def: "This is the root node of the ontology to provide controlled vocabulary terms protein separation based experiments." [PSI:GEL "The PSI Working group for gels"]
[Term]
id: sep:00002
name: abstract
def: "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." [SUMO:abstract "Suggested Upper Merged Ontology"]
is_a: sep:00001 ! entity
[Term]
id: sep:00003
name: physical
def: "An entity that has a location in space-time. Note that locations are themselves understood to have a location in space-time." [SUMO:physical "Suggested Upper Merged Ontology"]
is_a: sep:00001 ! entity
[Term]
id: sep:00004
name: attribute
def: "An attribute is an abstraction which belongs to or is a characteristic of an entity." [WordNet:attribute "http://wordnet.princeton.edu/"]
is_a: sep:00002 ! abstract
[Term]
id: sep:00005
name: quality
def: "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." [PATO:http\://purl.org/obo/owl/PATO "Phenotypic quality ontology"]
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.
is_a: sep:00002 ! abstract
[Term]
id: sep:00006
name: identifier
def: "An identifier is an attribute which characterises the identification of an entity." [PSI:GEL "The PSI Workging Group for gel based experiments"]
is_a: sep:00004 ! attribute
[Term]
id: sep:00007
name: format
def: "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." [PSI:GEL "The PSI working groups for gel based experiments"]
is_a: sep:00005 ! quality
[Term]
id: sep:00008
name: parameter
def: "A parameter is an attribute that defines a system and determines (or limits) its performance." [Wordnet:parameter "Wordnet"]
is_a: sep:00004 ! attribute
[Term]
id: sep:00009
name: distribution
def: "A distribution is a quality that specifies an arrangement of values of a variable showing their observed or theoretical frequency of occurrence." [WordNet:statistical distribution "WordNet 1.7.1"]
is_a: sep:00005 ! quality
[Term]
id: sep:00010
name: role
def: "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." [PSI:GEL "The PSI Working Group for Gel based experiments"]
is_a: sep:00004 ! attribute
[Term]
id: sep:00011
name: digital data set
def: "A digital data set is is a digital entity that is a collection of the same or heterogenous digital entities." [PSI:Gel "The PSI Working group for gel based experiments"]
is_a: sep:00109 ! digital entity
[Term]
id: sep:00012
name: product attribute
def: "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." [PSI:Gel "The PSI Working group for gel based experiments"]
is_a: sep:00004 ! attribute
[Term]
id: sep:00013
name: proteomics standards initiative working group
def: "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." [PSI:Gel "The PSI Working group for gel based experiments for gel based experiments"]
exact_synonym: "PSI WG" []
is_a: sep:00078 ! organization
[Term]
id: sep:00014
name: Uniform Resource Identifier
def: "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." [IETF:rfc3986 "The Internet Engineering Task Force http://tools.ietf.org/html/rfc3986"]
exact_synonym: "URI" []
is_a: sep:00006 ! identifier
[Term]
id: sep:00015
name: batch identifier
def: "A batch identifier is a product attribute which is a token which identifies the batch or lot number of a product." [PSI:GEL "The PSI Workign group for gel based experiments"]
exact_synonym: "batch number" []
exact_synonym: "lot number" []
is_a: sep:00012 ! product attribute
[Term]
id: sep:00016
name: catalogue identifier
def: "A catalogue identifier is a product attribute which is designated by a manufacture, seller, or producer of a product." [PSI:Gel "The PSI working group for gel based experiments"]
exact_synonym: "catalogue number" []
is_a: sep:00012 ! product attribute
[Term]
id: sep:00017
name: model identifier
def: "A model identifier is a product attribute assigned to a product." [PSI:Gel "The PSI working group for gel based experiments"]
related_synonym: "model number" []
is_a: sep:00012 ! product attribute
[Term]
id: sep:00018
name: linear distribution
def: "A linear distribution is a statsitical distribution that is equally sequential." [PSI:Gel "The PSI working group for gel based experiments"]
is_a: sep:00009 ! distribution
[Term]
id: sep:00019
name: logarithmic distribution
def: "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." [McGraw-Hill Dictionary of Scientific and Technical Terms:logarithmic "McGraw-Hill Companies Inc. 2003. Answers.com 14 Nov. 2006. http://www.answers.com/topic/logarithmic-scale-2"]
is_a: sep:00009 ! distribution
[Term]
id: sep:00020
name: maximum parameter
def: "A maximum parameter is a parameter which has he largest possible value for a parameter." [PSI:Gel "The PSi Working group for gel based experiments"]
is_a: sep:00008 ! parameter
[Term]
id: sep:00021
name: minimum parameter
def: "A minimum parameter is a parameter which has the smallest possible value for a parameter." [PSI:Gel "The PSI Working group for gel based experiments"]
is_a: sep:00008 ! parameter
[Term]
id: sep:00022
name: state
def: "A state is a quality that is the manner of being or form of existence." [:The American Heritage Dictionary of the English Language, Fourth Edition:state "Houghton Mifflin Company 2004. Answers.com 14 Nov. 2006. http://www.answers.com/topic/state"]
is_a: sep:00005 ! quality
[Term]
id: sep:00023
name: electrical mode
def: "Electric mode is a mode that represents one of several alternative conditions of a measure of electric from a device." [PSI:Gel "The PSI Working group for gel based experiments"]
is_a: sep:00026 ! mode
[Term]
id: sep:00024
name: gradient mode
def: "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." [PSI:Gel "The PSI working group for gel based experiments"]
related_synonym: "ramp" []
is_a: sep:00023 ! electrical mode
[Term]
id: sep:00025
name: social role
def: "A social role is a role that specify the position or status of a entity within an Organization or other Group." [SUMO:social role "Suggested Upper Merged Ontology"]
is_a: sep:00010 ! role
[Term]
id: sep:00026
name: mode
def: "A mode is a state that is one of several alternative conditions or methods of operation of a device." [McGraw-Hill Dictionary of Scientific and Technical Terms:mode "McGraw-Hill Companies Inc. 2003. Answers.com 14 Nov. 2006. http://www.answers.com/topic/mode-14"]
is_a: sep:00022 ! state
[Term]
id: sep:00027
name: hold mode
def: "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." [PSI:Gel "The PSI Working group for gel based experiments"]
