255 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000255 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000255 STATO http://purl.obolibrary.org/obo/STATO_0000255 http://purl.obolibrary.org/obo/STATO_0000255 between group comparison objective http://purl.obolibrary.org/obo/STATO_0000256 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000256 a manhattan plot for gwas is a kind of scatter plot used to facilitate presentation of genome-wide association study (GWAS) data. Genomic coordinates are displayed along the X-axis, with the negative logarithm of the association P-value for each single nucleotide polymorphism displayed on the Y-axis. http://purl.obolibrary.org/obo/STATO_0000256 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000256 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000256 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000256 http://en.wikipedia.org/wiki/Manhattan_plot http://purl.obolibrary.org/obo/STATO_0000256 http://purl.obolibrary.org/obo/STATO_0000256 plotGrandLinear(obj, ..., facets, space.skip = 0.01, geom = NULL, cutoff = NULL, cutoff.color = "red", cutoff.size = 1, legend = FALSE, xlim, ylim, xlab, ylab, main) http://www.tengfei.name/ggbio/docs/man/plotGrandLinear.html http://purl.obolibrary.org/obo/STATO_0000256 manhattan plot for gwas http://purl.obolibrary.org/obo/STATO_0000257 import from Population and Community Ontology: http://www.ontobee.org/browser/rdf.php?o=PCO&iri=http://purl.obolibrary.org/obo/PCO_0000020 http://purl.obolibrary.org/obo/STATO_0000257 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000257 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000257 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000257 family http://purl.obolibrary.org/obo/STATO_0000258 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000258 a variable is a data item which can assume any of a set of values, either as determined by an agent or as randomly occuring through observation. http://purl.obolibrary.org/obo/STATO_0000258 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000258 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000258 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000258 STATO http://purl.obolibrary.org/obo/STATO_0000258 adapted from wolfram-alpha (http://www.wolframalpha.com/input/?i=variable) definition 2. and from Oxford English Dictionary: http://www.oed.com/view/Entry/221514?redirectedFrom=variable#eid, definition B,1 http://purl.obolibrary.org/obo/STATO_0000258 http://purl.obolibrary.org/obo/STATO_0000258 variable http://purl.obolibrary.org/obo/STATO_0000259 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000259 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000259 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000259 has denominator http://purl.obolibrary.org/obo/STATO_0000260 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000260 repeated measure ANOVA is a kind of ANOVA specifically developed for non-independent observations as found when repeated measurements on the sample experimental unit. repeated measure ANOVA is sensitive to departure of normality (evaluation using Bartlett's test), departure of sphericity (evaluation using Mauchly'test) and unbalanced groups (i.e. different sizes of sample populations). Repeated measure ANOVA use in case of unbalanced design is discouraged as it leads to violation of conditions of applicability http://purl.obolibrary.org/obo/STATO_0000260 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000260 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000260 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000260 ANOVA for correlated samples http://purl.obolibrary.org/obo/STATO_0000260 adapted from wikipedia and https://statistics.laerd.com/statistical-guides/repeated-measures-anova-statistical-guide-3.php http://purl.obolibrary.org/obo/STATO_0000260 http://www.ats.ucla.edu/stat/sas/library/repeated_ut.htm http://purl.obolibrary.org/obo/STATO_0000260 ANOVA for correlated samples http://purl.obolibrary.org/obo/STATO_0000260 http://cran.r-project.org/doc/contrib/Lemon-kickstart/kr_repms.html http://purl.obolibrary.org/obo/STATO_0000260 repeated measure ANOVA http://purl.obolibrary.org/obo/STATO_0000261 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000261 The Newman–Keuls or Student–Newman–Keuls (SNK) method is a stepwise multiple comparisons procedure used to identify sample means that are significantly different from each other. It was named after Student (1927), D. Newman, and M. Keuls. This procedure is often used as a post-hoc test whenever a significant difference between three or more sample means has been revealed by an analysis of variance (ANOVA). The Newman–Keuls method is similar to Tukey's range test as both procedures use Studentized range statistics.Compared to Tukey's range test, the Newman–Keuls method is more powerful but less conservative. http://purl.obolibrary.org/obo/STATO_0000261 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000261 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000261 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000261 adapted from wikipedia: last accessed: 2013-11-15 http://purl.obolibrary.org/obo/STATO_0000261 SNK.test(y, trt, DFerror, MSerror, alpha = 0.05, group=TRUE, main = NULL) http://artax.karlin.mff.cuni.cz/r-help/library/agricolae/html/SNK.test.html http://purl.obolibrary.org/obo/STATO_0000261 Newman-Keuls test post-hoc analysis http://purl.obolibrary.org/obo/STATO_0000262 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000262 Bernoulli distribution is a binomial distribution where the number of trials is equal to 1. notation: B(1,p) The mean is p The variance is p*q http://purl.obolibrary.org/obo/STATO_0000262 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000262 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000262 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000262 http://purl.obolibrary.org/obo/STATO_0000262 Bernoulli distribution http://purl.obolibrary.org/obo/STATO_0000263 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000263 Galbraith (Radial) plot is a scatter plot which can be used in the meta-analytic context to examine the data for heterogeneity. For a fixed-effects model, the plot shows the inverse of the standard errors on the horizontal axis against the individual observed effect sizes or outcomes standardized by their corresponding standard errors on the vertical axis. Radial plots were introduced by Rex Galbraith (1988a, 1988b, 1994). http://purl.obolibrary.org/obo/STATO_0000263 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000263 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000263 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000263 Galbraith, Rex (1988). "Graphical display of estimates having differing standard errors". Technometrics (Technometrics, Vol. 30, No. 3) 30 (3): 271–281. doi:10.2307/1270081. JSTOR 1270081 http://purl.obolibrary.org/obo/STATO_0000263 radial Galbraith plot http://purl.obolibrary.org/obo/STATO_0000263 http://www.inside-r.org/packages/cran/Luminescence/docs/plot_RadialPlot plot_RadialPlot(data, na.exclude = TRUE, negatives = "remove", log.z = TRUE, central.value, centrality = "mean.weighted", plot.ratio, bar.col, grid.col, legend.text, summary = FALSE, stats, line, line.col, line.label, output = FALSE, ...) http://purl.obolibrary.org/obo/STATO_0000263 http://www.metafor-project.org/doku.php/plots:radial_plot http://purl.obolibrary.org/obo/STATO_0000263 Galbraith plot http://purl.obolibrary.org/obo/STATO_0000264 http://isogenic.info/html/9__treatments.html#factorial http://purl.obolibrary.org/obo/STATO_0000264 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000264 a factor level combination is one a possible sets of factor levels resulting from the cartesian product of sets of factor and their