Software Ontology
type: Ontology
version IRI: swo.owl
creator: Allyson Lister
creator: Andy Brown
creator: Duncan Hull
creator: Helen Parkinson
creator: James Malone
creator: Jon Ison
creator: Nandini Badarinarayan
creator: Robert Stevens
description: The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community.
license: https://creativecommons.org/licenses/by/4.0/
comment: The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, licensing, provenance and associated data. It contains SWO-specific classes and axioms as well as imports from: 1. BFO 2. IAO 3. OBI 4. EDAM
version info: 2023-03-05

editor preferred label
type: AnnotationProperty
editor preferred label: editor preferred label
editor preferred label: editor preferred term
editor preferred label: editor preferred term~editor preferred label
IAO_0000114: IAO_0000122
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: editor preferred term
label: editor preferred term~editor preferred label

example of usage
type: AnnotationProperty
editor preferred label: example of usage
IAO_0000114: IAO_0000122
definition: 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.
definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: IAO

definition
type: AnnotationProperty
editor preferred label: definition
editor preferred label: textual definition
IAO_0000114: IAO_0000122
definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
IAO_0000116: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: textual definition

term editor
type: AnnotationProperty
editor preferred label: term editor
IAO_0000114: IAO_0000122
definition: 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
IAO_0000116: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

alternative term
type: AnnotationProperty
editor preferred label: alternative label
editor preferred label: alternative term
IAO_0000114: IAO_0000125
definition: A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
term editor: OBO Operations committee
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
comment: Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
label: alternative label

definition source
type: AnnotationProperty
editor preferred label: definition source
IAO_0000114: IAO_0000122
definition: 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
term editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

term tracker item
type: AnnotationProperty
editor preferred label: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
IAO_0000114: IAO_0000125
definition: An IRI or similar locator for a request or discussion of an ontology term.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

imported from
type: AnnotationProperty
editor preferred label: imported from
IAO_0000114: IAO_0000125
definition: For external terms/classes, the ontology from which the term was imported
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

term replaced by
type: AnnotationProperty
editor preferred label: term replaced by
IAO_0000114: IAO_0000125
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

is a defining property chain axiom
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL

is a defining property chain axiom where second argument is reflexive
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.

Contributor
type: AnnotationProperty
description: Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.
comment: An entity responsible for making contributions to the content of the resource.

description
type: AnnotationProperty

license
type: AnnotationProperty
term editor: Mark Miller
date: 2018-05-11T13:47:29Z

title
type: AnnotationProperty

obsoleted in version
type: AnnotationProperty
definition: The version in which a class or property has been made obsolete
creator: EFO Development Team

isDefinedBy
type: AnnotationProperty
IAO_0000589: is defined by

Axiom
annotated source: isDefinedBy
annotated property: IAO_0000589
annotated target: is defined by
comment: This is an experimental annotation

label
type: AnnotationProperty
editor preferred label: label

deprecated
type: AnnotationProperty
range: boolean

exactMatch
type: AnnotationProperty
comment: Allyson Lister 14.9.22: Added as a temporary workaround with issues relating to equivalentClass axioms between IAO software and SWO software.

is about
type: ObjectProperty
domain: information content entity
definition: 'is about' relates an information entity to other entities in which the information entity holds some information which dscribes some facet of the other entity, such as the arrow direction on a sign.
definition source: IAO
definition source: James Malone
creator: Alan Ruttenberg

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
editor preferred label: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
IAO_0000116: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative term: part_of
RO_0001900: RO_0001901
RO_0040042: continuant
RO_0040042: occurrent
RO_0040042: independent continuant
RO_0040042: realizable entity
RO_0040042: quality
RO_0040042: specifically dependent continuant
RO_0040042: generically dependent continuant
in subset: valid for go annotation extension
in subset: valid for go gp2term
in subset: valid for go ontology
in subset: valid for gocam

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
editor preferred label: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
IAO_0000116: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
alternative term: has_part
RO_0001900: RO_0001901
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

realized in
type: ObjectProperty
inverse of: realizes
domain: realizable entity
range: process
editor preferred label: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative term: is realized by
alternative term: realized_in
IAO_0000600: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
domain: process
range: realizable entity
editor preferred label: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
IAO_0000600: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
editor preferred label: preceded by
definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
IAO_0000116: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative term: is preceded by
alternative term: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in subset: ro-eco

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
editor preferred label: precedes
definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
in subset: ro-eco

is about
type: ObjectProperty
domain: information content entity
example of usage: This document is about information artifacts and their representations
IAO_0000114: IAO_0000125
definition: A (currently) primitive relation that relates an information artifact to an entity.
IAO_0000116: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
term editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

has_specified_input
type: ObjectProperty
equivalent property:
  inverse of: is_specified_input_of
sub property of: has participant
inverse of: is_specified_input_of
domain: planned process
editor preferred label: has_specified_input
example of usage: see is_input_of example_of_usage
IAO_0000114: IAO_0000122
definition: The inverse property of is_specified_input_of
IAO_0000116: 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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Coutot
imported from: obi.owl

is_specified_input_of
type: ObjectProperty
sub property of: participates in
range: planned process
editor preferred label: is_specified_input_of
example of usage: 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
IAO_0000114: IAO_0000122
definition: 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.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has participant
inverse of: is_specified_output_of
domain: planned process
editor preferred label: has_specified_output
IAO_0000114: IAO_0000122
definition: The inverse property of is_specified_output_of
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Courtot
imported from: obi.owl

is manufactured by
type: ObjectProperty
domain: material entity
range: organization
range: Class
  union of: Homo sapiens
  union of: organization
editor preferred label: is_manufactured_by
example of usage: http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
IAO_0000114: IAO_0000123
definition: c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
term editor: Alan Ruttenberg
term editor: Liju Fan
alternative term: has_make
alternative term: has_manufacturer
definition source: OBI
label: is_manufactured_by

is_specified_output_of
type: ObjectProperty
sub property of: participates in
range: planned process
editor preferred label: is_specified_output_of
IAO_0000114: IAO_0000122
definition: 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.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters
imported from: obi.owl

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: planned process
range: objective specification
editor preferred label: achieves_planned_objective
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
IAO_0000114: IAO_0000120
definition: 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.
term editor: BP, AR, PPPB branch
definition source: PPPB branch derived
IAO_0000232: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch

objective_achieved_by
type: ObjectProperty
domain: objective specification
range: planned process
editor preferred label: objective_achieved_by
IAO_0000114: IAO_0000122
definition: This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
term editor: OBI
definition source: OBI

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: bearer of
type: FunctionalProperty
editor preferred label: inheres in
example of usage: this fragility inheres in this vase
example of usage: this fragility is a characteristic of this vase
example of usage: this red color inheres in this apple
example of usage: this red color is a characteristic of this apple
definition: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
IAO_0000116: A dependent inheres in its bearer at all times for which the dependent exists.
alternative term: inheres_in
RO_0001900: RO_0001901
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
label: inheres in

bearer of
type: ObjectProperty
type: InverseFunctionalProperty
range: specifically dependent continuant
editor preferred label: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: Inverse of characteristic_of
definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative term: bearer_of
alternative term: is bearer of
RO_0001900: RO_0001901
label: has characteristic

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
editor preferred label: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative term: participates_in
creator: Andy Brown
comment: Please see the official RO definition for the inverse of this property, 'has participant.'

has participant
type: ObjectProperty
domain: occurrent
range: continuant
property chain axiom: has part
editor preferred label: has participant
example of usage: The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process.
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
IAO_0000116: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
alternative term: has_participant
definition source: http://obo-relations.googlecode.com/svn/trunk/src/ontology/core.owl
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
creator: Andy Brown

is concretized as
type: ObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.

concretizes
type: ObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
IAO_0000116: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative term: function_of
alternative term: is function of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

quality of
type: ObjectProperty
sub property of: characteristic of
inverse of: has quality
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
IAO_0000116: A quality inheres in its bearer at all times for which the quality exists.
alternative term: is quality of
alternative term: quality_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has_role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
IAO_0000116: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative term: is role of
alternative term: role_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has function
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
alternative term: has_function

has quality
type: ObjectProperty
sub property of: bearer of
range: quality
example of usage: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
alternative term: has_quality

has_role
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
alternative term: has_role
label: has role

has disposition
type: ObjectProperty
sub property of: bearer of
inverse of: disposition of
domain: independent continuant
range: disposition
definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

disposition of
type: ObjectProperty
sub property of: characteristic of
definition: inverse of has disposition
in subset: RO_0002259
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has regulatory component activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulated by
definition: A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
created by: dos
creation date: 2017-05-24T09:30:46Z

has negative regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: negatively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
created by: dos
creation date: 2017-05-24T09:31:01Z
comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.

has positive regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: positively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
created by: dos
creation date: 2017-05-24T09:31:17Z
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.

has component activity
type: ObjectProperty
sub property of: has component process
created by: dos
creation date: 2017-05-24T09:44:33Z
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.

has component process
type: ObjectProperty
sub property of: has component
domain: process
range: process
definition: w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
created by: dos
creation date: 2017-05-24T09:49:21Z

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates
created by: dos
creation date: 2017-09-17T13:52:24Z
comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.

Axiom
annotated source: directly regulated by
annotated property: comment
annotated target: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
has db xref: GOC:dos

directly negatively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly negatively regulates
definition: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
created by: dos
creation date: 2017-09-17T13:52:38Z

Axiom
annotated source: directly negatively regulated by
annotated property: definition
annotated target: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
has db xref: GOC:dos

directly positively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly positively regulates
definition: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
created by: dos
creation date: 2017-09-17T13:52:47Z

Axiom
annotated source: directly positively regulated by
annotated property: definition
annotated target: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
has db xref: GOC:dos

has effector activity
type: ObjectProperty
sub property of: has component activity
type: FunctionalProperty
definition: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
created by: dos
creation date: 2017-09-22T14:14:36Z
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.

Axiom
annotated source: has effector activity
annotated property: definition
annotated target: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
has db xref: GOC:dos

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
term editor: David Osumi-Sutherland
in subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
term editor: David Osumi-Sutherland
alternative term: starts_at_end_of
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

immediately precedes
type: ObjectProperty
sub property of: precedes
term editor: https://orcid.org/0000-0002-7073-9172
term editor: David Osumi-Sutherland
alternative term: ends_at_start_of
alternative term: meets
RO_0002575: precedes
in subset: ro-eco
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: part of
property chain axiom: has part
IAO_0000114: IAO_0000125
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO_0001900: RO_0001901
in subset: valid for go annotation extension
in subset: valid for gocam
in subset: ro-eco

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: has part
annotated target: part of
RO_0002582: true

has component
type: ObjectProperty
sub property of: has part
IAO_0000114: IAO_0000125
definition: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
IAO_0000116: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
IAO_0000232: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO_0001900: RO_0001901
in subset: ro-eco

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: has effector activity
property chain axiom: directly regulates
definition: p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
term editor: https://orcid.org/0000-0001-7476-6306
term editor: https://orcid.org/0000-0002-3837-8864
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
definition source: GO
IAO_0000232: Regulation precludes parthood; the regulatory process may not be within the regulated process.
IAO_0000589: regulates (processual)
IAO_0000600: false
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
definition: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
IAO_0000589: negatively regulates (process to process)
RO_0004050: regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
definition: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
IAO_0000589: positively regulates (process to process)
RO_0004049: regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
example of usage: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
example of usage: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
term editor: https://orcid.org/0000-0002-6601-2165
alternative term: has function realized in
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20123131
definition source: http://www.ncbi.nlm.nih.gov/pubmed/21208450
IAO_0000232: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
in subset: ro-eco

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative term: has function in

Axiom
annotated source: capable of part of
annotated property: propertyChainAxiom
annotated target: capable of
annotated target: part of
RO_0002582: true

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
IAO_0000114: IAO_0000125
term editor: https://orcid.org/0000-0002-6601-2165
definition source: Allen's interval algebra
IAO_0000232: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
IAO_0000114: IAO_0000125
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative term: consumes
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
in subset: ro-eco

has output
type: ObjectProperty
sub property of: has participant
inverse of: output of
IAO_0000114: IAO_0000125
definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative term: produces
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
in subset: ro-eco

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
example of usage: A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
definition: c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
in subset: valid for go gp2term

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: enables
property chain axiom: causally upstream of or within
example of usage: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
definition: c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
has related synonym: affects
in subset: valid for go gp2term

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
definition: p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
RO_0004049: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for gocam
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
definition: p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
RO_0004050: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for gocam

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: characteristic of
property chain axiom: part of
definition: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
IAO_0000116: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
term editor: https://orcid.org/0000-0002-6601-2165
alternative term: inheres in part of
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
RO_0001900: RO_0001901

Axiom
annotated source: characteristic of part of
annotated property: propertyChainAxiom
annotated target: characteristic of
annotated target: part of
RO_0002582: true

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
term editor: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
property chain axiom: has component activity
example of usage: a particular instances of akt-2 enables some instance of protein kinase activity
definition: c enables p iff c is capable of p and c acts to execute p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative term: catalyzes
alternative term: executes
alternative term: has
alternative term: is catalyzing
alternative term: is executing
IAO_0000232: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
in subset: valid for go gp2term

functionally related to
type: ObjectProperty
definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
term editor: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This is a grouping relation that collects relations used for the purpose of connecting structure and function

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: part of
property chain axiom: capable of
definition: this relation holds between c and p when c is part of some c', and c' is capable of p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative term: false

Axiom
annotated source: part of structure that is capable of
annotated property: propertyChainAxiom
annotated target: part of
annotated target: capable of
is a defining property chain axiom: true

involved in
type: ObjectProperty
sub property of: participates in
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: part of
definition: c involved_in p if and only if c enables some process p', and p' is part of p
term editor: https://orcid.org/0000-0002-6601-2165
alternative term: actively involved in
alternative term: enables part of

enabled by
type: ObjectProperty
sub property of: has participant
sub property of: functionally related to
definition: inverse of enables
term editor: https://orcid.org/0000-0002-6601-2165
in subset: valid for gocam

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
definition: inverse of regulates
term editor: https://orcid.org/0000-0002-6601-2165
IAO_0000589: regulated by (processual)
in subset: RO_0002259

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
term editor: https://orcid.org/0000-0002-6601-2165
in subset: RO_0002259

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
term editor: https://orcid.org/0000-0002-6601-2165
in subset: RO_0002259

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
example of usage: An organism that is a member of a population of organisms
definition: is member of is a mereological relation between a item and a collection.
alternative term: is member of
alternative term: member part of
definition source: SIO
RO_0001900: RO_0001901

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.
definition source: SIO
RO_0001900: RO_0001901

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: An entity A is the 'input of' another entity B if A was put into the system, entity or software represented by B.
definition: inverse of has input
term editor: https://orcid.org/0000-0002-6601-2165
definition source: Allyson Lister
in subset: RO_0002259
in subset: ro-eco

output of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
example of usage: A piece of software can be the output of a particular software company via a software publishing process; data might be the output of a particular piece of data-producing software.
definition: An entity A is the 'output of' another entity B if it was produced as a result of the functioning of entity B.
definition: inverse of has output
term editor: https://orcid.org/0000-0002-6601-2165
definition source: Allyson Lister
in subset: RO_0002259
in subset: ro-eco

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
IAO_0000114: IAO_0000428
definition: inverse of upstream of
term editor: https://orcid.org/0000-0002-6601-2165

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of
IAO_0000114: IAO_0000428
term editor: https://orcid.org/0000-0002-6601-2165

indirectly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly positively regulates
property chain axiom: indirectly negatively regulates
definition: p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
term editor: https://orcid.org/0000-0002-6601-2165
alternative term: indirectly activates
RO_0002579: positively regulates

indirectly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly negatively regulates
definition: p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
term editor: https://orcid.org/0000-0002-6601-2165
alternative term: indirectly inhibits
RO_0002579: negatively regulates

causally related to
type: ObjectProperty
definition: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
IAO_0000116: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yie…
term editor: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

Axiom
annotated source: causally related to
annotated property: definition
annotated target: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
has db xref: https://en.wikipedia.org/wiki/Causality

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
definition: p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
term editor: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for gocam

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
definition: p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
term editor: https://orcid.org/0000-0002-6601-2165
RO_0002575: causally upstream of

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
definition: p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
IAO_0000116: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
term editor: https://orcid.org/0000-0002-6601-2165
alternative term: influences (processual)
has related synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
in subset: RO_0002259

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' regulates some p
term editor: https://orcid.org/0000-0002-6601-2165

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
term editor: https://orcid.org/0000-0002-6601-2165
RO_0004049: involved in regulation of

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
term editor: https://orcid.org/0000-0002-6601-2165
RO_0004050: involved in regulation of

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process
definition: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
IAO_0000116: OWL does not allow defining object properties via a Union
term editor: https://orcid.org/0000-0002-6601-2165
alternative term: involved in or reguates

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
definition: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
IAO_0000116: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
IAO_0000116: Considering relabeling as 'pairwise interacts with'
term editor: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
has exact synonym: in pairwise interaction with
in subset: ro-eco

molecularly interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
definition: An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
term editor: https://orcid.org/0000-0002-6601-2165
alternative term: binds
alternative term: molecularly binds with

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
IAO_0000116: Axiomatization to GO to be added later
term editor: https://orcid.org/0000-0002-6601-2165
alternative term: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431
has exact synonym: molecularly controls

directly negatively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly negatively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431
alternative term: directly inhibits
has exact synonym: molecularly decreases activity of

directly positively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly positively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431
alternative term: directly activates
has exact synonym: molecularly increases activity of

helper property (not for use in curation)
type: ObjectProperty
term editor: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.

is kinase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
term editor: https://orcid.org/0000-0002-6601-2165

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
definition source: causal-relations

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: occurrent
range: occurrent
definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

depends on
type: ObjectProperty
term editor: https://orcid.org/0000-0002-6601-2165

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: continuant
range: continuant
IAO_0000116: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
IAO_0000589: causally influenced by (entity-centric)

interaction relation helper property
type: ObjectProperty
sub property of: helper property (not for use in curation)
term editor: https://orcid.org/0000-0002-6601-2165

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property
term editor: https://orcid.org/0000-0002-6601-2165

causally influences
type: ObjectProperty
sub property of: causal relation between entities
domain: continuant
range: continuant
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
definition: The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431
definition source: causal-relations
IAO_0000589: causally influences (entity-centric)

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
definition: p directly regulates q iff p is immediately causally upstream of q and p regulates q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
IAO_0000589: directly regulates (processual)
RO_0002575: regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

has part structure that is capable of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: has part
property chain axiom: capable of
example of usage: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
definition: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
term editor: https://orcid.org/0000-0002-6601-2165

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
definition: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
IAO_0000116: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

capable of regulating
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: regulates
example of usage: pyrethroid -> growth
definition: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
definition source: causal-relations

capable of negatively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates
definition: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
definition source: causal-relations

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
example of usage: renin -> arteriolar smooth muscle contraction
definition: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
definition source: causal-relations

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
definition source: causal-relations

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
definition: p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
definition source: causal-relations
IAO_0000589: directly positively regulates (process to process)
RO_0004049: directly regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
definition: p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
definition source: causal-relations
IAO_0000589: directly negatively regulates (process to process)
RO_0004050: directly regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

enables subfunction
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: has part
definition: Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-25T23:20:13Z

acts upstream of or within, positive effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, positive effect
RO_0004049: acts upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:49:30Z
in subset: valid for go gp2term

acts upstream of or within, negative effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, negative effect
RO_0004050: acts upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:49:51Z
in subset: valid for go gp2term

acts upstream of, positive effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect
property chain axiom: enables
property chain axiom: causally upstream of, positive effect
definition: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
RO_0004049: acts upstream of
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:53:14Z
in subset: valid for go gp2term

acts upstream of, negative effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect
property chain axiom: enables
property chain axiom: causally upstream of, negative effect
definition: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
RO_0004050: acts upstream of
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:53:22Z
in subset: valid for go gp2term

