STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots.
Statistical Method, Design of Experiment, Plots, Statistical Model
Alejandra Gonzalez-Beltran (http://orcid.org/0000-0003-3499-8262)
This Ontology is distributed under a Creative Commons Attribution License
Philippe Rocca-Serra (http://orcid.org/0000-0001-9853-5668)
This statement can actually be inferred from 'plan specification', because 'independent variable specification' is a subclass of 'is part of' some 'plan specification'
entity
continuant
a heart
a person
a symphony orchestra
the color of a tomato
the disposition of blood to coagulate
the lawn and atmosphere in front of our building
the mass of a cloud
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
endurant
occurrent
a surgical operation as processual context for a nosocomical infection
the life of an organism
the most interesting part of Van Gogh's life
the spatiotemporal context occupied by a process of cellular meiosis
the spatiotemporal region occupied by the development of a cancer tumor
An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
perdurant
independent continuant
a chair
a leg
an organism
the bottom right portion of a human torso
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
substantial entity
dependent continuant
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
spatial region
parts of the sum total of all space in the universe
the sum total of all space in the universe
A continuant that is neither bearer of quality entities nor inheres in any other entities.
All instances of continuant [snap:Continuant] are spatial entities, that is, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself.
An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe, a designated individual, which is thus itself a spatial region [snap:SpatialRegion].
Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO, the class site [snap:Site] allows for a so-called relational view of space, that is to say, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities, they are nevertheless spatial entities.
process
the process of cell-division
the process of sleeping
A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
two dimensional region
the surface of a cube-shaped part of space
the surface of a rectilinear planar figure-shaped part of space
the surface of a sphere-shaped part of space
A spatial region with two dimensions.
disposition
the disposition of a patient with a weakened immune system to contract disease
the disposition of a vase to brake if dropped
the disposition of metal to conduct electricity
the disposition of vegetables to decay when not refrigerated
A realizable entity that essentially causes a specific process or transformation in the object in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object has the disposition D to (transform, initiate a process) R under conditions C.
realizable entity
the function of the reproductive organs
the role of being a doctor
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
zero dimensional region
a point
A spatial region with no dimensions.
quality
the ambient temperature of air
the circumference of a waist
the mass of a piece of gold
the shape of a nose
the weight of a chimpanzee
A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property).
specifically dependent continuant
the disposition of fish to decay
the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
the liquidity of blood
the smell of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
mode
property
trope
role
the role of a biological grandfather as legal guardian in the context of a system of laws
the role of a chemical compound in an experiment
the role of a patient relative as defined by a hospital administrative form
the role of a person as a surgeon
the role of a student in a university
the role of a woman as a legal mother in the context of system of laws
the role of ingested matter in digestion
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
one dimensional region
an edge of a cube-shaped part of space
the part of space that is a line stretching from one end of absolute space to the other
A spatial region with one dimension.
three dimensional region
a cube-shaped part of space
a sphere-shaped part of space
A spatial region with three dimensions.
generically dependent continuant
a certain PDF file that exists in different and in several hard drives
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
function
the digestive function of the stomach to nutriate the body
the function of a birth canal to enable transport
the function of a computer program to compute mathematical equations
the function of a hammer to drive in nails
the function of a judge in a court of law
the function of an automobile to provide transportation
the function of reproduction in the transmission of genetic material
A realizable entity the manifestation of which is an essentially end-directed activity of a continuant entity in virtue of that continuant entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
material entity
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
Examples: collection of random bacteria, a chair, dorsal surface of the body
Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
is part of
There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else
part of
part_of
has part
has_part
inheres in
inheres_in
is bearer of
bearer of
bearer_of
is realized by
realized by
realized_by
realizes
participates in
participates_in
has participant
has_participant
is concretized as
concretizes
is preceded by
preceded by
preceded_by
precedes
s depends on
s_depends_on
is function of
function of
function_of
is role of
role of
role_of
is located in
located in
located_in
has function
has_function
has quality
has_quality
has role
has_role
gross anatomical part
Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells.
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
polymer
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules.
conditional specification
a directive information entity that specifies what should happen if the trigger condition is fulfilled
PlanAndPlannedProcess Branch
OBI branch derived
example to be eventually removed
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A data item label that denotes a unit of measure.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
objective specification
a directive information entity that describes an intended process endpoint.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
OBI Plan and Planned Process/Roles Branch
action specification
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
Alan Ruttenberg
OBI Plan and Planned Process branch
data item label
An information content entity that is part of some data item and is used to partially define the denotation of that data item.
GROUP: IAO
information carrier
In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
A quality of an information bearer that imparts the information content
12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method that reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
symbol
A written proper name such as “OBI”; a serial number such as “12324X”; a stop sign.
An information content entity that is a mark or character used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
an information content entity is an entity that is generically dependent on some material entity and stands in relation of aboutness to some entity
scalar measurement datum
10 feet. 3 ml.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
directive information entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Philly2013 - AR: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
dot plot
Dot plot of SSC-H and FSC-H.
A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
person:Allyson Lister
person:Chris Stoeckert
graph
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
PERSON: Lawrence Hunter
person:Alan Ruttenberg
has measurement unit label
A relation between a value specification and its unit of measurement.
rule
example to be added
a rule is an executable which guides, defines, restricts actions
MSI
PRS
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
Philippe Rocca-Serra
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
report
journal article, patent application, grant progress report, case report (not patient record)
An information content entity assembled by an author for the purpose of providing information for an audience, and that is meant to provide an accurate account of something that happened.
2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
PERSON:Chris Stoeckert
GROUP: OBI
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
image
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
data about an ontology part
data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
To lose weight, go running daily for at least 30 minutes. To isolate plasma from blood, centrifuge tubes at 1100-1300 rpm for 15 minutes.
a directive information entity that, when concretized, is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
measurement data item
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A data item that is a recording of the output of an assay.
2/2/2009 is_specified_output of some assay?
editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
editor preferred term
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
has curation status
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
version number
A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
is about
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
conclusion textual entity
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
2009/10/23 Alan Ruttenberg: We need to work on the definition still
Person:Alan Ruttenberg
material information bearer
A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. Additional examples: a hard drive, a brain.
A material entity in which a concretization of an information content entity inheres.
scatter plot
Comparison of gene expression values in two samples can be displayed in a scatter plot
A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
PERSON:James Malone
scattergraph
WEB: http://en.wikipedia.org/wiki/Scatterplot
denotes
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
curator note
An administrative note of use for a curator but of no use for a user
textual entity
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
text
table
A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
figure
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
diagram
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
A figure that expresses one or more propositions
cartesian spatial coordinate datum
A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
one dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
two dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
has x coordinate value
has y coordinate value
has coordinate unit label
relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
imported from
For external terms/classes, the ontology from which the term was imported
is duration of
relates a process to a time-measurement-datum that represents the duration of the process
mass measurement datum
A scalar measurement datum that is the result of measurement of mass quality
time measurement datum
A scalar measurement datum that is the result of measuring a temporal interval
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
documenting
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. Copying the readout from an instrument into a spreadsheet.
a planned process in which input information is used to create or add to a report
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
Bjoern Peters
wikipedia http://en.wikipedia.org/wiki/Documenting
line graph
line chart
WEB: http://en.wikipedia.org/wiki/Line_chart
CRID
PubMed identifier “PMID:12345”
A symbol that is sufficient to look up information about the corresponding entity from its CRID (centrally registered identifier) registry.
IAO call, 20101124: 12345 is not a CRID symbol. To be a CRID symbol you need to have some information about the registry within which the CRID is recorded.
PERSON: Bill Hogan
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier
Entries in a Column of which the header is "Pubmed ID"
The following URL: "http://www.ncbi.nlm.nih.gov/pubmed/19918065"
The following sentence contains a CRID: "The article with Pubmed ID: 19918065".
An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
CRID registry
PubMed and GenBank both have CRID registries as parts of their database systems.
A data set that consists of CRIDs (centrally registered identifier) and additional information about their corresponding entities, that were recorded in the dataset through an assigning a centrally registered identifier process.
IAO call, 20101124: PubMed registry is an instance of CRID registry
centrally registered identifier registry
has time stamp
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
time stamped measurement datum
has measurement datum
relates a time stamped measurement datum to the measurement datum that was measured
time sampled measurement data set
pmid:20604925 - time-lapse live cell microscopy
A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
experimental time series
fluorescent reporter intensity
A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.
From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem.
planned process
Injecting mice with a vaccine in order to test its efficacy
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
biological feature identification objective
Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
Jennifer Fostel
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
investigation
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
Could add specific objective specification
evaluant role
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
measuring
scientific observation
quantitative confidence value
A data item which is used to indicate the degree of uncertainty about a measurement.
culture medium
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
Person: Jennifer Fostel, Jie Zheng
OBI
reagent role
Buffer, dye, a catalyst, a solvating agent.
A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
PERSON:Matthew Brush
material processing
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
participant under investigation role
A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
GROUP: Role Branch
biological vector role
1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.
Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280
a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission.
Feb 20, 2009. The material transmitted can be genetic information (as in cloning vector) or a pathogen (as in a disease vector)
6/12/2009 Alan made this a material to be added role, because it was, and because this speeded up reasoning
specimen role
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
sequence feature identification objective
Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
intervention design
PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
Philppe Rocca-Serra
gene list
Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis.
A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis.
kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object.
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
molecular feature identification objective
Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.
cDNA library
PMID:6110205. collection of cDNA derived from mouse splenocytes.
PERSON: Luisa Montecchi
PERSON: Philippe Rocca-Serra
GROUP: PSI
p-value
A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
Addition of restriction 'output of null hypothesis testing' by AGB and PRS while working on STATO
May be outside the scope of OBI long term, is needed so is retained
Alejandra Gonzalez-Beltran
WEB: http://en.wikipedia.org/wiki/P-value
population
PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
adapted from Oxford English Dictionnary
rem1: collection somehow always involve a selection process
imaging assay
An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
dye role
A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest.
A substance used to color materials www.answers.com/topic/dye 19feb09
protocol
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
adding a material entity into a target
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
analyte role
Glucose in blood (measured in an assay to determine the concentration of glucose).
A role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role
interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
qualities such as weight, color are not assayed but measured, so they do not fall into this category.
has_specified_input
see is_input_of example_of_usage
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
is_specified_input_of
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
is_specified_output_of
is_proxy_for
A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be.
material to be added role
drug added to a buffer contained in a tube; substance injected into an animal;
material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
9 March 09 from discussion with PA branch
drawing a conclusion based on data
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
planning
The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
a process of creating or modifying a plan specification
7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
light emission function
A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
contain function
A contain function is a function to constrain a material entities location in space
heat function
A heat function is a function that increases the internal kinetic energy of a material
material separation function
A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
excitation function
A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
filter function
A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
cool function
A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
solid support function
Taped, glued, pinned, dried or molecularly bonded to a solid support
A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
environment control function
An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
sort function
A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order.
cloning vector role
pBluescript plays the role of a cloning vector
a vector role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
cloning insert role
cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process.
Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process"
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
extract
Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
an extract is a material entity which results from an extraction process
extracted material
transcription profiling assay
Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot
gene expression profiling
averaging objective
A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
James Malone
enzyme
adding material objective
creating a mouse infected with LCM virus
is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
genotyping assay
High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923
genotype profiling, SNP genotyping
analyte measurement objective
The objective to measure the concentration of glucose in a blood sample
an assay objective to determine the presence or concentration of an analyte in the evaluant
assay objective
the objective to determine the weight of a mouse.
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
analyte assay
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.
PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
target of material addition role
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
target of material addition role is a role realized by an entity into which a material is added in a material addition process
From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
normalized data set
A data set that is produced as the output of a normalization data transformation.
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
material transformation objective
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
a planned process that realizes the concretization of a study design
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858
DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is an objective to transform a material entity into spatially separated components.
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
data set of features
A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set.
differential expression analysis data transformation
A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of
Melanie Courtot
Monnie McGee
Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
A planned process with the objective of collecting a specimen.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
error corrected data set
A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for).
error correction data transformation
An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation.
a material obtained from an organism in order to be a representative of the whole
we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
statistical hypothesis test
"A statistical test provides a mechanism for making quantitative decisions about a process or processes".
A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.
PERSON: James Malone
statistical hypothesis testing
center value
A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
PRS and AGB added restriction about 'measure of central tendency' and quartile, june 2013
statistical hypothesis test objective
is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation
WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing
The objective to obtain multiple aliquots of an enzyme preparation.
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
average value
A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
PRS and AGB added restriction about 'measure of central tendency', june 2013
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
is an objective to obtain an output material that contains several input materials.
PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y.
is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
adapted from information provided by Solid web site
A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector.
is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site.
Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value.
WEB: http://en.wikipedia.org/wiki/T-test
t.test(dependent variable ~ independant variable, data = dataset, var.equal = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html
a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
A material entity that has the material sample role
study design independent variable
In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable.
a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
explanatory variable
study design dependent variable
In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable.
PRS-AGB: a dependent variable is a variable which assumes only values set by the operator according to a plan and are expected to influence the ranges of values assumed by a response variable aka independent variable.
dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies.
2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
response variable
A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring.
Application of the Bonferroni correction
A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously
multiple comparison correction objective
An objective specification maintains some or all of the qualities of a material over time.
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
A ruler, a microarray scanner, a Geiger counter.
A device in which a measure function inheres.
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
Likelihood-ratio test is a statistical test which evaluates the goodness-of-fit between two models and whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one)
date: March 2013 AGB and PRS provide formal definition expressed the test in terms of output and input, specifying the nature of the variables, the purpose of the test and the distribution used.
Alejandra Gonzales-Beltran
lrtest() http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/lmtest/html/lrtest.html
survival curve
A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
WEB: http://www.graphpad.com/www/book/survive.htm
Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody.
An assay that uses a flow cytometer to detect fluorescence in individual particles that flow by a laser in solution.
