Term IRI Term label Parent term IRI Parent term label Alternative term Definition
http://purl.obolibrary.org/obo/OBCS_0000144 R squared value http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value coefficient of determination A quantitative confidence value that indicates how well data points fit a statistical model - sometimes simply a line or curve. It is a statistic used in the context of statistical models whose main purpose is either the prediction of future outcomes or the testing of hypotheses, on the basis of other related information. It provides a measure of how well observed outcomes are replicated by the model, as the proportion of total variation of outcomes explained by the model.
http://purl.obolibrary.org/obo/OBI_0001970 multiplexed sequencing library http://purl.obolibrary.org/obo/OBI_0000047 processed material DNA-barcoded sequencing library a multiplexed library is a material entity which is the output of a library preparation process that uses a ligation step to attach a unique multiplexing sequence identifier to a specific sample, then mixes several such tagged samples prior to the library amplification process proper. A multiplexed library allows the sequencing of several samples in one sequencing run.
http://purl.obolibrary.org/obo/IAO_0000005 objective specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity goal specification a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
http://purl.obolibrary.org/obo/IAO_0000027 data item http://purl.obolibrary.org/obo/IAO_0000030 information content entity data a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
http://purl.obolibrary.org/obo/IAO_0000100 data set http://purl.obolibrary.org/obo/IAO_0000027 data item data list A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
http://purl.obolibrary.org/obo/IAO_0000184 scatter plot http://purl.obolibrary.org/obo/IAO_0000038 graph scattergraph A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
http://purl.obolibrary.org/obo/IAO_0000300 textual entity http://purl.obolibrary.org/obo/IAO_0000030 information content entity text A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
http://purl.obolibrary.org/obo/IAO_0000573 line graph http://purl.obolibrary.org/obo/IAO_0000038 graph line chart A line graph is a type of graph created by connecting a series of data
points together with a line.
http://purl.obolibrary.org/obo/IAO_0000579 centrally registered identifier registry http://purl.obolibrary.org/obo/IAO_0000100 data set CRID registry A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
http://purl.obolibrary.org/obo/IAO_0000584 time sampled measurement data set http://purl.obolibrary.org/obo/IAO_0000100 data set experimental time series A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
http://purl.obolibrary.org/obo/OBI_0000023 classified data set http://purl.obolibrary.org/obo/OBCS_0000220 derived data from inferential statistical analysis data set with assigned class labels A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels.
http://purl.obolibrary.org/obo/OBI_0000070 assay http://purl.obolibrary.org/obo/OBI_0000011 planned process scientific observation A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
http://purl.obolibrary.org/obo/OBI_0000086 reagent role http://purl.obolibrary.org/obo/BFO_0000023 role reagent A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
http://purl.obolibrary.org/obo/OBI_0000094 material processing http://purl.obolibrary.org/obo/OBI_0000011 planned process material transformation A planned process which results in physical changes in a specified input material
http://purl.obolibrary.org/obo/OBI_0000392 information processor function http://purl.obolibrary.org/obo/BFO_0000034 function data processor function An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process.
http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification artifact creation objective an objective specifiction that creates an specific output object from input materials.
http://purl.obolibrary.org/obo/OBI_0000648 clustered data set http://purl.obolibrary.org/obo/OBCS_0000220 derived data from inferential statistical analysis data set with assigned discovered class labels A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
http://purl.obolibrary.org/obo/OBI_0000658 data representational model http://purl.obolibrary.org/obo/OBCS_0000035 statistical model data structure specification Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax.
http://purl.obolibrary.org/obo/OBI_0000659 specimen collection process http://purl.obolibrary.org/obo/OBI_0000011 planned process specimen collection A planned process with the objective of collecting a specimen.
http://purl.obolibrary.org/obo/OBI_0000663 class prediction data transformation http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis supervised classification data transformation A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
http://purl.obolibrary.org/obo/OBI_0000674 center value http://purl.obolibrary.org/obo/OBCS_0000219 derived data from descriptive statistical analysis median A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
http://purl.obolibrary.org/obo/OBI_0000675 statistical hypothesis test objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective hypothesis test objective is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation
http://purl.obolibrary.org/obo/OBI_0000679 average value http://purl.obolibrary.org/obo/OBCS_0000219 derived data from descriptive statistical analysis mean A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
http://purl.obolibrary.org/obo/OBI_0000700 support vector machine http://purl.obolibrary.org/obo/OBI_0000663 class prediction data transformation SVM A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space.
http://purl.obolibrary.org/obo/OBI_0000701 self-organizing map http://purl.obolibrary.org/obo/OBI_0200175 class discovery data transformation SOM A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these.
http://purl.obolibrary.org/obo/OBI_0000711 library preparation http://purl.obolibrary.org/obo/OBI_0000094 material processing library construction is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors.
http://purl.obolibrary.org/obo/OBI_0000722 paired-end library http://purl.obolibrary.org/obo/OBI_0000047 processed material paired-end tag (PET) library is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
http://purl.obolibrary.org/obo/OBI_0000727 k-nearest neighbors http://purl.obolibrary.org/obo/OBI_0200175 class discovery data transformation k-NN A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned.
http://purl.obolibrary.org/obo/OBI_0000736 single fragment library http://purl.obolibrary.org/obo/OBI_0000047 processed material fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
http://purl.obolibrary.org/obo/OBI_0000749 CART http://purl.obolibrary.org/obo/OBI_0000707 decision tree building data transformation classification and regression trees A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
http://purl.obolibrary.org/obo/OBI_0000750 study design independent variable http://purl.obolibrary.org/obo/IAO_0000033 directive information entity independent variable a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
http://purl.obolibrary.org/obo/OBI_0000751 study design dependent variable http://purl.obolibrary.org/obo/IAO_0000033 directive information entity dependent variable dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies.
http://purl.obolibrary.org/obo/OBI_0000791 multiple testing correction objective http://purl.obolibrary.org/obo/OBI_0200186 error correction objective multiple comparison correction objective A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously
http://purl.obolibrary.org/obo/OBI_0000801 spike train datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum spike train measurement A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time.
http://purl.obolibrary.org/obo/OBI_0000938 categorical measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum nominal mesurement datum A measurement datum that is reported on a categorical scale
http://purl.obolibrary.org/obo/OBI_0000944 handedness assay http://purl.obolibrary.org/obo/OBI_0000070 assay handedness test A handedness assay measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure.
http://purl.obolibrary.org/obo/OBI_0000968 device http://purl.obolibrary.org/obo/OBI_0000047 processed material instrument A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
http://purl.obolibrary.org/obo/OBI_0000970 scalar score from composite inputs http://purl.obolibrary.org/obo/OBCS_0000233 transformed data item questionaire score A measurement datum which is the result of combining multiple datum. For example, a mean or summary score.
http://purl.obolibrary.org/obo/OBI_0001171 half life datum (t 1/2) http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum t 1/2 The time it takes for 50% of a class of stochastic processes to occur.
http://purl.obolibrary.org/obo/OBI_0001442 q-value http://purl.obolibrary.org/obo/OBI_0000662 error corrected data set FDR adjusted p-value A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant.
To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level.
http://purl.obolibrary.org/obo/OBI_0001508 sampling time measurement datum http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum time point A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
http://purl.obolibrary.org/obo/OBI_0001566 50% dissociation of binding temperature (Tm) http://purl.obolibrary.org/obo/OBI_0001181 binding datum melting temperature (Tm) A binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound.
http://purl.obolibrary.org/obo/OBI_0001619 specimen collection time measurement datum http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum collection date A time measurement datum that is the measure of the time when the specimens are collected.
http://purl.obolibrary.org/obo/OBI_0001620 latitude coordinate measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum latitude A measurement datum that is the measure of the latitude coordinate of a site.
http://purl.obolibrary.org/obo/OBI_0001621 longitude coordinate measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum longitude A measurement datum that is the measure of the longitude coordinate of a site.
http://purl.obolibrary.org/obo/OBI_0001877 random access memory http://purl.obolibrary.org/obo/IAO_0000178 material information bearer RAM Random-access memory (RAM) is a form of computer data storage. A random-access device allows stored data to be accessed directly in any random order. In contrast, other data storage media such as hard disks, CDs, DVDs and magnetic tape, as well as early primary memory types such as drum memory, read and write data only in a predetermined order, consecutively, because of mechanical design limitations. Therefore, the time to access a given data location varies significantly depending on its physical location
http://purl.obolibrary.org/obo/OBI_0001908 testable hypothesis http://purl.obolibrary.org/obo/IAO_0000030 information content entity hypothesis An information content entity that expresses an assertion that is intended to be tested.
http://purl.obolibrary.org/obo/OBI_0001913 computation run time http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum computation run time datum computation run time is a time measurement datum which corresponds the time expressed in second, minute, hour necessary for a computer program to complete a process execution, for example genome assembly. It is an important metrics as it indicates the resource occupancy and computer program efficiency.
http://purl.obolibrary.org/obo/OBI_0001940 N50 http://purl.obolibrary.org/obo/OBCS_0000233 transformed data item weighted median item size the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly
http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://purl.obolibrary.org/obo/OBI_0000011 planned process data operation A planned process that produces output data from input data.
http://purl.obolibrary.org/obo/OBI_0200022 variance stabilizing transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation variance stabilising transformation A variance stabilizing transformation is a data transformation, described in PMID 12169536, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (6) in this paper. One of the goals is to obtain an output matrix whose rows have equal variances. The method relies on various assumptions described in the paper.
http://purl.obolibrary.org/obo/OBI_0200029 mean centering http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation mean centring A mean centering is a data transformation that takes as input an n-dimensional (real) vector, performs a mean calculation on its components, and subtracts the resulting mean from each component of the input.
http://purl.obolibrary.org/obo/OBI_0200030 median centering http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation median centring A median centering is a data transformation that takes as input an n-dimensional (real) vector, performs a median calculation on its components, and subtracts the resulting median from each component of the input.
http://purl.obolibrary.org/obo/OBI_0200034 jackknifing method http://purl.obolibrary.org/obo/OBI_0000792 statistical model validation jackknifing Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method
http://purl.obolibrary.org/obo/OBI_0200050 dimensionality reduction http://purl.obolibrary.org/obo/OBI_0200175 class discovery data transformation data projection A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m.
http://purl.obolibrary.org/obo/OBI_0200051 principal components analysis dimensionality reduction http://purl.obolibrary.org/obo/OBI_0200050 dimensionality reduction pca data reduction A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones.
http://purl.obolibrary.org/obo/OBI_0200064 centroid mass spectrum http://purl.obolibrary.org/obo/OBI_0200085 mass spectrometry analysis centroiding A centroid mass spectrum is a data transformation in which many points are used to delineate a mass spectral peak, is converted into mass-centroided data by a data compression algorithm. The centroided mass peak is located at the weighted center of mass of the profile peak. The normalized area of the peak provides the mass intensity data.
http://purl.obolibrary.org/obo/OBI_0200073 family wise error rate correction method http://purl.obolibrary.org/obo/OBI_0200089 multiple testing correction method FWER correction A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive.
