An ontology that defines plant phenological classes and is used to run the plantphenology.org data portal. Reuses terms from PO and PATO where possible. Plant Phenology Ontology 2024-07-09 The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. definition A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. alternative label The NPN phenophase name that means the same thing as the PPO phenological stage name. USA-NPN term The BBCH code that means the same thing as the PPO phenological stage name. BBCH code description license title a core relation that holds between a part and its whole part of part of a core relation that holds between a whole and its part has part has part x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. preceded by x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes A (currently) primitive relation that relates an information artifact to an entity. is about The inverse property of is_specified_input_of has specified input has_specified_input 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. is_specified_input_of The inverse property of is_specified_output_of has specified output has_specified_output 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. is_specified_output_of 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. achieves_planned_objective This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. objective_achieved_by A relationship between two plant structures p and q such that p 'abscised' q indicates that plant structure q was formerly a part of p and that q was removed from p due to some abscission process. abscised A relationship between two plant structures p and q such that q 'abscised from' p indicates that plant structure q was formerly a part of p and that q was removed from p due to some abscission process. abscised from Relates an IAO:data item to a PATO:quality. This is similar to IAO:'is quality measurement of', but the IAO property uses BFO:'quality' for its range, and we use PATO:'quality'. quality datum of Relates a PATO:quality to an IAO:data item. has quality datum depends on structure has visible part visible part of A relationship between one data item that is the output of a phenology observing process and another data item. generated from A relationship that indicates the object was part of the subject at some point in time, but might no longer be so. is or was part of TRUE a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in characteristic of Inverse of characteristic_of bearer_of is bearer of has characteristic has characteristic a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in a relation between a process and a continuant, in which the continuant is somehow involved in the process has_participant has participant has participant A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence function_of is function of function of a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence is quality of quality_of quality of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence is role of role_of role of a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence has_function has function a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence has_quality has quality a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition disposition of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. has positive regulatory component activity has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. has component process directly regulated by directly negatively regulated by directly positively regulated by has effector activity ends after starts_at_end_of immediately preceded by ends_at_start_of meets immediately precedes x overlaps y if and only if there exists some z such that x has part z and z part of y overlaps x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. only in taxon x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. in taxon w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. has component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y develops from inverse of develops from develops into p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. positively regulates A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. has function realized in capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. has function in capable of part of temporally related to inverse of ends with ends x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. finished by ends with p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. consumes has input x has developmental contribution from y iff x has some part z such that z develops from y has developmental contribution from inverse of has developmental contribution from developmentally contributes to Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p developmentally preceded by c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. acts upstream of or within Inverse of developmentally preceded by developmentally succeeded by p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. inheres in part of characteristic of part of A relationship that holds via some environmental process evolutionarily related to A mereological relationship or a topological relationship mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) developmentally related to c enables p iff c is capable of p and c acts to execute p. catalyzes executes has is catalyzing is executing enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. false part of structure that is capable of c involved_in p if and only if c enables some process p', and p' is part of p actively involved in enables part of involved in inverse of enables enabled by enabled by inverse of regulates regulated by inverse of negatively regulates negatively regulated by inverse of positively regulates positively regulated by is member of is a mereological relation between a item and a collection. is member of member part of member of has member is a mereological relation between a collection and an item. has member inverse of has input input of x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y has potential to developmentally contribute to x has the potential to develop into y iff x develops into y or if x is capable of developing into y has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y has potential to directly develop into inverse of upstream of causally downstream of immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly activates indirectly positively regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits indirectly negatively regulates causally related to p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. immediately causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. influences (processual) causally upstream of or within inverse of causally upstream of or within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p involved in or reguates involved in or involved in regulation of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. interacts with An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. binds molecularly binds with molecularly interacts with An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. directly inhibits directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. directly activates directly positively regulates activity of helper property (not for use in curation) is kinase activity A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. causal relation between processes depends on causal relation between entities causally influenced by interaction relation helper property molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). causally influences p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. causal relation between material entity and a process Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. enables subfunction acts upstream of or within, positive effect acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative acts upstream of, negative effect causally upstream of or within, negative effect causally upstream of or within, positive effect A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. generically depends on *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* is carrier of The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. regulates activity of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. indirectly regulates X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. device utilizes material A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic A relationship between a data item and the inclusive lower endpoint of a non-negative integer range that contains the datum's value. lower count A relationship between a data item and the inclusive upper endpoint of a non-negative integer range that contains the datum's value. upper count A relationship between a data item and the inclusive lower endpoint of a real number range within [0.0,100.0] that contains the datum's value. lower percent A relationship between a data item and the inclusive upper endpoint of a real number range within [0.0,100.0] that contains the datum's value. upper percent A process in which a person or machine sees or detects a material entity and selects it as worthy of observation, and which has as output an information content entity about the selected material entity. observing process entity 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. continuant An entity that has temporal parts and that happens, unfolds or develops through time. occurrent