en An ontology for the planning, execution and analysis of clinical research including logitudinal studies and clinical trials. This is designed to be used in conjunction with domain specific models of diseases and measurements which conform to the shared ontology of clinical concepts to provide specific models of studies and trials. An ontology of objects and relationships in statistics that are useful for describing statistical analysis used in human studies. It is part of the Ontology for Clinical Research (OCRe). An ontology of study design descriptors and categorization of study design types in terms of their design descriptors. Concept imported from BRIDG that related to the defined activities and schedules of a study protocol. $Revision$ Revision 315 editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> editor note definition editor Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note is denotator type relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by deprecated:definition is administrative relation of Modeling constraints based on the freqency of events has operator has argument has upper bound obsolete start, stop, time of has time point extractor has upper bound has lower bound has permitted value range has permitted values has lower bound has value has constraint has context modifier An encompassing statement of what the investigator's objectives are. The main objective o a study may be to compare drug A and B, and other objectives may be to evaluate the compliance to treatment and the side effects. has study objective is related to has sampling method has intervention assignment scheme has study characteristic has temporal constraint has participant administrative property has laboratory agreement is study assessment/intervention agreement of has study performance agreement is laboratory agreement of has funding relation is IRB process of has sponsoring relation has oversight agreement is sponsoring relation of is recruitment agreement of has actor has study assessment/intervention agreement is oversight agreement of has variable has recruitment agreement has IRB process has blinding type is funding relation of is study objective of is study performance agreement of is an actor of has administrative relation Old definition to be updated: The hypothesis of a study pertains the result of primary outcome (also used to calculate sample size) has study hypothesis has relation between cases and non-cases has control group type has outcomes occurred before or after study start has phase has priority is study hypothesis of is predictor variable of is outcome variable of has study design has allocation concealment method value is defined by value of has comparative intent is dependent variable of has allocation type has non-temporal constraint has target subject is independent variable of "has study design characteristics" is a superproperty of "has study design" and "has design characteristics". Therefore, if a study has design X, and X has design characteristics Y, then the study has study design characteristics Y. has study design characteristic has individuals assigned to has study status defines group The reference time point against which a relative time is defined (e.g., the "enrollment" time in "3 weeks after enrollment"). has anchor time annotation has biospecimen availability has biospecimen preservation method has biospecimen tissue source has biospecimen type A code is the terminology code of a concept code for The duration of an interval or the offset from an anchor time point. has duration The finding associated with a clinical event has finding "elements" denotes members in the sense of a collection (i.e., object aggregate) containing its elements. It is distinguished from "members" in the sense of social relationship between an organization and its members. has element has predictor variable The population is composed of the indicated study subjects. has member has variable characteristic A single research event (a clinical situation itself) has multiple clinical situations as part of its definition. includes situation is defined by is code for is element of is member of has offset A performed activity operationalize a planned activity operationalize operationalized_by If C and C' are entities or events, C has_part C' if C' is in "part of" relationship with C has part A component of is a "part-whole" relationship with another component. The component can either be an entity or an event. part of The first event occurs before the second event in time. precedes The procedured performed in a Performed procedure clinical event procedure has_semantic_constraint links syntactic criterion (e.g., eligibility criteria) to a class expression involving other entities and events that describes the things that satisfy the meaning of the criterion has semantic constraint The start time (lower bound) of a time interval has start time The stop time (upper bound) of a time interval has stop time The first event is the last event occuring immediately before the second event in time. immediately_precedes derives An outcome is_analyzied_using some statistical method has analysis method has analysis type has assessment method HL7 RIM has effective time has biospecimen collected A statistical analysis is performed on the outcome variables of designated groups of subjects has group has health condition studied has population ocre:is_derived_from o ocre:has_outcome_phenomenon has study phenomenon has study protocol A relationship between instances Variable specification signifying that the domain variable specification is derived from the range variable specification through some function involving the range variable specification Samson is derived from is studied in trial is design characteristic of is study phenomenon of has outcome analysis The property chain "outcome phenomenon o term code => outcome code, causes Pellet to complain about subproperty chain being unsupported feature. has outcome code has outcome variable The study has the identified events. has study event The study has the identified populations. has study population study population property The study has the identified subjects. has study subject The identified clinical situation has the identified clinical subject as its sole or primary subject. has subject has age restriction has eligibility criterion is eligibility criterion of has gender restriction The substrance administered in a Substance Administration event has substance administered The unit component of a Quantity has unit The identified clinical subject is the sole or primary subject of the identified clinical situation. is subject of executed at A StudySite executes some Study Protocol (from BRIDG 1.1.1) executes A healthcare organization functions as a study site (from BRIDG 1).1.1 function as has address has contact for public queries has identifier has principal investigator has recruitment status has scheme is address of is principal investigator of has unit of allocation has noun phrase Some 'Variable specification' has data generated from 'Planned activity' has data generated from is structurally related to A property of a statistical concept statistics property The probability distribution of a variable in a plan for statistical analysis has distribution has dependent variable Specifies that a Variable specification is an independent variable of an Outcome analysis specification has independent variable A statistical analysis for which a statistical method is permissible, given the data types of the variables involved is permissible method of A permissible statistical method of a statistical analysis, given the data types of the variables involved has permissible method The data type of a variable in a plan for statistical analysis has measurement dimension has design characteristic has allocation concealment method entity conclusions are about entity directly observed entity assigned entity recruited or selected entity subject to intervention or exposure finest-grained entity available for analysis This is a relationship between two acts. This relationship asserts that an epoch must be a division of one and only one study protocol. This relationship also asserts that a study protocol must be divided into one or more epochs. is divided into This is a relationship between two acts. This relationship asserts that an epoch must be a division of one and only one study protocol. This relationship also asserts that a study protocol must be divided into one or more epochs. is a division of The relationship between an arm of a study and the specific intervention (whose effects are being evaluated) of the arm has intervention The quantity of a substance or medication to be administered (e.g., 5 mg; 20 mg of drug per kg of subject weight) Simona Adapted from BRIDG 3.2 definition of DefinedSubstanceAdministration.productDose Available at http://bridgmodel.nci.nih.gov/ has dose The "composite" entity in a reified decomposition relationship. The reified decomposition relationship links a "component" entity to the composite entity. composite Simona: generalized from has dose frequency code has frequency code has code has planned composition relationship occurs in The "component" entity in a reified decomposition relationship. The reified decomposition relationship links a component entity to the "composite" entity. component To hold a discrete entity within contains has route of administration is upper bound closed is lower bound closed has original text has context modifier has public description has value has scientific description has country has funding number A postal code designating a region defined by the postal service. Simona has zip has recruitment in the past has actual sample size has case definition has planned sample size has power calculation Source of participants and method of recruitment has recruitment administrative data property has address string has date of first enrollment has date of last enrollment has public title has scientific title has description date has recruitment in the present has recruitment in the future concept descriptor property The plain code symbol defined by the code system, or an expression in a syntax defined by the code system which describes the concept. The unique code of a term in a controlled vocabulary. Simona HL7 Abstract Data Type specification Release 2 has concept id The common name of the coding system. The code system name has no computational value. Note: The purpose of a code system name is to assist an unaided human interpreter of a code value to interpret code system. Simona HL7 Abstract Data Type specification Release 2 has code system name If applicable, a version descriptor defined specifically for the given code system. Simona HL7 Abstract Data Type specification Release 2 has code system version A name, title, or representation for the code or expression as it exists in the code system. The preferred name of a term in a coding system Was: has preferred name Simona HL7 Abstract Data Type specification Release 2 has display name Textual description has description has name first name of a person has first name last name of a person has last name The number of subjects expected to be included in the given population, either for statistical power calculations or based on demographic prediction. has target number The number of individuals who failed to complete the process, procedure or assessment specified because the subject died during the events. has number lost because of death The number of individuals who failed to complete the process, procedure or assessment specified because the subject chose not to complete. has number lost because of refusal The number of individuals who failed to complete the process, procedure or assessment specified because the clinician chose not to complete. has number lost because of rejection The number of individuals who failed to completed the process, procedure or assessment specified for whatever reason. N(considered) = N(completed) + N(lost) has number lost The number of individuals who successfully completed the process, procedure or assessment specified. N(considered) = N(completed) + N(lost) has completed population number The number of individuals who started the process, procedure or assessment specified. N(considered) = N(completed) + N(lost) has considered population number has study population number A unique identifier that guarantees the global uniqueness of the instance identifier. The root alone may be the entire instance identifier. has root A character string as a unique identifier within the scope of the identifier root. has extension This is a human-readable name for the namespace represented in the root. It is a descriptive name for the actual namespace. e.g. "California, U.S. Driver's License Number, 1970-". has identifier name instance identifier property study design data property [In a case-control study:] Choosing one or more controls with particular matching attributes for each case. Researchers match cases and controls according to particular variables that are thought to be important, such as age and sex. In cohort and cross-sectional studies, matching is done for analysis. Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary has matching In a pooled data study, the analysis is performed on subject-level results collected in two or more studies, with their own protocol(s). A study can include both original (de novo) data collection and the use of data pooled from one or more other studies. This is different from meta-analysis, where summary results from different studies are combined. Simona Simona: used to be a class. has pooled data has sequence number has repeat quantity The textual representation of dosing amounts or a range of dosing information used in a substance administration. Note: This is used for more complex dosages such as scaling and tapering doses, uncertain dosage ranges, differing morning and evening doses and other instructions that can't be expressed with a simple PQ. Simona Adapted from BRIDG 3.2 definition of DefinedSubstanceAdministration.productDoseDescription Available at http://bridgmodel.nci.nih.gov/ of "product dose description" has dose description IAO:0000027 data item IAO:0000030 information content entity IAO:0000078 curation status specification 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. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification IAO:0000102 data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part IAO:0000225 obsolescence reason specification 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. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification IAO:0000409 The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type OCRE000000 Aggregation operator OCRE000006 Comparison operator OCRE000012 Semantic relation OCRE000013 Time point extractor OCRE000018 Time interval comparison operator OCRE000019 Time literal OCRE000020 Time point reference OCRE000022 Integer OCRE000023 Real OCRE000024 Interval 1 1 OCRE000029 If 'has operator' is used, then only lower or upper bound but not both is specified. Numeric value constraint OCRE000030 Value set constraint OCRE000036 Constraint on variable 1 1 OCRE000037 Simple constraint on variable 1 OCRE000038 Boolean combination of constrained variables OCRE000040 Augmented noun phrase OCRE000041 This class is used to encode, in simple way, SNOMED finding with context such as "clinical finding absent with associated-finding noun_phrase" or "family history of noun phrase) Context-dependent noun phrase OCRE000042 Context term OCRE000146 Boolean combination of generalized ERGO annotation OCRE001000 A study status applied to a study that has been approved by the relevant regulatory agency (if applicable) and for which protocol-dictated activities are occurring. Simona Study active false false true OCRE085000 A "recruitment not yet started study" is a study for which participants are not yet being recruited. Simona Recruitment not yet started study OCRE099000 a logical combination (and, or, not) of Clinical statements Boolean combination statement 1 OCRE174569 Boolean combination of non-temporal constraints OCRE182000 A cohort population whose members share the same assigned intervention. Note: arm population is defined only within the context of an interventional study. Simona An arm population is an intention-to-treat group Arm population OCRe:OCRE200107 A univariate analysis where the independent variable is dichotomous and the dependent variable is quantitative I dichotomous D quantitative OCRE224000 Periodic event constraint OCRE261000 A recruitment status applied to a study for which participants will not be recruited, because the study is withdrawn. Simona Recruitment will not start OCRE314540 Boolean operator OCRE316000 A "terminated study" is a study that was halted prematurely and will not resume. Simona Terminated study OCRE317000 Simple statements are statements about Assessments made about a person, Interventions done to him, or his Behaviors. All Simple statements have noun phrases (e.g., LDL_cholesterol) as the core of the statements, an effective time, and a mood. The effective time property specifies the time during which the statement is valid. For example, the effective time of a blood test result may be the time when the sample is taken. Similar to HL7 RIM mood codes, a mood modifies the simple clinical statement to specify whether the statement indicates an event that happened, an intent, or an order. Simple statement OCRE364000 Priority OCRE386000 A "suspended study" is a study for which protocol-dictated activities have halted prematurely but potentially will resume. Simona Suspended study OCRE400000 A study status applied to a study in the planning stage: protocol is being developed and has not yet been submitted for regulatory approval (if applicable). Simona Study planned OCRE400001 An instance identifier is an identifier that uniquely identifies a thing or object. Examples are object identifier for HL7 RIM objects, medical record number, order id, service catalog item id, Vehicle Identification Number (VIN), etc. Instance identifiers are defined based on ISO object identifiers. Simona HL7 Data Types Abstract specification. Available at http://healthinfo.med.dal.ca/hl7intro/CDA_R2_NormativeWebEdition/infrastructure/datatypes/datatypes.htm Instance identifier OCRE400002 A term imported from some external standard terminology Domain term OCRE400003 The recruitment status describes the overall accrual (enrollment) activity for the study. Simona Recruitment status OCRE400004 An event is a processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities. Examples: the life of an organism, the process of sleeping, the process of cell-division Simona BFO Process Event OCRE400005 The scheme used to describe the telecommunication address (e.g., ftp, http, etc.) Simona Telecommunication scheme OCRE400006 A study status applied to a study halted prematurely, prior to enrollment of first participant. Simona ClinicalTrials.gov Protocol Data Element Definitions for Overall recruitment status Withdrawn. Available at http://prsinfo.clinicaltrials.gov/definitions.html Study withdrawn true false true OCRE400009 A "recruitment suspended study" is a study for which recruiting or enrolling participants has halted prematurely but potentially will resume. Simona Recruitment suspended study OCRE400010 Classes that define sets of permissible values. Simona Value set OCRE400012 A relative time point is a time point defined in terms of an offset duration before or after a reference or anchor time point (e.g., 2 months after the start of treatment). Relative time point OCRE400013 Biospecimen availability describes whether, for a study, biospecimens are available. Simona Biospecimen availability OCRE400014 A telecommunications address specified according to Internet standard RFC 2396 [http://www.ietf.org/rfc/rfc2396.txt]. The URI specifies the protocol and the contact point defined by that protocol for the resource. Notable uses of the telecommunication address data type are for telephone and telefax numbers, e-mail addresses, Hypertext references, FTP references, etc. Samson HL7 Data Types Abstract specification. Available at http://healthinfo.med.dal.ca/hl7intro/CDA_R2_NormativeWebEdition/infrastructure/datatypes/datatypes.htm Telecommunication address OCRE400015 A physical entity is an entity that has existence in time and space. An entity is that which is perceived or known or inferred to have its own distinct existence (living or nonliving) Simona bfo:material entity Physical entity OCRE400016 A recruitment status applied to a study for which participants are currently being recruited. Simona ClinicalTrials.gov Protocol Data Element Definition for Overall recruitment status Recruiting. Available at http://prsinfo.clinicaltrials.gov/definitions.html Recruitment active OCRE400018 OTC media is a biospecimen preservation method whereby a fresh specimen is frozen onto a sectioning planchet using OCT (Optimum Cutting Temperature) and then stored frozen Herb OCT media OCRE400019 Fast freeze is a biospecimen preservation method whereby the specimen is placed into typically liquid nitrogen or dry ice so the specimen is frozen in seconds then stored colder than (-160° C) Herb Fast freeze OCRE400020 Biospecimen preservation method describes the method used to preserve a biospecimen. Simona Biospecimen preservation method OCRE400021 A physical substance. For example, drug, device, specimen Simona BRIDG 3.0 Available at http://bridgmodel.nci.nih.gov/ Material OCRE400022 Formalin fixation is a biospecimen preservation method whereby the specimen is typically fixed overnight in buffered formalin and then embedded in paraffin and stored at room temperature Herb Formalin fixation OCRE400023 The quantity data type is an abstract generalization for all data types (1) whose value set has an order relation (less-or-equal) and (2) where difference is defined in all of the data type's totally ordered value subsets Quantity OCRE400024 A point on the time axis of a coordinate system. Time point OCRE400025 An anatomical structure consisting of similarly specialized cells and intercellular matrix, aggregated according to genetically determined spatial relationships, performing a specific function. Simona NCI thesaurus entry for Tissue. Available at http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C12801 Tissue OCRE400026 A variable is a placeholder for one or a set of data values Variable OCRE400027 The function played by entity in some process. When applied to person it implies a set of behavior, rights, and obligations. Role OCRE400028 A description of the variables whose data are collected in the study. Samson Study data specification OCRE400029 A study is a program of data collection and of analysis of the data collected to answer a particular question, to reach conclusions about subject(s) or situation(s). Study OCRE400030 A recruitment status applied to a study that has concluded recruitment as planned (i.e., last patient in has occurred) Simona Recruitment completed OCRE400031 An abstract data type that is the generalization of all concrete data types Data value OCRE400032 A physical thing, group of physical things, an organization or information content that can exist in multiple forms. Entity OCRE400033 A collection of organisms. Simona Organism collection OCRE400034 A tissue with red blood cells, white blood cells, platelets, and other substances suspended in fluid called plasma. Blood takes oxygen and nutrients to the tissues, and carries away wastes. Simona NCI Glossary Blood OCRE400035 One or more of the smallest units of living structure capable of independent existence, composed of a membrane-enclosed mass of protoplasm and containing a nucleus or nucleoid. Simona NCI Thesaurus entry for Cell. Available at http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C12508 Cells OCRE400038 An interval on the time axis of a coordinate system Time interval OCRE400039 A postal address is a mailing and home or office address. A sequence of address parts, such as street or post office Box, city, postal code, country, etc. Simona HL7 Data Types Abstract specification. Available at http://healthinfo.med.dal.ca/hl7intro/CDA_R2_NormativeWebEdition/infrastructure/datatypes/datatypes.htm Postal address OCRE400040 An address includes the particulars of where a person or organization has the mail delivered (postal address) or can be reached with means other than mail (telecommunication address). Simona Address 1 1 OCRE400041 A phenomenon is a fact or event of interest susceptible to scientific description and explanation Simona Merriam-Webster's Dictionary entry for phenomenon. Available at http://www.merriam-webster.com/dictionary/phenomenon Study phenomenon OCRE400042 Criterion is a placeholder class that represent a Boolean expression (e.g., an eligibility criterion) Constraint OCRE400044 A collection is a group of things or people. Simona New Oxford American Dictionary Collection OCRE400047 A meta-level characterization of a study Study characteristic OCRE400048 A "withdrawn study" is a study halted prematurely, prior to enrollment of first participant. Simona Withdrawn study OCRE400049 Method for assessing an outcome, such as a questionnaire or laboratory test. Samson Assessment method specification 1 1 1 OCRE400050 A description of the variable whose values are the quantitative or enumerable data collected in a study Samson Variable specification true false false OCRE400052 A "recruitment terminated study" is a study for which recruiting or enrolling participants has halted prematurely and will not resume. Simona Recruitment terminated study OCRE400053 A study status applied to a study in which all data has been collected (last patient's last visit has occurred) and the analysis performed. Results may or may not have been published. Simona Study completed OCRE400054 Any fluid in the body including blood, urine, saliva, sputum, tears, semen, milk, or vaginal secretions Simona Bodily fluid OCRE400055 OCRe:OCRE400055 A CD (concept descriptor) represents any kind of concept usually by giving a code defined in a code system. A concept descriptor can contain the original text or phrase that served as the basis of the coding and one or more translations into different coding systems. A concept descriptor can also contain qualifiers to describe, e.g., the concept of a "left foot" as a postcoordinated term built from the primary code "FOOT" and the qualifier "LEFT". In cases of an exceptional value, the concept descriptor need not contain a code but only the original text describing that concept. CD (concept descriptor) is a more general form of Coded value (CV). In HL7 datatype specification CV constrains CE so that there can be neither qualifiers not translations, and only a single concept is allowed. Samson HL7 Abstract Data Type specification Release 2 CD OCRE400056 An ecologic study is a non individual-human study in which the unit of observation is a population or community. Simona Adapted from: Epidemiology for the Uninitiated. Available at: http://www.bmj.com/epidem/epid.html Ecologic study OCRE400057 The quantity of time as measured in some unit Duration OCRE400059 Information entity is a structure whose purpose is to hold information. The structure itself is not a model of world. For example, a terminology code has properties such as terminology system, the code for a term (e.g.,"heart failure"), but the code is not a representation of thing that the term designate. Samson Tu Information entity OCRE400061 The collection of organisms that are formally enrolled in a study. Simona Enrolled population Study population OCRE400064 DEFINITION: Any individual living (or previously living) being. Simona BRIDG 3.0.3 definition of BiologicEntity. Available at http://bridgmodel.nci.nih.gov/ Organism OCRE400065 Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions. Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products. Simona NCI Thesaurus entry for Biospecimen. Available at http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C70699 Biospecimen OCRE400066 Slow freeze is a biospecimen preservation method whereby a specimen placed into environment (>or= -80° C) and allowed to freeze over minutes Herb Slow freeze OCRE400067 Para-formaldehyde fixation is a biospecimen preservation method whereby a specimen is typically fixed in para-formaldehyde for hours to days and then embedded in plastic and stored at room temperature Herb Para-formaldehyde fixation OCRE400068 A recruitment status applied to a study for which recruiting or enrolling participants has halted prematurely and will not resume. Simona ClinicalTrials.gov Protocol Data Element Definition Overall recruitment status Terminated (only the part pertaining enrollment). Available at http://prsinfo.clinicaltrials.gov/definitions.html Recruitment terminated true OCRE400069 A "recruitment active study" is a study for which participants are currently being recruited. Simona Recruitment active study OCRE400070 A clinical event is an event during which an assessment of, or intervention on a study subject occurs. Simona Clinical event true false false OCRE400071 A "recruitment completed study" is a study that has concluded recruitment (i.e., last patient in has occurred). Simona Recruitment completed study OCRE400072 The specification of how an outcome of the study should be analyzed through the use of statistical methods. It includes the specification of the relevant outcome and predictor variables, the cohort groups, time of outcome assessments, and the statistical method to be used. Samson Outcome analysis specification OCRE400073 A recruitment status applied to a study for which participants are not yet being recruited. Simona ClinicalTrials.gov Protocol Data Element Definition for Overall recruitment status Not yet recruiting. Available at http://prsinfo.clinicaltrials.gov/definitions.html Recruitment not yet started OCRE400074 The study status describes where the study is in its life-cycle. Simona Study status OCRE400075 A recruitment status applied to a study for which recruiting or enrolling participants has halted prematurely but potentially will resume. Simona ClinicalTrials.gov Protocol Data Element Definition for Overall recruitment status Suspended. Available at http://prsinfo.clinicaltrials.gov/definitions.html Recruitment suspended OCRE400076 A human being Person OCRE400078 OCRe:OCRE400078 Expression is an information entity that represent a data value or an entity that can be evaluated to yield a data value. Expression OCRE400079 A formalized group of persons or other organizations collected together for a common purpose (such as administrative, legal, political) and the infrastructure to carry out that purpose. Simona BRIDG 3.0.3 Available at http://bridgmodel.nci.nih.gov/ Organization OCRE400080 The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances. Simona NCI Thesaurus entry for Biospecimen type. Available at: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C70713 Biospecimen type OCRE400115 A physical quantity is a dimensioned quantity expressing the result of measuring. Simona HL7 Data Types Abstract specification. Available at http://healthinfo.med.dal.ca/hl7intro/CDA_R2_NormativeWebEdition/infrastructure/datatypes/datatypes.htm Physical quantity OCRE414000 Simple time constraint 1 OCRE434000 Relational constraint OCRE449000 An "completed study" is a study in which all data has been collected (last patient's last visit has occurred) and the analysis performed. Results may or may not have been published. Simona Completed study OCRE468000 Time-point constraint OCRE492000 Duration constraint OCRE50034 DEFINITION: Fiscal support for research from industry, government, or non-commercial, non-governmental organizations. EXAMPLE(S): Funding from pharmaceutical, device or biotechnology companies, the US NIH or the Gates Foundation. Simona BRIDG 3.0.3 Available at http://bridgmodel.nci.nih.gov/ Funding OCRE50048 Study administrative relation is a kind of relationship that an entity enters into in the design, conduct, and analysis of a study. The relationship starts when the organization agrees to undertake the activity entailed by the relationship. "Agreement to perform study activity"doesn't mean performance of a specific study activity (e.g., administration of a drug) itself, but agreement to do so. An organization becomes a "participating site" once it agrees to perform activities specified in the study protocol. It doesn't have to perform any of activities yet. Samson Study administrative relation OCRE513134 "Agreement to perform study activity" is a study administrative relation. It doesn't mean performance of a specific study activity (e.g., administration of a drug) itself, but agreement to do so. Simona Agreement to perform study activity OCRE535847 "Agreement to perform overisight" is a study administrative relation that entails agreement to perform some study activity. It doesn't mean performance of oversight per se (e.g., data safety monitoring), but agreement to do so. Simona Agreement to perform oversight OCRE541581 An established society, corporation, foundation or other organization founded and united for a specific purpose, e.g. for health-related research. NCI Thesaurus entry for Institution. Available at http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C41206 Simona Social institution OCRE557116 A person's permanent place of residence. Simona NCI Thesaurus entry for Home. Available at: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C18002 Home OCRE568687 The ethics approval process is a study administrative relation whereby a study is submitted to a committee that is formally designated to approve, monitor, and review biomedical and behavioral research involving humans with the aim to protect the rights and welfare of the research subjects. Simona Ethics approval process OCRE581634 Sponsoring is a study administrative relation whereby a person or organization takes responsibility for the initiation and management, and financing (or arranging the financing) of a clinical trial. Simona Sponsoring OCRE584000 An "active study" is a study for which protocol-dictated activities are occurring. Simona Active study OCRE590011 "Agreement to perform study subject assessment" is a study administrative relation that entails agreement to perform some study subject assessment. It doesn't mean performance of study subject assessment per se (e.g., neorologic evaluation), but agreement to do so. Simona Agreement to perform study subject assessment or intervention OCRE591890 "Agreement to perform study laboratory processing" is a study administrative relation that entails agreement to perform some study activity. It doesn't mean performance of study laboratory processing per se (e.g., blood or urine tests), but agreement to do so. Simona Agreement to perform study laboratory processing OCRE595405 Agreement to recruit OCRE596000 Non-temporal constraints operate on the root noun phrase (code) or value of criterion statements Non-temporal constraint OCRE693433 Value constraint OCRE722000 Generalized ERGO annotation OCRE733000 Time-interval constraint OCRE740000 A "planned study" is a study in the planning stage: protocol is being developed and has not yet been submitted for regulatory approval (if applicable). Simona Planned study 1 OCRE763000 Boolean combination of simple time constraints OCRE793000 Objective OCRE824000 A status applied to a study for which protocol-dictated activities have halted prematurely but potentially will resume. Simona Study suspended OCRE826211 A study that has "Ramdon" allocation scheme Samson Tu Defined in order to assert that random allocation study must be a study with parallel or cross-over study design Random allocation study OCRE831288 Study classified by study status OCRE832477 Study that recruit study subjects OCRE834838 Post-hoc group OCRE846075 Study subpopulation OCRE850429 Pre-defined group 2 OCRE870591 Created this class for the purpose of asserting "if study is parallel group or cross-over, then should have more than 1 arm" Parallel or cross-over study OCRE873851 The collection of screened organisms that satisfies all eligibility criteria for a study. Simona Eligible population OCRE882000 Hypothesis OCRe:OCRE900300 A univariate analysis where the independent variable is dichotomous and the dependent variable is nominal with cardinality greater than 2 I dichotomous D nominalGT2 OCRe:OCRE900301 A univariate analysis where the independent variable nominal with cardinality greater than 2 and the dependent dependent variable is nominal with cardinality greater than 2 I nominalGT2 D nominalGT2 OCRe:OCRE900302 A univariate analysis where the independent variable is ordinal and the dependent variable is nominal with cardinality greater than 2 I ordinal D nominalGT2 OCRe:OCRE900303 A univariate analysis where the independent variable is quantitative and the dependent variable is nominal with cardinality greater than 2 I quantitative D nominalGT2 OCRe:OCRE900304 A univariate analysis where the independent variable is dichotomous and the dependent variable is ordinal I dichotomous D ordinal OCRe:OCRE900305 A univariate analysis where the independent variable is nominal with cardinality greater than 2 and the dependent variable is ordinal I nominalGT2 D ordinal OCRe:OCRE900306 A univariate analysis where the independent variable is ordinal and the dependent variable is ordinal I ordinal D ordinal OCRe:OCRE900307 A univariate analysis where the independent variable is quantitative and the dependent variable is ordinal I quantitative D ordinal OCRe:OCRE900308 A univariate analysis where the independent variable is nominal with cardinality greater than 2 and the dependent variable is quantitative I nominalGT2 D quantitative OCRe:OCRE900309 A univariate analysis where the independent variable is ordinal and the dependent variable is quantitative I ordinal D quantitative OCRe:OCRE900310 A univariate analysis where the independent variable is quantitative and the dependent variable is quantitative I quantitative D quantitative OCRe:OCRE900311 A univariate analysis where the independent variable is dichotomous and the dependent variable is survival I dichotomous D survival data OCRe:OCRE900312 A univariate analysis where the independent variable is ordinal and the dependent variable is survival I ordinal D survival data OCRE908000 A status applied to a study for which protocol-dictated activities have halted prematurely and will not resume. Simona Study terminated OCRE920000 Clinical statements have valid time/interval and may have "value" associated with them. Clinical statement false false false OCRE992000 A "recruitment will not start study" is a study for which participants have not, are not, and will not be recruited. Simona Recruitment will not start study OCRE200000 Variables whose values are one or more labels for predefined categories that enumerate possble states of some characteristic (e.g., blood types A, B, AB, or O). AKA "categorical data" Nominal scale level OCRE200001 Measurements whose values are in one of two possible states, these often being labeled 0 and 1. Samson adapted from Cambridge Dictionary of Statistics 3rd edition Dichotomous OCRE200002 A typology of scales measure Dimensions about how data can be ordered Samson Variable dimension OCRE200003 A numeric characteristic of a distribution or of a random variable Samson Descriptive statistics Distributional metric OCRE200004 A chi-square test (also chi squared test or χ2 test) is any statistical hypothesis test in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough. Simona Wikipedia entry for Chi-square test. Available at http://en.wikipedia.org/wiki/Chi-square_test Chi-square test OCRE200005 Mixed linear model OCRE200006 [see standard reference] Linear regression OCRE200007 The range is the difference between the lowest and highest numerical values; the limits or scale of variation. Simona NCI Thesaurus entry for Range. Available at http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C38013 Range OCRE200008 The right boundary is not included in the interval [ ) Simona Right open OCRE200009 [see standard reference] Poisson regression OCRE200010 An index of performance of a discriminant test calculated as the percentage of correct positives in all true postives Samson recall Sensitivity OCRE200011 A ratio is a quotient of quantities of the same kind for different components within the same system. Simona NCI Thesaurus entry for Ratio. Available at http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C44256 Ratio OCRE200012 Exact test OCRE200013 The Kruskal-Wallis one-way analysis of variance by ranks (named after William Kruskal and W. Allen Wallis) is a non-parametric method for testing equality of population medians among groups. It is identical to a one-way analysis of variance with the data replaced by their ranks. It is an extension of the Mann-Whitney U test to 3 or more groups. Simona Wikipedia entry for Kruskal–Wallis one-way analysis of variance. Available at http://en.wikipedia.org/wiki/Wallis_statistic Kruskal Wallis method OCRE200014 A plan for multivariate analysis where the independent