is_a: sep:00023 ! electrical mode
[Term]
id: sep:00028
name: step and hold mode
def: "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." [PSI:Gel "The PSI Working group for gel based experiments"]
is_a: sep:00023 ! electrical mode
[Term]
id: sep:00029
name: substance role
def: "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." [SUMO:role "Suggested Upper Merged Ontology"]
is_a: sep:00010 ! role
[Term]
id: sep:00030
name: position
def: "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." [SUMO:position "Suggested Upper Merged Ontology"]
is_a: sep:00025 ! social role
[Term]
id: sep:00031
name: lecturer
def: "Lecturer is a position." [PSI:Gel "The PSI Working group for gel based experiments for gel based experiments"]
is_a: sep:00030 ! position
[Term]
id: sep:00032
name: professor
def: "Professor is a postion." [PSI:Gel "The PSI working group for gel based experiments"]
is_a: sep:00030 ! position
[Term]
id: sep:00033
name: reader
def: "Reader is a position." [PSI :Gel "The PSI Working group for gel based experiments"]
is_a: sep:00030 ! position
[Term]
id: sep:00034
name: researcher
def: "A researcher is a position." [PSI:Gel "The PSI working group for gel based experiments"]
is_a: sep:00030 ! position
[Term]
id: sep:00035
name: principle investigator
def: "A principle investigator is a position." [PSI:GEL "The PSI working group for gel based experiments"]
is_a: sep:00030 ! position
[Term]
id: sep:00036
name: cross linker
def: "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." [Wikkipedia:cross linker "http://en.wikipedia.org/wiki/Cross-linker"]
is_a: sep:00029 ! substance role
[Term]
id: sep:00037
name: medium
def: "A medium is a substance role which an intervening substance through which something else is transmitted or carried on." [:The American Heritage Dictionary of the English Language, Fourth Edition:medium "Houghton Mifflin Company 2004. Answers.com 14 Nov. 2006. http://www.answers.com/topic/medium"]
is_a: sep:00029 ! substance role
[Term]
id: sep:00038
name: detection medium
def: "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." [PSI:Gel "The PSI Working group for gel based experiments"]
is_a: sep:00037 ! medium
[Term]
id: sep:00039
name: separation medium
def: "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." [PSI:Gel "The PSI Working group for gel based experiments"]
is_a: sep:00037 ! medium
[Term]
id: sep:00040
name: transfer medium
def: "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." [PSI:Gel "The PSI Working group for gel based experiments"]
is_a: sep:00037 ! medium
[Term]
id: sep:00041
name: gelling agent
def: "A gelling agent is a substance role of a substance to react with another substance to form a gel." [PSI:Gel "The PSI working groupfor gel based experiments"]
is_a: sep:00029 ! substance role
[Term]
id: sep:00042
name: sample
def: "A sample is a substance role played by a biological substance as an input substance to a protocol." [PSI:Gel "The PSI Working group for gel based experiments"]
is_a: sep:00029 ! substance role
[Term]
id: sep:00043
name: permission
def: "A permission is an attribute which is a formal authorization." [Wordnet:permission "WordNet 1.7.1."]
is_a: sep:00004 ! attribute
[Term]
id: sep:00044
name: security access
def: "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." [FUGE:security access "Functional genomics experiment"]
is_a: sep:00043 ! permission
[Term]
id: sep:00045
name: read access
def: "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." [PSI :Gel "The PSI Working Group of gel based experiments"]
is_a: sep:00044 ! security access
[Term]
id: sep:00046
name: write access
def: "Write access is a security access permission attribute that is the access right to record or update stored data." [PSI:Gel "The PSI Working group for gel based experiments"]
is_a: sep:00044 ! security access
[Term]
id: sep:00047
name: data format
def: "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." [PSI:Gel "The PSI Working group for gel based experiments"]
is_a: sep:00007 ! format
[Term]
id: sep:00048
name: image file format
def: "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." [PSI:Gel "The PSI Working group for gel based experiments"]
is_a: sep:00047 ! data format
[Term]
id: sep:00049
name: graphics interchange format
def: "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." [Wikipedia:graphics interchange format "http://en.wikipedia.org/wiki/Graphics_file_format"]
exact_synonym: "gif" []
is_a: sep:00048 ! image file format
[Term]
id: sep:00050
name: Joint Photographic Experts Group
def: "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." [WIkipedia:Joint Photography Experts Group "http://en.wikipedia.org/wiki/Graphics_file_format"]
exact_synonym: "jpeg" []
exact_synonym: "jpg" []
is_a: sep:00048 ! image file format
[Term]
id: sep:00051
name: Portable Network Graphics
def: "A Portable Network Graphics is an image file format which lossless compression, offering bit depths from 1 to 48." [Wikipedia:Portable Network Graphics "http://en.wikipedia.org/wiki/Graphics_file_format"]
exact_synonym: "png" []
is_a: sep:00048 ! image file format
[Term]
id: sep:00052
name: Scalable Vector Graphics
def: "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." [Wikipedia:Scalable Vector Graphics "http://en.wikipedia.org/wiki/Graphics_file_format"]
exact_synonym: "svg" []
is_a: sep:00048 ! image file format
[Term]
id: sep:00053
name: Tagged Image File Format
def: "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." [Wikipedia:Tagged Image File Format "http://en.wikipedia.org/wiki/Graphics_file_format"]
exact_synonym: "tif" []
exact_synonym: "tiff" []
is_a: sep:00048 ! image file format
[Term]
id: sep:00054
name: Windows Bitmap
def: "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." [Wikipedia:Windows Bitmap "http://en.wikipedia.org/wiki/Graphics_file_format"]
exact_synonym: "bmp" []
is_a: sep:00048 ! image file format
[Term]
id: sep:00055
name: quantity
def: "A quantity is an abstract concept which is any specification of how many or how much of something there is." [SUMO:quality "Suggested Upper Merged Ontology"]
is_a: sep:00002 ! abstract
[Term]
id: sep:00056
name: unit of measure
def: "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." [SUMO:unit of measure "Suggested Upper Merged Ontology"]
comment: Units of measure should be imported from PATO units ontology under this node http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/.