independent continuant process disposition 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. realizable realizable entity quality characteristic specifically dependent continuant 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. role generically dependent continuant function An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity developmental process involved in reproduction gene product or complex activity molecular_function catalytic activity multicellular organism development A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. biological process biological_process response to radiation response to light stimulus response to abiotic stimulus post-embryonic development abscission seed germination flower development photoprotection true kinase activity transferase activity transferase activity, transferring phosphorus-containing groups reproductive process dormancy process multicellular organismal process developmental process shoot system development floral organ development reproductive structure development system development anatomical structure development response to stimulus leaf abscission reproductive system development floral organ senescence seedling development reproductive shoot system development plant organ senescence bud dormancy process entry into dormancy exit from dormancy plant organ development A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. goal specification objective specification A directive information entity that describes an action the bearer will take. action specification A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label datum label Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. software A quality of an information bearer that imparts the information content information carrier 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 which reliably tends to produce (approximately) truthful statements. data data item A generically dependent continuant that is about some thing. information content entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. directive information entity 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. dot plot 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. graph A plan specification which describes the inputs and 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. algorithm 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. curation status specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file data format specification 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. data set 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. image Data about an ontology part is a data item about a part of an ontology, for example a term data about an ontology part A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. plan specification A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. measurement datum A material entity in which a concretization of an information content entity inheres. material information bearer A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. histogram A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. heatmap A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. dendrogram 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. scattergraph scatter plot The reason for which a term has been deprecated. 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. obsolescence reason specification An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. figure A figure that expresses one or more propositions diagram A collection of information content entities intended to be understood together as a whole document A document that is the output of a publishing process. published document publication A denotator type indicates how a term should be interpreted from an ontological perspective. denotator type A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free. publishing process root cellular organisms Eukaryota Viridiplantae A process that realizes a plan which is the concretization of a plan specification. planned process a regulatory role involved with making and/or enforcing relevant legislation and governmental orders regulator regulator role a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. regulatory role a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. material provider role supplier material supplier role A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. data set with assigned class labels classified data set 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 specimen role 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. organization A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. regulatory agency Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. manufacturer role A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. data set with assigned discovered class labels clustered data set A planned process with the objective of collecting a specimen. specimen collection specimen collection process A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. supervised classification data transformation class prediction data transformation A objective specification to obtain a material entity for potential use as an input during an investigation. specimen collection objective A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. SVM support vector machine A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. decision tree induction objective A decision tree building data transformation is a data transformation that has objective decision tree induction. decision tree building data transformation a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. GenePattern software Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold peak matching A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. k-NN k-nearest neighbors A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. classification and regression trees CART A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. statistical model validation A person or organization that has a manufacturer role. manufacturer is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person service provider role A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. categorical label A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. questionnaire A value specification that is specifies one category out of a fixed number of nominal categories categorical value specification An information content entity that specifies a value within a classification scheme or on a quantitative scale. value specification A material entity that has two or more specimens as its parts. collection of specimens A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. histologic grade according to AJCC 7th edition A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. Histologic Grade (Fuhrman Nuclear Grading System) histologic grade according to the Fuhrman Nuclear Grading System A categorical value specification that is a histologic grade assigned to a ovarian tumor. histologic grade for ovarian tumor A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. histologic grade for ovarian tumor according to a two-tier grading system A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). histologic grade for ovarian tumor according to the World Health Organization A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) pathologic primary tumor stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. pT: Pathologic spread lung primary tumor (AJCC 7th Edition) pathologic primary tumor stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) pathologic primary tumor stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) pathologic primary tumor stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) pathologic lymph node stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) pathologic lymph node stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) pathologic lymph node stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) pathologic lymph node stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. M: colon distant metastases (AJCC 7th Edition) pathologic distant metastases stage for colon according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. M: lung distant metastases (AJCC 7th Edition) pathologic distant metastases stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. M: kidney distant Metastases (AJCC 7th Edition) pathologic distant metastases stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. M: ovarian distant metastases (AJCC 7th Edition) pathologic distant metastases stage for ovary according to AJCC 7th edition A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. Clinical tumor stage group (AJCC 7th Edition) clinical tumor stage group according to AJCC 7th edition A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. Clinical FIGO stage International Federation of Gynecology and Obstetrics cervical cancer stage value specification A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) International Federation of Gynecology and Obstetrics ovarian cancer stage value specification A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). Performance Status Scale performance status value specification A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. ECOG score Eastern Cooperative Oncology Group score value specification A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. Karnofsky Score Karnofsky score vaue specification A person or organization that