variable is nominal and the dependent variable is quantitative Simona: needs review; labels and definitions in this subtree are not clear. Multivariate I nominal D quantitative OCRE200015 A measurement that allows a sample of individuals to be ranked with respect to some characteristics but where differences at different points of the scale are not necessarily equivalent. (Cambridge Dictionary of Statistics 3nd ed.) Ordinal scale level OCRE200016 A univariate analysis where the independent variable is nominal Independent variable nominal OCRE200017 In S. Steven's typology of measurement scale, a variable is "a continuous variable that has an arbitrary zero point." Cannot meaningfully compute ratios Cambridge Dictionary of Statistics 3rd edition Interval scale level OCRE200018 A univariate analysis where the independent variable is quantitative and the dependent variable is dichotomous I quantitative D dichotomous OCRE200019 [see standard reference] Robust regression OCRE200020 In point observation, the width of the censoring interval is 0. The frequency of measurements prevents one from being more accurate in time, or one of the possible states cannot be observed. Example: we are all biallelic, but sometimes we cannot observe both allels [x, y] x=y Simona Point observation OCRE200021 The event occurred within an interval, but it is not known exactly when. Example: the last measurement day one person was HIV negative and the first measurement day the person was positive are known, but when the seroconversion happened within that interval is not known [x, y] x~=y Simona Interval censored OCRE200022 A univariate analysis where the independent variable is nominal with cardinality greater than 2 and the dependent variable is dichotomous I nominalGT2 D dichotomous OCRE200023 A distribution function used to describe the occurrence of rare events or to describe the sampling distribution of isolated counts in a continuum of time or space. This special probability distribution can apply to the number of discrete independent random events occurring in a given interval when knowing their average rate of occurrence over a very long interval. Simona NCI Thesaurus entry for Poisson distribution. Available at http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C53212 Poisson distribution OCRE200024 A metric measuring the "middle" or "expected" value of a distribution or of a random variable Samson Central tendency OCRE200025 A proportion is a measure of the frequency of some phenomenon of interest within an average population Ranges from 0 to 1. One way to summarize count data. Proportion OCRE200026 Method for deriving a variable by scoring from multiple observations or aggregating from multiple events in a subject or from multiple subjects E.g., population-level variables Scoring or aggregation method OCRE200027 [see standard reference] Logistic regression OCRE200028 A quotient is the result obtained by dividing one quantity by another Simona Quotient OCRE200029 [see standard reference] Z-test OCRE200030 Infinite non-countable OCRE200031 Both boundaries are included in the interval [ ] Simona Closed OCRE200032 A univariate analysis where the dependent variable is nominal with cardinality greater than 2 Dependent variable nominalGT2 OCRE200033 The analysis of variance is a collection of statistical models, and their associated procedures, in which the observed variance is partitioned into components due to different explanatory variables. [source: Wikipedia] The total variation displayed by a set of observations, as measured by the sums of squares of deviations from the mean, may in certain circumstances be separated into components associated with defined sources of variation used as criteria of classification for the observations. Such an analysis is called an analysis of variance, although in the strict sense it is an analysis of sums of squares. Simona OECD Glossary of Statistical Terms entry for Variance Analysis. Available at http://stats.oecd.org/glossary/detail.asp?ID=3885 Analysis of variance OCRE200034 How measurements of "equal value" of interval data can be differentiated Whether 0, 1 or both interval boundaries are included. Simona Interval data tie-breaking distinction OCRE200035 Variables derived from taking the sum of two other variables Sum OCRE200036 Variables whose values are unitary measurements that cannot be defined from other variables Scale level OCRE200037 The lambda co-efficient of an exponential distribution Lambda OCRE200038 Ties are exact Discrete OCRE200039 The median is the middle value in a data set: i.e., the value which has an equal number of values greater and less than it. Simona Median OCRE200040 Variables derived from taking the difference of two other variables. For example, the first difference of a time series {yt} is defined as Dyt = yt - yt-1 Difference OCRE200041 In probability theory and statistics, the exponential distribution (a.k.a. negative exponential distribution) is a family of continuous probability distributions. It describes the time between events in a Poisson process, i.e. a process in which events occur continuously and independently at a constant average rate. A class of probability distribution with probability density function (pdf) of f(x;lambda) = 1 - exp(-lambda*x) for x >-0 ; 0 otherwise Simona Wikipedia entry for Exponential distribution. Available at http://en.wikipedia.org/wiki/Exponential_distribution Exponential distribution OCRE200042 A rate is a quantity per unit of time. (Cambridge Dictionary of Statistics 3nd ed.) A measure of the frequency of some phenomenon of interest given by rate: number of events in specified period / average population during the period. The (Cambridge Dictionary of Statistics 3nd ed.) definition of rate is our definition of proportion. Rate OCRE200043 In probability theory, a log-normal distribution is a probability distribution of a random variable whose logarithm is normally distributed. If X is a random variable with a normal distribution, then Y = exp(X) has a log-normal distribution; likewise, if Y is log-normally distributed, then X = log(Y) is normally distributed. (This is true regardless of the base of the logarithmic function: if loga(Y) is normally distributed, then so is logb(Y), for any two positive numbers a, b ≠ 1.) Simona Wikipedia entry for Log-normal distribution. Available at http://en.wikipedia.org/wiki/Log-normal_distribution Log-normal distribution OCRE200044 [see standard reference] Polychotomous regression OCRE200045 A univariate analysis where the independent variable is dichotomous and the dependent variable is dichotomous I dichotomous D dichotomous OCRE200046 A plan for multivariate analysis where the independent variable is nominal and the dependent variable is nominal with cardinality greater than 2 Simona: needs review; labels and definitions in this subtree are not clear. Multivariate I nominal D nominalGT2 OCRE200047 A categorical method is a statistical technique that uses categorical (nominal) data. Simona Categorical method OCRE200048 The left boundary is not included in the interval ( ] Simona Left open OCRE200049 Quantitative scale level OCRE200050 In probability theory and statistics, the chi-square distribution (also chi-squared or χ²-distribution) with k degrees of freedom is the distribution of a sum of the squares of k independent standard normal random variables. Simona Wikipedia entry for Chi-square distribution. Available at http://en.wikipedia.org/wiki/Chi-square_distribution Chi-square distribution OCRE200051 Non-linear model OCRE200052 Neither boundary is included in the interval ( ) Simona Open OCRE200053 statistics:OCRE200053 Meta data characterizing the plan to analyze a set of data Statistical analysis type 2 OCRE200054 [see standard reference] Cox regression OCRE200055 The variate distance between the upper and lower quartiles. This range contains one half of the total frequency and provides a simple measure of dispersion which is useful in descriptive statistics OECD glossary of Statistical Terms entry for Interquartile range. Available at http://stats.oecd.org/glossary/detail.asp?ID=3761 Interquartile range OCRE200056 [see standard reference] Quantile regression OCRE200057 The mean is the sum of a set of values divided by the number of values in the set. Simona NCI thesaurus entry for Mean Available at http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C53319 Statistical mean Mean OCRE200058 The mode is the value which occurs most often in a set of values. If no value is repeated, there is no mode. If more than one value occurs with the same greatest frequency, each value is a mode. Simona NCI thesaurus entry for Mode. Available at http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C53320 Mode OCRE200059 A univariate analysis where the independent variable is ordinal with cardinality greater than 2 and the dependent variable is dichotomous I ordinalGT2 D dichotomous OCRE200060 A univariate analysis where the dependent variable is ordinal Dependent variable ordinal OCRE200061 statistics:OCRE200061 A procedure for performing statistical inference Note that we are excluding descriptive statistical method Statistical method OCRE200062 Ties are not exact Continuous OCRE200063 In probability theory and statistics, the gamma distribution is a two-parameter family of continuous probability distributions. It has a scale parameter θ and a shape parameter k. If k is an integer, then the distribution represents an Erlang distribution, i.e., the sum of k independent exponentially distributed random variables, each of which has a mean of θ (which is equivalent to a rate parameter of θ −1) . The gamma distribution is frequently a probability model for waiting times; for instance, in life testing, the waiting time until death is a random variable that is frequently modeled with a gamma distribution. Simona Wikipedia entry for Gamma distribution. Available at http://en.wikipedia.org/wiki/Gamma_distribution Gamma distribution OCRE200064 The event occurred some time before the last measurement, but it is not known exactly when. Example: one person tests HIV positive, but there is no negative test result, so it is not possible to estalish a time interval for seroconversion [x, y], x unknown Simona Left censored OCRE200065 In probability theory and statistics, the binomial distribution is the discrete probability distribution of the number of successes in a sequence of n independent yes/no experiments, each of which yields success with probability p. Such a success/failure experiment is also called a Bernoulli experiment or Bernoulli trial. Simona Wikipedia entry for Binomial distribution. Available at http://en.wikipedia.org/wiki/Binomial_distribution Binomial distribution OCRE200066 [see standard reference] Spearmans rank correlation coefficient OCRE200067 General estimating equation OCRE200068 Odds is a quotient in which the relative likelihood that an event will occur is divided by the the relative likelihood that it won't. In probability theory and statistics, where the variable "p" is the probability in favor of the event, and the probability against the event is 1-p, "the odds" of the event are the quotient of the two, or p / (1-p) Simona Odds OCRE200069 A plan for multivariate analysis where the independent variable is multivariate and the dependent variable is ordinal Simona: needs review; labels and definitions in this subtree are not clear. Multivariate D ordinal OCRE200070 [see standard reference] Student's t-test OCRE200071 Generalized linear model OCRE200072 Object and values that related to the description of statistical analysis Statistical concept 1 OCRE200073 Logrank test Simona: changed label to 'Product limit estimation', which can be tested with a logrank test and the result is the Kaplan-Meier curve. The logrank test allows to compare two or more KM curves Product limit estimation OCRE200074 The analysis of covariance (ANCOVA) is a general linear model with one continuous outcome variable (quantitative) and one or more factor variables (qualitative). ANCOVA is a merger of ANOVA and regression for continuous variables. ANCOVA tests whether certain factors have an effect on the outcome variable after removing the variance for which quantitative predictors (covariates) account. Simona Wikipedia entry for Analysis of covariance. Available at: http://en.wikipedia.org/wiki/Analysis_of_covariance Analysis of covariance OCRE200075 The variance is the mean square deviation of the variable around the average value. It reflects the dispersion of the empirical values around its mean. (http://stats.oecd.org/glossary/detail.asp?ID=5160) Variance OCRE200076 Number of possible outcomes Describe background of data, how to present data when you plot it Granularity OCRE200077 A plot of the sensitivity of a discriminant test against one minus its specificity ROC curve OCRE200078 The normal distribution is a family of probability density functions whose mean, median and mode are identical. The function generates a symmetrical curve, whose position and shape is determined by its location and scale parameters, the mean and standard deviation respectively. The standard normal distribution has a location parameter of 0 and a scale parameter of 1. Simona NCI Thesaurus entry for Normal distribution. Available at http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C53215 Normal distribution OCRE200079 A univariate analysis where the dependent variable is dichotomous Dependent variable dichotomous OCRE200080 A distribution metric of the exponential distribution Exponential distribution metric OCRE200081 [see standard reference] Wilcoxon rank sum test OCRE200082 A plan for multivariate analysis where the independent variable is multivariate and the