is_a: sep:00055 ! quantity
[Term]
id: sep:00057
name: measurement range
def: "A measurement range is a quantity which consists of a lower value, an upper value and a unit of measure." [PSI:Gel "The PSI Working Group for gel based experiments"]
is_a: sep:00055 ! quantity
[Term]
id: sep:00058
name: pH range
def: "A pH range is a measurement range which has a unit of measure of pH." [PSI:Gel "The PSI Working Group for gel based experiments"]
is_a: sep:00057 ! measurement range
[Term]
id: sep:00059
name: molecular weight range
def: "A molecular weight range is a measurement range which has a measurement unit of Kilo Daltons." [PSI:Gel "The PSI Working group for gel based experiments"]
is_a: sep:00057 ! measurement range
[Term]
id: sep:00060
name: software
def: "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." [West's Encyclopedia of American Law:software "The Gale Group Inc 1998. Answers.com 15 Nov. 2006. http://www.answers.com/topic/computer-software."]
is_a: sep:00109 ! digital entity
[Term]
id: sep:00061
name: image acquistion software
def: "Image acquisition software is software that is designed to aquire a digitised image of a physical object." [PSI:GEL "The PSI working group for gel based Experiments."]
is_a: sep:00060 ! software
[Term]
id: sep:00062
name: image analysis software
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00060 ! software
[Term]
id: sep:00063
name: progenisis
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00062 ! image analysis software
[Term]
id: sep:00064
name: software attribute
def: "A software attribute is an attribute that is associated with software." [PSI:GEL "The PSI Working Group for gel based experiments"]
is_a: sep:00004 ! attribute
[Term]
id: sep:00065
name: software version number
def: "A software version number is a software attribute that represents the version of software." [PSI:GEL "The PSI Working Group for gel based experiments"]
is_a: sep:00064 ! software attribute
[Term]
id: sep:00066
name: progenisis PG200
def: "Progenisis PG200 is a progenisis image analysis software that offers an advanced workflow and powerful data analysis for the proteomics researcher." [PSI:GEL "The PSI working Group fro gel based experiments"]
is_a: sep:00063 ! progenisis
[Term]
id: sep:00067
name: progeniss PG220
def: "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." [PSI:GEL "The PSI Working Group for gel based experiments"]
is_a: sep:00063 ! progenisis
[Term]
id: sep:00068
name: progenisis PG240
def: "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." [PSI:GEL "The PSI Working Group for gel based experiments"]
is_a: sep:00063 ! progenisis
[Term]
id: sep:00069
name: SameSpots
def: "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." [PSI:GEL "The PSI working group for gel based experiments"]
is_a: sep:00062 ! image analysis software
[Term]
id: sep:00070
name: DeCyder
def: "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." [PSI:GEL "The PSI working group for gel based experiments"]
is_a: sep:00062 ! image analysis software
[Term]
id: sep:00071
name: Delta2D
def: "Delata2D is image analysis software that is manufactured by Decodon." [PSI:GEL "The PSI working group for gel based experiments"]
is_a: sep:00062 ! image analysis software
[Term]
id: sep:00072
name: object
def: "An object is a physical concept that has independent material existence and is a separate and distinct portion of matter." [Roget's II: The New Thesaurus, Third Edition:object "Houghton Mifflin Company 1995. Answers.com 15 Nov. 2006. http://www.answers.com/topic/object."]
