sep.owl
type: Ontology
version IRI: sep.owl
imports: unit.obo
auto-generated-by: OBO-Edit 1.101
date: 17:12:2019 17:10
default-namespace: default_namespace
has_obo_format_version: 1.0
saved-by: jonesar

definition
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_units
type: ObjectProperty
has_obo_namespace: default_namespace
id: has_units

entity
type: Class
definition: This is the root node of the ontology to provide controlled vocabulary terms protein separation based experiments.
has_obo_namespace: default_namespace
id: sep:00001

Axiom
annotated source: entity
annotated property: definition
annotated target: This is the root node of the ontology to provide controlled vocabulary terms protein separation based experiments.
database_cross_reference: PSI:GEL

abstract
type: Class
subclass of: entity
definition: Properties or qualities as distinguished from any particular embodiment of the properties/qualities in a physical medium. Instances of Abstract can be said to exist in the same sense as mathematical objects such as sets and relations, but they cannot exist at a particular place and time without some physical encoding or embodiment.
has_obo_namespace: default_namespace
id: sep:00002

Axiom
annotated source: abstract
annotated property: definition
annotated target: Properties or qualities as distinguished from any particular embodiment of the properties/qualities in a physical medium. Instances of Abstract can be said to exist in the same sense as mathematical objects such as sets and relations, but they cannot exist at a particular place and time without some physical encoding or embodiment.
database_cross_reference: SUMO:abstract

physical
type: Class
subclass of: entity
definition: An entity that has a location in space-time. Note that locations are themselves understood to have a location in space-time.
has_obo_namespace: default_namespace
id: sep:00003

Axiom
annotated source: physical
annotated property: definition
annotated target: An entity that has a location in space-time. Note that locations are themselves understood to have a location in space-time.
database_cross_reference: SUMO:physical

attribute
type: Class
subclass of: abstract
definition: An attribute is an abstraction which belongs to or is a characteristic of an entity.
has_obo_namespace: default_namespace
id: sep:00004

Axiom
annotated source: attribute
annotated property: definition
annotated target: An attribute is an abstraction which belongs to or is a characteristic of an entity.
database_cross_reference: WordNet:attribute

quality
type: Class
subclass of: abstract
definition: An abstract concept that is exhibited in full if it is possessed by an object at all (a categorical property), that inheres in a bearer by virtue of how the bearer is related to other entities. Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee.
has_obo_namespace: default_namespace
id: sep:00005
comment: Quality should be used to describe abstract qualities of entitiys such as color, shape and state. PATO (http://obo.sourceforge.net/cgi-bin/detail.cgi?quality) should be consulted and imported under this node before creating sepCV specific terms.

Axiom
annotated source: quality
annotated property: definition
annotated target: An abstract concept that is exhibited in full if it is possessed by an object at all (a categorical property), that inheres in a bearer by virtue of how the bearer is related to other entities. Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee.
database_cross_reference: PATO:http://purl.org/obo/owl/PATO

identifier
type: Class
subclass of: attribute
definition: An identifier is an attribute which characterises the identification of an entity.
has_obo_namespace: default_namespace
id: sep:00006

Axiom
annotated source: identifier
annotated property: definition
annotated target: An identifier is an attribute which characterises the identification of an entity.
database_cross_reference: PSI:GEL

format
type: Class
subclass of: quality
definition: A format is a quality that is a specificiation or arrangement of a specified form. The structure, layout, or the digital manifestation of an entity.
has_obo_namespace: default_namespace
id: sep:00007

Axiom
annotated source: format
annotated property: definition
annotated target: A format is a quality that is a specificiation or arrangement of a specified form. The structure, layout, or the digital manifestation of an entity.
database_cross_reference: PSI:GEL

parameter
type: Class
subclass of: attribute
definition: A parameter is an attribute that defines a system and determines (or limits) its performance.
has_obo_namespace: default_namespace
id: sep:00008

Axiom
annotated source: parameter
annotated property: definition
annotated target: A parameter is an attribute that defines a system and determines (or limits) its performance.
database_cross_reference: Wordnet:parameter

distribution
type: Class
subclass of: quality
definition: A distribution is a quality that specifies an arrangement of values of a variable showing their observed or theoretical frequency of occurrence.
has_obo_namespace: default_namespace
id: sep:00009

Axiom
annotated source: distribution
annotated property: definition
annotated target: A distribution is a quality that specifies an arrangement of values of a variable showing their observed or theoretical frequency of occurrence.
database_cross_reference: WordNet:statistical distribution

role
type: Class
subclass of: attribute
definition: A role is an attribute that is the activity assigned to or required or expected of an entiy within the context of a particular process.
has_obo_namespace: default_namespace
id: sep:00010

Axiom
annotated source: role
annotated property: definition
annotated target: A role is an attribute that is the activity assigned to or required or expected of an entiy within the context of a particular process.
database_cross_reference: PSI:GEL

digital data set
type: Class
subclass of: digital entity
definition: A digital data set is is a digital entity that is a collection of the same or heterogenous digital entities.
has_obo_namespace: default_namespace
id: sep:00011

Axiom
annotated source: digital data set
annotated property: definition
annotated target: A digital data set is is a digital entity that is a collection of the same or heterogenous digital entities.
database_cross_reference: PSI:Gel

product attribute
type: Class
subclass of: attribute
definition: A product attribute is an attribute that is assigned to a physical object which has been produced by human or mechanical effort or by a natural process.
has_obo_namespace: default_namespace
id: sep:00012

Axiom
annotated source: product attribute
annotated property: definition
annotated target: A product attribute is an attribute that is assigned to a physical object which has been produced by human or mechanical effort or by a natural process.
database_cross_reference: PSI:Gel

proteomics standards initiative working group
type: Class
subclass of: organization
definition: The proteomics standards intiative working group name is an identifier for the Proteomics Standards Initiative (PSI) working groups. The primary functions of creating, editing, maintaining and obsoleting recommendations are the task of a Working Group.
has_exact_synonym: PSI WG
has_obo_namespace: default_namespace
id: sep:00013

Axiom
annotated source: proteomics standards initiative working group
annotated property: definition
annotated target: The proteomics standards intiative working group name is an identifier for the Proteomics Standards Initiative (PSI) working groups. The primary functions of creating, editing, maintaining and obsoleting recommendations are the task of a Working Group.
database_cross_reference: PSI:Gel

Uniform Resource Identifier
type: Class
subclass of: identifier
definition: A Uniform Resource Identifier (URI) is an identifier which is a compact sequence of characters that identifies an abstract or physical resource. This specification defines the generic URI syntax and a process for resolving URI references that might be in relative form, along with guidelines and security considerations for the use of URIs on the Internet. The URI syntax defines a grammar that is a superset of all valid URIs, allowing an implementation to parse the common components of a URI reference without knowing the scheme-specific requirements of every possible identifier. This specification does not define a generative grammar for URIs; that task is performed by the individual specifications of each URI scheme. http://tools.ietf.org/html/rfc3986.
has_exact_synonym: URI
has_obo_namespace: default_namespace
id: sep:00014

Axiom
annotated source: Uniform Resource Identifier
annotated property: definition
annotated target: A Uniform Resource Identifier (URI) is an identifier which is a compact sequence of characters that identifies an abstract or physical resource. This specification defines the generic URI syntax and a process for resolving URI references that might be in relative form, along with guidelines and security considerations for the use of URIs on the Internet. The URI syntax defines a grammar that is a superset of all valid URIs, allowing an implementation to parse the common components of a URI reference without knowing the scheme-specific requirements of every possible identifier. This specification does not define a generative grammar for URIs; that task is performed by the individual specifications of each URI scheme. http://tools.ietf.org/html/rfc3986.
database_cross_reference: IETF:rfc3986

batch identifier
type: Class
subclass of: product attribute
definition: A batch identifier is a product attribute which is a token which identifies the batch or lot number of a product.
has_exact_synonym: batch number
has_exact_synonym: lot number
has_obo_namespace: default_namespace
id: sep:00015

Axiom
annotated source: batch identifier
annotated property: definition
annotated target: A batch identifier is a product attribute which is a token which identifies the batch or lot number of a product.
database_cross_reference: PSI:GEL

catalogue identifier
type: Class
subclass of: product attribute
definition: A catalogue identifier is a product attribute which is designated by a manufacture, seller, or producer of a product.
has_exact_synonym: catalogue number
has_obo_namespace: default_namespace
id: sep:00016

Axiom
annotated source: catalogue identifier
annotated property: definition
annotated target: A catalogue identifier is a product attribute which is designated by a manufacture, seller, or producer of a product.
database_cross_reference: PSI:Gel

model identifier
type: Class
subclass of: product attribute
definition: A model identifier is a product attribute assigned to a product.
has_obo_namespace: default_namespace
has_related_synonym: model number
id: sep:00017

Axiom
annotated source: model identifier
annotated property: definition
annotated target: A model identifier is a product attribute assigned to a product.
database_cross_reference: PSI:Gel

linear distribution
type: Class
subclass of: distribution
definition: A linear distribution is a statsitical distribution that is equally sequential.
has_obo_namespace: default_namespace
id: sep:00018

Axiom
annotated source: linear distribution
annotated property: definition
annotated target: A linear distribution is a statsitical distribution that is equally sequential.
database_cross_reference: PSI:Gel

logarithmic distribution
type: Class
subclass of: distribution
definition: A logarithmic distribution is a statistical distribution which is a scale in which the distances that numbers are at from a reference point are proportional to their logarithms.
has_obo_namespace: default_namespace
id: sep:00019

Axiom
annotated source: logarithmic distribution
annotated property: definition
annotated target: A logarithmic distribution is a statistical distribution which is a scale in which the distances that numbers are at from a reference point are proportional to their logarithms.
database_cross_reference: McGraw-Hill Dictionary of Scientific and Technical Terms:logarithmic

non-linear distribution
type: Class
subclass of: distribution
definition: A non-linear distribution is a statsitical distribution that is not equally sequential.
has_obo_namespace: default_namespace
id: sep:000199

Axiom
annotated source: non-linear distribution
annotated property: definition
annotated target: A non-linear distribution is a statsitical distribution that is not equally sequential.
database_cross_reference: PSI:Gel

maximum parameter
type: Class
subclass of: parameter
definition: A maximum parameter is a parameter which has he largest possible value for a parameter.
has_obo_namespace: default_namespace
id: sep:00020

Axiom
annotated source: maximum parameter
annotated property: definition
annotated target: A maximum parameter is a parameter which has he largest possible value for a parameter.
database_cross_reference: PSI:Gel

minimum parameter
type: Class
subclass of: parameter
definition: A minimum parameter is a parameter which has the smallest possible value for a parameter.
has_obo_namespace: default_namespace
id: sep:00021

Axiom
annotated source: minimum parameter
annotated property: definition
annotated target: A minimum parameter is a parameter which has the smallest possible value for a parameter.
database_cross_reference: PSI:Gel

state
type: Class
subclass of: quality
definition: A state is a quality that is the manner of being or form of existence.
has_obo_namespace: default_namespace
id: sep:00022

Axiom
annotated source: state
annotated property: definition
annotated target: A state is a quality that is the manner of being or form of existence.
database_cross_reference: :The American Heritage Dictionary of the English Language
database_cross_reference: Fourth Edition:state

electrical mode
type: Class
subclass of: mode
definition: Electric mode is a mode that represents one of several alternative conditions of a measure of electric from a device.
has_obo_namespace: default_namespace
id: sep:00023

Axiom
annotated source: electrical mode
annotated property: definition
annotated target: Electric mode is a mode that represents one of several alternative conditions of a measure of electric from a device.
database_cross_reference: PSI:Gel

gradient mode
type: Class
subclass of: electrical mode
definition: A gradient mode is an electic mode that is a graded process of increases or decreases for a given period in time in the context of use within a process.
has_obo_namespace: default_namespace
has_related_synonym: ramp
id: sep:00024

Axiom
annotated source: gradient mode
annotated property: definition
annotated target: A gradient mode is an electic mode that is a graded process of increases or decreases for a given period in time in the context of use within a process.
database_cross_reference: PSI:Gel

social role
type: Class
subclass of: role
definition: A social role is a role that specify the position or status of a entity within an Organization or other Group.
has_obo_namespace: default_namespace
id: sep:00025

Axiom
annotated source: social role
annotated property: definition
annotated target: A social role is a role that specify the position or status of a entity within an Organization or other Group.
database_cross_reference: SUMO:social role

mode
type: Class
subclass of: state
definition: A mode is a state that is one of several alternative conditions or methods of operation of a device.
has_obo_namespace: default_namespace
id: sep:00026

Axiom
annotated source: mode
annotated property: definition
annotated target: A mode is a state that is one of several alternative conditions or methods of operation of a device.
database_cross_reference: McGraw-Hill Dictionary of Scientific and Technical Terms:mode

hold mode
type: Class
subclass of: electrical mode
definition: A hold mode is an electric mode where the measure of electric remains constant for a given period in time in the context of use within a process.
has_obo_namespace: default_namespace
id: sep:00027

Axiom
annotated source: hold mode
annotated property: definition
annotated target: A hold mode is an electric mode where the measure of electric remains constant for a given period in time in the context of use within a process.
database_cross_reference: PSI:Gel

step and hold mode
type: Class
subclass of: electrical mode
definition: a step and hold mode is an electrical mode which the measure of electric is increased (or decreased) in a defined series of increases (or decreases) from a low electric measure value to a high electric measure value and then remains constant (is held) for a given period in time in the context of use within a process.
has_obo_namespace: default_namespace
id: sep:00028

Axiom
annotated source: step and hold mode
annotated property: definition
annotated target: a step and hold mode is an electrical mode which the measure of electric is increased (or decreased) in a defined series of increases (or decreases) from a low electric measure value to a high electric measure value and then remains constant (is held) for a given period in time in the context of use within a process.
database_cross_reference: PSI:Gel

substance role
type: Class
subclass of: role
definition: A susbtance role is a role that the function or part assigned to or required or expected of a substance within the context of a particular process.
has_obo_namespace: default_namespace
id: sep:00029

Axiom
annotated source: substance role
annotated property: definition
annotated target: A susbtance role is a role that the function or part assigned to or required or expected of a substance within the context of a particular process.
database_cross_reference: SUMO:role

position
type: Class
subclass of: social role
definition: A position is a social role that is a formal declaration of reponsibility within an Organization. Examples of Positions include president, laboratory director, senior researcher, sales representative, etc.
has_obo_namespace: default_namespace
id: sep:00030