provides material supplies to other people or organizations. material supplier 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. organism A material entity that has the specimen role. specimen A planned process that produces output data from input data. data analysis data processing data transformation is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data leave one out cross validation method A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). k-means clustering A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). hierarchical clustering A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. data projection dimensionality reduction A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. pca data reduction principal components analysis dimensionality reduction A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations. data encoding as image visualization data visualization An objective specification to transformation input data into output data data transformation objective A partitioning data transformation is a data transformation that has objective partitioning. partitioning data transformation A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. partitioning objective A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. clustering data transformation unsupervised classification data transformation class discovery data transformation A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. clustering objective discriminant analysis objective unsupervised classification objective class discovery objective A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. classification objective supervised classification objective class prediction objective A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. rotation estimation objective cross validation objective A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. clustered data visualization quality whole plant cotyledon primordium vascular leaf primordium ovule primordium gynoecium primordium shoot axis apex bud flower bud inflorescence bud vegetative bud peripheral zone flower meristem fruit development stage leaf development stage vascular leaf initiation stage vascular leaf expansion stage vascular leaf post-expansion stage vascular leaf senescent stage inflorescence development stage plant zygote stage seed development stage meristematic cell fertilized ovule stage developing seed stage shoot-borne shoot system stamen primordium microsporangiate strobilus megasporangiate strobilus phyllome shoot system meristem anther primordium protoderm whole plant flowering stage whole plant development stage seed germination stage sporophyte reproductive stage sporophyte vegetative stage flower development stage flowering stage seed maturation stage endosperm development stage vegetative shoot apical meristem reproductive shoot apical meristem fruit plant cell shoot system portion of plant tissue plant organ plant embryo seed plant structure plant structure development stage portion of meristem tissue vascular leaf sporophyll microsporophyll stamen flower bract lemma palea glume flower inflorescence spikelet inflorescence bract bract androecium gynoecium anther spikelet floret plant ovule cotyledon apical meristem shoot apical meristem plant axis collective plant organ structure collective phyllome structure embryo plant cell shoot axis leaf reproductive shoot system strobilus reproductive bud sporangium embryo plant structure primordium phyllome primordium plant anatomical entity microsporangium reproductive shoot apex vegetative shoot apex portion of embryo plant tissue pollen sac life of whole plant stage collective plant organ structure development stage plant organ development stage floral organ phyllome anlagen vascular leaf anlagen cotyledon anlagen floral organ primordium androecium primordium bract anlagen stamen anlagen bract primordium flower bract primordium inflorescence bract primordium multi-tissue plant structure collective plant structure fruit ripening stage shoot system development stage bud development stage reproductive shoot system development stage bud swell stage bud burst stage vascular leaf development stage multi-tissue plant structure development stage vascular leaf differentiation stage phyllome development stage floral organ formation stage flower meristem transition stage native plant cell vegetative shoot system sporophyte development stage herbaceous plant woody plant perennial plant A vegetative shoot system that does not yet have any unfolded true leaves. new shoot system new above-ground shoot-borne shoot system new shoot system emerging from ground new shoot system emerging from ground in first growth cycle seedling new shoot system emerging from ground in later growth cycle A vegetative bud that is participating in a bud dormancy process. dormant leaf bud A vegetative bud that is not participating in a bud dormancy process. non-dormant leaf bud A non-dormant leaf bud that is in the bud swell stage. swelling leaf bud A non-dormant leaf bud that is in the bud burst stage. If a breaking leaf bud is present, it implies that a new shoot system and unfolding true leaf are also present and observable, hence the “subclass of” axiom. breaking leaf bud A vascular leaf that is not a cotyledon. true leaf An expanding true leaf that is in the vascular leaf unfolding stage. unfolding true leaf A true leaf that is in the vascular leaf expanding unfolded stage or vascular leaf post-expansion stage or vascular leaf senescent stage. unfolded true leaf A unfolded true leaf that is in the vascular leaf expanding unfolded stage or vascular leaf post-expansion stage. non-senescing unfolded true leaf A unfolded true leaf that is in the vascular leaf senescent stage. senescing true leaf A non-senescing unfolded true leaf that is in the vascular leaf expanding unfolded stage or vascular leaf expanded immature stage. immature unfolded true leaf A non-senescing unfolded true leaf that is in the vascular leaf mature stage. mature true leaf An expanding true leaf that is in the vascular leaf expanding unfolded stage. expanding unfolded true leaf An immature unfolded true leaf that is in the vascular leaf expanded immature stage. expanded immature true leaf A true leaf that is in the vascular leaf expansion stage. expanding true leaf A plant structure that is either a reproductive shoot system or a fruit. reproductive structure A seed that has participated in a seed maturation stage. mature seed floral structure non-senesced floral structure unopened floral structure open floral structure pollen-releasing floral structure A floral structure that has completed floral organ senescence. senesced floral structure A flower in which all the petaloid floral organs floral organ have not completed floral organ senescence. Petaloid floral organs generally are the petals, sepal, or tepals, but may also be floral bracts or petaloid anthers anther. For scoring phenology in grasses, petaloid floral organs can include lemma, palea or glume, even though a glume is not strictly a floral organ, because it encloses an inflorescence. non-senesced flower A 'non-senesced flower' that is in the 'unopened flower stage'. unopened flower A 'non-senesced flower' that is in the 'open flower stage'. open flower An 'open flower' that is in the 'pollen-releasing flower stage'. pollen-releasing flower A flower in which all of the petaloid floral organs floral organ have completed floral organ senescence. Petaloid floral organs generally are the petals, sepal, or tepals, but may also be floral bracts or petaloid anthers anther. For scoring phenology in grasses, petaloid floral organs can include lemma, palea or glume, even though a glume is not strictly a floral organ, because it encloses an inflorescence. senesced flower An inflorescence with at least one non-senesced flower. In the case of an unopened flower head, the non-senesced flower(s) might not be visible. non-senesced flower head A non-senesced flower head in which all flowers are unopened flowers unopened flower. The unopened flowers might not yet be visible. unopened flower head A non-senesced flower head with at least one open flower. open flower head An open flower head with at least one pollen-releasing flower. pollen-releasing flower head An inflorescence on which there are no remaining non-senesced flowers non-senesced flower. senesced flower head compound fruit simple fruit or compound fruit A simple fruit or compound fruit that is in the fruit ripening stage. ripening fruit A ripening fruit that is in the fruit unripe stage. unripe fruit A ripening fruit that is in the fruit ripe stage. ripe fruit A microsporangiate strobilus that has not yet completed the pollen-releasing strobilus stage. fresh pollen cone A fresh pollen cone that is in the open microsporangiate strobilus stage. open pollen cone A open pollen cone that is in the pollen-releasing strobilus stage. pollen-releasing pollen cone A megasporangiate strobilus that has not yet been abscised and has not yet releases all of its seeds. fresh seed cone A fresh seed cone that is in the megasporangiate strobilus ripening stage. ripening seed cone A ripening seed cone that is in the megasporangiate strobilus unripe stage. unripe seed cone A ripening seed cone that is in the megasporangiate strobilus ripe stage. ripe seed cone A plant structure that is not a whole plant; i.e. a proper part of a whole plant. Note that a portion of a plant need no longer be