is_a: sep:00003 ! physical
[Term]
id: sep:00073
name: process
def: "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." [SUMO:process "Suggested Upper Merged Ontology"]
is_a: sep:00003 ! physical
[Term]
id: sep:00074
name: collection
def: "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." [SUMO:collection "Suggested Upper Merged Ontology"]
is_a: sep:00072 ! object
[Term]
id: sep:00075
name: device
def: "A device is an object which provides a mechanical advantage when used in a process." [PSI:Gel "The PSI working group for gel based experiments"]
is_a: sep:00072 ! object
[Term]
id: sep:00076
name: substance
def: "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." [SUMO:substance "Suggested Upper Merged Ontology"]
is_a: sep:00072 ! object
[Term]
id: sep:00077
name: group
def: "A group is a defnined collection of objects, e.g. a flock of sheep, a herd of goats, or the local Boy Scout troop." [SUMO:group "Suggested Upper Merged Ontology"]
is_a: sep:00074 ! collection
[Term]
id: sep:00078
name: organization
def: "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." [SUMO:organisation "The PSI working group for gel based experiments"]
is_a: sep:00077 ! group
[Term]
id: sep:00079
name: consortium
def: "A consortium is an association of organisations for some definite purpose." [SUMO:consortium "Suggested Upper Merged Ontology"]
is_a: sep:00078 ! organization
[Term]
id: sep:00080
name: The Human Proteome Organisation
def: "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." [PSI :GEL "The PSI working group for gel based experiments"]
exact_synonym: "HUPO" []
is_a: sep:00079 ! consortium
[Term]
id: sep:00081
name: The Human Proteome Organisation Proteomics Standards Initiative
def: "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)." [PSI:GEL "The PSI Working group for gel based experiments"]
def: "The PSI working group for Gel-based methods of analysis (GEL)." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00013 ! proteomics standards initiative working group
[Term]
id: sep:00083
name: PSI MI
def: "The PSI working group for Molecular Interactions (MI)." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00013 ! proteomics standards initiative working group
[Term]
id: sep:00084
name: PSI MOD
def: "The PSI working group for Protein Modifications (MOD)." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00013 ! proteomics standards initiative working group
[Term]
id: sep:00085
name: PSI MS
def: "The PSI working group for Mass Spectrometry Data Interchange (MS)." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00013 ! proteomics standards initiative working group
[Term]
id: sep:00086
name: PSI PI
def: "The PSI working group for Proteomics Informatics (PI)." [PSI :GEL "The PSI Working group for gel based experiments"]
is_a: sep:00013 ! proteomics standards initiative working group
[Term]
id: sep:00087
name: PSI SP
def: "The PSI working group for Separations and Sample Preparation (SP)." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00013 ! proteomics standards initiative working group
[Term]
id: sep:00088
name: vendor
def: "A vendor is an organisation that supplier of goods or services of a commercial nature may be a manufacturer, importer, or wholesale distributor." [Dictionary of Finance and Investment Terms:vendor "Dictionary of Finance and Investment Terms. Barron's Educational Series Inc 2006. Answers.com 24 Apr. 2007. http://www.answers.com/topic/vendor"]
is_a: sep:00078 ! organization
[Term]
id: sep:00089
name: educational organisation
def: "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." [SUMO:educational organisation "Suggested Upper Merged Ontology"]
is_a: sep:00078 ! organization
[Term]
id: sep:00090
name: university
def: "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." [SUMO:university "Suggested Upper Merged Ontology"]
is_a: sep:00089 ! educational organisation
[Term]
id: sep:00091
name: government organisation
def: "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." [SUMO:government organisation "Suggested Upper Merged Ontology"]
is_a: sep:00078 ! organization
[Term]
id: sep:00092
name: blot module
def: "A blot module is a device which permits the protocol of blotting to be performed." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00075 ! device
[Term]
id: sep:00093
name: electrical power supply
def: "An electrical power supply is a device that supplies electricity. For example a power pack." [PSI:GEL "The PSI Working group for gel based experiments"]
exact_synonym: "power pack" []
is_a: sep:00075 ! device
[Term]
id: sep:00094
name: gel dryer
def: "A gel dryer is a device which permits drying of gels." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00075 ! device
[Term]
id: sep:00095
name: gel tank
def: "A gel tank is a device which holds a gel and running buffers to allow electrophoresis to be performed." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00075 ! device
[Term]
id: sep:00096
name: image acquisition device
def: "An image acquisition device is a device which captures a digitiesed image of an object." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00075 ! device
[Term]
id: sep:00097
name: isoelectric focusing device
def: "An isoelectric focussing device is a device in which isoelectric focusing can be performed." [PSI:GEL "The PSI Working group for gel based experiments"]
exact_synonym: "isoelctric focusing unit" []
is_a: sep:00075 ! device
[Term]
id: sep:00098
name: thermostatic circulator
def: "A thermostatic circulator is a device which cools or heats a circulating liquid." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00075 ! device
[Term]
id: sep:00099
name: camera
def: "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)." [Wordnet:camera "The PSI Working group for gel based experiments"]
is_a: sep:00096 ! image acquisition device
[Term]
id: sep:00100
name: scanner
def: "A scanner is an image acquistion device that generates a digital representation of an image for data input to a computer." [Wordnet:scanner "Wordnet"]
is_a: sep:00096 ! image acquisition device
[Term]
id: sep:00101
name: protocol
def: "A protocol is a process which is a parameterizable description of a process." [FUGE:protocol "Functional Genomics Experiment"]
is_a: sep:00073 ! process
[Term]
id: sep:00102
name: protein blocking
def: "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." [Wikipedia:Blocking "http://en.wikipedia.org/wiki/Western_blot"]
is_a: sep:00101 ! protocol
[Term]
id: sep:00103
name: biological substance
def: "A biological substance is a substance which originates from a biological organism." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00076 ! substance
[Term]
id: sep:00104
name: chemical substance
def: "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." [SUMO:chemical agent "Suggeste Upper Merged Ontology"]
comment: The ontology of chemical entities should be imported under this node, or created under this node, if not included in Chebi.
is_a: sep:00076 ! substance
[Term]
id: sep:00105
name: gas substance
def: "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." [SUMO:compound gas "Suggested Upper Merged Ontology"]
is_a: sep:00076 ! substance
[Term]
id: sep:00106
name: compound liquid
def: "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." [SUMO:liquid mixture "Suggested Upper Merged Ontology"]
is_a: sep:00076 ! substance
[Term]
id: sep:00107
name: filter paper
def: "Fliter paper is a compund substance which is a porous unsized paper used for filtering." [WordNet:filter paper "WordNet"]
is_a: sep:00076 ! substance
[Term]
id: sep:00108
name: mobile phase
def: "Need DEF" [to:add]
is_a: sep:00029 ! substance role
[Term]
id: sep:00109
name: digital entity
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00002 ! abstract
[Term]
id: sep:00110
name: gel
def: "A gel is a compund substance which is a colloid in a more solid form than a solution." [Wordnet:gel "Wordnet"]
is_a: sep:00076 ! substance
[Term]
id: sep:00111
name: gel excised analyte
def: "A gel excised analyte is a compound substance which is a location on a gel which has been excised, cut out or removed." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00076 ! substance
[Term]
id: sep:00112
name: membrane substance
def: "A membrane compound is a compound substance which is a thin sheet of natural or synthetic material that is permeable to substances in solution." [:The American Heritage Dictionary of the English Language, Fourth Edition:membrane "Houghton Mifflin Company 2004. Answers.com 15 Nov. 2006. http://www.answers.com/topic/membrane."]