Axiom
annotated source: position
annotated property: definition
annotated target: A position is a social role that is a formal declaration of reponsibility within an Organization. Examples of Positions include president, laboratory director, senior researcher, sales representative, etc.
database_cross_reference: SUMO:position

lecturer
type: Class
subclass of: position
definition: Lecturer is a position.
has_obo_namespace: default_namespace
id: sep:00031

Axiom
annotated source: lecturer
annotated property: definition
annotated target: Lecturer is a position.
database_cross_reference: PSI:Gel

professor
type: Class
subclass of: position
definition: Professor is a postion.
has_obo_namespace: default_namespace
id: sep:00032

Axiom
annotated source: professor
annotated property: definition
annotated target: Professor is a postion.
database_cross_reference: PSI:Gel

reader
type: Class
subclass of: position
definition: Reader is a position.
has_obo_namespace: default_namespace
id: sep:00033

Axiom
annotated source: reader
annotated property: definition
annotated target: Reader is a position.
database_cross_reference: PSI :Gel

researcher
type: Class
subclass of: position
definition: A researcher is a position.
has_obo_namespace: default_namespace
id: sep:00034

Axiom
annotated source: researcher
annotated property: definition
annotated target: A researcher is a position.
database_cross_reference: PSI:Gel

principle investigator
type: Class
subclass of: position
definition: A principle investigator is a position.
has_obo_namespace: default_namespace
id: sep:00035

Axiom
annotated source: principle investigator
annotated property: definition
annotated target: A principle investigator is a position.
database_cross_reference: PSI:GEL

cross linker
type: Class
subclass of: substance role
definition: A cross linker is a substance role that induces covalent bonds linking one polymer chain to another They are the characteristic property of thermosetting plastics materials. In biology, cross-linking has applications in forming polyacrylamide gels for gel electrophoresis.
has_obo_namespace: default_namespace
id: sep:00036

Axiom
annotated source: cross linker
annotated property: definition
annotated target: A cross linker is a substance role that induces covalent bonds linking one polymer chain to another They are the characteristic property of thermosetting plastics materials. In biology, cross-linking has applications in forming polyacrylamide gels for gel electrophoresis.
database_cross_reference: Wikkipedia:cross linker

medium
type: Class
subclass of: substance role
definition: A medium is a substance role which an intervening substance through which something else is transmitted or carried on.
has_obo_namespace: default_namespace
id: sep:00037

Axiom
annotated source: medium
annotated property: definition
annotated target: A medium is a substance role which an intervening substance through which something else is transmitted or carried on.
database_cross_reference: :The American Heritage Dictionary of the English Language
database_cross_reference: Fourth Edition:medium

detection medium
type: Class
subclass of: medium
definition: A detection medium is a medium role of function of a substance to act as a medium which faciliates the detection of an entity. MAIPE.GE: If the proteins on the gel matrix must be exposed to another medium to permit detection (e.g. photographic film for radiolabel samples) then give details of name, model, manufacture, of detection medium.If the proteins on the gel matrix must be exposed to another medium to permit detection (e.g. photographic film for radiolabel samples) then give details of name, model, manufacture, of detection medium.
has_obo_namespace: default_namespace
id: sep:00038

Axiom
annotated source: detection medium
annotated property: definition
annotated target: A detection medium is a medium role of function of a substance to act as a medium which faciliates the detection of an entity. MAIPE.GE: If the proteins on the gel matrix must be exposed to another medium to permit detection (e.g. photographic film for radiolabel samples) then give details of name, model, manufacture, of detection medium.If the proteins on the gel matrix must be exposed to another medium to permit detection (e.g. photographic film for radiolabel samples) then give details of name, model, manufacture, of detection medium.
database_cross_reference: PSI:Gel

separation medium
type: Class
subclass of: medium
definition: A separation medium is a medium role of a substance that is used to separate a substance in the context of use within a protocol. In gel electrophoresis the gel is the separation medium.
has_obo_namespace: default_namespace
id: sep:00039

Axiom
annotated source: separation medium
annotated property: definition
annotated target: A separation medium is a medium role of a substance that is used to separate a substance in the context of use within a protocol. In gel electrophoresis the gel is the separation medium.
database_cross_reference: PSI:Gel

transfer medium
type: Class
subclass of: medium
definition: A transfer medium is a medium role in which a substance facilitates the transfer of a substance to another substance in the context of a process MIAPE.GE: If the proteins separated along the gel, are transferred to another medium to aid detection (such as a nitrocellulose membrane as used in immunoblots) then give details of the name and type of medium, models and manufacturers, where appropriate.
has_obo_namespace: default_namespace
id: sep:00040

Axiom
annotated source: transfer medium
annotated property: definition
annotated target: A transfer medium is a medium role in which a substance facilitates the transfer of a substance to another substance in the context of a process MIAPE.GE: If the proteins separated along the gel, are transferred to another medium to aid detection (such as a nitrocellulose membrane as used in immunoblots) then give details of the name and type of medium, models and manufacturers, where appropriate.
database_cross_reference: PSI:Gel

gelling agent
type: Class
subclass of: substance role
definition: A gelling agent is a substance role of a substance to react with another substance to form a gel.
has_obo_namespace: default_namespace
id: sep:00041

Axiom
annotated source: gelling agent
annotated property: definition
annotated target: A gelling agent is a substance role of a substance to react with another substance to form a gel.
database_cross_reference: PSI:Gel

sample
type: Class
subclass of: substance role
definition: A sample is a substance role played by a biological substance as an input substance to a protocol.
has_obo_namespace: default_namespace
id: sep:00042

Axiom
annotated source: sample
annotated property: definition
annotated target: A sample is a substance role played by a biological substance as an input substance to a protocol.
database_cross_reference: PSI:Gel

permission
type: Class
subclass of: attribute
definition: A permission is an attribute which is a formal authorization.
has_obo_namespace: default_namespace
id: sep:00043

Axiom
annotated source: permission
annotated property: definition
annotated target: A permission is an attribute which is a formal authorization.
database_cross_reference: Wordnet:permission

security access
type: Class
subclass of: permission
definition: Security access is an permission attribute which is specification of the access right (e.g read or write) that is specified on a particular object.
has_obo_namespace: default_namespace
id: sep:00044

Axiom
annotated source: security access
annotated property: definition
annotated target: Security access is an permission attribute which is specification of the access right (e.g read or write) that is specified on a particular object.
database_cross_reference: FUGE:security access

read access
type: Class
subclass of: security access
definition: Read access is a security access permission attribute which is the access right to obtain (data) from a storage medium, such as a magnetic disk.
has_obo_namespace: default_namespace
id: sep:00045

Axiom
annotated source: read access
annotated property: definition
annotated target: Read access is a security access permission attribute which is the access right to obtain (data) from a storage medium, such as a magnetic disk.
database_cross_reference: PSI :Gel

write access
type: Class
subclass of: security access
definition: Write access is a security access permission attribute that is the access right to record or update stored data.
has_obo_namespace: default_namespace
id: sep:00046

Axiom
annotated source: write access
annotated property: definition
annotated target: Write access is a security access permission attribute that is the access right to record or update stored data.
database_cross_reference: PSI:Gel

data format
type: Class
subclass of: format
definition: A data format is a format of data Each has its own headers, codes and rules for laying out the content. There are many different file structures for each kind of file, including executable programs, word processing documents, graphics files and databases.
has_obo_namespace: default_namespace
id: sep:00047

Axiom
annotated source: data format
annotated property: definition
annotated target: A data format is a format of data Each has its own headers, codes and rules for laying out the content. There are many different file structures for each kind of file, including executable programs, word processing documents, graphics files and databases.
database_cross_reference: PSI:Gel

image file format
type: Class
subclass of: data format
definition: An image file format is a data format that provides a standardized method of organizing and storing image data. Image files are made up of picture elements, called pixels. The pixels that comprise an image are in the form of a grid of columns and rows. Each of the pixels in an image stores digital numbers representing brightness and color.
has_obo_namespace: default_namespace
id: sep:00048

Axiom
annotated source: image file format
annotated property: definition
annotated target: An image file format is a data format that provides a standardized method of organizing and storing image data. Image files are made up of picture elements, called pixels. The pixels that comprise an image are in the form of a grid of columns and rows. Each of the pixels in an image stores digital numbers representing brightness and color.
database_cross_reference: PSI:Gel

graphics interchange format
type: Class
subclass of: image file format
definition: A graphics interchange format is an image file format that supports animated images. Supports only 255 colors per frame, so requires lossy quantization for full-color photos (dithering); using multiple frames can improve color precision.
has_exact_synonym: gif
has_obo_namespace: default_namespace
id: sep:00049

Axiom
annotated source: graphics interchange format
annotated property: definition
annotated target: A graphics interchange format is an image file format that supports animated images. Supports only 255 colors per frame, so requires lossy quantization for full-color photos (dithering); using multiple frames can improve color precision.
database_cross_reference: Wikipedia:graphics interchange format

Joint Photographic Experts Group
type: Class
subclass of: image file format
definition: A Joint Photographic Experts Group is an image file format which is used extensively for photos and other continuous tone images on the web. Uses lossy compression by trying to equalize eight by eight pixel blocks; the quality can vary greatly depending on the compression settings.
has_exact_synonym: jpeg
has_exact_synonym: jpg
has_obo_namespace: default_namespace
id: sep:00050

Axiom
annotated source: Joint Photographic Experts Group
annotated property: definition
annotated target: A Joint Photographic Experts Group is an image file format which is used extensively for photos and other continuous tone images on the web. Uses lossy compression by trying to equalize eight by eight pixel blocks; the quality can vary greatly depending on the compression settings.
database_cross_reference: WIkipedia:Joint Photography Experts Group

Portable Network Graphics
type: Class
subclass of: image file format
definition: A Portable Network Graphics is an image file format which lossless compression, offering bit depths from 1 to 48.
has_exact_synonym: png
has_obo_namespace: default_namespace
id: sep:00051

Axiom
annotated source: Portable Network Graphics
annotated property: definition
annotated target: A Portable Network Graphics is an image file format which lossless compression, offering bit depths from 1 to 48.
database_cross_reference: Wikipedia:Portable Network Graphics

Scalable Vector Graphics
type: Class
subclass of: image file format
definition: Scalable Vector Graphics is an image file format which is an XML based vector graphics format, as defined by the World Wide Web Consortium for use in web browsers.
has_exact_synonym: svg
has_obo_namespace: default_namespace
id: sep:00052

Axiom
annotated source: Scalable Vector Graphics
annotated property: definition
annotated target: Scalable Vector Graphics is an image file format which is an XML based vector graphics format, as defined by the World Wide Web Consortium for use in web browsers.
database_cross_reference: Wikipedia:Scalable Vector Graphics

Tagged Image File Format
type: Class
subclass of: image file format
definition: A Tagged Image File Format is an image file format which is used extensively for traditional print graphics. Lossy and lossless compression available, but many programs only support a subset of available options.
has_exact_synonym: tif
has_exact_synonym: tiff
has_obo_namespace: default_namespace
id: sep:00053

Axiom
annotated source: Tagged Image File Format
annotated property: definition
annotated target: A Tagged Image File Format is an image file format which is used extensively for traditional print graphics. Lossy and lossless compression available, but many programs only support a subset of available options.
database_cross_reference: Wikipedia:Tagged Image File Format

Windows Bitmap
type: Class
subclass of: image file format
definition: A Windows Bitmap is a image file format which is commonly used by Microsoft Windows programs, and the Windows operating system itself. Lossless compression can be specified, but some programs use only uncompressed files.
has_exact_synonym: bmp
has_obo_namespace: default_namespace
id: sep:00054

Axiom
annotated source: Windows Bitmap
annotated property: definition
annotated target: A Windows Bitmap is a image file format which is commonly used by Microsoft Windows programs, and the Windows operating system itself. Lossless compression can be specified, but some programs use only uncompressed files.
database_cross_reference: Wikipedia:Windows Bitmap

quantity
type: Class
subclass of: abstract
definition: A quantity is an abstract concept which is any specification of how many or how much of something there is.
has_obo_namespace: default_namespace
id: sep:00055

Axiom
annotated source: quantity
annotated property: definition
annotated target: A quantity is an abstract concept which is any specification of how many or how much of something there is.
database_cross_reference: SUMO:quality

unit of measure
type: Class
subclass of: quantity
definition: A unit of measure is a quantity which is a standard of measurement for some dimension. For example, the Meter is a Unit O fMeasure for the dimension of length, as is the Inch. There is no intrinsic property of a UnitOfMeasure that makes it primitive or fundamental; rather, a system of units (e.g. Systeme International Unit) defines a set of orthogonal dimensions and assigns units for each.
has_obo_namespace: default_namespace
id: sep:00056
comment: Units of measure should be imported from PATO units ontology under this node http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/.

