Natasha Karp (WTSI) and Helen Parkinson (EBI), on behalf of the KOMP2 partners, and IMPC. 1.0 definition_editor definition deprecated_from_version xref reason_for_obsolesence definition editor reason for obsolesence xref definition medo:MEDO_0000001 A description of the genetic background of the animals used as controls. control mouse genetic background medo:MEDO_0000002 B6Brd;B6N-Tyr<c-Brd> medo:MEDO_0000003 C57BL/6J-Tyr<c-Brd>;C57BL/6N medo:MEDO_0000004 C57BL/6N medo:MEDO_0000005 C57BL/6NCrl medo:MEDO_0000006 C57BL/6NTac medo:MEDO_0000007 Jax Stock 5304 C57BL/6NJ medo:MEDO_0000008 The organization from which the core animal colony was obtained, may be distinct from the production location. This class will be extended as new locations are added. core colony source medo:MEDO_0000009 Baylor College of Medicine medo:MEDO_0000010 MRC Harwell medo:MEDO_0000011 Wellcome Trust Sanger Institute medo:MEDO_0000012 The processes by which mouse phenotyping experimental design control for sources of bias. mouse phenotyping experimental design strategy medo:MEDO_0000019 The process by which experimental design determines the knowledge of the operator about the subjects. The blinding strategy describes whether the person performing the procedure (analysis, phenotyping etc) has access to the experiment design information. In a mouse phenotyping experiment this includes genotype and allele information. Blinding is performed on a per test basis. Where possible, experiments should be performed “blind” with respect to the treatments, particularly for tests with outcomes dependent on personal judgement. Ie. Providing the mice are not visually different, the operator should not know which is the knockout and which is the control mouse. If you are not running controls, this question is still relevant; the operator should not know the specific details of the knockout. This includes both the genotype and the allele. blinding strategy medo:MEDO_0000020 A process in which the person performing the procedure has access to the allele, but not the genotype information. allele free blinding medo:MEDO_0000021 A process in which the person performing the phenotyping does not have access to either genotype or allele information. blinded medo:MEDO_0000022 A process in which the person performing the procedure knows the genotype information but not the allele information of the subject being phenotyped. genotype free blinding medo:MEDO_0000023 A process in which the experiment is run with no blinding, i.e. both genotype and allele are visible to the person performing the phenotyping procedure. unblinded medo:MEDO_0000024 The process by which animals are grouped into batches for phenotyping. Usually a batch is a group processed on a single day. batch processing strategy medo:MEDO_0000027 The process by which animals were assigned to a batch where animals in a batch are mixed sex, male and female single batch mixed sex medo:MEDO_0000028 The process by which animals are assigned to a single batch per sex, i.e. all animals of the same sex were processed as a group. single batch per sex medo:MEDO_0000033 The control design process in a mouse phenotyping experiment describing which controls are used as a baseline to measure phenotypic variations. control design medo:MEDO_0000034 The process of using control wild type mice that are generated from a breeding programme of HET*HET or HET*WT crosses used to generate the mutant of interest. line mate control medo:MEDO_0000035 The process of using WT mice that are true siblings and hence were generated from a HET*HET, or a HET*WT cross that generated the mutant of interest. If HET mice are the controls, the control mice are true siblings from a HOM*HET or a HET*HET cross that generated the mutant of interest. littermate control medo:MEDO_0000036 The process of using WT mice from HET*HET or HET*WT breeding that generate mutant mice. This can be from matings that generate a variety of KO alelles all of which are on the same genetic background. pooled genetic control medo:MEDO_0000037 A process where WT mice from a breeding colony of the same genetic background is used. production colony control medo:MEDO_0000038 The organization at which the control animal was produced. This class will be extended as new locations are added. control mouse production location medo:MEDO_0000039 The process by which control stocks are managed to avoid genetic drift and maintaining the start genotype. control stock management medo:MEDO_0000040 The process of refreshing the core nucleus/pedigree at a set generational point e.g. by 10 generations and subsequent cryopreservation. control breeding medo:MEDO_0000041 The process by which controls are outsourced and new animals are acquired. externally managed control medo:MEDO_0000042 The process of managing control stocks is uncontrolled. uncontrolled stock management medo:MEDO_0000043 The process by which the core colony is sourced e.g. internally or externally acquired. core colony provider medo:MEDO_0000044 The core colony is provided from some external source externally sourced medo:MEDO_0000045 The core colony is internally sourced. internally sourced medo:MEDO_0000046 The process of controlling and managing instrumentation bias per test, for example in control only a single instrument is used per institute for DEXA instrumentation bias management medo:MEDO_0000047 The process by which instrument differences are managed by randomly assigning the subjects, processed within a defined time frame of one day, to the different