levels as defined in a factorial design http://purl.obolibrary.org/obo/STATO_0000264 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000264 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000264 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000264 treatment combination http://purl.obolibrary.org/obo/STATO_0000264 STATO http://purl.obolibrary.org/obo/STATO_0000264 http://purl.obolibrary.org/obo/STATO_0000264 factor level combination http://purl.obolibrary.org/obo/STATO_0000265 http://isogenic.info/html/9__treatments.html#factorial http://purl.obolibrary.org/obo/STATO_0000265 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000265 A factor level is data item which corresponds to one of the value assumed by a factor or independent variable manipulated and set by the experimentalist. In the context of factorial design, a factor level is assumed to be or treated as a category in a categorical variable http://purl.obolibrary.org/obo/STATO_0000265 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000265 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000265 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000265 treatment http://purl.obolibrary.org/obo/STATO_0000265 AGB-PRS http://purl.obolibrary.org/obo/STATO_0000265 https://onlinecourses.science.psu.edu/stat503/node/7 http://purl.obolibrary.org/obo/STATO_0000265 http://purl.obolibrary.org/obo/STATO_0000265 factor level http://purl.obolibrary.org/obo/STATO_0000266 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000266 Bayes factor is a ratio between 2 probabilities of observing data according 2 distinct models. It is used in Bayes model selection to evaluate which model best explains the data. if K<0, the model used in the denominator term is supported, if K>1, the model used in the numerator term is supported. The Bayes factor is about the plausibility of 2 different models http://purl.obolibrary.org/obo/STATO_0000266 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000266 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000266 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000266 adapted from Wikipedia last accessed 2013-11-13 http://purl.obolibrary.org/obo/STATO_0000266 http://purl.obolibrary.org/obo/STATO_0000266 Bayes factor http://purl.obolibrary.org/obo/STATO_0000267 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000267 grouped bar chart is a kind of bar chart which juxtaposes the discrete values for each of the possible value of a given categorical variable, thus providing within group comparison. Grouped bar charts are good for comparing between each element in the categories, and comparing elements across categories. However, the grouping can make it harder to tell the difference between the total of each group. http://purl.obolibrary.org/obo/STATO_0000267 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000267 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000267 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000267 adapter from http://www2.le.ac.uk/offices/ld/resources/numeracy/bar-charts and http://blog.visual.ly/how-groups-stack-up-when-to-use-grouped-vs-stacked-column-charts/ [last accessed: 2014-03-04] http://purl.obolibrary.org/obo/STATO_0000267 barplot(height....) set argument " beside = TRUE " http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/barplot.html http://purl.obolibrary.org/obo/STATO_0000267 grouped bar chart http://purl.obolibrary.org/obo/STATO_0000268 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000268 A gamma distribution is a general type of continous statistical distribution (related to the beta distribution) that arises naturally in processes for which the waiting times between Poisson distributed events are relevant. Gamma distributions have two free parameters shape k and scale denoted theta . http://purl.obolibrary.org/obo/STATO_0000268 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000268 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000268 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000268 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000268 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000268 http://mathworld.wolfram.com/GammaDistribution.html http://purl.obolibrary.org/obo/STATO_0000268 http://purl.obolibrary.org/obo/STATO_0000268 dgamma(x, shape, rate = 1, scale = 1/rate, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/GammaDist.html http://purl.obolibrary.org/obo/STATO_0000268 Gamma distribution http://purl.obolibrary.org/obo/STATO_0000269 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000269 polychoric correlation coefficient is a correlation coefficient which is computed over 2 variables to characterise an association by proxy with 2 (latent) variables which are assumed to be continuous and normally distributed. http://purl.obolibrary.org/obo/STATO_0000269 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000269 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000269 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000269 adapted from: http://www.rasch.org/rmt/rmt193c.htm and http://en.wikipedia.org/wiki/Polychoric_correlation http://purl.obolibrary.org/obo/STATO_0000269 http://cran.r-project.org/web/packages/polycor/ polychor(x, y, ML = FALSE, control = list(), std.err = FALSE, maxcor=.9999) http://purl.obolibrary.org/obo/STATO_0000269 polychoric correlation coefficient http://purl.obolibrary.org/obo/STATO_0000270 a full factorial design is a factorial design which ensures that all possible factor level combinations are defined and used so all between group differences can be explored http://purl.obolibrary.org/obo/STATO_0000270 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000270 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000270 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000270 http://purl.obolibrary.org/obo/STATO_0000270 full factorial design http://purl.obolibrary.org/obo/STATO_0000271 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000271 permutation numbering is a data tranformation allowing to count the number of possible permutations of elements in a set of size n, each element occurring exactly once. This number is factorial n. http://purl.obolibrary.org/obo/STATO_0000271 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000271 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000271 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000271 STATO http://purl.obolibrary.org/obo/STATO_0000271 http://purl.obolibrary.org/obo/STATO_0000271 permutation numbering http://purl.obolibrary.org/obo/STATO_0000272 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000272 The Michaelis constant is the substrate concentration at which the reaction rate is at half-maximum, and is an inverse measure of the substrate's affinity for the enzyme—as a small indicates high affinity, meaning that the rate will approach more quickly.