Axiom
annotated source: unit of measure
annotated property: definition
annotated target: A unit of measure is a quantity which is a standard of measurement for some dimension. For example, the Meter is a Unit O fMeasure for the dimension of length, as is the Inch. There is no intrinsic property of a UnitOfMeasure that makes it primitive or fundamental; rather, a system of units (e.g. Systeme International Unit) defines a set of orthogonal dimensions and assigns units for each.
database_cross_reference: SUMO:unit of measure

measurement range
type: Class
subclass of: quantity
definition: A measurement range is a quantity which consists of a lower value, an upper value and a unit of measure.
has_obo_namespace: default_namespace
id: sep:00057

Axiom
annotated source: measurement range
annotated property: definition
annotated target: A measurement range is a quantity which consists of a lower value, an upper value and a unit of measure.
database_cross_reference: PSI:Gel

pH range
type: Class
subclass of: measurement range
definition: A pH range is a measurement range which has a unit of measure of pH.
has_obo_namespace: default_namespace
id: sep:00058

Axiom
annotated source: pH range
annotated property: definition
annotated target: A pH range is a measurement range which has a unit of measure of pH.
database_cross_reference: PSI:Gel

molecular weight range
type: Class
subclass of: measurement range
definition: A molecular weight range is a measurement range which has a measurement unit of Kilo Daltons.
has_obo_namespace: default_namespace
id: sep:00059

Axiom
annotated source: molecular weight range
annotated property: definition
annotated target: A molecular weight range is a measurement range which has a measurement unit of Kilo Daltons.
database_cross_reference: PSI:Gel

software
type: Class
subclass of: digital entity
definition: Software is a digital entity that is the general term for a variety of procedures and routines that harness the computational power of a computer to produce, for example, a general operating system that coordinates the basic workings of the computer or specific applications. A common misconception is that software is data. It is not. Software tells the hardware how to process the data.
has_obo_namespace: default_namespace
id: sep:00060

Axiom
annotated source: software
annotated property: definition
annotated target: Software is a digital entity that is the general term for a variety of procedures and routines that harness the computational power of a computer to produce, for example, a general operating system that coordinates the basic workings of the computer or specific applications. A common misconception is that software is data. It is not. Software tells the hardware how to process the data.
database_cross_reference: West's Encyclopedia of American Law:software

image acquistion software
type: Class
subclass of: software
definition: Image acquisition software is software that is designed to aquire a digitised image of a physical object.
has_obo_namespace: default_namespace
id: sep:00061

Axiom
annotated source: image acquistion software
annotated property: definition
annotated target: Image acquisition software is software that is designed to aquire a digitised image of a physical object.
database_cross_reference: PSI:GEL

image analysis software
type: Class
subclass of: software
definition: Image analysis software is software which is the extraction of meaningful information from images; mainly from digital images by means of digital image processing techniques. Image analysis tasks can be as simple as reading bar coded tags or as sophisticated as identifying a person from their face.
has_obo_namespace: default_namespace
id: sep:00062

Axiom
annotated source: image analysis software
annotated property: definition
annotated target: Image analysis software is software which is the extraction of meaningful information from images; mainly from digital images by means of digital image processing techniques. Image analysis tasks can be as simple as reading bar coded tags or as sophisticated as identifying a person from their face.
database_cross_reference: PSI:GEL

progenisis
type: Class
subclass of: image analysis software
definition: The progenesis range is image analysis software manufactured by Nonlinear Dynamics that offers analysis and data-mining software for 2D electrophoresis and MS applications, including biomarker discovery.
has_obo_namespace: default_namespace
id: sep:00063

Axiom
annotated source: progenisis
annotated property: definition
annotated target: The progenesis range is image analysis software manufactured by Nonlinear Dynamics that offers analysis and data-mining software for 2D electrophoresis and MS applications, including biomarker discovery.
database_cross_reference: PSI:GEL

software attribute
type: Class
subclass of: attribute
definition: A software attribute is an attribute that is associated with software.
has_obo_namespace: default_namespace
id: sep:00064

Axiom
annotated source: software attribute
annotated property: definition
annotated target: A software attribute is an attribute that is associated with software.
database_cross_reference: PSI:GEL

software version number
type: Class
subclass of: software attribute
definition: A software version number is a software attribute that represents the version of software.
has_obo_namespace: default_namespace
id: sep:00065

Axiom
annotated source: software version number
annotated property: definition
annotated target: A software version number is a software attribute that represents the version of software.
database_cross_reference: PSI:GEL

progenisis PG200
type: Class
subclass of: progenisis
definition: Progenisis PG200 is a progenisis image analysis software that offers an advanced workflow and powerful data analysis for the proteomics researcher.
has_obo_namespace: default_namespace
id: sep:00066

Axiom
annotated source: progenisis PG200
annotated property: definition
annotated target: Progenisis PG200 is a progenisis image analysis software that offers an advanced workflow and powerful data analysis for the proteomics researcher.
database_cross_reference: PSI:GEL

progeniss PG220
type: Class
subclass of: progenisis
definition: Progenisis PG220 is a progensis image analysis software that has all the features of the PG200 plus a range of additional tools designed specifically for the analysis of DIGE experiments.
has_obo_namespace: default_namespace
id: sep:00067

Axiom
annotated source: progeniss PG220
annotated property: definition
annotated target: Progenisis PG220 is a progensis image analysis software that has all the features of the PG200 plus a range of additional tools designed specifically for the analysis of DIGE experiments.
database_cross_reference: PSI:GEL

progenisis PG240
type: Class
subclass of: progenisis
definition: The Progenisis PG240 is a progensis image analysis software that is the flagship of traditional and 2D DIGE gel analysis products, the PG240 caters for the needs of the most advanced users.
has_obo_namespace: default_namespace
id: sep:00068

Axiom
annotated source: progenisis PG240
annotated property: definition
annotated target: The Progenisis PG240 is a progensis image analysis software that is the flagship of traditional and 2D DIGE gel analysis products, the PG240 caters for the needs of the most advanced users.
database_cross_reference: PSI:GEL

SameSpots
type: Class
subclass of: image analysis software
definition: SameSpots is image analysis software by Nonlinear Dynamice that is unique technology delivering a major advance for the analysis of single stain or 2D DIGE images, allowing you to match and compare all the proteins in your experiment. SameSpots redefines the 2D image analysis workflow, delivering significant improvements in speed, objectivity and statistical power that create new possibilities for proteomics research.
has_obo_namespace: default_namespace
id: sep:00069

Axiom
annotated source: SameSpots
annotated property: definition
annotated target: SameSpots is image analysis software by Nonlinear Dynamice that is unique technology delivering a major advance for the analysis of single stain or 2D DIGE images, allowing you to match and compare all the proteins in your experiment. SameSpots redefines the 2D image analysis workflow, delivering significant improvements in speed, objectivity and statistical power that create new possibilities for proteomics research.
database_cross_reference: PSI:GEL

DeCyder
type: Class
subclass of: image analysis software
definition: Decyder is image analysis software that significantly increases throughput by accurately addressing measurement of protein differences with statistical confidence . DeCyder Differential Analysis Software automatically detects, matches and analyzes protein spots in multiplexed fluorescent images, and is able to give routine detection of < 10% differences with > 95 % confidence. Statistical analysis is carried out on each and every difference.
has_obo_namespace: default_namespace
id: sep:00070

Axiom
annotated source: DeCyder
annotated property: definition
annotated target: Decyder is image analysis software that significantly increases throughput by accurately addressing measurement of protein differences with statistical confidence . DeCyder Differential Analysis Software automatically detects, matches and analyzes protein spots in multiplexed fluorescent images, and is able to give routine detection of < 10% differences with > 95 % confidence. Statistical analysis is carried out on each and every difference.
database_cross_reference: PSI:GEL

Delta2D
type: Class
subclass of: image analysis software
definition: Delata2D is image analysis software that is manufactured by Decodon.
has_obo_namespace: default_namespace
id: sep:00071

Axiom
annotated source: Delta2D
annotated property: definition
annotated target: Delata2D is image analysis software that is manufactured by Decodon.
database_cross_reference: PSI:GEL

object
type: Class
subclass of: physical
definition: An object is a physical concept that has independent material existence and is a separate and distinct portion of matter.
has_obo_namespace: default_namespace
id: sep:00072

Axiom
annotated source: object
annotated property: definition
annotated target: An object is a physical concept that has independent material existence and is a separate and distinct portion of matter.
database_cross_reference: Roget's II: The New Thesaurus
database_cross_reference: Third Edition:object

process
type: Class
subclass of: physical
definition: A process is a physical concpet that has temporal parts or stages. Examples include extended events like a football match or a race, actions like Pursuing and Reading, and biological processes. The formal definition is: anything that lasts for a time but is not an Object. Note that a Process may have participants 'inside' it which are Objects, such as the players in a football match. In a 4D ontology, a Process is something whose spatiotemporal extent is thought of as dividing into temporal stages roughly perpendicular to the time-axis.
has_obo_namespace: default_namespace
id: sep:00073

Axiom
annotated source: process
annotated property: definition
annotated target: A process is a physical concpet that has temporal parts or stages. Examples include extended events like a football match or a race, actions like Pursuing and Reading, and biological processes. The formal definition is: anything that lasts for a time but is not an Object. Note that a Process may have participants 'inside' it which are Objects, such as the players in a football match. In a 4D ontology, a Process is something whose spatiotemporal extent is thought of as dividing into temporal stages roughly perpendicular to the time-axis.
database_cross_reference: SUMO:process

collection
type: Class
subclass of: object
definition: A collection is an object which have members and a position in space-time and members can be added and subtracted without thereby changing the identity of the Collection. Some examples are toolkits, football teams, and flocks of sheep.
has_obo_namespace: default_namespace
id: sep:00074

Axiom
annotated source: collection
annotated property: definition
annotated target: A collection is an object which have members and a position in space-time and members can be added and subtracted without thereby changing the identity of the Collection. Some examples are toolkits, football teams, and flocks of sheep.
database_cross_reference: SUMO:collection

device
type: Class
subclass of: object
definition: A device is an object which provides a mechanical advantage when used in a process.
has_obo_namespace: default_namespace
id: sep:00075

Axiom
annotated source: device
annotated property: definition
annotated target: A device is an object which provides a mechanical advantage when used in a process.
database_cross_reference: PSI:Gel

substance
type: Class
subclass of: object
definition: A substance is an Object in which every part is similar to every other in every relevant respect. More precisely, something is a Substance when it has only arbitrary pieces as parts - any parts have properties which are similar to those of the whole. Note that a Substance may nonetheless have physical properties that vary. For example, the temperature, chemical constitution, density, etc. may change from one part to another. An example would be a body of water.
has_obo_namespace: default_namespace
id: sep:00076

Axiom
annotated source: substance
annotated property: definition
annotated target: A substance is an Object in which every part is similar to every other in every relevant respect. More precisely, something is a Substance when it has only arbitrary pieces as parts - any parts have properties which are similar to those of the whole. Note that a Substance may nonetheless have physical properties that vary. For example, the temperature, chemical constitution, density, etc. may change from one part to another. An example would be a body of water.
database_cross_reference: SUMO:substance

group
type: Class
subclass of: collection
definition: A group is a defnined collection of objects, e.g. a flock of sheep, a herd of goats, or the local Boy Scout troop.
has_obo_namespace: default_namespace
id: sep:00077

Axiom
annotated source: group
annotated property: definition
annotated target: A group is a defnined collection of objects, e.g. a flock of sheep, a herd of goats, or the local Boy Scout troop.
database_cross_reference: SUMO:group

organization
type: Class
subclass of: group
definition: An organization is a group which the members of an Organization typically have a common purpose or function. Note that this class also covers divisions, departments, etc. of organizations. For example, both the Shell Corporation and the accounting department at Shell would both be instances of Organization. Note too that the existence of an Organization is dependent on the existence of at least one member (since Organization is a subclass of Collection). Accordingly, in cases of purely legal organizations, a fictitious member should be assumed.
has_obo_namespace: default_namespace
id: sep:00078

Axiom
annotated source: organization
annotated property: definition
annotated target: An organization is a group which the members of an Organization typically have a common purpose or function. Note that this class also covers divisions, departments, etc. of organizations. For example, both the Shell Corporation and the accounting department at Shell would both be instances of Organization. Note too that the existence of an Organization is dependent on the existence of at least one member (since Organization is a subclass of Collection). Accordingly, in cases of purely legal organizations, a fictitious member should be assumed.
database_cross_reference: SUMO:organisation

consortium
type: Class
subclass of: organization
definition: A consortium is an association of organisations for some definite purpose.
has_obo_namespace: default_namespace
id: sep:00079

Axiom
annotated source: consortium
annotated property: definition
annotated target: A consortium is an association of organisations for some definite purpose.
database_cross_reference: SUMO:consortium

The Human Proteome Organisation
type: Class
subclass of: consortium
definition: The Human Proteome Organisation (HUPO) is an international consortium of national proteomics research associations, government researchers, academic institutions, and industry partners. HUPO promotes the development and awareness of proteomics research, advocates on behalf of proteomics researchers throughout the world, and facilitates scientific collaborations between HUPO members and Initiatives.
has_exact_synonym: HUPO
has_obo_namespace: default_namespace
id: sep:00080

Axiom
annotated source: The Human Proteome Organisation
annotated property: definition
annotated target: The Human Proteome Organisation (HUPO) is an international consortium of national proteomics research associations, government researchers, academic institutions, and industry partners. HUPO promotes the development and awareness of proteomics research, advocates on behalf of proteomics researchers throughout the world, and facilitates scientific collaborations between HUPO members and Initiatives.
database_cross_reference: PSI :GEL

The Human Proteome Organisation Proteomics Standards Initiative
type: Class
subclass of: consortium
definition: The HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparision, exchange and verification. The PSI was founded at the HUPO meeting in Washington, April 28-29, 2002 (see Science 296, 827).
has_exact_synonym: HUPO PSI
has_exact_synonym: HUPO Proteomics Standards Initiative
has_exact_synonym: PSI
has_obo_namespace: default_namespace
id: sep:00081

Axiom
annotated source: The Human Proteome Organisation Proteomics Standards Initiative
annotated property: definition
annotated target: The HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparision, exchange and verification. The PSI was founded at the HUPO meeting in Washington, April 28-29, 2002 (see Science 296, 827).
database_cross_reference: PSI:GEL

PSI GEL
type: Class
subclass of: proteomics standards initiative working group
definition: The PSI working group for Gel-based methods of analysis (GEL).
has_obo_namespace: default_namespace
id: sep:00082

Axiom
annotated source: PSI GEL
annotated property: definition
annotated target: The PSI working group for Gel-based methods of analysis (GEL).
database_cross_reference: PSI:GEL

PSI MI
type: Class
subclass of: proteomics standards initiative working group
definition: The PSI working group for Molecular Interactions (MI).
has_obo_namespace: default_namespace
id: sep:00083

Axiom
annotated source: PSI MI
annotated property: definition
annotated target: The PSI working group for Molecular Interactions (MI).
database_cross_reference: PSI:GEL

PSI MOD
type: Class
subclass of: proteomics standards initiative working group
definition: The PSI working group for Protein Modifications (MOD).
has_obo_namespace: default_namespace
id: sep:00084

Axiom
annotated source: PSI MOD
annotated property: definition
annotated target: The PSI working group for Protein Modifications (MOD).
database_cross_reference: PSI:GEL

PSI MS
type: Class
subclass of: proteomics standards initiative working group
definition: The PSI working group for Mass Spectrometry Data Interchange (MS).
has_obo_namespace: default_namespace
id: sep:00085

Axiom
annotated source: PSI MS
annotated property: definition
annotated target: The PSI working group for Mass Spectrometry Data Interchange (MS).
database_cross_reference: PSI:GEL

PSI PI
type: Class
subclass of: proteomics standards initiative working group
definition: The PSI working group for Proteomics Informatics (PI).
has_obo_namespace: default_namespace
id: sep:00086

Axiom
annotated source: PSI PI
annotated property: definition
annotated target: The PSI working group for Proteomics Informatics (PI).
database_cross_reference: PSI :GEL

PSI SP
type: Class
subclass of: proteomics standards initiative working group
definition: The PSI working group for Separations and Sample Preparation (SP).
has_obo_namespace: default_namespace
id: sep:00087