http://purl.obolibrary.org/obo/OBI_0200080 network analysis http://purl.obolibrary.org/obo/OBI_0200000 data transformation network topology analysis A data transformation that takes as input data that describes biological networks in terms of the node (a.k.a. vertex) and edge graph elements and their characteristics and generates as output properties of the constituent nodes and edges, the sub-graphs, and the entire network.
http://purl.obolibrary.org/obo/OBI_0200082 longitudinal data analysis http://purl.obolibrary.org/obo/OBI_0200000 data transformation longitudinal data analysis Longitudinal analysis is a data transformation used to perform repeated observations of the same items over long periods of time.
http://purl.obolibrary.org/obo/OBI_0200083 survival analysis objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective survival analysis A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables
http://purl.obolibrary.org/obo/OBI_0200089 multiple testing correction method http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis multiple testing procedure A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate
http://purl.obolibrary.org/obo/OBI_0200091 inter-rater reliability objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective inter-rater agreement a data transformation objective of determining the concordance or agreement between human judges.
http://purl.obolibrary.org/obo/OBI_0200092 Westfall and Young family wise error rate correction http://purl.obolibrary.org/obo/OBI_0200073 family wise error rate correction method Westfall and Young FWER correction Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing
http://purl.obolibrary.org/obo/OBI_0200098 soft independent modeling of class analogy analysis http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation SIMCA Soft independent modeling by class analogy (SIMCA) is a descriptive statistics method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes.
http://purl.obolibrary.org/obo/OBI_0200100 canonical variate analysis http://purl.obolibrary.org/obo/OBI_0200171 partitioning data transformation CVA canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form.
http://purl.obolibrary.org/obo/OBI_0200105 partial least square regression analysis http://purl.obolibrary.org/obo/OBI_0200102 regression analysis method PLS-RA Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that
Y = b0 + b1X1 + b2X2 + ... + bpXp
In this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data.
http://purl.obolibrary.org/obo/OBI_0200107 partial least square discriminant analysis http://purl.obolibrary.org/obo/OBI_0200106 discriminant analysis PLS-DA PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information.
http://purl.obolibrary.org/obo/OBI_0200111 data visualization http://purl.obolibrary.org/obo/OBI_0000011 planned process visualization An planned process that creates images, diagrams or animations from the input data.
http://purl.obolibrary.org/obo/OBI_0200125 data combination http://purl.obolibrary.org/obo/OBI_0200000 data transformation data pooling A data transformation in which individual input data elements and values are merged together into a output set of data elements and values.
http://purl.obolibrary.org/obo/OBI_0200141 log base http://purl.obolibrary.org/obo/OBI_0200140 mathematical feature logarithmic base The log base is a feature of a logarithmic function which is defined in http://en.wikipedia.org/wiki/Logarithm. Its value can be any positive real number different from 1.
http://purl.obolibrary.org/obo/OBI_0200149 unit-variance scaling http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation autoscaling A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable.
http://purl.obolibrary.org/obo/OBI_0200154 agglomerative hierarchical clustering http://purl.obolibrary.org/obo/OBI_0200042 hierarchical clustering bottom-up hierarchical clustering An agglomerative hierarchical clustering is a hierarchical clustering which starts with separate clusters and then successively combines these clusters until there is only one cluster remaining.
http://purl.obolibrary.org/obo/OBI_0200155 divisive hierarchical clustering http://purl.obolibrary.org/obo/OBI_0200042 hierarchical clustering top-down hierarchical clustering A divisive hierarchical clustering is a hierarchical clustering which starts with a single cluster and then successively splits resulting clusters until only clusters of individual objects remain.
http://purl.obolibrary.org/obo/OBI_0200160 generalized family wise error rate correction method http://purl.obolibrary.org/obo/OBI_0200089 multiple testing correction method gFWER correction A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer.
http://purl.obolibrary.org/obo/OBI_0200161 quantile number of false positives correction method http://purl.obolibrary.org/obo/OBI_0200089 multiple testing correction method QNFP A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed'
http://purl.obolibrary.org/obo/OBI_0200162 tail probability for the proportion of false positives correction method http://purl.obolibrary.org/obo/OBI_0200089 multiple testing correction method TPPFP correction method A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1.
http://purl.obolibrary.org/obo/OBI_0200163 false discovery rate correction method http://purl.obolibrary.org/obo/OBI_0200089 multiple testing correction method FDR correction method The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. .
http://purl.obolibrary.org/obo/OBI_0200164 proportion of expected false positives correction method http://purl.obolibrary.org/obo/OBI_0200089 multiple testing correction method PEFP correction method A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses.
http://purl.obolibrary.org/obo/OBI_0200165 quantile proportion of false positives correction method http://purl.obolibrary.org/obo/OBI_0200089 multiple testing correction method QPFP correction method A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate).
http://purl.obolibrary.org/obo/OBI_0200175 class discovery data transformation http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis unsupervised classification data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
http://purl.obolibrary.org/obo/OBI_0200178 class discovery objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective unsupervised classification objective A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
http://purl.obolibrary.org/obo/OBI_0200179 class prediction objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective supervised classification objective A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and
class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data.
http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation http://purl.obolibrary.org/obo/OBCS_0000001 statistical data analysis descriptive statistical data analysis A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
http://purl.obolibrary.org/obo/OBI_0200188 cross validation objective http://purl.obolibrary.org/obo/OBI_0200172 partitioning objective rotation estimation objective A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis.
http://purl.obolibrary.org/obo/OBI_0200189 merging objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective combining objective A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets.
http://purl.obolibrary.org/obo/OBI_0200195 proportional hazards model estimation http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis Cox proportional hazards model Proportional hazards model is a data transformation model to estimate the effects of different covariates influencing the times-to-failure of a system.
http://purl.obolibrary.org/obo/OBI_0500000 study design http://purl.obolibrary.org/obo/IAO_0000104 plan specification experimental design A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
http://purl.obolibrary.org/obo/OBI_0600015 group assignment http://purl.obolibrary.org/obo/OBI_0000011 planned process study assignment group assignment is a process which has an organism as specified input and during which a role is assigned
http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation http://purl.obolibrary.org/obo/OBI_0000094 material processing genetic modification the introduction. alteration or integration of genetic material into a cell or organism
http://purl.obolibrary.org/obo/OBI_0600064 recombinant vector cloning http://purl.obolibrary.org/obo/OBI_0000094 material processing molecular cloning a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material
http://purl.obolibrary.org/obo/OBI_1000029 phage display library http://purl.obolibrary.org/obo/OBI_0000731 recombinant vector display library a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified.
http://purl.obolibrary.org/obo/SO_0000001 region http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant sequence A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
http://purl.obolibrary.org/obo/OBCS_0000003 F distribution http://purl.obolibrary.org/obo/OBCS_0000066 continuous probability distribution Fisher-Snedecor distribution A continuous probability distribution that is associated with the f statistic.
http://purl.obolibrary.org/obo/OBCS_0000005 normal distribution http://purl.obolibrary.org/obo/OBCS_0000066 continuous probability distribution Gaussian distribution A continuous probability distribution that has a symmetrical curve, whose position and shape is determined by its location and scale parameters, the mean and standard deviation respectively.
http://purl.obolibrary.org/obo/OBCS_0000006 Student's t distribution http://purl.obolibrary.org/obo/OBCS_0000066 continuous probability distribution t-distribution A continuous probability distribution that is is used to estimate population parameters when the sample size is small and/or when the population variance is unknown.
http://purl.obolibrary.org/obo/OBCS_0000007 bivariate normal distribution http://purl.obolibrary.org/obo/OBCS_0000066 continuous probability distribution bivariate normality A continuous probability distribution of two variables that has the traditional bell shape and the distribution of one variable is normal to each and every value of the other variable.
http://purl.obolibrary.org/obo/OBCS_0000008 log-normal distribution http://purl.obolibrary.org/obo/OBCS_0000066 continuous probability distribution log normal, lognormal A continuous probability that is the distribution of a random variable X if ln(X) is normally distributed
http://purl.obolibrary.org/obo/OBCS_0000011 measurement scale http://purl.obolibrary.org/obo/IAO_0000030 information content entity scale of measure An information content entity that represents a type of scale on which a variable is measured, including nominal, ordinal, interval, ratio.
http://purl.obolibrary.org/obo/OBCS_0000017 cohen's kappa measurement http://purl.obolibrary.org/obo/OBCS_0000109 kappa statistic inter-rater agreement, inter-annotator agreement A statistical measure of agreement for categorical data; a measure of inter-rater agreement or inter-annotator agreement.
http://purl.obolibrary.org/obo/OBCS_0000022 multilevel model http://purl.obolibrary.org/obo/OBCS_0000035 statistical model hierarchical models A statistical model of parameters that vary at more than one level; a type of regression model that explicitly takes into account structured/nested data
http://purl.obolibrary.org/obo/OBCS_0000028 data collapsing http://purl.obolibrary.org/obo/OBI_0200000 data transformation bracketing, grouping A data transformation that combines categories or ranges of values to produce a smaller number of categories
http://purl.obolibrary.org/obo/OBCS_0000031 kolmogorov-smirnov two sample test http://purl.obolibrary.org/obo/OBCS_0000025 univariate analysis Kolmogorov-Smirnov An univariate nonparametric test for the equality of continuous, one-dimensional probability distributions that can be used to compare a sample with a reference probability distribution (one-sample K鈥揝 test), or to compare two samples (two-sample K鈥揝 test).
http://purl.obolibrary.org/obo/OBCS_0000035 statistical model http://purl.obolibrary.org/obo/IAO_0000033 directive information entity model A directive information entity that represents a mathematical relationship which relates changes in a given response to changes in one or more factors. A statistical model is a formalization of relationships between variables in the form of mathematical equations.
http://purl.obolibrary.org/obo/OBCS_0000036 partitioning of variance components http://purl.obolibrary.org/obo/OBI_0200000 data transformation variance components Partitioning of the overall variation into assignable components
http://purl.obolibrary.org/obo/OBCS_0000037 statistical effect http://purl.obolibrary.org/obo/IAO_0000033 directive information entity effect A directive information entity that shows how changing the settings of a factor changes the response. The effect of a single factor is also called a main effect.
http://purl.obolibrary.org/obo/OBCS_0000038 statistical variable http://purl.obolibrary.org/obo/IAO_0000033 directive information entity variable A directive information entity that specifies a data item that can be measured or counted and is used in a statistical analysis.
http://purl.obolibrary.org/obo/OBCS_0000039 confounding variable specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity confounders A variable specification that specifies a variable that may have a causal impact on both the independent variable and dependent variable; ignoring a confounding variable may bias empirical estimates of the causal effect of the independent variable.
http://purl.obolibrary.org/obo/OBCS_0000040 covariate specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity covariate A variable specification that specifies a variable used in statistical analysis to correct, adjust, or modify the values of a dependent variable; an independent variable not manipulated by the investigator
http://purl.obolibrary.org/obo/OBCS_0000041 dichotomous variable specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity dichotomous variable A variable that has only two categories.