is_a: sep:00076 ! substance
[Term]
id: sep:00113
name: Parafilm
def: "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." [Wikipedia:Parafilm "http://en.wikipedia.org/wiki/Parafilm."]
is_a: sep:00076 ! substance
[Term]
id: sep:00114
name: Coomassie blue
def: "Coomassie blue is a chemical agent that nonspecifically stains proteins a strong blue colour. It is often used in gel electrophoresis." [Wikipedia:Coomassie blue "http://en.wikipedia.org/wiki/Coomassie."]
exact_synonym: "Acid Blue 90" []
exact_synonym: "Brilliant Blue" []
exact_synonym: "Brilliant Blue G" []
exact_synonym: "Brilliant Blue G 250" []
exact_synonym: "C.I. 42655" []
is_a: sep:00104 ! chemical substance
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: has_units UO:0000205 ! volume per unit volume
relationship: has_units UO:0000176 ! milligram per milliliter
relationship: has_units UO:0000101 ! microliter
relationship: has_units UO:0000173 ! gram per milliliter
relationship: has_units UO:0000098 ! milliliter
[Term]
id: sep:00115
name: solution
def: "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." [:The American Heritage Dictionary of the English Language, Fourth Edition:solution "Houghton Mifflin Company 2004. Answers.com 15 Nov. 2006. http://www.answers.com/topic/solution."]
is_a: sep:00106 ! compound liquid
[Term]
id: sep:00116
name: suspension
def: "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." [The American Heritage Dictionary of the English Language Fourth Edition:suspension "Houghton Mifflin Company 2004. Answers.com 15 Nov. 2006. http://www.answers.com/topic/suspension."]
is_a: sep:00106 ! compound liquid
[Term]
id: sep:00117
name: agarose sealing solution
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00115 ! solution
[Term]
id: sep:00118
name: buffer solution
def: "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." [McGraw-Hill Encyclopedia of Science and Technology:buffer solution "The McGraw-Hill Companies Inc. 2005. Answers.com 15 Nov. 2006. http://www.answers.com/topic/buffers-chemistry."]
exact_synonym: "chemical buffer" []
is_a: sep:00115 ! solution
[Term]
id: sep:00119
name: fixation solution
def: "A fixing solution is a solution used to fix proteins in a gel after gel electrophoresis has been performed." [PSI:GEL "The PSI Working group for gel based experiments"]
related_synonym: "fixing solution" []
is_a: sep:00115 ! solution
[Term]
id: sep:00120
name: carrier ampholyte buffer
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
def: "An electrophoresis buffer is a buffer solution which is used to perform electrophoresis." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00118 ! buffer solution
[Term]
id: sep:00122
name: loading buffer
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00118 ! buffer solution
[Term]
id: sep:00123
name: rehydration buffer
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00118 ! buffer solution
[Term]
id: sep:00124
name: sample buffer
def: "A sample buffer is a buffer solution which contains a biological substance used in the role of a sample." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00118 ! buffer solution
[Term]
id: sep:00125
name: transfer buffer
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00118 ! buffer solution
[Term]
id: sep:00126
name: Laemelli buffer
def: "Laemmli bufferis an electrophoresis buffer which is used as a running buffer in gel electrophoresis." [PubMed:PMID\:236308 "www.pubmed.org"]
is_a: sep:00121 ! electrophoresis buffer
[Term]
id: sep:00127
name: gel matrix
def: "A gel matrix is a gel which the constituants of a gel form a matirx structure." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00110 ! gel
[Term]
id: sep:00128
name: agarose gel
def: "An agarose gel is a gel matrix which is composed of the chemical agent agarose." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00127 ! gel matrix
[Term]
id: sep:00129
name: polyacrylamide gel
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00127 ! gel matrix
[Term]
id: sep:00130
name: immobilized pH gradient gel
def: "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." [Pubmed:PMID\:7142660 "www.pubmed.org"]
exact_synonym: "IPG Gel" []
exact_synonym: "IPG strip" []
is_a: sep:00129 ! polyacrylamide gel
[Term]
id: sep:00131
name: immobiline dry strip
def: "An immobiline dry strip is a immobilized pH gradinet gel which is a product of GE healthcare." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00130 ! immobilized pH gradient gel
[Term]
id: sep:00132
name: excised band
def: "An excised band is a gel excised analyte which has the geometric shape approximately that of a cuboid." [PSI:GEL "The PSI Working group for gel based experiments"]
related_synonym: "gel band" []
exact_synonym: "band" []
exact_synonym: "protein band" []
is_a: sep:00111 ! gel excised analyte
[Term]
id: sep:00133
name: excised spot
def: "An excised spot is a gel excised analyte which is approximately circlar in geometric shape." [PSI:GEL "The PSI Working group for gel based experiments"]
exact_synonym: "gel spot" []
exact_synonym: "protein spot" []
exact_synonym: "spot" []
is_a: sep:00111 ! gel excised analyte
[Term]
id: sep:00134
name: nitrocellulose memebrane
def: "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." [Wikipedia:Nitrocellulose "http://en.wikipedia.org/wiki/Nitrocellulose"]
exact_synonym: "nitrocellulose paper" []
is_a: sep:00112 ! membrane substance
[Term]
id: sep:00135
name: PolyVinylidine DiFluoride
def: "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." [Wikipedia:PVDF "http://en.wikipedia.org/wiki/PVDF"]
related_synonym: "KYNAR" []
exact_synonym: "PVDF" []
exact_synonym: "PVDF membrane" []
is_a: sep:00112 ! membrane substance
[Term]
id: sep:00136
name: biological stain product
def: "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." [Wikipedia:Staining Biology "http://en.wikipedia.org/wiki/Staining_%28biology%29"]
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
is_a: sep:00076 ! substance
[Term]
id: sep:00137
name: SimplyBlue SafeStain
def: "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." [Invitrogen:SimplyBlue SafeStain "www.invitrogen.com"]
is_a: sep:00136 ! biological stain product
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: has_units UO:0000205 ! volume per unit volume
