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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.

Open in the Ontology Lookup Service (OLS)

1 - 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.

CART

ID: OBI_0000749

Class

A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.

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Classification

2 - 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 label

ID: OBI_0000963

Class

A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.

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Classification

3 - categorical value specification [OBI_0001930]

A value specification that is specifies one category out of a fixed number of nominal categories

categorical value specification

ID: OBI_0001930

Class

A value specification that is specifies one category out of a fixed number of nominal categories

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Classification

4 - 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 culture splitting

ID: OBI_0600037

Class

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

An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone.

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Classification

Relationships

5 - 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.

cell freezing medium

ID: OBI_0001912

Class

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.

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Classification

6 - 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 data transformation

ID: OBI_0200175

Class

A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.

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Classification

7 - 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 discovery objective

ID: OBI_0200178

Class

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.

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Classification

8 - 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 data transformation

ID: OBI_0000663

Class

A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.

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Classification

9 - 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.

class prediction objective

ID: OBI_0200179

Class

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.

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Classification

10 - 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.

classified data set

ID: OBI_0000023

Class

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.

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Classification

Relationships

11 - 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.

clinical tumor stage group according to AJCC 7th edition

ID: OBI_0002314

Class

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.

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Classification

12 - 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 set

ID: OBI_0000648

Class

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.

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Classification

Relationships

13 - 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.

clustered data visualization

ID: OBI_0200190

Class

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.

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Classification

14 - collection of specimens [OBI_0002076]

A material entity that has two or more specimens as its parts.

Open collection of specimens in VFB

Term Information

  • ID: OBI_0002076
  • Name: collection of specimens
  • Definition: A material entity that has two or more specimens as its parts.
  • Synonyms:
  • Type:
  • Comment:

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/OBI_0002076",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "OBI_0002076",
            "unique_facets": [
                "Class"
            ],
            "label": "collection of specimens"
        },
        "description": [
            "A material entity that has two or more specimens as its parts."
        ],
        "comment": []
    },
    "query": "Get JSON for Class",
    "version": "3b19da3",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/BFO_0000040",
            "types": [
                "Entity",
                "Class",
                "has_subClass"
            ],
            "short_form": "BFO_0000040",
            "unique_facets": [
                "Class"
            ],
            "label": "material entity"
        }
    ],
    "relationships": [],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [],
    "def_pubs": [
        {
            "core": {
                "symbol": "",
                "iri": "http://flybase.org/reports/Unattributed",
                "types": [
                    "Entity",
                    "Individual",
                    "pub"
                ],
                "short_form": "Unattributed",
                "unique_facets": [
                    "pub"
                ],
                "label": ""
            },
            "FlyBase": "",
            "PubMed": "",
            "DOI": ""
        }
    ]
}

15 - collection of specimens [OBI_0002076]

A material entity that has two or more specimens as its parts.

collection of specimens

ID: OBI_0002076

Class

A material entity that has two or more specimens as its parts.

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Classification

16 - 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.

cross validation objective

ID: OBI_0200188

Class

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.

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Classification

17 - culture medium [OBI_0000079]

a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.

culture medium

ID: OBI_0000079

Class

a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.

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Classification

18 - 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.

cultured cell population

ID: OBI_0100060

Class

A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.

The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.

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Classification

Relationships

19 - data transformation [OBI_0200000]

A planned process that produces output data from input data.

data transformation

ID: OBI_0200000

Class

A planned process that produces output data from input data.

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Classification

Relationships

20 - data transformation objective [OBI_0200166]

An objective specification to transformation input data into output data

data transformation objective

ID: OBI_0200166

Class

An objective specification to transformation input data into output data

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Classification

21 - data visualization [OBI_0200111]

An planned process that creates images, diagrams or animations from the input data.

data visualization

ID: OBI_0200111

Class

An planned process that creates images, diagrams or animations from the input data.

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Classification

Relationships

22 - 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 building data transformation

ID: OBI_0000707

Class

A decision tree building data transformation is a data transformation that has objective decision tree induction.

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Classification

Relationships

23 - 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.

decision tree induction objective

ID: OBI_0000704

Class

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.

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Classification

24 - 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.

dimensionality reduction

ID: OBI_0200050

Class

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.