dependent variable is survival data Simona: needs review; labels and definitions in this subtree are not clear. Multivariate D survival data OCRE200083 In probability theory and statistics, the discrete uniform distribution is a probability distribution whereby a finite number of equally spaced values are equally likely to be observed; every one of n values has equal probability 1/n. Another way of saying "discrete uniform distribution" would be "a known, finite number of equally spaced outcomes equally likely to happen." If a random variable has any of n possible values that are equally spaced and equally probable, then it has a discrete uniform distribution. The probability of any outcome ki is 1 / n. A simple example of the discrete uniform distribution is throwing a fair die. Simona Wikipedia entry for Uniform distribution (discrete). Available at http://en.wikipedia.org/wiki/Uniform_distribution_(discrete) Discrete uniform distribution OCRE200084 Categorical variables with more than two categories Polychotomous OCRE200085 How measurements of "equal value" can be differentiated Simona Tie-breaking distinction OCRE200086 A measure of a test's accuracy defined as the harmonic mean of sensitivity and specificity F= 2*(specificity * sensitivity)/(specificity + sensitivity) F1 score F measure OCRE200087 For a discrete random variable, a mathematical formula that gives the probability of each value of the variable. For a continuous random variable, a curve described by a mathematical formula which specifies, by way of areas under the curve, the probability that the variable falls within a particular interval. Cambridge Dictionary of Statistics 3rd edition Probability distribution OCRE200088 Censoring type is a particular type of interval creation. Censoring means that one event prevents another event from being observed (e.g., end of study prevents possible evidence of success or failure from being observed). Though usually employed in the context of time-to-failure, this is not only about time, but it can be about any dimension of interest (e.g., if the measurement is above the maximum value in the scale used, then the measurement is right censored; if it is lower than the minimum detectable, then it is left censored). Simona Censoring type OCRE200089 In S. Steven's typology of measurement scale, a ratio variable is "a continuous variable that has a fixed rather than an arbitrary zero point." Examples: weight, height, temperature measured in degrees Kelvin Can compute ratios Cambridge Dictionary of Statistics 3rd edition Absolute scale level OCRE200090 An index of performance of a discriminant test calculated as the percentage of negatives in all true negatives Samson Specificity OCRE200091 Polychotomous finite 1 OCRE200092 A plan for statistical analysis where there is only one independent variable Univariate analysis OCRE200093 A metric measuring the variability of a distribution or of a random variable Dispersion OCRE200094 Polarity OCRE200095 An time-to-failure method is a statistical technique relating to preparation of mortality and other analytical tables. It uses data from the past to predict the future. Simona Time-to-failure method OCRE200096 In probability theory and statistics, the continuous uniform distribution or rectangular distribution is a family of probability distributions such that for each member of the family, all intervals of the same length on the distribution's support are equally probable. The support is defined by the two parameters, a and b, which are its minimum and maximum values. The distribution is often abbreviated U(a,b). Simona Wikipedia entry for Uniform distribution (continuous). Available at http://en.wikipedia.org/wiki/Uniform_distribution_(continuous) Simona: Wikipedia entry "does not cite any references or sources" Confirmation needed Continuous uniform distribution 2 OCRE200097 A plan for statistical analysis where there is more than one independent variable and some of those variables are not of the ordinal scale Multivariate analysis I non-ordinal OCRE200098 A univariate analysis where the dependent variable is interval/absolute scale level Dependent variable quantitative scale OCRE200099 A plan for multivariate analysis where some independent variables are non-ordinal and the dependent variable is dichotomous Simona: needs review; labels and definitions in this subtree are not clear. Multivariate I non-ordinal D dichotomous OCRE200100 An index of performance of a discriminant test with binary outcome Samson Classification analysis metric OCRE200101 In mathematics, a countable set is a set with the same cardinality (number of elements) as some subset of the set of natural numbers. Simona Wikipedia entry for Countable set. Available at http://en.wikipedia.org/wiki/Countable_set Infinite countable OCRE200102 Linear mixed effect model OCRE200103 Data representing the times of the occurrances of events of interest On scale of time. Often censored. A difference in time. Also whether an event occurs (lowerbound of time to event) Measurement can be one number or an interval. 3 categories: same L & Ul, right censoring (know lowerbound), an interval Survival data Time to event OCRE200104 Non linear mixed effect model OCRE200105 The event my have occurred some time after the last measurement, but it is not known exactly whether it has, because there are no further observations. Example: one person tests HIV negative at some point, but there are no further observations (e.g., the individual moved, or died), so it is not known whether the person has seroconverted or not [x, y], x unknown Simona Right censored OCRE200106 A univariate analysis where the dependent variable is survival data Dependent variable survival data OCRE693000 How measurements of "equal value" of point data can be differentiated Simona Point data tie-breaking distinction study_design:Non-standard_allocation_concealment_method Non-standard allocation concealment method study_design:OCRE100001 Each case serves as its own control Simona Case and control in same experimental unit study_design:OCRE100002 In the context of a study where the main comparison is within experimental units, investigator assigns regimen of interventions to an allocation group made up of one (single) or of more than one (multiple) experimental unit. Simona Allocation group cardinality study_design:OCRE100003 The scheme used to assign regimens of interventions: single factor or factorial. Simona Intervention assignment scheme study_design:OCRE100004 Cases and controls (or exposed and unexposed) are drawn from the same study cohort/sample. Simona Nested study_design:OCRE100005 A meta-level characterization of the design of a study Simona Study design characteristic study_design:OCRE100006 Probability sampling is an exclusively random process to guarantee that each participant or population has specified chance of selection, such as simple random sampling, systematic sampling, stratified random sampling, cluster sampling, and consecutive patient sampling Simona ClinicalTrials.gov Protocol Data Element Definitions (DRAFT). Available at http://prsinfo.clinicaltrials.gov/definitions.html Probability sampling study_design:OCRE100007 An interventional study is a quantitative study that prospectively assigns experimental units (human participants or groups of humans or part of human participants) to one or more health-related interventions to evaluate the effects on health outcomes. Interventions include but are not restricted to drugs, cells and other biological products, surgical procedures, radiologic procedures, devices, behavioural treatments, process-of-care changes, preventive care, etc. Simona WHO Available at: http://www.who.int/ictrp/en/ Simona: to be reviewed Interventional study design study_design:OCRE100008 Open label indicates that no blinding is in effect: the investigator and participant are aware which intervention is being used for which participant (i.e. not blinded) Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Open label study_design:OCRE100009 The investigator does not actively assign study experimental units to regimens of interventions. Simona Investigator assigns no intervention study_design:OCRE100011 Superiority is a type of comparative intent. When the aim of the study is to show that an experimental (E) treatment is superior to a control (C) treatment, the RCT is called a superiority trial and the associated statistical test is a superiority test. With a significant result, one concludes in a superiority trial that E is different in effect from C, and when the observed result is in favor of E, we conclude that E is statistically, significantly better performing than C. Simona Bull NYU Hosp Jt Dis. 2008;66(2):150-4. Superiority study_design:OCRE100012 Equivalence is a type of comparative intent. An equivalence trial is designed to determine whether the response to two or more treatments differs by an amount that is clinically unimportant. This is usually demonstrated by showing that the true treatment difference is likely to lie between a lower and an upper equivalence level of clinically acceptable differences. Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Equivalence study_design:OCRE100013 In an observational study, the main variable on which the selection of experimental units is based is a predictor variable. In this study, prospective inference occurs, i.e., from exposure to outcome. Simona Experimental unit selection based on predictor variable study_design:OCRE100014 The outcome assessor does not know to which treatment group a particular participant belongs Simona Outcome assessor blinded study_design:OCRE100015 A case-crossover study is an observational study that aims to answer the question, "Was this event triggered by something unusual that happened just before?" The key feature of the design is that each case serves as its own control. The method is analogous to a crossover experiment viewed retrospectively, except that the investigator does not control when an experimental unit starts and stops being exposed to the potential trigger. Also, the exposure frequency is typically measured in only a sample of the total time when the experimental unit was at risk of the injury or disease onset. Thus it usually resembles a case-control study more than a retrospective cohort study. The simplest case-crossover design is closely analogous to a traditional matched-pair case-control design. In both designs, each case has a matched control. In a traditional matched-pair case-control study, the control is a different experimental unit at a similar time. In the matched-pair case-crossover design, the control is the same experimental unit at a different time. Simona Annu Rev Public Health. 2000;21:193-221. Case-crossover study design study_design:OCRE100016 The concept of phase is not applicable to trials studying certain interventions (e.g., device, procedure, behavioral) Simona Phase not applicable study_design:OCRE100018 A case control study is an observational study that compares people with a specific disease or outcome of interest (cases) to people from the same population without that disease or outcome (controls), and which seeks to find associations between the outcome and prior exposure to particular risk factors. [Glossary of Terms in The Cochrane Collaboration] Simona Case-control study design study_design:OCRE100019 Non-probability sampling is any one of a variety of non random sampling processes, such as convenience sampling or invitation to volunteer Simona ClinicalTrials.gov Protocol Data Element Definitions (DRAFT). Available at http://prsinfo.clinicaltrials.gov/definitions.html Non-probability sampling study_design:OCRE100020 A crossover study is an interventional study where the population is a more than a single experimental unit, in which at least two regimens of interventions are given alternatingly. Upon completion of one regimen, experimental units are switched to the other. For example, for a comparison of regimens A and B, the experimental units are randomly allocated to receive them in either the order A, B or the order B, A. Regimens are assigned to and data are analyzed within more than one experimental unit at a time. Simona Crossover study design study_design:OCRE100021 Allocation scheme describes the way in which each experimental unit in an interventional trial is allocated to a treatment group. Simona Allocation scheme study_design:OCRE100022 Whether cases and controls (or exposed and unexposed) are drawn from the same study cohort/sample. Not applicable to case-crossover studies. Simona Control group type study_design:OCRE100023 A cohort study in which outcomes occurred after the start of the study. Simona Prospective study_design:OCRE100024 An N-of-1 crossover study is an interventional study where the population is a single human subject and in which at least two regimens of interventions are given alternatingly. Regimens are assigned to and data are analyzed within one participant at a time. Simona Simona: to be reviewed N-of-1 crossover study design study_design:OCRE100025 Stratified randomization is restricted randomization used to ensure that equal numbers of participants with a characteristic thought to affect prognosis or response to the intervention will be allocated to each comparison group. For example, in a trial of women with breast cancer, it may be important to have similar numbers of pre-menopausal and postmenopausal women in each comparison group. Stratified randomisation could be used to allocate equal numbers of pre- and post-menopausal women to each treatment group. Stratified randomisation is performed by performing separate randomisation (often using random permuted blocks) for each strata. Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Stratified randomization study_design:OCRE100026 The investigator actively assigns the study experimental units to one or more regimens of interventions (each including one or more interventions, or no intervention). Simona Investigator assigns intervention study_design:OCRE100027 A parallel group study is an interventional study that compares across at least two allocation groups concurrently, each receiving a regimen of interventions (which can be "no intervention"). Simona Simona: to be reviewed. Parallel group study design study_design:OCRE100028 Mode of inquiry refers to the research method used in a study Simona Mode of inquiry study_design:OCRE100029 In the context of a study where the main comparison is within experimental units, investigator assigns regimen of interventions to an allocation group made up of more than one experimental unit. Simona Multiple experimental unit allocation group study_design:OCRE100030 Restricted randomization is a random allocation scheme used to control the randomization to achieve balance between groups in size (or other characteristics). Different types of restricted randomization are as follows: - Blocking: Blocking is used to ensure close balance of the numbers in each group at any time during the study. After every block the number of participants in each group would be equal. Of course blocking tends to reduce the unpredictability of randomization. Therefore it is recommended to use random block sizes when using block randomization. - Stratification: Stratification ensures that the numbers of participants receiving each intervention are closely balanced within each stratum. Stratified randomization is achieved by performing a separate randomization procedure within each of two or more subsets of participants - Minimization: Minimization is not a method of randomization. Indeed it is the only non-random method which is an acceptable alternative to randomization. Minimization ensures balance between intervention groups for several patient factors. Randomization lists are not set up in advance. The first patient is truly randomly allocated; for each subsequent patient, the treatment allocation is identified, which minimizes the imbalance between groups at that time. Simona http://mahmoodsaghaei.tripod.com/Softwares/randalloc.html Simona: should we put the 3 schemes elsewhere? Restricted randomization study_design:OCRE100031 A quantitative research method is a deductive research process that uses statistical techniques to test a specific claim or statement about a phenomenon (a hypothesis) by collecting and analyzing data to decide whether the claim is true (i.e., accept or reject the null or alternative hypothesis). Simona http://www.utexas.edu/academic/ctl/assessment/iar/research/plan/types.php Quantitative inquiry mode study_design:OCRE100032 Quasi-random allocation is an allocation scheme that is not random, but is intended to produce similar groups when used to allocate experimental units. Quasi-random methods include: allocation by the person's date of birth, by the day of the week or month of the year, by a person's medical record number, or just allocating every alternate person. In practice, these methods of allocation are relatively easy to manipulate, introducing selection bias. Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Quasi-random allocation study_design:OCRE100033 Random allocation is an allocation scheme that uses the play of chance to assign participants to comparison groups in a trial, e.g. by using a random numbers table or a computer-generated random sequence. Random allocation implies that each individual or unit being entered into a trial has the same chance of receiving each of the possible interventions. It also implies that the probability that an individual will receive a particular intervention is independent of the probability that any other individual will receive the same intervention. Randomization is the process of randomly allocating experimental units into one of the arms of a controlled trial. There are two components to randomisation: the generation of a random sequence [allocation scheme], and its implementation [allocation concealment method], ideally in a way so that those entering participants into a study are not aware of the sequence (concealment of allocation). Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Random allocation study_design:OCRE100034 Non-cases were selected based on genetic relation Simona Genetically related non-cases study_design:OCRE100035 Multiple regimens of intervention, each including one or more individual interventions (treatments) or no treatment, each assigned to one allocation group. This means the study has at least one contemporaneous comparison group. Simona Multiple regimen study_design:OCRE100036 The caregiver does not know to which treatment group a particular participant belongs Simona Caregiver blinded study_design:OCRE100037 A single regimen of intervention, which includes one or more individual interventions (treatments), is assigned to one allocation group. This means the study has no contemporaneous comparison group. Simona Single regimen study_design:OCRE100038 Phase describes the level of a trial required of drugs before (and after) they are routinely used in clinical practice: - Phase 1 trials assess toxic effects on humans (not many people participate in them, and usually without controls); - Phase 2 trials assess therapeutic benefit (usually involving a few hundred people, usually with controls, but not always); - Phase 3 trials compare the new treatment against standard (or placebo) treatment (usually a full randomised controlled trial). At this point, a drug can be approved for community use. - Phase 4 monitors a new treatment in the community, often to evaluate longterm safety and effectiveness. [Glossary of Terms in The Cochrane Collaboration] A trial can be of a combination phase (e.g., 1/2). The concept of phase is not applicable to trials studying certain interventions (e.g., device, procedure, behavioral) Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Phase study_design:OCRE100039 A cross-sectional study is an observational study measuring the distribution of some characteristic(s) in a population at a particular point in time. (Also called survey.) Simona Glossary in The Cochrane Collaboration. Available at: http://www.cochrane.org/glossary Cross-sectional study design study_design:OCRE100040 Block randomization (or Random permuted blocks) is a restricted randomisation that ensures that, at any point in a trial, roughly equal numbers of participants have been allocated to all the comparison groups. Permuted blocks should be used in trials using stratified randomisation. Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Block randomization study_design:OCRE100041 The unit that is assigned to the alternative regimens of interventions being investigated in a trial. Most commonly, the unit will be an individual person, but in a cluster randomised trial, groups of people will be assigned together to one or the other of the regimens of interventions. In some other trials, different parts of a person (such as the left or right eye) might be assigned to receive different regimens of interventions. Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Unit of allocation study_design:OCRE100042 The number of regimens of interventions in a study. Each regimen includes one or more individual interventions (treatments) or no intervention. Simona Simona: to be reviewed Regimen cardinality study_design:OCRE100043 The unit that is assigned to the alternative regimens of interventions being investigated in a trial. In a cluster randomised trial, groups of experimental units will be assigned together to one or the other of the regimens of interventions. Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Cluster as unit of allocation study_design:OCRE100044 A quantitative study is an individual-human study whose primary mode of inquiry is quantitative. Simona Quantitative study design study_design:OCRE100045 [In a controlled trial:] Blinding is the process of preventing those involved in a trial from knowing to which comparison group a particular participant belongs. The risk of bias is minimised when as few people as possible know who is receiving the experimental intervention and who the control intervention. Participants, caregivers, outcome assessors, and analysts are all candidates for being blinded. Blinding of certain groups is not always possible, for example surgeons in surgical trials. The terms single blind, double blind and triple blind are in common use, but are not used consistently and so are ambiguous unless the specific people who are blinded are listed. (Also called masking) Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Blinding type study_design:OCRE100046 In the context of a study where the main comparison is within experimental units, whether data is analyzed within a single study experimental unit or within multiple experimental units. Simona Data analysis within experimental units study_design:OCRE100047 A qualitative study is an individual-human study whose primary mode of inquiry is qualitative. Simona Qualitative study design study_design:OCRE100048 Characteristics of the assignment experimental units (e.g., participant, eye) to a regimen of interventions Simona Assignment characteristics study_design:OCRE100049 Method of sampling in observational studies. Simona Sampling method study_design:OCRE100052 A single group study is an interventional study that has only a single allocation group and no contemporaneuos comparison group. A study in which an individual acts has his/her own comparison does not fall into this category, since an individual is not a group. Simona Simona: to be reviewed Single group study design study_design:OCRE100053 The care provider does not know to which treatment group a particular participant belongs Simona Care provider blinded study_design:OCRE100055 An observational study is a quantitative study in which the investigators do not seek to intervene, and simply observe the course of events. Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Observational study design study_design:OCRE100056 A study design is a common pattern of relationships (in time and causation) among various study elements (e.g., time of intervention to outcomes assessment in which participants). Simona Study design study_design:OCRE100057 A qualitative research method is an inductive research process that involves the collection and analysis of qualitative (i.e., non-numerical) data to search for patterns, themes, and holistic features. Simona http://www.utexas.edu/academic/ctl/assessment/iar/research/plan/types.php For other definitions, see http://www.google.com/search?hl=en&client=safari&rls=en&defl=en&q=define:Qualitative+research Qualitative inquiry mode study_design:OCRE100058 The role the investigator plays in the assignment of study experimental units to one or more regimens of interventions (each including one or more interventions, or no intervention). Simona Investigator assignment role study_design:OCRE100059 In a retrospective observational study (i.e., an observational study where the main variable on which experimental units selection is based is an outcome variable), experimental units with the same outcome (cases) can be compared to themselves or to other experimental units (controls). Simona Comparison of experimental units with the main outcome study_design:OCRE100060 Have outcomes occurred before the study start? If yes, the cohort study is historical; if no, the cohort study is prospective. Simona Outcomes occurred before or after study start study_design:OCRE100061 The main comparison is across study experimental units. Simona Main comparison across experimental units study_design:OCRE100062 Cases and controls (or exposed and unexposed) are not drawn from the same cohort/sample. [aka double cohort for cohort studies] Simona Non-nested study_design:OCRE100063 Data is analyzed within multiple study experimental units. Simona Data analyzed within multiple experimental units study_design:OCRE100064 The subject or individual participant does not know to which treatment group he or she or each experimental unit on him/her belongs. or Individual participant blinded Simona Subject blinded study_design:OCRE100065 In a single-factor design, an intervention is compared with one or more alternatives, or a placebo. Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Single-factor study_design:OCRE100066 A Phase 4 study monitors FDA-approved drug to delineate additional information including the drug's risks, benefits, and optimal use. Simona ClinicalTrials.gov Protocol Data Element Definitions (DRAFT). Available at http://prsinfo.clinicaltrials.gov/definitions.html Phase 4 study_design:OCRE100067 A Phase 1 trial includes initial studies to determine the metabolism and pharmacologic actions of drugs in humans, the side effects associated with increasing doses, and to gain early evidence of effectiveness; may include healthy participants and/or patients. Simona ClinicalTrials.gov Protocol Data Element Definitions (DRAFT). Available at http://prsinfo.clinicaltrials.gov/definitions.html Phase 1 study_design:OCRE100068 A Phase 0 trial is an exploratory trial involving very limited human exposure, with no therapeutic or diagnostic intent (e.g., screening study, microdose study). Simona ClinicalTrials.gov Protocol Data Element Definitions (DRAFT). Available at http://prsinfo.clinicaltrials.gov/definitions.html Phase 0 study_design:OCRE100069 A Phase 3 trial includes expanded controlled and uncontrolled trials after preliminary evidence suggesting effectiveness of the drug has been obtained, and are intended to gather additional information to evaluate the overall benefit-risk relationship of the drug and provide an adequate basis for physician labeling. Simona ClinicalTrials.gov Protocol Data Element Definitions (DRAFT). Available at http://prsinfo.clinicaltrials.gov/definitions.html Phase 3 study_design:OCRE100070 A Phase 2 trial includes controlled clinical studies conducted to evaluate the effectiveness of the drug for a particular indication or indications in patients with the disease or condition under study and to determine the common short-term side effects and risks. Simona ClinicalTrials.gov Protocol Data Element Definitions (DRAFT). Available at http://prsinfo.clinicaltrials.gov/definitions.html Phase 2 study_design:OCRE100071 The unit that is assigned to the alternative regimens of interventions being investigated in a trial. Most commonly, the unit will be an individual person. In some other trials, different parts of a person (such as the left or right eye) might be assigned to receive different regimens of interventions. Simona Individual as unit of allocation study_design:OCRE100072 Comparative intent is an additional descriptor: Intent of comparison made in a study with two or more arms. Simona Comparative intent study_design:OCRE100073 Whether the main comparison is across or within study experimental units Simona Main comparison and experimental units study_design:OCRE100074 A method of allocation used to provide comparison groups that are closely similar for several variables. The next participant is assessed with regard to several characteristics, and assigned to the treatment group that has so far had fewer such people assigned to it. It can be done with a component of randomisation, where the chance of allocation to the group with fewer similar participants is less than one. Minimisation is best performed centrally with the aid of a computer program to ensure concealment of allocation. Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Minimization study_design:OCRE100075 In the context of a study where the main comparison is within experimental units, investigator assigns regimen of interventions to an allocation group made up of a single experimental unit. Simona Single experimental unit allocation group study_design:OCRE100076 A non-inferiority trial is designed to determine whether the effect of a new treatment is not worse than a standard treatment by more than a pre-specified amount. A one-sided version of an equivalence trial. [Glossary of Terms in The Cochrane Collaboration] Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Non-inferiority study_design:OCRE100077 Non-random (or Deterministic) allocation is an allocation scheme that follows a non-random rule (e.g., sequential allocation). Simona Non-random allocation study_design:OCRE100078 A cohort study is an observational study in which a defined group of people (the cohort) is followed over time. The outcomes of people in subsets of this cohort are compared, to examine people who were exposed or not exposed (or exposed at different levels) to a particular intervention or other factor of interest. A prospective cohort study assembles participants and follows them into the future. A retrospective (or historical) cohort study identifies subjects from past records and follows them from the time of those records to the present. Simona Glossary in The Cochrane Collaboration. Available at: http://www.cochrane.org/glossary The DL definiition of cohort study design says that a cohort study design has the characteristics "Main control group defined by exposure status" and "outcome measured after measurement of predictors." A study design involves identification of factor variables and outcome variables. Factor variables are measured before the measurement of outcome variables. Let C be a member of the control groups of a study S Let SA be the set of statistical analysis of S Let F(sa) be the independent variables of a statistical analysis sa in SA Let O(sa) be the set of dependent variables of sa S has 'cohort study design" if and only if For all sa in SA, There exists times t1 < t2 such that there exists f in F(sa) such that for all c in C, f is measured at time t1 and f(c) = constant AND for all o in O(sa), o is measured at t2 Cohort study design study_design:OCRE100079 In an observational study, the main variable on which the selection of experimental units is based is an outcome variable. In this study, retrospectie inference occurs, i.e., from outcome to exposure. Simona Experimental unit selection based on outcome variable study_design:OCRE100080 The statistician does not know to which treatment group a particular participant belongs Simona Statistician blinded study_design:OCRE100081 The main comparison is within study experimental units. Simona Main comparison within experimental units study_design:OCRE100082 Relation between cases and non-cases Simona Relation between cases and non-cases study_design:OCRE100083 Simple randomization is a random allocation scheme that has no restriction, i.e. a single sequence of random assignment. When the sample size is relatively large, simple randomization is expected to produce equal sized treatment groups. Simona http://mahmoodsaghaei.tripod.com/Softwares/randalloc.html Simple randomization study_design:OCRE100084 The investigator does not know to which treatment group a particular participant belongs Simona Investigator blinded study_design:OCRE100085 Data is analyzed within a single study experimental unit. Simona Data analyzed within single experimental unit study_design:OCRE100086 Non-cases were not selected based on genetic relation Simona Genetically unrelated non-cases study_design:OCRE100087 A cohort study in which outcomes occurred before the start of the study. Simona Historical study_design:OCRE100088 A case does not serve as its own control Simona Case and control not in same experimental unit study_design:OCRE100089 Factorial design is a trial design used to assess the individual contribution of treatments given in combination, as well as any interactive effect they may have... In a trial using a 2x2 factorial design, participants are allocated to one of four possible combinations... This type of study is usually carried out in circumstances where no interaction is likely. Example: in a factorial-design study where regimens of interventions A and B are tested, the 4 possible combinations are: A, B, A and B, neither A nor B (placebo). Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Factorial study_design:OCRE101000 Sequentially numbered opaque sealed envelopes study_design:OCRE260000 Central randomization study_design:OCRE297000 Sequentially numbered drug containers study_design:OCRE475000 Allocation concealment method study_design:OCRE498000 In an observational study, the main varibale on which the selection of experimental units is based is neither an outcome nor an exposure variable. Simona Experimental unit selection based on neither outcome nor predictor variable study_design:OCRE606000 Natural history study design is a kind of cohort study design, where the inclusion criteria consists almost entirely of having some condition (usually a new one, e.g., SARS) or being at risk of developing a condition. A natural history study collects health information in order to understand how the medical condition or disease develops and how to treat it. (Such studies are usually prospectively, but could be a historical cohort study.) Simona Natural history study design study_design:OCRE629000 Case series study design is a collection of stories about cases, with narrative outcomes Case series study design study_design:OCRE710000 Allocation concealment method value study_design:OCRE866187 Case-only study design study_design:OCRE9000030 An aggregated human study is a human study in which the entity observed, recruited or selected, or subject to intervention or exposure is a population that contains persons Simona Aggregated-human study study_design:OCRE9000031 An individual-human study is a human study in which the entity observed, recruited or selected, or subject to intervention or exposure is a person, or a part of a person. Simona Individual-human study study_design:OCRE900028 A human study is a study in which the entity observed, recruited or selected, or subject to intervention or exposure is a person, a population of persons, or a part of a person. Human study study_design:OCRE900029 A non-organismal study is a study in which neither the entity observed, nor the entity recruited or selected, nor the entity subject to intervention or exposure is an organism, a population of organisms, or a part of an organism. Simona Non-organismal study study_design:OCRE900032 A decision analysis is a non-organismal study technique that formally identifies the options in a decision-making process, quantifies the probable outcomes (and costs) of each (and the uncertainty around them), determines the option that best meets the objectives of the decision-maker and assesses the robustness of this conclusion. Cost-benefit analysis, cost-effectiveness analysis and cost-utility analysis are special cases of decision analysis. Note that this type of analysis can also be applied to outcomes in a human study. Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Decision analysis study_design:OCRE900033 A policy analysis is a non-organismal study that can be defined as determining which of various alternative policies will most achieve a given set of goals in light of the relations between the policies and the goals. Policy analysis emphasizes systematic analytic methods that can be quantitative or qualitative. Simona Nagel, Stuart S. (Ed.), 1999, Policy Analysis Methods. New Science Publishers, Inc., pages 3 and 4 Policy analysis study_design:OCRE900034 A technology study is a non-organismal study that uses or collects measurements or assessments about a man-made object (e.g., a device) in terms of its technical/physical performance. Simona Technology study study_design:OCRE900036 An organismal study is a study in which the entity observed, recruited or selected, or subject to intervention or exposure is an organism, a population of organisms, or a part of an organism. Organismal study study_design:OCRE900037 A non-human organism study is a study in which the entity observed, recruited or selected, and subject to intervention or exposure is non-human organism, a population of non-human organisms, or a part of a non-human organism. Simona Non-human organism study study_design:OCRE900040 A systematic review is a meta study (i.e., a study in which observations are acquired from journal articles, abstracts, etc. reporting on other studies). A systematic review uses systematic and explicit methods to identify, select, and critically appraise relevant research, and to collect and analyse data from the studies that are included in the review. Statistical methods (meta-analysis) may or may not be used to analyse and summarise the results of the included studies. Meta-analysis is the use of statistical techniques in a systematic review to integrate the summary results of included studies. Sometimes misused as a synonym for systematic reviews, where the review includes a meta-analysis. Simona Glossary in The Cochrane Collaboration. Available at http://www.cochrane.org/glossary Systematic review study_design:OCRE942000 In an observational study, the main variable on which the selection of experimental units is based can be an outcome variable, a predictor variable, or a variable that is neither an outcome nor a predictor one. Simona Main variable on which experimental unit selection is based OCRE300000 study_protocol:OCRE300000 DEFINITION: One of a set of ordered partitions of an experimental unit's participation in a study. An Epoch represents a state within a study such that subjects in separate arms within that state are comparable. Each epoch serves a purpose in the trial as a whole, typically exposing the subject to a treatment or preparing them for a treatment, or gathering post-treatment data.  Activities and activity results control the subject's movement from one epoch to another. EXAMPLE(S): A study designed to assess the effects of treatments might have 3 epochs. A Screening Epoch in which subjects' eligibility is determined and baseline measurements are made. A Treatment Epoch during which treatments are given and effects of treatment are assessed. A Follow-up Epoch during which post-treatment assessments are conducted.  NOTE(S): A subject moves from one epoch to another and can only be in one epoch at a time. The subject can only move to an epoch with a greater sequenceNumber. Activities in the same epoch but a different arm need not be similar in time and pattern. Subjects in different arms will not necessarily pass through the same epochs. DEFINITION: One of a set of ordered partitions of an experimental unit's planned time in a study. Each Epoch serves a purpose in the trial as a whole, typically exposing the subject to a treatment or preparing them for a treatment, or gathering post-treatment data. Epoch-specific (state) transition rules control the subject's movement from one Epoch to another. For example, a study designed to assess the effects of treatments might have 3 epochs, a Screening epoch in which subjects' eligibility is determined and baseline measurements are made, a Treatment epoch during which treatments are given and effects of treatment are assessed, and a Follow-up epoch during which post-treatment assessments are conducted. NOTE: A subject moves from one Epoch to another and can only be in one epoch at a time. The subject can only move to an Epoch with a greater sequenceNumber. The main purpose of the Epoch is to organize the Arms for comparison purposes. Activities in the same Epoch but a different Arm need not be similar in time and pattern. [BRIDG Release 3] Simona BRIDG 3.0.3 Available at http://bridgmodel.nci.nih.gov/ Epoch OCRE300001 study_protocol:OCRE300001 DEFINITION: A path through the study which describes what activities the study subject or experimental unit will be involved in as they pass through the study, and is typically equivalent to a treatment group in a parallel design trial. Generally, each subject is assigned to an arm, and the design of the study is reflected in the number and composition of the individual arms. This intended path through which the subject progresses in a trial is composed of time point events for each epoch of the study. Each time point event, in turn, has a pattern of child time points through which the subject would pass. This planned path thus describes how subjects assigned to the arm will be treated. EXAMPLE(S): A study could have 2 arms named IV-Oral and Oral-IV.  