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004050: causally upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004049: causally upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-13T23:55:19Z

regulates activity of
type: ObjectProperty
sub property of: causally influences
domain: material entity
range: material entity
definition: The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
term editor: https://orcid.org/0000-0003-4639-4431

indirectly causally upstream of
type: ObjectProperty
sub property of: causally upstream of
definition: p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
created by: pg
creation date: 2022-09-26T06:07:17Z

indirectly regulates
type: ObjectProperty
sub property of: regulates
sub property of: indirectly causally upstream of
definition: p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
created by: pg
creation date: 2022-09-26T06:08:01Z

device utilizes material
type: ObjectProperty
property chain axiom: capable of
property chain axiom: has input
example of usage: A diagnostic testing device utilizes a specimen.
definition: X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
term editor: https://orcid.org/0000-0001-9625-1899
term editor: https://orcid.org/0000-0003-2620-0345
IAO_0000232: A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
IAO_0000232: See github ticket https://github.com/oborel/obo-relations/issues/497
creation date: 2021-11-08T12:00:00Z
has broad synonym: utilizes

regulates characteristic
type: ObjectProperty
sub property of: causally related to
domain: process
range: quality
property chain axiom: regulates
definition: A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599

positively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: positively regulates
definition: A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599

negatively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: negatively regulates
property chain axiom: positively regulates characteristic
property chain axiom: positively regulates
definition: A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599

obsolete reason_for_obsolescence
type: ObjectProperty
sub property of: obsolete object property
term tracker item: https://github.com/allysonlister/swo/issues/59
comment: AL 2023-03-05: Replaced by rdfs:comment as no longer within the EFO release files.
deprecated: true

obsolete is developed by
type: ObjectProperty
sub property of: obsolete object property
term tracker item: https://github.com/allysonlister/swo/issues/59
term replaced by: is developed by
comment: AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs.
deprecated: true

obsolete_is_published_by
type: ObjectProperty
sub property of: obsolete object property
domain: software
definition: The relationship between software and a software publisher.
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: 0.5
comment: This class can be entirely replaced with 'is published by', SWO_0004004. Please use SWO_0004004 instead.
deprecated: true

has legal status
type: ObjectProperty
sub property of: obsolete object property
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: 1.4
comment: This property was not in use anywhere in the ontology. Further, it had no definition and therefore its intended usage was unclear. Until a time when this property is required and an official definition created, this property is obsolete so as not to introduce inconsistent usage.
deprecated: true

obsolete implements
type: ObjectProperty
sub property of: obsolete object property
term tracker item: https://github.com/allysonlister/swo/issues/59
term replaced by: implements
comment: AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs.
deprecated: true

obsolete is encoded in
type: ObjectProperty
sub property of: obsolete object property
term tracker item: https://github.com/allysonlister/swo/issues/59
term replaced by: is encoded in
comment: AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs.
deprecated: true

is version of
type: ObjectProperty
inverse of: has version
domain: version name
definition: 'is version of' provides a link between a 'version name' and the entity with that version.
creator: Allyson Lister
comment: For further information, please see http://softwareontology.wordpress.com/2012/06/20/versioning-in-swo/

uses software
type: ObjectProperty
inverse of: is software for
domain: software
range: software
example of usage: Cytoscape plugins would be linked to the Cytoscape application via uses software, while Microsoft Excel is linked to Microsoft Office via has_part.
definition: This property allows the linkage of two different pieces of software such that one directly executes or uses the other. The has_part relationship should instead be used to describe related but independent members of a larger software package, and 'uses platform' relationship should be used to describe which operating system(s) a particular piece of software can use.
definition source: Allyson Lister

is implemented by
type: ObjectProperty
inverse of: implements
domain: algorithm
range: software
definition: is implemented by is the relationship between an algorithm and a piece of software which includes an implementation of that software for use when the software is executed.
creator: James Malone

has specified data input
type: ObjectProperty
inverse of: is specified data input of
domain: software
range: data item
definition: The relationship between input data which is permitted to a piece of software.
creator: James Malone
comment: AL 2.9.22: This cannot be a child of 'has specified input' because the restrictions on domain and range for that hierarchy would create issues for us, as both software and data item (our domain and range, respectively) are continuants. For now, the solution is to take it out of that hierarchy completely.
comment: See also http://softwareontology.wordpress.com/2011/04/15/ins-and-outs-of-software/

has specified data output
type: ObjectProperty
inverse of: is specified data output of
domain: software
range: data item
definition: The relationship between a piece of software and the data that it is possible to output.
creator: James Malone
comment: AL 2.9.22: This cannot be a child of 'has specified output' because the restrictions on domain and range for that hierarchy would create issues for us, as both software and data item (our domain and range, respectively) are continuants. For now, the solution is to take it out of that hierarchy completely.
comment: See also http://softwareontology.wordpress.com/2011/04/15/ins-and-outs-of-software/

is specified data input of
type: ObjectProperty
domain: data item
range: software
definition: The relationship between a data and the software which can possibly take this data as input.
creator: James Malone
comment: AL 2.9.22: This cannot be a child of 'is specified input of' or 'input of' because the restrictions on domain and range for that hierarchy would create issues for us, as both software and data item (our range and domain, respectively) are continuants. For now, the solution is to take it out of that hierarchy completely.

is specified data output of
type: ObjectProperty
domain: data item
range: software
definition: The relationship between a data and the software which can possibly produce this data as output.
creator: James Malone
comment: AL 2.9.22: This cannot be a child of 'is specified output of' or 'output of' because the restrictions on domain and range for that hierarchy would create issues for us, as both software and data item (our range and domain, respectively) are continuants. For now, the solution is to take it out of that hierarchy completely.

directly preceded by
type: ObjectProperty
sub property of: follows
inverse of: directly followed by
example of usage: Microsoft version 2007 is directly preceded by Microsoft version 2003.
definition: Entity A is 'directly preceded by' entity B if there are no intermediate entities temporally between the two entities. WIthin SWO this property is mainly used to describe versions of entities such as software.
definition source: Allyson Lister
creator: OBO Foundry

directly followed by
type: ObjectProperty
sub property of: followed by
definition: 'directly followed by' is an object property which further specializes the parent 'followed by' property. In the assertion 'C directly followed by C1', says that Cs generally are immediately followed by C1s.
definition source: Allyson Lister

uses platform
type: ObjectProperty
domain: software
range: operating system
definition: 'uses platform' should be used to link a particular piece of software to one or more operating systems which that software can run on. This is in contrast to both 'uses software' (which describes one piece of software directly executing another), and has_part, which can be used to describe related but independent software in a package, for example.
creator: Allyson Lister
comment: This property, together with 'uses software', is probably best modelled as a child of has_part. Its current position in the property hierarchy is based on simplicity of use. 'uses platform' was deemed an appropriate addition (rather than making use of already extant has_part or 'uses software') due to the already present definitions of those classes which restrict their use to particular situations.

is software for
type: ObjectProperty
domain: software
range: software

followed by
type: ObjectProperty
comment: AL 2.9.22: When incorporating all BFO annotations, it became clear that we were using BFO 'precedes' (which was the original parent for 'directly followed by') incorrectly. 'precedes' has a range and domain of occurent, and the IAO version number class is an ICE, which is a continuant. This led to an inconsistent ontology. To fix this for now, we have created a new class that performs a similar function to BFO 'precedes' but without the domain/range restrictions.

follows
type: ObjectProperty
comment: AL 2.9.22: When incorporating all BFO annotations, it became clear that we were using BFO 'precedes' and 'preceded by' (which was the original parent for 'directly preceded by') incorrectly. 'precedes' has a range and domain of occurent, and the IAO version number class is an ICE, which is a continuant. This led to an inconsistent ontology. To fix this for now, we have created a new class (and this, its inverse) that performs a similar function to BFO 'precedes' but without the domain/range restrictions.

is developed by
type: ObjectProperty
domain: software
definition: The relationship between a software and software developer.

implements
type: ObjectProperty
domain: software
range: algorithm
definition: implements is the relationship between software and an algorithm that is defined for use within that software when executed.
creator: James Malone

is encoded in
type: ObjectProperty
sub property of: is about
example of usage: Linking a type of software to its particular programming language.
definition: Is encoded in is an "is about" relationship which describes the type of encoding used for the referenced class.
definition source: Allyson Lister

has version
type: ObjectProperty
range: version name
definition: relationship between an entity and a version name or number
comment: For further information, please see http://softwareontology.wordpress.com/2012/06/20/versioning-in-swo/

has interface
type: ObjectProperty
range: software interface
definition: Provides a method of asserting what type of interactions are possible for the class in question. The interface must be from the 'software interface' hierarchy.
definition source: Allyson Lister
definition source: Andy Brown
creator: Andy Brown

has format specification
type: ObjectProperty
sub property of: is encoded in
domain: data item
range: data format specification
definition: Has format specification is a type of "is encoded in" relationship which specifically describes the relationship between data and a data format specification.
definition source: Allyson Lister

obsolete_is developed by
type: ObjectProperty
sub property of: obsolete object property
Contributor: Marked as obsolete by Allyson Lister.
creator: James Malone
obsoleted in version: 0.3
comment: is developed by and is_developed_by. The former is from the core file and originally had no identifier (though it is now identified via SWO_0004003), and the latter is from the original file (SWO_0000394). SWO_0000394 was retained and SWO_0004003 marked as obsolete as SWO_0004003 had no usages while SWO_0000394 has many usages. Finally, the underscores were removed from the label of SWO_0000394 so it would conform to our naming scheme. Please use SWO_0000394 instead.
deprecated: true

is published by
type: ObjectProperty
sub property of: topObjectProperty
domain: Class
  union of: data format specification
  union of: software
range: organization
definition: 'is published by' elucidates the relationship between a piece of software or a data format specification and its owning organization. Please note that this is not the same as authorship of the software. For instance, affy is published within Bioconductor, but has its own distinct authorship list.
creator: Allyson Lister
creator: James Malone

obsolete object property
type: ObjectProperty
definition: Stores those object properties which are no longer appropriate for use within SWO.
Contributor: Marked as obsolete by Allyson Lister
creator: Allyson Lister

is executed in
type: ObjectProperty
domain: software
range: data transformation
range: data visualization
definition: is executed in defines the relationship between a software class and an appropriate process in the information processing hierarchy. Specifically, it allows the linking of a particular piece of software to a process of a particular purpose,
definition source: Allyson Lister
creator: Allyson Lister
creator: OBI

obsolete_is specified output of
type: ObjectProperty
sub property of: obsolete object property
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: 0.3
comment: There is an object property duplication for is specified output of, where one is from OBI (OBI_0000312) and one is from SWO (SWO_9000058); additionally, the reasoner infers these two object properties as equivalent. Both are the inverse properties for has specified output. It makes sense to retain the OBI object property. The SWO class URI was renamed to the OBI term URI (to make the moving of the axioms across to the OBI term simple), and then an SWO class with the original URI was marked as obsolete. Please use OBI_0000312 instead.
deprecated: true

has clause
type: ObjectProperty
sub property of: is about
range: clause
definition: Axioms using the 'has clause' property, e.g. C 'has clause' C1, provide links from the left hand class to the instances within the 'license clause' hierarchy. This provides a way to more precisely assert the constraints of the licensing applied.
definition source: Allyson Lister

has license
type: ObjectProperty
sub property of: is about
inverse of: is license for
definition: The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between software and a software license.

is license for
type: ObjectProperty
sub property of: is about
definition: The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between a software license and the software which implements it.

is alternative format of
type: ObjectProperty
type: SymmetricProperty
domain: data format specification
range: data format specification
example of usage: The format for BioPAX Manchester OWL syntax is an alternative format of the BioPAX RDF/XML format.
definition: With both a domain and range of 'data format specification', this property provides a means of stating that two different data format specifications are valid specifications for the same type of data.
definition source: Allyson Lister

is compatible license of
type: ObjectProperty
type: SymmetricProperty
domain: software license
range: software license
definition: 'is compatible license of' provides a method of marking two software licenses as compatible and without conflicts, e.g. that the Apache License version 2 is compatible with GNU GPL version 3. If two licenses are connected with this property, it means code released under one license can be released with code from the other license in a larger program.
definition source: http://www.gnu.org/licenses/gpl-faq.html#WhatDoesCompatMean, accessed 12 June 2013.
creator: Allyson Lister

has declared status
type: ObjectProperty
sub property of: is about
range: SWO_9000061
definition: 'has declared status' provides a way to assert the developmental status of a class, such as whether it is stable or under development. Is especially useful for software that might not be complete or stable yet, and when combined with version information.
definition source: Allyson Lister

obsolete_has_participant
type: ObjectProperty
sub property of: obsolete object property
obsoleted in version: 1.4
comment: Exact equivalence with RO class http://purl.obolibrary.org/obo/RO_0000057, to the extent that the inverse of RO_0000057 was already present in this ontology as the inverse of this SWO class.
deprecated: true

has part
type: ObjectProperty
inverse of: part of
type: TransitiveProperty
comment: The inverse property. 'part of', contains the full official RO definition.
label: has_part

part of
type: ObjectProperty
type: TransitiveProperty
example of usage: Cytoscape plugins would be linked to the Cytoscape application via uses software, while Microsoft Excel is linked to Microsoft Office via has_part.
definition: For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
definition: This property can be used to describe related but independent members of a larger software package. In other cases, where parts of a larger software package are independent of one another in development but one piece of software executes another directly, please use "uses software".
definition source: OBO Foundry RO

has documentation
type: DatatypeProperty
range: string
definition: Should be used to link a particular class (e.g. a piece of software or an algorithm) with a publication(s) which act as the primary reference(s) for that class.
creator: Allyson Lister

has download location
type: DatatypeProperty
sub property of: has website homepage
range: string
definition: The location from where the software can be downloaded.
definition source: Allyson Lister
creator: Allyson Lister

has website homepage
type: DatatypeProperty
range: Literal
definition: The URL of the homepage for the resource this property is associated with.
definition source: Allyson Lister

has release date
type: DatatypeProperty
range: string
creator: Andy Brown
comment: The official date of release of software

has support URL
type: DatatypeProperty
range: Literal
creator: Andy Brown
comment: A URL for a source of support information about software

Ontology
type: Class
subclass of: data item
definition: An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc.
alternative term: Ontologies
imported from: EDAM.owl

Heat map
type: Class
subclass of: Image
subclass of: Clustered gene expression profiles
definition: A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment.
imported from: EDAM.owl
label: Heatmap

Gene expression data
type: Class
subclass of: data item
definition: Image, hybridisation or some other data arising from a study of gene expression, typically profiling or quantification.
alternative term: Gene product profile
alternative term: Gene product quantification data
alternative term: Gene transcription profile
alternative term: Gene transcription quantification data
alternative term: Microarray data
alternative term: Non-coding RNA profile
alternative term: Non-coding RNA quantification data
alternative term: RNA profile
alternative term: RNA quantification data
alternative term: RNA-seq data
alternative term: Transcriptome profile
alternative term: Transcriptome quantification data
alternative term: mRNA profile
alternative term: mRNA quantification data
imported from: EDAM.owl
label: Microarray data

Image
type: Class
subclass of: data item
definition: Biological or biomedical data has been rendered into an image, typically for display on screen.
alternative term: Image data
imported from: EDAM.owl

Clustered gene expression profiles
type: Class
subclass of: Gene expression data
definition: Groupings of gene expression profiles according to a clustering algorithm.
imported from: EDAM.owl

PDBML
type: Class
subclass of: XML

Taverna workflow format
type: Class
subclass of: XML
definition: Format of Taverna workflows.

newick
type: Class
subclass of: Textual format

FASTA format
type: Class
subclass of: Textual format

GenBank format
type: Class
subclass of: data format specification
definition: Genbank entry format.
alternative term: GenBank
imported from: EDAM.owl

GFF
type: Class
subclass of: Textual format

Textual format
type: Class
subclass of: data format specification

HTML
type: Class
subclass of: SWO_3000013
definition: html, or HyperText Markup Language in full, is a data format specification is a markup language for web pages and is the publishing language of the World Wide Web.
definition source: http://www.w3.org/TR/html401/
creator: James Malone

XML
type: Class
subclass of: data format specification
definition: Extensible Markup Language (XML) is a standard set of rules for encoding documents in a machine-readable form defined by the W3C.
creator: James Malone

binary format
type: Class
subclass of: data format specification

OBO Flat File Format
type: Class
subclass of: Textual format
definition: OBO format is the text file format used by OBO-Edit, the open source, platform-independent application for viewing and editing ontologies.
alternative term: OBO flat file format

SBML
type: Class
subclass of: XML
definition: Systems Biology Markup Language (SBML) is a machine-readable format for representing models. It's oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time.
alternative term: Systems Biology Markup Language
definition source: http://sbml.org

BED format
type: Class
subclass of: Textual format

format 3158
type: Class
subclass of: XML
definition: The PSI-MI format is an acronym for the Proteomics Standards Initiative - Molecular Interaction format. It provides an XML standard for molecular interactions and is supported by many molecular interaction databases and tools.
alternative term: PSI-MI format
alternative term: PSI-MIF
definition source: Modified from http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012.
creator: Allyson Lister

MAGE-ML
type: Class
subclass of: XML

MAGE-TAB
type: Class
subclass of: SWO_3000046
definition: MAGE-TAB is a tab delimited data format comprimising of ADF file for array design, IDFfor experimental design, SDRF for sample data relationships and associated data files.
definition source: http://www.mged.org/mage-tab/
comment: A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.

CopasiML
type: Class
subclass of: XML
definition: CopasiML, the native format of COPASI.
imported from: EDAM.owl

Query and retrieval
type: Class
subclass of: data transformation
definition: Search or query a data resource and retrieve entries and / or annotation.
alternative term: Database retrieval
alternative term: Query
imported from: EDAM.owl

Genome annotation
type: Class
subclass of: data transformation
definition: Annotate a genome sequence with terms from a controlled vocabulary.
alternative term: Metagenome annotation
imported from: EDAM.owl

Modelling and simulation
type: Class
subclass of: data transformation
definition: Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models.
alternative term: Mathematical modelling
imported from: EDAM.owl

data visualization algorithm
type: Class
subclass of: algorithm

data cleaning algorithm
type: Class
subclass of: data processing algorithm

data selection algorithm
type: Class
subclass of: data processing algorithm

data integration algorithm
type: Class
subclass of: data processing algorithm

data processing task
type: Class
subclass of: data transformation
comment: A data processing task is an information processing objective that specifies the objective that a data processing algorithm execution process needs to achieve when executed on a dataset to produce as output a new dataset.

data construction algorithm
type: Class
subclass of: data processing algorithm

generalization specification
type: Class
subclass of: directive information entity
definition: Generalization specification of a directive informational entity class that specifies the type of generalization. It includes information about the types of data used to produced the generalization and the language in which the generalization is expressed.
definition source: OntoDM

data processing algorithm
type: Class
subclass of: algorithm
definition source: Allyson Lister
comment: A data processing algorithm is an algorithm that has as its objective a data processing task and has data items both as input and output.

data visualization task
type: Class
subclass of: ObsoleteClass
term replaced by: data visualization
obsoleted in version: 1.7
comment: AL 25.9.19: Already obsoleted in originating ontology (OntoDM) so added here so people could see the history of the term.
comment: data visualization task is information processing objective achieved by a data visualization algorithm execution process.
deprecated: true

software development
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      union of: software
      union of: source code module
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: software
    union of: source code module
definition: A planned process that has specified output a software product and that involves the creation of source code.
term editor: Mathias Brochhausen
term editor: William R. Hogan
definition source: http://en.wikipedia.org/wiki/Software_development
IAO_0000600: A planned process resulting in a software product involving the creation of source code.

dataset creating
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: data set
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: data set
editor preferred label: creating a data set
definition: A planned process that has a data set as its specified output.
term editor: William R. Hogan
alternative term: data set creation
alternative term: dataset creation

entity
type: Class
disjoint with: ObsoleteClass
BFO_0000179: entity
BFO_0000180: Entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
IAO_0000116: BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
IAO_0000116: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
IAO_0000600: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

Axiom
annotated source: entity
annotated property: IAO_0000116
annotated target: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

Axiom
annotated source: entity
annotated property: IAO_0000600
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/001-001

continuant
type: Class
subclass of: entity
subclass of: Restriction
  on property: part of
  all values from: continuant
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
BFO_0000179: continuant
BFO_0000180: Continuant
editor preferred label: continuant
definition: 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.
IAO_0000116: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
IAO_0000116: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
imported from: pato.owl
IAO_0000600: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
IAO_0000601: if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
IAO_0000601: if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
IAO_0000601: if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
IAO_0000602: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
IAO_0000602: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
IAO_0000602: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
IAO_0000602: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
annotated source: continuant
annotated property: IAO_0000116
annotated target: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000007

Axiom
annotated source: continuant
annotated property: IAO_0000600
annotated target: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: IAO_0000601
annotated target: if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: IAO_0000601
annotated target: if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: IAO_0000601
annotated target: if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/011-002

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/011-002

occurrent
type: Class
subclass of: entity
subclass of: Restriction
  on property: part of
  all values from: occurrent
disjoint with: Restriction
  on property: part of
  some values from: continuant
BFO_0000179: occurrent
BFO_0000180: Occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
IAO_0000116: BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
IAO_0000116: BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
IAO_0000116: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
IAO_0000116: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
IAO_0000600: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
IAO_0000601: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
IAO_0000601: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
IAO_0000602: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
IAO_0000602: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
annotated source: occurrent
annotated property: IAO_0000116
annotated target: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: occurrent
annotated property: IAO_0000116
annotated target: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000012

Axiom
annotated source: occurrent
annotated property: IAO_0000600
annotated target: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/077-002

Axiom
annotated source: occurrent
annotated property: IAO_0000601
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: IAO_0000601
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/079-001

Axiom
annotated source: occurrent
annotated property: IAO_0000602
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: IAO_0000602
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/079-001

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: independent continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
BFO_0000179: ic
BFO_0000180: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
IAO_0000601: For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
IAO_0000601: For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
IAO_0000602: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
IAO_0000602: (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
IAO_0000602: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

Axiom
annotated source: independent continuant
annotated property: definition
annotated target: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated source: independent continuant
annotated property: IAO_0000601
annotated target: For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: IAO_0000601
annotated target: For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: IAO_0000602
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: IAO_0000602
annotated target: (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: IAO_0000602
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/017-002

process
type: Class
subclass of: occurrent
BFO_0000179: process
BFO_0000180: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
definition: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
IAO_0000116: BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
IAO_0000602: (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]

Axiom
annotated source: process
annotated property: definition
annotated target: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: IAO_0000602
annotated target: (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable entity
disjoint with: role
BFO_0000179: disposition
BFO_0000180: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
IAO_0000116: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
IAO_0000600: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
IAO_0000601: If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
IAO_0000602: (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
IAO_0000602: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

Axiom
annotated source: disposition
annotated property: IAO_0000600
annotated target: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/062-002

Axiom
annotated source: disposition
annotated property: IAO_0000601
annotated target: If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: IAO_0000602
annotated target: (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: IAO_0000602
annotated target: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/062-002

realizable entity
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of
  all values from: realizable entity
disjoint with: quality
BFO_0000179: realizable
BFO_0000180: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: 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.
IAO_0000600: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
IAO_0000601: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
IAO_0000602: (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
IAO_0000602: (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]

Axiom
annotated source: realizable entity
annotated property: IAO_0000600
annotated target: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
annotated source: realizable entity
annotated property: IAO_0000601
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: IAO_0000602
annotated target: (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: IAO_0000602
annotated target: (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/058-002

quality
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of
  all values from: quality
BFO_0000179: quality
BFO_0000180: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
IAO_0000600: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
IAO_0000601: If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
IAO_0000602: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
IAO_0000602: (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]

Axiom
annotated source: quality
annotated property: IAO_0000600
annotated target: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: IAO_0000601
annotated target: If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
annotated source: quality
annotated property: IAO_0000602
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: IAO_0000602
annotated target: (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/105-001

specifically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: specifically dependent continuant
disjoint with: generically dependent continuant
BFO_0000179: sdc
BFO_0000180: SpecificallyDependentContinuant
editor preferred label: specifically dependent continuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: 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.
definition: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
IAO_0000116: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
imported from: pato.owl
IAO_0000602: (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
IAO_0000602: (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: specifically dependent continuant
annotated property: IAO_0000116
annotated target: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

Axiom
annotated source: specifically dependent continuant
annotated property: IAO_0000602
annotated target: (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated source: specifically dependent continuant
annotated property: IAO_0000602
annotated target: (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable entity
BFO_0000179: role
BFO_0000180: Role
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
definition: 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.
IAO_0000116: BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
IAO_0000600: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
IAO_0000602: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
annotated source: role
annotated property: IAO_0000600
annotated target: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/061-001

Axiom
annotated source: role
annotated property: IAO_0000602
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/061-001

generically dependent continuant
type: Class
subclass of: continuant
BFO_0000179: gdc
BFO_0000180: GenericallyDependentContinuant
example of usage: The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: 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.
definition: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
IAO_0000602: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

Axiom
annotated source: generically dependent continuant
annotated property: definition
annotated target: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/074-001

Axiom
annotated source: generically dependent continuant
annotated property: IAO_0000602
annotated target: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/074-001

function
type: Class
subclass of: disposition
BFO_0000179: function
BFO_0000180: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
IAO_0000116: BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
IAO_0000600: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
IAO_0000602: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

Axiom
annotated source: function
annotated property: IAO_0000600
annotated target: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/064-001

Axiom
annotated source: function
annotated property: IAO_0000602
annotated target: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/064-001

material entity
type: Class
subclass of: independent continuant
BFO_0000179: material
BFO_0000180: MaterialEntity
editor preferred label: material entity
example of usage: Collection of random bacteria, a chair, dorsal surface of the body.
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: 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.
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
IAO_0000116: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
IAO_0000116: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
IAO_0000116: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
definition source: BFO
imported from: cl.owl
imported from: ido.owl
imported from: uberon.owl
IAO_0000600: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
IAO_0000601: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
IAO_0000601: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
IAO_0000602: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
IAO_0000602: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
IAO_0000602: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]

Axiom
annotated source: material entity
annotated property: IAO_0000600
annotated target: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: IAO_0000601
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
annotated source: material entity
annotated property: IAO_0000601
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: IAO_0000602
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: IAO_0000602
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: IAO_0000602
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/020-002

molecular_function
type: Class
definition: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
has exact synonym: molecular function
id: GO:0003674
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.