Axiom
annotated source: PSI SP
annotated property: definition
annotated target: The PSI working group for Separations and Sample Preparation (SP).
database_cross_reference: PSI:GEL

vendor
type: Class
subclass of: organization
definition: A vendor is an organisation that supplier of goods or services of a commercial nature may be a manufacturer, importer, or wholesale distributor.
has_obo_namespace: default_namespace
id: sep:00088

Axiom
annotated source: vendor
annotated property: definition
annotated target: A vendor is an organisation that supplier of goods or services of a commercial nature may be a manufacturer, importer, or wholesale distributor.
database_cross_reference: Dictionary of Finance and Investment Terms:vendor

educational organisation
type: Class
subclass of: organization
definition: An educational organization is an organisation which is an institution of learning. Some examples are public and private K-12 schools, and colleges and universities.
has_obo_namespace: default_namespace
id: sep:00089

Axiom
annotated source: educational organisation
annotated property: definition
annotated target: An educational organization is an organisation which is an institution of learning. Some examples are public and private K-12 schools, and colleges and universities.
database_cross_reference: SUMO:educational organisation

university
type: Class
subclass of: educational organisation
definition: A university is an educational organisations which admits students that have graduated from high school (known as undergraduate students) and students who have received a bachelor's degree (known as graduate students). A University confers both bachelor's and graduate degrees.
has_obo_namespace: default_namespace
id: sep:00090

Axiom
annotated source: university
annotated property: definition
annotated target: A university is an educational organisations which admits students that have graduated from high school (known as undergraduate students) and students who have received a bachelor's degree (known as graduate students). A University confers both bachelor's and graduate degrees.
database_cross_reference: SUMO:university

government organisation
type: Class
subclass of: organization
definition: A Government organization is the is an organisation that is concerned with the government of a Geopolitical Area at some level. They may be a suborganization of a government.
has_obo_namespace: default_namespace
id: sep:00091

Axiom
annotated source: government organisation
annotated property: definition
annotated target: A Government organization is the is an organisation that is concerned with the government of a Geopolitical Area at some level. They may be a suborganization of a government.
database_cross_reference: SUMO:government organisation

blot module
type: Class
subclass of: device
definition: A blot module is a device which permits the protocol of blotting to be performed.
has_obo_namespace: default_namespace
id: sep:00092

Axiom
annotated source: blot module
annotated property: definition
annotated target: A blot module is a device which permits the protocol of blotting to be performed.
database_cross_reference: PSI:GEL

electrical power supply
type: Class
subclass of: device
definition: An electrical power supply is a device that supplies electricity. For example a power pack.
has_exact_synonym: power pack
has_obo_namespace: default_namespace
id: sep:00093

Axiom
annotated source: electrical power supply
annotated property: definition
annotated target: An electrical power supply is a device that supplies electricity. For example a power pack.
database_cross_reference: PSI:GEL

gel dryer
type: Class
subclass of: device
definition: A gel dryer is a device which permits drying of gels.
has_obo_namespace: default_namespace
id: sep:00094

Axiom
annotated source: gel dryer
annotated property: definition
annotated target: A gel dryer is a device which permits drying of gels.
database_cross_reference: PSI:GEL

gel tank
type: Class
subclass of: device
definition: A gel tank is a device which holds a gel and running buffers to allow electrophoresis to be performed.
has_obo_namespace: default_namespace
id: sep:00095

Axiom
annotated source: gel tank
annotated property: definition
annotated target: A gel tank is a device which holds a gel and running buffers to allow electrophoresis to be performed.
database_cross_reference: PSI:GEL

image acquisition device
type: Class
subclass of: device
definition: An image acquisition device is a device which captures a digitiesed image of an object.
has_obo_namespace: default_namespace
id: sep:00096

Axiom
annotated source: image acquisition device
annotated property: definition
annotated target: An image acquisition device is a device which captures a digitiesed image of an object.
database_cross_reference: PSI:GEL

isoelectric focusing device
type: Class
subclass of: device
definition: An isoelectric focussing device is a device in which isoelectric focusing can be performed.
has_exact_synonym: isoelctric focusing unit
has_obo_namespace: default_namespace
id: sep:00097

Axiom
annotated source: isoelectric focusing device
annotated property: definition
annotated target: An isoelectric focussing device is a device in which isoelectric focusing can be performed.
database_cross_reference: PSI:GEL

thermostatic circulator
type: Class
subclass of: device
definition: A thermostatic circulator is a device which cools or heats a circulating liquid.
has_obo_namespace: default_namespace
id: sep:00098

Axiom
annotated source: thermostatic circulator
annotated property: definition
annotated target: A thermostatic circulator is a device which cools or heats a circulating liquid.
database_cross_reference: PSI:GEL

camera
type: Class
subclass of: image acquisition device
definition: A camera is an image acquistion device which is used for taking photographs (usually consisting of a lightproof box with a lens at one end and light-sensitive film at the other).
has_obo_namespace: default_namespace
id: sep:00099

Axiom
annotated source: camera
annotated property: definition
annotated target: A camera is an image acquistion device which is used for taking photographs (usually consisting of a lightproof box with a lens at one end and light-sensitive film at the other).
database_cross_reference: Wordnet:camera

scanner
type: Class
subclass of: image acquisition device
definition: A scanner is an image acquistion device that generates a digital representation of an image for data input to a computer.
has_obo_namespace: default_namespace
id: sep:00100

Axiom
annotated source: scanner
annotated property: definition
annotated target: A scanner is an image acquistion device that generates a digital representation of an image for data input to a computer.
database_cross_reference: Wordnet:scanner

protocol
type: Class
subclass of: process
definition: A protocol is a process which is a parameterizable description of a process.
has_obo_namespace: default_namespace
id: sep:00101

Axiom
annotated source: protocol
annotated property: definition
annotated target: A protocol is a process which is a parameterizable description of a process.
database_cross_reference: FUGE:protocol

protein blocking
type: Class
subclass of: protocol
definition: A blocking protocol is a protocol to prevent non-specific protein interactions between it and the antibody used for detection of the target protein. Blocking of non-specific binding is achieved by placing the membrane in a dilute solution of protein - typically Bovine serum albumin (BSA) or non-fat dry milk, with a minute percentage of detergent such as Tween 20 or colloidal carbon.
has_obo_namespace: default_namespace
id: sep:00102

Axiom
annotated source: protein blocking
annotated property: definition
annotated target: A blocking protocol is a protocol to prevent non-specific protein interactions between it and the antibody used for detection of the target protein. Blocking of non-specific binding is achieved by placing the membrane in a dilute solution of protein - typically Bovine serum albumin (BSA) or non-fat dry milk, with a minute percentage of detergent such as Tween 20 or colloidal carbon.
database_cross_reference: Wikipedia:Blocking

biological substance
type: Class
subclass of: substance
definition: A biological substance is a substance which originates from a biological organism.
has_obo_namespace: default_namespace
id: sep:00103

Axiom
annotated source: biological substance
annotated property: definition
annotated target: A biological substance is a substance which originates from a biological organism.
database_cross_reference: PSI:GEL

chemical substance
type: Class
subclass of: substance
definition: A chemical agent is a substance that is synthetic compounds that are not an analogue of anything occurring naturally and that can result in serious burns, paralysis, and death to Organisms.
has_obo_namespace: default_namespace
id: sep:00104
comment: The ontology of chemical entities should be imported under this node, or created under this node, if not included in Chebi.

Axiom
annotated source: chemical substance
annotated property: definition
annotated target: A chemical agent is a substance that is synthetic compounds that are not an analogue of anything occurring naturally and that can result in serious burns, paralysis, and death to Organisms.
database_cross_reference: SUMO:chemical agent

gas substance
type: Class
subclass of: substance
definition: A compound gas is a compound substance that is a mixture that satisfies two conditions.it is made up predominantly of things which are a Gas and any component other than Gas in the Mixture is in the form of fine particles which are suspended in the Gas.
has_obo_namespace: default_namespace
id: sep:00105

Axiom
annotated source: gas substance
annotated property: definition
annotated target: A compound gas is a compound substance that is a mixture that satisfies two conditions.it is made up predominantly of things which are a Gas and any component other than Gas in the Mixture is in the form of fine particles which are suspended in the Gas.
database_cross_reference: SUMO:compound gas

compound liquid
type: Class
subclass of: substance
definition: A compound liquid is a compound substance that satisfies two conditions. It is made up predominantly of things which are a Liquid and any component other than Liquid in the Mixture is in the form of fine particles which are suspended in the Liquid.
has_obo_namespace: default_namespace
id: sep:00106

Axiom
annotated source: compound liquid
annotated property: definition
annotated target: A compound liquid is a compound substance that satisfies two conditions. It is made up predominantly of things which are a Liquid and any component other than Liquid in the Mixture is in the form of fine particles which are suspended in the Liquid.
database_cross_reference: SUMO:liquid mixture

filter paper
type: Class
subclass of: substance
definition: Fliter paper is a compund substance which is a porous unsized paper used for filtering.
has_obo_namespace: default_namespace
id: sep:00107

Axiom
annotated source: filter paper
annotated property: definition
annotated target: Fliter paper is a compund substance which is a porous unsized paper used for filtering.
database_cross_reference: WordNet:filter paper

mobile phase
type: Class
subclass of: substance role
definition: Need DEF
has_obo_namespace: default_namespace
id: sep:00108

Axiom
annotated source: mobile phase
annotated property: definition
annotated target: Need DEF
database_cross_reference: to:add

digital entity
type: Class
subclass of: abstract
definition: A digital entity is an abstract concept that is a binary representation of information; facts, concepts, or instructions in a formalized manner suitable for communication, interpretation, or processing by humans or by automatic means. Any representations such as characters or analog quantities to which meaning is or might be assigned.
has_obo_namespace: default_namespace
id: sep:00109

Axiom
annotated source: digital entity
annotated property: definition
annotated target: A digital entity is an abstract concept that is a binary representation of information; facts, concepts, or instructions in a formalized manner suitable for communication, interpretation, or processing by humans or by automatic means. Any representations such as characters or analog quantities to which meaning is or might be assigned.
database_cross_reference: PSI:GEL

gel
type: Class
subclass of: substance
definition: A gel is a compund substance which is a colloid in a more solid form than a solution.
has_obo_namespace: default_namespace
id: sep:00110

Axiom
annotated source: gel
annotated property: definition
annotated target: A gel is a compund substance which is a colloid in a more solid form than a solution.
database_cross_reference: Wordnet:gel

gel excised analyte
type: Class
subclass of: substance
definition: A gel excised analyte is a compound substance which is a location on a gel which has been excised, cut out or removed.
has_obo_namespace: default_namespace
id: sep:00111

Axiom
annotated source: gel excised analyte
annotated property: definition
annotated target: A gel excised analyte is a compound substance which is a location on a gel which has been excised, cut out or removed.
database_cross_reference: PSI:GEL

membrane substance
type: Class
subclass of: substance
definition: A membrane compound is a compound substance which is a thin sheet of natural or synthetic material that is permeable to substances in solution.
has_obo_namespace: default_namespace
id: sep:00112

Axiom
annotated source: membrane substance
annotated property: definition
annotated target: A membrane compound is a compound substance which is a thin sheet of natural or synthetic material that is permeable to substances in solution.
database_cross_reference: :The American Heritage Dictionary of the English Language
database_cross_reference: Fourth Edition:membrane

Parafilm
type: Class
subclass of: substance
definition: Parafilm is a compound substance which is a product of the American Can Company, consisting of a flexible film that is commonly used for sealing or protecting vessels. Because it is stretchy, moldable, waterproof, odorless, thermoplastic, semitransparent and self-adhering, it can be used to make a temporary flexible seal on open vessels (such as flasks or cuvettes) as one might employ plastic wrap. It can also be used to further seal a lidded container against moisture for long term storage.
has_obo_namespace: default_namespace
id: sep:00113

Axiom
annotated source: Parafilm
annotated property: definition
annotated target: Parafilm is a compound substance which is a product of the American Can Company, consisting of a flexible film that is commonly used for sealing or protecting vessels. Because it is stretchy, moldable, waterproof, odorless, thermoplastic, semitransparent and self-adhering, it can be used to make a temporary flexible seal on open vessels (such as flasks or cuvettes) as one might employ plastic wrap. It can also be used to further seal a lidded container against moisture for long term storage.
database_cross_reference: Wikipedia:Parafilm

Coomassie blue
type: Class
subclass of: chemical substance
subclass of: Restriction
  on property: has_units
  some values from: UO_0000062
subclass of: Restriction
  on property: has_units
  some values from: UO_0000063
subclass of: Restriction
  on property: has_units
  some values from: UO_0000098
subclass of: Restriction
  on property: has_units
  some values from: UO_0000101
subclass of: Restriction
  on property: has_units
  some values from: UO_0000165
subclass of: Restriction
  on property: has_units
  some values from: UO_0000173
subclass of: Restriction
  on property: has_units
  some values from: UO_0000176
subclass of: Restriction
  on property: has_units
  some values from: UO_0000187
subclass of: Restriction
  on property: has_units
  some values from: UO_0000205
definition: Coomassie blue is a chemical agent that nonspecifically stains proteins a strong blue colour. It is often used in gel electrophoresis.
database_cross_reference: value-type:xsd:float
has_exact_synonym: Acid Blue 90
has_exact_synonym: Brilliant Blue
has_exact_synonym: Brilliant Blue G
has_exact_synonym: Brilliant Blue G 250
has_exact_synonym: C.I. 42655
has_obo_namespace: default_namespace
id: sep:00114

Axiom
annotated source: Coomassie blue
annotated property: definition
annotated target: Coomassie blue is a chemical agent that nonspecifically stains proteins a strong blue colour. It is often used in gel electrophoresis.
database_cross_reference: Wikipedia:Coomassie blue

The allowed value-type for this CV term.
type: Axiom
annotated source: Coomassie blue
annotated property: database_cross_reference
annotated target: value-type:xsd:float

solution
type: Class
subclass of: compound liquid
definition: A solution is a compund liquid which is a homogeneous mixture of two or more substances, which may be solids, liquids, gases, or a combination of these.
has_obo_namespace: default_namespace
id: sep:00115

Axiom
annotated source: solution
annotated property: definition
annotated target: A solution is a compund liquid which is a homogeneous mixture of two or more substances, which may be solids, liquids, gases, or a combination of these.
database_cross_reference: :The American Heritage Dictionary of the English Language
database_cross_reference: Fourth Edition:solution

suspension
type: Class
subclass of: compound liquid
definition: A suspension is a compund liquid in which microscopically visible particles are dispersed throughout a less dense liquid or gas from which they are easily filtered but not easily settled because of system viscocity or molecular interactions.
has_obo_namespace: default_namespace
id: sep:00116