A specimen that has been modified in order to be able to detect it in future experiments
the part of the execution of an intervention design study which is varied between two or more subjects in the study
A device with a separation function realized in a planed process
A measurement datum that is reported on a categorical scale
A specimen that has been intentionally physically modified.
A tissue sample that has been sliced and stained for a histology study.
The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
An assay in which a measurement is made by observing entities located in a live cell.
A device that can be used to restrict the location of material entities over time
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
sequence data
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
An organism has been injected 1ml of vaccine
A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)
a device which has a function to emit light.
A growth chamber is an environmental control device.
An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve.
Philippe Rocca-Serra, Alejandra Gonzalez-Beltran
genetic population background information
genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
a genetic characteristics information which is a part of genotype information that identifies the population of organisms
proposed and discussed on San Diego OBI workshop, March 2011
Group: OBI group
A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests
Addition of restriction 'output of null hypothesis testing' and specified output by AGB and PRS while working on STATO
PERS:Philippe Rocca-Serra
adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate)
RNA-seq assay
An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance
transcription profiling by high throughput sequencing
EFO_0002770 transcription profiling by high throughput sequencing
JZ: should be inferred as 'DNA sequencing'. Will check in the future.
genotype information
Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
discussed on San Diego OBI workshop, March 2011
transcription profiling identification objective
A molecular feature identification objective that aims to characterize the abundance of transcripts
Person: Chris Stoeckert, Jie Zheng
Group: Penn Group
allele information
genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
genetic alteration information
a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
genetic characteristics information
a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
MO_66 IndividualGeneticCharacteristics
FDR adjusted p-value
genotyping design
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
MO_560 genotyping_design
tissue specimen
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.
A scalar measurement datum that represents the number of events occuring over a time interval
The part of a FASTA file that contains the letters ACTGGGAA
A sequence data item that is about the primary structure of DNA
8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
selection criterion
rats should be aged between 6 and 8 weeks and weight between 180-250grams
A directive information entity which defines and states a principle of standard by which selection process may take place.
Person: Philippe Rocca-Serra
selection rule
OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
A planned process in which new information is inferred from existing information.
ISA alternative term
An alternative term used by the ISA tools project (http://isa-tools.org).
ISA tools project (http://isa-tools.org)
assay array
A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface.
PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg
An information content entity that is inferred from data.
In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
cell freezing medium
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
A relation between a value specification and an entity which the specification is about.
A value specification that is specifies one category out of a fixed number of nominal categories
A value specification that consists of two parts: a numeral and a unit label
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay
A relation between a value specification and a number that quantifies it.
A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
A relation between an information content entity and a value specification that specifies its value.
organism
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
WEB: http://en.wikipedia.org/wiki/Organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
screening library
PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library]
a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process?
7/13/09: Need to clarify if this meets reagent role definition
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
differential expression analysis objective
Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software
A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
PERSON: Elisabetta Manduchi
Benjamini and Hochberg false discovery rate correction method
Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate)
A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate
Benjamini and Yekutieli false discovery rate correction method
The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli)
A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate
Holm-Bonferroni family-wise error rate correction method
t-tests were used with the type I error adjusted for multiple comparisons, Holm's correction (HOLM 1979), and false discovery rate, http://www.genetics.org/cgi/content/full/172/2/1179
a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction
WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method
family wise error rate correction method
A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive.
FWER correction
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19
descriptive statistical calculation objective
A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
PERSON: Monnie McGee
survival analysis objective
A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables
multiple testing correction method
A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate
multiple testing procedure
PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10.
logarithmic transformation
A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm.
WEB: http://en.wikipedia.org/wiki/Logarithm
regression analysis method
Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data.
Date:2013-11-15 Person: AGB,PRS Adding restrictions, specifying model + parameter estimation process change of label from 'regression analysis method' to 'regression analysis'
BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048
data visualization
Generation of a heatmap from a microarray dataset
An planned process that creates images, diagrams or animations from the input data.
Tina Boussard
visualization
PERSON: Tina Boussard
mode calculation
A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data.
From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008)
median calculation
A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values.
false discovery rate correction method
The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. .
FDR correction method
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
data normalization objective
Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
correction objective
Type I error correction
A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself
normalization data transformation
A normalization data transformation is a data transformation that has objective normalization.
averaging data transformation
An averaging data transformation is a data transformation that has objective averaging.
Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests.
center calculation objective
A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
center calculation data transformation
A center calculation data transformation is a data transformation that has objective of center calculation.
descriptive statistical calculation data transformation
A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
error correction objective
Application of a multiple testing correction method
An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself.
James Malone, Helen Parkinson
Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type.
A data transformation which has the objective of performing survival analysis.
The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough.
negociation with OBI hence definition and definition source are missing from this class
ANalysis Of VAriance (ANOVA) is a data transformation in which a statistical test is performed to evaluate the null hypothesis that the means computed over the different groups as specified by the investigator do not differ. The test compares an F-statistics (a ratio of means) to an F-distribution and produces a p-value, used to reject or accept the null hypothesis given a false positive rate. The test assumes normality and equivariance of the data.
AGB and PRS augmented the class with formal definitions as part of STATO extension
stat.anova()
observation design
PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
extraction
nucleic acid extraction using phenol chloroform
A material separation in which a desired component of an input material is separated from the remainder
group randomization
PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6.
A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up.
adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization]
nucleic acid hybridization
PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.
a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity.
adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]
flow cell
Biofilm Flow Cell
Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell.
Person:John Quinn
flow cytometer
FACS Calibur
A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium.
John Quinn
light source
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
Elizabeth M. Goralczyk
Olga Tchuvatkina
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
obscuration bar
obscuration bar in a flow cytometer
An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device.
Daniel Schober
Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249
optical filter
720 LP filter, 580/30 BP filter
An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length.
photodetector
A photomultiplier tube, a photo diode
A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye.
DNA sequencer
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Trish Whetzel
hybridization chamber
Glass Array Hybridization Cassette
A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide.
MO_563 hybridization_chamber
cytometer
A cytometer is an instrument for counting and measuring cells.
microarray
An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays.
A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position.
DNA microarray
Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115
A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample.
PERSON: Daniel Schober
DNA Chip
DNA-array
droplet sorter
study design
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
repeated measure design
PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations.
a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs
cross over design
PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity.
a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control
(source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html)
matched pairs design
PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs.
A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment.
parallel group design
PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR.
A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment
independent measure design
randomized complete block design
http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd))
A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups.
latin square design
PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables). The 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once.
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
graeco latin square design
PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes.
graeco-latin square design is a block design which declares 3 blocking variables (aka nuisance variables) in addition to the treatment variable
only 2 articles in pubmed ->probably irrelevant
Euler square design
orthogonal latin squares design
hyper graeco latin square design
hyper graeco-latin square design is a block design which declares 4 blocking variables (aka nuisance variables) in addition to the treatment variable
no example found in pubmed->not in use in the community
factorial design
factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable.
http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment)
2x2 factorial design
PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed.
a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors
PMID: 17561240
fractional factorial design
A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run
http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control
dye swap design
PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip
Philippe Rocca-Serra on behalf of MO
MO_858
time series design
PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources.
Groups of assays that are related as part of a time series.
PRS-AGB adding formal restriction on independent variable specification about time (march 2013) and making time series design class a defined class.
MO_887
collecting specimen from organism
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
PERSON:Bjoern Peters
IEDB
material component separation
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
group assignment
Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation
group assignment is a process which has an organism as specified input and during which a role is assigned
OBI Plan
maintaining cell culture
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.
addition of molecular label
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay
OBI developer call, 3-12-12
sequencing assay
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
the use of a chemical or biochemical means to infer the sequence of a biomaterial
has_output should be sequence of input; we don't have sequence well defined yet
recombinant vector cloning
a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material
pa_branch (Alan, Randi, Kevin, Jay, Bjoern)
nucleic acid extraction
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
a material separation to recover the nucleic acid fraction of an input material
requested by Helen Parkinson for MO. Could be defined class
phage display library
PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides]
a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified.
display library
WEB: http://www.immuneepitope.org/home.do
A mixture of peptides that is being added into a cell culture.
a material that is added to another one in a material combination process
10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export
2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes
A cell culture into which a mixture of peptides is being added.
A material entity into which another is being added in a material combinatino process
10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
molecular label role
a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.
MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role)
a molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay
derives from
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
primary structure of sequence macromolecule
declares
digital images may be stored as electronic file in TIFF format on mass memory storage devices
an electronic file is an information content entity which conforms to a specification or format and which is meant to hold data and information in digital form, accessible to software agents
STATO
digital file
a balanced design is a an experimental design where all experimental group have the an equal number of subject observations
balanced design
is declared by
a single factor design is a study design which declares exactly 1 independent variable
single factor design
x-axis is a cartesian coordinate axis which is orthogonal to the y-axis and the z-axis
x-axis
an axis is a line graph used as reference line for the measurement of coordinates.
axis
y-axis is a cartesian coordinate axis which is orthogonal to the x-axis and the z-axis
y-axis
A Cartesian coordinate system is a coordinate system that specifies each point uniquely in a plane by a pair of numerical coordinates, which are the signed distances from the point to two fixed perpendicular directed lines, measured in the same unit of length.
cartesian coordinate system
In geometry, a coordinate system is a system which uses one or more numbers, or coordinates, to uniquely determine the position of a point or other geometric element on a manifold such as Euclidean space.
coordinate system
a cartesian axis is one of 3 the axis in a cartesian coordinate system defining a referential in 3 dimensions. each of the axis is orthogonal to the other 2
rectangular coordinate axis
adapted from Wolfram Alpha: https://www.wolframalpha.com/input/?i=cartesian+coordinates&lk=4&num=6&lk=4&num=6
cartesian coordinate axis
z-axis is a cartesian coordinate axis which is orthogonal to the x-axis and the y-axis
z-axis
a 2 dimensional cartesian coordinate system is a cartesian coordinate system which defines 2 orthogonal one dimensional axes and which may be used to describe a 2 dimensional spatial region
two dimensional cartesian coordinate system
spherical coordinate system
cylindrical coordinate system
In mathematics, the polar coordinate system is a two-dimensional coordinate system in which each point on a plane is determined by a distance from a fixed point and an angle from a fixed direction.
polar coordinate system
Wilks' lambda distribution (named for Samuel S. Wilks), is a probability distribution used in multivariate hypothesis testing, especially with regard to the likelihood-ratio test and Multivariate analysis of variance. It is a multivariate generalization of the univariate F-distribution, and generalizes the F-distribution in the same way that the Hotelling's T-squared distribution generalizes Student's t-distribution.
wikipedia: last accessed: 2013-09-11 http://en.wikipedia.org/wiki/Wilks%27_lambda_distribution
Wilk's lambda distribution
three dimensional cartesian spatial coordinage origin
normal distribution hypothesis is a goodness of fit hypothesis stating that the distribution computed from the sample population fits a normal distribution
normal distribution hypothesis
two dimensional cartesian spatial coordinate origin
a confidence interval which covers 90% of the sampling distribution, meaning that there is a 90% risk of false positive (type I error)
90% confidence interval
a three dimensional cartesian coordinate system is a cartesian coordinate system which defines 3 orthogonal one dimensional axis and which may be used to describe a 3 dimensional spatial region
one dimensional cartesian coordinate system
The studentized range (q) distribution is a probability distribution used by the Tukey Honestly Significant Difference test. The distribution of the statistic [x̄(k)- x̄(1)]/(s/√n) where random samples of size n have been taken from k independent and identically distributed normal populations, with x̄(1) and x̄(k) being, respectively, the smallest and largest of the k sample means, and s2 being the pooled estimate of the common variance. This statistic is particularly used in multiple comparison tests.
q distribution
A Dictionary of Statistics (2 rev ed.), OUP. ISBN-13: 9780199541454 http://www.oxfordreference.com/view/10.1093/acref/9780199541454.001.0001/acref-9780199541454-e-1588
studentized range distribution
a three dimensional cartesian coordinate system is a cartesian coordinate system which defines 3 orthogonal one dimensional axes and which may be used to describe a 3 dimensional spatial region
three dimensional cartesian coordinate system
one dimensional cartesian spatial coordinate origin
placeholder, more work needed
cartesian spatial coordinate origin
linkage between 2 categorical variable test is a statistical test which evaluates if there is an association between a predictor variable assuming discrete values and a response variable also assuming discrete values
test of association
test of independence
test of independence between variables
test of association between categorical variables
measure of variation or statistical dispersion is a data item which describes how much a theoritical distribution or dataset is spread.
measure of dispersion
measure of variation
a measure of central tendency is a data item which attempts to describe a set of data by identifying the value of its centre.
measure of central tendency
Chi-squared statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Chi-Squared distribution.
Chi-Squared statistic
binary classification (or binomial classification) is a data transformation which aims to cast members of a set into 2 disjoint groups depending on whether the element have a given property/feature or not.
adapted from wikipedia: http://en.wikipedia.org/wiki/Binary_classifier last accessed: 2013-11-21
binomial classification
binary classification
an alternative term used for STATO statistical ontology and ISA team
STATO alternative term
The mode is a data item which corresponds to the most frequently occurring number in a set of numbers.
a model parameter is a data item which is part of a model and which is meant to characterize an theoritecal or unknown population. a model parameter may be estimated by considering the properties of samples presumably taken from the theoritecal population
model parameter
the range is a measure of variation which describes the difference between the lowest score and the highest score in a set of numbers (a data set)
range(..., na.rm = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/base/html/range.html
range
Outliers are deviant scores that have been legitimately gathered and are not due to equipment failures.
outlier
The standard error of the mean (SEM) is data item denoting the the standard deviation of the sample-mean's estimate of a population mean. It is calculated by dividing the sample standard deviation (i.e., the sample-based estimate of the standard deviation of the population) by the square root of n , the size (number of observations) of the sample.
SEM
adapted from wikipedia (https://en.wikipedia.org/wiki/Standard_error)
standard error of the mean
a set of 2 subjects which result from a pairing process which assigns subject to a set based on a pairing rule/criteria
possibly submit to 'Population and Community Ontology'
matched pair of subjects
a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data.