[5] The value of is dependent on both the enzyme and the substrate, as well as conditions such as temperature and pH. http://purl.obolibrary.org/obo/STATO_0000272 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000272 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000272 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000272 adapted from wikipedia: http://en.wikipedia.org/wiki/Michaelis–Menten_constant last accessed: 22-11-2013 http://purl.obolibrary.org/obo/STATO_0000272 half maximal reaction rate substrate concentration (Km) http://purl.obolibrary.org/obo/STATO_0000272 Michaelis-Menten constant http://purl.obolibrary.org/obo/STATO_0000273 possibly submit to 'Population and Community Ontology' http://purl.obolibrary.org/obo/STATO_0000273 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000273 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000273 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000273 child-parents trio http://purl.obolibrary.org/obo/STATO_0000274 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000274 receiver operational characteristics curve is a graphical plot which illustrates the performance of a binary classifier system as its discrimination threshold (aka cut-off point) is varied by plotting sensitivity vs (1 − specificity) http://purl.obolibrary.org/obo/STATO_0000274 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000274 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000274 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000274 http://en.wikipedia.org/wiki/Receiver_operating_characteristic http://purl.obolibrary.org/obo/STATO_0000274 roc.from.table(table, graph = TRUE, add = FALSE, title = FALSE, line.col = "red", auc.coords = NULL, ...) http://rss.acs.unt.edu/Rdoc/library/epicalc/html/roc.html http://purl.obolibrary.org/obo/STATO_0000274 receiver operational characteristics curve http://purl.obolibrary.org/obo/STATO_0000275 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000275 The transmission disequilibrium test is a statistical test for genetic linkage between genetic marker and a trait in families. The test is robust to population structure. http://purl.obolibrary.org/obo/STATO_0000275 TODO: need to modify restrictions to include family and trio http://purl.obolibrary.org/obo/STATO_0000275 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000275 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000275 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000275 TDT http://purl.obolibrary.org/obo/STATO_0000275 STATO , adapted wikipedia (from http://en.wikipedia.org/wiki/Transmission_disequilibrium_test), polled on June,2013 http://purl.obolibrary.org/obo/STATO_0000275 http://purl.obolibrary.org/obo/STATO_0000275 transmission disequilibrium test http://purl.obolibrary.org/obo/STATO_0000276 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000276 The binomial distribution is a discrete probability distribution which describes the probability of k successes in n draws with replacement from a finite population of size N. The binomial distribution is frequently used to model the number of successes in a sample of size n drawn with replacement from a population of size N. The binomial distribution gives the discrete probability distribution of obtaining exactly n successes out of N Bernoulli trials (where the result of each Bernoulli trial is true with probability p and false with probability q=1-p ) notation: B(n,p) The mean is N*p The variance is N*p*q http://purl.obolibrary.org/obo/STATO_0000276 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000276 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000276 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000276 http://en.wikipedia.org/wiki/Binomial_distribution http://purl.obolibrary.org/obo/STATO_0000276 http://purl.obolibrary.org/obo/STATO_0000276 dbinom(x, size, prob, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Binomial.html http://purl.obolibrary.org/obo/STATO_0000276 binomial distribution http://purl.obolibrary.org/obo/STATO_0000277 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000277 hit selection is a planned process which in screening processes such as high-throughput screening, lead to the identification of perturbing agent which cause the typical signal generated by a standardized assay to significantly differ from the negative control. The selection hitself results from meeting or exceeding selection threshold (for instance 6 sigma from the mean or SSMD value beyond 5 when compared to positive controls or below -5 when compared to negative controls http://purl.obolibrary.org/obo/STATO_0000277 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000277 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000277 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000277 AGB, PRS http://purl.obolibrary.org/obo/STATO_0000277 adapted from: http://en.wikipedia.org/wiki/SSMD http://purl.obolibrary.org/obo/STATO_0000277 adapted from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789971/ http://purl.obolibrary.org/obo/STATO_0000277 http://purl.obolibrary.org/obo/STATO_0000277 hit selection http://purl.obolibrary.org/obo/STATO_0000278 TODO http://purl.obolibrary.org/obo/STATO_0000278 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000278 pairing rule is a rule which is specifies the criteria for deciding on how to associated any 2 entities. http://purl.obolibrary.org/obo/STATO_0000278 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000278 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000278 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000278 STATO http://purl.obolibrary.org/obo/STATO_0000278 http://purl.obolibrary.org/obo/STATO_0000278 pairing rule http://purl.obolibrary.org/obo/STATO_0000279 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000279 between group comparison statistical test is a statistical test which aims to detect difference between the means computing for each of the study group populations http://purl.obolibrary.org/obo/STATO_0000279 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000279 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000279 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000279 http://purl.obolibrary.org/obo/STATO_0000279 between group comparison statistical test http://purl.obolibrary.org/obo/STATO_0000280 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000280 The Pearson's correlation coefficient is a correlation coefficient which evaluates two continuous variables for association strength in a data sample. It assumes that both variables are normally distributed and linearity exists. The coefficient is calculated by dividing their covariance with the product of their individual standard deviations. It is a normalized measurement of how the two are linearly related. http://purl.obolibrary.org/obo/STATO_0000280 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000280 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000280 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000280 Pearson product-moment correlation coefficient http://purl.obolibrary.org/obo/STATO_0000280 Pearson's r http://purl.obolibrary.org/obo/STATO_0000280 r statistics http://purl.obolibrary.org/obo/STATO_0000280 STATO, adapted from http://www.r-tutor.com/elementary-statistics/numerical-measures/correlation-coefficient and from: http://stamash.org/pearsons-correlation-coefficient/ http://stamash.org/kendalls-tau-correlation/ http://purl.obolibrary.org/obo/STATO_0000280 http://purl.obolibrary.org/obo/STATO_0000280 cor(x, y = NULL, use = "everything",method = c("pearson")) http://purl.obolibrary.org/obo/STATO_0000280 http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cor.html http://purl.obolibrary.org/obo/STATO_0000280 Pearson's correlation coefficient http://purl.obolibrary.org/obo/STATO_0000282 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000282 F statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a F distribution. the F statistic is the ratio of two scaled sums of squares reflecting different sources of variability http://purl.obolibrary.org/obo/STATO_0000282 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000282 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000282 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000282 STATO http://purl.obolibrary.org/obo/STATO_0000282 F-statistic http://purl.obolibrary.org/obo/STATO_0000283 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000283 negative binomial probability distribution is a discrete probability distribution of the number of successes in a sequence of Bernoulli trials before a specified (non-random) number of failures (denoted r) occur. The negative binomial distribution, also known as the Pascal distribution or Pólya distribution, gives the probability of