Axiom
annotated source: suspension
annotated property: definition
annotated target: A suspension is a compund liquid in which microscopically visible particles are dispersed throughout a less dense liquid or gas from which they are easily filtered but not easily settled because of system viscocity or molecular interactions.
database_cross_reference: The American Heritage Dictionary of the English Language Fourth Edition:suspension

agarose sealing solution
type: Class
subclass of: solution
definition: Agarose sealing solution is a solution which is an agarose/buffer solution used to seal the first dimension gel to the second dimension gel in Two dimensional gel electrophoresis.
has_obo_namespace: default_namespace
id: sep:00117

Axiom
annotated source: agarose sealing solution
annotated property: definition
annotated target: Agarose sealing solution is a solution which is an agarose/buffer solution used to seal the first dimension gel to the second dimension gel in Two dimensional gel electrophoresis.
database_cross_reference: PSI:GEL

buffer solution
type: Class
subclass of: solution
definition: A solution selected or prepared to minimize changes in hydrogen ion concentration which would otherwise tend to occur as a result of a chemical reaction. In general, chemical buffers are systems which, once constituted, tend to resist further change due to external influences. Thus it is possible, for example, to make buffers resistant to changes in temperature, pressure, volume, redox potential, or acidity. The commonest buffer in chemical solution systems is the acid-base buffer, which resists changes in pH.
has_exact_synonym: chemical buffer
has_obo_namespace: default_namespace
id: sep:00118

Axiom
annotated source: buffer solution
annotated property: definition
annotated target: A solution selected or prepared to minimize changes in hydrogen ion concentration which would otherwise tend to occur as a result of a chemical reaction. In general, chemical buffers are systems which, once constituted, tend to resist further change due to external influences. Thus it is possible, for example, to make buffers resistant to changes in temperature, pressure, volume, redox potential, or acidity. The commonest buffer in chemical solution systems is the acid-base buffer, which resists changes in pH.
database_cross_reference: McGraw-Hill Encyclopedia of Science and Technology:buffer solution

fixation solution
type: Class
subclass of: solution
definition: A fixing solution is a solution used to fix proteins in a gel after gel electrophoresis has been performed.
has_obo_namespace: default_namespace
has_related_synonym: fixing solution
id: sep:00119

Axiom
annotated source: fixation solution
annotated property: definition
annotated target: A fixing solution is a solution used to fix proteins in a gel after gel electrophoresis has been performed.
database_cross_reference: PSI:GEL

carrier ampholyte buffer
type: Class
subclass of: buffer solution
definition: A carrier ampholyte buffer is a buffer solutions which contains Carrier ampholytes. They enhance protein solubility by minimizing protein aggregation due to charge-charge interactions.
has_exact_synonym: IPG Buffer
has_obo_namespace: default_namespace
has_related_synonym: Immobilized pH gradient Buffer
id: sep:00120

Axiom
annotated source: carrier ampholyte buffer
annotated property: definition
annotated target: A carrier ampholyte buffer is a buffer solutions which contains Carrier ampholytes. They enhance protein solubility by minimizing protein aggregation due to charge-charge interactions.
database_cross_reference: PSI:GEL

electrophoresis buffer
type: Class
subclass of: buffer solution
definition: An electrophoresis buffer is a buffer solution which is used to perform electrophoresis.
has_obo_namespace: default_namespace
id: sep:00121

Axiom
annotated source: electrophoresis buffer
annotated property: definition
annotated target: An electrophoresis buffer is a buffer solution which is used to perform electrophoresis.
database_cross_reference: PSI:GEL

loading buffer
type: Class
subclass of: buffer solution
definition: A loading buffer is a buffer solution which contains a suspended substance and facilitates loading onto another substance. For example in gel electrophoresis a sample is suspended in a loading buffer prior to application onto a gel matrix.
has_obo_namespace: default_namespace
id: sep:00122

Axiom
annotated source: loading buffer
annotated property: definition
annotated target: A loading buffer is a buffer solution which contains a suspended substance and facilitates loading onto another substance. For example in gel electrophoresis a sample is suspended in a loading buffer prior to application onto a gel matrix.
database_cross_reference: PSI:GEL

rehydration buffer
type: Class
subclass of: buffer solution
definition: A rehydration buffer is a buffer solution used to rehydrate a substance. For example in two dimensional gel electrophoresis the first dimension gel is rehydrated prior to the second dimension of electrophoresis.
has_obo_namespace: default_namespace
id: sep:00123

Axiom
annotated source: rehydration buffer
annotated property: definition
annotated target: A rehydration buffer is a buffer solution used to rehydrate a substance. For example in two dimensional gel electrophoresis the first dimension gel is rehydrated prior to the second dimension of electrophoresis.
database_cross_reference: PSI:GEL

sample buffer
type: Class
subclass of: buffer solution
definition: A sample buffer is a buffer solution which contains a biological substance used in the role of a sample.
has_obo_namespace: default_namespace
id: sep:00124

Axiom
annotated source: sample buffer
annotated property: definition
annotated target: A sample buffer is a buffer solution which contains a biological substance used in the role of a sample.
database_cross_reference: PSI:GEL

transfer buffer
type: Class
subclass of: buffer solution
definition: A transfer buffer is a buffer solution used to facilitate the transfer of one substance to another substance. For example; The buffer used in protein transfer procedure in immuno blots.
has_obo_namespace: default_namespace
id: sep:00125

Axiom
annotated source: transfer buffer
annotated property: definition
annotated target: A transfer buffer is a buffer solution used to facilitate the transfer of one substance to another substance. For example; The buffer used in protein transfer procedure in immuno blots.
database_cross_reference: PSI:GEL

Laemelli buffer
type: Class
subclass of: electrophoresis buffer
definition: Laemmli bufferis an electrophoresis buffer which is used as a running buffer in gel electrophoresis.
has_obo_namespace: default_namespace
id: sep:00126

Axiom
annotated source: Laemelli buffer
annotated property: definition
annotated target: Laemmli bufferis an electrophoresis buffer which is used as a running buffer in gel electrophoresis.
database_cross_reference: PubMed:PMID:236308

gel matrix
type: Class
subclass of: gel
definition: A gel matrix is a gel which the constituants of a gel form a matirx structure.
has_obo_namespace: default_namespace
id: sep:00127

Axiom
annotated source: gel matrix
annotated property: definition
annotated target: A gel matrix is a gel which the constituants of a gel form a matirx structure.
database_cross_reference: PSI:GEL

agarose gel
type: Class
subclass of: gel matrix
definition: An agarose gel is a gel matrix which is composed of the chemical agent agarose.
has_obo_namespace: default_namespace
id: sep:00128

Axiom
annotated source: agarose gel
annotated property: definition
annotated target: An agarose gel is a gel matrix which is composed of the chemical agent agarose.
database_cross_reference: PSI:GEL

polyacrylamide gel
type: Class
subclass of: gel matrix
definition: A polyacrylamide gel is a gel matrix which is the results of a chemical reactions of the chemical agent acrylamide and a chemical agent used in the role of a cross linker.
has_obo_namespace: default_namespace
id: sep:00129

Axiom
annotated source: polyacrylamide gel
annotated property: definition
annotated target: A polyacrylamide gel is a gel matrix which is the results of a chemical reactions of the chemical agent acrylamide and a chemical agent used in the role of a cross linker.
database_cross_reference: PSI:GEL

immobilized pH gradient gel
type: Class
subclass of: polyacrylamide gel
definition: An immobilised pH gradient gel is a polyacrylamide gel which has an immobilized pH gradient (IPG). It is created by covalently incorporating a gradient of acidic and basic buffering groups into a polyacrylamide gel at the time it is cast.
has_exact_synonym: IPG Gel
has_exact_synonym: IPG strip
has_obo_namespace: default_namespace
id: sep:00130

Axiom
annotated source: immobilized pH gradient gel
annotated property: definition
annotated target: An immobilised pH gradient gel is a polyacrylamide gel which has an immobilized pH gradient (IPG). It is created by covalently incorporating a gradient of acidic and basic buffering groups into a polyacrylamide gel at the time it is cast.
database_cross_reference: Pubmed:PMID:7142660

immobiline dry strip
type: Class
subclass of: immobilized pH gradient gel
definition: An immobiline dry strip is a immobilized pH gradinet gel which is a product of GE healthcare.
has_obo_namespace: default_namespace
id: sep:00131

Axiom
annotated source: immobiline dry strip
annotated property: definition
annotated target: An immobiline dry strip is a immobilized pH gradinet gel which is a product of GE healthcare.
database_cross_reference: PSI:GEL

excised band
type: Class
subclass of: gel excised analyte
definition: An excised band is a gel excised analyte which has the geometric shape approximately that of a cuboid.
has_exact_synonym: band
has_exact_synonym: protein band
has_obo_namespace: default_namespace
has_related_synonym: gel band
id: sep:00132

Axiom
annotated source: excised band
annotated property: definition
annotated target: An excised band is a gel excised analyte which has the geometric shape approximately that of a cuboid.
database_cross_reference: PSI:GEL

excised spot
type: Class
subclass of: gel excised analyte
definition: An excised spot is a gel excised analyte which is approximately circlar in geometric shape.
has_exact_synonym: gel spot
has_exact_synonym: protein spot
has_exact_synonym: spot
has_obo_namespace: default_namespace
id: sep:00133

Axiom
annotated source: excised spot
annotated property: definition
annotated target: An excised spot is a gel excised analyte which is approximately circlar in geometric shape.
database_cross_reference: PSI:GEL

nitrocellulose memebrane
type: Class
subclass of: membrane substance
definition: A nitrocellulose membrane is a memebrane compune which is a sticky membrane used for Western blots and immobilizing DNA. It is also used for immobilization of proteins, due to its non-specific affinity for amino acids. Nitrocellulose is widely used as support in diagnostic tests where antigen-antibody binding occur, e.g. pregnancy tests, U-Albumin tests and CRP.
has_exact_synonym: nitrocellulose paper
has_obo_namespace: default_namespace
id: sep:00134

Axiom
annotated source: nitrocellulose memebrane
annotated property: definition
annotated target: A nitrocellulose membrane is a memebrane compune which is a sticky membrane used for Western blots and immobilizing DNA. It is also used for immobilization of proteins, due to its non-specific affinity for amino acids. Nitrocellulose is widely used as support in diagnostic tests where antigen-antibody binding occur, e.g. pregnancy tests, U-Albumin tests and CRP.
database_cross_reference: Wikipedia:Nitrocellulose

PolyVinylidine DiFluoride
type: Class
subclass of: membrane substance
definition: A PolyVinylidine DiFluoride membrane is a membrane compound which is a highly non-reactive and pure thermoplastic fluoropolymer. It Can be used for binding proteins that are transferred from a variety of gel matrices.
has_exact_synonym: PVDF
has_exact_synonym: PVDF membrane
has_obo_namespace: default_namespace
has_related_synonym: KYNAR
id: sep:00135

Axiom
annotated source: PolyVinylidine DiFluoride
annotated property: definition
annotated target: A PolyVinylidine DiFluoride membrane is a membrane compound which is a highly non-reactive and pure thermoplastic fluoropolymer. It Can be used for binding proteins that are transferred from a variety of gel matrices.
database_cross_reference: Wikipedia:PVDF

biological stain product
type: Class
subclass of: substance
definition: A biological stain product is a compound substance which has been manufactued and sold as a product. A biological stain product reacts or concentrates in different parts of a cell or tissue. It is these properties that are used to highlight or identifiy specific parts or areas or substances.
has_obo_namespace: default_namespace
id: sep:00136
comment: Substances which are chemical substances in their own right should be recorded directly under chemical substance and should not be confused with a manufactured staining product, rather than a chemical susbtance which has been used in a role as a stain

Axiom
annotated source: biological stain product
annotated property: definition
annotated target: A biological stain product is a compound substance which has been manufactued and sold as a product. A biological stain product reacts or concentrates in different parts of a cell or tissue. It is these properties that are used to highlight or identifiy specific parts or areas or substances.
database_cross_reference: Wikipedia:Staining Biology

SimplyBlue SafeStain
type: Class
subclass of: biological stain product
subclass of: Restriction
  on property: has_units
  some values from: UO_0000062
subclass of: Restriction
  on property: has_units
  some values from: UO_0000063
subclass of: Restriction
  on property: has_units
  some values from: UO_0000098
subclass of: Restriction
  on property: has_units
  some values from: UO_0000101
subclass of: Restriction
  on property: has_units
  some values from: UO_0000165
subclass of: Restriction
  on property: has_units
  some values from: UO_0000173
subclass of: Restriction
  on property: has_units
  some values from: UO_0000176
subclass of: Restriction
  on property: has_units
  some values from: UO_0000187
subclass of: Restriction
  on property: has_units
  some values from: UO_0000205
definition: A SimplyBlue SafeStain is a biological stain product which is a fast, sensitive and safe Colloidal Coomassie G-250-based stain for nanogram-level detections of proteins, manufactured by Invitrogen.
database_cross_reference: value-type:xsd:float
has_obo_namespace: default_namespace
id: sep:00137

Axiom
annotated source: SimplyBlue SafeStain
annotated property: definition
annotated target: A SimplyBlue SafeStain is a biological stain product which is a fast, sensitive and safe Colloidal Coomassie G-250-based stain for nanogram-level detections of proteins, manufactured by Invitrogen.
database_cross_reference: Invitrogen:SimplyBlue SafeStain

The allowed value-type for this CV term.
type: Axiom
annotated source: SimplyBlue SafeStain
annotated property: database_cross_reference
annotated target: value-type:xsd:float

SilverQuest Silver Stain
type: Class
subclass of: biological stain product
subclass of: Restriction
  on property: has_units
  some values from: UO_0000062
subclass of: Restriction
  on property: has_units
  some values from: UO_0000063
subclass of: Restriction
  on property: has_units
  some values from: UO_0000098
subclass of: Restriction
  on property: has_units
  some values from: UO_0000101
subclass of: Restriction
  on property: has_units
  some values from: UO_0000165
subclass of: Restriction
  on property: has_units
  some values from: UO_0000173
subclass of: Restriction
  on property: has_units
  some values from: UO_0000176
subclass of: Restriction
  on property: has_units
  some values from: UO_0000187
subclass of: Restriction
  on property: has_units
  some values from: UO_0000205
definition: SilverQuest Silver Staining is a biological stain product that provides maximal silver staining sensitivity with minimal protein modification for optimal mass spectrometry results, manufactured by invitrogen.
database_cross_reference: value-type:xsd:float
has_obo_namespace: default_namespace
id: sep:00138