physically part of the whole plant from which it originated (e.g., a herbarium specimen). portion of a plant TRUE A quality of a a whole plant that provides phenologically relevant information about the whole plant. plant phenological trait A plant phenological trait that represents whether a plant structure is present or absent on a whole plant. plant structure presence A plant phenological trait}that is measured by the number of some plant structure that a whole plant has abscised. The number can be 0 or more. abscised plant structure presence A plant structure presence that represents whether a new shoot system is present or absent on a whole plant. new shoot system presence A plant structure presence that represents whether a new above-ground shoot-borne shoot system is present or absent on a whole plant. new above-ground shoot-borne shoot system presence A plant structure presence that represents whether a new shoot system emerging from ground is present or absent on a whole plant. new shoot system emerging from ground presence A plant structure presence that represents whether a new shoot system emerging from ground in first growth cycle is present or absent on a whole plant. new shoot system emerging from ground in first growth cycle presence A plant phenological trait that is measured by whether or not a whole plant is a seedling. For consistency with other trait measurements, seedling presence'is also measured with a count, which must be a binary value: 0 if the plant is a seedling, 1 if it is not. seedling presence A plant structure presence that represents whether a new shoot system emerging from ground in later growth cycle is present or absent on a whole plant. new shoot system emerging from ground in later growth cycle presence A plant structure presence that represents whether a vegetative bud is present or absent on a whole plant. vegetative bud presence A plant structure presence that represents whether a dormant leaf bud is present or absent on a whole plant. dormant leaf bud presence A plant structure presence that represents whether a non-dormant leaf bud is present or absent on a whole plant. non-dormant leaf bud presence A plant structure presence that represents whether a swelling leaf bud is present or absent on a whole plant. swelling leaf bud presence A plant structure presence that represents whether a breaking leaf bud is present or absent on a whole plant. breaking leaf bud presence A plant structure presence that represents whether a vascular leaf is present or absent on a whole plant. vascular leaf presence A plant structure presence that represents whether a true leaf is present or absent on a whole plant. true leaf presence A plant structure presence that represents whether a unfolding true leaf is present or absent on a whole plant. unfolding true leaf presence A plant structure presence that represents whether a unfolded true leaf is present or absent on a whole plant. unfolded true leaf presence A plant structure presence that represents whether a non-senescing unfolded true leaf is present or absent on a whole plant. non-senescing unfolded true leaf presence A plant structure presence that represents whether a senescing true leaf is present or absent on a whole plant. senescing true leaf presence A plant structure presence that represents whether a immature unfolded true leaf is present or absent on a whole plant. immature unfolded true leaf presence A plant structure presence that represents whether a mature true leaf is present or absent on a whole plant. mature true leaf presence A plant structure presence that represents whether a expanding unfolded true leaf is present or absent on a whole plant. expanding unfolded true leaf presence A plant structure presence that represents whether a expanded immature true leaf is present or absent on a whole plant. expanded immature true leaf presence A plant structure presence that represents whether a expanding true leaf is present or absent on a whole plant. expanding true leaf presence A plant structure presence that represents whether a reproductive structure is present or absent on a whole plant. reproductive structure presence A plant structure presence that represents whether a floral structure is present or absent on a whole plant. floral structure presence A plant structure presence that represents whether a non-senesced floral structure is present or absent on a whole plant. non-senesced floral structure presence A plant structure presence that represents whether a unopened floral structure is present or absent on a whole plant. unopened floral structure presence A plant structure presence that represents whether a open floral structure is present or absent on a whole plant. open floral structure presence A plant structure presence that represents whether a pollen-releasing floral structure is present or absent on a whole plant. pollen-releasing floral structure presence A plant structure presence that represents whether a senesced floral structure is present or absent on a whole plant. senesced floral structure presence A plant structure presence that represents whether a flower is present or absent on a whole plant. flower presence A plant structure presence that represents whether a non-senesced flower is present or absent on a whole plant. non-senesced flower presence A plant structure presence that represents whether a unopened flower is present or absent on a whole plant. unopened flower presence A plant structure presence that represents whether a open flower is present or absent on a whole plant. open flower presence A plant structure presence that represents whether a pollen-releasing flower is present or absent on a whole plant. pollen-releasing flower presence A plant structure presence that represents whether a senesced flower is present or absent on a whole plant. senesced flower presence A plant structure presence that represents whether a inflorescence is present or absent on a whole plant. inflorescence presence A plant structure presence that represents whether a non-senesced flower head is present or absent on a whole plant. non-senesced flower head presence A plant structure presence that represents whether a unopened flower head is present or absent on a whole plant. unopened flower head presence A plant structure presence that represents whether a open flower head is present or absent on a whole plant. open flower head presence A plant structure presence that represents whether a pollen-releasing flower head is present or absent on a whole plant. pollen-releasing flower head presence A plant structure presence that represents whether a senesced flower head is present or absent on a whole plant. senesced flower head presence A plant structure presence that represents whether a simple fruit or compound fruit is present or absent on a whole plant. simple fruit or compound fruit presence A plant structure presence that represents whether a ripening fruit is present or absent on a whole plant. ripening fruit presence A plant structure presence that represents whether a unripe fruit is present or absent on a whole plant. unripe fruit presence A plant structure presence that represents whether a ripe fruit is present or absent on a whole plant. ripe fruit presence A plant structure presence that represents whether a strobilus is present or absent on a whole plant. strobilus presence A plant structure presence that represents whether a microsporangiate strobilus is present or absent on a whole plant. microsporangiate strobilus presence A plant structure presence that represents whether a fresh pollen cone is present or absent on a whole plant. fresh pollen cone presence A plant structure presence that represents whether a open pollen cone is present or absent on a whole plant. open pollen cone presence A plant structure presence that represents whether a pollen-releasing pollen cone is present or absent on a whole plant. pollen-releasing pollen cone presence A plant structure presence that represents whether a megasporangiate strobilus is present or absent on a whole plant. megasporangiate strobilus presence A plant structure presence that represents whether a fresh seed cone is present or absent on a whole plant. fresh seed cone presence A plant structure presence that represents whether a ripening seed cone is present or absent on a whole plant. ripening seed cone presence A plant structure presence that represents whether a unripe seed cone is present or absent on a whole plant. unripe seed cone presence A plant structure presence that represents whether a ripe seed cone is present or absent on a whole plant. ripe seed cone presence A plant phenological trait that is measured by the number of true leaves true leaf that a whole plant has abscised. The number can be 0 or more abscised leaf presence A plant phenological trait that is measured by the number of a whole plant's ripe fruits ripe fruit that have been abscised or removed by an herbivore and/or the number of ripe fruits on a whole plant that have abscised at least one mature seed. The number can be 0 or more. abscised fruit or seed presence A plant phenological trait that is measured by the number of a whole plant's ripe seed cones that have been abscised or removed by an herbivore and/or the number of ripe seed cones on a whole plant that have abscised at least one mature seed. The number can be 0 or more and only includes the most recent cone crop. abscised