http://purl.obolibrary.org/obo/OBCS_0000043 intervening variable specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity intervening variable, mediating variable A variable postulated to be a predictor of one or more dependent variables, and simultaneously predicted by one or more independent variables
http://purl.obolibrary.org/obo/OBCS_0000050 censored data http://purl.obolibrary.org/obo/IAO_0000027 data item censoring A data item collected from censoring that the value of a measurement or observation is only partially known.
http://purl.obolibrary.org/obo/OBCS_0000052 Incidence rate http://purl.obolibrary.org/obo/OBCS_0000220 derived data from inferential statistical analysis incidence A data item that refers to the number of new events that have occurred in a specific time interval divided by the population at risk at the beginning of the time interval. The result gives the likelihood of developing an event in that time interval.
http://purl.obolibrary.org/obo/OBCS_0000055 prevalence rate http://purl.obolibrary.org/obo/OBCS_0000220 derived data from inferential statistical analysis prevalence A data item that refers to the number of individuals with a given disease at a given point in time divided by the population at risk at a specified point in time or over a specified period of time.
http://purl.obolibrary.org/obo/OBCS_0000062 data sampling design http://purl.obolibrary.org/obo/OBCS_0000137 data collection design sampling plan A plan specification that provides a detailed outline of which measurements will be taken at what times, on which material, in what manner, and by whom. Sampling plans should be designed in such a way that the resulting data will contain a representative sample of the parameters of interest and allow for all questions, as stated in the goals, to be answered.
http://purl.obolibrary.org/obo/OBCS_0000078 type 1 error rate http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value false positive rate A quantitative confidence value that refers to the probability of incorrectly concluding that there is a statistically significant difference in a dataset. Alpha is the number after a p-value. Thus, a statistically significant difference reported as p<0.05 means that there is less than a 5 percent chance that the difference could have occurred by chance.
http://purl.obolibrary.org/obo/OBCS_0000079 type 2 error rate http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value false negative rate A quantitative confidence value that refers to the probability of incorrectly concluding that there was no statistically significant difference in a dataset. This error often reflects insufficient power of the study.
http://purl.obolibrary.org/obo/OBCS_0000081 coefficient of variation http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value variation coefficient A quantitative confidence value that is the standard deviation of a data set divided by the mean of the same data set; a normalized measure of dispersion of a probability distribution
http://purl.obolibrary.org/obo/OBCS_0000082 statistical error http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value error A quantitative confidence value that represents unexplained variation in a collection of observations; comopnents of error include random error and lack of fit error
http://purl.obolibrary.org/obo/OBCS_0000084 intraclass correlation coefficient http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value ICC A quantitative confidence value that is a descriptive statistic and can be used to describe how strongly units in the same group resemble each other; unlike other correlation measures it operates on data structured as groups, rather than data structured as paired observations.
http://purl.obolibrary.org/obo/OBCS_0000086 logit regression http://purl.obolibrary.org/obo/OBI_0200102 regression analysis method logistic regression A type of regression analysis used for predicting the outcome of a categorical dependent variable
http://purl.obolibrary.org/obo/OBCS_0000088 non-randomization sampling design http://purl.obolibrary.org/obo/OBCS_0000062 data sampling design non-randomization sampling plan A data sampling design that does not use randomization for sample selection
http://purl.obolibrary.org/obo/OBCS_0000089 randomization sampling design http://purl.obolibrary.org/obo/OBCS_0000062 data sampling design randomization sampling plan A data sampling design that uses randomization for sample selection
http://purl.obolibrary.org/obo/OBCS_0000097 interaction effect http://purl.obolibrary.org/obo/OBCS_0000037 statistical effect moderation A statistical effect that represents the role of a variable in an estimated model (most often a regression model) and its effect on the dependent variable. A variable that has an interaction effect will have a different effect on the dependent variable, depending on the level of some third variable.
http://purl.obolibrary.org/obo/OBCS_0000100 type I error http://purl.obolibrary.org/obo/OBCS_0000082 statistical error false positive A statistical error that the null hypothesis is true but has been rejected; a test result that indicates a given condition has been fulfilled, when it actually has not been fulfilled
http://purl.obolibrary.org/obo/OBCS_0000101 type II error http://purl.obolibrary.org/obo/OBCS_0000082 statistical error false negative A statistical error that the null hypothesis is false but has been accepted; a test result indicates that a condition failed, while it actually was successful.
http://purl.obolibrary.org/obo/OBCS_0000103 mann-whitney U test http://purl.obolibrary.org/obo/OBI_0000673 statistical hypothesis test Wilcoxon rank-sum test A non-parametric test of the null hypothesis that two populations are the same against an alternative hypothesis
http://purl.obolibrary.org/obo/OBCS_0000111 mediating variable http://purl.obolibrary.org/obo/OBCS_0000038 statistical variable mediating variable, mediation A statistical variable that specifies a variable describing how, rather than when, effects will occur by accounting for the relationship between the independent and dependent variables. A mediating relationship is one in which the path relating A to C is mediated by a third variable (B).
http://purl.obolibrary.org/obo/OBCS_0000112 moderator variable http://purl.obolibrary.org/obo/OBCS_0000038 statistical variable moderator, interaction A statistical variable that specifies a variable affecting the direction and/or strength of the relation between dependent and independent variables; occurs when the relationship between two variables depends on a third variable
http://purl.obolibrary.org/obo/OBCS_0000116 probability density function http://purl.obolibrary.org/obo/OBI_0200000 data transformation density function A data transformation that represents a mathematical function describing the relative likelihood of a continuous random variable to take on a value.
http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis http://purl.obolibrary.org/obo/OBCS_0000001 statistical data analysis significantly statistical data analysis
A statistical data analysis that uses patterns in the sample data to draw inferences about the population represented, accounting for randomness.
http://purl.obolibrary.org/obo/OBCS_0000122 transformed data matrix http://purl.obolibrary.org/obo/OBCS_0000120 data matrix set of transformed data sets A data item that consists of two or more data sets that are produced as the output of a data transformation.
http://purl.obolibrary.org/obo/OBCS_0000132 data collection by sampling http://purl.obolibrary.org/obo/OBCS_0000002 data collection data sampling A data collection process that results in a collection of data from a sampling process.
http://purl.obolibrary.org/obo/OBCS_0000133 dependent variable http://purl.obolibrary.org/obo/OBCS_0000038 statistical variable dependent variable A statistical variable that represents the output or effect, or is tested to see if it is the effect in an experiment or a modeling.
http://purl.obolibrary.org/obo/OBCS_0000136 numerical data item http://purl.obolibrary.org/obo/IAO_0000027 data item numeric data A data item which consists of digits as opposed to letters of the alphabet of special characters
http://purl.obolibrary.org/obo/OBCS_0000140 robust multi-array average normalization http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation RMA normalization A normalization data transformation that used to create normalized gene expression level from microarray raw data. The raw intensity values are background corrected, log2 transformed and then quantile normalized in the RMA normalization process.
http://purl.obolibrary.org/obo/OBCS_0000141 significance analysis of microarrays http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis SAM An inferential statistical data analysis that is established in 2001 by Virginia Tusher, Robert Tibshirani and Gilbert Chu, for determining whether changes in gene expression are statistically significant.
http://purl.obolibrary.org/obo/OBCS_0000142 signal-2-noise statistical analysis http://purl.obolibrary.org/obo/OBCS_0000025 univariate analysis signal-2-noise statistic A univariate analysis that calculates the level of a desired signal to the level of background noise to identify which detected signal is more signal than noise. It can be used to identify differentially expressed genes.
http://purl.obolibrary.org/obo/OBCS_0000145 contingency table http://purl.obolibrary.org/obo/IAO_0000030 information content entity error matrix A data item with a specific table layout that allows visualization of the performance of an algorithm. Each column of the matrix represents the instances in a predicted class, while each row represents the instances in an actual class.
http://purl.obolibrary.org/obo/OBCS_0000147 Gene Set Enrichment Analysis http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis GSEA An inferential statistical data analysis that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).
http://purl.obolibrary.org/obo/OBCS_0000150 standardized mortality ratio http://purl.obolibrary.org/obo/OBCS_0000220 derived data from inferential statistical analysis SMR A data item which is the ratio of observed deaths in the study group to expected deaths in the general population.
http://purl.obolibrary.org/obo/OBCS_0000162 representation validity http://purl.obolibrary.org/obo/OBCS_0000158 content validity translation validity A content validity that refers to the extent to which an abstract theoretical construct can be turned into a specific practical test.
http://purl.obolibrary.org/obo/OBCS_0000163 face validity http://purl.obolibrary.org/obo/OBCS_0000158 content validity translation validity A content validity that estimates whether a test appears to measure a certain criterion. It is not guaranteed that the test actually measures phenomena in that domain. When the test does not appear to be measuring what it is, it has low face validity.
http://purl.obolibrary.org/obo/OBCS_0000168 differential expression analysis using LIMMA linear models for microarry data http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis LIMMA data analysis A differential expression analysis using LIMMA linear model to identify differential expression for microarray data.
http://purl.obolibrary.org/obo/OBCS_0000169 summing data values http://purl.obolibrary.org/obo/OBI_0200000 data transformation summing data transformation A data transformation that add two or more numbers, magnitudes, quantities, or particulars as determined by or as if by the mathematical process of addition.
http://purl.obolibrary.org/obo/OBCS_0000173 data collection by web crawling http://purl.obolibrary.org/obo/OBCS_0000171 data collection from online resource data collection using Web spider An online data collection process that extracts data from online using a web crawler. A Web crawler is an Internet bot which systematically browses the World Wide Web and gets data from WWW.
http://purl.obolibrary.org/obo/OBCS_0000175 web crawling software http://purl.obolibrary.org/obo/IAO_0000010 software web spider A software that is used to browses the World Wide Web in a methodical, automated manner.
http://purl.obolibrary.org/obo/OBCS_0000182 Kriging http://purl.obolibrary.org/obo/OBI_0200102 regression analysis method Gaussian process regression A regression method of interpolation for which the interpolated values are modeled by a Gaussian process governed by prior covariances, as opposed to a piecewise-polynomial spline chosen to optimize smoothness of the fitted values.
http://purl.obolibrary.org/obo/OBCS_0000193 numerical data value http://purl.obolibrary.org/obo/IAO_0000030 information content entity mathematical value an information content entity that refers to a number value of a data item.
http://purl.obolibrary.org/obo/OBCS_0000198 undirected graph http://purl.obolibrary.org/obo/OBCS_0000216 mathematic graph undirected network A mathematic graph that a set of objects (vertices or nodes) that are connected together, where all the edges between two objects are bidirectional.
http://purl.obolibrary.org/obo/OBCS_0000201 discrete variable http://purl.obolibrary.org/obo/OBCS_0000038 statistical variable categorical variable A statistical variable over a particular range of real values is one for which, for any value in the range that the variable is permitted to take on, there is a positive minimum distance to the nearest other permissible value.