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Classification

25 - 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.

Eastern Cooperative Oncology Group score value specification

ID: OBI_0002357

Class

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.

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Classification

26 - 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

Epstein Barr virus transformed B cell

ID: OBI_0100010

Class

A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity

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Classification

27 - 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 culture

ID: OBI_0600036

Class

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).

A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.

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Classification

Relationships

28 - 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).

establishing cell line

ID: OBI_0001867

Class

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).

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Classification

Relationships

29 - 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.

GenePattern software

ID: OBI_0000713

Class

a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.

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Classification

30 - 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).

hierarchical clustering

ID: OBI_0200042

Class

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).

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Classification

31 - 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 AJCC 7th edition

ID: OBI_0002205

Class

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.

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Classification

32 - 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 according to the Fuhrman Nuclear Grading System

ID: OBI_0002210

Class

A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.

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Classification

33 - 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

ID: OBI_0002215

Class

A categorical value specification that is a histologic grade assigned to a ovarian tumor.

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Classification

34 - 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 a two-tier grading system

ID: OBI_0002216

Class

A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.

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Classification

35 - 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).

histologic grade for ovarian tumor according to the World Health Organization

ID: OBI_0002219

Class

A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).

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Classification

36 - 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 cervical cancer stage value specification

ID: OBI_0002326

Class

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.

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Classification

37 - 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.

International Federation of Gynecology and Obstetrics ovarian cancer stage value specification

ID: OBI_0002341

Class

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.

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Classification

38 - 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-means clustering

ID: OBI_0200041

Class

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).

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Classification

39 - 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.

k-nearest neighbors

ID: OBI_0000727

Class

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.

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Classification

40 - 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.

Karnofsky score vaue specification

ID: OBI_0002363

Class

A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.

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Classification

41 - 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

leave one out cross validation method

ID: OBI_0200033

Class

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

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Classification

42 - 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

maintaining cell culture

ID: OBI_0600024

Class

a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing

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Classification

Relationships

43 - manufacturer [OBI_0000835]

A person or organization that has a manufacturer role

manufacturer

ID: OBI_0000835

Class

A person or organization that has a manufacturer role

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Classification

Relationships

44 - manufacturer role [OBI_0000571]

Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.

manufacturer role

ID: OBI_0000571

Class

Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.

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Classification

45 - 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

ID: OBI_0000457

Class

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

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Classification

Relationships

46 - manufacturing objective [OBI_0000458]

is the objective to manufacture a material of a certain function (device)

manufacturing objective

ID: OBI_0000458

Class

is the objective to manufacture a material of a certain function (device)

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Classification

47 - material component separation [OBI_0600014]

a material processing in which components of an input material become segregated in space

material component separation

ID: OBI_0600014

Class

a material processing in which components of an input material become segregated in space

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Classification

Relationships

48 - 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

ID: OBI_0000838

Class

a process with that achieves the objective to maintain some or all of the characteristics of an input material over time

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Classification

Relationships

49 - material maintenance objective [OBI_0000806]

An objective specification maintains some or all of the qualities of a material over time.

material maintenance objective

ID: OBI_0000806

Class

An objective specification maintains some or all of the qualities of a material over time.

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Classification

50 - material processing [OBI_0000094]

A planned process which results in physical changes in a specified input material

material processing

ID: OBI_0000094

Class

A planned process which results in physical changes in a specified input material

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Classification

Relationships

51 - material separation objective [OBI_0000639]

is an objective to transform a material entity into spatially separated components.

material separation objective

ID: OBI_0000639

Class

is an objective to transform a material entity into spatially separated components.

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Classification

52 - material supplier [OBI_0002989]

A person or organization that provides material supplies to other people or organizations.

material supplier

ID: OBI_0002989

Class

A person or organization that provides material supplies to other people or organizations.

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Classification

Relationships

53 - 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 supplier role

ID: OBI_0000018

Class

a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.

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Classification

54 - material transformation objective [OBI_0000456]

an objective specifiction that creates an specific output object from input materials.

material transformation objective

ID: OBI_0000456

Class

an objective specifiction that creates an specific output object from input materials.