r-1 successes and x failures in x+r-1 trials, and success on the (x+r)th trial. http://purl.obolibrary.org/obo/STATO_0000283 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000283 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000283 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000283 Pascal distribution http://purl.obolibrary.org/obo/STATO_0000283 Pólya distribution http://purl.obolibrary.org/obo/STATO_0000283 http://mathworld.wolfram.com/NegativeBinomialDistribution.html http://purl.obolibrary.org/obo/STATO_0000283 http://purl.obolibrary.org/obo/STATO_0000283 dnbinom(x, size, prob, mu, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/NegBinomial.html http://purl.obolibrary.org/obo/STATO_0000283 negative binomial distribution http://purl.obolibrary.org/obo/STATO_0000284 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000284 Breusch-Pagan test is a statistical test which computes a score test of the hypothesis of constant error variance against the alternative that the error variance changes with the level of the response (fitted values), or with a linear combination of predictors. http://purl.obolibrary.org/obo/STATO_0000284 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000284 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000284 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000284 Breusch, T. S. and Pagan, A. R. (1979) A simple test for heteroscedasticity and random coefficient variation. Econometrica 47, 1287--1294. and adapted from: http://www.inside-r.org/packages/cran/car/docs/ncvTest last accessed [2014-03-15] http://purl.obolibrary.org/obo/STATO_0000284 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000284 http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/lmtest/html/bptest.html bptest(formula, varformula = NULL, studentize = TRUE, data = list()) or http://www.inside-r.org/packages/cran/car/docs/ncvTest http://purl.obolibrary.org/obo/STATO_0000284 Breusch-Pagan test http://purl.obolibrary.org/obo/STATO_0000285 http://www.ncbi.nlm.nih.gov/pubmed/?term=17182697 Bioinformatics. 2007 Feb 15;23(4):401-7. Enrichment or depletion of a GO category within a class of genes: which test? Rivals I1, Personnaz L, Taing L, Potier MC. http://purl.obolibrary.org/obo/STATO_0000285 hypergeometric test is a null hypothesis test which evaluates if a random variable follows a hypergeometric distribution. It is a test of goodness of fit to that distribution. The test is suited for situation aimed at assessing cases of sampling from a finite set without replacements. For instance, testing for enrichment or depletion of elements (e.g GO categories, genes) http://purl.obolibrary.org/obo/STATO_0000285 Added following a term request by Chris Mungall: https://github.com/ISA-tools/stato/issues/6 http://purl.obolibrary.org/obo/STATO_0000285 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000285 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000285 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000285 phyper(q, m, n, k, lower.tail = TRUE, log.p = FALSE) lower.tail logical; if TRUE (default), probabilities are P[X ≤ x], otherwise, P[X > x]. http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Hypergeometric.html http://purl.obolibrary.org/obo/STATO_0000285 hypergeometric test http://purl.obolibrary.org/obo/STATO_0000286 http://purl.obolibrary.org/obo/STATO_0000286 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000286 a one-tailed test is a statistical test which, assuming an unskewed probability distribution, allocates all of the significance level to evaluate only one hypothesis to explain a difference. The one-tailed test provides more power to detect an effect in one direction by not testing the effect in the other direction. one-tailed test should be preceded by two-tailed test in order to avoid missing out on detecting alternate effect explaining an observed difference. http://purl.obolibrary.org/obo/STATO_0000286 Added following a term request by Chris Mungall: https://github.com/ISA-tools/stato/issues/6 http://purl.obolibrary.org/obo/STATO_0000286 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000286 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000286 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000286 one sided test http://purl.obolibrary.org/obo/STATO_0000286 adapted from: http://www.ats.ucla.edu/stat/mult_pkg/faq/general/tail_tests.htm http://purl.obolibrary.org/obo/STATO_0000286 http://purl.obolibrary.org/obo/STATO_0000286 one tailed test http://purl.obolibrary.org/obo/STATO_0000287 For example, we may wish to compare the mean of a sample to a given value x using a t-test. Our null hypothesis is that the mean is equal to x. A two-tailed test will test both if the mean is significantly greater than x and if the mean significantly less than x. The mean is considered significantly different from x if the test statistic is in the top 2.5% or bottom 2.5% of its probability distribution, resulting in a p-value less than 0.05. http://purl.obolibrary.org/obo/STATO_0000287 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000287 a two tailed test is a statistical test which assess the null hypothesis of absence of difference assuming a symmetric (not skewed) underlying probability distribution by allocating half of the significance level selected to each of the direction of change which could explain a difference (for example, a difference can be an excess or a loss). http://purl.obolibrary.org/obo/STATO_0000287 Added following a term request by Chris Mungall: https://github.com/ISA-tools/stato/issues/6 http://purl.obolibrary.org/obo/STATO_0000287 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000287 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000287 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000287 two sided test http://purl.obolibrary.org/obo/STATO_0000287 adapted from: http://www.ats.ucla.edu/stat/mult_pkg/faq/general/tail_tests.htm http://purl.obolibrary.org/obo/STATO_0000287 http://purl.obolibrary.org/obo/STATO_0000287 two tailed test http://purl.obolibrary.org/obo/STATO_0000288 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000288 a null hypothesis which states that no difference exists between 2 or more groups being considered http://purl.obolibrary.org/obo/STATO_0000288 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000288 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000288 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000288 STATO http://purl.obolibrary.org/obo/STATO_0000288 absence of difference hypothesis http://purl.obolibrary.org/obo/STATO_0000289 let's consider an experiment evaluating 2 compounds (aspirin & ibuprofen) at 3 distinct dose levels (low, medium, high) and 4 time points post exposure (0h, 6h, 12h, 24h). Assuming the treatments are applied only once (no replication), the number of observation in a full factorial design is 2 x 3 x 4 = 24 so the design matrix would have 24 rows and 3 columns (1 per factor (independent variable). http://purl.obolibrary.org/obo/STATO_0000289 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000289 a design matrix is an information content entity which denotes a study design. The design matrix is a n by m matrix where n the number of rows, corresponds to the number of observations (4 rows if quadruplicates) and where m, the number of columns corresponds to the number of independent variables. Each element in the matrix correspond to a discretized value representing one of the factor levels for a given factor. A design matrix can be used as input to statistical modeling or statistical analysis. The design matrix contains data on the independent variables (also called explanatory variables) in statistical models which attempt to explain observed data on a response variable (often called a dependent variable) in terms of the explanatory