cone or seed presence A plant structure presence trait that is a quality of a whole plant that has at least one plant structure as part plant structure present A new shoot system presence trait that is a quality of a whole plant that has at least one new shoot system as part new shoot system present A new above-ground shoot-borne shoot system presence trait that is a quality of a whole plant that has at least one new above-ground shoot-borne shoot system as part new above-ground shoot-borne shoot system present A new shoot system emerging from ground presence trait that is a quality of a whole plant that has at least one new shoot system emerging from ground as part new shoot system emerging from ground present A new shoot system emerging from ground in first growth cycle presence trait that is a quality of a whole plant that has at least one new shoot system emerging from ground in first growth cycle as part new shoot system emerging from ground in first growth cycle present A seedling presence trait that is a quality of a whole plant that has at least one seedling as part seedling present A new shoot system emerging from ground in later growth cycle presence trait that is a quality of a whole plant that has at least one new shoot system emerging from ground in later growth cycle as part new shoot system emerging from ground in later growth cycle present A vegetative bud presence trait that is a quality of a whole plant that has at least one vegetative bud as part vegetative bud present A dormant leaf bud presence trait that is a quality of a whole plant that has at least one dormant leaf bud as part dormant leaf bud present A non-dormant leaf bud presence trait that is a quality of a whole plant that has at least one non-dormant leaf bud as part non-dormant leaf bud present A swelling leaf bud presence trait that is a quality of a whole plant that has at least one swelling leaf bud as part swelling leaf bud present A breaking leaf bud presence trait that is a quality of a whole plant that has at least one breaking leaf bud as part breaking leaf bud present A vascular leaf presence trait that is a quality of a whole plant that has at least one vascular leaf as part vascular leaf present A true leaf presence trait that is a quality of a whole plant that has at least one true leaf as part true leaf present A unfolding true leaf presence trait that is a quality of a whole plant that has at least one unfolding true leaf as part unfolding true leaf present A unfolded true leaf presence trait that is a quality of a whole plant that has at least one unfolded true leaf as part unfolded true leaf present A non-senescing unfolded true leaf presence trait that is a quality of a whole plant that has at least one non-senescing unfolded true leaf as part non-senescing unfolded true leaf present A senescing true leaf presence trait that is a quality of a whole plant that has at least one senescing true leaf as part senescing true leaf present A immature unfolded true leaf presence trait that is a quality of a whole plant that has at least one immature unfolded true leaf as part immature unfolded true leaf present A mature true leaf presence trait that is a quality of a whole plant that has at least one mature true leaf as part mature true leaf present A expanding unfolded true leaf presence trait that is a quality of a whole plant that has at least one expanding unfolded true leaf as part expanding unfolded true leaf present A expanded immature true leaf presence trait that is a quality of a whole plant that has at least one expanded immature true leaf as part expanded immature true leaf present A expanding true leaf presence trait that is a quality of a whole plant that has at least one expanding true leaf as part expanding true leaf present A reproductive structure presence trait that is a quality of a whole plant that has at least one reproductive structure as part reproductive structure present A floral structure presence trait that is a quality of a whole plant that has at least one floral structure as part floral structure present A non-senesced floral structure presence trait that is a quality of a whole plant that has at least one non-senesced floral structure as part non-senesced floral structure present A unopened floral structure presence trait that is a quality of a whole plant that has at least one unopened floral structure as part unopened floral structure present A open floral structure presence trait that is a quality of a whole plant that has at least one open floral structure as part open floral structure present A pollen-releasing floral structure presence trait that is a quality of a whole plant that has at least one pollen-releasing floral structure as part pollen-releasing floral structure present A senesced floral structure presence trait that is a quality of a whole plant that has at least one senesced floral structure as part senesced floral structure present A flower presence trait that is a quality of a whole plant that has at least one flower as part flower present A non-senesced flower presence trait that is a quality of a whole plant that has at least one non-senesced flower as part non-senesced flower present A unopened flower presence trait that is a quality of a whole plant that has at least one unopened flower as part unopened flower present A open flower presence trait that is a quality of a whole plant that has at least one open flower as part open flower present A pollen-releasing flower presence trait that is a quality of a whole plant that has at least one pollen-releasing flower as part pollen-releasing flower present A senesced flower presence trait that is a quality of a whole plant that has at least one senesced flower as part senesced flower present A inflorescence presence trait that is a quality of a whole plant that has at least one inflorescence as part inflorescence present A non-senesced flower head presence trait that is a quality of a whole plant that has at least one non-senesced flower head as part non-senesced flower head present A unopened flower head presence trait that is a quality of a whole plant that has at least one unopened flower head as part unopened flower head present A open flower head presence trait that is a quality of a whole plant that has at least one open flower head as part open flower head present A pollen-releasing flower head presence trait that is a quality of a whole plant that has at least one pollen-releasing flower head as part pollen-releasing flower head present A senesced flower head presence trait that is a quality of a whole plant that has at least one senesced flower head as part senesced flower head present A simple fruit or compound fruit presence trait that is a quality of a whole plant that has at least one simple fruit or compound fruit as part simple fruit or compound fruit present A ripening fruit presence trait that is a quality of a whole plant that has at least one ripening fruit as part ripening fruit present A unripe fruit presence trait that is a quality of a whole plant that has at least one unripe fruit as part unripe fruit present A ripe fruit presence trait that is a quality of a whole plant that has at least one ripe fruit as part ripe fruit present A strobilus presence trait that is a quality of a whole plant that has at least one strobilus as part strobilus present A microsporangiate strobilus presence trait that is a quality of a whole plant that has at least one microsporangiate strobilus as part microsporangiate strobilus present A fresh pollen cone presence trait that is a quality of a whole plant that has at least one fresh pollen cone as part fresh pollen cone present A open pollen cone presence trait that is a quality of a whole plant that has at least one open pollen cone as part open pollen cone present A pollen-releasing pollen cone presence trait that is a quality of a whole plant that has at least one pollen-releasing pollen cone as part pollen-releasing pollen cone present A megasporangiate strobilus presence trait that is a quality of a whole plant that has at least one megasporangiate strobilus as part megasporangiate strobilus present A fresh seed cone presence trait that is a quality of a whole plant that has at least one fresh seed cone as part fresh seed cone present A ripening seed cone presence trait that is a quality of a whole plant that has at least one ripening seed cone as part ripening seed cone present A unripe seed cone presence trait that is a quality of a whole plant that has at least one unripe seed cone as part unripe seed cone present A ripe seed cone presence trait that is a quality of a whole plant that has at least one ripe seed cone as part ripe seed cone present An abscised plant structure presence trait that is a quality of a whole plant from which at least one of some plant structure has been abscised or removed. abscised plant structure present An abscised leaf presence trait that is a quality of a whole plant from which at least one true leaf has been abscised. abscised leaf present An abscised fruit or seed presence trait that is a quality of a whole plant from which at least one ripe fruit has been abscised or removed by an herbivore or that has at least one ripe fruit from which at least one mature seed has been abscised. abscised fruit or seed present An abscised cone or seed presence trait that is a quality of a whole plant from which at least one ripe seed cone has been