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Classification

55 - organism [OBI_0100026]

Category=external. [object; organismal entity; organism]

Open organism in VFB

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/OBI_0100026",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "OBI_0100026",
            "label": "organism"
        },
        "description": [],
        "comment": [
            "Category=external."
        ]
    },
    "query": "Get JSON for Class",
    "version": "44725ae",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/BFO_0000030",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "BFO_0000030",
            "label": "object"
        },
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/GENO_0000904",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "GENO_0000904",
            "label": "organismal entity"
        }
    ],
    "relationships": [],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [],
    "def_pubs": []
}

56 - 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.

organism

ID: OBI_0100026

Class

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.

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Classification

57 - 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.

organization

ID: OBI_0000245

Class

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.

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Classification

58 - partitioning data transformation [OBI_0200171]

A partitioning data transformation is a data transformation that has objective partitioning.

partitioning data transformation

ID: OBI_0200171

Class

A partitioning data transformation is a data transformation that has objective partitioning.

Open in VFB 3D Browser →

Classification

Relationships

59 - 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.

partitioning objective

ID: OBI_0200172

Class

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.

Open in VFB 3D Browser →

Classification

60 - 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 colon according to AJCC 7th edition

ID: OBI_0002290

Class

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.

Open in VFB 3D Browser →

Classification

61 - 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 kidney according to AJCC 7th edition

ID: OBI_0002306

Class

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.

Open in VFB 3D Browser →

Classification

62 - 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 lung according to AJCC 7th edition

ID: OBI_0002298

Class

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.

Open in VFB 3D Browser →

Classification

63 - 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 distant metastases stage for ovary according to AJCC 7th edition

ID: OBI_0002310

Class

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.

Open in VFB 3D Browser →

Classification

64 - 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 colon and rectum according to AJCC 7th edition

ID: OBI_0002270

Class

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.

Open in VFB 3D Browser →

Classification

65 - 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 kidney according to AJCC 7th edition

ID: OBI_0002284

Class

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.

Open in VFB 3D Browser →

Classification

66 - 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 lung according to AJCC 7th edition

ID: OBI_0002279

Class

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.

Open in VFB 3D Browser →

Classification

67 - 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 lymph node stage for ovary according to AJCC 7th edition

ID: OBI_0002287

Class

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.

Open in VFB 3D Browser →

Classification

68 - 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 colon and rectum according to AJCC 7th edition

ID: OBI_0002224

Class

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.

Open in VFB 3D Browser →

Classification

69 - 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 kidney according to AJCC 7th edition

ID: OBI_0002243

Class

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.

Open in VFB 3D Browser →

Classification

70 - 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 lung according to AJCC 7th edition

ID: OBI_0002232

Class

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.

Open in VFB 3D Browser →

Classification

71 - 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.

pathologic primary tumor stage for ovary according to AJCC 7th edition

ID: OBI_0002256

Class

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.

Open in VFB 3D Browser →

Classification

72 - 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

peak matching

ID: OBI_0000726

Class

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

Open in VFB 3D Browser →

Classification

73 - 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).

performance status value specification

ID: OBI_0002356

Class

A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).

Open in VFB 3D Browser →

Classification

74 - planned process [OBI_0000011]

A processual entity that realizes a plan which is the concretization of a plan specification.

Open planned process in VFB

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/OBI_0000011",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "OBI_0000011",
            "label": "planned process"
        },
        "description": [
            "A processual entity that realizes a plan which is the concretization of a plan specification."
        ],
        "comment": []
    },
    "query": "Get JSON for Class",
    "version": "44725ae",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/BFO_0000015",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "BFO_0000015",
            "label": "process"
        }
    ],
    "relationships": [],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [],
    "def_pubs": [
        {
            "core": {
                "symbol": "",
                "iri": "http://flybase.org/reports/Unattributed",
                "types": [
                    "Entity",
                    "Individual",
                    "pub"
                ],
                "short_form": "Unattributed",
                "label": ""
            },
            "FlyBase": "",
            "PubMed": "",
            "DOI": ""
        }
    ]
}

75 - planned process [OBI_0000011]

A processual entity that realizes a plan which is the concretization of a plan specification.

planned process

ID: OBI_0000011

Class

A processual entity that realizes a plan which is the concretization of a plan specification.