http://purl.obolibrary.org/obo/OBCS_0000211 Box-Cox distribution http://purl.obolibrary.org/obo/OBCS_0000005 normal distribution power-normal distribution A normal distribution that is the distribution of a random variable X for which the Box–Cox transformation on X follows a truncated normal distribution.
http://purl.obolibrary.org/obo/OBCS_0000215 bipartite graph http://purl.obolibrary.org/obo/OBCS_0000216 mathematic graph bigraph A mathematic graph that contains a set of objects (vertices or nodes) decomposed into two disjoint sets such that no two objects within the same set are adjacent.
http://purl.obolibrary.org/obo/OBCS_0000218 derived data from statistical analysis http://purl.obolibrary.org/obo/OBCS_0000233 transformed data item statistic A data item that is derived from a statistical data analysis.
http://purl.obolibrary.org/obo/OBCS_0000219 derived data from descriptive statistical analysis http://purl.obolibrary.org/obo/OBCS_0000218 derived data from statistical analysis descriptive statistic A data item that is derived from a descriptive statistical data analysis.
http://purl.obolibrary.org/obo/OBCS_0000220 derived data from inferential statistical analysis http://purl.obolibrary.org/obo/OBCS_0000218 derived data from statistical analysis inferential statistic A data item that is derived from an inferential statistical data analysis.
http://purl.obolibrary.org/obo/CHEBI_33839 macromolecule http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity polymer A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
http://purl.obolibrary.org/obo/OBCS_0000164 Extraction of Differential Gene Expression software http://purl.obolibrary.org/obo/IAO_0000010 software EDGE A software that is used for the differential gene expression significance analysis of DNA microarray experiments for both standard and time course experiments. The outputs consist of bothe p-values and q-values.
http://purl.obolibrary.org/obo/OBCS_0000165 Patterns from Gene Expression software http://purl.obolibrary.org/obo/IAO_0000010 software PaGE A software that can be used to produce lists of differentially expressed genes with confidence measures attached. These lists are generated via a False Discovery Rate (FDR) method of controlling the false positives. Patterns from Gene Expression (PaGE) is more than a differential expression analysis tool. PaGE is a tool to attach descriptive, dependable, and easily interpretable expression patterns to genes across multiple conditions, each represented by a set of replicated array experiments.
http://purl.obolibrary.org/obo/OBCS_0000166 GLobal Identifier of Target Regions software http://purl.obolibrary.org/obo/IAO_0000010 software GLITR A software that is used to identify transcription factor binding sites in a genome that have been enriched with aligned reads generated from ChIP-Seq technology.
http://purl.obolibrary.org/obo/OBCS_0000058 sensitivity http://purl.obolibrary.org/obo/OBCS_0000220 derived data from inferential statistical analysis true positive rate, recall A data item that measures the proportion of actual positives which are correctly identified as such (e.g. the percentage of sick people who are correctly identified as having the condition).
http://purl.obolibrary.org/obo/OBCS_0000059 specificity http://purl.obolibrary.org/obo/OBCS_0000220 derived data from inferential statistical analysis true negative rate A data item that refers to the proportion of negatives in a binary classification test which are correctly identified
http://purl.obolibrary.org/obo/OBCS_0000120 data matrix http://purl.obolibrary.org/obo/IAO_0000027 data item set of data sets A data item that is more specifically a rectangular array of numbers, symbols, or expressions, arranged in rows and columns.
http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/BFO_0000040 material entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
http://purl.obolibrary.org/obo/PATO_0000161 rate http://purl.obolibrary.org/obo/BFO_0000019 quality A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.
http://purl.obolibrary.org/obo/BFO_0000002 continuant http://purl.obolibrary.org/obo/BFO_0000001 entity An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000001 entity An entity that has temporal parts and that happens, unfolds or develops through time.
http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/BFO_0000003 occurrent An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
http://purl.obolibrary.org/obo/BFO_0000023 role http://purl.obolibrary.org/obo/BFO_0000017 realizable entity A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
http://purl.obolibrary.org/obo/BFO_0000035 process boundary http://purl.obolibrary.org/obo/BFO_0000003 occurrent p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000004 independent continuant An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/IAO_0000009 datum label A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
http://purl.obolibrary.org/obo/IAO_0000007 action specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity a directive information entity that describes an action the bearer will take
http://purl.obolibrary.org/obo/IAO_0000009 datum label http://purl.obolibrary.org/obo/IAO_0000030 information content entity A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
http://purl.obolibrary.org/obo/IAO_0000010 software http://purl.obolibrary.org/obo/IAO_0000104 plan specification Software is a plan specification composed of a series of instructions that can be
interpreted by or directly executed by a processing unit.
http://purl.obolibrary.org/obo/IAO_0000030 information content entity http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant A generically dependent continuant that is about some thing.
http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
http://purl.obolibrary.org/obo/IAO_0000033 directive information entity http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity whose concretizations indicate to their bearer how to realize them in a process.
http://purl.obolibrary.org/obo/IAO_0000037 dot plot http://purl.obolibrary.org/obo/IAO_0000038 graph A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
http://purl.obolibrary.org/obo/IAO_0000038 graph http://purl.obolibrary.org/obo/IAO_0000309 diagram A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://purl.obolibrary.org/obo/IAO_0000104 plan specification A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
http://purl.obolibrary.org/obo/IAO_0000078 curation status specification http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
http://purl.obolibrary.org/obo/IAO_0000079 density plot http://purl.obolibrary.org/obo/IAO_0000038 graph A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity A data format specification is the information content borne by the document published defining the specification.
Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
http://purl.obolibrary.org/obo/IAO_0000101 image http://purl.obolibrary.org/obo/IAO_0000308 figure An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part http://purl.obolibrary.org/obo/IAO_0000027 data item data about an ontology part is a data item about a part of an ontology, for example a term
http://purl.obolibrary.org/obo/IAO_0000104 plan specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
http://purl.obolibrary.org/obo/IAO_0000109 measurement datum http://purl.obolibrary.org/obo/IAO_0000027 data item A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
http://purl.obolibrary.org/obo/IAO_0000140 setting datum http://purl.obolibrary.org/obo/IAO_0000027 data item A settings datum is a datum that denotes some configuration of an instrument.
http://purl.obolibrary.org/obo/IAO_0000144 conclusion textual entity http://purl.obolibrary.org/obo/OBI_0001909 conclusion based on data A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
http://purl.obolibrary.org/obo/IAO_0000178 material information bearer http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity in which a concretization of an information content entity inheres.
http://purl.obolibrary.org/obo/IAO_0000179 histogram http://purl.obolibrary.org/obo/IAO_0000038 graph A histogram is a report graph which is a statistical description of a
distribution in terms of occurrence frequencies of different event classes.
http://purl.obolibrary.org/obo/IAO_0000180 heatmap http://purl.obolibrary.org/obo/IAO_0000038 graph A heatmap is a report graph which is a graphical representation of data
where the values taken by a variable(s) are shown as colors in a
two-dimensional map.
http://purl.obolibrary.org/obo/IAO_0000183 dendrogram http://purl.obolibrary.org/obo/IAO_0000038 graph A dendrogram is a report graph which is a tree diagram
frequently used to illustrate the arrangement of the clusters produced by a
clustering algorithm.
http://purl.obolibrary.org/obo/IAO_0000225 obsolescence reason specification http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part 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.
http://purl.obolibrary.org/obo/IAO_0000306 table http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
http://purl.obolibrary.org/obo/IAO_0000308 figure http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
http://purl.obolibrary.org/obo/IAO_0000309 diagram http://purl.obolibrary.org/obo/IAO_0000308 figure A figure that expresses one or more propositions
http://purl.obolibrary.org/obo/IAO_0000310 document http://purl.obolibrary.org/obo/IAO_0000030 information content entity A collection of information content entities intended to be understood together as a whole
http://purl.obolibrary.org/obo/IAO_0000400 cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000027 data item A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
http://purl.obolibrary.org/obo/IAO_0000401 one dimensional cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000400 cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
http://purl.obolibrary.org/obo/IAO_0000402 two dimensional cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000400 cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
http://purl.obolibrary.org/obo/IAO_0000403 three dimensional cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000400 cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
http://purl.obolibrary.org/obo/IAO_0000408 length measurement datum http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum A scalar measurement datum that is the result of measurement of length quality
http://purl.obolibrary.org/obo/IAO_0000409 denotator type http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part A denotator type indicates how a term should be interpreted from an ontological perspective.
http://purl.obolibrary.org/obo/IAO_0000414 mass measurement datum http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum A scalar measurement datum that is the result of measurement of mass quality
http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum A scalar measurement datum that is the result of measuring a temporal interval
http://purl.obolibrary.org/obo/IAO_0000572 documenting http://purl.obolibrary.org/obo/OBI_0000011 planned process a planned process in which a document is created or added to by including the specified input in it.
http://purl.obolibrary.org/obo/IAO_0000591 software method http://purl.obolibrary.org/obo/IAO_0000010 software A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
http://purl.obolibrary.org/obo/IAO_0000592 software module http://purl.obolibrary.org/obo/IAO_0000010 software A software module is software composed of a collection of software methods.
http://purl.obolibrary.org/obo/IAO_0000593 software library http://purl.obolibrary.org/obo/IAO_0000010 software A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
http://purl.obolibrary.org/obo/IAO_0000594 software application http://purl.obolibrary.org/obo/IAO_0000010 software A software application is software that can be directly executed by some processing unit.
http://purl.obolibrary.org/obo/IAO_0000595 software script http://purl.obolibrary.org/obo/IAO_0000010 software A software script is software whose instructions can be executed using a software
interpreter.
http://purl.obolibrary.org/obo/OBI_0000010 fluorescent reporter intensity http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.
http://purl.obolibrary.org/obo/OBI_0000011 planned process http://purl.obolibrary.org/obo/BFO_0000015 process A processual entity that realizes a plan which is the concretization of a plan specification.
http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
http://purl.obolibrary.org/obo/OBI_0000047 processed material http://purl.obolibrary.org/obo/BFO_0000040 material entity Is a material entity that is created or changed during material processing.
http://purl.obolibrary.org/obo/OBI_0000054 ratio of collected to emitted light http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role
http://purl.obolibrary.org/obo/OBI_0000066 investigation http://purl.obolibrary.org/obo/OBI_0000011 planned process a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
http://purl.obolibrary.org/obo/OBI_0000067 evaluant role http://purl.obolibrary.org/obo/BFO_0000023 role a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value http://purl.obolibrary.org/obo/OBCS_0000220 derived data from inferential statistical analysis A data item which is used to indicate the degree of uncertainty about a measurement.
http://purl.obolibrary.org/obo/OBI_0000075 diagnosis textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
http://purl.obolibrary.org/obo/OBI_0000078 eMedical record http://purl.obolibrary.org/obo/IAO_0000030 information content entity An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11.
http://purl.obolibrary.org/obo/OBI_0000101 measured expression level http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts.
http://purl.obolibrary.org/obo/OBI_0000112 specimen role http://purl.obolibrary.org/obo/BFO_0000023 role a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
http://purl.obolibrary.org/obo/OBI_0000115 intervention design http://purl.obolibrary.org/obo/OBI_0500000 study design An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
http://purl.obolibrary.org/obo/OBI_0000118 gene list http://purl.obolibrary.org/obo/IAO_0000100 data set A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis.
http://purl.obolibrary.org/obo/OBI_0000119 number of particles in subset http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role
http://purl.obolibrary.org/obo/OBI_0000125 number of lost events electronic http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role.
http://purl.obolibrary.org/obo/OBI_0000164 cDNA library http://purl.obolibrary.org/obo/OBI_0000731 recombinant vector Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.
ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications.
http://purl.obolibrary.org/obo/OBI_0000172 parameter threshold http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role
http://purl.obolibrary.org/obo/OBI_0000175 p-value http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
http://purl.obolibrary.org/obo/OBI_0000208 methodology testing objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies.
http://purl.obolibrary.org/obo/OBI_0000235 standard error http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution.
http://purl.obolibrary.org/obo/OBI_0000242 software testing objective http://purl.obolibrary.org/obo/OBI_0000208 methodology testing objective Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software.
http://purl.obolibrary.org/obo/OBI_0000245 organization http://purl.obolibrary.org/obo/BFO_0000040 material entity An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
http://purl.obolibrary.org/obo/OBI_0000251 cluster http://purl.obolibrary.org/obo/IAO_0000100 data set A data set which is a subset of data that are a similar to each other in some way.
http://purl.obolibrary.org/obo/OBI_0000268 organism feature identification objective http://purl.obolibrary.org/obo/OBI_0000015 biological feature identification objective Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
http://purl.obolibrary.org/obo/OBI_0000269 number of lost events computer http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role
http://purl.obolibrary.org/obo/OBI_0000272 protocol http://purl.obolibrary.org/obo/IAO_0000104 plan specification A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
http://purl.obolibrary.org/obo/OBI_0000274 adding a material entity into a target http://purl.obolibrary.org/obo/OBI_0000652 material combination is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
http://purl.obolibrary.org/obo/OBI_0000319 material to be added role http://purl.obolibrary.org/obo/BFO_0000023 role material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
http://purl.obolibrary.org/obo/OBI_0000338 drawing a conclusion based on data http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
http://purl.obolibrary.org/obo/OBI_0000339 planning http://purl.obolibrary.org/obo/BFO_0000015 process a process of creating or modifying a plan specification
http://purl.obolibrary.org/obo/OBI_0000343 inductive reasoning http://purl.obolibrary.org/obo/OBI_0000338 drawing a conclusion based on data a interpreting data that is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns.
http://purl.obolibrary.org/obo/OBI_0000355 hypothesis driven investigation http://purl.obolibrary.org/obo/OBI_0000066 investigation is an investigation with the goal to test one or more hypothesis
http://purl.obolibrary.org/obo/OBI_0000356 hypothesis generating investigation http://purl.obolibrary.org/obo/OBI_0000066 investigation is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis
http://purl.obolibrary.org/obo/OBI_0000411 cloning vector role http://purl.obolibrary.org/obo/OBI_0000319 material to be added role A material to be added role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
http://purl.obolibrary.org/obo/OBI_0000416 cloning insert role http://purl.obolibrary.org/obo/BFO_0000023 role cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process.
http://purl.obolibrary.org/obo/OBI_0000425 averaging objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
http://purl.obolibrary.org/obo/OBI_0000434 adding material objective http://purl.obolibrary.org/obo/OBI_0000686 material combination objective is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
http://purl.obolibrary.org/obo/OBI_0000441 assay objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
http://purl.obolibrary.org/obo/OBI_0000444 target of material addition role http://purl.obolibrary.org/obo/BFO_0000023 role target of material addition role is a role realized by an entity into which a material is added in a material addition process
http://purl.obolibrary.org/obo/OBI_0000451 normalized data set http://purl.obolibrary.org/obo/OBCS_0000123 transformed data set A data set that is produced as the output of a normalization data transformation.
http://purl.obolibrary.org/obo/OBI_0000453 measure function http://purl.obolibrary.org/obo/BFO_0000034 function Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
http://purl.obolibrary.org/obo/OBI_0000455 consume data function http://purl.obolibrary.org/obo/BFO_0000034 function Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data.
http://purl.obolibrary.org/obo/OBI_0000471 study design execution http://purl.obolibrary.org/obo/OBI_0000011 planned process a planned process that realizes the concretization of a study design
http://purl.obolibrary.org/obo/OBI_0000626 DNA sequencing http://purl.obolibrary.org/obo/OBI_0600047 sequencing assay DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.
http://purl.obolibrary.org/obo/OBI_0000649 data set of features http://purl.obolibrary.org/obo/OBCS_0000219 derived data from descriptive statistical analysis A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set.
http://purl.obolibrary.org/obo/OBI_0000652 material combination http://purl.obolibrary.org/obo/OBI_0000094 material processing is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
http://purl.obolibrary.org/obo/OBI_0000653 fuzzy clustering objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori.
http://purl.obolibrary.org/obo/OBI_0000656 data set of predicted values according to fitted curve http://purl.obolibrary.org/obo/OBCS_0000220 derived data from inferential statistical analysis A data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints.
http://purl.obolibrary.org/obo/OBI_0000660 background corrected data set http://purl.obolibrary.org/obo/OBCS_0000123 transformed data set A data set that is produced as the output of a background correction data transformation.
http://purl.obolibrary.org/obo/OBI_0000662 error corrected data set http://purl.obolibrary.org/obo/OBCS_0000123 transformed data set A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for).
http://purl.obolibrary.org/obo/OBI_0000666 background correction data transformation http://purl.obolibrary.org/obo/OBCS_0000188 data transformation in statistics A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction.
http://purl.obolibrary.org/obo/OBI_0000668 error correction data transformation http://purl.obolibrary.org/obo/OBCS_0000188 data transformation in statistics An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation.
http://purl.obolibrary.org/obo/OBI_0000673 statistical hypothesis test http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.
http://purl.obolibrary.org/obo/OBI_0000676 reduced dimension data set http://purl.obolibrary.org/obo/OBCS_0000220 derived data from inferential statistical analysis A data set that is produced as the output of a data vector reduction data transformation and consists of producing a data set which has fewer vectors than the input data set.
http://purl.obolibrary.org/obo/OBI_0000684 specimen collection objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification A objective specification to obtain a material entity for potential use as an input during an investigation.
http://purl.obolibrary.org/obo/OBI_0000686 material combination objective http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective is an objective to obtain an output material that contains several input materials.
http://purl.obolibrary.org/obo/OBI_0000704 decision tree induction objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
http://purl.obolibrary.org/obo/OBI_0000707 decision tree building data transformation http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis A decision tree building data transformation is a data transformation that has objective decision tree induction.
http://purl.obolibrary.org/obo/OBI_0000713 GenePattern software http://purl.obolibrary.org/obo/IAO_0000010 software a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
http://purl.obolibrary.org/obo/OBI_0000726 peak matching http://purl.obolibrary.org/obo/OBI_0200000 data transformation Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold
http://purl.obolibrary.org/obo/OBI_0000731 recombinant vector http://purl.obolibrary.org/obo/OBI_0000047 processed material A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector.
http://purl.obolibrary.org/obo/OBI_0000737 cloning vector http://purl.obolibrary.org/obo/OBI_1110108 material to be added A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site.
http://purl.obolibrary.org/obo/OBI_0000739 Student's t-test http://purl.obolibrary.org/obo/OBI_0000673 statistical hypothesis test Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value.
http://purl.obolibrary.org/obo/OBI_0000741 topologically preserved clustered data set http://purl.obolibrary.org/obo/OBI_0000648 clustered data set A clustered data set in which the topology, i.e. the spatial properties between data points, is preserved from the original input data from which it was derived.
http://purl.obolibrary.org/obo/OBI_0000789 survival rate http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring.
http://purl.obolibrary.org/obo/OBI_0000792 statistical model validation http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
http://purl.obolibrary.org/obo/OBI_0000811 primary structure of DNA macromolecule http://purl.obolibrary.org/obo/SO_0000001 region a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
http://purl.obolibrary.org/obo/OBI_0000832 measurement device http://purl.obolibrary.org/obo/OBI_0000968 device A device in which a measure function inheres.
http://purl.obolibrary.org/obo/OBI_0000861 Likelihood-ratio test http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis Likelihood-ratio is a data transformation which tests whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one); tests of the goodness-of-fit between two models.
http://purl.obolibrary.org/obo/OBI_0000868 pattern matching objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees.
http://purl.obolibrary.org/obo/OBI_0000931 study intervention http://purl.obolibrary.org/obo/OBI_0000011 planned process the part of the execution of an intervention design study which is varied between two or more subjects in the study
http://purl.obolibrary.org/obo/OBI_0000951 compound treatment design http://purl.obolibrary.org/obo/OBI_0000115 intervention design an intervention design in which the treatment is the administration of a compound
http://purl.obolibrary.org/obo/OBI_0000963 categorical label http://purl.obolibrary.org/obo/IAO_0000009 datum label A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
http://purl.obolibrary.org/obo/OBI_0000973 sequence data http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
http://purl.obolibrary.org/obo/OBI_0000976 handedness categorical measurement datum http://purl.obolibrary.org/obo/OBI_0000938 categorical measurement datum A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally
http://purl.obolibrary.org/obo/OBI_0000984 dose http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
http://purl.obolibrary.org/obo/OBI_0000985 growth condition intervention design http://purl.obolibrary.org/obo/OBI_0000115 intervention design A study design in which the independent variable is the environmental condition in which the specimen is growing
http://purl.obolibrary.org/obo/OBI_0000988 performing a diagnosis http://purl.obolibrary.org/obo/OBI_0200000 data transformation The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis
http://purl.obolibrary.org/obo/OBI_0000991 Edinburgh score http://purl.obolibrary.org/obo/OBI_0000970 scalar score from composite inputs A score that measures the dominance of a person's right or left hand in everyday activities.
http://purl.obolibrary.org/obo/OBI_0000995 administration of material to specimen http://purl.obolibrary.org/obo/OBI_0000274 adding a material entity into a target The directed combination of a material entity with a specimen.
http://purl.obolibrary.org/obo/OBI_0000997 growth environment http://purl.obolibrary.org/obo/BFO_0000040 material entity The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth.
http://purl.obolibrary.org/obo/OBI_0001000 questionnaire http://purl.obolibrary.org/obo/IAO_0000310 document A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
http://purl.obolibrary.org/obo/OBI_0001001 Edinburgh handedness assay http://purl.obolibrary.org/obo/OBI_0000944 handedness assay The Edinburgh Handedness assay is an assay in which a set of questions = the Edinburgh Handedness inventory - is asked and the answers to these questions are turned into a score, used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand.