abscised or removed by an herbivore or that has at least one ripe seed cone that has at least one mature seed that has abscised. abscised cone or seed present A new shoot system presence trait that is a quality of a whole plant that does not have a new shoot system as part new shoot system absent A new above-ground shoot-borne shoot system presence trait that is a quality of a whole plant that does not have a new above-ground shoot-borne shoot system as part new above-ground shoot-borne shoot system absent A new shoot system emerging from ground presence trait that is a quality of a whole plant that does not have a new shoot system emerging from ground as part new shoot system emerging from ground absent A new shoot system emerging from ground in first growth cycle presence trait that is a quality of a whole plant that does not have a new shoot system emerging from ground in first growth cycle as part new shoot system emerging from ground in first growth cycle absent A seedling presence trait that is a quality of a whole plant that does not have a seedling as part seedling absent A new shoot system emerging from ground in later growth cycle presence trait that is a quality of a whole plant that does not have a new shoot system emerging from ground in later growth cycle as part new shoot system emerging from ground in later growth cycle absent A vegetative bud presence trait that is a quality of a whole plant that does not have a vegetative bud as part vegetative bud absent A dormant leaf bud presence trait that is a quality of a whole plant that does not have a dormant leaf bud as part dormant leaf bud absent A non-dormant leaf bud presence trait that is a quality of a whole plant that does not have a non-dormant leaf bud as part non-dormant leaf bud absent A swelling leaf bud presence trait that is a quality of a whole plant that does not have a swelling leaf bud as part swelling leaf bud absent A breaking leaf bud presence trait that is a quality of a whole plant that does not have a breaking leaf bud as part breaking leaf bud absent A vascular leaf presence trait that is a quality of a whole plant that does not have a vascular leaf as part vascular leaf absent A true leaf presence trait that is a quality of a whole plant that does not have a true leaf as part true leaf absent A unfolding true leaf presence trait that is a quality of a whole plant that does not have a unfolding true leaf as part unfolding true leaf absent A unfolded true leaf presence trait that is a quality of a whole plant that does not have a unfolded true leaf as part unfolded true leaf absent A non-senescing unfolded true leaf presence trait that is a quality of a whole plant that does not have a non-senescing unfolded true leaf as part non-senescing unfolded true leaf absent A senescing true leaf presence trait that is a quality of a whole plant that does not have a senescing true leaf as part senescing true leaf absent A immature unfolded true leaf presence trait that is a quality of a whole plant that does not have a immature unfolded true leaf as part immature unfolded true leaf absent A mature true leaf presence trait that is a quality of a whole plant that does not have a mature true leaf as part mature true leaf absent A expanding unfolded true leaf presence trait that is a quality of a whole plant that does not have a expanding unfolded true leaf as part expanding unfolded true leaf absent A expanded immature true leaf presence trait that is a quality of a whole plant that does not have a expanded immature true leaf as part expanded immature true leaf absent A expanding true leaf presence trait that is a quality of a whole plant that does not have a expanding true leaf as part expanding true leaf absent A reproductive structure presence trait that is a quality of a whole plant that does not have a reproductive structure as part reproductive structure absent A floral structure presence trait that is a quality of a whole plant that does not have a floral structure as part floral structure absent A non-senesced floral structure presence trait that is a quality of a whole plant that does not have a non-senesced floral structure as part non-senesced floral structure absent A unopened floral structure presence trait that is a quality of a whole plant that does not have a unopened floral structure as part unopened floral structure absent A open floral structure presence trait that is a quality of a whole plant that does not have a open floral structure as part open floral structure absent A pollen-releasing floral structure presence trait that is a quality of a whole plant that does not have a pollen-releasing floral structure as part pollen-releasing floral structure absent A senesced floral structure presence trait that is a quality of a whole plant that does not have a senesced floral structure as part senesced floral structure absent A flower presence trait that is a quality of a whole plant that does not have a flower as part flower absent A non-senesced flower presence trait that is a quality of a whole plant that does not have a non-senesced flower as part non-senesced flower absent A unopened flower presence trait that is a quality of a whole plant that does not have a unopened flower as part unopened flower absent A open flower presence trait that is a quality of a whole plant that does not have a open flower as part open flower absent A pollen-releasing flower presence trait that is a quality of a whole plant that does not have a pollen-releasing flower as part pollen-releasing flower absent A senesced flower presence trait that is a quality of a whole plant that does not have a senesced flower as part senesced flower absent A inflorescence presence trait that is a quality of a whole plant that does not have a inflorescence as part inflorescence absent A non-senesced flower head presence trait that is a quality of a whole plant that does not have a non-senesced flower head as part non-senesced flower head absent A unopened flower head presence trait that is a quality of a whole plant that does not have a unopened flower head as part unopened flower head absent A open flower head presence trait that is a quality of a whole plant that does not have a open flower head as part open flower head absent A pollen-releasing flower head presence trait that is a quality of a whole plant that does not have a pollen-releasing flower head as part pollen-releasing flower head absent A senesced flower head presence trait that is a quality of a whole plant that does not have a senesced flower head as part senesced flower head absent A simple fruit or compound fruit presence trait that is a quality of a whole plant that does not have a simple fruit or compound fruit as part simple fruit or compound fruit absent A ripening fruit presence trait that is a quality of a whole plant that does not have a ripening fruit as part ripening fruit absent A unripe fruit presence trait that is a quality of a whole plant that does not have a unripe fruit as part unripe fruit absent A ripe fruit presence trait that is a quality of a whole plant that does not have a ripe fruit as part ripe fruit absent A strobilus presence trait that is a quality of a whole plant that does not have a strobilus as part strobilus absent A microsporangiate strobilus presence trait that is a quality of a whole plant that does not have a microsporangiate strobilus as part microsporangiate strobilus absent A fresh pollen cone presence trait that is a quality of a whole plant that does not have a fresh pollen cone as part fresh pollen cone absent A open pollen cone presence trait that is a quality of a whole plant that does not have a open pollen cone as part open pollen cone absent A pollen-releasing pollen cone presence trait that is a quality of a whole plant that does not have a pollen-releasing pollen cone as part pollen-releasing pollen cone absent A megasporangiate strobilus presence trait that is a quality of a whole plant that does not have a megasporangiate strobilus as part megasporangiate strobilus absent A fresh seed cone presence trait that is a quality of a whole plant that does not have a fresh seed cone as part fresh seed cone absent A ripening seed cone presence trait that is a quality of a whole plant that does not have a ripening seed cone as part ripening seed cone absent A unripe seed cone presence trait that is a quality of a whole plant that does not have a unripe seed cone as part unripe seed cone absent A ripe seed cone presence trait that is a quality of a whole plant that does not have a ripe seed cone as part ripe seed cone absent An abscised plant structure presence trait that is a quality of a whole plant from which none of some plant structure have been abscised or removed. abscised plant structure absent An abscised leaf presence trait that is a quality of a whole plant from which no true leaves PPO:0001013 have been abscised. abscised leaf absent An abscised fruit or seed presence trait that is a quality of a whole plant from which no ripe fruits have been abscised or removed by herbivores and that does not have any ripe fruits from which any mature seeds have abscised. abscised fruit or seed absent An abscised cone or seed presence trait that is a quality of a whole plant from which no ripe seed cones PPO:0001052 have been abscised or removed by herbivores and that does not have any ripe seed cones from which any mature seeds have abscised. abscised cone or seed