Axiom
annotated source: molecular_function
annotated property: definition
annotated target: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
has db xref: GOC:pdt

biological_process
type: Class
definition: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
created by: jl
creation date: 2012-09-19T15:05:24Z
has db xref: Wikipedia:Biological_process
has exact synonym: biological process
has exact synonym: physiological process
has related synonym: single organism process
has related synonym: single-organism process
id: GO:0008150
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.

Axiom
annotated source: biological_process
annotated property: definition
annotated target: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
has db xref: GOC:pdt

kinase activity
type: Class
subclass of: molecular_function
subclass of: Restriction
  on property: is kinase activity
  has self: true
definition: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
has db xref: Reactome:R-HSA-6788855
has db xref: Reactome:R-HSA-6788867
has exact synonym: phosphokinase activity
id: GO:0016301
comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.

Axiom
annotated source: kinase activity
annotated property: definition
annotated target: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
has db xref: ISBN:0198506732

FN3KRP phosphorylates PsiAm, RibAm
type: Axiom
annotated source: kinase activity
annotated property: hasDbXref
annotated target: Reactome:R-HSA-6788855

FN3K phosphorylates ketosamines
type: Axiom
annotated source: kinase activity
annotated property: hasDbXref
annotated target: Reactome:R-HSA-6788867

measurement unit label
type: Class
subclass of: datum label
editor preferred label: measurement unit label
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
IAO_0000114: IAO_0000125
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
IAO_0000116: 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
IAO_0000116: 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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

objective specification
type: Class
subclass of: directive information entity
editor preferred label: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
IAO_0000114: IAO_0000122
definition: A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
IAO_0000116: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
IAO_0000116: 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
IAO_0000116: Answers the question, why did you do this experiment?
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
alternative term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217

action specification
type: Class
subclass of: directive information entity
example of usage: Pour the contents of flask 1 into flask 2
IAO_0000114: IAO_0000122
definition: A directive information entity that describes an action the bearer will take.
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch

datum label
type: Class
subclass of: information content entity
editor preferred label: datum label
IAO_0000114: IAO_0000123
definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
IAO_0000116: http://www.golovchenko.org/cgi-bin/wnsearch#4n
term editor: GROUP: IAO
IAO_0000232: 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.

software
type: Class
subclass of: plan specification
editor preferred label: software
IAO_0000114: IAO_0000120
definition: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
IAO_0000116: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Melanie Courtot
definition source: GROUP: OBI

programming language
type: Class
subclass of: plan specification
editor preferred label: programming language
example of usage: R, Perl, Java
IAO_0000114: IAO_0000120
definition: A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
definition: A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
definition source: IAO
definition source: OBI_0000058
definition source: group:OBI

data item
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is encoded in
  some values from: data format specification
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
IAO_0000114: IAO_0000125
definition: 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 which reliably tends to produce (approximately) truthful statements.
IAO_0000116: 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.
IAO_0000116: 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.
IAO_0000116: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
IAO_0000116: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
IAO_0000116: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
alternative term: data

symbol
type: Class
subclass of: information content entity
editor preferred label: symbol
example of usage: a serial number such as "12324X"
example of usage: a stop sign
example of usage: a written proper name such as "OBI"
IAO_0000114: IAO_0000125
definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
IAO_0000116: 20091104, MC: this needs work and will most probably change
IAO_0000116: 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
term editor: PERSON: James A. Overton
term editor: PERSON: Jonathan Rees
definition source: based on Oxford English Dictionary

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
editor preferred label: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
IAO_0000114: IAO_0000122
definition: A generically dependent continuant that is about some thing.
definition: An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity.
IAO_0000116: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
IAO_0000116: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
term editor: PERSON: Chris Stoeckert
definition source: IAO
definition source: OBI_0000142

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
IAO_0000114: IAO_0000122
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
IAO_0000116: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".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.
IAO_0000116: 2013-05-30 Alan Ruttenberg: 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.
IAO_0000116: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
IAO_0000116: 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters

dot plot
type: Class
subclass of: graph
editor preferred label: dot plot
example of usage: Dot plot of SSC-H and FSC-H.
IAO_0000114: IAO_0000002
definition: 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.
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000123
definition source: group:OBI

graph
type: Class
subclass of: diagram
editor preferred label: graph
IAO_0000114: IAO_0000125
definition: 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.
term editor: PERSON: Lawrence Hunter
term editor: person:Alan Ruttenberg
term editor: person:Allyson Lister
definition source: OBI_0000240
definition source: group:OBI

algorithm
type: Class
subclass of: plan specification
editor preferred label: algorithm
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
IAO_0000114: IAO_0000120
definition: 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.
definition: A plan specification which describes the inputs and 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.
term editor: Philippe Rocca-Serra
term editor: PlanAndPlannedProcess Branch
definition source: IAO
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)

curation status specification
type: Class
equivalent class: Class
  one of: IAO_0000002
  one of: IAO_0000120
  one of: IAO_0000121
  one of: IAO_0000122
  one of: IAO_0000123
  one of: IAO_0000124
  one of: IAO_0000125
  one of: IAO_0000423
  one of: IAO_0000428
subclass of: data about an ontology part
editor preferred label: curation status specification
IAO_0000114: IAO_0000125
definition: 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.
IAO_0000116: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
term editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266

source code module
type: Class
subclass of: directive information entity
editor preferred label: source code module
example of usage: The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
IAO_0000114: IAO_0000123
definition: A source code module is a directive information entity that specifies, using a programming language, some algorithm.
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
definition source: OBI_0000039
definition source: group:OBI

data format specification
type: Class
subclass of: directive information entity
editor preferred label: data format specification
IAO_0000114: IAO_0000123
definition: A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
IAO_0000116: 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
term editor: PERSON: Alan Ruttenberg
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
definition source: OBI_0000187

data set
type: Class
subclass of: data item
editor preferred label: data set
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
IAO_0000114: IAO_0000125
definition: 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.
IAO_0000116: 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
IAO_0000116: 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI

image
type: Class
subclass of: figure
editor preferred label: image
IAO_0000114: IAO_0000122
definition: 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.
term editor: person:Alan Ruttenberg
term editor: person:Allyson
term editor: person:Chris Stoeckert
definition source: OBI_0000030
definition source: group:OBI

data about an ontology part
type: Class
subclass of: data item
editor preferred label: data about an ontology part
definition: Data about an ontology part is a data item about a part of an ontology, for example a term
term editor: Person:Alan Ruttenberg

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
editor preferred label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
IAO_0000114: IAO_0000122
definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
definition: A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
IAO_0000116: 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.
IAO_0000116: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
IAO_0000116: 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
IAO_0000116: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
term editor: Alan Ruttenberg
term editor: Clint Dowland
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them

version name
type: Class
subclass of: symbol
subclass of: Restriction
  on property: is version of
  all values from: Class
    union of: programming language
    union of: algorithm
    union of: data format specification
    union of: software
editor preferred label: version number
IAO_0000114: IAO_0000123
definition: 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.
IAO_0000116: 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
term editor: GROUP: IAO
label: version number

material information bearer
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes
      some values from: information content entity
subclass of: material entity
subclass of: Restriction
  on property: bearer of
  some values from: Restriction
    on property: concretizes
    some values from: information content entity
editor preferred label: material information bearer
example of usage: 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.
example of usage: a brain
example of usage: a hard drive
IAO_0000114: IAO_0000122
definition: A material entity in which a concretization of an information content entity inheres.
term editor: GROUP: IAO

histogram
type: Class
subclass of: graph
editor preferred label: histogram
IAO_0000114: IAO_0000122
definition: A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI

heatmap
type: Class
subclass of: graph
editor preferred label: heatmap
IAO_0000114: IAO_0000122
definition: A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI

dendrogram
type: Class
subclass of: graph
editor preferred label: dendrogram
example of usage: Dendrograms are often used in computational biology to illustrate the clustering of genes.
IAO_0000114: IAO_0000122
definition: A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Dendrogram

scatter plot
type: Class
subclass of: graph
editor preferred label: scatter plot
example of usage: Comparison of gene expression values in two samples can be displayed in a scatter plot
IAO_0000114: IAO_0000122
definition: 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.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
alternative term: scattergraph
definition source: WEB: http://en.wikipedia.org/wiki/Scatterplot

obsolescence reason specification
type: Class
equivalent class: Class
  one of: IAO_0000103
  one of: IAO_0000226
  one of: IAO_0000227
  one of: IAO_0000228
  one of: IAO_0000229
equivalent class: Class
  one of: IAO_0000103
  one of: IAO_0000226
  one of: IAO_0000227
  one of: IAO_0000228
  one of: IAO_0000229
  one of: OMO_0001000
subclass of: data about an ontology part
editor preferred label: obsolescence reason specification
IAO_0000114: IAO_0000125
definition: The reason for which a term has been deprecated. 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.
IAO_0000116: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

figure
type: Class
subclass of: information content entity
editor preferred label: figure
example of usage: Any picture, diagram or table
IAO_0000114: IAO_0000120
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
term editor: PERSON: Lawrence Hunter

diagram
type: Class
subclass of: figure
editor preferred label: diagram
example of usage: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
IAO_0000114: IAO_0000120
definition: A figure that expresses one or more propositions
term editor: PERSON: Lawrence Hunter

document
type: Class
subclass of: information content entity
editor preferred label: document
example of usage: A journal article, patent application, laboratory notebook, or a book
IAO_0000114: IAO_0000120
definition: A collection of information content entities intended to be understood together as a whole
term editor: PERSON: Lawrence Hunter

denotator type
type: Class
equivalent class: Class
  one of: IAO_0000410
  one of: IAO_0000420
  one of: IAO_0000421
subclass of: data about an ontology part
editor preferred label: denotator type
example of usage: The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
term editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters

Viruses
type: Class
subclass of: organism
editor preferred label: Viruses
imported from: ncbitaxon.owl

Euteleostomi
type: Class
subclass of: Vertebrata <vertebrates>
editor preferred label: Euteleostomi
alternative term: bony vertebrates
imported from: ncbitaxon.owl

Bacteria
type: Class
subclass of: organism
editor preferred label: Bacteria
alternative term: eubacteria
imported from: ncbitaxon.owl

Archaea
type: Class
subclass of: organism
editor preferred label: Archaea
imported from: ncbitaxon.owl

Eukaryota
type: Class
subclass of: organism
editor preferred label: Eukaryota
alternative term: eucaryotes
alternative term: eukaryotes
imported from: ncbitaxon.owl

Euarchontoglires
type: Class
subclass of: Mammalia
editor preferred label: Euarchontoglires
imported from: ncbitaxon.owl

Tetrapoda
type: Class
subclass of: Euteleostomi
editor preferred label: Tetrapoda
alternative term: tetrapods
imported from: ncbitaxon.owl

Amniota
type: Class
subclass of: Tetrapoda
editor preferred label: Amniota
alternative term: amniotes
imported from: ncbitaxon.owl

Opisthokonta
type: Class
subclass of: Eukaryota
editor preferred label: Opisthokonta
imported from: ncbitaxon.owl

Metazoa
type: Class
subclass of: Opisthokonta
editor preferred label: Metazoa
alternative term: metazoans
alternative term: multicellular animals
imported from: ncbitaxon.owl

Bilateria
type: Class
subclass of: Metazoa
editor preferred label: Bilateria
imported from: ncbitaxon.owl

Mammalia
type: Class
subclass of: Amniota
editor preferred label: Mammalia
alternative term: mammals
imported from: ncbitaxon.owl

Vertebrata <vertebrates>
type: Class
subclass of: Bilateria
editor preferred label: Vertebrata <vertebrates>
alternative term: Vertebrata
alternative term: vertebrates
imported from: ncbitaxon.owl

Homo sapiens
type: Class
subclass of: Euarchontoglires
editor preferred label: Homo sapiens
alternative term: human
alternative term: human being
imported from: ncbitaxon.owl

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
IAO_0000114: IAO_0000122
definition: A process that realizes a plan which is the concretization of a plan specification.
IAO_0000116: '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.)
IAO_0000116: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
term editor: Bjoern Peters
definition source: branch derived
IAO_0000232: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
IAO_0000232: 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)
imported from: obi.owl

regulator role
type: Class
subclass of: regulatory role
editor preferred label: regulator role
example of usage: Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
IAO_0000114: IAO_0000120
definition: a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
term editor: Person:Jennifer Fostel
alternative term: regulator
definition source: OBI

regulatory role
type: Class
subclass of: role
editor preferred label: regulatory role
example of usage: Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
IAO_0000114: IAO_0000120
definition: a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
term editor: GROUP: Role branch
definition source: OBI, CDISC
IAO_0000232: govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent

material supplier role
type: Class
subclass of: service provider role
editor preferred label: material supplier role
example of usage: Jackson Labs is an organization which provide mice as experimental material
IAO_0000114: IAO_0000120
definition: a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
IAO_0000116: Supplier role is a special kind of service, e.g. biobank
term editor: PERSON:Jennifer Fostel
alternative term: material provider role
alternative term: supplier

classified data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: class prediction data transformation
subclass of: data set
subclass of: Restriction
  on property: is_specified_output_of
  some values from: class prediction data transformation
editor preferred label: classified data set
IAO_0000114: IAO_0000125
definition: A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: data set with assigned class labels

processed material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: material processing
subclass of: material entity
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
editor preferred label: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
IAO_0000114: IAO_0000122
definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg

material processing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_input
  all values from: material entity
editor preferred label: material processing
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
IAO_0000114: IAO_0000122
definition: A planned process which results in physical changes in a specified input material
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca Serra
alternative term: material transformation
definition source: OBI branch derived

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
editor preferred label: specimen role
example of usage: 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.
IAO_0000114: IAO_0000122
definition: a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
IAO_0000116: 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.
IAO_0000116: 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.
IAO_0000116: blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
IAO_0000116: parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
term editor: GROUP: Role Branch
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/1013

organization
type: Class
subclass of: material entity
editor preferred label: organization
example of usage: 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.
IAO_0000114: IAO_0000122
definition: 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.
IAO_0000116: BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Susanna Sansone
definition source: GROUP: OBI

regulatory agency
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: has_role
    some values from: regulator role
subclass of: organization
subclass of: Restriction
  on property: has_role
  some values from: regulator role
editor preferred label: regulatory agency
example of usage: The US Environmental Protection Agency
IAO_0000114: IAO_0000122
definition: A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: en.wikipedia.org/wiki/Regulator

material transformation objective
type: Class
subclass of: objective specification
editor preferred label: material transformation objective
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
IAO_0000114: IAO_0000122
definition: an objective specifiction that creates an specific output object from input materials.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
alternative term: artifact creation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: manufacturing objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: manufacturing objective
editor preferred label: manufacturing
IAO_0000114: IAO_0000122
definition: Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
IAO_0000116: Manufacturing implies reproducibility and responsibility AR
IAO_0000116: This includes a single scientist making a processed material for personal use.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturing objective
type: Class
subclass of: material transformation objective
editor preferred label: manufacturing objective
IAO_0000114: IAO_0000122
definition: is the objective to manufacture a material of a certain function (device)
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturer role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    union of: Homo sapiens
    union of: organization
subclass of: Restriction
  on property: realized in
  all values from: manufacturing
editor preferred label: manufacturer role
example of usage: With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
IAO_0000114: IAO_0000123
definition: Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
term editor: GROUP: Role Branch
definition source: OBI

clustered data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: class discovery data transformation
subclass of: data set
subclass of: Restriction
  on property: is_specified_output_of
  some values from: class discovery data transformation
editor preferred label: clustered data set
example of usage: A clustered data set is the output of a K means clustering data transformation
IAO_0000114: IAO_0000125
definition: A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: data set with assigned discovered class labels
IAO_0000232: AR thinks could be a data item instead

specimen collection process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
editor preferred label: specimen collection process
example of usage: 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
IAO_0000114: IAO_0000122
definition: A planned process with the objective of collecting a specimen.
IAO_0000116: 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.
IAO_0000116: 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.
IAO_0000116: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
IAO_0000116: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
term editor: Bjoern Peters
alternative term: specimen collection
IAO_0000232: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
IAO_0000232: 6/9/09: used at workshop

class prediction data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: classified data set
  union of: Restriction
    on property: achieves_planned_objective
    some values from: class prediction objective
subclass of: data transformation
editor preferred label: class prediction data transformation
IAO_0000114: IAO_0000122
definition: A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
term editor: James Malone
alternative term: supervised classification data transformation
definition source: PERSON: James Malone

specimen collection objective
type: Class
subclass of: objective specification
editor preferred label: specimen collection objective
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
IAO_0000114: IAO_0000122
definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
term editor: Bjoern Peters
definition source: Bjoern Peters

support vector machine
type: Class
subclass of: class prediction data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: class prediction objective
editor preferred label: support vector machine
IAO_0000114: IAO_0000123
definition: A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space.
term editor: James Malone
term editor: Ryan Brinkman
alternative term: SVM
definition source: PERSON: Ryan Brinkman

decision tree induction objective
type: Class
subclass of: data transformation objective
editor preferred label: decision tree induction objective
IAO_0000114: IAO_0000123
definition: A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
term editor: James Malone

decision tree building data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: decision tree induction objective
subclass of: data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: decision tree induction objective
editor preferred label: decision tree building data transformation
IAO_0000114: IAO_0000120
definition: A decision tree building data transformation is a data transformation that has objective decision tree induction.
term editor: James Malone
definition source: PERSON: James Malone

GenePattern software
type: Class
subclass of: software
editor preferred label: GenePattern software
IAO_0000114: IAO_0000120
definition: a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
term editor: James Malone
term editor: Person:Helen Parkinson
definition source: WEB: http://www.broadinstitute.org/cancer/software/genepattern/

peak matching
type: Class
subclass of: data transformation
editor preferred label: peak matching
IAO_0000114: IAO_0000123
definition: Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold
term editor: James Malone
term editor: Ryan Brinkman
definition source: PERSON: Ryan Brinkman

k-nearest neighbors
type: Class
subclass of: dataset creating
subclass of: partitioning data transformation
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
editor preferred label: k-nearest neighbors
IAO_0000114: IAO_0000125
definition: A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned.
term editor: James Malone
alternative term: k-NN
definition source: PERSON: James Malone

CART
type: Class
subclass of: decision tree building data transformation
editor preferred label: CART
IAO_0000114: IAO_0000122
definition: A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
term editor: James Malone
alternative term: classification and regression trees
definition source: BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.

statistical model validation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: cross validation objective
subclass of: partitioning data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: cross validation objective
editor preferred label: statistical model validation
example of usage: Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia
IAO_0000114: IAO_0000120
definition: A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
term editor: Helen Parkinson
definition source: http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29

manufacturer
type: Class
equivalent class: Class
  intersection of: Class
    union of: Homo sapiens
    union of: organization
  intersection of: Restriction
    on property: has_role
    some values from: manufacturer role
subclass of: material entity
subclass of: Restriction
  on property: has_role
  some values from: manufacturer role
editor preferred label: manufacturer
IAO_0000114: IAO_0000123
definition: A person or organization that has a manufacturer role

service provider role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    union of: Homo sapiens
    union of: organization
subclass of: Restriction
  on property: realized in
  all values from: planned process
editor preferred label: service provider role
example of usage: Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
IAO_0000114: IAO_0000123
definition: is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
term editor: PERSON:Helen Parkinson

processed specimen
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: specimen
subclass of: processed material
subclass of: specimen
editor preferred label: processed specimen
example of usage: A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
IAO_0000114: IAO_0000122
definition: A specimen that has been intentionally physically modified.
term editor: Bjoern Peters
definition source: Bjoern Peters
comment: A tissue sample that has been sliced and stained for a histology study.