relationship: has_units UO:0000176 ! milligram per milliliter
relationship: has_units UO:0000101 ! microliter
relationship: has_units UO:0000173 ! gram per milliliter
relationship: has_units UO:0000098 ! milliliter
[Term]
id: sep:00138
name: SilverQuest Silver Stain
def: "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." [Invitrogen:SilverQuest Silver Stain "www.invitrogen.com"]
is_a: sep:00136 ! biological stain product
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: has_units UO:0000205 ! volume per unit volume
relationship: has_units UO:0000176 ! milligram per milliliter
relationship: has_units UO:0000101 ! microliter
relationship: has_units UO:0000173 ! gram per milliliter
relationship: has_units UO:0000098 ! milliliter
[Term]
id: sep:00139
name: biological blot protocol
def: "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." [Wikipedia:Blot (Biology) "http://en.wikipedia.org/wiki/Blot_%28biology%29"]
is_a: sep:00101 ! protocol
[Term]
id: sep:00140
name: capillary electrophoresis
def: "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." [Wikipedia:Capillary Electrophroesis "http://en.wikipedia.org/wiki/Capillary_electrophoresis"]
exact_synonym: "CE" []
is_a: sep:00101 ! protocol
[Term]
id: sep:00141
name: detection
def: "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)." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00101 ! protocol
[Term]
id: sep:00142
name: enzyme digestion
def: "Enzyme digestion is a protocol that describes the digestion of a protein by an enzyme." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00101 ! protocol
[Term]
id: sep:00143
name: electrophoresis
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00101 ! protocol
[Term]
id: sep:00144
name: equilibration
def: "Equilibration is a protocol to bring to a chemical stasis or equilibrium." [Wordnet:equilibrium "WordNet 1.7.1"]
is_a: sep:00101 ! protocol
[Term]
id: sep:00145
name: first dimension gel equilibration
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
related_synonym: "equilibration step" []
exact_synonym: "equlibration" []
exact_synonym: "gel equilibration" []
is_a: sep:00144 ! equilibration
[Term]
id: sep:00146
name: excision
def: "An excision is a protocol that described removal of a defined location from a substance." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00101 ! protocol
[Term]
id: sep:00147
name: image acquisition
def: "Image acquisition is a protocol which is used to acquire a digitised image." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00101 ! protocol
[Term]
id: sep:00148
name: inter dimension protocol
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00101 ! protocol
[Term]
id: sep:00149
name: isoelectric focusing
def: "Isoelectric focussing is a protocol that separates a sample (ususally protein) along a separation matrix (usually gel) based on Isoelectric point (pI)." [PubMed:PMID\:7142660 "www.pubmed.org"]
is_a: sep:00101 ! protocol
[Term]
id: sep:00150
name: one dimensional gel electrophoresis
def: "One dimensional gel electrophoresis is a protocol which separates a substance based on a single characteristic or dimension of the substance." [PSI:GEL "The PSI Working group for gel based experiments"]
exact_synonym: "1D" []
is_a: sep:00101 ! protocol
[Term]
id: sep:00151
name: sample loading protocol
def: "Sample loading protocol is a protocol which is the loading a substance (sample) onto another substance." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00101 ! protocol
[Term]
id: sep:00152
name: image analysis
def: "Image analysis protocol is a protocol which is the process of the analysis of digitised images." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00101 ! protocol
[Term]
id: sep:00153
name: transfer protocol
def: "A transfer protocol is a protocol which is the conveyance or removal an entity from one location to another." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00101 ! protocol
[Term]
id: sep:00154
name: protein transfer protocol
def: "A protein transfer protocol is a protocol which is the movement of proteins from one substance to another substance, possibly via a transfer medium." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00153 ! transfer protocol
[Term]
id: sep:00155
name: two dimensional gel electrophoresis
def: "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." [Pubmed:PMID\:236308 "www.pubmed.org"]
exact_synonym: "2DG" []
exact_synonym: "2DGE" []
is_a: sep:00101 ! protocol
[Term]
id: sep:00156
name: northern blot
def: "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." [Wikipeda:northern blot "http://en.wikipedia.org/wiki/Northern_blot"]
is_a: sep:00139 ! biological blot protocol
[Term]
id: sep:00157
name: Southern blot
def: "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." [Wikipedia:Southern blot "http://en.wikipedia.org/wiki/Southern_blot"]
is_a: sep:00139 ! biological blot protocol
[Term]
id: sep:00158
name: western blot
def: "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." [Wikipedia:western blot "http://en.wikipedia.org/wiki/Western_blot"]
related_synonym: "immunoblot" []
is_a: sep:00139 ! biological blot protocol
[Term]
id: sep:00159
name: direct detection
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00141 ! detection
[Term]
id: sep:00160
name: indirect detection
def: "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)." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00141 ! detection
[Term]
id: sep:00161
name: staining
def: "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." [Wikipedia:staining "http://en.wikipedia.org/wiki/Staining"]
is_a: sep:00159 ! direct detection
[Term]
id: sep:00162
name: Coomassie staining
def: "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." [WIkipedia:Coomassie staining "http://en.wikipedia.org/wiki/Staining#Coomassie_blue"]
is_a: sep:00161 ! staining
[Term]
id: sep:00163
name: silver staining
def: "Silver staining is a staining which uses silver to stain a substance." [Wikipedia:silver staining "http://en.wikipedia.org/wiki/Staining#Silver_staining"]
is_a: sep:00161 ! staining
[Term]
id: sep:00164
name: chemilumninescent detect