http://purl.obolibrary.org/obo/OBI_0001028 feature extraction http://purl.obolibrary.org/obo/OBCS_0000188 data transformation in statistics A planed process with objective of obtaining quantified values from an image.
http://purl.obolibrary.org/obo/OBI_0001144 binding constant http://purl.obolibrary.org/obo/OBI_0001181 binding datum A binding datum about the disposition of two or more material entities to form complexes which comes in the form of a scalar and unit that are utilized in equations that model the binding process
http://purl.obolibrary.org/obo/OBI_0001151 genetically modified material http://purl.obolibrary.org/obo/OBI_0000047 processed material a material entity, organism or cell, that is the output of a genetic transformation process.
http://purl.obolibrary.org/obo/OBI_0001153 genetic transformation objective http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective a material transformation objective aims to create genetically modified organism or cell
http://purl.obolibrary.org/obo/OBI_0001155 3D structural organization datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum that describes the structural orientation of a material entity in 3D space.
http://purl.obolibrary.org/obo/OBI_0001156 age since planting measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing.
http://purl.obolibrary.org/obo/OBI_0001157 age since hatching measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg.
http://purl.obolibrary.org/obo/OBI_0001158 age measurement assay http://purl.obolibrary.org/obo/OBI_0000070 assay An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted.
http://purl.obolibrary.org/obo/OBI_0001159 age since egg laying measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism.
http://purl.obolibrary.org/obo/OBI_0001161 age since germination measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth.
http://purl.obolibrary.org/obo/OBI_0001163 age since eclosion measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon.
http://purl.obolibrary.org/obo/OBI_0001164 age since sowing measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination.
http://purl.obolibrary.org/obo/OBI_0001165 age since coitus measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction.
http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum A time measurement datum that is the result of measurement of age of an organism
http://purl.obolibrary.org/obo/OBI_0001168 age since fertilization measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote.
http://purl.obolibrary.org/obo/OBI_0001169 age since birth measurement datum http://purl.obolibrary.org/obo/OBI_0001167 age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
http://purl.obolibrary.org/obo/OBI_0001172 dose response curve http://purl.obolibrary.org/obo/IAO_0000573 line graph A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve.
http://purl.obolibrary.org/obo/OBI_0001180 half maximal effective concentration (EC50) http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time.
http://purl.obolibrary.org/obo/OBI_0001181 binding datum http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is.
http://purl.obolibrary.org/obo/OBI_0001182 negative binding datum http://purl.obolibrary.org/obo/OBI_0001181 binding datum A binding datum that states that there is no significant disposition of two or more entities to form a complex
http://purl.obolibrary.org/obo/OBI_0001191 half maximal inhibitory concentration (IC50) http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect.
http://purl.obolibrary.org/obo/OBI_0001214 normalization testing design http://purl.obolibrary.org/obo/OBI_0500000 study design A study design that tests different normalization procedures.
http://purl.obolibrary.org/obo/OBI_0001225 genetic population background information http://purl.obolibrary.org/obo/OBI_0001404 genetic characteristics information a genetic characteristics information which is a part of genotype information that identifies the population of organisms
http://purl.obolibrary.org/obo/OBI_0001265 FWER adjusted p-value http://purl.obolibrary.org/obo/OBI_0000662 error corrected data set A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests
http://purl.obolibrary.org/obo/OBI_0001294 wild type organism genotype information http://purl.obolibrary.org/obo/OBI_0001305 genotype information a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms.
http://purl.obolibrary.org/obo/OBI_0001305 genotype information http://purl.obolibrary.org/obo/OBI_0001404 genetic characteristics information a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
http://purl.obolibrary.org/obo/OBI_0001352 allele information http://purl.obolibrary.org/obo/OBI_0001364 genetic alteration information a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
http://purl.obolibrary.org/obo/OBI_0001358 post-transcriptional modification design http://purl.obolibrary.org/obo/OBI_0000115 intervention design A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
http://purl.obolibrary.org/obo/OBI_0001364 genetic alteration information http://purl.obolibrary.org/obo/OBI_0001404 genetic characteristics information a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
http://purl.obolibrary.org/obo/OBI_0001369 wild type allele information http://purl.obolibrary.org/obo/OBI_0001352 allele information an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism.
http://purl.obolibrary.org/obo/OBI_0001396 stimulus or stress design http://purl.obolibrary.org/obo/OBI_0000115 intervention design A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc.
http://purl.obolibrary.org/obo/OBI_0001404 genetic characteristics information http://purl.obolibrary.org/obo/IAO_0000027 data item a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
http://purl.obolibrary.org/obo/OBI_0001418 dose response design http://purl.obolibrary.org/obo/OBI_0000951 compound treatment design A study design that examines the relationship between the size of the administered dose and the extent of the response.
http://purl.obolibrary.org/obo/OBI_0001460 genetic modification design http://purl.obolibrary.org/obo/OBI_0000115 intervention design A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out.
http://purl.obolibrary.org/obo/OBI_0001474 lowess group transformation http://purl.obolibrary.org/obo/OBI_0001477 lowess transformation A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed.
http://purl.obolibrary.org/obo/OBI_0001477 lowess transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria.
http://purl.obolibrary.org/obo/OBI_0001481 lowess global transformation http://purl.obolibrary.org/obo/OBI_0001477 lowess transformation A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample.
http://purl.obolibrary.org/obo/OBI_0001514 minimal inhibitory concentration http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound.
http://purl.obolibrary.org/obo/OBI_0001522 sequence assembly algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured.
http://purl.obolibrary.org/obo/OBI_0001525 PDB file http://purl.obolibrary.org/obo/OBI_0001155 3D structural organization datum A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned.
http://purl.obolibrary.org/obo/OBI_0001536 equilibrium dissociation constant (KD) http://purl.obolibrary.org/obo/OBI_0001144 binding constant A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate)
http://purl.obolibrary.org/obo/OBI_0001546 comparative phenotypic assessment http://purl.obolibrary.org/obo/OBI_0001834 drawing a conclusion Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference
http://purl.obolibrary.org/obo/OBI_0001548 equilibrium association constant (KA) http://purl.obolibrary.org/obo/OBI_0001144 binding constant A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate)
http://purl.obolibrary.org/obo/OBI_0001554 rate measurement datum http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum A scalar measurement datum that represents the number of events occuring over a time interval
http://purl.obolibrary.org/obo/OBI_0001571 equilibrium dissociation constant (KD) approximated by IC50 http://purl.obolibrary.org/obo/OBI_0001191 half maximal inhibitory concentration (IC50) A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor.
http://purl.obolibrary.org/obo/OBI_0001573 DNA sequence data http://purl.obolibrary.org/obo/OBI_0000973 sequence data A sequence data item that is about the primary structure of DNA
http://purl.obolibrary.org/obo/OBI_0001575 assigning gene property based on phenotypic assessment http://purl.obolibrary.org/obo/OBI_0000338 drawing a conclusion based on data Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms that have a defined genetic difference, and assigning a property to the product of the targeted gene as a result.
http://purl.obolibrary.org/obo/OBI_0001581 equilibrium dissociation constant (KD) approximated by EC50 http://purl.obolibrary.org/obo/OBI_0001180 half maximal effective concentration (EC50) A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand.
http://purl.obolibrary.org/obo/OBI_0001583 half life of binding datum http://purl.obolibrary.org/obo/OBI_0001171 half life datum (t 1/2) A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association.
http://purl.obolibrary.org/obo/OBI_0001588 binding http://purl.obolibrary.org/obo/GO_0008150 biological_process The process of material entities forming complexes.
http://purl.obolibrary.org/obo/OBI_0001596 PDB file chain http://purl.obolibrary.org/obo/OBI_0001155 3D structural organization datum A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities
http://purl.obolibrary.org/obo/OBI_0001603 binding off rate measurement datum (koff) http://purl.obolibrary.org/obo/OBI_0001554 rate measurement datum A rate measurement datum of how quickly bound complexes disassociate
http://purl.obolibrary.org/obo/OBI_0001605 binding on rate measurement datum (kon) http://purl.obolibrary.org/obo/OBI_0001554 rate measurement datum A rate measurement datum of how quickly bound complexes form
http://purl.obolibrary.org/obo/OBI_0001618 average depth of sequence coverage http://purl.obolibrary.org/obo/OBI_0000679 average value An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size.
http://purl.obolibrary.org/obo/OBI_0001834 drawing a conclusion http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process in which new information is inferred from existing information.
http://purl.obolibrary.org/obo/OBI_0001872 sequence assembly process http://purl.obolibrary.org/obo/OBI_0200000 data transformation A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs).
http://purl.obolibrary.org/obo/OBI_0001873 number of errors http://purl.obolibrary.org/obo/OBI_0001933 value specification a data item that is the number of times that a given process failed, as an integer
http://purl.obolibrary.org/obo/OBI_0001874 random access memory size http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum random access memory size is a scalar measurement datum which denotes the amount of physical memory know as random access memory present of a computer or required by a computational process or data transformation
http://purl.obolibrary.org/obo/OBI_0001909 conclusion based on data http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that is inferred from data.
http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification http://purl.obolibrary.org/obo/OBI_0001933 value specification A value specification that is specifies one category out of a fixed number of nominal categories
http://purl.obolibrary.org/obo/OBI_0001931 scalar value specification http://purl.obolibrary.org/obo/OBI_0001933 value specification A value specification that consists of two parts: a numeral and a unit label
http://purl.obolibrary.org/obo/OBI_0001933 value specification http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that specifies a value within a classification scheme or on a quantitative scale.
http://purl.obolibrary.org/obo/OBI_0001939 genome coverage http://purl.obolibrary.org/obo/OBCS_0000233 transformed data item A data item that is the total number of bases in reads, divided by genome size, assumed to be the reference size (for instance of 3.10 Gb for human and 2.73 Gb for mouse) and refers to the percentage of the genome that is contained in the assembly based on size estimates; these are usually based on cytological techniques. Genome coverage of 90–95% is generally considered to be good, as most genomes contain a considerable fraction of repetitive regions that are difficult to sequence. So it is not a cause for concern if the genome coverage of an assembly is a bit less than 100%.
http://purl.obolibrary.org/obo/OBI_0001941 contig N50 http://purl.obolibrary.org/obo/OBI_0001940 N50 N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list.
http://purl.obolibrary.org/obo/OBI_0001945 scaffold N50 http://purl.obolibrary.org/obo/OBI_0001940 N50 N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information
http://purl.obolibrary.org/obo/OBI_0001959 sequencing library multiplexing http://purl.obolibrary.org/obo/OBI_0000094 material processing a planned process which consists in running a set of samples as a pool in one single instrument run of data acquisition process while retaining the ability to associate individual results to each of the individual input samples thanks to the use of a multiplex identifier, introduced during the ligation step of the individual library preparation and specific to a given sample.