absent A whole plant development stage that begins with seed germination or exit from dormancy, ends with death or entry into dormancy, and during which the participant plant is not dormant. This class is not intended to apply to in vitro-grown plants such as tissue culture, where growth can begin with cell division. plant growth cycle TRUE A plant growth cycle that begins with seed germination. initial growth cycle TRUE A plant growth cycle that begins with exit from dormancy of the participating plant. This cycle cannot begin with the exit from dormancy of a seed. later growth cycle TRUE plant regreening process TRUE An observing process that has as input a whole plant and has as output a measurement datum that is a quality datum of some plant phenological trait. phenology observing process A vascular leaf expansion stage during which a vascular leaf participates in the process of unfolding. This stage ends when a leaf is considered unfolded, which varies by species, but generally occurs once the leaf blade has unfolded enough to appear more or less like a small version of the adult leaf. For species with scaled buds, this is generally once the entire leaf blade has emerged from a breaking bud; for conifers, once a needle begins to spread away at an angle from the developing stem or from other needles in a bundle (e.g. pines); for grasses, once the leaf blade unrolls slightly from around the stem and begins to fall away at an angle; for sedges, once the leaf has grown long enough that the two halves of the blade have begun to spread apart like an open book; for rushes, once the exposed, green portion of the leaf has reached a specified length. vascular leaf unfolding stage A vascular leaf expansion stage during which a vascular leaf has completed the process of unfolding but is still expanding in size. This stage begins when a leaf is considered unfolded, which varies by species, but generally occurs once the leaf blade has unfolded enough to appear more or less like a small version of the adult leaf. For species with scaled buds, this is generally once the entire leaf blade has emerged from a breaking bud; for conifers, once a needle begins to spread away at an angle from the developing stem or from other needles in a bundle (e.g. pines); for grasses, once the leaf blade unrolls slightly from around the stem and begins to fall away at an angle; for sedges, once the leaf has grown long enough that the two halves of the blade have begun to spread apart like an open book; for rushes, once the exposed, green portion of the leaf has reached a specified length. vascular leaf expanding unfolded stage A vascular leaf post-expansion stage during which a vascular leaf has not yet completed the process of maturing. In this stage, the leaf is fully expanded but not yet the same color and texture as fully mature leaves. vascular leaf expanded immature stage A vascular leaf post-expansion stage during which a vascular leaf has completed the process of maturing. vascular leaf mature stage A flower development stage in which a flower has not yet opened. unopened flower stage A flower development stage in which a flower has opened. open flower stage An open flower stage in which the anthers are releasing pollen. pollen-releasing flower stage A fruit ripening stage in which the ripening fruit has not yet reached the fruit ripe stage. fruit unripe stage A fruit ripening stage in which the ripening fruit has completed ripening to the taxon-specific point at which it is widely considered by botanical experts to have seeds $seed that are developed enough to be ready for dispersal, or, in the case of agricultural crops, the point at which the fruit is considered palatable for human consumption. fruit ripe stage A reproductive shoot system development stage that has as primary participant a strobilus. strobilus development stage A microsporangiate strobilus (pollen cone) ripening stage during the pollen cone is open. open microsporangiate strobilus stage A open microsporangiate strobilus (pollen cone) stage during the pollen cone is releasing pollen. pollen-releasing microsporangiate strobilus stage A strobilus (cone) development that has as primary participant a megasporangiate strobilus (seed cone). megasporangiate strobilus ripening stage A megasporangiate strobilus (seed cone) ripening stage in which the ripening seed cone has not yet reached the megasporangiate strobilus ripe stage. megasporangiate strobilus unripe stage A megasporangiate strobilus(seed cone) ripening stage in which the ripening seed cone has completed ripening to the taxon-specific point at which it is widely considered by botanical experts to have seeds that are developed enough to be ready for dispersal. megasporangiate strobilus ripe stage A strobilus development that has as primary participant a microsporangiate strobilus (pollen cone). microsporangiate strobilus ripening stage processual entity death stage life cycle life cycle stage anatomical entity specimen collection process X material entity A material entity B material entity C specimen collection process Y incorrect identifier format, replaced example to be eventually removed The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job failed exploratory term 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. metadata complete Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term 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." ready for release Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated 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. pending final vetting placeholder removed terms merged term imported term split universal A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal defined class A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expression Terms with this status should eventually replaced with a term from another ontology. to be replaced with external ontology term 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. requires discussion Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf) Transformation-ML ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/) ACS XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/) XML RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/) RDF zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/) zip tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/) tar FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/) FCS Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf) Compensation-ML Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/) Gating-ML OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/) OWL An organization which supplies technology, tools and protocols for use in high throughput applications Affymetrix Thermo Waters BIO-RAD GenePattern hierarchical clustering Ambion Helicos Roche Illumina GenePattern PCA GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. GenePattern module SVM GenePattern k-nearest neighbors GenePattern LOOCV GenePattern k-means clustering Agilent GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. GenePattern module KMeansClustering GenePattern CART GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. GenePattern module CARTXValidation Li-Cor Bruker Corporation GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. GenePattern module KNNXValidation GenePattern module PeakMatch GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. GenePattern module KNN GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. GenePattern module HierarchicalClustering GenePattern SVM Applied Biosystems GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. GenePattern module PCA GenePattern peak matching Bruker Daltonics The GenePattern process of generating Heat Maps from clustered data. GenePattern HeatMapViewer data visualization The GenePattern process of generating hierarchical clustering visualization from clustered data. GenePattern HierarchicalClusteringViewer data visualization A GenePattern software module which is used to generate a heatmap view of data. GenePattern module HeatMapViewer A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. GenePattern module HierarchicalClusteringViewer Sysmex Corporation, Kobe, Japan FDA U.S. Food and Drug Administration right handed ambidexterous left handed The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities. Edingburgh handedness inventory eBioscience Cytopeia Exalpha Biological Apogee Flow Systems Exbio Antibodies Becton Dickinson (BD Biosciences) Dako Cytomation Millipore Antigenix Partec Beckman Coulter Advanced Instruments Inc. (AI Companies) Miltenyi Biotec AES Chemunex Bentley Instruments Invitrogen Luminex CytoBuoy An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. Nimblegen An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. Pacific Biosciences An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. NanoString Technologies An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. Thermo Fisher Scientific A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. G1 G1: Well differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. G2 G2: Moderately differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. G3 G3: Poorly differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. G4 G4: Undifferentiated A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. Grade 1 G1 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. Grade 2 G2 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. Grade 