Open in VFB 3D Browser →

Classification

76 - 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

Open population in VFB

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/OBI_0000181",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "OBI_0000181",
            "label": "population"
        },
        "description": [
            "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"
        ],
        "comment": []
    },
    "query": "Get JSON for Class",
    "version": "44725ae",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/GENO_0000113",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "GENO_0000113",
            "label": "taxonomic group"
        }
    ],
    "relationships": [],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [],
    "def_pubs": [
        {
            "core": {
                "symbol": "",
                "iri": "http://flybase.org/reports/Unattributed",
                "types": [
                    "Entity",
                    "Individual",
                    "pub"
                ],
                "short_form": "Unattributed",
                "label": ""
            },
            "FlyBase": "",
            "PubMed": "",
            "DOI": ""
        }
    ]
}

77 - 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

ID: OBI_0000181

Class

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

Open in VFB 3D Browser →

Classification

78 - 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.

portioning objective

ID: OBI_0000678

Class

A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.

Open in VFB 3D Browser →

Classification

79 - 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.

principal components analysis dimensionality reduction

ID: OBI_0200051

Class

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.

Open in VFB 3D Browser →

Classification

80 - processed material [OBI_0000047]

Is a material entity that is created or changed during material processing.

processed material

ID: OBI_0000047

Class

Is a material entity that is created or changed during material processing.

Open in VFB 3D Browser →

Classification

Relationships

81 - processed specimen [OBI_0000953]

A specimen that has been intentionally physically modified.

processed specimen

ID: OBI_0000953

Class

A specimen that has been intentionally physically modified.

A tissue sample that has been sliced and stained for a histology study.

Open in VFB 3D Browser →

Classification

82 - 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.

questionnaire

ID: OBI_0001000

Class

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.

Open in VFB 3D Browser →

Classification

83 - 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

ID: OBI_0001879

Class

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.

(copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).

Open in VFB 3D Browser →

Classification

Relationships

84 - reagent role [OBI_0000086]

[reagent role]

Open reagent role in VFB

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/OBI_0000086",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "OBI_0000086",
            "label": "reagent role"
        },
        "description": [],
        "comment": []
    },
    "query": "Get JSON for Class",
    "version": "44725ae",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/BFO_0000023",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "BFO_0000023",
            "label": "role"
        }
    ],
    "relationships": [],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [],
    "def_pubs": []
}

85 - 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.

reagent role

ID: OBI_0000086

Class

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.

(copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).

Open in VFB 3D Browser →

Classification

86 - regulator role [OBI_0000014]

a regulatory role involved with making and/or enforcing relevant legislation and governmental orders

regulator role

ID: OBI_0000014

Class

a regulatory role involved with making and/or enforcing relevant legislation and governmental orders

Open in VFB 3D Browser →

Classification

87 - 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 agency

ID: OBI_0000450

Class

A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.

Open in VFB 3D Browser →

Classification

Relationships

88 - 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.

regulatory role

ID: OBI_0000017

Class

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.

Open in VFB 3D Browser →

Classification

89 - 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

ID: OBI_0001866

Class

A cultured cell that has been passaged or derives from a cell that has been passaged in culture.

A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture.

Open in VFB 3D Browser →

Classification

Relationships

90 - secondary cultured cell population [OBI_0001905]

A cultured cell population that is derived through one or more passages in culture.

secondary cultured cell population

ID: OBI_0001905

Class

A cultured cell population that is derived through one or more passages in culture.

The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally.

Open in VFB 3D Browser →

Classification

Relationships

91 - 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).

separation into different composition objective

ID: OBI_0000681

Class

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).

Open in VFB 3D Browser →

Classification

92 - 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

service provider role

ID: OBI_0000947

Class

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

Open in VFB 3D Browser →

Classification

93 - specimen [OBI_0100051]

A material entity that has the specimen role.