categorical label
type: Class
subclass of: datum label
editor preferred label: categorical label
example of usage: 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.
IAO_0000114: IAO_0000120
definition: A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
term editor: Bjoern Peters
definition source: Bjoern Peters

questionnaire
type: Class
subclass of: document
editor preferred label: questionnaire
IAO_0000114: IAO_0000120
definition: A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
IAO_0000116: JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
IAO_0000116: Need to clarify if this is a document or a directive information entity (or what their connection is))
term editor: PERSON: Jessica Turner
definition source: Merriam-Webster

categorical value specification
type: Class
subclass of: value specification
editor preferred label: categorical value specification
IAO_0000114: IAO_0000123
definition: A value specification that is specifies one category out of a fixed number of nominal categories
term editor: PERSON:Bjoern Peters

value specification
type: Class
subclass of: information content entity
editor preferred label: value specification
example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
IAO_0000114: IAO_0000122
definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
IAO_0000116: 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.
term editor: PERSON:Bjoern Peters

collection of specimens
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has member
    all values from: specimen
subclass of: material entity
editor preferred label: collection of specimens
example of usage: Blood cells collected from multiple donors over the course of a study.
IAO_0000114: IAO_0000125
definition: A material entity that has two or more specimens as its parts.
IAO_0000116: Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: OBIB, OBI
source: Biobank

histologic grade according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: histologic grade according to AJCC 7th edition
example of usage: G1:Well differentiated
example of usage: G4: Undifferentiated
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

histologic grade according to the Fuhrman Nuclear Grading System
type: Class
subclass of: categorical value specification
editor preferred label: histologic grade according to the Fuhrman Nuclear Grading System
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Histologic Grade (Fuhrman Nuclear Grading System)
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

histologic grade for ovarian tumor
type: Class
subclass of: categorical value specification
editor preferred label: histologic grade for ovarian tumor
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a histologic grade assigned to a ovarian tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

histologic grade for ovarian tumor according to a two-tier grading system
type: Class
subclass of: histologic grade for ovarian tumor
editor preferred label: histologic grade for ovarian tumor according to a two-tier grading system
IAO_0000114: IAO_0000120
definition: A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

histologic grade for ovarian tumor according to the World Health Organization
type: Class
subclass of: histologic grade for ovarian tumor
editor preferred label: histologic grade for ovarian tumor according to the World Health Organization
IAO_0000114: IAO_0000120
definition: A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

pathologic primary tumor stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for lung according to AJCC 7th edition
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

pathologic primary tumor stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for kidney according to AJCC 7th edition
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

pathologic primary tumor stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for ovary according to AJCC 7th edition
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

pathologic lymph node stage for colon and rectum according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

pathologic lymph node stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for lung according to AJCC 7th edition
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

pathologic lymph node stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for kidney according to AJCC 7th edition
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

pathologic lymph node stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for ovary according to AJCC 7th edition
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

pathologic distant metastases stage for colon according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for colon according to AJCC 7th edition
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: M: colon distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

pathologic distant metastases stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for lung according to AJCC 7th edition
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: M: lung distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

pathologic distant metastases stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for kidney according to AJCC 7th edition
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: M: kidney distant Metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

pathologic distant metastases stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for ovary according to AJCC 7th edition
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative term: M: ovarian distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

clinical tumor stage group according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: clinical tumor stage group according to AJCC 7th edition
IAO_0000114: IAO_0000120
definition: A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Clinical tumor stage group (AJCC 7th Edition)
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

International Federation of Gynecology and Obstetrics cervical cancer stage value specification
type: Class
subclass of: categorical value specification
editor preferred label: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
IAO_0000114: IAO_0000120
definition: A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Clinical FIGO stage
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
type: Class
subclass of: categorical value specification
editor preferred label: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
IAO_0000114: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

performance status value specification
type: Class
subclass of: categorical value specification
editor preferred label: performance status value specification
IAO_0000114: IAO_0000120
definition: A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).
term editor: Chris Stoeckert, Helena Ellis
alternative term: Performance Status Scale
definition source: https://en.wikipedia.org/wiki/Performance_status
IAO_0000234: NCI BBRB

Eastern Cooperative Oncology Group score value specification
type: Class
subclass of: performance status value specification
editor preferred label: Eastern Cooperative Oncology Group score value specification
IAO_0000114: IAO_0000120
definition: A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient.
term editor: Chris Stoeckert, Helena Ellis
alternative term: ECOG score
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

Karnofsky score vaue specification
type: Class
subclass of: performance status value specification
editor preferred label: Karnofsky score vaue specification
IAO_0000114: IAO_0000120
definition: A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
term editor: Chris Stoeckert, Helena Ellis
alternative term: Karnofsky Score
definition source: NCI BBRB, OBI
IAO_0000234: NCI BBRB

material supplier
type: Class
equivalent class: Class
  intersection of: Class
    union of: Homo sapiens
    union of: organization
  intersection of: Restriction
    on property: has_role
    some values from: material supplier role
subclass of: material entity
subclass of: Restriction
  on property: has_role
  some values from: material supplier role
editor preferred label: material supplier
IAO_0000114: IAO_0000123
definition: A person or organization that provides material supplies to other people or organizations.
term editor: Rebecca Jackson
term tracker item: https://github.com/obi-ontology/obi/issues/1289

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material entity
editor preferred label: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
IAO_0000114: IAO_0000122
definition: 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.
IAO_0000116: 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')
IAO_0000116: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism

specimen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has_role
    some values from: specimen role
subclass of: material entity
subclass of: Restriction
  on property: has_role
  some values from: specimen role
editor preferred label: specimen
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
IAO_0000114: IAO_0000122
definition: A material entity that has the specimen role.
IAO_0000116: 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.
term editor: PERSON: James Malone
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch
term tracker item: https://github.com/obi-ontology/obi/issues/1013

data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: data transformation objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: Class
      intersection of: algorithm
      intersection of: Restriction
        on property: has part
        some values from: objective specification
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: data transformation objective
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
editor preferred label: data transformation
example of usage: 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.
IAO_0000114: IAO_0000122
definition: A planned process that produces output data from input data.
term editor: Elisabetta Manduchi
term editor: Helen Parkinson
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
term editor: Richard Scheuermann
term editor: Ryan Brinkman
term editor: Tina Hernandez-Boussard
alternative term: data analysis
alternative term: data processing
definition source: Branch editors
imported from: obi.owl

leave one out cross validation method
type: Class
subclass of: statistical model validation
editor preferred label: leave one out cross validation method
example of usage: The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368
IAO_0000114: IAO_0000123
definition: is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data
IAO_0000116: 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178
term editor: Person:Helen Parkinson

k-means clustering
type: Class
subclass of: dataset creating
subclass of: partitioning data transformation
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
editor preferred label: k-means clustering
IAO_0000114: IAO_0000125
definition: A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Philippe Rocca-Serra
definition source: WEB: http://en.wikipedia.org/wiki/K-means

hierarchical clustering
type: Class
subclass of: dataset creating
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
editor preferred label: hierarchical clustering
IAO_0000114: IAO_0000125
definition: A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root).
term editor: James Malone
definition source: WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering

dimensionality reduction
type: Class
subclass of: dataset creating
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
editor preferred label: dimensionality reduction
IAO_0000114: IAO_0000122
definition: A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
alternative term: data projection
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot

principal components analysis dimensionality reduction
type: Class
subclass of: dimensionality reduction
editor preferred label: principal components analysis dimensionality reduction
IAO_0000114: IAO_0000122
definition: A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
alternative term: pca data reduction
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot

data visualization
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: graph
    union of: image
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
subclass of: Restriction
  on property: has_specified_output
  all values from: Class
    union of: graph
    union of: image
editor preferred label: data visualization
example of usage: Generation of a heatmap from a microarray dataset
IAO_0000114: IAO_0000122
definition: An planned process that creates images, diagrams or animations from the input data.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
term editor: Tina Boussard
alternative term: data encoding as image
alternative term: visualization
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot
definition source: PERSON: Tina Boussard
IAO_0000232: Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding

data transformation objective
type: Class
subclass of: objective specification
editor preferred label: data transformation objective
example of usage: normalize objective
IAO_0000114: IAO_0000122
definition: An objective specification to transformation input data into output data
IAO_0000116: Modified definition in 2013 Philly OBI workshop
term editor: James Malone
definition source: PERSON: James Malone

partitioning data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: partitioning objective
subclass of: data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: partitioning objective
editor preferred label: partitioning data transformation
IAO_0000114: IAO_0000123
definition: A partitioning data transformation is a data transformation that has objective partitioning.
term editor: James Malone
definition source: PERSON: James Malone

partitioning objective
type: Class
subclass of: data transformation objective
editor preferred label: partitioning objective
example of usage: A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
IAO_0000114: IAO_0000122
definition: A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set.
term editor: Elisabetta Manduchi
term editor: James Malone
definition source: PERSON: Elisabetta Manduchi

class discovery data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  union of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
subclass of: data transformation
editor preferred label: class discovery data transformation
IAO_0000114: IAO_0000122
definition: A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
term editor: James Malone
alternative term: clustering data transformation
alternative term: unsupervised classification data transformation
definition source: PERSON: James Malone

class discovery objective
type: Class
subclass of: data transformation objective
editor preferred label: class discovery objective
IAO_0000114: IAO_0000122
definition: A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
term editor: James Malone
alternative term: clustering objective
alternative term: discriminant analysis objective
alternative term: unsupervised classification objective
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone

class prediction objective
type: Class
subclass of: data transformation objective
editor preferred label: class prediction objective
IAO_0000114: IAO_0000122
definition: A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data.
term editor: James Malone
alternative term: classification objective
alternative term: supervised classification objective
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone

cross validation objective
type: Class
subclass of: partitioning objective
editor preferred label: cross validation objective
IAO_0000114: IAO_0000125
definition: A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis.
term editor: James Malone
alternative term: rotation estimation objective
definition source: WEB: http://en.wikipedia.org/wiki/Cross_validation

clustered data visualization
type: Class
subclass of: data visualization
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: dot plot
    union of: histogram
    union of: heatmap
    union of: dendrogram
    union of: scatter plot
subclass of: Restriction
  on property: has_specified_input
  all values from: clustered data set
editor preferred label: clustered data visualization
IAO_0000114: IAO_0000123
definition: A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type.
term editor: James Malone

quality
type: Class
subclass of: specifically dependent continuant
definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
id: PATO:0000001

Axiom
annotated source: quality
annotated property: definition
annotated target: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
has db xref: PATOC:GVG

length unit
type: Class
subclass of: measurement unit label
editor preferred label: length unit
definition: A unit which is a standard measure of the distance between two points.
imported from: uo.owl

mass unit
type: Class
subclass of: measurement unit label
editor preferred label: mass unit
definition: A unit which is a standard measure of the amount of matter/energy of a physical object.
imported from: uo.owl

time unit
type: Class
subclass of: measurement unit label
editor preferred label: time unit
definition: A unit which is a standard measure of the dimension in which events occur in sequence.
imported from: uo.owl

temperature unit
type: Class
subclass of: measurement unit label
editor preferred label: temperature unit
imported from: uo.owl

substance unit
type: Class
subclass of: measurement unit label
editor preferred label: substance unit
imported from: uo.owl

concentration unit
type: Class
subclass of: measurement unit label
editor preferred label: concentration unit
imported from: uo.owl

volume unit
type: Class
subclass of: measurement unit label
editor preferred label: volume unit
imported from: uo.owl

frequency unit
type: Class
subclass of: measurement unit label
editor preferred label: frequency unit
imported from: uo.owl

volumetric flow rate unit
type: Class
subclass of: measurement unit label
editor preferred label: volumetric flow rate unit
imported from: uo.owl

rate unit
type: Class
subclass of: measurement unit label
editor preferred label: rate unit
imported from: uo.owl

obsolete sequence feature format
type: Class
subclass of: ObsoleteClass
term replaced by: http://www.ebi.ac.uk/swo/data/SWO_3000069
obsoleted in version: 1.7
comment: AL 2.10.2019: Incorrectly-formatted IRI. See also https://github.com/allysonlister/swo/issues/16
deprecated: true

obsolete matlab software
type: Class
subclass of: ObsoleteClass
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 2-sample pooled t-test
type: Class
subclass of: ObsoleteClass
term replaced by: 2-sample pooled t-test
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 50-50 MANOVA
type: Class
subclass of: ObsoleteClass
term replaced by: 50-50 MANOVA
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ABarray
type: Class
subclass of: ObsoleteClass
term replaced by: ABarray
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'ACME'
type: Class
subclass of: ObsoleteClass
term replaced by: 'ACME'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Algorithms for Calculating Microarray Enrichment
type: Class
subclass of: ObsoleteClass
term replaced by: Algorithms for Calculating Microarray Enrichment
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Affymetrix Expression Console
type: Class
subclass of: ObsoleteClass
term replaced by: Affymetrix Expression Console
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete AIDA
type: Class
subclass of: ObsoleteClass
term replaced by: AIDA
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Average log expression across arrays (ALE)
type: Class
subclass of: ObsoleteClass
term replaced by: Average log expression across arrays (ALE)
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ALL/AML data set
type: Class
subclass of: ObsoleteClass
term replaced by: ALL/AML data set
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete AMDIS
type: Class
subclass of: ObsoleteClass
term replaced by: AMDIS
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ANCOVA
type: Class
subclass of: ObsoleteClass
term replaced by: ANCOVA
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'ANOVA'
type: Class
subclass of: ObsoleteClass
term replaced by: 'ANOVA'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete AP-MS data
type: Class
subclass of: ObsoleteClass
term replaced by: AP-MS data
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ARACNE algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: ARACNE algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ARR
type: Class
subclass of: ObsoleteClass
term replaced by: ARR
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete AWS algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: AWS algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Absolute Expression Analysis
type: Class
subclass of: ObsoleteClass
term replaced by: Absolute Expression Analysis
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Absolute Expression Analysis
type: Class
subclass of: ObsoleteClass
term replaced by: Absolute Expression Analysis
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'AffyCompatible'
type: Class
subclass of: ObsoleteClass
term replaced by: 'AffyCompatible'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'AffyExpress'
type: Class
subclass of: ObsoleteClass
term replaced by: 'AffyExpress'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Affymetrix GCOS v1.2
type: Class
subclass of: ObsoleteClass
term replaced by: Affymetrix GCOS v1.2
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Affymetrix GeneChip Operating Software
type: Class
subclass of: ObsoleteClass
term replaced by: Affymetrix GeneChip Operating Software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Affymetrix Software
type: Class
subclass of: ObsoleteClass
term replaced by: Affymetrix Software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Agi4x44PreProcess
type: Class
subclass of: ObsoleteClass
term replaced by: Agi4x44PreProcess
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Agilent Feature Extraction 5.1.1
type: Class
subclass of: ObsoleteClass
term replaced by: Agilent Feature Extraction 5.1.1
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Agilent Feature Extraction software version 7.1
type: Class
subclass of: ObsoleteClass
term replaced by: Agilent Feature Extraction software version 7.1
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Agilent Feature Extraction software version 7.5
type: Class
subclass of: ObsoleteClass
term replaced by: Agilent Feature Extraction software version 7.5
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Agilent Feature Extraction software version A.5.1.1
type: Class
subclass of: ObsoleteClass
term replaced by: Agilent Feature Extraction software version A.5.1.1
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Agilent Scan Control
type: Class
subclass of: ObsoleteClass
term replaced by: Agilent Scan Control
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Agilent Technologies Software
type: Class
subclass of: ObsoleteClass
term replaced by: Agilent Technologies Software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'AnnotationDbi'
type: Class
subclass of: ObsoleteClass
term replaced by: 'AnnotationDbi'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Applied Biosystems 1700 Expression Array System Software
type: Class
subclass of: ObsoleteClass
term replaced by: Applied Biosystems 1700 Expression Array System Software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ArrayGauge
type: Class
subclass of: ObsoleteClass
term replaced by: ArrayGauge
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ArrayNorm
type: Class
subclass of: ObsoleteClass
term replaced by: ArrayNorm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'ArrayTools'
type: Class
subclass of: ObsoleteClass
term replaced by: 'ArrayTools'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ArrayVision
type: Class
subclass of: ObsoleteClass
term replaced by: ArrayVision
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ArrayVision 6.0 (Imaging Research Inc.)
type: Class
subclass of: ObsoleteClass
term replaced by: ArrayVision 6.0 (Imaging Research Inc.)
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Array_vision_(Interfocus)
type: Class
subclass of: ObsoleteClass
term replaced by: Array_vision_(Interfocus)
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete AtlasImage
type: Class
subclass of: ObsoleteClass
term replaced by: has download location
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Axon GenePix Pro 3
type: Class
subclass of: ObsoleteClass
term replaced by: Axon GenePix Pro 3
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete BAC
type: Class
subclass of: ObsoleteClass
term replaced by: BAC
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Binning clustering method
type: Class
subclass of: ObsoleteClass
term replaced by: Binning clustering method
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'BCRANK'
type: Class
subclass of: ObsoleteClass
term replaced by: 'BCRANK'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_BED format
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: After 0.4 release.
comment: Equivalence with EDAM term "BED" (format_3003).
deprecated: true

obsolete BGL
type: Class
subclass of: ObsoleteClass
term replaced by: BGL
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'BGmix'
type: Class
subclass of: ObsoleteClass
term replaced by: 'BGmix'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete BLAST
type: Class
subclass of: ObsoleteClass
term replaced by: BLAST
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Iterative Bayesian Model Averaging (BMA)
type: Class
subclass of: ObsoleteClass
term replaced by: Iterative Bayesian Model Averaging (BMA)
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Base-Pair-Distance Kernel
type: Class
subclass of: ObsoleteClass
term replaced by: Base-Pair-Distance Kernel
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete BPMAP
type: Class
subclass of: ObsoleteClass
term replaced by: BPMAP
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete BRB-ArrayTools
type: Class
subclass of: ObsoleteClass
term replaced by: BRB-ArrayTools
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'BSgenome'
type: Class
subclass of: ObsoleteClass
term replaced by: 'BSgenome'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete BZScan
type: Class
subclass of: ObsoleteClass
term replaced by: BZScan
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete BaldiLongT
type: Class
subclass of: ObsoleteClass
term replaced by: BaldiLongT
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete BasReader 3.01
type: Class
subclass of: ObsoleteClass
term replaced by: BasReader 3.01
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Bayesian Model
type: Class
subclass of: ObsoleteClass
term replaced by: Bayesian Model
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Beadstudio
type: Class
subclass of: ObsoleteClass
term replaced by: Beadstudio
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'BicARE'
type: Class
subclass of: ObsoleteClass
term replaced by: 'BicARE'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'BioMVCClass'
type: Class
subclass of: ObsoleteClass
term replaced by: 'BioMVCClass'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'Biobase'
type: Class
subclass of: ObsoleteClass
term replaced by: 'Biobase'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'BiocCaseStudies'
type: Class
subclass of: ObsoleteClass
term replaced by: 'BiocCaseStudies'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete BioConductor Software
type: Class
subclass of: ObsoleteClass
term replaced by: BioConductor Software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'Biostrings'
type: Class
subclass of: ObsoleteClass
term replaced by: 'Biostrings'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete BlueFuse
type: Class
subclass of: ObsoleteClass
term replaced by: BlueFuse
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'BufferedMatrix'
type: Class
subclass of: ObsoleteClass
term replaced by: 'BufferedMatrix'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'BufferedMatrixMethods'
type: Class
subclass of: ObsoleteClass
term replaced by: 'BufferedMatrixMethods'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'CALIB'
type: Class
subclass of: ObsoleteClass
term replaced by: 'CALIB'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'CAMERA'
type: Class
subclass of: ObsoleteClass
term replaced by: 'CAMERA'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete CBS
type: Class
subclass of: ObsoleteClass
term replaced by: is version of
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete CBS algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: uses software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete CDF binary format
type: Class
subclass of: ObsoleteClass
term replaced by: CDF binary format
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete CEL binary format
type: Class
subclass of: ObsoleteClass
term replaced by: CEL binary format
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'CGHbase'
type: Class
subclass of: ObsoleteClass
term replaced by: is implemented by
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'CGHcall'
type: Class
subclass of: ObsoleteClass
term replaced by: has specified data input
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'CGHregions'
type: Class
subclass of: ObsoleteClass
term replaced by: has specified data output
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete CHP binary format
type: Class
subclass of: ObsoleteClass
term replaced by: is specified data input of
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete CLR algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: is specified data output of
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'CMA'
type: Class
subclass of: ObsoleteClass
term replaced by: 'CMA'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete CMA
type: Class
subclass of: ObsoleteClass
term replaced by: CMA
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'CORREP'
type: Class
subclass of: ObsoleteClass
term replaced by: 'CORREP'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete CRLMM algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: CRLMM algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Continuous Wavelet Transform (CWT)-based peak detection algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Continuous Wavelet Transform (CWT)-based peak detection algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete CARMAweb
type: Class
subclass of: ObsoleteClass
term replaced by: CARMAweb
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Category analysis
type: Class
subclass of: ObsoleteClass
term replaced by: Category analysis
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Category
type: Class
subclass of: ObsoleteClass
term replaced by: Category
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'ChemmineR'
type: Class
subclass of: ObsoleteClass
term replaced by: 'ChemmineR'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ChipReader 3.1
type: Class
subclass of: ObsoleteClass
term replaced by: ChipReader 3.1
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ChipSkipper
type: Class
subclass of: ObsoleteClass
term replaced by: ChipSkipper
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ChipSkipper V0.99
type: Class
subclass of: ObsoleteClass
term replaced by: ChipSkipper V0.99
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete multiscan
type: Class
subclass of: ObsoleteClass
term replaced by: multiscan
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete affy
type: Class
subclass of: ObsoleteClass
term replaced by: affy
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete affycomp
type: Class
subclass of: ObsoleteClass
term replaced by: affycomp
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete PCMG
type: Class
subclass of: ObsoleteClass
term replaced by: PCMG
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Feature Extraction Software
type: Class
subclass of: ObsoleteClass
term replaced by: Feature Extraction Software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Chi-square
type: Class
subclass of: ObsoleteClass
term replaced by: Chi-square
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Annotation-Driven Clustering
type: Class
subclass of: ObsoleteClass
term replaced by: Annotation-Driven Clustering
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete distance calculation
type: Class
subclass of: ObsoleteClass
term replaced by: distance calculation
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete R software
type: Class
subclass of: ObsoleteClass
term replaced by: R software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete BCRANK
type: Class
subclass of: ObsoleteClass
term replaced by: BCRANK
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Cosmo
type: Class
subclass of: ObsoleteClass
term replaced by: Cosmo
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete F test
type: Class
subclass of: ObsoleteClass
term replaced by: F test
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MAGE-TAB inputting software
type: Class
subclass of: ObsoleteClass
term replaced by: MAGE-TAB inputting software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Text data set
type: Class
subclass of: ObsoleteClass
term replaced by: Text data set
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete CSV data set
type: Class
subclass of: ObsoleteClass
term replaced by: CSV data set
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Non-linear functional regression model
type: Class
subclass of: ObsoleteClass
term replaced by: Non-linear functional regression model
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'CoCiteStats'
type: Class
subclass of: ObsoleteClass
term replaced by: 'CoCiteStats'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete CodeLink Expression Analysis Software
type: Class
subclass of: ObsoleteClass
term replaced by: CodeLink Expression Analysis Software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete CodeLink Expression Scanning Software
type: Class
subclass of: ObsoleteClass
term replaced by: CodeLink Expression Scanning Software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Complex Estimation Algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Complex Estimation Algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Cyber-T
type: Class
subclass of: ObsoleteClass
term replaced by: Cyber-T
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'DEDS'
type: Class
subclass of: ObsoleteClass
term replaced by: 'DEDS'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'DFP'
type: Class
subclass of: ObsoleteClass
term replaced by: 'DFP'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Discriminant Fuzzy Pattern Algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Discriminant Fuzzy Pattern Algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete DFW
type: Class
subclass of: ObsoleteClass
term replaced by: DFW
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Digital gene expression (DGE) datasets
type: Class
subclass of: ObsoleteClass
term replaced by: Digital gene expression (DGE) datasets
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'DNAcopy'
type: Class
subclass of: ObsoleteClass
term replaced by: 'DNAcopy'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'DynDoc'
type: Class
subclass of: ObsoleteClass
term replaced by: directly followed by
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'EBImage'
type: Class
subclass of: ObsoleteClass
term replaced by: 'EBImage'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'EBarrays'
type: Class
subclass of: ObsoleteClass
term replaced by: 'EBarrays'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Expectation-Maximization(EM) algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Expectation-Maximization(EM) algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Empirical Bayes rule
type: Class
subclass of: ObsoleteClass
term replaced by: Empirical Bayes rule
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Expert 2100
type: Class
subclass of: ObsoleteClass
term replaced by: Expert 2100
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_FACS ( fluorescence-activated cell sorter)
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: 0.5
comment: This class had no definition, and seemed incorrectly placed as an algorithm, as from its name it seemed to only be an experimental method.
deprecated: true