http://purl.obolibrary.org/obo/OBI_0001966 sequence library deconvolution http://purl.obolibrary.org/obo/OBI_0200187 sequence analysis data transformation is a data transformation which uses sequence alignment and 'multiplex identifier sequence' information to pull together all reads belonging to a given single sample following the sequencing of a multiplexed library which combining several samples in one sequencing event
http://purl.obolibrary.org/obo/OBI_0001967 multiplexing sequence identifier http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acid A multiplexing sequence identifier is a nucleic acid sequence which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library
http://purl.obolibrary.org/obo/OBI_0001968 operational taxonomic unit matrix http://purl.obolibrary.org/obo/OBCS_0000233 transformed data item Operational Taxonomic Unit matrix is a data item, organized as a table, where organismal taxonomic units, computed by sequence analysis and genetic distance calculation, are counted in a set of biological or environmental samples. The table is used to appraise biodiversity of a population or community of living organism.
http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
http://purl.obolibrary.org/obo/OBI_0100051 specimen http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity that has the specimen role.
http://purl.obolibrary.org/obo/OBI_0200002 logistic-log curve fitting http://purl.obolibrary.org/obo/OBI_0200072 curve fitting data transformation A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n).
http://purl.obolibrary.org/obo/OBI_0200003 logit-log curve fitting http://purl.obolibrary.org/obo/OBI_0200072 curve fitting data transformation A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points.
http://purl.obolibrary.org/obo/OBI_0200004 log-log curve fitting http://purl.obolibrary.org/obo/OBI_0200072 curve fitting data transformation A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points.
http://purl.obolibrary.org/obo/OBI_0200005 feature extraction objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image.
http://purl.obolibrary.org/obo/OBI_0200006 biexponential transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation.
http://purl.obolibrary.org/obo/OBI_0200007 box-cox transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A box-cox transformation is a data transformation according to the methods of Box and Cox as described in the article Box, G. E. P. and Cox, D.R. (1964) An analysis of transformations. Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246.
http://purl.obolibrary.org/obo/OBI_0200008 hyperlog transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation.
http://purl.obolibrary.org/obo/OBI_0200010 loess scale group transformation one-channel http://purl.obolibrary.org/obo/OBI_0200025 loess scale group transformation A loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar.
http://purl.obolibrary.org/obo/OBI_0200011 logical transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A logical transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation.
http://purl.obolibrary.org/obo/OBI_0200012 loess scale group transformation two-channel http://purl.obolibrary.org/obo/OBI_0200025 loess scale group transformation A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar.
http://purl.obolibrary.org/obo/OBI_0200013 loess global transformation one-channel http://purl.obolibrary.org/obo/OBI_0200023 loess global transformation A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
http://purl.obolibrary.org/obo/OBI_0200014 split-scale transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t.
http://purl.obolibrary.org/obo/OBI_0200015 loess global transformation two-channel http://purl.obolibrary.org/obo/OBI_0200023 loess global transformation A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
http://purl.obolibrary.org/obo/OBI_0200016 sine transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html.
http://purl.obolibrary.org/obo/OBI_0200017 cosine transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A cosine transformation is a data transformation which consists in applying the cosine function to a (one dimensional) real number input. The cosine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Cosine.html.
http://purl.obolibrary.org/obo/OBI_0200018 loess group transformation one-channel http://purl.obolibrary.org/obo/OBI_0200024 loess group transformation A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
http://purl.obolibrary.org/obo/OBI_0200019 loess group transformation two-channel http://purl.obolibrary.org/obo/OBI_0200024 loess group transformation A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
http://purl.obolibrary.org/obo/OBI_0200020 homogeneous polynomial transformation http://purl.obolibrary.org/obo/OBI_0200093 polynomial transformation A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree.
http://purl.obolibrary.org/obo/OBI_0200021 linlog transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm.
http://purl.obolibrary.org/obo/OBI_0200023 loess global transformation http://purl.obolibrary.org/obo/OBI_0200071 loess transformation A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation.
http://purl.obolibrary.org/obo/OBI_0200024 loess group transformation http://purl.obolibrary.org/obo/OBI_0200071 loess transformation A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs.
http://purl.obolibrary.org/obo/OBI_0200025 loess scale group transformation http://purl.obolibrary.org/obo/OBI_0200185 scaling data transformation A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling.
http://purl.obolibrary.org/obo/OBI_0200026 total intensity transformation single http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice.
http://purl.obolibrary.org/obo/OBI_0200027 total intensity transformation paired http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors).
http://purl.obolibrary.org/obo/OBI_0200028 quantile transformation http://purl.obolibrary.org/obo/OBI_0200181 center calculation data transformation A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles.
http://purl.obolibrary.org/obo/OBI_0200031 differential expression analysis objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
http://purl.obolibrary.org/obo/OBI_0200032 K-fold cross validation method http://purl.obolibrary.org/obo/OBI_0000792 statistical model validation K-fold cross-validation randomly partitions the original sample into K subsamples. Of the K subsamples, a single subsample is retained as the validation data for testing the model, and the remaining K - 1 subsamples are used as training data. The cross-validation process is then repeated K times (the folds), with each of the K subsamples used exactly once as the validation data. The K results from the folds then can be averaged (or otherwise combined) to produce a single estimation. The advantage of this method over repeated random sub-sampling is that all observations are used for both training and validation, and each observation is used for validation exactly once. 10-fold cross-validation is commonly used
http://purl.obolibrary.org/obo/OBI_0200033 leave one out cross validation method http://purl.obolibrary.org/obo/OBI_0000792 statistical model validation is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data
http://purl.obolibrary.org/obo/OBI_0200035 boostrapping http://purl.obolibrary.org/obo/OBI_0000792 statistical model validation Bootstrapping is a statistical method for estimating the sampling distribution of a statistic by sampling with replacement from the original data, most often with the purpose of deriving robust estimates of standard errors and confidence intervals of a population parameter like a mean, median, proportion, odds ratio, correlation coefficient or regression coefficient
http://purl.obolibrary.org/obo/OBI_0200036 Benjamini and Hochberg false discovery rate correction method http://purl.obolibrary.org/obo/OBI_0200163 false discovery rate correction method A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate
http://purl.obolibrary.org/obo/OBI_0200037 pareto scaling http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable.
http://purl.obolibrary.org/obo/OBI_0200040 modular decomposition http://purl.obolibrary.org/obo/OBI_0200080 network analysis Molecular decomposition is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins.
http://purl.obolibrary.org/obo/OBI_0200041 k-means clustering http://purl.obolibrary.org/obo/OBI_0200175 class discovery data transformation A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).
http://purl.obolibrary.org/obo/OBI_0200042 hierarchical clustering http://purl.obolibrary.org/obo/OBI_0200175 class discovery data transformation A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root).
http://purl.obolibrary.org/obo/OBI_0200043 average linkage hierarchical clustering http://purl.obolibrary.org/obo/OBI_0200154 agglomerative hierarchical clustering An average linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the average distance between objects from the first cluster and objects from the second cluster.
http://purl.obolibrary.org/obo/OBI_0200044 complete linkage hierarchical clustering http://purl.obolibrary.org/obo/OBI_0200154 agglomerative hierarchical clustering an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster.
http://purl.obolibrary.org/obo/OBI_0200045 single linkage hierarchical clustering http://purl.obolibrary.org/obo/OBI_0200154 agglomerative hierarchical clustering A single linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the minimum distance between objects from the first cluster and objects from the second cluster.
http://purl.obolibrary.org/obo/OBI_0200049 Benjamini and Yekutieli false discovery rate correction method http://purl.obolibrary.org/obo/OBI_0200163 false discovery rate correction method A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate
http://purl.obolibrary.org/obo/OBI_0200052 probabilistic algorithm http://purl.obolibrary.org/obo/OBI_0200000 data transformation A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data.
http://purl.obolibrary.org/obo/OBI_0200053 expectation maximization http://purl.obolibrary.org/obo/OBI_0200052 probabilistic algorithm EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximated probability function.
http://purl.obolibrary.org/obo/OBI_0200054 global modularity calculation http://purl.obolibrary.org/obo/OBI_0200147 network graph quality calculation A network graph quality calculation in which an input data set of subgraph modules and their in-degree and out-degree qualities is used to calculate the average modularity of subgraphs within the network.
http://purl.obolibrary.org/obo/OBI_0200055 dye swap merge http://purl.obolibrary.org/obo/OBI_0200057 replicate analysis A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met.
http://purl.obolibrary.org/obo/OBI_0200056 moving average http://purl.obolibrary.org/obo/OBI_0200170 averaging data transformation A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set.
http://purl.obolibrary.org/obo/OBI_0200057 replicate analysis http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc.
http://purl.obolibrary.org/obo/OBI_0200058 b cell epitope prediction http://purl.obolibrary.org/obo/OBI_0200187 sequence analysis data transformation A B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope.
http://purl.obolibrary.org/obo/OBI_0200059 mhc binding prediction http://purl.obolibrary.org/obo/OBI_0200187 sequence analysis data transformation An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule.
http://purl.obolibrary.org/obo/OBI_0200060 t cell epitope prediction http://purl.obolibrary.org/obo/OBI_0200187 sequence analysis data transformation A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope.
http://purl.obolibrary.org/obo/OBI_0200061 data imputation http://purl.obolibrary.org/obo/OBI_0200000 data transformation Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm.
http://purl.obolibrary.org/obo/OBI_0200062 continuum mass spectrum http://purl.obolibrary.org/obo/OBI_0200085 mass spectrometry analysis A continuum mass spectrum is a data transformation that contains the full profile of the detected signals for a given ion.
http://purl.obolibrary.org/obo/OBI_0200063 characteristic path length calculation http://purl.obolibrary.org/obo/OBI_0200085 mass spectrometry analysis Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices
http://purl.obolibrary.org/obo/OBI_0200066 Holm-Bonferroni family-wise error rate correction method http://purl.obolibrary.org/obo/OBI_0200073 family wise error rate correction method a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level ? in the strong sense. Objective: multiple testing correction
http://purl.obolibrary.org/obo/OBI_0200070 edge weighting http://purl.obolibrary.org/obo/OBI_0200080 network analysis Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network.
http://purl.obolibrary.org/obo/OBI_0200071 loess transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves.
http://purl.obolibrary.org/obo/OBI_0200072 curve fitting data transformation http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints.
http://purl.obolibrary.org/obo/OBI_0200074 submatrix extraction http://purl.obolibrary.org/obo/OBI_0200050 dimensionality reduction A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.)
http://purl.obolibrary.org/obo/OBI_0200075 row submatrix extraction http://purl.obolibrary.org/obo/OBI_0200074 submatrix extraction A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows.
http://purl.obolibrary.org/obo/OBI_0200076 column submatrix extraction http://purl.obolibrary.org/obo/OBI_0200074 submatrix extraction A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns.
http://purl.obolibrary.org/obo/OBI_0200077 gating http://purl.obolibrary.org/obo/OBI_0200182 data vector reduction data transformation Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry.