instruments using a randomisation technique (e.g. alternate allocation or odd or even last digit of sample number). Steps are also taken to minimise the potential effect of differences in instrumentation e.g. calibration of scales between instruments. active randomisation and minimisation instrumentation strategy medo:MEDO_0000048 The process by which instrumentation differences are actively managed by randomly assigning subjects (e.g. mice), processing these in a defined time frame of 24 hours, with assignment managed by a randomisation technique such as alternate allocation, or odd/even last digit sample number allocation. active randomisation instrumentation strategy medo:MEDO_0000049 The process by which instrument effects are manged. Instrument effects will affect subjects (e.g. mice) equally as equal numbers of the control and knockout mice are processed by a specific instrument. Steps are also taken to minimise the potential effect of differences in instrumentation e.g. calibration of scales. balanced and minimisation instrumentation strategy medo:MEDO_0000050 The process by which instrument effects affecting the ‘local’ subjects are managed. These affect the local subjects (e.g. control and knockout mice) equally as equal numbers of subjects of different genotypes are processed by a specific instrument. balanced instrumentation strategy medo:MEDO_0000051 The process by which instrument differences are managed by randomly assigning subjects, processed within a defined time frame of 24h, to the different instruments using an operator to randomly place the mice. Steps are also taken to minimise the potential effect of differences in instrumentation e.g. calibration of scales. casual randomisation and minimisation instrumentation strategy medo:MEDO_0000052 The process by which instrument differences are managed by randomly assigning the subjects, processed within a defined time frame of 24h, to the different instruments using an operator to randomly place the mice. casual randomisation instrumentation strategy medo:MEDO_0000053 The process by which instrumentation effects are minimised as the same instrument is used for all subjects. controlled instrumentation strategy medo:MEDO_0000054 The process by which steps are taken to minimise the potential effect of differences in instrumentation e.g. calibration of scales. minimisation instrumentation strategy medo:MEDO_0000059 The process by which operator effects are controlled operator effect control strategy medo:MEDO_0000060 The process by which operator effect is controlled actively. Operator effects will affect the ‘local’ control (controls collected at same time) and experimental siubjects equally as these are randomly assigned to an operator using a randomisation technique (e.g. alternate allocation or odd or even last digit of sample number). active operator randomisation medo:MEDO_0000061 The process by which operator effects are controlled by randomisation and minimisation. Operator effects will affect the ‘local’ control (controls collected at same time) and knockout subjects equally as the control and knockouts are randomly assigned to an operator using a randomisation technique (e.g. alternate allocation or odd or even last digit of sample number). Steps are also taken to minimise the potential differences in the effector by training and monitoring of operator. active operator randomisation and minimisation medo:MEDO_0000062 The process by which equal numbers of control and experimental subjects are run. Operator effects will affect the ‘local’ control (controls collected at same time) and knockout subjects equally in this scenario. balanced operator medo:MEDO_0000063 The process by which steps are taken to minimise the potential differences in the effector by training and monitoring of operator. minimized operator medo:MEDO_0000064 The process by which order effects are managed. Ideally observations collected for a test on a day are recorded in a random order. This is to avoid potential order effects. For example in annotation an operator might become less stringent with time or within a day an instrument might drift in its base value. The randomisation is to avoid an unexpected experimental effect becoming associated with the genotype difference of interest. order effect control strategy medo:MEDO_0000065 The process by which order effects a controlled with a batch as alternate wildtype and knockout are processed alternate mouse order medo:MEDO_0000066 A process in which the order of the cages selected for processing (where a cage houses mice of one genotype or one mouse) is actively randomised by the use of a randomisation technique (e.g. alternate cage or odd or even last digit of cage number). cage active randomisation medo:MEDO_0000067 A process in which on a given day, the order of the cage (where a cage houses mice of one genotype or one mouse) is casually randomised by the operator selecting the cage randomly from those being processed in the day. cage casual randomisation medo:MEDO_0000068 The process by which subject selection strategies are used to minimise selection effects. subject selection strategy medo:MEDO_0000069 The process by which subjects are seleted subject to timetabling constraints such as availabiility of personnel and equipment. active selection strategy medo:MEDO_0000070 The process by which the first subjects available from the production pipeline are processed first. first subject availability strategy medo:MEDO_0000071 The process by which subjects are