obsolete FACS data
type: Class
subclass of: ObsoleteClass
term replaced by: FACS data
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete FARMS
type: Class
subclass of: ObsoleteClass
term replaced by: FARMS
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_FASTA
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: Obsoleted after the 0.4 release.
comment: Equivalence with EDAM term format_1929. Please use this term instead.
deprecated: true

obsolete FC
type: Class
subclass of: ObsoleteClass
term replaced by: FC
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_FCS
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister
obsoleted in version: 0.5
comment: Obsoleted as it was a generic term where there was no way of knowing for sure which format it was - or which version the format was in. Perhaps could have been annotated and moved, but this class was only identified after a new class (http://www.ebi.ac.uk/swo/data/SWO_3000061) had been created. Please use the new class (SWO_3000061) or its versioned children instead of this obsolete class.
deprecated: true

obsolete 'FDR'
type: Class
subclass of: ObsoleteClass
term replaced by: 'FDR'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Fixed effect model
type: Class
subclass of: ObsoleteClass
term replaced by: Fixed effect model
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Agilent Feature Extraction Software
type: Class
subclass of: ObsoleteClass
term replaced by: Agilent Feature Extraction Software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Firth's bias reduction procedure
type: Class
subclass of: ObsoleteClass
term replaced by: Firth's bias reduction procedure
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Fischer's Exact Test
type: Class
subclass of: ObsoleteClass
term replaced by: Fischer's Exact Test
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete FoxDimmicT
type: Class
subclass of: ObsoleteClass
term replaced by: uses platform
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GACK
type: Class
subclass of: ObsoleteClass
term replaced by: GACK
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GASSCO method
type: Class
subclass of: ObsoleteClass
term replaced by: GASSCO method
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GC-RMA Quantification
type: Class
subclass of: ObsoleteClass
term replaced by: GC-RMA Quantification
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GEMTools 2.4
type: Class
subclass of: ObsoleteClass
term replaced by: GEMTools 2.4
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GEO data type
type: Class
subclass of: ObsoleteClass
term replaced by: GEO data type
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GEO Matrix Series format
type: Class
subclass of: ObsoleteClass
term replaced by: is software for
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GEOmetadb
type: Class
subclass of: ObsoleteClass
term replaced by: GEOmetadb
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GEOquery
type: Class
subclass of: ObsoleteClass
term replaced by: GEOquery
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GGBase
type: Class
subclass of: ObsoleteClass
term replaced by: GGBase
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Gamma Gamma Model
type: Class
subclass of: ObsoleteClass
term replaced by: Gamma Gamma Model
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GGtools
type: Class
subclass of: ObsoleteClass
term replaced by: GGtools
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GLAD
type: Class
subclass of: ObsoleteClass
term replaced by: GLAD
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)
type: Class
subclass of: ObsoleteClass
term replaced by: Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GLEAMS software
type: Class
subclass of: ObsoleteClass
term replaced by: GLEAMS software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GMS
type: Class
subclass of: ObsoleteClass
term replaced by: GMS
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GOstats
type: Class
subclass of: ObsoleteClass
term replaced by: GOstats
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Gene Recommender algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Gene Recommender algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GSEABase
type: Class
subclass of: ObsoleteClass
term replaced by: GSEABase
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GSEAlm
type: Class
subclass of: ObsoleteClass
term replaced by: GSEAlm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Gamma-Gamma hierarchical model
type: Class
subclass of: ObsoleteClass
term replaced by: Gamma-Gamma hierarchical model
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Gaussian locally weighted regression
type: Class
subclass of: ObsoleteClass
term replaced by: Gaussian locally weighted regression
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Gene-Set Enrichment Analysis
type: Class
subclass of: ObsoleteClass
term replaced by: Gene-Set Enrichment Analysis
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GeneData Expressionist Analyst v4.0.5
type: Class
subclass of: ObsoleteClass
term replaced by: GeneData Expressionist Analyst v4.0.5
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Gene Pix
type: Class
subclass of: ObsoleteClass
term replaced by: Gene Pix
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GenePix 3.0.6
type: Class
subclass of: ObsoleteClass
term replaced by: GenePix 3.0.6
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GenePix 4.1
type: Class
subclass of: ObsoleteClass
term replaced by: GenePix 4.1
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GenePix 4100A
type: Class
subclass of: ObsoleteClass
term replaced by: GenePix 4100A
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GenePix 5.0.1
type: Class
subclass of: ObsoleteClass
term replaced by: GenePix 5.0.1
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GenePix
type: Class
subclass of: ObsoleteClass
term replaced by: GenePix
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GenePix Pro
type: Class
subclass of: ObsoleteClass
term replaced by: GenePix Pro
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GenePix Pro 3
type: Class
subclass of: ObsoleteClass
term replaced by: GenePix Pro 3
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GenePix Pro 5.0
type: Class
subclass of: ObsoleteClass
term replaced by: GenePix Pro 5.0
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GenePix Pro 6.0
type: Class
subclass of: ObsoleteClass
term replaced by: GenePix Pro 6.0
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GenePix Pro 6 [Axon Instruments]
type: Class
subclass of: ObsoleteClass
term replaced by: GenePix Pro 6 [Axon Instruments]
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GenePix Pro [Axon Instruments]
type: Class
subclass of: ObsoleteClass
term replaced by: GenePix Pro [Axon Instruments]
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GeneR
type: Class
subclass of: ObsoleteClass
term replaced by: GeneR
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GeneRegionScan
type: Class
subclass of: ObsoleteClass
term replaced by: GeneRegionScan
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GeneRfold
type: Class
subclass of: ObsoleteClass
term replaced by: GeneRfold
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GeneSelectMMD
type: Class
subclass of: ObsoleteClass
term replaced by: GeneSelectMMD
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GeneSelector
type: Class
subclass of: ObsoleteClass
term replaced by: GeneSelector
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GeneSpring
type: Class
subclass of: ObsoleteClass
term replaced by: GeneSpring
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GeneSpringGX
type: Class
subclass of: ObsoleteClass
term replaced by: GeneSpringGX
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GeneTac Analyser
type: Class
subclass of: ObsoleteClass
term replaced by: GeneTac Analyser
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GeneTraffic
type: Class
subclass of: ObsoleteClass
term replaced by: GeneTraffic
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GenePix Pro 4.0
type: Class
subclass of: ObsoleteClass
term replaced by: GenePix Pro 4.0
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GenePix Pro 3.0
type: Class
subclass of: ObsoleteClass
term replaced by: GenePix Pro 3.0
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GeneticsBase
type: Class
subclass of: ObsoleteClass
term replaced by: GeneticsBase
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GeneticsDesign
type: Class
subclass of: ObsoleteClass
term replaced by: GeneticsDesign
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GeneticsPed
type: Class
subclass of: ObsoleteClass
term replaced by: GeneticsPed
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GenomeGraphs
type: Class
subclass of: ObsoleteClass
term replaced by: GenomeGraphs
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GlobalAncova
type: Class
subclass of: ObsoleteClass
term replaced by: GlobalAncova
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GOSemSim
type: Class
subclass of: ObsoleteClass
term replaced by: GOSemSim
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GraphAT
type: Class
subclass of: ObsoleteClass
term replaced by: GraphAT
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GraphAlignment
type: Class
subclass of: ObsoleteClass
term replaced by: GraphAlignment
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete GridGrinder
type: Class
subclass of: ObsoleteClass
term replaced by: GridGrinder
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Hexagon binning algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Hexagon binning algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete HELP
type: Class
subclass of: ObsoleteClass
term replaced by: HELP
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete HEM
type: Class
subclass of: ObsoleteClass
term replaced by: HEM
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Heterogeneous Error Model (HEM)
type: Class
subclass of: ObsoleteClass
term replaced by: Heterogeneous Error Model (HEM)
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Hubert’s gamma
type: Class
subclass of: ObsoleteClass
term replaced by: Hubert’s gamma
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Hidden Markov Model
type: Class
subclass of: ObsoleteClass
term replaced by: Hidden Markov Model
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Hidden Variable Dynamic Modelling HVDM)
type: Class
subclass of: ObsoleteClass
term replaced by: Hidden Variable Dynamic Modelling HVDM)
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete HaarSeg algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: HaarSeg algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Hardy-Weinberg equilibrium
type: Class
subclass of: ObsoleteClass
term replaced by: Hardy-Weinberg equilibrium
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Harshlight
type: Class
subclass of: ObsoleteClass
term replaced by: Harshlight
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Heatplus
type: Class
subclass of: ObsoleteClass
term replaced by: Heatplus
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete HilbertVis
type: Class
subclass of: ObsoleteClass
term replaced by: HilbertVis
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete HilbertVisGUI
type: Class
subclass of: ObsoleteClass
term replaced by: HilbertVisGUI
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Hypergeometric probability
type: Class
subclass of: ObsoleteClass
term replaced by: Hypergeometric probability
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ICS-501 (version 2.3) Image Capture System
type: Class
subclass of: ObsoleteClass
term replaced by: ICS-501 (version 2.3) Image Capture System
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Iteratively ReWeighted Least Squares
type: Class
subclass of: ObsoleteClass
term replaced by: Iteratively ReWeighted Least Squares
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete IRanges
type: Class
subclass of: ObsoleteClass
term replaced by: IRanges
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ITALICS
type: Class
subclass of: ObsoleteClass
term replaced by: ITALICS
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ILLUMINA data
type: Class
subclass of: ObsoleteClass
term replaced by: ILLUMINA data
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ImaGene4.1 software
type: Class
subclass of: ObsoleteClass
term replaced by: ImaGene4.1 software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ImaGene 3.0
type: Class
subclass of: ObsoleteClass
term replaced by: ImaGene 3.0
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ImageQuant
type: Class
subclass of: ObsoleteClass
term replaced by: ImageQuant
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ImageReader
type: Class
subclass of: ObsoleteClass
term replaced by: ImageReader
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ImaGene
type: Class
subclass of: ObsoleteClass
term replaced by: ImaGene
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Imagene v4.0
type: Class
subclass of: ObsoleteClass
term replaced by: Imagene v4.0
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Initial microarray data processing (data filtering, local normalisation and quality control)
type: Class
subclass of: ObsoleteClass
term replaced by: Initial microarray data processing (data filtering, local normalisation and quality control)
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Jaccard’s index
type: Class
subclass of: ObsoleteClass
term replaced by: Jaccard’s index
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Jaguar
type: Class
subclass of: ObsoleteClass
term replaced by: Jaguar
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete KCsmart
type: Class
subclass of: ObsoleteClass
term replaced by: KCsmart
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete KEGGSOAP
type: Class
subclass of: ObsoleteClass
term replaced by: KEGGSOAP
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete KEGGgraph
type: Class
subclass of: ObsoleteClass
term replaced by: KEGGgraph
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete KGML
type: Class
subclass of: ObsoleteClass
term replaced by: KGML
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'KLD'
type: Class
subclass of: ObsoleteClass
term replaced by: 'KLD'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Kolmogorov Smirnov rank-sum based algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Kolmogorov Smirnov rank-sum based algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete LBE
type: Class
subclass of: ObsoleteClass
term replaced by: LBE
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete LC-MS data
type: Class
subclass of: ObsoleteClass
term replaced by: LC-MS data
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete LMGene
type: Class
subclass of: ObsoleteClass
term replaced by: LMGene
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Locally Moderated Weighted-t (LMW) method
type: Class
subclass of: ObsoleteClass
term replaced by: Locally Moderated Weighted-t (LMW) method
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Lognormal Normal Model
type: Class
subclass of: ObsoleteClass
term replaced by: Lognormal Normal Model
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Lognormal Normal with Modied Variance Model
type: Class
subclass of: ObsoleteClass
term replaced by: Lognormal Normal with Modied Variance Model
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete LPE
type: Class
subclass of: ObsoleteClass
term replaced by: LPE
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete LPEadj
type: Class
subclass of: ObsoleteClass
term replaced by: LPEadj
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete publisher role
type: Class
subclass of: ObsoleteClass
term replaced by: publisher role
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Langmuir Isotherm
type: Class
subclass of: ObsoleteClass
term replaced by: Langmuir Isotherm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Laplace mixture model
type: Class
subclass of: ObsoleteClass
term replaced by: Laplace mixture model
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Library Search Algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Library Search Algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Loess algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Loess algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Logic regression
type: Class
subclass of: ObsoleteClass
term replaced by: Logic regression
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MAANOVA v1.2 package for MATLAB
type: Class
subclass of: ObsoleteClass
term replaced by: MAANOVA v1.2 package for MATLAB
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Median Average Difference Algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Median Average Difference Algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_MAGE-ML
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: Obsoleted after the 0.4 release.
comment: Equivalence with EDAM format_3161.
deprecated: true

obsolete MANOR
type: Class
subclass of: ObsoleteClass
term replaced by: MANOR
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MAQC data
type: Class
subclass of: ObsoleteClass
term replaced by: MAQC data
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MIcroarray Analysis Suite
type: Class
subclass of: ObsoleteClass
term replaced by: MIcroarray Analysis Suite
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MicroArraySuite 5.0
type: Class
subclass of: ObsoleteClass
term replaced by: MicroArraySuite 5.0
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MATLAB language
type: Class
subclass of: ObsoleteClass
term replaced by: MATLAB language
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MAVI Pro
type: Class
subclass of: ObsoleteClass
term replaced by: MAVI Pro
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Multivariate correlation estimator
type: Class
subclass of: ObsoleteClass
term replaced by: Multivariate correlation estimator
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Markov Chain Monte Carlo
type: Class
subclass of: ObsoleteClass
term replaced by: Markov Chain Monte Carlo
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MCR algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: MCR algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MCRestimate
type: Class
subclass of: ObsoleteClass
term replaced by: MCRestimate
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MEDME
type: Class
subclass of: ObsoleteClass
term replaced by: MEDME
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'MI'
type: Class
subclass of: ObsoleteClass
term replaced by: 'MI'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Mutual information matrix (MIM)
type: Class
subclass of: ObsoleteClass
term replaced by: Mutual information matrix (MIM)
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MLInterfaces
type: Class
subclass of: ObsoleteClass
term replaced by: MLInterfaces
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MMD
type: Class
subclass of: ObsoleteClass
term replaced by: MMD
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MVCClass
type: Class
subclass of: ObsoleteClass
term replaced by: MVCClass
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Mahalanobis distance
type: Class
subclass of: ObsoleteClass
term replaced by: Mahalanobis distance
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MantelCorr
type: Class
subclass of: ObsoleteClass
term replaced by: MantelCorr
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MassSpecWavelet
type: Class
subclass of: ObsoleteClass
term replaced by: MassSpecWavelet
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MeasurementError.cor
type: Class
subclass of: ObsoleteClass
term replaced by: MeasurementError.cor
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MergeMaid
type: Class
subclass of: ObsoleteClass
term replaced by: MergeMaid
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Mfuzz
type: Class
subclass of: ObsoleteClass
term replaced by: Mfuzz
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MiPP
type: Class
subclass of: ObsoleteClass
term replaced by: MiPP
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Misclassification-Penalized Posteriors (MiPP)
type: Class
subclass of: ObsoleteClass
term replaced by: Misclassification-Penalized Posteriors (MiPP)
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete MicroArraySuite 4.0
type: Class
subclass of: ObsoleteClass
term replaced by: MicroArraySuite 4.0
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Mixed model equations
type: Class
subclass of: ObsoleteClass
term replaced by: Mixed model equations
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'Needleman-Wunsch'
type: Class
subclass of: ObsoleteClass
term replaced by: 'Needleman-Wunsch'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Nested Effects Models
type: Class
subclass of: ObsoleteClass
term replaced by: Nested Effects Models
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Nonlinear Estimation by Iterative Partial Least Squares
type: Class
subclass of: ObsoleteClass
term replaced by: Nonlinear Estimation by Iterative Partial Least Squares
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete OCplus
type: Class
subclass of: ObsoleteClass
term replaced by: OCplus
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete OLIN
type: Class
subclass of: ObsoleteClass
term replaced by: OLIN
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete OLINgui
type: Class
subclass of: ObsoleteClass
term replaced by: OLINgui
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Optiquant
type: Class
subclass of: ObsoleteClass
term replaced by: Optiquant
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete OrderedList
type: Class
subclass of: ObsoleteClass
term replaced by: OrderedList
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete OutlierD
type: Class
subclass of: ObsoleteClass
term replaced by: OutlierD
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Presence-Absence calls with Negative Probesets (PANP)
type: Class
subclass of: ObsoleteClass
term replaced by: Presence-Absence calls with Negative Probesets (PANP)
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete PAnnBuilder
type: Class
subclass of: ObsoleteClass
term replaced by: PAnnBuilder
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Pearson correlation estimator
type: Class
subclass of: ObsoleteClass
term replaced by: Pearson correlation estimator
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete PCpheno
type: Class
subclass of: ObsoleteClass
term replaced by: PCpheno
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete PGSEA
type: Class
subclass of: ObsoleteClass
term replaced by: PGSEA
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'PLM'
type: Class
subclass of: ObsoleteClass
term replaced by: 'PLM'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete PLPE
type: Class
subclass of: ObsoleteClass
term replaced by: PLPE
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Probe level Locally moderated Weighted median-t (PLW) method
type: Class
subclass of: ObsoleteClass
term replaced by: Probe level Locally moderated Weighted median-t (PLW) method
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete PPC algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: PPC algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete PROcess
type: Class
subclass of: ObsoleteClass
term replaced by: PROcess
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Propagation of uncertainty in microarray analysis
type: Class
subclass of: ObsoleteClass
term replaced by: Propagation of uncertainty in microarray analysis
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Pathways 2.01 software
type: Class
subclass of: ObsoleteClass
term replaced by: Pathways 2.01 software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Power Law Global Error Model (PLGEM) analysis method
type: Class
subclass of: ObsoleteClass
term replaced by: Power Law Global Error Model (PLGEM) analysis method
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Probe Cell Analysis
type: Class
subclass of: ObsoleteClass
term replaced by: Probe Cell Analysis
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete PLIER (Probe Logarithmic Error Intensity Estimate) method
type: Class
subclass of: ObsoleteClass
term replaced by: PLIER (Probe Logarithmic Error Intensity Estimate) method
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete QuantArray scanner software
type: Class
subclass of: ObsoleteClass
term replaced by: QuantArray scanner software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete QuantArray, PackaardBiochip technologies
type: Class
subclass of: ObsoleteClass
term replaced by: QuantArray, PackaardBiochip technologies
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete QuantArray version 2
type: Class
subclass of: ObsoleteClass
term replaced by: QuantArray version 2
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Radial basis function
type: Class
subclass of: ObsoleteClass
term replaced by: Radial basis function
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RBGL
type: Class
subclass of: ObsoleteClass
term replaced by: RBGL
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete R interface to boost graph library algorithm (RBGL)
type: Class
subclass of: ObsoleteClass
term replaced by: R interface to boost graph library algorithm (RBGL)
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RBioinf
type: Class
subclass of: ObsoleteClass
term replaced by: RBioinf
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Random effects model
type: Class
subclass of: ObsoleteClass
term replaced by: Random effects model
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Recursive Feature Elimination (RFE)
type: Class
subclass of: ObsoleteClass
term replaced by: Recursive Feature Elimination (RFE)
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RLMM
type: Class
subclass of: ObsoleteClass
term replaced by: RLMM
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Regression model
type: Class
subclass of: ObsoleteClass
term replaced by: Regression model
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RMA
type: Class
subclass of: ObsoleteClass
term replaced by: RMA
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RMA+
type: Class
subclass of: ObsoleteClass
term replaced by: RMA+
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RMA++
type: Class
subclass of: ObsoleteClass
term replaced by: RMA++
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RMAExpress
type: Class
subclass of: ObsoleteClass
term replaced by: RMAExpress
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RMAExpress 2.0
type: Class
subclass of: ObsoleteClass
term replaced by: RMAExpress 2.0
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RMAExpress quantification
type: Class
subclass of: ObsoleteClass
term replaced by: RMAExpress quantification
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RMAGEML
type: Class
subclass of: ObsoleteClass
term replaced by: RMAGEML
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RNAither
type: Class
subclass of: ObsoleteClass
term replaced by: RNAither
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ROC
type: Class
subclass of: ObsoleteClass
term replaced by: ROC
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RWebServices
type: Class
subclass of: ObsoleteClass
term replaced by: RWebServices
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RankProd
type: Class
subclass of: ObsoleteClass
term replaced by: RankProd
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RbcBook1
type: Class
subclass of: ObsoleteClass
term replaced by: RbcBook1
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Rdbi
type: Class
subclass of: ObsoleteClass
term replaced by: Rdbi
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RdbiPgSQL
type: Class
subclass of: ObsoleteClass
term replaced by: RdbiPgSQL
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Rdisop
type: Class
subclass of: ObsoleteClass
term replaced by: Rdisop
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RefPlus
type: Class
subclass of: ObsoleteClass
term replaced by: RefPlus
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Resourcerer
type: Class
subclass of: ObsoleteClass
term replaced by: Resourcerer
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Rgraphviz
type: Class
subclass of: ObsoleteClass
term replaced by: Rgraphviz
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Ringo
type: Class
subclass of: ObsoleteClass
term replaced by: Ringo
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Rintact
type: Class
subclass of: ObsoleteClass
term replaced by: Rintact
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Rmagpie
type: Class
subclass of: ObsoleteClass
term replaced by: Rmagpie
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Rnw
type: Class
subclass of: ObsoleteClass
term replaced by: Rnw
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Robust likelihood-based survival modeling
type: Class
subclass of: ObsoleteClass
term replaced by: Robust likelihood-based survival modeling
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Rosetta Resolver
type: Class
subclass of: ObsoleteClass
term replaced by: Rosetta Resolver
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete RpsiXML
type: Class
subclass of: ObsoleteClass
term replaced by: RpsiXML
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Rredland
type: Class
subclass of: ObsoleteClass
term replaced by: Rredland
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Rtreemix
type: Class
subclass of: ObsoleteClass
term replaced by: Rtreemix
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Ruuid
type: Class
subclass of: ObsoleteClass
term replaced by: Ruuid
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete S-Score algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: S-Score algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Serial Analysis of Gene Expression (SAGE)
type: Class
subclass of: ObsoleteClass
term replaced by: Serial Analysis of Gene Expression (SAGE)
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete SAGx
type: Class
subclass of: ObsoleteClass
term replaced by: SAGx
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete SAM
type: Class
subclass of: ObsoleteClass
term replaced by: SAM
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete SAS/STAT Software, Version 8
type: Class
subclass of: ObsoleteClass
term replaced by: SAS/STAT Software, Version 8
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete SBMLR
type: Class
subclass of: ObsoleteClass
term replaced by: SBMLR
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete SBMLR format
type: Class
subclass of: ObsoleteClass
term replaced by: SBMLR format
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_SBML file
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister
obsoleted in version: 0.4
comment: Identical to http://www.ebi.ac.uk/swo/data/SWO_3000037
deprecated: true