Axiom
annotated source: SilverQuest Silver Stain
annotated property: definition
annotated target: SilverQuest Silver Staining is a biological stain product that provides maximal silver staining sensitivity with minimal protein modification for optimal mass spectrometry results, manufactured by invitrogen.
database_cross_reference: Invitrogen:SilverQuest Silver Stain

The allowed value-type for this CV term.
type: Axiom
annotated source: SilverQuest Silver Stain
annotated property: database_cross_reference
annotated target: value-type:xsd:float

biological blot protocol
type: Class
subclass of: protocol
definition: A biological blot protocol is a protocol which defines the transfer of proteins, DNA or RNA, onto a carrier (for example, a nitrocellulose PVDF or nylon membrane). In many instances, this is done after a gel electrophoresis, transferring the molecules from the gel onto the blotting membrane, and other times adding the samples directly onto the membrane.
has_obo_namespace: default_namespace
id: sep:00139

Axiom
annotated source: biological blot protocol
annotated property: definition
annotated target: A biological blot protocol is a protocol which defines the transfer of proteins, DNA or RNA, onto a carrier (for example, a nitrocellulose PVDF or nylon membrane). In many instances, this is done after a gel electrophoresis, transferring the molecules from the gel onto the blotting membrane, and other times adding the samples directly onto the membrane.
database_cross_reference: Wikipedia:Blot (Biology)

capillary electrophoresis
type: Class
subclass of: protocol
definition: Capillary electrophoresis is a protocol which can be used to separate ionic species by their charge and frictional forces. In traditional electrophoresis, electrically charged analytes move in a conductive liquid medium under the influence of an electric . Introduced in the 1960s, the technique of capillary electrophoresis (CE) was designed to separate species based on their size to charge ratio in the interior of a small capillary filled with an electrolyte.
has_exact_synonym: CE
has_obo_namespace: default_namespace
id: sep:00140

Axiom
annotated source: capillary electrophoresis
annotated property: definition
annotated target: Capillary electrophoresis is a protocol which can be used to separate ionic species by their charge and frictional forces. In traditional electrophoresis, electrically charged analytes move in a conductive liquid medium under the influence of an electric . Introduced in the 1960s, the technique of capillary electrophoresis (CE) was designed to separate species based on their size to charge ratio in the interior of a small capillary filled with an electrolyte.
database_cross_reference: Wikipedia:Capillary Electrophroesis

detection
type: Class
subclass of: protocol
definition: A detection is a protocol which allows the detection, or permits the viewing of a substance. This can involve such process as; staining the proteins on the gel (direct detection), exposing the gel which contains radiolabel sample to photographic film, or transfer of proteins to a matrix such as in immunoblotting (indirect detection).
has_obo_namespace: default_namespace
id: sep:00141

Axiom
annotated source: detection
annotated property: definition
annotated target: A detection is a protocol which allows the detection, or permits the viewing of a substance. This can involve such process as; staining the proteins on the gel (direct detection), exposing the gel which contains radiolabel sample to photographic film, or transfer of proteins to a matrix such as in immunoblotting (indirect detection).
database_cross_reference: PSI:GEL

enzyme digestion
type: Class
subclass of: protocol
definition: Enzyme digestion is a protocol that describes the digestion of a protein by an enzyme.
has_obo_namespace: default_namespace
id: sep:00142

Axiom
annotated source: enzyme digestion
annotated property: definition
annotated target: Enzyme digestion is a protocol that describes the digestion of a protein by an enzyme.
database_cross_reference: PSI:GEL

electrophoresis
type: Class
subclass of: protocol
definition: An electrophoresis is a protocol for capturing the details of electrophoresis. The runnning conditions applied to an electrophoresis substrate in terms of voltage against time and temperature if appropriate.
has_obo_namespace: default_namespace
id: sep:00143

Axiom
annotated source: electrophoresis
annotated property: definition
annotated target: An electrophoresis is a protocol for capturing the details of electrophoresis. The runnning conditions applied to an electrophoresis substrate in terms of voltage against time and temperature if appropriate.
database_cross_reference: PSI:GEL

equilibration
type: Class
subclass of: protocol
definition: Equilibration is a protocol to bring to a chemical stasis or equilibrium.
has_obo_namespace: default_namespace
id: sep:00144

Axiom
annotated source: equilibration
annotated property: definition
annotated target: Equilibration is a protocol to bring to a chemical stasis or equilibrium.
database_cross_reference: Wordnet:equilibrium

first dimension gel equilibration
type: Class
subclass of: equilibration
definition: The first dimension gel equilibration is a protocol which equilibrates the first dimension gel in Two dimensional gel electrophoresis protocol with the buffer system required for the second-dimension separation.
has_exact_synonym: equlibration
has_exact_synonym: gel equilibration
has_obo_namespace: default_namespace
has_related_synonym: equilibration step
id: sep:00145

Axiom
annotated source: first dimension gel equilibration
annotated property: definition
annotated target: The first dimension gel equilibration is a protocol which equilibrates the first dimension gel in Two dimensional gel electrophoresis protocol with the buffer system required for the second-dimension separation.
database_cross_reference: PSI:GEL

excision
type: Class
subclass of: protocol
definition: An excision is a protocol that described removal of a defined location from a substance.
has_obo_namespace: default_namespace
id: sep:00146

Axiom
annotated source: excision
annotated property: definition
annotated target: An excision is a protocol that described removal of a defined location from a substance.
database_cross_reference: PSI:GEL

image acquisition
type: Class
subclass of: protocol
definition: Image acquisition is a protocol which is used to acquire a digitised image.
has_obo_namespace: default_namespace
id: sep:00147

Axiom
annotated source: image acquisition
annotated property: definition
annotated target: Image acquisition is a protocol which is used to acquire a digitised image.
database_cross_reference: PSI:GEL

inter dimension protocol
type: Class
subclass of: protocol
definition: Inter dimension protocol is a protocol which is used to record any process or processes applied to, or carried out between the dimensions of gel electrophoresis. This includes processes such as equilibration, reduction and alkylation.
has_obo_namespace: default_namespace
id: sep:00148

Axiom
annotated source: inter dimension protocol
annotated property: definition
annotated target: Inter dimension protocol is a protocol which is used to record any process or processes applied to, or carried out between the dimensions of gel electrophoresis. This includes processes such as equilibration, reduction and alkylation.
database_cross_reference: PSI:GEL

isoelectric focusing
type: Class
subclass of: protocol
definition: Isoelectric focussing is a protocol that separates a sample (ususally protein) along a separation matrix (usually gel) based on Isoelectric point (pI).
has_obo_namespace: default_namespace
id: sep:00149

Axiom
annotated source: isoelectric focusing
annotated property: definition
annotated target: Isoelectric focussing is a protocol that separates a sample (ususally protein) along a separation matrix (usually gel) based on Isoelectric point (pI).
database_cross_reference: PubMed:PMID:7142660

one dimensional gel electrophoresis
type: Class
subclass of: protocol
definition: One dimensional gel electrophoresis is a protocol which separates a substance based on a single characteristic or dimension of the substance.
has_exact_synonym: 1D
has_obo_namespace: default_namespace
id: sep:00150

Axiom
annotated source: one dimensional gel electrophoresis
annotated property: definition
annotated target: One dimensional gel electrophoresis is a protocol which separates a substance based on a single characteristic or dimension of the substance.
database_cross_reference: PSI:GEL

sample loading protocol
type: Class
subclass of: protocol
definition: Sample loading protocol is a protocol which is the loading a substance (sample) onto another substance.
has_obo_namespace: default_namespace
id: sep:00151

Axiom
annotated source: sample loading protocol
annotated property: definition
annotated target: Sample loading protocol is a protocol which is the loading a substance (sample) onto another substance.
database_cross_reference: PSI:GEL

image analysis
type: Class
subclass of: protocol
definition: Image analysis protocol is a protocol which is the process of the analysis of digitised images.
has_obo_namespace: default_namespace
id: sep:00152

Axiom
annotated source: image analysis
annotated property: definition
annotated target: Image analysis protocol is a protocol which is the process of the analysis of digitised images.
database_cross_reference: PSI:GEL

transfer protocol
type: Class
subclass of: protocol
definition: A transfer protocol is a protocol which is the conveyance or removal an entity from one location to another.
has_obo_namespace: default_namespace
id: sep:00153

Axiom
annotated source: transfer protocol
annotated property: definition
annotated target: A transfer protocol is a protocol which is the conveyance or removal an entity from one location to another.
database_cross_reference: PSI:GEL

protein transfer protocol
type: Class
subclass of: transfer protocol
definition: A protein transfer protocol is a protocol which is the movement of proteins from one substance to another substance, possibly via a transfer medium.
has_obo_namespace: default_namespace
id: sep:00154

Axiom
annotated source: protein transfer protocol
annotated property: definition
annotated target: A protein transfer protocol is a protocol which is the movement of proteins from one substance to another substance, possibly via a transfer medium.
database_cross_reference: PSI:GEL

two dimensional gel electrophoresis
type: Class
subclass of: protocol
definition: Two dimensional gel electrophoresis is a protocol which is the separation of proteins along two gel matrices based on a two characteristics or dimensions of the protein.
has_exact_synonym: 2DG
has_exact_synonym: 2DGE
has_obo_namespace: default_namespace
id: sep:00155

Axiom
annotated source: two dimensional gel electrophoresis
annotated property: definition
annotated target: Two dimensional gel electrophoresis is a protocol which is the separation of proteins along two gel matrices based on a two characteristics or dimensions of the protein.
database_cross_reference: Pubmed:PMID:236308

northern blot
type: Class
subclass of: biological blot protocol
definition: A northern blot is a biological blot protocol which is used in molecular biology research to study gene expression. It takes its name from the similarity of the procedure to the Southern blot procedure, named for biologist Edwin Southern, used to study DNA, with the key difference that RNA, rather than DNA, is the substance being analyzed by electrophoresis and detection with a hybridization probe.
has_obo_namespace: default_namespace
id: sep:00156

Axiom
annotated source: northern blot
annotated property: definition
annotated target: A northern blot is a biological blot protocol which is used in molecular biology research to study gene expression. It takes its name from the similarity of the procedure to the Southern blot procedure, named for biologist Edwin Southern, used to study DNA, with the key difference that RNA, rather than DNA, is the substance being analyzed by electrophoresis and detection with a hybridization probe.
database_cross_reference: Wikipeda:northern blot

Southern blot
type: Class
subclass of: biological blot protocol
definition: A Southern blot is a biological blot protocol which is used in molecular biology to enhancing the result of an agarose gel electrophoresis by marking specific DNA sequences. The method is named after its inventor, the British biologist Edwin Southern.
has_obo_namespace: default_namespace
id: sep:00157

Axiom
annotated source: Southern blot
annotated property: definition
annotated target: A Southern blot is a biological blot protocol which is used in molecular biology to enhancing the result of an agarose gel electrophoresis by marking specific DNA sequences. The method is named after its inventor, the British biologist Edwin Southern.
database_cross_reference: Wikipedia:Southern blot

western blot
type: Class
subclass of: biological blot protocol
definition: A western blot is a biological blot protocol which is used in molecular biology/biochemistry/immunogenetics to detect protein in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate denatured proteins by mass. The proteins are then transferred out of the gel and onto a membrane (typically nitrocellulose), where they are "probed" using antibodies specific to the protein.
has_obo_namespace: default_namespace
has_related_synonym: immunoblot
id: sep:00158

Axiom
annotated source: western blot
annotated property: definition
annotated target: A western blot is a biological blot protocol which is used in molecular biology/biochemistry/immunogenetics to detect protein in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate denatured proteins by mass. The proteins are then transferred out of the gel and onto a membrane (typically nitrocellulose), where they are "probed" using antibodies specific to the protein.
database_cross_reference: Wikipedia:western blot

direct detection
type: Class
subclass of: detection
definition: Direct detection is a detection protocol which is the detection of a substance directly on the susbtances location. For example in gel electrophoresis this can involve such process as; staining proteins on the gel.
has_obo_namespace: default_namespace
id: sep:00159

Axiom
annotated source: direct detection
annotated property: definition
annotated target: Direct detection is a detection protocol which is the detection of a substance directly on the susbtances location. For example in gel electrophoresis this can involve such process as; staining proteins on the gel.
database_cross_reference: PSI:GEL

indirect detection
type: Class
subclass of: detection
definition: Indirect detection is a detection protocol that allows one substance to be detected using an intermediate substance. For example in gel electrophoresis exposing the gel which contains radiolabel sample to photographic film, or transfer of proteins to a matrix such as in immunoblotting (indirect detection).
has_obo_namespace: default_namespace
id: sep:00160

Axiom
annotated source: indirect detection
annotated property: definition
annotated target: Indirect detection is a detection protocol that allows one substance to be detected using an intermediate substance. For example in gel electrophoresis exposing the gel which contains radiolabel sample to photographic film, or transfer of proteins to a matrix such as in immunoblotting (indirect detection).
database_cross_reference: PSI:GEL

staining
type: Class
subclass of: direct detection
definition: Staining is a direct detection which is a biochemical technique of adding a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
has_obo_namespace: default_namespace
id: sep:00161

Axiom
annotated source: staining
annotated property: definition
annotated target: Staining is a direct detection which is a biochemical technique of adding a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
database_cross_reference: Wikipedia:staining

Coomassie staining
type: Class
subclass of: staining
definition: Coomassie staining is a staining which uses the chemical susbstance Coomassie blue, nonspecifically stains proteins a strong blue colour. It is often used in gel electrophoresis.
has_obo_namespace: default_namespace
id: sep:00162

Axiom
annotated source: Coomassie staining
annotated property: definition
annotated target: Coomassie staining is a staining which uses the chemical susbstance Coomassie blue, nonspecifically stains proteins a strong blue colour. It is often used in gel electrophoresis.
database_cross_reference: WIkipedia:Coomassie staining

silver staining
type: Class
subclass of: staining
definition: Silver staining is a staining which uses silver to stain a substance.
has_obo_namespace: default_namespace
id: sep:00163

Axiom
annotated source: silver staining
annotated property: definition
annotated target: Silver staining is a staining which uses silver to stain a substance.
database_cross_reference: Wikipedia:silver staining

chemilumninescent detect
type: Class
subclass of: indirect detection
definition: Chemiluminescent detection is an indirect detection protocol that detects proteins with a substrate that will luminesce when exposed to the reporter on the secondary antibody. The light is then detected by photographic film, and more recently by CCD cameras which captures a digital image of the western blot.
has_obo_namespace: default_namespace
id: sep:00164