selected using a randomisation technique. passive subject selection strategy medo:MEDO_0000072 The process by which time effects are managed time effect strategy medo:MEDO_0000073 The process by which local control and knockout mice are consistently processed within a day per procedure. controlled time effect medo:MEDO_0000074 The process by which the controls are batched for phenotyping. For example, with knockouts, weekly, biweekly etc. control phenotyping design medo:MEDO_0000076 The process of running control phenotyping concurrently with knockouts. parallel control with knockout medo:MEDO_0000077 A process where control subjects are run biweekly biweekly control medo:MEDO_0000078 The process by which controls are run at some predetermined time interval e.g. weekly regular control medo:MEDO_0000079 A process where controls are processed monthly monthly control medo:MEDO_0000080 A process where controls are run weekly weekly control medo:MEDO_0000081 The process by which the mouse generation is designed and managed, for example how controls are selected (each organisation's definition of a control.) mouse production medo:MEDO_0000082 The process by which the knockouts are batched for phenotyping. For example one batch per sex etc. knockout phenotyping design medo:MEDO_0000083 The process by which animals are grouped into multiple batches for an allele, for example, seven mice are processed in three independent batches in time. multiple batch medo:MEDO_0000084 The process of grouping animals for phenotyping, in a single batch per sex, or a single batch mixed sex. In practice a phenotyping centre may use both these strategies. single batch medo:MEDO_0000085 The process by which animals are assigned to single, or multiple batches for an allele. Typically used when a single batch is preferred but for some alleles breeding issues prevent this and a a mixed single or multiple batch approach is then used. variable batch medo:MEDO_0000086 The process by which systematic bias is addressed. There is a need to minimise systematic bias, where the difference between the knockout and the control arises not from the genotype difference but from some experimental difference that correlates with the genotype difference. An example of workflow allowing potential systematic differences would occur if different operators performed the same test differently and all the control data were collected by one of the operators whilst the knockouts were collected by a different operator. Another example of how systematic difference can arise is when an institute has multiple machines for collecting data and all the controls are run on one machine whilst all the knockouts are run on a second machine. If you are not running controls, these questions are still relevant, as you will need to avoid systematic bias being associated with a particular knockout line. bias reduction management medo:MEDO_0000087 The process of minimisation of the potential differences in the effector by training and monitoring of operator and operator effects will affect the ‘local’ control (controls collected at same time) and knockout subjects equally as equal numbers of the control and knockout subjects are processed by an operator for a process. balanced operator and minimisation medo:MEDO_0000088 The process of using a single operator per test per allele. single operator medo:MEDO_0000089 An information entity is an entity that represents information about some other entity. For example, a measurement, a clustered data set, a description of a mouse strain. http://purl.obolibrary.org/obo/IAO_0000030 organisational class information medo:MEDO_0000090 A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray a mouse liver. http://www.ifomis.org/bfo/1.1/snap#MaterialEntity organisational class material medo:MEDO_0000091 A material entity is a property or characteristic of some other entity. For example, the mouse has the coat colour black. http://www.ifomis.org/bfo/1.1/snap#SpecificallyDependentContinuant organisational class material property medo:MEDO_0000092 A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs. http://www.ifomis.org/bfo/1.1/span#ProcessualEntity organisational class process medo:MEDO_0000093 A process where the the local control and knockout mice are not consistently processed within a day for a single procedure. uncontrolled time effect medo:MEDO_0000094 A process where control and knockout subjects are processed over multiple days using an alternate control and knockout scheme. randomised time effect MEDO_0000073 University of California Davis MEDO_0000094 Controls are run at regular intervals determined by the availability of knockout animals for a phenotyping experiment. regular control with phenotyping run MEDO_0000095 The Jackson Laboratory MEDO_0000097 A batch process where for an allele either a both sexes are phenotyped together, or separately depending on availability of knockout animals. single batch mixed MEDO_0000099 On a day the order of mice from a cage (where a cage houses a mixture of genotypes for an allele +/-, +/+ -/-) is casually randomised for genotype prior to phenotyping.( Used in scenarios where low throughput means controls and knocks are phenotyped in similar volumes, often on the same day). casual randomisation within a cage MEDO_0000100 The local controls and knockout animals are not consistently processed on the same day per procedure. uncontrolled time effect 1.0 Natasha Karp (WTSI) and Helen Parkinson (EBI), on behalf of the KOMP2 partners, and IMPC. 1.0