Open specimen in VFB

Term Information

  • ID: OBI_0100051
  • Name: specimen
  • Definition: A material entity that has the specimen role.
  • Synonyms:
  • Type:
  • Comment:

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/OBI_0100051",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "OBI_0100051",
            "unique_facets": [
                "Class"
            ],
            "label": "specimen"
        },
        "description": [
            "A material entity that has the specimen role."
        ],
        "comment": []
    },
    "query": "Get JSON for Class",
    "version": "3b19da3",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/BFO_0000040",
            "types": [
                "Entity",
                "Class",
                "has_subClass"
            ],
            "short_form": "BFO_0000040",
            "unique_facets": [
                "Class"
            ],
            "label": "material entity"
        }
    ],
    "relationships": [
        {
            "relation": {
                "iri": "http://purl.obolibrary.org/obo/RO_0000087",
                "label": "has role",
                "type": "has_role"
            },
            "object": {
                "symbol": "",
                "iri": "http://purl.obolibrary.org/obo/OBI_0000112",
                "types": [
                    "Entity",
                    "Class"
                ],
                "short_form": "OBI_0000112",
                "unique_facets": [
                    "Class"
                ],
                "label": "specimen role"
            }
        }
    ],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [],
    "def_pubs": [
        {
            "core": {
                "symbol": "",
                "iri": "http://flybase.org/reports/Unattributed",
                "types": [
                    "Entity",
                    "Individual",
                    "pub"
                ],
                "short_form": "Unattributed",
                "unique_facets": [
                    "pub"
                ],
                "label": ""
            },
            "FlyBase": "",
            "PubMed": "",
            "DOI": ""
        }
    ]
}

94 - specimen [OBI_0100051]

A material entity that has the specimen role.

specimen

ID: OBI_0100051

Class

A material entity that has the specimen role.

Open in VFB 3D Browser →

Classification

Relationships

95 - specimen collection objective [OBI_0000684]

A objective specification to obtain a material entity for potential use as an input during an investigation.

Open specimen collection objective in VFB

Term Information

  • ID: OBI_0000684
  • Name: specimen collection objective
  • Definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
  • Synonyms:
  • Type:
  • Comment:

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/OBI_0000684",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "OBI_0000684",
            "unique_facets": [
                "Class"
            ],
            "label": "specimen collection objective"
        },
        "description": [
            "A objective specification to obtain a material entity for potential use as an input during an investigation."
        ],
        "comment": []
    },
    "query": "Get JSON for Class",
    "version": "3b19da3",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/IAO_0000005",
            "types": [
                "Entity",
                "Class",
                "has_subClass"
            ],
            "short_form": "IAO_0000005",
            "unique_facets": [
                "Class"
            ],
            "label": "IAO_0000005"
        }
    ],
    "relationships": [],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [],
    "def_pubs": [
        {
            "core": {
                "symbol": "",
                "iri": "http://flybase.org/reports/Unattributed",
                "types": [
                    "Entity",
                    "Individual",
                    "pub"
                ],
                "short_form": "Unattributed",
                "unique_facets": [
                    "pub"
                ],
                "label": ""
            },
            "FlyBase": "",
            "PubMed": "",
            "DOI": ""
        }
    ]
}

96 - 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

ID: OBI_0000684

Class

A objective specification to obtain a material entity for potential use as an input during an investigation.

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Classification

97 - specimen collection process [OBI_0000659]

A planned process with the objective of collecting a specimen.

Open specimen collection process in VFB

Term Information

  • ID: OBI_0000659
  • Name: specimen collection process
  • Definition: A planned process with the objective of collecting a specimen.
  • Synonyms:
  • Type:
  • Comment:

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/OBI_0000659",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "OBI_0000659",
            "unique_facets": [
                "Class"
            ],
            "label": "specimen collection process"
        },
        "description": [
            "A planned process with the objective of collecting a specimen."
        ],
        "comment": []
    },
    "query": "Get JSON for Class",
    "version": "3b19da3",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/OBI_0000011",
            "types": [
                "Entity",
                "Class",
                "has_subClass"
            ],
            "short_form": "OBI_0000011",
            "unique_facets": [
                "Class"
            ],
            "label": "planned process"
        }
    ],
    "relationships": [
        {
            "relation": {
                "iri": "http://purl.obolibrary.org/obo/OBI_0000299",
                "label": "has_specified_output",
                "type": "has_specified_output"
            },
            "object": {
                "symbol": "",
                "iri": "http://purl.obolibrary.org/obo/OBI_0100051",
                "types": [
                    "Entity",
                    "Class"
                ],
                "short_form": "OBI_0100051",
                "unique_facets": [
                    "Class"
                ],
                "label": "specimen"
            }
        },
        {
            "relation": {
                "iri": "http://purl.obolibrary.org/obo/OBI_0000293",
                "label": "has_specified_input",
                "type": "has_specified_input"
            },
            "object": {
                "symbol": "",
                "iri": "http://purl.obolibrary.org/obo/BFO_0000040",
                "types": [
                    "Entity",
                    "Class",
                    "has_subClass"
                ],
                "short_form": "BFO_0000040",
                "unique_facets": [
                    "Class"
                ],
                "label": "material entity"
            }
        },
        {
            "relation": {
                "iri": "http://purl.obolibrary.org/obo/OBI_0000417",
                "label": "achieves_planned_objective",
                "type": "achieves_planned_objective"
            },
            "object": {
                "symbol": "",
                "iri": "http://purl.obolibrary.org/obo/OBI_0000684",
                "types": [
                    "Entity",
                    "Class"
                ],
                "short_form": "OBI_0000684",
                "unique_facets": [
                    "Class"
                ],
                "label": "specimen collection objective"
            }
        }
    ],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [],
    "def_pubs": [
        {
            "core": {
                "symbol": "",
                "iri": "http://flybase.org/reports/Unattributed",
                "types": [
                    "Entity",
                    "Individual",
                    "pub"
                ],
                "short_form": "Unattributed",
                "unique_facets": [
                    "pub"
                ],
                "label": ""
            },
            "FlyBase": "",
            "PubMed": "",
            "DOI": ""
        }
    ]
}

98 - specimen collection process [OBI_0000659]

A planned process with the objective of collecting a specimen.

specimen collection process

ID: OBI_0000659

Class

A planned process with the objective of collecting a specimen.

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Classification

Relationships

99 - 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).

Open specimen from organism in VFB

Term Information

  • ID:

  • Name: specimen from organism

  • Definition: 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).

  • Synonyms:

  • Type:

  • Comment:

VFB Term Json

{
    "term": {
        "core": {
            "short_form": "",
            "label": "specimen from organism",
            "types": [],
            "iri": "",
            "symbol": ""
        },
        "description": [
            "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). "
        ],
        "comment": [
            ""
        ]
    },
    "parents": [],
    "relationships": [],
    "xrefs": [],
    "pub_syn": [],
    "def_pubs": []
}

100 - 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 from organism

ID: OBI_0001479

Class

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).

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Classification

101 - 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

Open specimen role in VFB

Term Information

  • ID: OBI_0000112
  • Name: specimen role
  • Definition: 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
  • Synonyms:
  • Type:
  • Comment:

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/OBI_0000112",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "OBI_0000112",
            "unique_facets": [
                "Class"
            ],
            "label": "specimen role"
        },
        "description": [
            "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"
        ],
        "comment": []
    },
    "query": "Get JSON for Class",
    "version": "3b19da3",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/BFO_0000023",
            "types": [
                "Entity",
                "Class",
                "has_subClass"
            ],
            "short_form": "BFO_0000023",
            "unique_facets": [
                "Class"
            ],
            "label": "role"
        }
    ],
    "relationships": [],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [],
    "def_pubs": [
        {
            "core": {
                "symbol": "",
                "iri": "http://flybase.org/reports/Unattributed",
                "types": [
                    "Entity",
                    "Individual",
                    "pub"
                ],
                "short_form": "Unattributed",
                "unique_facets": [
                    "pub"
                ],
                "label": ""
            },
            "FlyBase": "",
            "PubMed": "",
            "DOI": ""
        }
    ]
}

102 - 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.

specimen role

ID: OBI_0000112

Class

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.

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Classification

103 - statistical model validation [OBI_0000792]

A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.

statistical model validation

ID: OBI_0000792

Class

A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.

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Classification

Relationships

104 - 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.

support vector machine

ID: OBI_0000700

Class

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.

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Classification

Relationships

105 - value specification [OBI_0001933]

An information content entity that specifies a value within a classification scheme or on a quantitative scale.

value specification

ID: OBI_0001933

Class

An information content entity that specifies a value within a classification scheme or on a quantitative scale.

Open in VFB 3D Browser →

Classification