Axiom
annotated source: chemilumninescent detect
annotated property: definition
annotated target: Chemiluminescent detection is an indirect detection protocol that detects proteins with a substrate that will luminesce when exposed to the reporter on the secondary antibody. The light is then detected by photographic film, and more recently by CCD cameras which captures a digital image of the western blot.
database_cross_reference: WIkipedia:Chemiluminescence

colorimetric detection
type: Class
subclass of: indirect detection
definition: Colorimetric detection is an indirect detection protocol that detects proteins with a substrate that reacts with the reporter enzyme (such as peroxidase) that is bound to the secondary antibody. This converts the soluble dye into an insoluble form of a different colour that precipitates next to the enzyme and thereby stains the nitrocellulose membrane. Development of the blot is then stopped by washing away the soluble dye. Protein levels are evaluated through densitometry (how intense the stain is) or spectrophotometry.
has_obo_namespace: default_namespace
id: sep:00165

Axiom
annotated source: colorimetric detection
annotated property: definition
annotated target: Colorimetric detection is an indirect detection protocol that detects proteins with a substrate that reacts with the reporter enzyme (such as peroxidase) that is bound to the secondary antibody. This converts the soluble dye into an insoluble form of a different colour that precipitates next to the enzyme and thereby stains the nitrocellulose membrane. Development of the blot is then stopped by washing away the soluble dye. Protein levels are evaluated through densitometry (how intense the stain is) or spectrophotometry.
database_cross_reference: WIkipedia:colormetric detection

flourescent detection
type: Class
subclass of: indirect detection
definition: Flourescent detection is a indirect detection protocol.The fluorescently labeled probe is excited by light and the emission of the excitation is then detected by a photosensor such as CCD camera equipped which appropriate emission filters which captures a digital image of the western blot and allows further data analysis such molecular weight analysis and a quantitative western blot analysis. Fluorescence is considered to be among the most sensitive detection methods for blotting analysis.
has_obo_namespace: default_namespace
id: sep:00166

Axiom
annotated source: flourescent detection
annotated property: definition
annotated target: Flourescent detection is a indirect detection protocol.The fluorescently labeled probe is excited by light and the emission of the excitation is then detected by a photosensor such as CCD camera equipped which appropriate emission filters which captures a digital image of the western blot and allows further data analysis such molecular weight analysis and a quantitative western blot analysis. Fluorescence is considered to be among the most sensitive detection methods for blotting analysis.
database_cross_reference: Wikipedia:flourescent detection

immuno detection
type: Class
subclass of: indirect detection
definition: Immuno detection is an indirect detection protocol which is the use of an antibody-based method to detect a specific protein in a sample.
has_obo_namespace: default_namespace
id: sep:00167

Axiom
annotated source: immuno detection
annotated property: definition
annotated target: Immuno detection is an indirect detection protocol which is the use of an antibody-based method to detect a specific protein in a sample.
database_cross_reference: Wikipedia:immunostaining

primary antibody probing
type: Class
subclass of: indirect detection
definition: Primary antibody probing is an indeirect detection protocol. Antibodies are generated when a host species or immune cell culture is exposed to the protein of interest (or a part thereof). Normally a part of the immune response, here they are harvested and used as sensitive and specific detection tools that bind the protein directly - hence "primary" antibody.
has_obo_namespace: default_namespace
id: sep:00168

Axiom
annotated source: primary antibody probing
annotated property: definition
annotated target: Primary antibody probing is an indeirect detection protocol. Antibodies are generated when a host species or immune cell culture is exposed to the protein of interest (or a part thereof). Normally a part of the immune response, here they are harvested and used as sensitive and specific detection tools that bind the protein directly - hence "primary" antibody.
database_cross_reference: Wikipedia:primary antibody probing

secondary antibody probing
type: Class
subclass of: indirect detection
definition: Secondary antibody probing is an indirect detection protocol. The unbound primary antibody, it is exposed to another antibody, directed at a species-specific portion of the primary antibody. This is known as a secondary antibody, and due to its targeting properties, tends to be referred to as "anti-mouse," "anti-goat," etc. The secondary antibody is usually linked to biotin or to a reporter enzyme such as alkaline phosphatase or horseradish peroxidase. This step confers an advantage in that several secondary antibodies will bind one primary antibody, providing enhanced signal.
has_obo_namespace: default_namespace
id: sep:00169

Axiom
annotated source: secondary antibody probing
annotated property: definition
annotated target: Secondary antibody probing is an indirect detection protocol. The unbound primary antibody, it is exposed to another antibody, directed at a species-specific portion of the primary antibody. This is known as a secondary antibody, and due to its targeting properties, tends to be referred to as "anti-mouse," "anti-goat," etc. The secondary antibody is usually linked to biotin or to a reporter enzyme such as alkaline phosphatase or horseradish peroxidase. This step confers an advantage in that several secondary antibodies will bind one primary antibody, providing enhanced signal.
database_cross_reference: Wikipedia:secondary antobody probing

radioactive detection
type: Class
subclass of: indirect detection
definition: Radio active detection is an indirect detection protocol that involves Radioactive labels that do not require enzyme substrates, but rather allow the placement of medical X-ray film directly against the radio active matierial which develops as it is exposed to the label and creates dark regions which correspond to the protein bands of interest (see image to the right).
has_obo_namespace: default_namespace
id: sep:00170

Axiom
annotated source: radioactive detection
annotated property: definition
annotated target: Radio active detection is an indirect detection protocol that involves Radioactive labels that do not require enzyme substrates, but rather allow the placement of medical X-ray film directly against the radio active matierial which develops as it is exposed to the label and creates dark regions which correspond to the protein bands of interest (see image to the right).
database_cross_reference: Wikipedia :radioactive detection

agarose gel electrophoresis
type: Class
subclass of: one dimensional gel electrophoresis
definition: Agarose gel electrophoresis is a one dimensional gel electrophoresis protocol which use the application of voltage to separate a sample along a separation medium which is a gel matrix made of agarose.
has_obo_namespace: default_namespace
id: sep:00171

Axiom
annotated source: agarose gel electrophoresis
annotated property: definition
annotated target: Agarose gel electrophoresis is a one dimensional gel electrophoresis protocol which use the application of voltage to separate a sample along a separation medium which is a gel matrix made of agarose.
database_cross_reference: PSI:GEL

polyacrylamide gel electrohoresis
type: Class
subclass of: one dimensional gel electrophoresis
definition: Polyacrylamide gel electrophoresis is a one dimensional gel electrophoresis protocol which use the application of voltage to separate a sample along a separation medium which is a gel matrix made of polyacrylamide.
has_obo_namespace: default_namespace
id: sep:00172

Axiom
annotated source: polyacrylamide gel electrohoresis
annotated property: definition
annotated target: Polyacrylamide gel electrophoresis is a one dimensional gel electrophoresis protocol which use the application of voltage to separate a sample along a separation medium which is a gel matrix made of polyacrylamide.
database_cross_reference: Pubmed:PMID:5432063

sodium dodecyl sulfate polyacrylamide gel electrophoresis
type: Class
subclass of: polyacrylamide gel electrohoresis
definition: Sodium dodecyl sulfate polyacrylamide gel electrophoresis is a polyacrylamide gel electrophoresis which which the charge of the proteins results from their binding SDS.
has_exact_synonym: SDS PAGE
has_obo_namespace: default_namespace
id: sep:00173

Axiom
annotated source: sodium dodecyl sulfate polyacrylamide gel electrophoresis
annotated property: definition
annotated target: Sodium dodecyl sulfate polyacrylamide gel electrophoresis is a polyacrylamide gel electrophoresis which which the charge of the proteins results from their binding SDS.
database_cross_reference: Pubmed:PMID: 5432063

cup loading
type: Class
subclass of: sample loading protocol
definition: A cup loading protocol is a sample loading protocol which the sample is pipetted into sample cups precisely positioned on the surface of the gels (usually in first dimension).
has_obo_namespace: default_namespace
id: sep:00174

Axiom
annotated source: cup loading
annotated property: definition
annotated target: A cup loading protocol is a sample loading protocol which the sample is pipetted into sample cups precisely positioned on the surface of the gels (usually in first dimension).
database_cross_reference: PSI:GEL

paper bridge loading
type: Class
subclass of: sample loading protocol
definition: Paper bridge loading is a sample loading protocol that is the loading of samples on a gel prior to electrophoresis using a paper bridge.
has_obo_namespace: default_namespace
id: sep:00175

Axiom
annotated source: paper bridge loading
annotated property: definition
annotated target: Paper bridge loading is a sample loading protocol that is the loading of samples on a gel prior to electrophoresis using a paper bridge.
database_cross_reference: Pubmed:PMID:11271483

rehydration loading
type: Class
subclass of: sample loading protocol
definition: Rehydration loading is a sample loading protocol which rehydrates the gel at the same time as the application of sample to a gel.
has_obo_namespace: default_namespace
id: sep:00176

Axiom
annotated source: rehydration loading
annotated property: definition
annotated target: Rehydration loading is a sample loading protocol which rehydrates the gel at the same time as the application of sample to a gel.
database_cross_reference: PSI:GEL

well loading
type: Class
subclass of: sample loading protocol
definition: Well loading is a sample loading protocols that directly loads a sample directly in the wells of a gel prior to electrophoresis.
has_obo_namespace: default_namespace
id: sep:00177

Axiom
annotated source: well loading
annotated property: definition
annotated target: Well loading is a sample loading protocols that directly loads a sample directly in the wells of a gel prior to electrophoresis.
database_cross_reference: PSI:GEL

one dimensional gel electrophoresis image analysis
type: Class
subclass of: image analysis
definition: One dimensional gel electrophoresis image analysis is an image analysis protocol which is the analysis of multiple images produces as a result of one dimensional gel electrophoresis.
has_obo_namespace: default_namespace
id: sep:00178

Axiom
annotated source: one dimensional gel electrophoresis image analysis
annotated property: definition
annotated target: One dimensional gel electrophoresis image analysis is an image analysis protocol which is the analysis of multiple images produces as a result of one dimensional gel electrophoresis.
database_cross_reference: PSI:GEL

two dimensional gel electrophoresis image analysis
type: Class
subclass of: image analysis
definition: Two dimensional gel electrophoresis image analysis is an image analysis protocol which is the analysis of multiple images produces as a result of two dimensional gel electrophoresis.
has_obo_namespace: default_namespace
id: sep:00179

Axiom
annotated source: two dimensional gel electrophoresis image analysis
annotated property: definition
annotated target: Two dimensional gel electrophoresis image analysis is an image analysis protocol which is the analysis of multiple images produces as a result of two dimensional gel electrophoresis.
database_cross_reference: PSI:GEL

difference gel electrophoresis
type: Class
subclass of: two dimensional gel electrophoresis
definition: Difference gel electrophoresis is a two dimensional gel electrophoresis protocol which is where three different protein samples can be labeled with fluorescent dyes (for example Cy3, Cy5, Cy2) prior to two-dimensional electrophoresis. After the gel electrophoresis, the gel is scanned with the excitation wavelength of each dye one after the other. This technique is used to see changes in protein abundancy (for example, between a sample of a healthy person and a sample of a diseased person).
has_exact_synonym: DIGE
has_obo_namespace: default_namespace
id: sep:00180

Axiom
annotated source: difference gel electrophoresis
annotated property: definition
annotated target: Difference gel electrophoresis is a two dimensional gel electrophoresis protocol which is where three different protein samples can be labeled with fluorescent dyes (for example Cy3, Cy5, Cy2) prior to two-dimensional electrophoresis. After the gel electrophoresis, the gel is scanned with the excitation wavelength of each dye one after the other. This technique is used to see changes in protein abundancy (for example, between a sample of a healthy person and a sample of a diseased person).
database_cross_reference: Pubmed:PMID:9420172

PubMed
type: Class
subclass of: digital data set
definition: PubMed is data which is a service of the U.S. National Library of Medicine that includes over 16 million citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. PubMed includes links to full text articles and other related resources. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed.
has_obo_namespace: default_namespace
id: sep:00181

Axiom
annotated source: PubMed
annotated property: definition
annotated target: PubMed is data which is a service of the U.S. National Library of Medicine that includes over 16 million citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. PubMed includes links to full text articles and other related resources. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed.
database_cross_reference: Pubmed:Pubmed

WordNet
type: Class
subclass of: digital data set
definition: WordNet is data which is an online lexical reference system whose design is inspired by current psycholinguistic theories of human lexical memory. English nouns, verbs, adjectives and adverbs are organized into synonym sets, each representing one underlying lexical concept. Different relations link the synonym sets.
has_obo_namespace: default_namespace
id: sep:00182

Axiom
annotated source: WordNet
annotated property: definition
annotated target: WordNet is data which is an online lexical reference system whose design is inspired by current psycholinguistic theories of human lexical memory. English nouns, verbs, adjectives and adverbs are organized into synonym sets, each representing one underlying lexical concept. Different relations link the synonym sets.
database_cross_reference: WordNet:WordNet

Cy2
type: Class
subclass of: chemical substance
definition: Cyanine is a chemical substance which is a polymer hydroxide formula achieved in 1986 by the Universal Chemical Society. It is used as a dye for CD-R and DVD-R media. Cyanine dyes are mostly green or light blue in color, and are chemically unstable. This made cyanine discs unsuitable for archival use, as they can fade and become unreadable in a few years.
has_exact_synonym: cyanine
has_obo_namespace: default_namespace
id: sep:00183

Axiom
annotated source: Cy2
annotated property: definition
annotated target: Cyanine is a chemical substance which is a polymer hydroxide formula achieved in 1986 by the Universal Chemical Society. It is used as a dye for CD-R and DVD-R media. Cyanine dyes are mostly green or light blue in color, and are chemically unstable. This made cyanine discs unsuitable for archival use, as they can fade and become unreadable in a few years.
database_cross_reference: Wikipedia:Cyanine

Cy3
type: Class
subclass of: chemical substance
definition: Cy3 is a chemical susbstance that has a reactive N-hydroxysuccinimide group. Cy3 is excited maximally at 550nm and emits maximally at 570nm, in the green part of the spectruum; quantum yield is 0.15; FW=766.
has_exact_synonym: indocarbocyanine
has_obo_namespace: default_namespace
id: sep:00184

Axiom
annotated source: Cy3
annotated property: definition
annotated target: Cy3 is a chemical susbstance that has a reactive N-hydroxysuccinimide group. Cy3 is excited maximally at 550nm and emits maximally at 570nm, in the green part of the spectruum; quantum yield is 0.15; FW=766.
database_cross_reference: Wikipedia:Cy3