obsolete_SBML model
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: 0.5
comment: 'SBML model' was classed as a child of algorithm, when this clearly isn't the case. As SWO already contained 'SBML file' (to cover the data format itself), there was no need for this class at all. The one class (SBMLR) which referenced this class had the relevant axiom deleted. For referencing the SBML format, please use the class 'SBML file'.
deprecated: true

obsolete SDF format
type: Class
subclass of: ObsoleteClass
term replaced by: SDF format
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete SIM
type: Class
subclass of: ObsoleteClass
term replaced by: SIM
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete SLGI
type: Class
subclass of: ObsoleteClass
term replaced by: SLGI
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete SLqPCR
type: Class
subclass of: ObsoleteClass
term replaced by: SLqPCR
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete SMAP
type: Class
subclass of: ObsoleteClass
term replaced by: SMAP
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete SNPRMA algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: SNPRMA algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete SNPchip
type: Class
subclass of: ObsoleteClass
term replaced by: SNPchip
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete SPIA
type: Class
subclass of: ObsoleteClass
term replaced by: SPIA
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Semantic Similarity Measures
type: Class
subclass of: ObsoleteClass
term replaced by: Semantic Similarity Measures
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete SSPA
type: Class
subclass of: ObsoleteClass
term replaced by: SSPA
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete SVDimpute algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: SVDimpute algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete software developer role
type: Class
subclass of: ObsoleteClass
term replaced by: software developer role
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_Information processing
type: Class
subclass of: ObsoleteClass
definition: Information processing is a process in which input information is analysed or transformed in order to produce information as output.
definition source: James Malone
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: 0.4
comment: Present both in the original file (SWO_0000393) and in the core file (SWO_0000003), and each have different identifiers. SWO_0000393 was initially created within the originalsoftwareontology.owl and later moved to swo_core.owl. SWO_0000003 was retained and SWO_0000393 deemed obsolete. Please use SWO_0000003 instead.
deprecated: true

obsolete software developer organization
type: Class
subclass of: ObsoleteClass
term replaced by: software developer organization
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete software publisher organization
type: Class
subclass of: ObsoleteClass
term replaced by: software publisher organization
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 50-50 MANOVA algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: 50-50 MANOVA algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_html
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: 0.4
comment: There is one EDAM html class (EDAM_format:2331) and one SWO class (SWO_0000399) within swo_data.owl. EDAM_format:2331 was retained and SWO_0000399 deemed obsolete, as EDAM_format:2331 has a better location in the hierarchy and is an imported term. All axioms belonging to SWO_0000399 were transferred to EDAM_format:2331. Please use EDAM_format:2331 (in this ontology via its full URI http://edamontology.org/format_2331) instead.
deprecated: true

obsolete ArrayExpress Bioconductor
type: Class
subclass of: ObsoleteClass
term replaced by: ArrayExpress Bioconductor
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Gene list
type: Class
subclass of: ObsoleteClass
term replaced by: Gene list
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Clustered data set
type: Class
subclass of: ObsoleteClass
term replaced by: Clustered data set
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete R data frame
type: Class
subclass of: ObsoleteClass
term replaced by: R data frame
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete R language
type: Class
subclass of: ObsoleteClass
term replaced by: R language
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ScISI
type: Class
subclass of: ObsoleteClass
term replaced by: ScISI
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ScanAlyze
type: Class
subclass of: ObsoleteClass
term replaced by: ScanAlyze
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ScanArray
type: Class
subclass of: ObsoleteClass
term replaced by: ScanArray
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ScanArray v3.1 software
type: Class
subclass of: ObsoleteClass
term replaced by: ScanArray v3.1 software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete scanning software
type: Class
subclass of: ObsoleteClass
term replaced by: scanning software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Scanning software G2565AA version A6.3.1
type: Class
subclass of: ObsoleteClass
term replaced by: Scanning software G2565AA version A6.3.1
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ShortRead
type: Class
subclass of: ObsoleteClass
term replaced by: ShortRead
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Signaling Pathway Impact Analysis (SPIA) algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Signaling Pathway Impact Analysis (SPIA) algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Silicon Genetics Genespring
type: Class
subclass of: ObsoleteClass
term replaced by: Silicon Genetics Genespring
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Similarity score
type: Class
subclass of: ObsoleteClass
term replaced by: Similarity score
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'Smith-Waterman'
type: Class
subclass of: ObsoleteClass
term replaced by: 'Smith-Waterman'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Spot quantification
type: Class
subclass of: ObsoleteClass
term replaced by: Spot quantification
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Spotfinder [TIGR]
type: Class
subclass of: ObsoleteClass
term replaced by: Spotfinder [TIGR]
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Spotfire
type: Class
subclass of: ObsoleteClass
term replaced by: Spotfire
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete TAS Software
type: Class
subclass of: ObsoleteClass
term replaced by: TAS Software
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_TIFF image
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: 0.4
comment: SWO_0000434 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000016, with the label 'TIFF', is also present, and stored within swo_data.owl. SWO_3000016 was retained and SWO_0000434 deemed obsolete, as SWO_3000016 has a better location in the hierarchy. All axioms belonging to SWO_0000434 were transferred to SWO_3000016. Please use SWO_3000016 instead.
deprecated: true

obsolete TargetSearch
type: Class
subclass of: ObsoleteClass
term replaced by: TargetSearch
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Theodore Ts’o’s
type: Class
subclass of: ObsoleteClass
term replaced by: Theodore Ts’o’s
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete TypeInfo
type: Class
subclass of: ObsoleteClass
term replaced by: TypeInfo
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Variance-stabilizing transformation (VST) algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Variance-stabilizing transformation (VST) algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete VanillaICE
type: Class
subclass of: ObsoleteClass
term replaced by: VanillaICE
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete WilcEbam
type: Class
subclass of: ObsoleteClass
term replaced by: WilcEbam
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Wilcoxon
type: Class
subclass of: ObsoleteClass
term replaced by: Wilcoxon
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete XDE
type: Class
subclass of: ObsoleteClass
term replaced by: XDE
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete XDotsReader
type: Class
subclass of: ObsoleteClass
term replaced by: XDotsReader
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_XML
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: 0.4
comment: 5. SWO_0000448 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000005 is also present within swo_data.owl. SWO_3000005 was retained and SWO_0000448 deemed obsolete, as SWO_3000005 has a better location in the hierarchy. All axioms belonging to SWO_0000448 were transferred to SWO_3000005. Please use SWO_3000005 instead.
deprecated: true

obsolete Xba.CQV and Xba.regions
type: Class
subclass of: ObsoleteClass
term replaced by: Xba.CQV and Xba.regions
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Array Comparative Genomic Hybridization
type: Class
subclass of: ObsoleteClass
term replaced by: Array Comparative Genomic Hybridization
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Acuity
type: Class
subclass of: ObsoleteClass
term replaced by: Acuity
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete affxparser
type: Class
subclass of: ObsoleteClass
term replaced by: affxparser
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete affyContam
type: Class
subclass of: ObsoleteClass
term replaced by: affyContam
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete affyImGUI
type: Class
subclass of: ObsoleteClass
term replaced by: affyImGUI
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'affyPLM'
type: Class
subclass of: ObsoleteClass
term replaced by: 'affyPLM'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete affyPara
type: Class
subclass of: ObsoleteClass
term replaced by: affyPara
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete affyQCReport
type: Class
subclass of: ObsoleteClass
term replaced by: affyQCReport
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete affyTiling
type: Class
subclass of: ObsoleteClass
term replaced by: affyTiling
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'affycoretools'
type: Class
subclass of: ObsoleteClass
term replaced by: 'affycoretools'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete affyio
type: Class
subclass of: ObsoleteClass
term replaced by: affyio
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete affypdnn
type: Class
subclass of: ObsoleteClass
term replaced by: affypdnn
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete altcdfenvs
type: Class
subclass of: ObsoleteClass
term replaced by: altcdfenvs
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete annaffy
type: Class
subclass of: ObsoleteClass
term replaced by: annaffy
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'annotate'
type: Class
subclass of: ObsoleteClass
term replaced by: 'annotate'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete data annotation
type: Class
subclass of: ObsoleteClass
term replaced by: data annotation
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete annotationTools
type: Class
subclass of: ObsoleteClass
term replaced by: annotationTools
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Annotation data packages
type: Class
subclass of: ObsoleteClass
term replaced by: Annotation data packages
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'apComplex'
type: Class
subclass of: ObsoleteClass
term replaced by: 'apComplex'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete aroma.light
type: Class
subclass of: ObsoleteClass
term replaced by: aroma.light
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete arrayMvout
type: Class
subclass of: ObsoleteClass
term replaced by: arrayMvout
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete arrayQuality
type: Class
subclass of: ObsoleteClass
term replaced by: arrayQuality
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete arrayQualityMetrics
type: Class
subclass of: ObsoleteClass
term replaced by: arrayQualityMetrics
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete arrayWoRx 2.0
type: Class
subclass of: ObsoleteClass
term replaced by: arrayWoRx 2.0
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete arrayWoRx
type: Class
subclass of: ObsoleteClass
term replaced by: arrayWoRx
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Associative T method
type: Class
subclass of: ObsoleteClass
term replaced by: Associative T method
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete AvgNRRs
type: Class
subclass of: ObsoleteClass
term replaced by: AvgNRRs
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'beadarray'
type: Class
subclass of: ObsoleteClass
term replaced by: 'beadarray'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'beadarraySNP'
type: Class
subclass of: ObsoleteClass
term replaced by: 'beadarraySNP'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'betr'
type: Class
subclass of: ObsoleteClass
term replaced by: 'betr'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete bgafun
type: Class
subclass of: ObsoleteClass
term replaced by: bgafun
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete bgx
type: Class
subclass of: ObsoleteClass
term replaced by: bgx
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Bitmap object
type: Class
subclass of: ObsoleteClass
term replaced by: Bitmap object
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete bioDist
type: Class
subclass of: ObsoleteClass
term replaced by: bioDist
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'biocDatasets'
type: Class
subclass of: ObsoleteClass
term replaced by: 'biocDatasets'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'biocGraph'
type: Class
subclass of: ObsoleteClass
term replaced by: 'biocGraph'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'biocViews'
type: Class
subclass of: ObsoleteClass
term replaced by: 'biocViews'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete biomaRT
type: Class
subclass of: ObsoleteClass
term replaced by: biomaRT
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Bootstrap
type: Class
subclass of: ObsoleteClass
term replaced by: Bootstrap
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'bridge'
type: Class
subclass of: ObsoleteClass
term replaced by: 'bridge'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete cdt
type: Class
subclass of: ObsoleteClass
term replaced by: cdt
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'cellHTS'
type: Class
subclass of: ObsoleteClass
term replaced by: 'cellHTS'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'cellHTS2'
type: Class
subclass of: ObsoleteClass
term replaced by: 'cellHTS2'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete cghMCR
type: Class
subclass of: ObsoleteClass
term replaced by: cghMCR
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete chamber slide format
type: Class
subclass of: ObsoleteClass
term replaced by: chamber slide format
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete cls
type: Class
subclass of: ObsoleteClass
term replaced by: cls
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'clusterStab'
type: Class
subclass of: ObsoleteClass
term replaced by: 'clusterStab'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_Clustering algorithm
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: 0.4
comment: The original label for this class, 'Clustering algorithm', was used in two separate class URIs. The first was SWO_0000500, initially created within the originalsoftwareontology.owl. The second URI is stored within swo_algorithms.owl and is an import from OntoDM (OntoDM_170075). As the SWO class contains no annotation beyond its label, and because OntoDM has more structure surrounding its algorithm classes, the OntoDM class was retained and the SWO class was deemed obsolete. The 6 usages of the SWO class were refactored to reference the OntoDM term and then the SWO class was marked as obsolete. Please use OntoDM_170075 instead.
deprecated: true

obsolete 'codelink'
type: Class
subclass of: ObsoleteClass
term replaced by: 'codelink'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete dataset comparison
type: Class
subclass of: ObsoleteClass
term replaced by: dataset comparison
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Concordance
type: Class
subclass of: ObsoleteClass
term replaced by: Concordance
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete convert
type: Class
subclass of: ObsoleteClass
term replaced by: convert
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete copa
type: Class
subclass of: ObsoleteClass
term replaced by: copa
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete cosmo
type: Class
subclass of: ObsoleteClass
term replaced by: cosmo
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete cosmoGUI
type: Class
subclass of: ObsoleteClass
term replaced by: cosmoGUI
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete covdesc file
type: Class
subclass of: ObsoleteClass
term replaced by: covdesc file
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete database creation
type: Class
subclass of: ObsoleteClass
term replaced by: database creation
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete crlmm
type: Class
subclass of: ObsoleteClass
term replaced by: crlmm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ctc
type: Class
subclass of: ObsoleteClass
term replaced by: ctc
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete dChip
type: Class
subclass of: ObsoleteClass
term replaced by: dChip
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete daMA
type: Class
subclass of: ObsoleteClass
term replaced by: daMA
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete .data
type: Class
subclass of: ObsoleteClass
term replaced by: .data
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete dcf
type: Class
subclass of: ObsoleteClass
term replaced by: dcf
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete design file
type: Class
subclass of: ObsoleteClass
term replaced by: design file
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'diffGeneAnalysis'
type: Class
subclass of: ObsoleteClass
term replaced by: 'diffGeneAnalysis'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'domainsignatures'
type: Class
subclass of: ObsoleteClass
term replaced by: 'domainsignatures'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'dualKS'
type: Class
subclass of: ObsoleteClass
term replaced by: 'dualKS'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete dyebias
type: Class
subclass of: ObsoleteClass
term replaced by: dyebias
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Dynamic programming algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Dynamic programming algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ecolitk
type: Class
subclass of: ObsoleteClass
term replaced by: ecolitk
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete edd
type: Class
subclass of: ObsoleteClass
term replaced by: edd
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'edgeR'
type: Class
subclass of: ObsoleteClass
term replaced by: 'edgeR'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete exonmap
type: Class
subclass of: ObsoleteClass
term replaced by: exonmap
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'explorase'
type: Class
subclass of: ObsoleteClass
term replaced by: 'explorase'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'externalVector'
type: Class
subclass of: ObsoleteClass
term replaced by: 'externalVector'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete f-test
type: Class
subclass of: ObsoleteClass
term replaced by: f-test
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete factDesign
type: Class
subclass of: ObsoleteClass
term replaced by: factDesign
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete fbat
type: Class
subclass of: ObsoleteClass
term replaced by: fbat
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete fdrame
type: Class
subclass of: ObsoleteClass
term replaced by: fdrame
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete flagme
type: Class
subclass of: ObsoleteClass
term replaced by: flagme
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete flowClust
type: Class
subclass of: ObsoleteClass
term replaced by: flowClust
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete flowCore
type: Class
subclass of: ObsoleteClass
term replaced by: flowCore
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete flowFlowJo
type: Class
subclass of: ObsoleteClass
term replaced by: flowFlowJo
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete flowQ
type: Class
subclass of: ObsoleteClass
term replaced by: flowQ
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete flowStats
type: Class
subclass of: ObsoleteClass
term replaced by: flowStats
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete flowUtils
type: Class
subclass of: ObsoleteClass
term replaced by: flowUtils
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete flowViz
type: Class
subclass of: ObsoleteClass
term replaced by: flowViz
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete gaga
type: Class
subclass of: ObsoleteClass
term replaced by: gaga
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'gaggle'
type: Class
subclass of: ObsoleteClass
term replaced by: 'gaggle'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete gcRMA quantification
type: Class
subclass of: ObsoleteClass
term replaced by: gcRMA quantification
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete gcrma
type: Class
subclass of: ObsoleteClass
term replaced by: gcrma
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete gct
type: Class
subclass of: ObsoleteClass
term replaced by: gct
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'genArise'
type: Class
subclass of: ObsoleteClass
term replaced by: 'genArise'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete gene2pathway
type: Class
subclass of: ObsoleteClass
term replaced by: gene2pathway
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete geneRecommender
type: Class
subclass of: ObsoleteClass
term replaced by: geneRecommender
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Gene array analysis algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Gene array analysis algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete gene expression analysis
type: Class
subclass of: ObsoleteClass
term replaced by: gene expression analysis
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Gene expression dataset
type: Class
subclass of: ObsoleteClass
term replaced by: Gene expression dataset
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete genefilter
type: Class
subclass of: ObsoleteClass
term replaced by: genefilter
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete genemeta
type: Class
subclass of: ObsoleteClass
term replaced by: genemeta
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete geneplotter
type: Class
subclass of: ObsoleteClass
term replaced by: geneplotter
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete genomeIntervals
type: Class
subclass of: ObsoleteClass
term replaced by: genomeIntervals
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_gff format
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: Obsoleted after the 0.4 release.
comment: Equivalence with EDAM format_2305.
deprecated: true