3 G3 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. Grade 4 G4 (Fuhrman) A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. Low grade Low grade ovarian tumor A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. High grade High grade ovarian tumor A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. G1 G1 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. G2 G2 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. G3 G3 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. G4 G4 (WHO) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. pT0 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). pTis (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. pT1 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. pT2 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. pT3 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. pT4a (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. pT4b (colon) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. pT0 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. pTis (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). pT1 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. pT1a (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. pT1b (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. pT2 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. pT2a (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. pT2b (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. pT3 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. pT4 (lung) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. pT0 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. pT1 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. pT1a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. pT1b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. pT2 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. pT2a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. pT2b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. pT3 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. pT3a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. pT3b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. pT3c (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). pT4 (kidney) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. pT0 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). pT1 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. pT1a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. pT1b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. pT1c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. pT2 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. pT2a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. pT2b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. pT2c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. pT3 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. pT3a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. pT3b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. pT3c (ovary) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. pN0 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. pN1 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. pN1a (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. pN1b (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. pN1c (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. pN2 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. pN2a (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. pN2b (colon) A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. pN0 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. pN1 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). pN2 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). pN3 (lung) A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. pN0 (kidney) A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. pN1 (kidney) A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. pN0 (ovary) A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. pN1 (ovary) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. cM0 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. cM1 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. cM1a (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. cM1b (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. pM1 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. pM1a (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. pM1b (colon) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. cM0 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. cM1 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. cM1a (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. cM1b (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. pM1 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. pM1a (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis. pM1b (lung) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. cM0 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. cM1 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. pM1 (kidney) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. cM0 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. cM1 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. pM1 (ovary) A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. Occult Carcinoma Occult Carcinoma (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. Stage 0 Stage 0 (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. Stage I Stage I (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. Stage IIA Stage IIA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. Stage IIB Stage IIB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. Stage IIC Stage IIC (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. Stage IIIA Stage IIIA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. Stage IIIB Stage IIIB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. Stage IIIC Stage IIIC (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. Stage IVA Stage IVA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. Stage IVB Stage IVB (AJCC 7th) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. Stage IA Stage IA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. Stage IA1 Stage IA1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. Stage IA2 Stage IA2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA Stage IB Stage IB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. Stage IB1 Stage IB1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. Stage IB2 Stage IB2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. Stage IIA Stage IIA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. Stage IIA1 Stage IIA1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. Stage IIA2 Stage IIA2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. Stage IIB Stage IIB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. Stage IIIA Stage IIIA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. Stage IIIB Stage IIIB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. Stage IVA Stage IVA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. Stage IVB Stage IVB (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. Stage 1 Stage 1 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. Stage 1A Stage 1A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. Stage 1B Stage 1B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. Stage 1C Stage 1C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. Stage 2 Stage 2 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. Stage 2A Stage 2A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. Stage 2B Stage 2B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. Stage 2C Stage 2C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). Stage 3 Stage 3 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . Stage 3A Stage 3A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . Stage 3B Stage 3B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). Stage 3C Stage 3C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. Stage 4 Stage 4 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). Stage Unknown Stage Unknown (FIGO) An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. 3: symptomatic in bed more than 50% of the day but not bed ridden An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. 2: symptomatic but in bed less than 50% of the day An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. 4: bed ridden An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. 0: asymptomatic An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. 1: symptomatic but fully ambulatory A Karnofsky score vaue specification indicating that a patient is asymptomatic. 100: asymptomatic A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. 80-90: symptomatic but fully ambulatory A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. 60-70: symptomatic but in bed less than 50% of the day A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden An organization that is developing and selling nanopore sequencing products and is based in the UK. Oxford Nanopore Technologies An organization that manufactures mosquito traps and other mosquito control products. BioGents A manufacturer of rapid point-of-care assay devices. Abbott A manufacturer of in vitro diagnostic assay kits in India. J. Mitra A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases. InBios inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).