Cy5
type: Class
subclass of: chemical substance
definition: Cy5 is a chemical substance that has a reactive N-hydroxysuccinimide group that reacts readily with amine groups. Cy5 instead is excited maximally at 649 and emits maximally at 670nm, in the red part of the spectruum; quantum yield is 0.28. FW=792.
has_exact_synonym: Indodicarbocyanine
has_obo_namespace: default_namespace
id: sep:00185

Axiom
annotated source: Cy5
annotated property: definition
annotated target: Cy5 is a chemical substance that has a reactive N-hydroxysuccinimide group that reacts readily with amine groups. Cy5 instead is excited maximally at 649 and emits maximally at 670nm, in the red part of the spectruum; quantum yield is 0.28. FW=792.
database_cross_reference: Wikipedia:Cy5

label
type: Class
subclass of: attribute
definition: A label is an attribute which is an identifying or descriptive marker or token that is attached to an object.
has_obo_namespace: default_namespace
id: sep:00186

Axiom
annotated source: label
annotated property: definition
annotated target: A label is an attribute which is an identifying or descriptive marker or token that is attached to an object.
database_cross_reference: Wordnet:label

flourescent label
type: Class
subclass of: label
definition: A fluorescent label is a label that is either a fluorescent molecule, or an enzyme system that generates a fluorescent product, which is linked to a ligand or binder tracer. The tracer is quantified by measuring the amount of light emitted by the tracer at a specific wavelength after exciting the tracer with incident light of a shorter wavelength. Fluorescent molecules include fluorescein and lanthanide chelates such as europium, samarium, and terbium.
has_obo_namespace: default_namespace
id: sep:00187

Axiom
annotated source: flourescent label
annotated property: definition
annotated target: A fluorescent label is a label that is either a fluorescent molecule, or an enzyme system that generates a fluorescent product, which is linked to a ligand or binder tracer. The tracer is quantified by measuring the amount of light emitted by the tracer at a specific wavelength after exciting the tracer with incident light of a shorter wavelength. Fluorescent molecules include fluorescein and lanthanide chelates such as europium, samarium, and terbium.
database_cross_reference: Brendan Glossart:flourescent label

SYPRO Ruby
type: Class
subclass of: biological stain product
subclass of: Restriction
  on property: has_units
  some values from: UO_0000062
subclass of: Restriction
  on property: has_units
  some values from: UO_0000063
subclass of: Restriction
  on property: has_units
  some values from: UO_0000098
subclass of: Restriction
  on property: has_units
  some values from: UO_0000101
subclass of: Restriction
  on property: has_units
  some values from: UO_0000165
subclass of: Restriction
  on property: has_units
  some values from: UO_0000173
subclass of: Restriction
  on property: has_units
  some values from: UO_0000176
subclass of: Restriction
  on property: has_units
  some values from: UO_0000187
subclass of: Restriction
  on property: has_units
  some values from: UO_0000205
definition: SYPRO Ruby is a biological stain product that is a ready to use, ultra sensitive, luminescent stain for the detection of proteins separated by PAGE. Designed especicially for 2D PAGE, SYPRO Ruby also performs impressively in PAGE and IEF gels. Stains glycoproteins, lipoproteins, calcium binding proteins, fibrillar proteins and others. Will not stain extraneous nucleic acids. Sensitive to 1 ng of protein.
database_cross_reference: value-type:xsd:float
has_obo_namespace: default_namespace
id: sep:00188

Axiom
annotated source: SYPRO Ruby
annotated property: definition
annotated target: SYPRO Ruby is a biological stain product that is a ready to use, ultra sensitive, luminescent stain for the detection of proteins separated by PAGE. Designed especicially for 2D PAGE, SYPRO Ruby also performs impressively in PAGE and IEF gels. Stains glycoproteins, lipoproteins, calcium binding proteins, fibrillar proteins and others. Will not stain extraneous nucleic acids. Sensitive to 1 ng of protein.
database_cross_reference: Invitrogen:SYPRO Ruby

The allowed value-type for this CV term.
type: Axiom
annotated source: SYPRO Ruby
annotated property: database_cross_reference
annotated target: value-type:xsd:float

manufacturer
type: Class
subclass of: role
definition: A person, an enterprise, or an entity that manufactures something.
has_obo_namespace: default_namespace
id: sep:00189

Axiom
annotated source: manufacturer
annotated property: definition
annotated target: A person, an enterprise, or an entity that manufactures something.
database_cross_reference: :The American Heritage Dictionary of the English Language
database_cross_reference: Fourth Edition:manufacturer

bisacrylamide
type: Class
subclass of: chemical substance
definition: A bisacrylaimde is a chemical substance that has a molecular formula of C7H10O2N2. Often a primary component of polyacrylamide gels used for sequencing and protein electrophoresis.
has_obo_namespace: default_namespace
id: sep:00190

Axiom
annotated source: bisacrylamide
annotated property: definition
annotated target: A bisacrylaimde is a chemical substance that has a molecular formula of C7H10O2N2. Often a primary component of polyacrylamide gels used for sequencing and protein electrophoresis.
database_cross_reference: http://www.leighlabs.com/MSDS/bisacry.htm:bisacrylamide

photographic film
type: Class
subclass of: substance
definition: need def
has_obo_namespace: default_namespace
id: sep:00191

Axiom
annotated source: photographic film
annotated property: definition
annotated target: need def
database_cross_reference: add:def

phosphor screen
type: Class
subclass of: substance
definition: def
has_obo_namespace: default_namespace
id: sep:00192

Axiom
annotated source: phosphor screen
annotated property: definition
annotated target: def
database_cross_reference: def:add

digital entity role
type: Class
subclass of: role
definition: def
has_obo_namespace: default_namespace
id: sep:00193

Axiom
annotated source: digital entity role
annotated property: definition
annotated target: def
database_cross_reference: def:add

picking gel feature location set
type: Class
subclass of: digital entity role
definition: def
has_obo_namespace: default_namespace
id: sep:00194

Axiom
annotated source: picking gel feature location set
annotated property: definition
annotated target: def
database_cross_reference: def:add

biological sample
type: Class
subclass of: biological substance
definition: A biological sample analysed by a particular technology.
has_obo_namespace: default_namespace
id: sep:00195

Axiom
annotated source: biological sample
annotated property: definition
annotated target: A biological sample analysed by a particular technology.
database_cross_reference: SP:9999

sample description
type: Class
subclass of: biological sample
definition: A description of the biological sample analysed.
database_cross_reference: value-type:xsd:string
has_obo_namespace: default_namespace
id: sep:00196

Axiom
annotated source: sample description
annotated property: definition
annotated target: A description of the biological sample analysed.
database_cross_reference: PSI:SP:9999

The allowed value-type for this CV term.
type: Axiom
annotated source: sample description
annotated property: database_cross_reference
annotated target: value-type:xsd:string

sample volume
type: Class
subclass of: biological sample
subclass of: Restriction
  on property: has_units
  some values from: UO_0000098
subclass of: Restriction
  on property: has_units
  some values from: UO_0000101
definition: Volume of sample analysed.
database_cross_reference: value-type:xsd:float
has_obo_namespace: default_namespace
id: sep:00197

Axiom
annotated source: sample volume
annotated property: definition
annotated target: Volume of sample analysed.
database_cross_reference: PSI:SP:9999

The allowed value-type for this CV term.
type: Axiom
annotated source: sample volume
annotated property: database_cross_reference
annotated target: value-type:xsd:float

equilibration buffer
type: Class
subclass of: buffer solution
definition: A buffer intended to maintain the pH in a range appropriate for electrophoresis.
has_obo_namespace: default_namespace
id: sep:00198

Axiom
annotated source: equilibration buffer
annotated property: definition
annotated target: A buffer intended to maintain the pH in a range appropriate for electrophoresis.
database_cross_reference: PSI:SP:9999

resolving buffer
type: Class
subclass of: buffer solution
definition: TO DO
has_obo_namespace: default_namespace
id: sep:00200

Axiom
annotated source: resolving buffer
annotated property: definition
annotated target: TO DO
database_cross_reference: PSI:Gel

stacking buffer
type: Class
subclass of: buffer solution
definition: TO DO
has_obo_namespace: default_namespace
id: sep:00201

Axiom
annotated source: stacking buffer
annotated property: definition
annotated target: TO DO
database_cross_reference: PSI:Gel

alkylation buffer
type: Class
subclass of: buffer solution
definition: TO DO
has_obo_namespace: default_namespace
id: sep:00202

Axiom
annotated source: alkylation buffer
annotated property: definition
annotated target: TO DO
database_cross_reference: PSI:Gel

reduction buffer
type: Class
subclass of: buffer solution
definition: TO DO
has_obo_namespace: default_namespace
id: sep:00203

Axiom
annotated source: reduction buffer
annotated property: definition
annotated target: TO DO
database_cross_reference: PSI:Gel

sample desalting
type: Class
subclass of: protocol
definition: Sample desalting and solid phase extraction. Desalting and/or enrichment procedures before to the measurement.
has_obo_namespace: default_namespace
id: sep:00204

Axiom
annotated source: sample desalting
annotated property: definition
annotated target: Sample desalting and solid phase extraction. Desalting and/or enrichment procedures before to the measurement.
database_cross_reference: PSI:Gel

microcolumn
type: Class
subclass of: sample desalting
definition: Small volume column packet with different chromatography resins
has_obo_namespace: default_namespace
id: sep:00205

Axiom
annotated source: microcolumn
annotated property: definition
annotated target: Small volume column packet with different chromatography resins
database_cross_reference: PSI:Gel

cartridge
type: Class
subclass of: sample desalting
definition: Large volume column packed with different chromatography resins
has_obo_namespace: default_namespace
id: sep:00206

Axiom
annotated source: cartridge
annotated property: definition
annotated target: Large volume column packed with different chromatography resins
database_cross_reference: PSI:Gel

beads
type: Class
subclass of: sample desalting
definition: Bulk chromatography resin applied to a sample
has_obo_namespace: default_namespace
id: sep:00207

Axiom
annotated source: beads
annotated property: definition
annotated target: Bulk chromatography resin applied to a sample
database_cross_reference: PSI:Gel

SPE surface
type: Class
subclass of: sample desalting
definition: Solid membrane combining different chromatographic affinities
has_obo_namespace: default_namespace
id: sep:00208

Axiom
annotated source: SPE surface
annotated property: definition
annotated target: Solid membrane combining different chromatographic affinities
database_cross_reference: PSI:Gel

liquid chromatography
type: Class
subclass of: protocol
definition: Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid. Liquid chromatography can be carried out either in a column or a plane. Present day liquid chromatography that generally utilizes very small packing particles and a relatively high pressure is referred to as high performance liquid chromatography
has_obo_namespace: default_namespace
has_related_synonym: HPLC
has_related_synonym: High Perfomance Liquid Chromatography
id: sep:00210

Axiom
annotated source: liquid chromatography
annotated property: definition
annotated target: Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid. Liquid chromatography can be carried out either in a column or a plane. Present day liquid chromatography that generally utilizes very small packing particles and a relatively high pressure is referred to as high performance liquid chromatography
database_cross_reference: Wikipedia:Chromatography

reversed-phase chromatography
type: Class
subclass of: liquid chromatography
definition: Reversed phase HPLC (RP-HPLC or RPC) has a non-polar stationary phase and an aqueous, moderately polar mobile phase. One common stationary phase is a silica which has been treated with RMe2SiCl, where R is a straight chain alkyl group such as C18H37 or C8H17. With these stationary phases, retention time is longer for molecules which are less polar, while polar molecules elute more readily.
has_obo_namespace: default_namespace
id: sep:00211

Axiom
annotated source: reversed-phase chromatography
annotated property: definition
annotated target: Reversed phase HPLC (RP-HPLC or RPC) has a non-polar stationary phase and an aqueous, moderately polar mobile phase. One common stationary phase is a silica which has been treated with RMe2SiCl, where R is a straight chain alkyl group such as C18H37 or C8H17. With these stationary phases, retention time is longer for molecules which are less polar, while polar molecules elute more readily.
database_cross_reference: Wikipedia:High-performance_liquid_chromatography

normal-phase chromatography
type: Class
subclass of: liquid chromatography
definition: Also known as normal-phase HPLC (NP-HPLC), or adsorption chromatography, this method separates analytes based on adsorption to a stationary surface chemistry and by polarity
has_obo_namespace: default_namespace
id: sep:00212

Axiom
annotated source: normal-phase chromatography
annotated property: definition
annotated target: Also known as normal-phase HPLC (NP-HPLC), or adsorption chromatography, this method separates analytes based on adsorption to a stationary surface chemistry and by polarity
database_cross_reference: Wikipedia:High-performance_liquid_chromatography

ion-exchange chromatography
type: Class
subclass of: liquid chromatography
definition: Ion-exchange chromatography (or ion chromatography) is a process that allows the separation of ions and polar molecules based on their charge.
has_obo_namespace: default_namespace
id: sep:00213

Axiom
annotated source: ion-exchange chromatography
annotated property: definition
annotated target: Ion-exchange chromatography (or ion chromatography) is a process that allows the separation of ions and polar molecules based on their charge.
database_cross_reference: Wikipedia:Ion-exchange_chromatography

affinity chromatography
type: Class
subclass of: liquid chromatography
definition: A method of separating biochemical mixtures and based on a highly specific biological interaction such as that between antigen and antibody, enzyme and substrate, or receptor and ligand. Affinity chromatography combines the size fractionation capability of gel permeation chromatography with the ability to design a chromatography that reversibly binds to a known subset of molecules.
has_obo_namespace: default_namespace
id: sep:00214

Axiom
annotated source: affinity chromatography
annotated property: definition
annotated target: A method of separating biochemical mixtures and based on a highly specific biological interaction such as that between antigen and antibody, enzyme and substrate, or receptor and ligand. Affinity chromatography combines the size fractionation capability of gel permeation chromatography with the ability to design a chromatography that reversibly binds to a known subset of molecules.
database_cross_reference: Wikipedia:Affinity_chromatography

size-exclusion chromatography
type: Class
subclass of: liquid chromatography
definition: Size-exclusion chromatography (SEC) is a chromatographic method in which molecules in solution are separated by their size, not by molecular weight. It is usually applied to large molecules or macromolecular complexes such as proteins and industrial polymers.
has_obo_namespace: default_namespace
id: sep:00215

Axiom
annotated source: size-exclusion chromatography
annotated property: definition
annotated target: Size-exclusion chromatography (SEC) is a chromatographic method in which molecules in solution are separated by their size, not by molecular weight. It is usually applied to large molecules or macromolecular complexes such as proteins and industrial polymers.
database_cross_reference: Wikipedia:Size-exclusion_chromatography