variables. The theory relating to such models makes substantial use of matrix manipulations involving the design matrix: see for example linear regression. A notable feature of the concept of a design matrix is that it is able to represent a number of different experimental designs and statistical models, e.g., ANOVA, ANCOVA, and linear regression http://purl.obolibrary.org/obo/STATO_0000289 Added following a term request by Nolan Nichols: https://github.com/ISA-tools/stato/issues/9 http://purl.obolibrary.org/obo/STATO_0000289 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000289 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000289 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000289 model matrix http://purl.obolibrary.org/obo/STATO_0000289 adapted from: Design of Experiments: Principles and Applications edited by Lennart Eriksson, 1999-2008 Umetrics. ISBN-13:978-91-973730-4-3 and http://en.wikipedia.org/wiki/Design_matrix [last accessed: 22-05-2014] http://purl.obolibrary.org/obo/STATO_0000289 model.matrix(object, data = environment(object), contrasts.arg = NULL, xlev = NULL, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/model.matrix.html http://purl.obolibrary.org/obo/STATO_0000289 design matrix http://purl.obolibrary.org/obo/STATO_0000290 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000290 a contrast is used to define a comparison between 2 or more means. it is the set of coefficients used to specify a comparison. when the sum of these coefficients is null, the contrast is said to be orthogonal. old definition now deprecated: A contrast is a data item which is the output of a linear combination of 2 or more factor level means with coefficients that sum to zero. http://purl.obolibrary.org/obo/STATO_0000290 Term request by Nolan Nichols via https://github.com/ISA-tools/stato/issues/9 http://purl.obolibrary.org/obo/STATO_0000290 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000290 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000290 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000290 http://www.itl.nist.gov/div898/handbook/prc/section4/prc426.htm http://purl.obolibrary.org/obo/STATO_0000290 contrasts(x, contrasts = TRUE, sparse = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrasts.html http://purl.obolibrary.org/obo/STATO_0000290 contrast http://purl.obolibrary.org/obo/STATO_0000291 http://purl.obolibrary.org/obo/STATO_0000291 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000291 a quantile is a data item which corresponds to specific elements x in the range of a variate X. the k-th n-tile P_k is that value of x, say x_k, which corresponds to a cumulative frequency of Nk/n (Kenney and Keeping 1962). If n=4, the quantity is called a quartile, and if n=100, it is called a percentile. http://purl.obolibrary.org/obo/STATO_0000291 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000291 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000291 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000291 Evans, M.; Hastings, N.; and Peacock, B. Statistical Distributions, 3rd ed. New York: Wiley, 2000. http://purl.obolibrary.org/obo/STATO_0000291 http://mathworld.wolfram.com/Quantile.html http://purl.obolibrary.org/obo/STATO_0000291 quantile http://purl.obolibrary.org/obo/STATO_0000292 http://purl.obolibrary.org/obo/STATO_0000292 a decile is a quantile where n=10 and which splits data into sections accrued of 10% of data, so the first decile delineates 10% of the data, the second decile delineates 20% of the data and the nineth decile, 90 % of the data http://purl.obolibrary.org/obo/STATO_0000292 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000292 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000292 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000292 STATO http://purl.obolibrary.org/obo/STATO_0000292 decile http://purl.obolibrary.org/obo/STATO_0000293 http://purl.obolibrary.org/obo/STATO_0000293 a percentile is a quantile which splits data into sections accrued of 1% of data, so the first percentile delineates 1% of the data, the second quartile delineates 2% of the data and the 99th percentile, 99 % of the data http://purl.obolibrary.org/obo/STATO_0000293 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000293 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000293 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000293 STATO http://purl.obolibrary.org/obo/STATO_0000293 percentile http://purl.obolibrary.org/obo/STATO_0000294 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/STATO_0000294 absence of negative difference hypothesis is a hypothesis which assumes that a difference significantly less than a threshold does not exist. http://purl.obolibrary.org/obo/STATO_0000294 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000294 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000294 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000294 STATO http://purl.obolibrary.org/obo/STATO_0000294 absence of negative difference hypothesis http://purl.obolibrary.org/obo/STATO_0000295 http://purl.obolibrary.org/obo/IAO_0000123 http://purl.obolibrary.org/obo/STATO_0000295 absence of negative difference hypothesis is a hypothesis which assumes that a difference significantly greater than a threshold does not exist. http://purl.obolibrary.org/obo/STATO_0000295 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000295 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000295 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000295 STATO http://purl.obolibrary.org/obo/STATO_0000295 absence of positive difference hypothesis http://purl.obolibrary.org/obo/STATO_0000299 Evaluation of statistical inference on empirical resting state fMRI. IEEE Trans Biomed Eng. 2014 Apr;61(4):1091-9. doi: 10.1109/TBME.2013.2294013. http://www.ncbi.nlm.nih.gov/pubmed/24658234 http://purl.obolibrary.org/obo/STATO_0000299 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000299 statistical inference is a process of drawing conclusions following data analysis using statistical methods (statistical tests) and evaluating whether to reject or accept null hypothesis http://purl.obolibrary.org/obo/STATO_0000299 Added following a term request by Nolan Nichols: https://github.com/ISA-tools/stato/issues/12 http://purl.obolibrary.org/obo/STATO_0000299 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000299 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000299 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000299 STATO http://purl.obolibrary.org/obo/STATO_0000299 statistical inference http://purl.obolibrary.org/obo/STATO_0000300 A ratio where the numerator and denominator are expressed in the same unit. http://purl.obolibrary.org/obo/STATO_0000300 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000300 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000300 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000300 STATO http://purl.obolibrary.org/obo/STATO_0000300 dimensionless ratio http://purl.obolibrary.org/obo/STATO_0000300 dimensionless ratio http://purl.obolibrary.org/obo/STATO_0000301 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000301 The covariance is a measurement data item about the strength of correlation between a set (2 or more) of random variables. The covariance is obtained by forming: cov(X,Y)=E([X-E(X)][Y-E(Y)] where E(X), E(Y) is the expected value (mean) of variable X and Y respectively. covariance is symmetric so cov(X,Y)=cov(Y,X). The covariance is usefull when looking at the variance of the sum of the 2 random variables since: var(X+Y) = var(X) +var(Y) +2cov(X,Y) The covariance cov(x,y) is used to obtain the coefficient of correlation cor(x,y) by normalizing (dividing) cov(x,y) but the product of the standard deviations of x and y. http://purl.obolibrary.org/obo/STATO_0000301 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000301 