The name IV-Oral reflects a path that passes through IV treatment, then Oral treatment. OTHER NAME(S): Group (CTRR Observational Studies) Simona BRIDG 3.0.3 Available at http://bridgmodel.nci.nih.gov/ Arm OCRE300004 The description of a planned activity that is not directly related to hypothesis evaluation or testing, but is typically essential to the efficient and/or effective coordination and execution of a study, such as obtaining informed consent, verifying eligibility criteria, and completing study visits. Samson Tu Adapted from BRIDG 3.1 definition of DefinedAdministrativeActivity Planned administrative activity specification OCRE300006 The description of a planned procedure that is an action of gathering samples that may be used for subsequent analysis. Samson Tu Adapted from BRIDG 3.1 definition of DefinedSpecimenCollection Planned specimen collection specification OCRE300008 The description of a planned activity whose immediate and primary intention is to obtain a result by observing, monitoring, measuring or otherwise qualitatively or quantitatively gathering data or information about some aspect of a subject's, study subject's or experimental unit's state and whose immediate and primary intention is NOT the alteration of the state of the subject, study subject or experimental unit. Samson Tu Adapted from BRIDG 3.1 definition of DefinedObservation. Planned observation specification OCRE300009 The description of a planned activity whose immediate and primary intention is the alteration of the state of the subject, study subject or experimental unit. Samson Tu Planned procedure specification OCRE300010 study_protocol:OCRE300010 DEFINITION: A relationship between a composite activity specification and the component activity specifications that comprise it, i.e. parent and child activity specifications where all specified activities are intended to occur at some point in the context of a particular study. Samson Tu BRIDG 3.0.3 Available at http://bridgmodel.nci.nih.gov/ cf BRIDG 3.1 DEFINITION of Planned composition relationship A relationship between a composite activity and the component activities that comprise it, i.e. parent and child activities where all activities are intended to occur at some point in the context of a particular study. EXAMPLE(S): A battery of tests may be composed of multiple routine labs that are always ordered together as a group. A glucose tolerance test which is comprised of administering glucose and taking multiple timed blood samples which are then tested for glucose. OTHER NAME(S): NOTE(S): This class helps represent an AND relationship between siblings with the same parent activity. Planned activities composition relationship specification 1 OCRE300011 study_protocol:OCRE300011 The description of an activity that is intended to occur or start at some point in the context of a particular study. Samson Tu Modified from BRIDG 3.1; Available at http://bridgmodel.nci.nih.gov/ Activity specification can be harmonized to BRIDG 3.1 'Planned activity,' which is defined as DEFINITION: An activity that is intended to occur or start at some point in the context of a particular study. EXAMPLE(S): Pregnancy tests are planned for study subjects who are females of childbearing potential. OTHER NAME(S): NOTE(S): A PlannedActivity may be a container of other activities and have a complex structure involving components, options and contingencies using the associated relationship classes. This structure allows the representation of concepts in previous versions of BRIDG such as StudyCells, StudySegments and StudySubjectEncounters. A PlannedActivity could also be thought of as an activity at a particular stage in the business process in which the activities occur, i.e., in the "planned" stage rather than the "scheduled" stage or the "performed" stage. An instance of a PlannedActivity is not assigned to a particular Subject, StudySubject, or ExperimentalUnit, but to a "kind of" Subject, StudySubject, or ExperimentalUnit. Planned activity specification OCRE300012 study_protocol:OCRE300012 A discrete, structured plan (that persists over time) of a formal investigation to assess some outcome phenomena in relation to other study phenomena. DEFINITION: A discrete, structured plan (that persists over time) of a formal investigation to assess the utility, impact, pharmacological, physiological, and/or psychological effects of a particular treatment, procedure, drug, device, biologic, food product, cosmetic, care plan, or subject characteristic. NOTE(S): The term "protocol" is somewhat overloaded and must be qualified to provide semantic context.  Therefore the term "study protocol" was chosen to disambiguate it from other protocols. In previous versions of BRIDG, there was one class for StudyProtocol.  However this too represented multiple distinct aspects of the semantics of study protocol, each of which have now been split into separate classes: - The StudyProtocol class represents the content of the study protocol and can exist even before the information is put into document form. - The details of the structured plan for the study protocol are represented by the StudyProtocolVersion, so named because any aspect of the definition can change from version to version.  These details include, but are not limited to, the characteristics, specifications, objective(s), background, the pre-study/study/post-study portions of the plan (including the design, methodology, statistical considerations, organization). - The protocol and its versions can each be represented in document form, respectively StudyProtocolDocument and StudyProtocolDocumentVersion.  A StudyProtocolDocument groups the various document versions (StudyProtocolDocumentVersions). - The conduct of a study based on a study protocol definition is represented by the StudyExecution class. BRIDG 3.0.3 Available at http://bridgmodel.nci.nih.gov/ Previous definition: An action plan for a pre-clinical or clinical study which defines all activities planned to achieve the objectives of the study. The plan specifies, for example, the design of the study, including the subject to be included, the outcome to be studied, data to be collected, and method of analysis. A study protocol is an informational entity that is ontologically distinct from events that occur as part of the study. BRIDG Release 2.2 definition: An action plan for a formal investigation to assess the utility, impact, pharmacological, physiological, and psychological effects of a particular treatment, procedure, drug, device, biologic, food product, cosmetic, care plan, or subject characteristic. Note: Among other things, the action plan may include the design, statistical considerations and all activities to test a particular hypothesis that is the basis of the study. The study may be of any type that involves StudySubjects, including prevention, therapeutic, interventional or observational. Subjects may be biological entities (human, animal, specimen, tissue, organ, etc.) or products. Simona Study protocol OCRE300015 The description of a collection of activities that are intended to occur or start for the same study subject at a specific point in the context of a particular study. EXAMPLE(S): Clinic visit during which a physical exam, a blood test, and a substance administration occur Telephone contact during which temperature, blood pressure and adverse events are reported Recording multiple observation results in a diary A treatment strategy that consists of drug administrations with rules for modifying doses Adapted from BRIDG 3.1 definition of PlannedSubjectActivityGroup. Cf BRIDG 3.1 PlannedSubjectActivityGroup DEFINITION: A collection of activities that are intended to occur or start for the same study subject at a specific point in the context of a particular study. EXAMPLE(S): Clinic visit during which a physical exam, a blood test, and a substance administration occur Telephone contact during which temperature, blood pressure and adverse events are reported Recording multiple observation results in a diary A treatment strategy that consists of drug administrations with rules for modifying doses OTHER NAME(S): visit, time point, study segment, course, treatment strategy, period, cycle NOTE(S): Planned subject activity group specification OCRE307000 study_protocol:OCRE307000 DEFINITION: A physical entity which is the primary unit of interest in a specific research objective. In an interventional study, the experimental unit is assigned to an intervention. The experimental unit is also the unit of primary statistical analysis. Commonly the individual study subject (animal, person or product) is the experimental unit. Different experimental units must be capable of receiving different experimental interventions. EXAMPLE(S): If all pigs in a pen receive the same intervention in their feed, and the primary observations and analyses of interest are associated with the entire pen (e.g. total feed consumed, total weight of all pigs combined), then the pen of pigs rather than the individual animal is the experimental unit. [CDISC/HL7 Study Participation RMIM, PORT_RM100001UV] A human StudySubject may have 10 patches of skin each considered an ExperimentalUnit, or a Product StudySubject may have 10 bearings in it, each considered an ExperimentalUnit.  Alternatively, each StudySubject may be an ExperimentalUnit. OTHER NAME(S): NOTE(S): Depending on the research objectives, a single study may have multiple levels of experimental units, such as whole people and patches of skin. Simona BRIDG 3.0.3 Available at http://bridgmodel.nci.nih.gov/ ExperimentalUnit OCRE817858 The description of a planned procedure that is an action of applying, introducing, or otherwise giving medication or other substance to a subject or experimental unit. Samson Tu Adapted from BRIDG 3.1 definition of DefinedSubstanceAdministration. Available at http://bridgmodel.nci.nih.gov/ Cf BRIDG 3.1 DefinedSubstanceAdministration definition An activity defined at a global library level that is an action of applying, introducing or otherwise giving medications or other substances to a subject or experimental unit. Example: Administration of methotrexate as part of chemotherapy. Planned substance administration specification OCRE892807 study_protocol:OCRE892807 Intervention study protocol fma3:OCRE9000027 A material anatomical entity is a physical anatomical entity which has mass. Examples: hemoglobin molecule, mitochondrion, hepatocyte, erythrocyte, heart, head, blood, urine. Simona Foundational Model of Anatomy (FMA) class definition of Material anatomical entity. Available at http://bioportal.bioontology.org/visualize/44507 Material anatomical entity oboInOwl:DbXref oboInOwl:Definition oboInOwl:Subset oboInOwl:Synonym oboInOwl:SynonymType snap:GenericallyDependentContinuant A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time. http://biomedgt.nci.nih.gov/wiki/index.php/Category:BFO_generically_dependent_continuant(GenericallyDependentContinuant) GeneriallyDependentContinuant owl:Thing Thing example to be eventually removed The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg 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 definition editor. pending final vetting Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot core placeholder removed An editor note should explain what were the merged terms and the reason for the merge. terms merged This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. We expect to be able to mine these new reasons and add instances as required. other Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal Alan Ruttenberg 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 expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI 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. Alan Ruttenberg group:OBI requires discussion NOT most recent Equals Greater than Less than first start stop time of secondary http mailto tel x-text-fax Biospecimen availability NA Biospecimen available Biospecimen not available primary AND OR $Revision$ Revision 315 en $Revision$ An ontology for the planning, execution and analysis of clinical research including logitudinal studies and clinical trials. This is designed to be used in conjunction with domain specific models of diseases and measurements which conform to the shared ontology of clinical concepts to provide specific models of studies and trials. Revision 315 An ontology of objects and relationships in statistics that are useful for describing statistical analysis used in human studies. It is part of the Ontology for Clinical Research (OCRe). An ontology of study design descriptors and categorization of study design types in terms of their design descriptors. Concept imported from BRIDG that related to the defined activities and schedules of a study protocol.