def: "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." [WIkipedia:Chemiluminescence "http://en.wikipedia.org/wiki/Western_blot#Chemiluminescence"]
is_a: sep:00160 ! indirect detection
[Term]
id: sep:00165
name: colorimetric detection
def: "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." [WIkipedia:colormetric detection "http://en.wikipedia.org/wiki/Western_blot#Colorimetric_detection"]
is_a: sep:00160 ! indirect detection
[Term]
id: sep:00166
name: flourescent detection
def: "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." [Wikipedia:flourescent detection "http://en.wikipedia.org/wiki/Western_blot#Fluorescent_detection"]
is_a: sep:00160 ! indirect detection
[Term]
id: sep:00167
name: immuno detection
def: "Immuno detection is an indirect detection protocol which is the use of an antibody-based method to detect a specific protein in a sample." [Wikipedia:immunostaining "http://en.wikipedia.org/wiki/Immunostaining"]
is_a: sep:00160 ! indirect detection
[Term]
id: sep:00168
name: primary antibody probing
def: "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." [Wikipedia:primary antibody probing "http://en.wikipedia.org/wiki/Western_blot#Two_step"]
is_a: sep:00160 ! indirect detection
[Term]
id: sep:00169
name: secondary antibody probing
def: "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." [Wikipedia:secondary antobody probing "http://en.wikipedia.org/wiki/Western_blot#Two_step"]
is_a: sep:00160 ! indirect detection
[Term]
id: sep:00170
name: radioactive detection
def: "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)." [Wikipedia :radioactive detection "http://en.wikipedia.org/wiki/Western_blot#Radioactive_detection"]
is_a: sep:00160 ! indirect detection
[Term]
id: sep:00171
name: agarose gel electrophoresis
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00150 ! one dimensional gel electrophoresis
[Term]
id: sep:00172
name: polyacrylamide gel electrohoresis
def: "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." [Pubmed:PMID\:5432063 "www.pubmed.org"]
is_a: sep:00150 ! one dimensional gel electrophoresis
[Term]
id: sep:00173
name: sodium dodecyl sulfate polyacrylamide gel electrophoresis
def: "Sodium dodecyl sulfate polyacrylamide gel electrophoresis is a polyacrylamide gel electrophoresis which which the charge of the proteins results from their binding SDS." [Pubmed:PMID\: 5432063 "www.pubmed.org"]
exact_synonym: "SDS PAGE" []
is_a: sep:00172 ! polyacrylamide gel electrohoresis
[Term]
id: sep:00174
name: cup loading
def: "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)." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00151 ! sample loading protocol
[Term]
id: sep:00175
name: paper bridge loading
def: "Paper bridge loading is a sample loading protocol that is the loading of samples on a gel prior to electrophoresis using a paper bridge." [Pubmed:PMID\:11271483 "www.pubmed.org"]
is_a: sep:00151 ! sample loading protocol
[Term]
id: sep:00176
name: rehydration loading
def: "Rehydration loading is a sample loading protocol which rehydrates the gel at the same time as the application of sample to a gel." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00151 ! sample loading protocol
[Term]
id: sep:00177
name: well loading
def: "Well loading is a sample loading protocols that directly loads a sample directly in the wells of a gel prior to electrophoresis." [PSI:GEL "The PSI GEL workin group"]
is_a: sep:00151 ! sample loading protocol
[Term]
id: sep:00178
name: one dimensional gel electrophoresis image analysis
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00152 ! image analysis
[Term]
id: sep:00179
name: two dimensional gel electrophoresis image analysis
def: "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." [PSI:GEL "The PSI Working group for gel based experiments"]
is_a: sep:00152 ! image analysis
[Term]
id: sep:00180
name: difference gel electrophoresis
def: "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)." [Pubmed:PMID\:9420172 "www.pubmed.org"]
exact_synonym: "DIGE" []
is_a: sep:00155 ! two dimensional gel electrophoresis
[Term]
id: sep:00181
name: PubMed
def: "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." [Pubmed:Pubmed "PubMed 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"]
is_a: sep:00011 ! digital data set
[Term]
id: sep:00182
name: WordNet
def: "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." [WordNet:WordNet "http://wordnet.princeton.edu/"]
is_a: sep:00011 ! digital data set
[Term]
id: sep:00183
name: Cy2
def: "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." [Wikipedia:Cyanine "http://en.wikipedia.org/wiki/Cyanine"]
exact_synonym: "cyanine" []
is_a: sep:00104 ! chemical substance
[Term]
id: sep:00184
name: Cy3
def: "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." [Wikipedia:Cy3 "http://en.wikipedia.org/wiki/Cy3"]
exact_synonym: "indocarbocyanine" []
is_a: sep:00104 ! chemical substance
[Term]
id: sep:00185
name: Cy5
def: "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." [Wikipedia:Cy5 "http://en.wikipedia.org/wiki/Cy3"]
exact_synonym: "Indodicarbocyanine" []
is_a: sep:00104 ! chemical substance
[Term]
id: sep:00186
name: label
def: "A label is an attribute which is an identifying or descriptive marker or token that is attached to an object." [Wordnet:label "WordNet"]
is_a: sep:00004 ! attribute
[Term]
id: sep:00187
name: flourescent label
def: "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." [Brendan Glossart:flourescent label "http://www.brendan.com/glossary.html#f"]
is_a: sep:00186 ! label
[Term]
id: sep:00188
name: SYPRO Ruby
def: "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." [Invitrogen:SYPRO Ruby "Invitrogen"]
is_a: sep:00136 ! biological stain product
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: has_units UO:0000205 ! volume per unit volume
relationship: has_units UO:0000176 ! milligram per milliliter
relationship: has_units UO:0000101 ! microliter
relationship: has_units UO:0000173 ! gram per milliliter
relationship: has_units UO:0000098 ! milliliter
[Term]
id: sep:00189
name: manufacturer
def: "A person, an enterprise, or an entity that manufactures something." [:The American Heritage Dictionary of the English Language, Fourth Edition:manufacturer "Houghton Mifflin Company 2004. Answers.com 28 Nov. 2006."]
