CART [OBI_0000749]
A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
Ontology for Biomedical Investigations (OBI)
The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
Categories:
categorical label [OBI_0000963]
A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
categorical value specification [OBI_0001930]
A value specification that is specifies one category out of a fixed number of nominal categories
cell culture splitting [OBI_0600037]
The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing
cell freezing medium [OBI_0001912]
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
class discovery data transformation [OBI_0200175]
A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
class discovery objective [OBI_0200178]
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.
class prediction data transformation [OBI_0000663]
A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
class prediction objective [OBI_0200179]
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.
classified data set [OBI_0000023]
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.
clinical tumor stage group according to AJCC 7th edition [OBI_0002314]
A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
clustered data set [OBI_0000648]
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.
clustered data visualization [OBI_0200190]
A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type.
collection of specimens [OBI_0002076]
A material entity that has two or more specimens as its parts.
collection of specimens [OBI_0002076]
A material entity that has two or more specimens as its parts.
cross validation objective [OBI_0200188]
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.
culture medium [OBI_0000079]
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
cultured cell population [OBI_0100060]
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
data transformation [OBI_0200000]
A planned process that produces output data from input data.
data transformation objective [OBI_0200166]
An objective specification to transformation input data into output data
data visualization [OBI_0200111]
An planned process that creates images, diagrams or animations from the input data.
decision tree building data transformation [OBI_0000707]
A decision tree building data transformation is a data transformation that has objective decision tree induction.
decision tree induction objective [OBI_0000704]
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.
dimensionality reduction [OBI_0200050]
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.
Eastern Cooperative Oncology Group score value specification [OBI_0002357]
A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient.
Epstein Barr virus transformed B cell [OBI_0100010]
A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity
establishing cell culture [OBI_0600036]
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
establishing cell line [OBI_0001867]
a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset).
GenePattern software [OBI_0000713]
a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
hierarchical clustering [OBI_0200042]
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).
histologic grade according to AJCC 7th edition [OBI_0002205]
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
histologic grade according to the Fuhrman Nuclear Grading System [OBI_0002210]
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
histologic grade for ovarian tumor [OBI_0002215]
A categorical value specification that is a histologic grade assigned to a ovarian tumor.
histologic grade for ovarian tumor according to a two-tier grading system [OBI_0002216]
A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
histologic grade for ovarian tumor according to the World Health Organization [OBI_0002219]
A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
International Federation of Gynecology and Obstetrics cervical cancer stage value specification [OBI_0002326]
A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
International Federation of Gynecology and Obstetrics ovarian cancer stage value specification [OBI_0002341]
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system.
k-means clustering [OBI_0200041]
A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).
k-nearest neighbors [OBI_0000727]
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.
Karnofsky score vaue specification [OBI_0002363]
A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
leave one out cross validation method [OBI_0200033]
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
maintaining cell culture [OBI_0600024]
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
manufacturer [OBI_0000835]
A person or organization that has a manufacturer role
manufacturer role [OBI_0000571]
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
manufacturing [OBI_0000457]
Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
manufacturing objective [OBI_0000458]
is the objective to manufacture a material of a certain function (device)
material component separation [OBI_0600014]
a material processing in which components of an input material become segregated in space
material maintenance [OBI_0000838]
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
material maintenance objective [OBI_0000806]
An objective specification maintains some or all of the qualities of a material over time.
material processing [OBI_0000094]
A planned process which results in physical changes in a specified input material
material separation objective [OBI_0000639]
is an objective to transform a material entity into spatially separated components.
material supplier [OBI_0002989]
A person or organization that provides material supplies to other people or organizations.
material supplier role [OBI_0000018]
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
material transformation objective [OBI_0000456]
an objective specifiction that creates an specific output object from input materials.
organism [OBI_0100026]
Category=external. [object; organismal entity; organism]
organism [OBI_0100026]
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
organization [OBI_0000245]
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
partitioning data transformation [OBI_0200171]
A partitioning data transformation is a data transformation that has objective partitioning.
partitioning objective [OBI_0200172]
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.
pathologic distant metastases stage for colon according to AJCC 7th edition [OBI_0002290]
A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pathologic distant metastases stage for kidney according to AJCC 7th edition [OBI_0002306]
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pathologic distant metastases stage for lung according to AJCC 7th edition [OBI_0002298]
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pathologic distant metastases stage for ovary according to AJCC 7th edition [OBI_0002310]
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pathologic lymph node stage for colon and rectum according to AJCC 7th edition [OBI_0002270]
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pathologic lymph node stage for kidney according to AJCC 7th edition [OBI_0002284]
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pathologic lymph node stage for lung according to AJCC 7th edition [OBI_0002279]
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pathologic lymph node stage for ovary according to AJCC 7th edition [OBI_0002287]
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pathologic primary tumor stage for colon and rectum according to AJCC 7th edition [OBI_0002224]
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pathologic primary tumor stage for kidney according to AJCC 7th edition [OBI_0002243]
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pathologic primary tumor stage for lung according to AJCC 7th edition [OBI_0002232]
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pathologic primary tumor stage for ovary according to AJCC 7th edition [OBI_0002256]
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
peak matching [OBI_0000726]
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
performance status value specification [OBI_0002356]
A categorical value specification that is an assessment of a participant’s performance status (general well-being and activities of daily life).
planned process [OBI_0000011]
A processual entity that realizes a plan which is the concretization of a plan specification.
planned process [OBI_0000011]
A processual entity that realizes a plan which is the concretization of a plan specification.
population [OBI_0000181]
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
population [OBI_0000181]
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
portioning objective [OBI_0000678]
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
principal components analysis dimensionality reduction [OBI_0200051]
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.
processed material [OBI_0000047]
Is a material entity that is created or changed during material processing.
processed specimen [OBI_0000953]
A specimen that has been intentionally physically modified.
questionnaire [OBI_0001000]
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.
reagent [OBI_0001879]
A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output.
reagent role [OBI_0000086]
[reagent role]
reagent role [OBI_0000086]
A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
regulator role [OBI_0000014]
a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
regulatory agency [OBI_0000450]
A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
regulatory role [OBI_0000017]
a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
secondary cultured cell [OBI_0001866]
A cultured cell that has been passaged or derives from a cell that has been passaged in culture.
secondary cultured cell population [OBI_0001905]
A cultured cell population that is derived through one or more passages in culture.
separation into different composition objective [OBI_0000681]
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
service provider role [OBI_0000947]
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
specimen [OBI_0100051]
A material entity that has the specimen role.
specimen [OBI_0100051]
A material entity that has the specimen role.
specimen collection objective [OBI_0000684]
A objective specification to obtain a material entity for potential use as an input during an investigation.
specimen collection objective [OBI_0000684]
A objective specification to obtain a material entity for potential use as an input during an investigation.
specimen collection process [OBI_0000659]
A planned process with the objective of collecting a specimen.
specimen collection process [OBI_0000659]
A planned process with the objective of collecting a specimen.
specimen from organism []
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
specimen from organism [OBI_0001479]
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
specimen role [OBI_0000112]
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
specimen role [OBI_0000112]
A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen.
statistical model validation [OBI_0000792]
A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
support vector machine [OBI_0000700]
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.
value specification [OBI_0001933]
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
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Last modified January 20, 2026: move out ontologies (362809c)