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000301 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000301 adapted from: http://mathworld.wolfram.com/Covariance.html http://purl.obolibrary.org/obo/STATO_0000301 covariance http://purl.obolibrary.org/obo/STATO_0000301 cov(x, y = NULL, use = "everything", method = c("pearson", "kendall", "spearman")) from: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cor.html http://purl.obolibrary.org/obo/STATO_0000301 covariance http://purl.obolibrary.org/obo/STATO_0000302 one sample t-test is a kind of Student's t-test which evaluates if a given sample can be reasonably assumed to be taken from the population. The test compares the sample statistic (m) to the population parameter (M). The one sample t-test is the small sample analog of the z test, which is suitable for large samples. http://purl.obolibrary.org/obo/STATO_0000302 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000302 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000302 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000302 adapted from various sources, including: Practical Statistics for Medical Research by D.Altman. ISBN: 0-412-27630-5 http://www.psychology.emory.edu/clinical/bliwise/Tutorials/TOM/meanstests/tone.htm http://purl.obolibrary.org/obo/STATO_0000302 one sample t-test http://purl.obolibrary.org/obo/STATO_0000302 t.test(x = NULL, alternative = c("two.sided", "less", "greater"), mu = 0, paired = FALSE, var.equal = FALSE, conf.level = 0.95, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html http://purl.obolibrary.org/obo/STATO_0000302 one sample t-test http://purl.obolibrary.org/obo/STATO_0000303 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000303 two sample t-test is a null hypothesis statistical test which is used to reject or accept the hypothesis of absence of difference between the means over 2 randomly sampled populations. It uses a t-distribution for the test and assumes that the variables in the population are normally distributed and with equal variances. http://purl.obolibrary.org/obo/STATO_0000303 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000303 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000303 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000303 two sample t-test http://purl.obolibrary.org/obo/STATO_0000303 adapted from: http://en.wikipedia.org/wiki/Student's_t-test#Independent_.28unpaired.29_samples and from: http://www.psychology.emory.edu/clinical/bliwise/Tutorials/TOM/meanstests/tind.htm http://purl.obolibrary.org/obo/STATO_0000303 t-test for independent means assuming equal variance http://purl.obolibrary.org/obo/STATO_0000303 t.test(x, y = NULL, alternative = c("two.sided", "less", "greater"), mu = 0, paired = FALSE, var.equal = TRUE, conf.level = 0.95, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html http://purl.obolibrary.org/obo/STATO_0000303 two sample t-test with equal variance http://purl.obolibrary.org/obo/STATO_0000304 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000304 Welch t-test is a two sample t-test used when the variances of the 2 populations/samples are thought to be unequal (homoskedasticity hypothesis not verified). In this version of the two-sample t-test, the denominator used to form the t-statistics, does not rely on a 'pooled variance' estimate. http://purl.obolibrary.org/obo/STATO_0000304 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000304 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000304 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000304 Welsh t-test http://purl.obolibrary.org/obo/STATO_0000304 Welch, B. L. (1947). "The generalization of "Student's" problem when several different population variances are involved". Biometrika 34 (1–2): 28–35. doi:10.1093/biomet/34.1-2.28 http://purl.obolibrary.org/obo/STATO_0000304 adapted from wikipedia: http://en.wikipedia.org/wiki/Welch's_t_test last accessed: 2014-05-06 http://purl.obolibrary.org/obo/STATO_0000304 t-test for independent means assuming unequal variance http://purl.obolibrary.org/obo/STATO_0000304 t.test(x, y = NULL, alternative = c("two.sided", "less", "greater"), mu = 0, paired = FALSE, var.equal = FALSE, conf.level = 0.95, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html http://purl.obolibrary.org/obo/STATO_0000304 two sample t-test with unequal variance http://purl.obolibrary.org/obo/STATO_0000305 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000305 a helmert contrast is a contrast in which the coefficients for the Helmert regressors compare each level with the average of the “preceding” ones http://purl.obolibrary.org/obo/STATO_0000305 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000305 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000305 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000305 http://www.clayford.net/statistics/tag/helmert-contrasts/ An R and S-Plus Companion to Applied Regression. John Fox ISBN-13: 978-0761922803 http://purl.obolibrary.org/obo/STATO_0000305 contr.helmert(n, contrasts = TRUE, sparse = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html http://purl.obolibrary.org/obo/STATO_0000305 helmert contrast http://purl.obolibrary.org/obo/STATO_0000306 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000306 a polynomial contrast is a contrast which... http://purl.obolibrary.org/obo/STATO_0000306 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000306 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000306 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000306 http://purl.obolibrary.org/obo/STATO_0000306 contr.poly(n, scores = 1:n, contrasts = TRUE, sparse = FALSE) from: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html http://purl.obolibrary.org/obo/STATO_0000306 polynomial contrast http://purl.obolibrary.org/obo/STATO_0000307 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000307 treatment contrast is a contrast which allows to test how linear model coefficients of categorical variables are interpreted in case where the “first” level (aka, the baseline) is included into the intercept and all subsequent levels have a coefficient that represents their difference from the baseline. http://purl.obolibrary.org/obo/STATO_0000307 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000307 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000307 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000307 adapted from multiple sources: http://pic.dhe.ibm.com/infocenter/spssstat/v20r0m0/index.jsp?topic=%2Fcom.ibm.spss.statistics.help%2Fidh_idd_genlin_emmeans.htm http://www.clayford.net/statistics/tag/helmert-contrasts/ http://www.aliquote.org/articles/tech/contrasts.html http://purl.obolibrary.org/obo/STATO_0000307 contr.treatment(n, base = 1, contrasts = TRUE, sparse = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html http://purl.obolibrary.org/obo/STATO_0000307 treatment contrast http://purl.obolibrary.org/obo/STATO_0000308 http://purl.obolibrary.org/obo/IAO_0000428 http://purl.obolibrary.org/obo/STATO_0000308 the sum contrast is a contrast in which each coefficient compares the corresponding level of the factor to the average of the other levels http://purl.obolibrary.org/obo/STATO_0000308 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000308 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000308 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000308 http://www.clayford.net/statistics/tag/helmert-contrasts/ An R and S-Plus Companion to Applied Regression. John Fox ISBN-13: 978-0761922803 http://purl.obolibrary.org/obo/STATO_0000308 contr.sum(n, contrasts = TRUE, sparse = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html http://purl.obolibrary.org/obo/STATO_0000308 sum contrast http://purl.obolibrary.org/obo/STATO_0000309 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000309 