obsolete Global test
type: Class
subclass of: ObsoleteClass
term replaced by: Global test
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete globaltest
type: Class
subclass of: ObsoleteClass
term replaced by: globaltest
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete gmt format
type: Class
subclass of: ObsoleteClass
term replaced by: gmt format
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete goProfiles
type: Class
subclass of: ObsoleteClass
term replaced by: goProfiles
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete goTools
type: Class
subclass of: ObsoleteClass
term replaced by: goTools
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete gpls
type: Class
subclass of: ObsoleteClass
term replaced by: gpls
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete gpr format
type: Class
subclass of: ObsoleteClass
term replaced by: gpr format
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete graph
type: Class
subclass of: ObsoleteClass
term replaced by: graph
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete gtr
type: Class
subclass of: ObsoleteClass
term replaced by: gtr
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete gxl format
type: Class
subclass of: ObsoleteClass
term replaced by: gxl format
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_Heatmap
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: Obsoleted after the 0.4 release.
comment: Equivalence with EDAM data_1636.
deprecated: true

obsolete hexbin
type: Class
subclass of: ObsoleteClass
term replaced by: hexbin
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Hierarchical clustering
type: Class
subclass of: ObsoleteClass
term replaced by: Hierarchical clustering
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete hopach
type: Class
subclass of: ObsoleteClass
term replaced by: hopach
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete HTML report
type: Class
subclass of: ObsoleteClass
term replaced by: HTML report
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Hypergeometric enrichment
type: Class
subclass of: ObsoleteClass
term replaced by: Hypergeometric enrichment
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete hypergraph
type: Class
subclass of: ObsoleteClass
term replaced by: hypergraph
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Icens
type: Class
subclass of: ObsoleteClass
term replaced by: Icens
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete idiogram
type: Class
subclass of: ObsoleteClass
term replaced by: idiogram
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_Image
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: Obsoleted after the 0.4 release.
comment: Equivalence with EDAM data_2968
deprecated: true

obsolete impute
type: Class
subclass of: ObsoleteClass
term replaced by: impute
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete iterativeBMA
type: Class
subclass of: ObsoleteClass
term replaced by: iterativeBMA
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete iterativeBMAsurv
type: Class
subclass of: ObsoleteClass
term replaced by: iterativeBMAsurv
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Iterative local regression and model selection
type: Class
subclass of: ObsoleteClass
term replaced by: Iterative local regression and model selection
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_.java file
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: 0.4
comment: The original label for this class, .java file, was used in two separate class URIs. The first was SWO_0000585, initially created within the originalsoftwareontology.owl. The second URI is stored within swo_data.owl and is SWO_3000034. As SWO_3000034 is properly modelled as a child of 'Programming language format' this class was retained and SWO_0000585 deemed obsolete. The usages of SWO_0000585 were refactored to reference 3. SWO_3000034, and SWO_0000585 was marked as obsolete. Please use SWO_3000034 instead.
deprecated: true

obsolete_jpeg
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: 0.4
comment: SWO_0000586 (jpeg) was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000017, with the label 'JPEG', is also present, and stored within swo_data.owl. SWO_3000017 was retained and SWO_ 0000586 deemed obsolete, as SWO_3000017 has a better location in the hierarchy. All axioms belonging to SWO_0000586 were transferred to SWO_3000017. Please use SWO_3000017 instead.
deprecated: true

obsolete k-cores
type: Class
subclass of: ObsoleteClass
term replaced by: k-cores
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete k-means
type: Class
subclass of: ObsoleteClass
term replaced by: k-means
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete k-nearest neighbour classification
type: Class
subclass of: ObsoleteClass
term replaced by: k-nearest neighbour classification
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete keggorth
type: Class
subclass of: ObsoleteClass
term replaced by: keggorth
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete lapmix
type: Class
subclass of: ObsoleteClass
term replaced by: lapmix
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Likelihood method
type: Class
subclass of: ObsoleteClass
term replaced by: Likelihood method
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete limma
type: Class
subclass of: ObsoleteClass
term replaced by: limma
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete limmaGUI
type: Class
subclass of: ObsoleteClass
term replaced by: limmaGUI
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Linear modelling
type: Class
subclass of: ObsoleteClass
term replaced by: Linear modelling
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete lma
type: Class
subclass of: ObsoleteClass
term replaced by: lma
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Local-pooled-error
type: Class
subclass of: ObsoleteClass
term replaced by: Local-pooled-error
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete log file
type: Class
subclass of: ObsoleteClass
term replaced by: log file
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete logicFS
type: Class
subclass of: ObsoleteClass
term replaced by: logicFS
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete logicFS dataset
type: Class
subclass of: ObsoleteClass
term replaced by: logicFS dataset
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete logitT
type: Class
subclass of: ObsoleteClass
term replaced by: logitT
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Logit-t algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: Logit-t algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete lumi
type: Class
subclass of: ObsoleteClass
term replaced by: lumi
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete maCorrPlot
type: Class
subclass of: ObsoleteClass
term replaced by: maCorrPlot
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete maDB
type: Class
subclass of: ObsoleteClass
term replaced by: maDB
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete maSigPro
type: Class
subclass of: ObsoleteClass
term replaced by: maSigPro
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete maanova
type: Class
subclass of: ObsoleteClass
term replaced by: maanova
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete macat
type: Class
subclass of: ObsoleteClass
term replaced by: macat
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete made4
type: Class
subclass of: ObsoleteClass
term replaced by: made4
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete maigesPack
type: Class
subclass of: ObsoleteClass
term replaced by: maigesPack
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete makePlatformDesign
type: Class
subclass of: ObsoleteClass
term replaced by: makePlatformDesign
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete makecdfenv
type: Class
subclass of: ObsoleteClass
term replaced by: makecdfenv
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete marray
type: Class
subclass of: ObsoleteClass
term replaced by: marray
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 'MAS5'
type: Class
subclass of: ObsoleteClass
term replaced by: 'MAS5'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete mas5 format
type: Class
subclass of: ObsoleteClass
term replaced by: mas5 format
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete matchprobes
type: Class
subclass of: ObsoleteClass
term replaced by: matchprobes
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete mdqc
type: Class
subclass of: ObsoleteClass
term replaced by: mdqc
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete M-estimation regression
type: Class
subclass of: ObsoleteClass
term replaced by: M-estimation regression
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete metaArray
type: Class
subclass of: ObsoleteClass
term replaced by: metaArray
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Meta data
type: Class
subclass of: ObsoleteClass
term replaced by: Meta data
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete metahdep
type: Class
subclass of: ObsoleteClass
term replaced by: metahdep
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete miRNApath
type: Class
subclass of: ObsoleteClass
term replaced by: miRNApath
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete microRNA
type: Class
subclass of: ObsoleteClass
term replaced by: microRNA
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_Microarray data
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: Obsoleted after the 0.4 release.
comment: Equivalent to EDAM class data_2603.
deprecated: true

obsolete minet
type: Class
subclass of: ObsoleteClass
term replaced by: minet
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete mrnet algorithm
type: Class
subclass of: ObsoleteClass
term replaced by: mrnet algorithm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Multinomial probit regression with Gaussian Process priors
type: Class
subclass of: ObsoleteClass
term replaced by: Multinomial probit regression with Gaussian Process priors
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Multiple testing
type: Class
subclass of: ObsoleteClass
term replaced by: Multiple testing
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Multivariate t mixture models
type: Class
subclass of: ObsoleteClass
term replaced by: Multivariate t mixture models
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete multtest
type: Class
subclass of: ObsoleteClass
term replaced by: multtest
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Negative binomial distribution
type: Class
subclass of: ObsoleteClass
term replaced by: Negative binomial distribution
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete nem
type: Class
subclass of: ObsoleteClass
term replaced by: nem
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Neural networks models
type: Class
subclass of: ObsoleteClass
term replaced by: Neural networks models
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_newick
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister
obsoleted in version: Obsoleted after the 0.4 release.
comment: Equivalence with EDAM format_1910.
deprecated: true

obsolete nnNorm
type: Class
subclass of: ObsoleteClass
term replaced by: nnNorm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete nudge
type: Class
subclass of: ObsoleteClass
term replaced by: nudge
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete occugene
type: Class
subclass of: ObsoleteClass
term replaced by: occugene
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete oligo
type: Class
subclass of: ObsoleteClass
term replaced by: oligo
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete oligoClasses
type: Class
subclass of: ObsoleteClass
term replaced by: oligoClasses
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete OMICS data
type: Class
subclass of: ObsoleteClass
term replaced by: OMICS data
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete oneChannelGUI
type: Class
subclass of: ObsoleteClass
term replaced by: oneChannelGUI
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ontoTools
type: Class
subclass of: ObsoleteClass
term replaced by: ontoTools
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete pair file
type: Class
subclass of: ObsoleteClass
term replaced by: pair file
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete pamr
type: Class
subclass of: ObsoleteClass
term replaced by: pamr
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete panp
type: Class
subclass of: ObsoleteClass
term replaced by: panp
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete parody
type: Class
subclass of: ObsoleteClass
term replaced by: parody
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete parse
type: Class
subclass of: ObsoleteClass
term replaced by: parse
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete pathRender
type: Class
subclass of: ObsoleteClass
term replaced by: pathRender
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete pcaMethods
type: Class
subclass of: ObsoleteClass
term replaced by: pcaMethods
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete pcot2
type: Class
subclass of: ObsoleteClass
term replaced by: pcot2
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_pdf
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: 0.4
comment: SWO_0000652 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000015 is also present and stored within swo_data.owl. SWO_3000015 was retained and SWO_0000652 deemed obsolete, as SWO_3000015 has a better location in the hierarchy. All axioms belonging to SWO_0000652 were transferred to SWO_3000015. Please use SWO_3000015 instead.
deprecated: true

obsolete pdInfoBuilder
type: Class
subclass of: ObsoleteClass
term replaced by: pdInfoBuilder
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete pdmclass
type: Class
subclass of: ObsoleteClass
term replaced by: pdmclass
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete pedigree data file
type: Class
subclass of: ObsoleteClass
term replaced by: pedigree data file
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete pgUtils
type: Class
subclass of: ObsoleteClass
term replaced by: pgUtils
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete pickgene
type: Class
subclass of: ObsoleteClass
term replaced by: pickgene
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete pkgDepTools
type: Class
subclass of: ObsoleteClass
term replaced by: pkgDepTools
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete plgem
type: Class
subclass of: ObsoleteClass
term replaced by: plgem
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete plier
type: Class
subclass of: ObsoleteClass
term replaced by: plier
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Graph plot
type: Class
subclass of: ObsoleteClass
term replaced by: Graph plot
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete plw
type: Class
subclass of: ObsoleteClass
term replaced by: plw
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_png
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: 0.4
comment: SWO_0000663 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000018 is also present and stored within swo_data.owl. SWO_3000018 was retained and SWO_0000663 deemed obsolete, as SWO_3000018 has a better location in the hierarchy. All axioms belonging to SWO_0000663 were transferred to SWO_3000018 . Please use SWO_3000018 instead.
deprecated: true

obsolete Position weight matrix (PWM )
type: Class
subclass of: ObsoleteClass
term replaced by: Position weight matrix (PWM )
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ppiStats
type: Class
subclass of: ObsoleteClass
term replaced by: ppiStats
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete prada
type: Class
subclass of: ObsoleteClass
term replaced by: prada
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete preprocessCore
type: Class
subclass of: ObsoleteClass
term replaced by: preprocessCore
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete_ps
type: Class
subclass of: ObsoleteClass
Contributor: Marked as obsolete by Allyson Lister.
obsoleted in version: 0.4
comment: An equivalence statement is already marked for these two classes. Removed equivalence statement as the location of the obsoleted class has been changed. SWO_0000668 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000024 is also present and stored within swo_data.owl. SWO_3000018 was retained and SWO_0000668 deemed obsolete, as SWO_3000024 has a better location in the hierarchy. All axioms belonging to SWO_0000668 were transferred to SWO_3000024. Please use SWO_3000024 instead.
deprecated: true

obsolete puma
type: Class
subclass of: ObsoleteClass
term replaced by: puma
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete qPCR data
type: Class
subclass of: ObsoleteClass
term replaced by: qPCR data
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete qpcrNorm
type: Class
subclass of: ObsoleteClass
term replaced by: qpcrNorm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete qpgraph
type: Class
subclass of: ObsoleteClass
term replaced by: qpgraph
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Quantile normalization
type: Class
subclass of: ObsoleteClass
term replaced by: Quantile normalization
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Quantile regression techniques
type: Class
subclass of: ObsoleteClass
term replaced by: Quantile regression techniques
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete quantsmooth
type: Class
subclass of: ObsoleteClass
term replaced by: quantsmooth
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete qvalue
type: Class
subclass of: ObsoleteClass
term replaced by: qvalue
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete rHVDM
type: Class
subclass of: ObsoleteClass
term replaced by: rHVDM
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete rMAT
type: Class
subclass of: ObsoleteClass
term replaced by: rMAT
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete rama
type: Class
subclass of: ObsoleteClass
term replaced by: rama
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Rank-invariant set normalization
type: Class
subclass of: ObsoleteClass
term replaced by: Rank-invariant set normalization
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Rank product non-parametric method
type: Class
subclass of: ObsoleteClass
term replaced by: Rank product non-parametric method
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete .raw files
type: Class
subclass of: ObsoleteClass
term replaced by: .raw files
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete rbsurv
type: Class
subclass of: ObsoleteClass
term replaced by: rbsurv
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete rda
type: Class
subclass of: ObsoleteClass
term replaced by: rda
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete reb
type: Class
subclass of: ObsoleteClass
term replaced by: reb
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete rflowcyt
type: Class
subclass of: ObsoleteClass
term replaced by: rflowcyt
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete .rma format
type: Class
subclass of: ObsoleteClass
term replaced by: .rma format
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete rsbml
type: Class
subclass of: ObsoleteClass
term replaced by: rsbml
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete rtracklayer
type: Class
subclass of: ObsoleteClass
term replaced by: rtracklayer
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete safe
type: Class
subclass of: ObsoleteClass
term replaced by: safe
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete sagenhaft
type: Class
subclass of: ObsoleteClass
term replaced by: sagenhaft
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete seqLogo
type: Class
subclass of: ObsoleteClass
term replaced by: seqLogo
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete sigPathway
type: Class
subclass of: ObsoleteClass
term replaced by: sigPathway
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete siggenes
type: Class
subclass of: ObsoleteClass
term replaced by: siggenes
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Sim method
type: Class
subclass of: ObsoleteClass
term replaced by: Sim method
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete simpleaffy
type: Class
subclass of: ObsoleteClass
term replaced by: simpleaffy
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete simulatorAPMS
type: Class
subclass of: ObsoleteClass
term replaced by: simulatorAPMS
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete sizepower
type: Class
subclass of: ObsoleteClass
term replaced by: sizepower
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete xmapbridge
type: Class
subclass of: ObsoleteClass
term replaced by: xmapbridge
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete snapCGH
type: Class
subclass of: ObsoleteClass
term replaced by: snapCGH
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete snpMatrix
type: Class
subclass of: ObsoleteClass
term replaced by: snpMatrix
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete spikeLI
type: Class
subclass of: ObsoleteClass
term replaced by: spikeLI
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete spkTools
type: Class
subclass of: ObsoleteClass
term replaced by: spkTools
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete splicegear
type: Class
subclass of: ObsoleteClass
term replaced by: splicegear
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete splots
type: Class
subclass of: ObsoleteClass
term replaced by: splots
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete spotSegmentation
type: Class
subclass of: ObsoleteClass
term replaced by: spotSegmentation
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete sproc
type: Class
subclass of: ObsoleteClass
term replaced by: sproc
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete sqlite
type: Class
subclass of: ObsoleteClass
term replaced by: sqlite
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete sscore
type: Class
subclass of: ObsoleteClass
term replaced by: sscore
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete ssize
type: Class
subclass of: ObsoleteClass
term replaced by: ssize
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete stam
type: Class
subclass of: ObsoleteClass
term replaced by: stam
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Statistical tests
type: Class
subclass of: ObsoleteClass
term replaced by: Statistical tests
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete stepNorm
type: Class
subclass of: ObsoleteClass
term replaced by: stepNorm
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete 't-test'
type: Class
subclass of: ObsoleteClass
term replaced by: 't-test'
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete tilingArray
type: Class
subclass of: ObsoleteClass
term replaced by: tilingArray
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete timecourse
type: Class
subclass of: ObsoleteClass
term replaced by: timecourse
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete tkWidgets
type: Class
subclass of: ObsoleteClass
term replaced by: tkWidgets
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete topGO
type: Class
subclass of: ObsoleteClass
term replaced by: topGO
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete tspair
type: Class
subclass of: ObsoleteClass
term replaced by: tspair
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete twilight
type: Class
subclass of: ObsoleteClass
term replaced by: twilight
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete Two-stage measurement error model
type: Class
subclass of: ObsoleteClass
term replaced by: Two-stage measurement error model
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete vbmp
type: Class
subclass of: ObsoleteClass
term replaced by: vbmp
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete data visualization
type: Class
subclass of: ObsoleteClass
term replaced by: data visualization
obsoleted in version: 1.7
comment: AL 25.9.19: Redundant with http://purl.obolibrary.org/obo/OBI_0200111
deprecated: true

obsolete vsn
type: Class
subclass of: ObsoleteClass
term replaced by: vsn
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete weaver
type: Class
subclass of: ObsoleteClass
term replaced by: weaver
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete webbioc
type: Class
subclass of: ObsoleteClass
term replaced by: webbioc
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete widgetTools
type: Class
subclass of: ObsoleteClass
term replaced by: widgetTools
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete xcms
type: Class
subclass of: ObsoleteClass
term replaced by: xcms
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete xps
type: Class
subclass of: ObsoleteClass
term replaced by: xps
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

obsolete yaqcaffy
type: Class
subclass of: ObsoleteClass
term replaced by: yaqcaffy
obsoleted in version: 1.7
comment: AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
deprecated: true

software
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: is executed in
  some values from: Class
    union of: data transformation
    union of: data visualization
definition: Computer software, or generally just software, is any set of machine-readable instructions (most often in the form of a computer program) that conform to a given syntax (sometimes referred to as a language) that is interpretable by a given processor and that directs a computer's processor to perform specific operations.
definition source: James Malone
definition source: Modified in parts from https://en.wikipedia.org/wiki/Software
definition source: Robert Stevens
comment: AL 7.9.22: There are some reasoning oddities associated with marking IAO and SWO software as equivalent; once these are sorted out, the equivalence statement will take the place of this current parent-child relationship.

software license
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property:
      inverse of: has license
    some values from: software
subclass of: information content entity
subclass of: Restriction
  on property:
    inverse of: has license
  some values from: software
definition: A licence is a legal instrument (usually by way of contract law, with or without printed material) governing the use or redistribution of the resource containing the licence.
definition source: Modified from http://en.wikipedia.org/wiki/Software_license
creator: James Malone
label: licence

obsolete information processing
type: Class
subclass of: ObsoleteClass
definition: Information processing is a process in which input information is analysed or transformed in order to produce information as output.
definition source: James Malone
term replaced by: data transformation
obsoleted in version: 1.7
comment: AL 18.9.2019: This class is identical (based on its definition) with OBI 'data transformation' and is no longer required.
deprecated: true

Microsoft Excel 2007
type: Class
subclass of: Microsoft Excel
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000046
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000003
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000046
subclass of: Restriction
  on property: directly followed by
  some values from: Microsoft Excel for Windows 2010
subclass of: Restriction
  on property: has version
  has value: SWO_2000007
subclass of: Restriction
  on property: has website homepage
  has value: http://office.microsoft.com/
subclass of: Restriction
  on property: has release date
  has value: 2007-01-30T0:00:00
definition: Microsoft Excel 2007 is a spreadsheet editing and viewing tool.

MATLAB
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000002
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000002
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000004
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000004
subclass of: Restriction
  on property: is executed in
  some values from: SWO_40000002
subclass of: Restriction
  on property: has license
  some values from: SWO_1000002
subclass of: Restriction
  on property: has website homepage
  has value: http://www.mathworks.com/products/matlab/
definition: MATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran
definition source: http://www.mathworks.com/products/matlab/
creator: Nandini Badarinarayan

Protege 4
type: Class
subclass of: ontology engineering software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000003
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000003
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Ontology
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000007
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Ontology
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000038
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Ontology
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000039
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Ontology
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000007
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Ontology
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000038
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Ontology
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000039
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000052
subclass of: Restriction
  on property: has license
  some values from: SWO_1000003
subclass of: Restriction
  on property: has website homepage
  has value: http://protege.stanford.edu/

OmniOutliner
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000004
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000004
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000027
subclass of: Restriction
  on property: is executed in
  some values from: SWO_4000003
subclass of: Restriction
  on property: has license
  some values from: SWO_1000002
subclass of: Restriction
  on property: has website homepage
  has value: http://www.omnigroup.com/products/omnioutliner/
definition: OmniOutliner is commercial outlining software for Mac OS X produced by The Omni Group

Racket
type: Class
subclass of: programming language
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000005
subclass of: Restriction
  on property: has license
  some values from: SWO_1000004
definition: Racket is a Scheme-based language interpreter and programming environment

Kakadu
type: Class
subclass of: software with image input
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000029
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000052
subclass of: Restriction
  on property: is executed in
  some values from: SWO_4000004
subclass of: Restriction
  on property: has website homepage
  has value: http://www.kakadusoftware.com

WordStar
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000006
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000031
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000031
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000052
subclass of: Restriction
  on property: is executed in
  some values from: SWO_4000006

IntelliJ IDEA
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000007
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000034
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000034
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000052
subclass of: Restriction
  on property: is executed in
  some values from: SWO_9000056
subclass of: Restriction
  on property: has license
  some values from: Class
    union of: SWO_1000002
    union of: SWO_1000005
subclass of: Restriction
  on property: has website homepage
  has value: http://www.jetbrains.com/idea/
definition: IntelliJ IDEA is a commercial Java IDE for developing software.
alternative term: IntelliJ

Java
type: Class
subclass of: programming language
subclass of: Restriction
  on property: has website homepage
  has value: http://www.java.com

COPASI
type: Class
subclass of: software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SBML
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: CopasiML
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SBML
subclass of: Restriction
  on property: uses platform
  some values from: Linux
subclass of: Restriction
  on property: uses platform
  some values from: OS X
subclass of: Restriction
  on property: uses platform
  some values from: SWO_9000072
subclass of: Restriction
  on property: implements
  some values from: SWO_4000006
subclass of: Restriction
  on property: implements
  some values from: SWO_4000007
subclass of: Restriction
  on property: is executed in
  some values from: SWO_4000008
subclass of: Restriction
  on property: has license
  some values from: SWO_1000057
subclass of: Restriction
  on property: has license
  all values from: SWO_1000057
subclass of: Restriction
  on property: has website homepage
  has value: http://www.copasi.org
definition: COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. COPASI provides an C++ API with language bindings for Perl, python, R, Java, and Octave and is able to communicate with the Systems Biology Workbench COPASI carries out several analyses of the network and its dynamics and has extensive support for parameter estimation and optimization. COPASI provides means to visualize data in customizable plots, histograms and animations of network diagrams.
definition source: http://sbml.org/SBML_Software_Guide/SBML_Software_Summary, accessed 24 March 2015.