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic).
statistic
an MA plot is a scatter plot of the log intensity ratios M = log_2(T/R) versus the average log intensities A = log_2(T*T)/2, where T and R represent the signal intensities in the test and reference channels respectively.
M vs A plot
MA plot
plot.mva()
a R command syntax or link to a R documentation in support of Statistical Ontology Classes or Data Transformations
R command
The Anderson–Darling test is a statistical test of whether a given sample of data is drawn from a given probability distribution.
ad.test(x) function, where x is a numeric vector
Anderson-Darling test
one-way anova is an analysis of variance where the different groups being compared are associated with the factor levels of only one independent variable. The null hypothesis is an absence of difference between the means calculated for each of the groups. The test assumes normality and equivariance of the data.
one factor ANOVA
one-way ANOVA
two-way anova is an analysis of variance where the different groups being compared are associated the factor levels of exatly 2 independent variables. The null hypothesis is an absence of difference between the means calculated for each of the groups. The test assumes normality and equivariance of the data.
two factor ANOVA
two-way ANOVA
a block design is a kind of study design which declares a blocking variable (also known as nuisance variable) in order to account for a known source of variation and reduce its impact on the acquisition of the signal
adapted from several sources including Wikipedia
block design
a count of 4 resulting from counting limbs in humans
a count is a data item denoted by an integer and represented the number of instances or occurences of an entity
count
Multi-way anova is an analysis of variance where the difference groups being compared are associated to the factor levels of more than 2 independent variables. The null hypothesis is an absence of difference between the means calculated for each of the groups. The test assumes normality and equivariance of the data.
multiway ANOVA
Hardy-Weinberg equilibrium hypothesis is a good of fit hypothesis which states that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences (non-random mating, mutation, selection, genetic drift, gene flow and meiotic drive).
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Hardy–Weinberg_principle)
signal to noise ratio is a measurement datum comparing the amount of meaningful, useful or interesting data (the signal) to the amount of irrelevant or false data (the noise). Depending on the field and domain of application, different variables will be used to determinate a 'signal to noise ratio'. In statistics, the definition of signal to noise ratio is the ratio of the mean of a measurement to its standard deviation. It thus corresponds to the inverse of the coefficient of variation
adapted from Wikipedia: http://en.wikipedia.org/wiki/Signal-to-noise_ratio#Alternative_definition last accessed: 2013-10-18
S/N
SNR
signal to noise ratio
Poisson distribution is a probability distribution used to model the number of events occurring within a given time interval. It is defined by a real number (λ) and an integer k representing the number of events and a function. The expected value of a Poisson-distributed random variable is equal to λ and so is its variance.
dpois(x, lambda, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Poisson.html
NIST: http://www.itl.nist.gov/div898/handbook/eda/section3/eda366j.htm
Poisson distribution
Z-test is a statistical test which evaluate the null hypothesis that the means of 2 populations are equal and returns a p-value.
simple.z.test(x, sigma, conf.level=0.95) http://www.inside-r.org/packages/cran/UsingR/docs/simple.z.test
Z-test
a false positive rate is a data item which accounts for the proportion of incorrect rejection of a true null hypothesis.
PRS,AGB adapted from wikipedia and wolfram alpha
significance level
type I error rate
false positive rate
homoskedasticity is a null hypothesis stating that all variances under consideration are homogenous
equality of variance
homoskedasticity hypothesis
http://www.ncbi.nlm.nih.gov/assembly/model/ chrX:35,000,000-36,000,000.
chromosome coordinate system is a genomic coordinate which uses chromosome of a particular assembly build process to define start and end positions. This coordinate system is unstable and will change with each new genome sequence assembly build.
chromosome coordinate system
a null hypothesis which states that no linkage exists between 2 categorical variables
no relationship between the variables
absence of association hypothesis
A null hypothesis is a statistical hypothesis that is tested for possible rejection under the assumption that it is true (usually that observations are the result of chance). The concept was introduced by R. A. Fisher. The hypothesis contrary to the null hypothesis, usually that the observations are the result of a real effect, is known as the alternative hypothesis.[wolfram alpha]
null hypothesis
goodness of fit hypothesis is a null hypothesis stating that the distribution computed from the sample population fits a theoretical distribution or that a dataset can be correctly explained by a model
goodness of fit hypothesis
the Student's t distribution is a continuous probability distribution which arises when estimating the mean of a normally distributed population in situations where the sample size is small and population standard deviation is unknown.
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Student's_t-distribution)
t distribution
dt(x, df, ncp, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/TDist.html
Student's t distribution
hypergeometric distribution is a probability distribution that describes the probability of k successes in n draws from a finite population of size N containing K successes without replacement
dhyper(x, m, n, k, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Hypergeometric.html
hypergeometric distribution
is a null hypothesis stating that there are no differences observed between group of subjects
absence of between group difference hypothesis
is a null hypothesis stating that there are no difference observed across a series of measurements made one same subject.
absence of within subject difference hypothesis
genomic coordinate datum is a data item which denotes a genomic position expressed using a genomic coordinate system
genomic coordinate datum
sequence read count is a data item determining how many sequence reads generated by a DNA sequencing assay for a given stretch of DNA can counted
sequence read count
In statistics, a statement that can be tested.[wolfram alpha]
hypothesis
Cleveland dot plot is a dot plot which plots points that each belong to one of several categories. They are an alternative to bar charts or pie charts, and look somewhat like a horizontal bar chart where the bars are replaced by a dots at the values associated with each category. Compared to (vertical) bar charts and pie charts, Cleveland argues that dot plots allow more accurate interpretation of the graph by readers by making the labels easier to read, reducing non-data ink (or graph clutter) and supporting table look-up.which
adapted from Wikipedia: http://en.wikipedia.org/wiki/Dot_plot_(statistics) and Cleveland, William S. (1993). Visualizing Data. Hobart Press. ISBN 0-9634884-0-6. hdl:2027/mdp.39015026891187.
http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/dotchart.html dotchart(x, labels = NULL, groups = NULL, gdata = NULL, cex = par("cex"), pch = 21, gpch = 21, bg = par("bg"), color = par("fg"), gcolor = par("fg"), lcolor = "gray", xlim = range(x[is.finite(x)]), main = NULL, xlab = NULL, ylab = NULL, ...)
a continuousprobability distribution is a probability distribution which is defined by a probability density function
adapted from Wikipedia http://en.wikipedia.org/wiki/Probability_distribution#Continuous_probability_distribution last accessed: 14/01/2014
continuous probability distribution
Skewness is a data item indicating of the degree of asymmetry of a distribution.
skewness(x, na.rm = FALSE, type = 3) http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/e1071/html/skewness.html
skewness
The number degree of freedom is a count evaluating the number of values in a calculation that can vary. In statistics, the number of degrees of freedom ν is equal to N-1 in the case of the direct measurement of a quantity estimated by the arithmetic mean of N independent observations.
the rank of the quadratic form (mathematical definition)
number of degrees of freedom
Yate's corrected Chi-Squared test is a statistical test which is used to test the association/linkage/independence of 2 dichotomous variables while introducing a correction for using the continous Chi-squared distribution for the test. To reduce the error in approximation, Frank Yates, an English statistician, suggested a correction for continuity that adjusts the formula for Pearson's chi-squared test by subtracting 0.5 from the difference between each observed value and its expected value in a 2 × 2 contingency table. This reduces the chi-squared value obtained and thus increases its p-value.
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Yates's_correction_for_continuity) polled in June 2013
Yate's correction for continuity
chisq.test(x, y = NULL, correct = TRUE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html
Yate's corrected Chi-Squared test
reaction rate is a measurement datum which represents the speed of a chemical reaction turning reactive species into product species of event (i.e the number of such conversions)s occuring over a time interval
reaction rate
substrate concentration is a scalar measurement datum which denotes the amount of molecular entity involved in an enzymatic reaction (or catalytic chemical reaction) and whose role in that reaction is as substrate.
substrate concentration
Fisher's exact test is a statistical test used to determine if there are nonrandom associations between two categorical variables.
duplicate with OBI_0200176. so either MIREOT and add metadata and axioms or move from OBI
fisher.test(x) function, where x is a matrix
Fisher's exact test
Cochran-Mantel-Haenzel test for repeated tests of independence is a statitiscal test which allows the comparison of two groups on a dichotomous/categorical response. It is used when the effect of the explanatory variable on the response variable is influenced by covariates that can be controlled. It is often used in observational studies where random assignment of subjects to different treatments cannot be controlled, but influencing covariates can. The null hypothesis is that the two nominal variables that are tested within each repetition are independent of each other. So there are 3 variables to consider: two categorical variables to be tested for independence of each other, and the third variable identifies the repeats.
STATO adapted from wikipedia (http://en.wikipedia.org/wiki/Cochran–Mantel–Haenszel_statistics) and from the Handbook of Biological Statistics (http://udel.edu/~mcdonald/statcmh.html)
cmh.test(x,y,z)
Cochran-Mantel-Haenzel test for repeated tests of independence
a rarefaction curve is a graph used for estimating species richness in ecology studies
>library(vegan) >rarefaction(x, subsample=5, plot=TRUE, color=TRUE, error=FALSE, legend=TRUE, symbol) http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/vegan/html/vegan-package.html
rarefaction curve
The Mann-Whitney U-test is a null hypothesis statistical testing procedure which allows two groups (or conditions or treatments) to be compared without making the assumption that values are normally distributed. The Mann-Whitney test is the non-parametric equivalent of the t-test for independent samples
rank-sum test for the comparison of two samples
adapted from http://udel.edu/~mcdonald/statkruskalwallis.html and from http://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U last accessed [2014-03-04]
Wilcoxon Rank-Sum test
wilcox.test(dependent variable ~ independant variable, data = dataset) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/wilcox.test.html
Mann-Whitney U-test
Shapiro-Wilk test is a goodness of fit test which evaluates the null hypothesis that the sample is drawn from a population following a normal distribution
STATO, adapted from wikipedia (https://en.wikipedia.org/wiki/Shapiro–Wilk_test)
shapiro.test(x) function, where x is a numeric vector https://stat.ethz.ch/R-manual/R-devel/library/stats/html/shapiro.test.html
Shapiro-Wilk test
Levene's test is a null hypothesis statistical test which evaluates the null hypothesis of equality of variance in several populations.
levene.test(x) function, where x is a numeric vector
Levene's test
Bartlett's test (see Snedecor and Cochran, 1989) is used to test if k samples are from populations with equal variances. Equal variances across samples is called homoscedasticity or homogeneity of variances. Some statistical tests, for example the analysis of variance, assume that variances are equal across groups or samples. The Bartlett test can be used to verify that assumption. Bartlett's test is sensitive to departures from normality. That is, if the samples come from non-normal distributions, then Bartlett's test may simply be testing for non-normality. Levene's test and the Brown–Forsythe test are alternatives to the Bartlett test that are less sensitive to departures from normality.
bartlett.test(x) function, where x is a numeric vector
Barlett's test
the Brown Forsythe test is a statistical test which evaluates if the variance of different groups are equal. It relies on computing the median rather than the mean, as used in the Levene's test for homoschedacity. This test maybe used to, for instance, ensure that the conditions of applications of ANOVA are met.
adapted from Wikipedia and Brown, M. B., and A. B. Forsythe. 1974a. The small sample behavior of some statistics which test the equality of several means. Technometrics, 16, 129-132.
http://www.statmethods.net/stats/anovaAssumptions.html The hovPlot( ) function in the HH package provides a graphic test of homogeneity of variances based on Brown-Forsyth. In the following example, y is numeric and G is a grouping factor. Note that G must be of type factor. # Homogeneity of Variance Plot library(HH) hov(y~G, data=mydata) hovPlot(y~G,data=mydata)
Brown Forsythe test
Pearson's Chi-Squared test is a statistical null hypothesis test which is used to either evaluate goodness of fit of dataset to a Chi-Squared distribution or used to test independence of 2 categorical variables (ie absence of association between those variables).
Chi2 test for independence
adapted from: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html and http://en.wikipedia.org/wiki/Pearson's_chi-squared_test
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html chisq.test(x, y = NULL, correct = TRUE, p = rep(1/length(x), length(x)), rescale.p = FALSE, simulate.p.value = FALSE, B = 2000)
http://www.inside-r.org/packages/cran/nortest/docs/pearson.test pearson.test(x) function, where x is a numeric vector
Pearson's Chi square test of independence between categorical variables
a fixed effect model is a statistical model which represents the observed quantities in terms of explanatory variables that are treated as if the quantities were non-random.
PRS: this is a stub and more work is needed to reconcile conflicting definitions
adapted from wikipedia: http://en.wikipedia.org/wiki/Fixed_effects_model
fixed effects model
Kolmogorov-Smirnov test is a goodness of fit test which evaluates the null hypothesis that a sample is drawn from a population that follows a specific continuous probability distribution.
STATO, adapted from wikipedia (https://en.wikipedia.org/wiki/Kolmogorov–Smirnov_test)
Kolmogorov-Smirnov test
multinomial logistic regression model is a model which attempts to explain data distribution associated with *polychotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is probit function.
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Multinomial_probit) polled in June 2013
multinomial probit regression for analysis of polychotomous dependent variable
effect size estimate is a data item about the direction and strength of the consequences of a causative agent as explored by statistical methods. Those methods produce estimates of the effect size, e.g. confidence interval
AGB,PRS
effect size
effect size estimate
an F-test is a statistical test which evaluates that the computed test statistics follows an F-distribution under the null hypothesis. The F-test is sensitive to departure from normality. F-test arise when decomposing the variability in a data set in terms of sum of squares.