Pearson's Chi-Squared test for goodnes of fit is a statistical null hypothesis test which is used to either evaluate goodness of fit of dataset to a Chi-Squared distribution http://purl.obolibrary.org/obo/STATO_0000309 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000309 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000309 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000309 Chi2 test for goodness of fit http://purl.obolibrary.org/obo/STATO_0000309 adapted from: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html and http://en.wikipedia.org/wiki/Pearson's_chi-squared_test http://purl.obolibrary.org/obo/STATO_0000309 http://purl.obolibrary.org/obo/STATO_0000309 http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html chisq.test(x = NULL, correct = FALSE, p = rep(1/length(x), length(x)), rescale.p = FALSE, simulate.p.value = FALSE, B = 2000) http://purl.obolibrary.org/obo/STATO_0000309 Pearson's Chi square test of goodness of fit http://purl.obolibrary.org/obo/STATO_0000310 http://purl.obolibrary.org/obo/IAO_0000122 http://purl.obolibrary.org/obo/STATO_0000310 Barnard's test is an exact statistical test used to determine if there are nonrandom associations between two categorical variables. It was developed in 1949 by Barnard and is a test which is, most times, more powerfull that the Fisher exact test http://purl.obolibrary.org/obo/STATO_0000310 duplicate with OBI_0200176. so either MIREOT and add metadata and axioms or move from OBI http://purl.obolibrary.org/obo/STATO_0000310 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000310 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000310 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000310 http://en.wikipedia.org/wiki/Barnard's_test and G A Barnard (1945) "A New Test for 2X2 Tables", Nature, 156, 177 & 783. http://purl.obolibrary.org/obo/STATO_0000310 Barnard's test http://purl.obolibrary.org/obo/STATO_0000310 barnardw.test(n1, n2, n3, n4, dp = 0.001, verbose = FALSE) from http://www.inside-r.org/packages/cran/Barnard/docs/barnardw.test http://purl.obolibrary.org/obo/STATO_0000310 Barnard's test http://purl.obolibrary.org/obo/STATO_0000311 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000311 a central composite design is a study design which contains an imbedded factorial or fractional factorial design with center points that is augmented with a group of so-called 'star points' that allow estimation of curvature. A CCD design with k factors has 2k star points. http://purl.obolibrary.org/obo/STATO_0000311 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000311 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000311 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000311 http://www.itl.nist.gov/div898/handbook/pri/section3/pri3361.htm http://purl.obolibrary.org/obo/STATO_0000311 Box-Wilson Central Composite Design http://purl.obolibrary.org/obo/STATO_0000311 cd(basis, generators, blocks = "Block", n0 = 4, alpha = "orthogonal", wbreps = 1, bbreps = 1, randomize = TRUE, inscribed = FALSE, coding) http://artax.karlin.mff.cuni.cz/r-help/library/rsm/html/ccd.html http://purl.obolibrary.org/obo/STATO_0000311 central composite design http://purl.obolibrary.org/obo/STATO_0000312 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000312 The Box-Behnken design is an independent quadratic design in that it does not contain an embedded factorial or fractional factorial design. In this design the treatment combinations are at the midpoints of edges of the process space and at the center. These designs are rotatable (or near rotatable) and require 3 levels of each factor. The designs have limited capability for orthogonal blocking compared to the central composite designs. http://purl.obolibrary.org/obo/STATO_0000312 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000312 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000312 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000312 http://www.itl.nist.gov/div898/handbook/pri/section3/pri3362.htm http://purl.obolibrary.org/obo/STATO_0000312 bbd(k, n0 = 4, block = (k == 4 | k == 5), randomize = TRUE, coding) from: http://artax.karlin.mff.cuni.cz/r-help/library/rsm/html/bbd.html http://purl.obolibrary.org/obo/STATO_0000312 Box–Behnkens design http://purl.obolibrary.org/obo/STATO_0000313 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000313 Plackett-Burman design is a type of study design optimizing multifactorial experiments characterized by their parsimony and economy with the run number a multiple of 4 (rather than a power of 2). Plackett-Burman design is often used for screening experiments where the main effect is often heavily confounded with two-factor interactions. This type of design is very useful for economically detecting large main effects, assuming all interactions are negligible when compared with the few important main effects. http://purl.obolibrary.org/obo/STATO_0000313 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000313 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000313 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000313 http://www.itl.nist.gov/div898/handbook/pri/section3/pri335.htm http://purl.obolibrary.org/obo/STATO_0000313 pb(nruns, nfactors = nruns - 1, factor.names = if (nfactors <= 50) Letters[1:nfactors] else paste("F", 1:nfactors, sep = ""), default.levels = c(-1, 1), ncenter=0, center.distribute=NULL, boxtyssedal = TRUE, n12.taguchi = FALSE, replications = 1, repeat.only = FALSE, randomize = TRUE, seed = NULL, oldver = FALSE, ...) from: http://www.inside-r.org/packages/cran/FrF2/docs/pb http://purl.obolibrary.org/obo/STATO_0000313 Plackett-Burman design http://purl.obolibrary.org/obo/STATO_0000314 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000314 upper confidence limit is a data item which is a largest value bounding a confidence interval http://purl.obolibrary.org/obo/STATO_0000314 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000314 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000314 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000314 STATO http://purl.obolibrary.org/obo/STATO_0000314 upper confidence limit http://purl.obolibrary.org/obo/STATO_0000315 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000315 lower confidence limit is a data item which is a lowest value bounding a confidence interval http://purl.obolibrary.org/obo/STATO_0000315 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000315 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000315 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000315 STATO http://purl.obolibrary.org/obo/STATO_0000315 lower confidence limit http://purl.obolibrary.org/obo/STATO_0000316 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000316 root-mean-square standardized effect is a data item which denotes effect size in the context of analysis of variance and corresponds to the square root of the arithmetic average of p standardized effects (effects normalized to be expressed in standard deviation units). http://purl.obolibrary.org/obo/STATO_0000316 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000316 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000316 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000316 Ψ http://purl.obolibrary.org/obo/STATO_0000316 http://www.statpower.net/Steiger%20Biblio/Steiger04.pdf http://purl.obolibrary.org/obo/STATO_0000316 RMSSE http://purl.obolibrary.org/obo/STATO_0000316 root-mean-square standardized effect http://purl.obolibrary.org/obo/STATO_0000317 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000317 Eta-squared is a biased estimator of the variance explained by the model in the population (it estimates only the effect size in the sample). Eta-squared describes the ratio of variance explained in the dependent variable by a predictor while controlling for other