is_a: sep:00010 ! role
[Term]
id: sep:00190
name: bisacrylamide
def: "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." [http://www.leighlabs.com/MSDS/bisacry.htm\:bisacrylamide "http://www.leighlabs.com/MSDS/bisacry.htm"]
is_a: sep:00104 ! chemical substance
[Term]
id: sep:00191
name: photographic film
def: "need def" [add:def]
is_a: sep:00076 ! substance
[Term]
id: sep:00192
name: phosphor screen
def: "def" [def:add]
is_a: sep:00076 ! substance
[Term]
id: sep:00193
name: digital entity role
def: "def" [def:add]
is_a: sep:00010 ! role
[Term]
id: sep:00194
name: picking gel feature location set
def: "def" [def:add]
is_a: sep:00193 ! digital entity role
[Term]
id: sep:00195
name: biological sample
def: "A biological sample analysed by a particular technology." [SP:9999]
is_a: sep:00103 ! biological substance
[Term]
id: sep:00196
name: sample description
def: "A description of the biological sample analysed." [PSI:SP\:9999 "SP"]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: sep:00195 ! biological sample
[Term]
id: sep:00197
name: sample volume
def: "Volume of sample analysed." [PSI:SP\:9999 "SP"]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: sep:00195 ! biological sample
relationship: has_units UO:0000098 ! milliliter
relationship: has_units UO:0000101 ! microliter
[Term]
id: sep:00198
name: equilibration buffer
def: "A buffer intended to maintain the pH in a range appropriate for electrophoresis." [PSI:SP\:9999 "SP"]
is_a: sep:00118 ! buffer solution
[Term]
id: sep:000199
name: non-linear distribution
def: "A non-linear distribution is a statsitical distribution that is not equally sequential." [PSI:Gel "The PSI working group for gel based experiments"]
is_a: sep:00009 ! distribution
[Term]
id: sep:00200
name: resolving buffer
def: "TO DO" [PSI:Gel "The PSI working group for gel based experiments"]
is_a: sep:00118 ! buffer solution
[Term]
id: sep:00201
name: stacking buffer
def: "TO DO" [PSI:Gel "The PSI working group for gel based experiments"]
is_a: sep:00118 ! buffer solution
[Term]
id: sep:00202
name: alkylation buffer
def: "TO DO" [PSI:Gel "The PSI working group for gel based experiments"]
is_a: sep:00118 ! buffer solution
[Term]
id: sep:00203
name: reduction buffer
def: "TO DO" [PSI:Gel "The PSI working group for gel based experiments"]
is_a: sep:00118 ! buffer solution
[Term]
id: sep:00204
name: sample desalting
def: "Sample desalting and solid phase extraction. Desalting and/or enrichment procedures before to the measurement." [PSI:Gel "The PSI working group for gel based experiments"]
is_a: sep:00101 ! protocol
[Term]
id: sep:00205
name: microcolumn
def: "Small volume column packet with different chromatography resins" [PSI:Gel "The PSI working group for gel based experiments"]
is_a: sep:00204 ! sample desalting
[Term]
id: sep:00206
name: cartridge
def: "Large volume column packed with different chromatography resins" [PSI:Gel "The PSI working group for gel based experiments"]
is_a: sep:00204 ! sample desalting
[Term]
id: sep:00207
name: beads
def: "Bulk chromatography resin applied to a sample" [PSI:Gel "The PSI working group for gel based experiments"]
is_a: sep:00204 ! sample desalting
[Term]
id: sep:00208
name: SPE surface
def: "Solid membrane combining different chromatographic affinities" [PSI:Gel "The PSI working group for gel based experiments"]
is_a: sep:00204 ! sample desalting
[Term]
id: sep:00210
name: liquid chromatography
def: "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" [Wikipedia:Chromatography "http://en.wikipedia.org/wiki/Chromatography"]
def: "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." [Wikipedia:High-performance_liquid_chromatography "http://en.wikipedia.org/wiki/High-performance_liquid_chromatography"]
is_a: sep:00210 ! liquid chromatography
[Term]
id: sep:00212
name: normal-phase chromatography
def: "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" [Wikipedia:High-performance_liquid_chromatography "http://en.wikipedia.org/wiki/High-performance_liquid_chromatography"]
is_a: sep:00210 ! liquid chromatography
[Term]
id: sep:00213
name: ion-exchange chromatography
def: "Ion-exchange chromatography (or ion chromatography) is a process that allows the separation of ions and polar molecules based on their charge." [Wikipedia:Ion-exchange_chromatography "http://en.wikipedia.org/wiki/Ion-exchange_chromatography"]
is_a: sep:00210 ! liquid chromatography
[Term]
id: sep:00214
name: affinity chromatography
def: "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." [Wikipedia:Affinity_chromatography "http://en.wikipedia.org/wiki/Affinity_chromatography"]
is_a: sep:00210 ! liquid chromatography
[Term]
id: sep:00215
name: size-exclusion chromatography
def: "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." [Wikipedia:Size-exclusion_chromatography "http://en.wikipedia.org/wiki/Size-exclusion_chromatography"]