F-test
a polychotomous variable is a categorical variable which is defined to have minimally 2 categories or possible values
polychotomous variable
statistical sample size is a count evaluating the number of individual experimental units
AGB-PRS
statistical sample size
study group population size
a case-control study design is a observation study design which assess the risk of particular outcome (a trait or a disease) associated with an event (either an exposure or endogenous factor). A case-control study design therefore declares an exposure variable which is dichotomous in nature (exposed/non-exposed) and an outcome variable, which is also dichotomous (case or control), thus giving the name to the design. During the execution of the design, a case control study defines a population and counts the events to determine their frequency.
STATO, adapted from: http://www.drcath.net/toolkit/casecontrol.html
case-control study design
a dichotomous variable is a categorical variable which is defined to have only 2 categories or possible values
'has part' exactly 1 ('categorical measurement datum' and ('has category label' exactly 2 'categorical label'))
dichotomous variable
Genome wide association study is a kind of study whose objective is to detect association between genetic markers (SNP or otherwise) accross the genome and a trait which may be a disease or another phenotype (e.g. trait of agronomic relevance in animal or plant studies). Genome wide association study compare the allele frequencies in 2 populations, one free of the trait used as control, the other one showing the trait use as 'case'. GWAS studies implement case-control design
AGB, PRS
GWAS study
whole genome association study
genome-wide association study
The Wilcoxon signed rank test is a statistical test which tests the null hypothesis that the median difference between pairs of observations is zero. This is the non-parametric analogue to the paired t-test, and should be used if the distribution of differences between pairs may be non-normally distributed. The procedure involves a ranking hence the name. The absolute value of the differences between observations are ranked from smallest to largest, with the smallest difference getting a rank of 1, then next larger difference getting a rank of 2, etc. Ties are given average ranks. The ranks of all differences in one direction are summed, and the ranks of all differences in the other direction are summed. The smaller of these two sums is the test statistic, W (sometimes symbolized Ts). Unlike most test statistics, smaller values of W are less likely under the null hypothesis.
signrank()
Wilcoxon signed rank test
date
The Kruskal–Wallis test is a null hypothesis statistical testing objective which allows multiple (n>=2) groups (or conditions or treatments) to be compared, without making the assumption that values are normally distributed. The Kruskal–Wallis test is the non-parametric equivalent of the independent samples ANOVA The Kruskal–Wallis test is most commonly used when there is one nominal variable and one measurement variable, and the measurement variable does not meet the normality assumption of an anova.
rank-sum test for the comparison of multiple (more than 2) samples
kruskal.test() http://stat.ethz.ch/R-manual/R-patched/library/stats/html/kruskal.test.html
Kruskal Wallis test
paired t-test is a statistical test which is specifically designed to analysis differences between paired observations in the case of studies realizing repeated measures design with only 2 repeated measurements per subject (before and after treatment for example)
t-test for dependent means
t-test for repeated measures
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html t.test(dependent variable ~ independant variable, data = dataset, var.equal = FALSE, paired= TRUE)
paired t-test
stratification is a planned process which executes a stratification rule using as input a population and assign it member to mutually exclusive subpopulation based on the values defined by the stratification rule
PRS+AGB adapted from wikipedia: http://en.wikipedia.org/wiki/Stratified_sampling polled on June 7th,2013
stratifying population
population stratification prior to sampling
stastical test power analysis is a data transformation which aims to determine the size of a statistical sample required to reach a desired significance level given a particular statistical test
statistical test power analysis
Hotelling's T2 test is a statistical test which is a generalization of Student's T-test to a assess if the means of a set of variables remains unchanged when studying 2 populations. It is a type of multivariate analysis
two sample Hotelling T2 test
a random effect(s) model, also called a variance components model, is a kind of hierarchical linear model. It assumes that the dataset being analysed consists of a hierarchy of different populations whose differences relate to that hierarchy.
variance components model
adapted from wikipedia: http://en.wikipedia.org/wiki/Random_effects_model#Qualitative_description
random effects model
standardized mean difference is data item computed by forming the difference between two means, divided by an estimate of the within-group standard deviation. It is used to provide an estimatation of the effect size between two treatments when the predictor (independent variable) is categorical and the response(dependent) variable is continuous
SMD
adapted from "Effect size, confidence interval and statistical significance: a practical guide for biologists" Nakagawa and Cuthill DOI: 10.1111/j.1469-185X.2007.00027.x
adapted from http://htaglossary.net/standardised+mean+difference+(SMD)
Cohen's d statistic
standardized mean difference
the multinomial distribution is a probability distribution which gives the probability of any particular combination of numbers of successes for various categories defined in the context of n independent trials each of which leads to a success for exactly one of k categories, with each category having a given fixed success probability.
adapted from http://mathworld.wolfram.com/MultinomialDistribution.html and http://en.wikipedia.org/wiki/Multinomial_distribution
dmultinom(x, size = NULL, prob, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Multinom.html
multinomial distribution
A z-score (also known as z-value, standard score, or normal score) is a measure of the divergence of an individual experimental result from the most probable result, the mean. Z is expressed in terms of the number of standard deviations from the mean value.
Orlaith Burke
normal score
standard score
z-score
log signal intensity ratio is a data item which corresponding the logarithmitic base 2 of the ratio between 2 signal intensity, each corresponding to a condition.
adapted from wikipedia: http://en.wikipedia.org/wiki/MA_plot last accessed: 2014-03-13
M-value
log signal intensity ratio
probit regression model is a model which attempts to explain data distribution associated with *dichotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is the probit function aka the quantile function, i.e., the inverse cumulative distribution function (CDF), associated with the standard normal distribution.
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Probit_model) polled in June 2013
probit regression for analysis of polychotomous dependent variable
a statistical model is an information content entity which is a formalization of relationships between variables in the form of mathematical equations. A statistical model describes how one or more random variables are related to one or more other variables. The model is statistical as the variables are not deterministically but stochastically related.
adapted from Wikipedia: http://en.wikipedia.org/wiki/Statistical_model last accessed: 14/01/2014
statistical model
linear regression model is a model which attempts to explain data distribution associated with response/dependent variable in terms of values assumed by the independent variable uses a linear function or linear combination of the regression parameters and the predictor/independent variable(s). linear regression modeling makes a number of assumptions, which includes homoskedasticity (constance of variance)
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Linear_regression) polled in June 2013
linear regression for analysis of continuous dependent variable
multinomial logistic regression model is a model which attempts to explain data distribution associated with *polychotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is logistic function.
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Multinomial_logistic_regression) polled in June 2013
multinomial logistic regression for analysis of dichotomous dependent variable
This is the inverse of 'specifies value of' and it is intended to say things such as 'compound' 'assumes values specified by' 'independent variable specification'
assumes values specified by
a sequence read is a DNA sequence data which is generated by a DNA sequencer
sequence read
a Funnel plot is a scatter plot of treatment effect versus a measure of study size and aims to provide a visual aid to detecting bias or systematic heterogeneity. A symmetric inverted funnel shape arises from a ‘well-behaved’ data set, in which publication bias is unlikely. An asymmetric funnel indicates a relationship between treatment effect and study size. Known caveats: If high precision studies really are different from low precision studies with respect to effect size (e.g., due to different populations examined) a funnel plot may give a wrong impression of publication bias. The appearance of the funnel plot can change quite dramatically depending on the scale on the y-axis — whether it is the inverse square error or the trial size. Funnel plot was introduced by Light and Palmer in 1984.
adapted from Wikipedia: http://en.wikipedia.org/wiki/Funnel_plot
Funnel plot
variance is a data item about a random variable or probability distribution. it is equivalent to the square of the standard deviation. It is one of several descriptors of a probability distribution, describing how far the numbers lie from the mean (expected value).The variance is the second moment of a distribution.
Alejandra Gonzalez-Belran
var(x, y = NULL, na.rm = FALSE, use) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cor.html
variance
is member of
has member
assess stastistical evidence
assess statistical evidence
a discrete probability distribution is a probability distribution which is defined by a probability mass function where the random variable can only assume a finite number of values or infinitely countable values
adapted from Wikipedia http://en.wikipedia.org/wiki/Probability_distribution#Discrete_probability_distribution last accessed: 14/01/2014
discrete probability distribution
ranking is a data transformation which turns a non-ordinal variable into a Ordinal variable by sorting the values of the input variable and replacing their value by their position in the sorting result
ranking
model parameter estimation is a data transformation that finds parameter values (the model parameter estimates) most compatible with the data as judged by the model.
textual definition modified following contributiong by Thomas Nichols: https://github.com/ISA-tools/stato/issues/18
model parameter estimation
beanplot is a plot in which (one or) multiple batches ("beans") are shown. Each bean consists of a density trace, which is mirrored to form a polygon shape. Next to that, a one-dimensional scatter plot shows all the individual measurements, like in a stripchart. The name beanplot stems from green beans. The density shape can be seen as the pod of a green bean, while the scatter plot shows the seeds inside the pod.
the objective of a data transformation to evaluate a null hypothesis of absence of linkage between variables.
association between categorical variables testing objective
a pedigree chart is a graph which plots parent child relations
STATO adapted from wikipedia (https://en.wikipedia.org/wiki/Pedigree_chart)
family tree
plot.pedigree {kinship} http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/kinship/html/plot.pedigree.html
pedigree chart
r2 is a correlation coefficient which is computed over the frequency of 2 dichotomous variable and is used as a measure of Linkage Disequilibrium and as input data item to the creation of an LD plot
a stratification rule/criteria is a criteria used to determine population strata so that a stratification process implementing the rule can result in any member of the total population being assigned to one and only one stratum
adapted from wikipedia: http://en.wikipedia.org/wiki/Stratified_sampling polled on June 7th,2013
stratification rule
The dot plot as a representation of a distribution consists of group of data points plotted on a simple scale. Dot plots are used for continuous, quantitative, univariate data. Data points may be labelled if there are few of them.
adapted from Wikipedia: Wilkinson, Leland (1999). "Dot plots". The American Statistician (American Statistical Association) 53 (3): 276–281. doi:10.2307/2686111
volcano plot is a kind of scatter plot which graphs the negative log of the p-value (significance) on the y-axis versus log2 of fold-change between 2 conditions on the x-axis. It is a popular method for visualizing differential occurence of variables between 2 conditions.
volcanoplot(fit, coef=1, highlight=0, names=fit$genes$ID, ...) http://rss.acs.unt.edu/Rdoc/library/limma/html/volcanoplot.html
volcano plot
a confidence interval which covers 99% of the sampling distribution, meaning that there is a 1% risk of false positive (type I error)
confidence interval at 1% of type I error rate
99% confidence interval
Altman Box and Whisker plot is a variation of Tukey Box and Whisker plot which use the criteria of Altman to create the 'whisker' of the plot.
Altman, D.G. Practical Statistics for Medical Research (Chapman and Hall, 1991).
has value
the Breslow-Day test is a statistical test which evaluates if the odds ratios are homogenous across N 2x2 contingency tables, for instance several 2x2 contingency tables associated with different strata of a stratified population when evaluating the relationship between exposure and outcome or associated with the different samples coming from several centres in a multicentric study in clinical trial context.
adapted from wikipedia: http://en.wikipedia.org/wiki/Odds_ratio#Statistical_inference polled on June 8th,2013
Breslow-Day test
Breslow-Day test for homogeneity of odds ratio
a sphericity test is a null hypothesis statistical testing procedure which posits a null hypothesis of equality of the variances of the differences between levels of the repeated measures factor
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Sphericity#Sphericity_in_statistics)
test of data sphericity
sphericity test
Hotelling T squared distribution is a probability distribution used in multivariate hypothesis testing, which is a univariate distribution proportional to the F-distribution and arises importantly as the distribution of a set of statistics which are natural generalizations of the statistics underlying Student's t-distribution. In particular, the distribution arises in multivariate statistics in undertaking tests of the differences between the (multivariate) means of different populations, where tests for univariate problems would make use of a t-test. The distribution is named for Harold Hotelling, who developed it[1] as a generalization of Student's t-distribution. This distribution is commonly used to describe the sample Mahalanobis distance between two populations.
adapted from Wikipedia "http://en.wikipedia.org/wiki/Hotelling's_T-squared_distribution" last polled: 2013-11-09
Hotelling T2 distribution
a post-hoc analysis is a statistical test carried out following an analysis of variance which ruled out the null hypothesis of absence of difference between group which allows identifying which groups differ.
a posteriori test
adapted from wikipedia: http://en.wikipedia.org/wiki/Post-hoc_analysis last accessed: 2013-11-15
post-hoc analysis
specificity is a measurement datum qualifying a binary classification test and is computed by substracting the false positive rate to the integral numeral 1
specificity
true negative rate
strictly standardized mean difference (SSMS) is a standardized mean difference which corresponds to the ratio of mean to the standard deviation of the difference between two groups. SSMD directly measures the magnitude of difference between two groups. SSMD is widely used in High Content Screen for hit selection and quality control. When the data is preprocessed using log-transformation as normally done in HTS experiments, SSMD is the mean of log fold change divided by the standard deviation of log fold change with respect to a negative reference. In other words, SSMD is the average fold change (on the log scale) penalized by the variability of fold change (on the log scale). For quality control, one index for the quality of an HTS assay is the magnitude of difference between a positive control and a negative reference in an assay plate. For hit selection, the size of effects of a compound (i.e., a small molecule or an siRNA) is represented by the magnitude of difference between the compound and a negative reference. SSMD directly measures the magnitude of difference between two groups. Therefore, SSMD can be used for both quality control and hit selection in HTS experiments.
strictly standardized mean difference
Tarone's test for homogeneity of odds ratio is a statistical test which evaluates the null hypothesis that odds ratio are homogeneous
> library("metafor") > calcTaronesTest <- function(mylist,referencerow=2) http://a-little-book-of-r-for-biomedical-statistics.readthedocs.org/en/latest/src/biomedicalstats.html#calculating-the-mantel-haenszel-odds-ratio-when-there-is-a-stratifying-variable
Tarone's test for homogeneity of odds ratio
an homoskedasticity test is a statistical test aiming at evaluate if the variances from several random samples are similar
equivariance test
homoskedasticity test
a 2x2 contingency table is a contingency table build for 2 dichotomous variables (i.e. 2 categorical variables, each with only 2 possible outcomes). It is the simplest of contingency tables
2x2 contingency table
xtabs(formula = ~., data = parent.frame(), subset, sparse = FALSE, na.action, exclude = c(NA, NaN), drop.unused.levels = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/xtabs.html flat contingency tables: ftable(x, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/ftable.html
2 by 2 contingency table
pairing patients by age, pairing animals by body weight range
a subject pairing is a planned process which executes a pairing rule and results in the creation of sets of 2 subjects meeting the pairing criteria
subject pairing
a contigency table is a data item which displays the (multivariate) frequency distribution of the possible values of categorical variables. The first row of the table corresponds to categories of one categorical variable, the first column of the table corresponds to categories of the other categorical variable, the cells corresponding to each combination of categories is filled with the observed occurences in the sample being considered. The table also contains marginal total (marginal sums) and grand total of the occurences The term contingency table was first used by Karl Pearson in "On the Theory of Contingency and Its Relation to Association and Normal Correlation", part of the Drapers' Company Research Memoirs Biometric Series I published in 1904.