predictors, making it analogous to the r2. This estimate shares the weakness with r2 that each additional variable will automatically increase the value of η2. In addition, it measures the variance explained of the sample, not the population, meaning that it will always overestimate the effect size, although the bias grows smaller as the sample grows larger. http://purl.obolibrary.org/obo/STATO_0000317 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000317 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000317 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000317 http://en.wikipedia.org/wiki/Effect_size#Eta-squared.2C_.CE.B72 http://purl.obolibrary.org/obo/STATO_0000317 η2 http://purl.obolibrary.org/obo/STATO_0000317 eta-squared http://purl.obolibrary.org/obo/STATO_0000318 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000318 omega-squared is a effect size estimate for variance explained which is less biased than the eta-squared coefficient. http://purl.obolibrary.org/obo/STATO_0000318 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000318 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000318 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000318 adapted from: http://en.wikipedia.org/wiki/Effect_size#Omega-squared.2C_.CF.892 http://purl.obolibrary.org/obo/STATO_0000318 ω2 http://purl.obolibrary.org/obo/STATO_0000318 omega-squared http://purl.obolibrary.org/obo/STATO_0000319 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000319 Hedges's g is an estimator of effect size which is similar to Cohen's d and is a measure based on a standardized difference however the denominator , corresponding to a pooled standard deviation, is computed differently from Cohen's d coefficient, by applying a correction factor (which involves a Gamma function) http://purl.obolibrary.org/obo/STATO_0000319 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000319 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000319 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000319 adapted from : http://en.wikipedia.org/wiki/Effect_size#Cohen.27s_d and http://blog.stata.com/tag/cohens-d/ http://purl.obolibrary.org/obo/STATO_0000319 Hedges's g http://purl.obolibrary.org/obo/STATO_0000320 http://purl.obolibrary.org/obo/IAO_0000125 http://purl.obolibrary.org/obo/STATO_0000320 Glass's delta is an estimator of effect size which is similar to Cohen's d but where the denominator corresponds only to the standard deviation of the control group (or second group). It is considered less biais than the Cohen's d for estimating effect sizes based on means and distances between means. http://purl.obolibrary.org/obo/STATO_0000320 Alejandra Gonzalez-Beltran http://purl.obolibrary.org/obo/STATO_0000320 Orlaith Burke http://purl.obolibrary.org/obo/STATO_0000320 Philippe Rocca-Serra http://purl.obolibrary.org/obo/STATO_0000320 adapted from : http://en.wikipedia.org/wiki/Effect_size#Cohen.27s_d and http://blog.stata.com/tag/cohens-d/ http://purl.obolibrary.org/obo/STATO_0000320 Glass's delta http://purl.obolibrary.org/obo/UO_0000001 length unit http://purl.obolibrary.org/obo/UO_0000001 A unit which is a standard measure of the distance between two points. http://purl.obolibrary.org/obo/UO_0000001 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/UO_0000001 http://purl.obolibrary.org/obo/uo.owl http://purl.obolibrary.org/obo/UO_0000001 length unit http://purl.obolibrary.org/obo/UO_0000003 time unit http://purl.obolibrary.org/obo/UO_0000003 A unit which is a standard measure of the dimension in which events occur in sequence. http://purl.obolibrary.org/obo/UO_0000003 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/UO_0000003 http://purl.obolibrary.org/obo/uo.owl http://purl.obolibrary.org/obo/UO_0000003 time unit #STATO_0000043 a false positive rate whose value is 5 per cent #STATO_0000043 Following discussion with OBCS, deprecated of class STATO_0000043 and creation of instance #STATO_0000043 Alejandra Gonzalez-Beltran #STATO_0000043 Orlaith Burke #STATO_0000043 Philippe Rocca-Serra #STATO_0000043 STATO #STATO_0000043 5 % false positive rate #STATO_0000281 a false positive rate whose value is 1 per cent #STATO_0000281 Following discussion with OBCS, deprecated of class STATO_0000281 and creation of instance #STATO_0000281 Alejandra Gonzalez-Beltran #STATO_0000281 Orlaith Burke #STATO_0000281 Philippe Rocca-Serra #STATO_0000281 STATO #STATO_0000281 1 % false positive rate #STATO_0000296 http://purl.obolibrary.org/obo/IAO_0000123 #STATO_0000296 absence of depletion difference hypothesis is a hypothesis which assumes that the representation of an element significantly greater than a threshold does not exist. #STATO_0000296 Alejandra Gonzalez-Beltran #STATO_0000296 Orlaith Burke #STATO_0000296 Philippe Rocca-Serra #STATO_0000296 absence of over representation hypothesis #STATO_0000296 STATO #STATO_0000296 absence of enrichment hypothesis #STATO_0000297 http://purl.obolibrary.org/obo/IAO_0000123 #STATO_0000297 absence of depletion difference hypothesis is a hypothesis which assumes that the representation of an element significantly less than a threshold does not exist. #STATO_0000297 Alejandra Gonzalez-Beltran #STATO_0000297 Orlaith Burke #STATO_0000297 Philippe Rocca-Serra #STATO_0000297 absence of under representation hypothesis #STATO_0000297 STATO #STATO_0000297 absence of depletion hypothesis #STATO_0000298 http://purl.obolibrary.org/obo/IAO_0000122 #STATO_0000298 a binomial test is a statistical hypothesis test which evaluates if the observations made about a Bernoulli experiment , that is an experiment which tests the statistical significance of deviations from a theoretically expected distribution (the binomial distribution) of observations into 2 categories. It is a goodness of fit test. #STATO_0000298 Added following a term request by Chris Mungall: https://github.com/ISA-tools/stato/issues/6 #STATO_0000298 Alejandra Gonzalez-Beltran #STATO_0000298 Orlaith Burke #STATO_0000298 Philippe Rocca-Serra #STATO_0000298 adapted from: http://en.wikipedia.org/wiki/Binomial_test #STATO_0000298 binomial test #STATO_0000298 binom.test(x, n, p = 0.5, alternative = c("two.sided", "less", "greater"), conf.level = 0.95) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/binom.test.html #STATO_0000298 exact binomial test http://purl.org/dc/elements/1.1/contributor http://purl.org/dc/elements/1.1/ http://purl.org/dc/elements/1.1/contributor Contributor http://purl.org/dc/elements/1.1/contributor Contributor http://purl.org/dc/elements/1.1/creator http://purl.org/dc/elements/1.1/ http://purl.org/dc/elements/1.1/creator Creator http://purl.org/dc/elements/1.1/creator Creator http://purl.org/dc/elements/1.1/date http://purl.org/dc/elements/1.1/ http://purl.org/dc/elements/1.1/date Date http://purl.org/dc/elements/1.1/date Date http://purl.org/dc/elements/1.1/description An account of the content of the resource. http://purl.org/dc/elements/1.1/description http://purl.org/dc/elements/1.1/ http://purl.org/dc/elements/1.1/description Description http://purl.org/dc/elements/1.1/description Description http://purl.org/dc/elements/1.1/format The physical or digital manifestation of the resource. http://purl.org/dc/elements/1.1/format http://purl.org/dc/elements/1.1/ http://purl.org/dc/elements/1.1/format Format http://purl.org/dc/elements/1.1/format Format http://purl.org/dc/elements/1.1/subject The topic of the content of the resource. http://purl.org/dc/elements/1.1/subject http://purl.org/dc/elements/1.1/ http://purl.org/dc/elements/1.1/subject Subject and Keywords http://purl.org/dc/elements/1.1/subject Subject and Keywords http://purl.org/dc/elements/1.1/title A name given to the resource. http://purl.org/dc/elements/1.1/title http://purl.org/dc/elements/1.1/ http://purl.org/dc/elements/1.1/title Title http://purl.org/dc/elements/1.1/title Title