http://purl.obolibrary.org/obo/OBI_0200078 descriptive statistical calculation objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
http://purl.obolibrary.org/obo/OBI_0200079 mean calculation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation A mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
http://purl.obolibrary.org/obo/OBI_0200081 sequence analysis objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns.
http://purl.obolibrary.org/obo/OBI_0200085 mass spectrometry analysis http://purl.obolibrary.org/obo/OBI_0200000 data transformation A data transformation which has the objective of spectrum analysis.
http://purl.obolibrary.org/obo/OBI_0200086 spread calculation data transformation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation A spread calculation is a data transformation that has objective spread calculation.
http://purl.obolibrary.org/obo/OBI_0200088 Kaplan Meier http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored)
http://purl.obolibrary.org/obo/OBI_0200093 polynomial transformation http://purl.obolibrary.org/obo/OBCS_0000188 data transformation in statistics A polynomial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted.
http://purl.obolibrary.org/obo/OBI_0200094 logarithmic transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm.
http://purl.obolibrary.org/obo/OBI_0200095 exponential transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function.
http://purl.obolibrary.org/obo/OBI_0200097 non-negative matrix factorization http://purl.obolibrary.org/obo/OBCS_0000188 data transformation in statistics Non negative matrix factorization is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero.
http://purl.obolibrary.org/obo/OBI_0200099 discriminant function analysis http://purl.obolibrary.org/obo/OBI_0200175 class discovery data transformation Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome.
http://purl.obolibrary.org/obo/OBI_0200101 linear discriminant functional analysis http://purl.obolibrary.org/obo/OBI_0200175 class discovery data transformation Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective.
http://purl.obolibrary.org/obo/OBI_0200102 regression analysis method http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data.
http://purl.obolibrary.org/obo/OBI_0200103 multiple linear regression analysis http://purl.obolibrary.org/obo/OBI_0200102 regression analysis method multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written as
Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon
where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression.
http://purl.obolibrary.org/obo/OBI_0200104 principal component regression http://purl.obolibrary.org/obo/OBI_0200175 class discovery data transformation The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores.
http://purl.obolibrary.org/obo/OBI_0200106 discriminant analysis http://purl.obolibrary.org/obo/OBCS_0000121 inferential statistical data analysis Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome.
http://purl.obolibrary.org/obo/OBI_0200108 eh transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization.
http://purl.obolibrary.org/obo/OBI_0200109 b transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization.
http://purl.obolibrary.org/obo/OBI_0200110 s transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization.
http://purl.obolibrary.org/obo/OBI_0200113 similarity calculation http://purl.obolibrary.org/obo/OBI_0200175 class discovery data transformation A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are.
http://purl.obolibrary.org/obo/OBI_0200114 euclidean distance calculation http://purl.obolibrary.org/obo/OBI_0200113 similarity calculation An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered.
http://purl.obolibrary.org/obo/OBI_0200115 pearson correlation coefficient calculation http://purl.obolibrary.org/obo/OBI_0200113 similarity calculation A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered.
http://purl.obolibrary.org/obo/OBI_0200116 loess fitting http://purl.obolibrary.org/obo/OBI_0200072 curve fitting data transformation A loess fitting is a curve fitting obtained by localized regression. The latter refers to fitting a polynomial (straight line, quadratic, cubic, etc) to data values within a window covering a fraction of the total number of observations. As the window slides along the axis, a new polynomial is fit to the observations falling within the window. This continues until all points are fit with a local polynomial. The results are then smoothed together to form a curve. The smoothness of loess fits is controlled by a smoothing parameter (often denoted as alpha, usually between 1/4 and 1) and the degree of the polynomial that is fitted by the method (usually denoted by lambda).
http://purl.obolibrary.org/obo/OBI_0200117 mode calculation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data.
http://purl.obolibrary.org/obo/OBI_0200118 quantile calculation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details.
http://purl.obolibrary.org/obo/OBI_0200119 median calculation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values.
http://purl.obolibrary.org/obo/OBI_0200120 variance calculation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment.
http://purl.obolibrary.org/obo/OBI_0200121 standard deviation calculation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean.
http://purl.obolibrary.org/obo/OBI_0200122 interquartile-range calculation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data.
http://purl.obolibrary.org/obo/OBI_0200123 skewness calculation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment
http://purl.obolibrary.org/obo/OBI_0200124 kurtosis calculation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation A kurtosis calculation is a descriptive statistics calculation defined as a parameter that measures how large or small the tails of a distribution are relative to the mean. For details, see http://davidmlane.com/hyperstat/A53638.html
http://purl.obolibrary.org/obo/OBI_0200126 network graph construction http://purl.obolibrary.org/obo/OBI_0200080 network analysis A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph.
http://purl.obolibrary.org/obo/OBI_0200127 weighted network graph construction http://purl.obolibrary.org/obo/OBI_0200126 network graph construction A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph.
http://purl.obolibrary.org/obo/OBI_0200128 directed network graph construction http://purl.obolibrary.org/obo/OBI_0200126 network graph construction A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph.
http://purl.obolibrary.org/obo/OBI_0200129 node quality calculation http://purl.obolibrary.org/obo/OBI_0200080 network analysis A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network.
http://purl.obolibrary.org/obo/OBI_0200130 node degree calculation http://purl.obolibrary.org/obo/OBI_0200129 node quality calculation A node quality calculation in which an input data set describing object nodes and relationship edges between object nodes is used to enumerate the number of unique relationships of an individual object node.
http://purl.obolibrary.org/obo/OBI_0200131 quantitative node degree calculation http://purl.obolibrary.org/obo/OBI_0200129 node quality calculation A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node.
http://purl.obolibrary.org/obo/OBI_0200132 node in-degree calculation http://purl.obolibrary.org/obo/OBI_0200129 node quality calculation A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing into an individual object node.
http://purl.obolibrary.org/obo/OBI_0200133 node out-degree calculation http://purl.obolibrary.org/obo/OBI_0200129 node quality calculation A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node.
http://purl.obolibrary.org/obo/OBI_0200134 node shortest path identification http://purl.obolibrary.org/obo/OBI_0200129 node quality calculation A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arrive at a specific target node in the network.
http://purl.obolibrary.org/obo/OBI_0200135 edge quality calculation http://purl.obolibrary.org/obo/OBI_0200080 network analysis A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network.
http://purl.obolibrary.org/obo/OBI_0200136 edge betweenness calculation http://purl.obolibrary.org/obo/OBI_0200135 edge quality calculation An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge.
http://purl.obolibrary.org/obo/OBI_0200137 network subgraph quality calculation http://purl.obolibrary.org/obo/OBI_0200080 network analysis A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network.
http://purl.obolibrary.org/obo/OBI_0200138 subgraph degree calculation http://purl.obolibrary.org/obo/OBI_0200137 network subgraph quality calculation A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph.
http://purl.obolibrary.org/obo/OBI_0200139 quantitative subgraph degree calculation http://purl.obolibrary.org/obo/OBI_0200137 network subgraph quality calculation A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph.
http://purl.obolibrary.org/obo/OBI_0200140 mathematical feature http://purl.obolibrary.org/obo/OBI_0200000 data transformation feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation
http://purl.obolibrary.org/obo/OBI_0200143 subgraph in-degree calculation http://purl.obolibrary.org/obo/OBI_0200137 network subgraph quality calculation A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph.
http://purl.obolibrary.org/obo/OBI_0200144 subgraph out-degree calculation http://purl.obolibrary.org/obo/OBI_0200137 network subgraph quality calculation A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph.
http://purl.obolibrary.org/obo/OBI_0200145 intra subgraph connectivity calculation http://purl.obolibrary.org/obo/OBI_0200137 network subgraph quality calculation A network subgraph quality calculation in which an input data set describing internal nodes, edges and node degrees is used to determine the average node degree within the subgraph.
http://purl.obolibrary.org/obo/OBI_0200146 subgraph modularity calculation http://purl.obolibrary.org/obo/OBI_0200137 network subgraph quality calculation A network subgraph quality calculation in which an input data set of subgraph in-degree and out-degree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity.
http://purl.obolibrary.org/obo/OBI_0200147 network graph quality calculation http://purl.obolibrary.org/obo/OBI_0200080 network analysis A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of the network as a whole.
http://purl.obolibrary.org/obo/OBI_0200150 MA transformation http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation.
http://purl.obolibrary.org/obo/OBI_0200151 exponential base http://purl.obolibrary.org/obo/OBI_0200140 mathematical feature The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1).
http://purl.obolibrary.org/obo/OBI_0200152 polynomial degree http://purl.obolibrary.org/obo/OBI_0200140 mathematical feature The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted.
http://purl.obolibrary.org/obo/OBI_0200153 number of variables http://purl.obolibrary.org/obo/OBI_0200140 mathematical feature The number of variables is a feature of any function (including polynomial functions) with domain contained in an n-dimensional vector space and is defined as n, the dimension of such space.
http://purl.obolibrary.org/obo/OBI_0200156 data partitioning http://purl.obolibrary.org/obo/OBI_0200000 data transformation Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets.
http://purl.obolibrary.org/obo/OBI_0200157 data vector reduction objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k.
http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification An objective specification to transformation input data into output data
http://purl.obolibrary.org/obo/OBI_0200167 data normalization objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A normalization objective is a data transformation objective where the aim is to remove
systematic sources of variation to put the data on equal footing in order
to create a common base for comparisons.
http://purl.obolibrary.org/obo/OBI_0200168 correction objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself
http://purl.obolibrary.org/obo/OBI_0200169 normalization data transformation http://purl.obolibrary.org/obo/OBCS_0000188 data transformation in statistics A normalization data transformation is a data transformation that has objective normalization.
http://purl.obolibrary.org/obo/OBI_0200170 averaging data transformation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation An averaging data transformation is a data transformation that has objective averaging.
http://purl.obolibrary.org/obo/OBI_0200171 partitioning data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A partitioning data transformation is a data transformation that has objective partitioning.
http://purl.obolibrary.org/obo/OBI_0200172 partitioning objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set.
http://purl.obolibrary.org/obo/OBI_0200173 background correction objective http://purl.obolibrary.org/obo/OBI_0200168 correction objective A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation.
http://purl.obolibrary.org/obo/OBI_0200174 curve fitting objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints.
http://purl.obolibrary.org/obo/OBI_0200176 Fisher's exact test http://purl.obolibrary.org/obo/OBI_0000673 statistical hypothesis test Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests.
http://purl.obolibrary.org/obo/OBI_0200177 center calculation objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
http://purl.obolibrary.org/obo/OBI_0200180 spread calculation objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set
http://purl.obolibrary.org/obo/OBI_0200181 center calculation data transformation http://purl.obolibrary.org/obo/OBI_0200184 descriptive statistical calculation data transformation A center calculation data transformation is a data transformation that has objective of center calculation.
http://purl.obolibrary.org/obo/OBI_0200182 data vector reduction data transformation http://purl.obolibrary.org/obo/OBI_0000707 decision tree building data transformation A data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of output vectors j, where j