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Contingency_table)
contingency table
acute toxicity study is an investigation which use interventions organized according to a factorial design and a parallel group design to observe the effect of use of high dose xenobiotics in animal models or cellular models
acute toxicity study
The correlation coefficient of two variables in a data sample is their covariance divided by the product of their individual standard deviations. It is a normalized measurement of how the two are linearly related.
r statistics
correlation coefficient
a Bayesian model selection is a data transformation which is based on Bayesian statistics to compute Bayes factor in order to evaluate which model best explains data.
adapted from wikipedia
Bayesian model selection
for example , model parameter estimates could be produced using regression analysis (used in a model estimation process) , which attempts to express the response variable in terms of function of predictor variable and model parameters.
a model parameter estimate is a data item which results from a model parameter estimation process and which provides a numerical value is about a model parameter.
Alejandra Gonzalez Beltran
model parameter estimate
the geometric distribution is a negative binomial distribution where r is 1. It is useful for modeling the runs of consecutive successes (or failures) in repeated independent trials of a system. The geometric distribution models the number of successes before one failure in an independent succession of tests where each test results in success or failure. The geometric distribution with prob = p has density p(x) = p (1-p)^x for x = 0, 1, 2, …, 0 < p ≤ 1. If an element of x is not integer, the result of dgeom is zero, with a warning. The quantile is defined as the smallest value x such that F(x) ≥ p, where F is the distribution function.
dgeom(x, prob, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Geometric.html
geometric distribution
a null hypothesis stating that there are differences observed between group of subjects
presence of between group difference hypothesis
Linkage Disequilibrium plot is a graph which represents pairwise linkage disequilibrium measures between SNP as a heatmap
STATO, adapted from R documentation (http://cran.r-project.org/web/packages/LDheatmap/index.html)
LD plot
The Cochran-Armitage test is a statistical test used in categorical data analysis when the aim is to assess for the presence of an association between a dichotomous variable (variable with two categories) and a polychotomous variable (a variable with k categories). The two-level variable represents the response, and the other represents an explanatory variable with ordered levels. The null hypothesis is the hypothesis of no trend, which means that the binomial proportion is the same for all levels of the explanatory variable For example, doses of a treatment can be ordered as 'low', 'medium', and 'high', and we may suspect that the treatment benefit cannot become smaller as the dose increases. The trend test is often used as a genotype-based test for case-control genetic association studies.
CATT
Cochran-Armitage test for trend
binomial logistic regression model is a model which attempts to explain data distribution associated with *dichotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is logistic function.
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Logistic_regression) polled in June 2013
binomial logistic regression for analysis of dichotomous dependent variable
a minimum value is a data item which denotes the smallest value found in a dataset or resulting from a calculation.
minimum value
maximum value is a data item which denotes the largest value found in a dataset or resulting from a calculation.
maximum value
a quartile is a quantile which splits data into sections accrued of 25% of data, so the first quartile delineates 25% of the data, the second quartile delineates 50% of the data and the third quartile, 75 % of the data
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Quartile)
quartile
one sample Hotelling T2 test
a violin plot is a plot combining the features of box plot and kernel density plot. The violin plot is therefore similar to box plot but it incorporated in the display the probability density of the data at different values. Typically violin plots will include a marker for the median of the data and a box indicating the interquartile range, as in standard box plots.
http://en.wikipedia.org/wiki/Violin_plot and Hintze, J. L. and R. D. Nelson (1998). Violin plots: a box plot-density trace synergism. The American Statistician, 52(2):181-4.
http://www.inside-r.org/packages/cran/vioplot/docs/vioplot vioplot( x, ..., range=1.5, h, ylim, names, horizontal=FALSE, col="magenta", border="black", lty=1, lwd=1, rectCol="black", colMed="white", pchMed=19, at, add=FALSE, wex=1, drawRect=TRUE)
meta-analysis is a data transformation which uses the effect size estimates from several independent quantitative scientific studies addressing the same question in order to assess finding consistency.
adapted from wikipedia: http://en.wikipedia.org/wiki/Metaanalysis last accessed: 2013-11-15
meta analysis
the Scheffe test is a data transformation which evaluates all possible contrasts and adjusting the levels significance by accounting for multiple comparison. The test is therefore conservative. Confidence intervals can be constructed for the corresponding linear regression. It was developped by American statistician Henry Scheffe in 1959.
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Scheffé's_method)
Scheffe test
the LSD test is a statistical test for multiple comparisons of treatments by means of least significant difference following an ANOVA analysis
Least significance different test
a null hypothesis which states that a linkage exists between 2 categorical variables
presence of association hypothesis
Stacked bar chart is a bar which is used to compare overall quantities across items while showing the contribution of category to the total amount. Stacked bar chart can be used for highlighting the total as they visually aggregate all of the categories in a group while indicating a part to whole relationship. The downside is that it becomes harder to compare the sizes of the individual categories.
adapter from http://www2.le.ac.uk/offices/ld/resources/numeracy/bar-charts and http://blog.visual.ly/how-groups-stack-up-when-to-use-grouped-vs-stacked-column-charts/ [last accessed: 2014-03-04]
barplot(height....) set argument " beside = FALSE " http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/barplot.html
The exponential distribution (a.k.a. negative exponential distribution) is the probability distribution that describes the time between events in a Poisson process, i.e. a process in which events occur continuously and independently at a constant average rate. It is the continuous analogue of the geometric distribution, and it has the key property of being memoryless.
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Exponential.html dexp(x, rate = 1, log = FALSE) pexp(q, rate = 1, lower.tail = TRUE, log.p = FALSE) qexp(p, rate = 1, lower.tail = TRUE, log.p = FALSE) rexp(n, rate = 1)
exponential distribution
variable distribution is data item which denotes the spatial resolution of data point making up a variable. variable distribution may be compared to a known probability distribution using goodness of fit test or plotting a quantile-quantile plot for visual assessment of the fit.
TODO: Probably need to drop it
data distribution
the role played by an entity part of study group as defined by an experimental design and realized in a data analysis and data interpretation
experimental unit role
trimmed mean or truncated mean is a measure of central tendency which involves the calculation of the mean after discarding given parts of a probability distribution or sample at the high and low end, and typically discarding an equal amount of both
adapted from wikipedia [last accessed 2014-03-04] http://en.wikipedia.org/wiki/Truncated_mean
trimmed mean
The interquartile range is a data item which corresponds to the difference between the upper quartile (3rd quartile) and lower quartile (1st quartile). The interquartile range contains the second quartile or median. The interquartile range is a data item providing a measure of data dispersion
STATO adapted from wikipedia, wolfram alpha and oxford dictionary of statistics
IQR(x, na.rm = FALSE, type = 7) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/IQR.html
inter quartile range
a pie chart is a graph in which a circular graph is divided into sector illustrating numerical proportion, meaning that the arc length of each sector (and consequently its central angle and area), is proportional to the quantity it represents.
adapted from Wikipedia, last accessed [2014-03-05] http://en.wikipedia.org/wiki/Pie_chart
pie(x, labels = names(x), edges = 200, radius = 0.8, clockwise = FALSE, init.angle = if(clockwise) 90 else 0, density = NULL, angle = 45, col = NULL, border = NULL, lty = NULL, main = NULL, ...) https://stat.ethz.ch/R-manual/R-devel/library/graphics/html/pie.html
pie chart
A bar chart is appropriate to represent counts of data.
the bart chart is a graph resulting from plotting rectangular bars with lengths proportional to the values that they represent.
adapted from wikipedia (http://en.wikipedia.org/wiki/Bar_chart) polled in June 2013
bar plot
barplot(height, ...) http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/barplot.html
bar chart
the first quartile is a quartile which splits the lower 25 % of the data
first quartile
a real time quantitative pcr plot is a line graph which plots the signal fluorescence intensity as a function of the number of PCR cycle
real time quantitative pcr plot
Fold change is a number describing how much a quantity changes going from an initial to a final value or one condition to another condition
30/04/2014 - removed restriction: 'is about' exactly 2 'study group population' - need more discussion for the relationship of fold change to study group populations for particular examples.
fold change
the first quartile is a quartile which splits the 75 % of the data
third quartile
Spear Box and Whisker plot is a variation of Tukey Box and Whisker plot which use the criteria of Spear to create the 'whisker' of the plot.
Spear, M.E. Charting Statistics (McGraw-Hill, 1952)
expected fragments per kilobase of transcript per million fragments mapped is a metric used to report transcript expression event as generated by RNA-Seq using paired-end library. The calculated value results from 2 types of normalization, one to take into account the difference in reads counts associated with transcript length (at equal abundance, longer transcripts will have more reads than shorter transcripts) , (hence the 'per kilobase of transcript') and the other one to take into account different sequencing depth during distinct sequencing runs (hence the 'per millions mapped fragment'. The metric is specifically produced by cufflink software.
FPKM
adapted from: http://seqanswers.com/forums/showthread.php?t=3254 and from http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
fragments per kilobase of transcript per million fragments mapped
homogeneity testing objective is the objective of a data transformation to test a null hypothesis that two or more sub-groups of a population share the same distribution of a single categorical variable. For example, do people of different countries have the same proportion of smokers to non-smokers
homogeneity test objective
A forest plot is a graph designed to illustrate the relative strength of treatment effects in multiple quantitative scientific studies addressing the same question.
metaplot(mn, se, nn=NULL, labels=NULL, conf.level=0.95, xlab="Odds ratio", ylab="Study Reference",xlim=NULL, summn=NULL, sumse=NULL, sumnn=NULL, summlabel="Summary", logeffect=FALSE, lwd=2, boxsize=1, zero=as.numeric(logeffect), colors=meta.colors(), xaxt="s", logticks=TRUE, ...) http://rss.acs.unt.edu/Rdoc/library/rmeta/html/metaplot.html
Forest plot
confidence interval calculation is a data transformation which determines a confidence interval for a given statistical parameter
confidence interval calculation
t-statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Student's t distribution.
t-statistic
the beta distribution is a continuous probability distributions defined on the interval [0, 1] parametrized by two positive shape parameters, denoted by α and β, that appear as exponents of the random variable and control the shape of the distribution
adapted from Wikipedia: http://en.wikipedia.org/wiki/Beta_distribution
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Beta.html dbeta(x, shape1, shape2, ncp = 0, log = FALSE) pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE) qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE) rbeta(n, shape1, shape2, ncp = 0)
Kurtosis is a data item which denotes the degree of peakedness of a distribution. It is defined as a normalized form of the fourth central moment of a distribution.
kurtosis
ANCOVA or analysis of covariance is a data transformation which evaluates if population means of a dependent variable are equal across levels of a categorical independent variables while controlling for the effects of other continuous variable s, known as covariates. Therefore, when performing ANCOVA, we are adjusting the dependent variable means to what they would be if all groups were equal on the covariates. It augments the ANOVA model with one or more additional quantitative variables, called covariates, which are related to the response variable. The covariates are included to reduce the variance in the error terms and provide more precise measurement of the treatment effects. ANCOVA is used to test the main and interaction effects of the factors, while controlling for the effects of the covariate
standard normal distribution is a normal distribution with variance = 1 and mean=0
we need to formally set value for mean and variance
dnorm(x, mean = 0, sd = 1, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Normal.html
standard normal distribution
Hardy-Weinberg equilibrium test is a statistical test which aims to evaluate if a population's proportion of allele is stable or not. It is used as means of quality control to evaluate possibility of genotyping error or population structure.
STATO: adapted from wikipedia (http://en.wikipedia.org/wiki/Hardy–Weinberg_principle)
> library(HardyWeinberg) > x <- c(298,489,213) > HW.test <- HWChisq(x,verbose=TRUE) http://cran.r-project.org/web/packages/HardyWeinberg/index.html
Hardy-Weinberg equilibrium testing
Odds ratio is a ratio that measures effect size, that is the strength of association between 2 dichotomous variables, one describing an exposure and one describing an outcome. It represents the odds that an outcome will occur given a particular exposure, compared to the odds of the outcome occurring in the absence of that exposure ( the probability of the event occuring divided by the probability of an event not occurring). The odds ratio is a ratio of describing the strength of association or non-independence between two binary data values by forming the ratio of the odds for the first group and the odds for the second group. Odds ratio are used when one wants to compare the odds of something occurring to two different groups.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938757/ http://www.stats.org/stories/2008/odds_ratios_april4_2008.html
sphericity testing objective is a statistical objective of a data transformation which aims to test a null hypothesis of sphericity holds.
sphericity testing objective
A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s.
review formal definition as both numerator and denominator should be of the same type, not just some data item
adapted from Wolfram Alpha: https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig76g7
a 2 by n contingency table is a contingency table built for one dichotomous variable (a categorical variable with only 2 outcomes) and one polychotomous variable (a polychomotomous variable with at least 2 outcomes)
2 by n contingency table
Lineweaver-Burk plot is a graph which is the graphical representation of the Lineweaver–Burk equation of enzyme kinetics, described by Hans Lineweaver and Dean Burk in 1934. The plot provides a useful graphical method for analysis of the Michaelis–Menten equation. It was widely used to determine important terms in enzymology and enzyme kinetics as the x-intercept of the graph represents −1/Km and the y-intercept of such a graph is equivalent to the inverse of Vmax
TODO: create 'inverse function' and replace 'data transformation' in the assertions
double reciprocal plot
Lineweaver-Burk plot
Tukey Honestly Significant Difference (HSD) test is a statistical test used following an ANOVA test yielding a statistically significant p-value in order to determine which means are different, to a given level of significance. The Tukey HSD test relies on the q-distribution. The procedure is conservative, meaning that if sample sizes (the sizes of different study groups) are equal, the risk of a Type I error is exactly α, and if sample sizes are unequal it’s less than α.
IMPORTANT: Do Not to confuse the Tukey HSD test with Tukey Mean Difference Test (Bland-Altman test)
Tukey's honestly significant difference
Tukey HSD for Post-Hoc Analysis
average log signal intensity is a data time which corresponds to the sum of 2 distinct logarithm base 2 transformed signal intensity, each corresponding to a distinct condition of signal acquisition, divided by 2.
A-value
average log signal intensity
A mixed model is a statistical model containing both fixed effects and random effects
mixed model
Threshold cycle (or Ct or Cq) is a count which is defined as the fractional PCR cycle number at which the reporter fluorescence is greater than the threshold in the context of the RT-qPCR assay. The Ct is a basic principle of real time PCR and is an essential component in producing accurate and reproducible data.
threshold cycle
a goodness of fit statistical test is a statistical test which aim to evaluate if a sample distribution can be considered equivalent to a theoretical distribution used as input
a cartesian product is a data transformation which operates on a n Sets to produce a set of all possible ordered n-tuples where each element of the tuple comes from a Set
adapted from math wolfram (http://mathworld.wolfram.com/CartesianProduct.html)
cartesian product
is a population whose individual members realize (may be expressed as) a combination of inclusion rule values specifications or resulting from a sampling process (e.g. recruitment followed by randomization to group) on which a number of measurements will be carried out, which may be used as input to statistical tests and statistical inference.
statistical sample
self explanatory
cartesian product 2 sets
A non-negative integer defining how many combination of factor levels (or treatments in the statistical sense) are to be used in a study.
number of factor level combinations
A confidence interval is a data item which defines an range of values in which a measurement or trial falls corresponding to a given probability.
confidence interval
a genomic coordinate system is a coordinate system to describe position of sequence on a genomic scaffold (assembly of chromosome, contig....)
ensembl, ucsc
genomic coordinate system
a statistical test which makes no assumption about the underlying data distribution
non-parametric test
the Mauchly's test for sphericity is a statistical test which evaluates if the variance of the differences between all combinations of the groups are equal, a property known as 'sphericity' in the context of repeated measures. It is used for instance prior to repeated measure ANOVA. The test works by assessing if a Wishart-distributed covariance matrix (or transformation thereof) is proportional to a given matrix.
AGB-PRS, adapted from wikipedia (http://en.wikipedia.org/wiki/Mauchly's_sphericity_test) polled on june,10th, 2013 and from R manual: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/mauchly.test.html
Mauchly's test for sphericity
mauchly.test(object, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/mauchly.test.html
the statistical test power is data item which is about a statistical test and is obtained by subtracting the false negative rate (type II error rate) to 1. The power of a statistical test is the probability that it will correctly lead to the rejection of a false null hypothesis (Greene 2000). The statistical power is the ability of a test to detect an effect, if the effect actually exists (High 2000).
adapted from wikipedia (http://en.wikipedia.org/wiki/Statistical_power), polled June 10th, 2013
statistical test power
Spearman's rank correlation coefficient is a correlation coefficient which is a nonparametric measure of statistical dependence between two ranked variables. It assesses how well the relationship between two variables can be described using a monotonic function. If there are no repeated data values, a perfect Spearman correlation of +1 or −1 occurs when each of the variables is a perfect monotone function of the other. Spearman's coefficient may be used when the conditions for computing Pearson's correlation are not met (e.g linearity, normality of the 2 continuous variables) but may require a ranking transformation of the variables
Spearman's rho
cor(x, y = NULL, use = "everything",method = c("spearman"))
Spearman's rank correlation coefficient
within subject comparison statistical test is a kind of statistical test which evaluates if a change occurs within one experimental unit over time following a treatment or an event
within subject comparison statistical test
a cohort is a study group population where the members are human beings which meet inclusion criteria and undergo a longitudinal design
the F-distribution is a continuous probability distribution which arises in the testing of whether two observed samples have the same variance.
Fisher distribution
Snedecor Fisher distribution
df(x, df1, df2, ncp, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Fdist.html
F-distribution
is denoted by
RPKM is a kind of count which numbers the sequence reads found per kilobase of transcript reported to million of sequence reads. RPKM is a metric generated by ERANGE software tool as reported by Mortazi et al, in 2008. The metric has been enhanced and replaced by FPKM to better take into account splice variant. FKPM uses a statistical model to perform the computation.
RPKM
reads per kilobase of transcript per million fragments mapped
a planned process which etablishes and states the different hypothesis to be evaluated during a null hypothesis statistical test
specifying null and alternate hypothesis
alternative hypothesis is an hyopthesis defined in a statistical which is the opposite of the null hypothesis
alternate hypothesis
PMID:12892658 "Two formulas for computation of the area under the curve represent measures of total hormone concentration versus time-dependent change."
area under curve is a measurement datum which corresponds to the surface define by the x-axis and bound by the line graph represented in a 2 dimensional plot resulting from an integration or integrative calculus. The interpretation of this measurement datum depends on the variables plotted in the graph
PRS: submit 'integral calculus' as a kind of data transformation in OBI:DT branch
area under curve
is a data item formed by dividing the fluorescence intensity obtained in one channel to that obtained in the other channel, typically the case when considering 2-color microarray data when imaging is done for Cy3 and Cy5 dyes.
channel1/channel2 fluorescence intensity ratio
odds ratio homogeneity hypothesis is a null hypothesis stating that all odds ratio are homogenous, that is remain within the same range
odds ratio homogeneity hypothesis
a tetrachoric correlation coefficient is a polychoric correlation coefficient for 2 dichotomous variables used as proxy for correlation between 2 continuous latent variables.
adapted from: http://www.rasch.org/rmt/rmt193c.htm and http://en.wikipedia.org/wiki/Polychoric_correlation
tetrachoric correlation coefficient
discretization as a processing converting a continuous variable into a polychotomous variable by concretizing a set of discretization rules
AGB,PRS adapted from wikipedia (http://en.wikipedia.org/wiki/Discretization)
continuous variable discretization
a confidence interval which covers 50% of the sampling distribution, meaning that there is a 50% risk of false positive (type I error)
confidence interval at 10% of type I error rate
50% confidence interval
probit regression model is a model which attempts to explain data distribution associated with *ordinal* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is the ordered probit function.
ordered probit regression for analysis of ordinal dependent variable
a stratum population is a population resulting from a population stratification prior to sampling process which aims to produce homogenous subpopulations from an heterogeneous population by applying one or more stratification criteria
a null hypothesis which states that a given matrix is proportional to a Wishart-distributed covariance matrix
hypothesis of sphericity
sphericity hypothesis
Model fitting is a data transformation process which evaluates if a model appropriately represents a dataset. A model fitting process tests the goodness of fit of the model to the data
model fitting
a real time pcr standard curve is a line graph which plots the fluorescence intensity signal as a function of the concentration of a sample used as reference and used to determine relative abundance of test samples
adapted from: http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/General_Information/qpcr_technical_guide.pdf and http://www.lifetechnologies.com/uk/en/home/life-science/pcr/real-time-pcr/qpcr-education/absolute-vs-relative-quantification-for-qpcr.html
RT-PCR standard curve
the false negative rate is a data item which denotes the proportion of missed detection of elements known to be meeting the detection criteria
type II error rate
false negative rate
a random variable (or aleatory variable or stochastic variable) in probability and statistics, is a variable whose value is subject to variations due to chance (i.e. randomness, in a mathematical sense)
aleatory variable
stochastic variable
wikipedia: http://en.wikipedia.org/wiki/Random_variable
random variable
graeco-latin square design is_a study design which allows in its simpler form controlling 3 levels of nuisance variables (also known as blocking variables). The 3 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once.
graeco-latin square design
group assignment based on blocking variable specification is a kind of group assignment process which takes into account the levels assumed by a blocking variable to allocate subjects or experimental units to a treatment group
group assignment based on blocking variable specification
A testing objective to ensure that the sample used in a statistical test actually follows a normal distribution.
goodness of fit testing objective
A probability distribution is a information content entity specifies the probability of the value of a random variable. For a discrete random variable, a mathematical formula that gives the probability of each value of the variable. For a continuous random variable, a curve described by a mathematical formula which specifies, by way of areas under the curve, the probability that the variable falls within a particular interval.
probability distribution
It is a testing objective to ensure the variances of the different groups used in a statistical test are similar (i.e. not too different).
equal variance testing objective
a normal distribution is a continuous probability distribution described by a probability distribution function described here: http://mathworld.wolfram.com/NormalDistribution.html
Gaussian distribution
normal distribution
ordinal variable is a categorical variable where the discrete possible values are ordered or correspond to an implicit ranking
Alejandra Gonzalez-Beltan
ranked variable
ordinal variable
Chi-square probability distribution with k degrees of freedom is a theoretical probability distribution which corresponds to the distribution of a sum of the squares of k independent standard normal random variables.
dchisq(x, df, ncp = 0, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Chisquare.html
Chi-square probability distribution
the expected value (or expectation, mathematical expectation, EV, mean, or the first moment) of a random variable is a data item which corresponds to the weighted average of all possible values that this random variable can take on. The weights used in computing this average correspond to the probabilities in case of a discrete random variable, or densities in case of a continuous random variable. From a rigorous theoretical standpoint, the expected value is the integral of the random variable with respect to its probability measure.
first moment
mean
expected value
a confidence interval which covers 95% of the sampling distribution, meaning that there is a 5% risk of false positive (type I error). If the number of observations made is large enough, the sampling distribution can be assumed to be normal, which entails that 95% of the sampling distributions falls within roughly2 (1.96) standard deviations from the mean.
confidence interval at 5% of type I error rate
95% confidence interval
number of PCR cycle is a count which enumerates how many iterations of 'annealing, renaturation, amplification,' rounds (or cycles) are performed during a polymerase chain reaction (PCR) or an assay relying on PCR.
adapted from various sources including: http://www.ncbi.nlm.nih.gov/genome/probe/doc/TechQPCR.shtml
number of PCR cycle
sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1
recall
sensitivity
adapted from: http://en.wikipedia.org/wiki/Sensitivity_and_specificity and http://mathworld.wolfram.com/Sensitivity.html
true positive rate
a residual is a data item which is the output of an error estimate or model fitting process and which is an observable estimate of the unobservable error
residual
A genetic association study is a kind of study whose objective is to detect associations between phenotypes, between a phenotype and a genetic polymorphism or between two genetic polymorphisms.
genetic association study
the coefficient of variation is a normalized measure fo dispersion of a probability distribution of frequency distribution.
http://en.wikipedia.org/wiki/Coefficient_of_variation last accessed: 2013-10-18
coefficient of variation
The standard deviation of a random variable, statistical population, data set, or probability distribution is a measure of variation which correspond to the average distance from the mean of the data set to any given point of that dataset. It also corresponds to the square root of its variance.
sd(x, na.rm = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/sd.html
standard deviation
high content screening is a kind of investigation which uses a standardized cellular assays to test the effect of substances (RNAi or small molecules) held in libraries on a cellular phenotype. it relies on microscopy imaging and or flow-cytometry, robotic handling to ensure fast and high-throughput.
high throughput screening
adapted from: http://en.wikipedia.org/wiki/High-content_screening
high-content screening
high throughput screening is a kind of investigation which uses a standardized assays (cell based, enzymatic or chemometric) to test the effect of substances (RNAi or small molecules) held in libraries on a very specific and measureable outcome (e.g fluorence intensity). it relies on robotic handling to ensure fast and high-throughput in assay performance, data acquisition and hit selection.
Kendall's correlation coefficient is a correlation coefficient between 2 ordinal variables (natively or following a ranking procedure) and may be used when the conditions for computing Pearson's correlation are not met (e.g linearity, normality of the 2 continuous variables)
Kendall rank correlation coefficient
Kendall's tau (τ) coefficient
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Kendall_tau_rank_correlation_coefficient), polled in june 2013 and from: http://stamash.org/pearsons-correlation-coefficient/ http://stamash.org/kendalls-tau-correlation/
cor(x, y = NULL, use = "everything",method = c("kendall"))
Kendall's correlation coefficient
Q-Q plot or quantile-quantile plot is the output of a graphical method for comparing two probability distributions by plotting their quantiles against each other
PRS,AGB: need to add the notion of quantile
quantile-quantile plot
qqplot(x, y, plot.it = TRUE, xlab = deparse(substitute(x)), ylab = deparse(substitute(y)), ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/qqnorm.html
Q-Q plot
statistical error is an data item denoting the amount by which an observation differs from the expected value, being based on the whole statistical population from which the statistical unit was chosen randomly
adapted from wikipedia: http://en.wikipedia.org/wiki/Errors_and_residuals_in_statistics last accessed: 18-11-2013
disturbance
statistical error
A box and whisker plot is appropriate to represent the characteristics oc a distribution.
a box plot is a graph which plots datasets relying on their quartiles and the interquartile range to create the box and the whiskers
Tukey box and whisker plot
box plot
Tukey, J. W. "Box-and-Whisker Plots." §2C in Exploratory Data Analysis. Reading, MA: Addison-Wesley, pp. 39-43, 1977.
boxplot
boxplot(x, ...) http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/boxplot.html
box and whisker plot
(Rn +) − (Rn −), where Rn + = (emission intensity of reporter dye)/(emission intensity of passive reference dye) in PCR with template and Rn − = (emission intensity of reporter dye)/(emission intensity of passive reference dye) in PCR without template or early cycles of a real-time reaction. Ct = threshold cycle, i.e., cycle at which a statistically significant increase in ΔRn is first detected
ΔRn
Relative risk is a measurement datum which denotes the risk of an 'event' relative to an 'exposure'. Relative risk is calculated by forming the ratio of the probability of the event occurring in the exposed group versus a the probability of this event occurring in the non-exposed group.
Woolf's test is a statistical test which evaluates the null hypothesis that odds ratio are the same accross all strata of population under investigation
woolf_test(x) where x is 2 x 2 x k contingency table http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/vcd/html/woolf_test.html
Woolf's test
odds ratio homogeneity test is a statistical test which aims to evaluate that null the hypothesis of consistency odds ratio accross different strata of population is true or not
odds ratio homogeneity test
https://onlinecourses.science.psu.edu/stat503/node/19 Often in medical studies, the blocking factor used is the type of institution. This provides a very useful blocking factor, hopefully removing institutionally related factors such as size of the institution, types of populations served, hospitals versus clinics, etc., that would influence the overall results of the experiment.
a blocking variable is a independent variable which is used in a blocking process part of an experiment with the purpose of maximizing the signal coming from the main variable.
blocking variable
a DNA microarray hybridization is an assay relying on nucleic acid hybridization , which uses a DNA microarray device and a nucleic acid as input. It precedes a data acquisition process
DNA microarray hybridization
group comparison objective is a data transformation objective which aims to determine if 2 or more study group differ with respect to the signal of a response variable
group comparison objective
"Time to solve an anagram problem" is continuous since it could take 2 minutes, 2.13 minutes etc. to finish a problem
A continuous variable is one for which, within the limits the variable ranges, any value is possible.
continuous variable
a categorical variable is a variable which that can only assume a finite number of value and cast observation in a small number of categories
discrete variable
nominal variable
categorical variable
the objective of a data transformation to test a null hypothesis of absence of difference within subject holds.
within subject comparison objective
The allele frequency is a data item which denotes the incidence of a gene variant in a population. It is calculated as a ratio, by dividing the number of copies of a particular allele by the number of copies of all alleles at the genetic place (locus) in a population.
the objective of a data transformation to test a null hypothesis of absence of difference withing subject holds.
between group comparison objective
a manhattan plot for gwas is a kind of scatter plot used to facilitate presentation of genome-wide association study (GWAS) data. Genomic coordinates are displayed along the X-axis, with the negative logarithm of the association P-value for each single nucleotide polymorphism displayed on the Y-axis.
plotGrandLinear(obj, ..., facets, space.skip = 0.01, geom = NULL, cutoff = NULL, cutoff.color = "red", cutoff.size = 1, legend = FALSE, xlim, ylim, xlab, ylab, main) http://www.tengfei.name/ggbio/docs/man/plotGrandLinear.html
manhattan plot for gwas
import from Population and Community Ontology: http://www.ontobee.org/browser/rdf.php?o=PCO&iri=http://purl.obolibrary.org/obo/PCO_0000020
family
a variable is a data item which can assume any of a set of values, either as determined by an agent or as randomly occuring through observation.
adapted from wolfram-alpha (http://www.wolframalpha.com/input/?i=variable) definition 2. and from Oxford English Dictionary: http://www.oed.com/view/Entry/221514?redirectedFrom=variable#eid, definition B,1
variable
repeated measure ANOVA is a kind of ANOVA specifically developed for non-independent observations as found when repeated measurements on the sample experimental unit. repeated measure ANOVA is sensitive to departure of normality (evaluation using Bartlett's test), departure of sphericity (evaluation using Mauchly'test) and unbalanced groups (i.e. different sizes of sample populations). Repeated measure ANOVA use in case of unbalanced design is discouraged as it leads to violation of conditions of applicability
ANOVA for correlated samples
adapted from wikipedia and https://statistics.laerd.com/statistical-guides/repeated-measures-anova-statistical-guide-3.php
The Newman–Keuls or Student–Newman–Keuls (SNK) method is a stepwise multiple comparisons procedure used to identify sample means that are significantly different from each other. It was named after Student (1927), D. Newman, and M. Keuls. This procedure is often used as a post-hoc test whenever a significant difference between three or more sample means has been revealed by an analysis of variance (ANOVA). The Newman–Keuls method is similar to Tukey's range test as both procedures use Studentized range statistics.Compared to Tukey's range test, the Newman–Keuls method is more powerful but less conservative.
adapted from wikipedia: last accessed: 2013-11-15
SNK.test(y, trt, DFerror, MSerror, alpha = 0.05, group=TRUE, main = NULL) http://artax.karlin.mff.cuni.cz/r-help/library/agricolae/html/SNK.test.html
Newman-Keuls test post-hoc analysis
Bernoulli distribution is a binomial distribution where the number of trials is equal to 1. notation: B(1,p) The mean is p The variance is p*q
Bernoulli distribution
Galbraith (Radial) plot is a scatter plot which can be used in the meta-analytic context to examine the data for heterogeneity. For a fixed-effects model, the plot shows the inverse of the standard errors on the horizontal axis against the individual observed effect sizes or outcomes standardized by their corresponding standard errors on the vertical axis. Radial plots were introduced by Rex Galbraith (1988a, 1988b, 1994).
Galbraith, Rex (1988). "Graphical display of estimates having differing standard errors". Technometrics (Technometrics, Vol. 30, No. 3) 30 (3): 271–281. doi:10.2307/1270081. JSTOR 1270081
radial Galbraith plot
http://www.inside-r.org/packages/cran/Luminescence/docs/plot_RadialPlot plot_RadialPlot(data, na.exclude = TRUE, negatives = "remove", log.z = TRUE, central.value, centrality = "mean.weighted", plot.ratio, bar.col, grid.col, legend.text, summary = FALSE, stats, line, line.col, line.label, output = FALSE, ...)
Galbraith plot
a factor level combination is one a possible sets of factor levels resulting from the cartesian product of sets of factor and their levels as defined in a factorial design
factor level combination
A factor level is data item which corresponds to one of the value assumed by a factor or independent variable manipulated and set by the experimentalist. In the context of factorial design, a factor level is assumed to be or treated as a category in a categorical variable
factor level
Bayes factor is a ratio between 2 probabilities of observing data according 2 distinct models. It is used in Bayes model selection to evaluate which model best explains the data. if K<0, the model used in the denominator term is supported, if K>1, the model used in the numerator term is supported. The Bayes factor is about the plausibility of 2 different models
adapted from Wikipedia last accessed 2013-11-13
Bayes factor
grouped bar chart is a kind of bar chart which juxtaposes the discrete values for each of the possible value of a given categorical variable, thus providing within group comparison. Grouped bar charts are good for comparing between each element in the categories, and comparing elements across categories. However, the grouping can make it harder to tell the difference between the total of each group.
barplot(height....) set argument " beside = TRUE " http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/barplot.html
A gamma distribution is a general type of continous statistical distribution (related to the beta distribution) that arises naturally in processes for which the waiting times between Poisson distributed events are relevant. Gamma distributions have two free parameters shape k and scale denoted theta .
dgamma(x, shape, rate = 1, scale = 1/rate, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/GammaDist.html
Gamma distribution
polychoric correlation coefficient is a correlation coefficient which is computed over 2 variables to characterise an association by proxy with 2 (latent) variables which are assumed to be continuous and normally distributed.
http://cran.r-project.org/web/packages/polycor/ polychor(x, y, ML = FALSE, control = list(), std.err = FALSE, maxcor=.9999)
polychoric correlation coefficient
a full factorial design is a factorial design which ensures that all possible factor level combinations are defined and used so all between group differences can be explored
full factorial design
permutation numbering is a data tranformation allowing to count the number of possible permutations of elements in a set of size n, each element occurring exactly once. This number is factorial n.
permutation numbering
The Michaelis constant is the substrate concentration at which the reaction rate is at half-maximum, and is an inverse measure of the substrate's affinity for the enzyme—as a small indicates high affinity, meaning that the rate will approach more quickly.[5] The value of is dependent on both the enzyme and the substrate, as well as conditions such as temperature and pH.
adapted from wikipedia: http://en.wikipedia.org/wiki/Michaelis–Menten_constant last accessed: 22-11-2013
half maximal reaction rate substrate concentration (Km)
Michaelis-Menten constant
child-parents trio
receiver operational characteristics curve is a graphical plot which illustrates the performance of a binary classifier system as its discrimination threshold (aka cut-off point) is varied by plotting sensitivity vs (1 − specificity)
roc.from.table(table, graph = TRUE, add = FALSE, title = FALSE, line.col = "red", auc.coords = NULL, ...) http://rss.acs.unt.edu/Rdoc/library/epicalc/html/roc.html
receiver operational characteristics curve
The transmission disequilibrium test is a statistical test for genetic linkage between genetic marker and a trait in families. The test is robust to population structure.
TODO: need to modify restrictions to include family and trio
TDT
STATO , adapted wikipedia (from http://en.wikipedia.org/wiki/Transmission_disequilibrium_test), polled on June,2013
transmission disequilibrium test
The binomial distribution is a discrete probability distribution which describes the probability of k successes in n draws with replacement from a finite population of size N. The binomial distribution is frequently used to model the number of successes in a sample of size n drawn with replacement from a population of size N. The binomial distribution gives the discrete probability distribution of obtaining exactly n successes out of N Bernoulli trials (where the result of each Bernoulli trial is true with probability p and false with probability q=1-p ) notation: B(n,p) The mean is N*p The variance is N*p*q
dbinom(x, size, prob, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Binomial.html
binomial distribution
hit selection is a planned process which in screening processes such as high-throughput screening, lead to the identification of perturbing agent which cause the typical signal generated by a standardized assay to significantly differ from the negative control. The selection hitself results from meeting or exceeding selection threshold (for instance 6 sigma from the mean or SSMD value beyond 5 when compared to positive controls or below -5 when compared to negative controls
adapted from: http://en.wikipedia.org/wiki/SSMD
adapted from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789971/
hit selection
TODO
pairing rule is a rule which is specifies the criteria for deciding on how to associated any 2 entities.
pairing rule
between group comparison statistical test is a statistical test which aims to detect difference between the means computing for each of the study group populations
between group comparison statistical test
The Pearson's correlation coefficient is a correlation coefficient which evaluates two continuous variables for association strength in a data sample. It assumes that both variables are normally distributed and linearity exists. The coefficient is calculated by dividing their covariance with the product of their individual standard deviations. It is a normalized measurement of how the two are linearly related.
Pearson product-moment correlation coefficient
Pearson's r
STATO, adapted from http://www.r-tutor.com/elementary-statistics/numerical-measures/correlation-coefficient and from: http://stamash.org/pearsons-correlation-coefficient/ http://stamash.org/kendalls-tau-correlation/
cor(x, y = NULL, use = "everything",method = c("pearson"))
Pearson's correlation coefficient
F statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a F distribution. the F statistic is the ratio of two scaled sums of squares reflecting different sources of variability
F-statistic
negative binomial probability distribution is a discrete probability distribution of the number of successes in a sequence of Bernoulli trials before a specified (non-random) number of failures (denoted r) occur. The negative binomial distribution, also known as the Pascal distribution or Pólya distribution, gives the probability of r-1 successes and x failures in x+r-1 trials, and success on the (x+r)th trial.
Pascal distribution
Pólya distribution
dnbinom(x, size, prob, mu, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/NegBinomial.html
negative binomial distribution
Breusch-Pagan test is a statistical test which computes a score test of the hypothesis of constant error variance against the alternative that the error variance changes with the level of the response (fitted values), or with a linear combination of predictors.
Breusch, T. S. and Pagan, A. R. (1979) A simple test for heteroscedasticity and random coefficient variation. Econometrica 47, 1287--1294. and adapted from: http://www.inside-r.org/packages/cran/car/docs/ncvTest last accessed [2014-03-15]
http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/lmtest/html/bptest.html bptest(formula, varformula = NULL, studentize = TRUE, data = list()) or http://www.inside-r.org/packages/cran/car/docs/ncvTest
Breusch-Pagan test
http://www.ncbi.nlm.nih.gov/pubmed/?term=17182697 Bioinformatics. 2007 Feb 15;23(4):401-7. Enrichment or depletion of a GO category within a class of genes: which test? Rivals I1, Personnaz L, Taing L, Potier MC.
hypergeometric test is a null hypothesis test which evaluates if a random variable follows a hypergeometric distribution. It is a test of goodness of fit to that distribution. The test is suited for situation aimed at assessing cases of sampling from a finite set without replacements. For instance, testing for enrichment or depletion of elements (e.g GO categories, genes)
Added following a term request by Chris Mungall: https://github.com/ISA-tools/stato/issues/6
phyper(q, m, n, k, lower.tail = TRUE, log.p = FALSE) lower.tail logical; if TRUE (default), probabilities are P[X ≤ x], otherwise, P[X > x]. http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Hypergeometric.html
hypergeometric test
a one-tailed test is a statistical test which, assuming an unskewed probability distribution, allocates all of the significance level to evaluate only one hypothesis to explain a difference. The one-tailed test provides more power to detect an effect in one direction by not testing the effect in the other direction. one-tailed test should be preceded by two-tailed test in order to avoid missing out on detecting alternate effect explaining an observed difference.
one sided test
adapted from: http://www.ats.ucla.edu/stat/mult_pkg/faq/general/tail_tests.htm
one tailed test
For example, we may wish to compare the mean of a sample to a given value x using a t-test. Our null hypothesis is that the mean is equal to x. A two-tailed test will test both if the mean is significantly greater than x and if the mean significantly less than x. The mean is considered significantly different from x if the test statistic is in the top 2.5% or bottom 2.5% of its probability distribution, resulting in a p-value less than 0.05.
a two tailed test is a statistical test which assess the null hypothesis of absence of difference assuming a symmetric (not skewed) underlying probability distribution by allocating half of the significance level selected to each of the direction of change which could explain a difference (for example, a difference can be an excess or a loss).
two sided test
two tailed test
a null hypothesis which states that no difference exists between 2 or more groups being considered
absence of difference hypothesis
let's consider an experiment evaluating 2 compounds (aspirin & ibuprofen) at 3 distinct dose levels (low, medium, high) and 4 time points post exposure (0h, 6h, 12h, 24h). Assuming the treatments are applied only once (no replication), the number of observation in a full factorial design is 2 x 3 x 4 = 24 so the design matrix would have 24 rows and 3 columns (1 per factor (independent variable).
a design matrix is an information content entity which denotes a study design. The design matrix is a n by m matrix where n the number of rows, corresponds to the number of observations (4 rows if quadruplicates) and where m, the number of columns corresponds to the number of independent variables. Each element in the matrix correspond to a discretized value representing one of the factor levels for a given factor. A design matrix can be used as input to statistical modeling or statistical analysis. The design matrix contains data on the independent variables (also called explanatory variables) in statistical models which attempt to explain observed data on a response variable (often called a dependent variable) in terms of the explanatory variables. The theory relating to such models makes substantial use of matrix manipulations involving the design matrix: see for example linear regression. A notable feature of the concept of a design matrix is that it is able to represent a number of different experimental designs and statistical models, e.g., ANOVA, ANCOVA, and linear regression
Added following a term request by Nolan Nichols: https://github.com/ISA-tools/stato/issues/9
model matrix
adapted from: Design of Experiments: Principles and Applications edited by Lennart Eriksson, 1999-2008 Umetrics. ISBN-13:978-91-973730-4-3 and http://en.wikipedia.org/wiki/Design_matrix [last accessed: 22-05-2014]
model.matrix(object, data = environment(object), contrasts.arg = NULL, xlev = NULL, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/model.matrix.html
design matrix
a contrast is used to define a comparison between 2 or more means. it is the set of coefficients used to specify a comparison. when the sum of these coefficients is null, the contrast is said to be orthogonal. old definition now deprecated: A contrast is a data item which is the output of a linear combination of 2 or more factor level means with coefficients that sum to zero.
Term request by Nolan Nichols via https://github.com/ISA-tools/stato/issues/9
contrasts(x, contrasts = TRUE, sparse = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrasts.html
contrast
a quantile is a data item which corresponds to specific elements x in the range of a variate X. the k-th n-tile P_k is that value of x, say x_k, which corresponds to a cumulative frequency of Nk/n (Kenney and Keeping 1962). If n=4, the quantity is called a quartile, and if n=100, it is called a percentile.
Evans, M.; Hastings, N.; and Peacock, B. Statistical Distributions, 3rd ed. New York: Wiley, 2000.
quantile
a decile is a quantile where n=10 and which splits data into sections accrued of 10% of data, so the first decile delineates 10% of the data, the second decile delineates 20% of the data and the nineth decile, 90 % of the data
decile
a percentile is a quantile which splits data into sections accrued of 1% of data, so the first percentile delineates 1% of the data, the second quartile delineates 2% of the data and the 99th percentile, 99 % of the data
percentile
absence of negative difference hypothesis is a hypothesis which assumes that a difference significantly less than a threshold does not exist.
absence of negative difference hypothesis
absence of negative difference hypothesis is a hypothesis which assumes that a difference significantly greater than a threshold does not exist.
absence of positive difference hypothesis
Evaluation of statistical inference on empirical resting state fMRI. IEEE Trans Biomed Eng. 2014 Apr;61(4):1091-9. doi: 10.1109/TBME.2013.2294013. http://www.ncbi.nlm.nih.gov/pubmed/24658234
statistical inference is a process of drawing conclusions following data analysis using statistical methods (statistical tests) and evaluating whether to reject or accept null hypothesis
Added following a term request by Nolan Nichols: https://github.com/ISA-tools/stato/issues/12
statistical inference
A ratio where the numerator and denominator are expressed in the same unit.
dimensionless ratio
The covariance is a measurement data item about the strength of correlation between a set (2 or more) of random variables. The covariance is obtained by forming: cov(X,Y)=E([X-E(X)][Y-E(Y)] where E(X), E(Y) is the expected value (mean) of variable X and Y respectively. covariance is symmetric so cov(X,Y)=cov(Y,X). The covariance is usefull when looking at the variance of the sum of the 2 random variables since: var(X+Y) = var(X) +var(Y) +2cov(X,Y) The covariance cov(x,y) is used to obtain the coefficient of correlation cor(x,y) by normalizing (dividing) cov(x,y) but the product of the standard deviations of x and y.
adapted from: http://mathworld.wolfram.com/Covariance.html
covariance
cov(x, y = NULL, use = "everything", method = c("pearson", "kendall", "spearman")) from: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cor.html
one sample t-test is a kind of Student's t-test which evaluates if a given sample can be reasonably assumed to be taken from the population. The test compares the sample statistic (m) to the population parameter (M). The one sample t-test is the small sample analog of the z test, which is suitable for large samples.
adapted from various sources, including: Practical Statistics for Medical Research by D.Altman. ISBN: 0-412-27630-5 http://www.psychology.emory.edu/clinical/bliwise/Tutorials/TOM/meanstests/tone.htm
one sample t-test
t.test(x = NULL, alternative = c("two.sided", "less", "greater"), mu = 0, paired = FALSE, var.equal = FALSE, conf.level = 0.95, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html
two sample t-test is a null hypothesis statistical test which is used to reject or accept the hypothesis of absence of difference between the means over 2 randomly sampled populations. It uses a t-distribution for the test and assumes that the variables in the population are normally distributed and with equal variances.
two sample t-test
adapted from: http://en.wikipedia.org/wiki/Student's_t-test#Independent_.28unpaired.29_samples and from: http://www.psychology.emory.edu/clinical/bliwise/Tutorials/TOM/meanstests/tind.htm
t-test for independent means assuming equal variance
t.test(x, y = NULL, alternative = c("two.sided", "less", "greater"), mu = 0, paired = FALSE, var.equal = TRUE, conf.level = 0.95, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html
two sample t-test with equal variance
Welch t-test is a two sample t-test used when the variances of the 2 populations/samples are thought to be unequal (homoskedasticity hypothesis not verified). In this version of the two-sample t-test, the denominator used to form the t-statistics, does not rely on a 'pooled variance' estimate.
Welsh t-test
Welch, B. L. (1947). "The generalization of "Student's" problem when several different population variances are involved". Biometrika 34 (1–2): 28–35. doi:10.1093/biomet/34.1-2.28
adapted from wikipedia: http://en.wikipedia.org/wiki/Welch's_t_test last accessed: 2014-05-06
t-test for independent means assuming unequal variance
t.test(x, y = NULL, alternative = c("two.sided", "less", "greater"), mu = 0, paired = FALSE, var.equal = FALSE, conf.level = 0.95, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html
two sample t-test with unequal variance
a helmert contrast is a contrast in which the coefficients for the Helmert regressors compare each level with the average of the “preceding” ones
http://www.clayford.net/statistics/tag/helmert-contrasts/ An R and S-Plus Companion to Applied Regression. John Fox ISBN-13: 978-0761922803
contr.helmert(n, contrasts = TRUE, sparse = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html
helmert contrast
a polynomial contrast is a contrast which...
contr.poly(n, scores = 1:n, contrasts = TRUE, sparse = FALSE) from: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html
polynomial contrast
treatment contrast is a contrast which allows to test how linear model coefficients of categorical variables are interpreted in case where the “first” level (aka, the baseline) is included into the intercept and all subsequent levels have a coefficient that represents their difference from the baseline.
adapted from multiple sources: http://pic.dhe.ibm.com/infocenter/spssstat/v20r0m0/index.jsp?topic=%2Fcom.ibm.spss.statistics.help%2Fidh_idd_genlin_emmeans.htm http://www.clayford.net/statistics/tag/helmert-contrasts/ http://www.aliquote.org/articles/tech/contrasts.html
contr.treatment(n, base = 1, contrasts = TRUE, sparse = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html
treatment contrast
the sum contrast is a contrast in which each coefficient compares the corresponding level of the factor to the average of the other levels
contr.sum(n, contrasts = TRUE, sparse = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html
sum contrast
Pearson's Chi-Squared test for goodnes of fit is a statistical null hypothesis test which is used to either evaluate goodness of fit of dataset to a Chi-Squared distribution
Chi2 test for goodness of fit
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html chisq.test(x = NULL, correct = FALSE, p = rep(1/length(x), length(x)), rescale.p = FALSE, simulate.p.value = FALSE, B = 2000)
Pearson's Chi square test of goodness of fit
Barnard's test is an exact statistical test used to determine if there are nonrandom associations between two categorical variables. It was developed in 1949 by Barnard and is a test which is, most times, more powerfull that the Fisher exact test
http://en.wikipedia.org/wiki/Barnard's_test and G A Barnard (1945) "A New Test for 2X2 Tables", Nature, 156, 177 & 783.
Barnard's test
barnardw.test(n1, n2, n3, n4, dp = 0.001, verbose = FALSE) from http://www.inside-r.org/packages/cran/Barnard/docs/barnardw.test
a central composite design is a study design which contains an imbedded factorial or fractional factorial design with center points that is augmented with a group of so-called 'star points' that allow estimation of curvature. A CCD design with k factors has 2k star points.
Box-Wilson Central Composite Design
cd(basis, generators, blocks = "Block", n0 = 4, alpha = "orthogonal", wbreps = 1, bbreps = 1, randomize = TRUE, inscribed = FALSE, coding) http://artax.karlin.mff.cuni.cz/r-help/library/rsm/html/ccd.html
central composite design
The Box-Behnken design is an independent quadratic design in that it does not contain an embedded factorial or fractional factorial design. In this design the treatment combinations are at the midpoints of edges of the process space and at the center. These designs are rotatable (or near rotatable) and require 3 levels of each factor. The designs have limited capability for orthogonal blocking compared to the central composite designs.
bbd(k, n0 = 4, block = (k == 4 | k == 5), randomize = TRUE, coding) from: http://artax.karlin.mff.cuni.cz/r-help/library/rsm/html/bbd.html
Box–Behnkens design
Plackett-Burman design is a type of study design optimizing multifactorial experiments characterized by their parsimony and economy with the run number a multiple of 4 (rather than a power of 2). Plackett-Burman design is often used for screening experiments where the main effect is often heavily confounded with two-factor interactions. This type of design is very useful for economically detecting large main effects, assuming all interactions are negligible when compared with the few important main effects.
pb(nruns, nfactors = nruns - 1, factor.names = if (nfactors <= 50) Letters[1:nfactors] else paste("F", 1:nfactors, sep = ""), default.levels = c(-1, 1), ncenter=0, center.distribute=NULL, boxtyssedal = TRUE, n12.taguchi = FALSE, replications = 1, repeat.only = FALSE, randomize = TRUE, seed = NULL, oldver = FALSE, ...) from: http://www.inside-r.org/packages/cran/FrF2/docs/pb
Plackett-Burman design
upper confidence limit is a data item which is a largest value bounding a confidence interval
upper confidence limit
lower confidence limit is a data item which is a lowest value bounding a confidence interval
lower confidence limit
root-mean-square standardized effect is a data item which denotes effect size in the context of analysis of variance and corresponds to the square root of the arithmetic average of p standardized effects (effects normalized to be expressed in standard deviation units).
RMSSE
root-mean-square standardized effect
Eta-squared is a biased estimator of the variance explained by the model in the population (it estimates only the effect size in the sample). Eta-squared describes the ratio of variance explained in the dependent variable by a predictor while controlling for other predictors, making it analogous to the r2. This estimate shares the weakness with r2 that each additional variable will automatically increase the value of η2. In addition, it measures the variance explained of the sample, not the population, meaning that it will always overestimate the effect size, although the bias grows smaller as the sample grows larger.
eta-squared
omega-squared is a effect size estimate for variance explained which is less biased than the eta-squared coefficient.
adapted from: http://en.wikipedia.org/wiki/Effect_size#Omega-squared.2C_.CF.892
omega-squared
Hedges's g is an estimator of effect size which is similar to Cohen's d and is a measure based on a standardized difference however the denominator , corresponding to a pooled standard deviation, is computed differently from Cohen's d coefficient, by applying a correction factor (which involves a Gamma function)
adapted from : http://en.wikipedia.org/wiki/Effect_size#Cohen.27s_d and http://blog.stata.com/tag/cohens-d/
Hedges's g
Glass's delta is an estimator of effect size which is similar to Cohen's d but where the denominator corresponds only to the standard deviation of the control group (or second group). It is considered less biais than the Cohen's d for estimating effect sizes based on means and distances between means.
Glass's delta
A unit which is a standard measure of the distance between two points.
A unit which is a standard measure of the dimension in which events occur in sequence.
a false positive rate whose value is 5 per cent
Following discussion with OBCS, deprecated of class STATO_0000043 and creation of instance
5 % false positive rate
a false positive rate whose value is 1 per cent
Following discussion with OBCS, deprecated of class STATO_0000281 and creation of instance
1 % false positive rate
absence of depletion difference hypothesis is a hypothesis which assumes that the representation of an element significantly greater than a threshold does not exist.
absence of over representation hypothesis
absence of enrichment hypothesis
absence of depletion difference hypothesis is a hypothesis which assumes that the representation of an element significantly less than a threshold does not exist.
absence of under representation hypothesis
absence of depletion hypothesis
a binomial test is a statistical hypothesis test which evaluates if the observations made about a Bernoulli experiment , that is an experiment which tests the statistical significance of deviations from a theoretically expected distribution (the binomial distribution) of observations into 2 categories. It is a goodness of fit test.
adapted from: http://en.wikipedia.org/wiki/Binomial_test
binomial test
binom.test(x, n, p = 0.5, alternative = c("two.sided", "less", "greater"), conf.level = 0.95) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/binom.test.html
exact binomial test
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