Microsoft Excel 2003
type: Class
subclass of: software before Microsoft 2007
subclass of: Microsoft Excel
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000003
subclass of: Restriction
  on property: has version
  has value: SWO_2000005
definition: Microsoft Excel 2003 is a spreadsheet editing and viewing tool.

Microsoft Excel 2002
type: Class
subclass of: Microsoft Excel
subclass of: Restriction
  on property: has version
  has value: SWO_2000004

MATLAB 7
type: Class
subclass of: MATLAB
subclass of: Restriction
  on property: has version
  has value: SWO_2000011

MATLAB 6
type: Class
subclass of: MATLAB
subclass of: Restriction
  on property: has version
  has value: SWO_2000012

MATLAB 7.12
type: Class
subclass of: MATLAB
subclass of: Restriction
  on property: has version
  has value: SWO_2000013

STARLIMS
type: Class
subclass of: software
subclass of: Restriction
  on property: is executed in
  some values from: SWO_4000009

Unix
type: Class
subclass of: operating system
subclass of: software with command line interface

operating system
type: Class
equivalent class: Restriction
  on property: is executed in
  some values from: SWO_4000010
subclass of: software
subclass of: Restriction
  on property: is executed in
  some values from: SWO_4000010
definition: An operating system is a piece of software which is responsible for managing software that runs on a computer and the interactions of that software with the hardware and system resources.

Linux
type: Class
subclass of: operating system
subclass of: software with command line interface

Microsoft Word 2001
type: Class
subclass of: Microsoft Word

Adobe Illustrator 10
type: Class
subclass of: software with image input
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000009
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000009
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000010
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000011
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000012
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000015
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000016
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000017
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000018
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000022
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000023
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000032
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000009
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000010
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000011
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000015
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000017
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000019
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000022
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000023
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000052
definition: Adobe Illustrator is a graphics editor for creating and editing vector graphics.
creator: James Malone

Microsoft Word
type: Class
subclass of: Microsoft developed software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000001
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000032
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000032
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000052
subclass of: Restriction
  on property: is executed in
  some values from: SWO_4000006

software with image input
type: Class
equivalent class: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008

OBO-Edit
type: Class
subclass of: ontology engineering software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Ontology
    intersection of: Restriction
      on property: has format specification
      some values from: OBO Flat File Format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Ontology
    intersection of: Restriction
      on property: has format specification
      some values from: OBO Flat File Format
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000052
subclass of: Restriction
  on property: has website homepage
  has value: http://oboedit.org/
definition: OBO-Edit is an open source ontology editor optimized for the OBO biological ontology file format. It features an easy to use editing interface, a simple but fast reasoner, and powerful search capabilities.
alternative term: OBO edit

ontology engineering software
type: Class
equivalent class: Restriction
  on property: is executed in
  some values from: SWO_4000005
subclass of: software
subclass of: Restriction
  on property: is executed in
  some values from: SWO_4000005

Microsoft developed software
type: Class
equivalent class: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000001
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000001

software with command line interface
type: Class
equivalent class: Restriction
  on property: has interface
  some values from: SWO_9000053
subclass of: software
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000053

Smultron
type: Class
subclass of: software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Ontology
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: is executed in
  some values from: SWO_4000011
subclass of: Restriction
  on property: has declared status
  some values from: SWO_9000072
subclass of: Restriction
  on property: has version
  has value: SWO_2000017
subclass of: Restriction
  on property: has website homepage
  has value: http://www.peterborgapps.com/smultron/

Agilent Scan Control
type: Class
subclass of: Agilent Technologies Software
definition: Scan Control Software is the user interface software that controls the Agilent scanner. This software is usable only with the Agilent high-resolution scanner (G2565CA) or high-resolution scanner upgrade. It will not function with earlier scanner versions
alternative term: Scan Control Application software
definition source: http://www.chem.agilent.com/
creator: Nandini Badarinarayan

Agilent Technologies Software
type: Class
equivalent class: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000033
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000033
creator: Nandini Badarinarayan

'AnnotationDbi'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: sqlite
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Bitmap object
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
definition: This package provides user interface and database connection code for annotation data packages using SQLite data storage.
definition source: http://bioconductor.org/packages/2.4/bioc/html/AnnotationDbi.html
creator: Nandini Badarinarayan

Applied Biosystems 1700 Expression Array System Software
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000036
definition: Microarrays are powerful tools for discovering levels of gene expression. Geneservice have invested in the latest gene expression microarray system from Applied Biosystems so that the widest choice of platform is available to our customers. The key features of this system are: Sensitivity: a detection threshold of as little as a femtomole of expresseed mRNA and requiring as little as 500ng of starting total RNA. Content: each probe is associated with a gene sequence buiult on unique Celera data and validated by public RefSeqs all of which have been curated. Pipeline: complete integrated solutions for gene expression research including Applied Biosystems Bioinformatic tools and ready-to-go gene expression TaqMan assays for validation of results.
definition source: http://www.geneservice.co.uk/services/geneexpression/overview_1700.jsp
creator: Nandini Badarinarayan

ArrayGauge
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200010
definition: Fujifilm ArrayGauge™ software is specifically designed for Macroarray and Microarray samples, with all the practical functions necessary for the most powerful array analysis. Its ultra-friendly navigation and functions can handle any kind of array (CLONTECH, Genome Systems, Research Genetics - even hand-made arrays). It already includes virtually every contemporary cDNA membrane template on the market, with the flexibility to handle others as they develop.
alternative term: ArrayGauge [FUJIFILM]
definition source: http://www.fujifilm.com/products/life_science_systems/science_imaging/arraygauge/
creator: Nandini Badarinarayan

ArrayNorm
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000242
definition: ArrayNorm is an platform-independent Java tool for normalization and statistical analysis for microarray-experiment data. It provides modules for visualization (scatterplot, histogram, boxplot, etc.), normalization and analysis.
definition source: http://bin.tugraz.at/Tools/ArrayNorm.html
creator: Nandini Badarinarayan

'ArrayTools'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene list
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: HTML report
    intersection of: Restriction
      on property: has format specification
      some values from: HTML
subclass of: Restriction
  on property: implements
  some values from: RMA
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays.
definition source: http://bioconductor.org/packages/2.4/bioc/html/ArrayTools.html
creator: Nandini Badarinarayan

ArrayVision
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200011
definition: This software implements a robust algorithm for spot finding and quantitation, quality metrics, and use of pre-made protocols ensure accuracy and reproducibility. Choices for background correction, normalization, and ratio calculation between arrays provides flexibility.Wizard guides simplify operation.Automatic batch processing increases throughput and saves time.Data easily exported to Microsoft™ Excel or database programs for flexibility in reporting.
creator: Nandini Badarinarayan

BLAST+ 2.2.26
type: Class
subclass of: software with command line interface
subclass of: BLAST
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: SWO_3000065
    intersection of: Restriction
      on property: has format specification
      some values from: FASTA format
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: SWO_3000065
    intersection of: Restriction
      on property: has format specification
      some values from: GenBank format
subclass of: Restriction
  on property: has interface
  some values from: SWO_5000002
subclass of: Restriction
  on property: has version
  has value: SWO_2000027
subclass of: Restriction
  on property: has download location
  has value: ftp://ftp.ncbi.nih.gov/blast/executables/
definition: The C++ version of the command line BLAST+ tool made by the NCBI. (See also http://www.ncbi.nlm.nih.gov/books/NBK1763)
creator: Allyson Lister

Array_vision_(Interfocus)
type: Class
subclass of: ArrayVision
creator: Nandini Badarinarayan

Axon GenePix Pro 3
type: Class
subclass of: GenePix Pro [Axon Instruments]
creator: Nandini Badarinarayan

BAC
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    some values from: BED format
subclass of: Restriction
  on property: implements
  some values from: Bayesian Model
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments
definition source: http://bioconductor.org/packages/2.4/bioc/html/BAC.html
creator: Nandini Badarinarayan

Binning clustering method
type: Class
subclass of: algorithm
definition: binning clustering method- The algorithm uses single-linkage clustering to join compounds into similarity groups, where every member in a cluster shares with at least one other member a similarity value above a user-specified threshold. The algorithm is optimized for speed and memory eciency by avoiding the calculation of an all-against-all distance matrix.

Ensembl
type: Class
subclass of: software

Clustal
type: Class
subclass of: software
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000003
definition: Multiple alignment program for nucleic acid or protein sequences.
definition source: http://www.clustal.org/, Accessed 13 June 2012.
creator: Allyson Lister

Clustal Omega
type: Class
subclass of: Clustal
definition: Clustal Omega provides improved scalability over previous Clustal versions, allowing hundreds of thousands of sequences to be aligned in a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks.
definition source: http://www.clustal.org/omega/, Accessed 13 June 2012
creator: Allyson Lister

ClustalW
type: Class
subclass of: Clustal
creator: Allyson Lister

ClustalX
type: Class
subclass of: Clustal
creator: Allyson Lister

Clustal Omega 1.1
type: Class
subclass of: Clustal Omega
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000061
subclass of: Restriction
  on property: has interface
  all values from: SWO_9000053
subclass of: Restriction
  on property: has version
  has value: SWO_2000030
subclass of: Restriction
  on property: has documentation
  has value: http://dx.doi.org/10.1038/msb.2011.75
creator: Allyson Lister

ClustalW 2.1
type: Class
subclass of: ClustalW
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000061
subclass of: Restriction
  on property: has interface
  all values from: SWO_9000053
subclass of: Restriction
  on property: has version
  has value: SWO_2000028
subclass of: Restriction
  on property: has documentation
  has value: http://dx.doi.org/10.1093/bioinformatics/btm404
creator: Allyson Lister

ClustalX 2.1
type: Class
subclass of: ClustalX
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000061
subclass of: Restriction
  on property: has interface
  all values from: SWO_9000052
subclass of: Restriction
  on property: has version
  has value: SWO_2000029
subclass of: Restriction
  on property: has documentation
  has value: http://dx.doi.org/10.1093/bioinformatics/btm404
creator: Allyson Lister

EBI Clustal W2 Web Tool
type: Class
subclass of: Clustal
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000019
subclass of: Restriction
  on property: uses software
  some values from: ClustalW 2.1
subclass of: Restriction
  on property: has interface
  some values from: SWO_5000002
creator: Allyson Lister

EBI Clustal Omega Web Tool
type: Class
subclass of: Clustal
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000019
subclass of: Restriction
  on property: uses software
  some values from: Clustal Omega 1.1
subclass of: Restriction
  on property: has interface
  some values from: SWO_5000002
creator: Allyson Lister

MUSCLE
type: Class
subclass of: software
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000003
creator: Allyson Lister

EBI Muscle Web Tool
type: Class
subclass of: MUSCLE
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000019
subclass of: Restriction
  on property: uses software
  some values from: MUSCLE 3.8.31
subclass of: Restriction
  on property: has interface
  some values from: SWO_5000002
creator: Allyson Lister

MUSCLE 3.8.31
type: Class
subclass of: software with command line interface
subclass of: Drive5 MUSCLE
subclass of: Restriction
  on property: has version
  has value: SWO_2000031
subclass of: Restriction
  on property: has documentation
  has value: http://dx.doi.org/10.1093/nar/gkh340
subclass of: Restriction
  on property: has documentation
  has value: http://www.drive5.com/muscle/muscle_userguide3.8.html
subclass of: Restriction
  on property: has download location
  has value: http://www.drive5.com/muscle/downloads.htm
creator: Allyson Lister

Drive5 MUSCLE
type: Class
subclass of: MUSCLE
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000060
creator: Allyson Lister

TCoffee
type: Class
subclass of: software
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000003
creator: Allyson Lister

CRG TCoffee
type: Class
subclass of: TCoffee
subclass of: Restriction
  on property: has documentation
  has value: http://dx.doi.org/10.1006/jmbi.2000.4042
definition: TCoffee is a multiple sequence alignment program with a number of different modes.
creator: Allyson Lister

EBI TCoffee Web Tool
type: Class
subclass of: TCoffee
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000019
subclass of: Restriction
  on property: uses software
  some values from: CRG TCoffee 9.02.r1228
subclass of: Restriction
  on property: has interface
  some values from: SWO_5000002
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000051
definition: Performs an alignment of DNA, RNA or Proteins with the standard TCoffee mode. This Web tool provides both interactive access via a Web browser and programmatic SOAP Web service access. Currently only the Web service interface is modelled in OWL.
creator: Allyson Lister

CRG RCoffee Web Tool
type: Class
subclass of: TCoffee
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000062
subclass of: Restriction
  on property: uses software
  some values from: CRG TCoffee 9.02.r1228
subclass of: Restriction
  on property: has interface
  some values from: SWO_5000002
subclass of: Restriction
  on property: has documentation
  has value: http://dx.doi.org/10.1093/nar/gkn278
definition: Aligns RNA sequences using predicted secondary structures by accessing the RCoffee mode of the underlying TCoffee software.
definition source: http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012
creator: Allyson Lister

CRG TCoffee Web Tool
type: Class
subclass of: TCoffee
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000062
subclass of: Restriction
  on property: uses software
  some values from: CRG TCoffee 9.02.r1228
subclass of: Restriction
  on property: has interface
  some values from: SWO_5000002
subclass of: Restriction
  on property: has documentation
  has value: http://dx.doi.org/10.1093/nar/gkr245
definition: Performs an alignment of DNA, RNA or Proteins with the standard TCoffee mode.
definition source: http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012
creator: Allyson Lister

CRG MCoffee Web Tool
type: Class
subclass of: TCoffee
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000062
subclass of: Restriction
  on property: uses software
  some values from: CRG TCoffee 9.02.r1228
subclass of: Restriction
  on property: has interface
  some values from: SWO_5000002
subclass of: Restriction
  on property: has documentation
  has value: http://dx.doi.org/10.1093/nar/gkm333
definition: Aligns DNA, RNA or Proteins by combining the output of popular aligners and by accessing the MCoffee mode of the underlying TCoffee software.
definition source: http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012
creator: Allyson Lister

CRG Expresso Web Tool
type: Class
subclass of: TCoffee
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000062
subclass of: Restriction
  on property: uses software
  some values from: CRG TCoffee 9.02.r1228
subclass of: Restriction
  on property: has interface
  some values from: SWO_5000002
subclass of: Restriction
  on property: has documentation
  has value: http://dx.doi.org/10.1093/nar/gkl092
definition: Aligns protein sequences using structural information by accessing the 3DCoffee/Expresso mode of the underlying TCoffee software.
definition source: http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012
creator: Allyson Lister

CRG PSICoffee Web Tool
type: Class
subclass of: TCoffee
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000062
subclass of: Restriction
  on property: uses software
  some values from: CRG TCoffee 9.02.r1228
subclass of: Restriction
  on property: has interface
  some values from: SWO_5000002
subclass of: Restriction
  on property: has documentation
  has value: http://dx.doi.org/10.1093/nar/gkr245
definition: Aligns distantly related proteins using homology extension (slow and accurate) by accessing the PSICoffee mode of the underlying TCoffee software.
definition source: http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012
creator: Allyson Lister

CRG TCoffee 9.02.r1228
type: Class
subclass of: software with command line interface
subclass of: CRG TCoffee
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000062
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000052
subclass of: Restriction
  on property: has version
  has value: SWO_2000032
definition: The initial interface is via the command line. Depending on the options and inputs provided at the command line, an appropriate alignment takes place and is then presented to the user via a Graphical User Interface.
creator: Allyson Lister

Q
type: Class
subclass of: software
subclass of: Restriction
  on property: is executed in
  some values from: data processing task
subclass of: Restriction
  on property: is executed in
  some values from: data visualization
subclass of: Restriction
  on property: has website homepage
  has value: http://xray.bmc.uu.se/~aqwww/q/
definition: Q is a set of tools tailored for some specific kinds of free energy calculations, namely: (I) Free energy perturbation (FEP) simulations. (II) Empirical valence bond (EVB) calculations of reaction free energies. (III) Linear interaction energy (LIE) calculations of receptor-ligand binding affinities.
creator: Allyson Lister

Axiom
annotated source: Q
annotated property: definition
annotated target: Q is a set of tools tailored for some specific kinds of free energy calculations, namely: (I) Free energy perturbation (FEP) simulations. (II) Empirical valence bond (EVB) calculations of reaction free energies. (III) Linear interaction energy (LIE) calculations of receptor-ligand binding affinities.
definition source: http://xray.bmc.uu.se/~aqwww/q

Q 4.2
type: Class
subclass of: Q
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000064

SPSS
type: Class
subclass of: software
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000052
subclass of: Restriction
  on property: is executed in
  some values from: data processing task
subclass of: Restriction
  on property: is executed in
  some values from: data visualization
definition: Data analysis software which performs a variety of statistical, summarising, analytical and visualization tasks.
creator: Allyson Lister

SPSS 20.0
type: Class
subclass of: SPSS
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000063
subclass of: Restriction
  on property: has download location
  has value: http://www-01.ibm.com/software/uk/analytics/spss/downloads.html
creator: Allyson Lister

Sequence Alignment and Modeling System
type: Class
subclass of: software
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000003
definition: Sequence Alignment and Modeling System, a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis.
alternative term: SAM
definition source: http://bioinformatics.org/wiki/SAM, Accessed 19 June 2012.
creator: Allyson Lister

SAM 3.5
type: Class
subclass of: Sequence Alignment and Modeling System
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000065
subclass of: Restriction
  on property: implements
  some values from: Hidden Markov Model

Cytoscape
type: Class
subclass of: software
subclass of: Restriction
  on property: is executed in
  some values from: data visualization
subclass of: Restriction
  on property: has specified data input
  all values from: SWO_3000052
subclass of: Restriction
  on property: has documentation
  has value: http://dx.doi.org/10.1101/gr.1239303
definition: Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
definition source: http://www.cytoscape.org/what_is_cytoscape.html, Accessed June 20, 2012.
creator: Allyson Lister

Cytoscape 2.8
type: Class
subclass of: Cytoscape
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: SWO_3000052
    intersection of: Restriction
      on property: has format specification
      some values from: Class
        union of: SBML
        union of: format 3158
        union of: SWO_3000049
        union of: SWO_3000050
        union of: SWO_3000051
        union of: SWO_3000055
subclass of: Restriction
  on property: has download location
  has value: http://www.cytoscape.org/download.html

Plugin
type: Class
subclass of: role
definition: This role can be borne by any software which is a plugin for another piece of software. It can be used, for example, with an axiom such as "ParentSoftware 'uses software' some (PluginSoftware has_role some Plugin)"
creator: Allyson Lister

CEL binary format
type: Class
subclass of: binary format
subclass of: Restriction
  on property: is published by
  has value: SWO_1200000
definition: CEL binary format is a binary data format specification created by Affymetrix where values are stored in little-endian format. The CEL format stores the results of the intensity calculations on the pixel values of the DAT file. This includes an intensity value, standard deviation of the intensity, the number of pixels used to calculate the intensity value, a flag to indicate an outlier as calculated by the algorithm and a user defined flag indicating the feature should be excluded from future analysis. The file stores the previously stated data for each feature on the probe array.
definition source: http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html, accessed 22 May 2013.
creator: Allyson Lister
comment: It is unclear whether, originally, this format was intended to be the ASCII or binary version of the CEL format. As such, this class has been renamed as the binary format, and a new class created (CEL ASCII format) to make both options available. (22/05/2013)

Gene Expression Atlas at EBI R statistics package
type: Class
subclass of: software
subclass of: Restriction
  on property: has support URL
  has value: https://github.com/gxa/gxa/blob/develop/atlas-analytics/src/main/resources/R/analytics.R
definition: R package for producing statistics that populate the Gene Expression Atlas. https://github.com/gxa/gxa/blob/develop/atlas-analytics/src/main/resources/R/analytics.R

ActionScript
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/ActionScript

Ada
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Ada_(programming_language)

AppleScript
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/AppleScript

Assembly
type: Class
subclass of: programming language

C
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/C_(programming_language)

C Sharp
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/C_Sharp_(programming_language)

C++
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/C++

COBOL
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/COBOL

ColdFusion
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/ColdFusion_Markup_Language

D
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/D_(programming_language)

Delphi
type: Class
subclass of: programming language

Dylan
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Dylan_(programming_language)

Eiffel
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Eiffel_(programming_language)

Forth
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Forth_(programming_language)

Fortran
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Fortran

Groovy
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Groovy_(programming_language)

Haskell
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Haskell_(programming_language)

JavaScript
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/JavaScript

LabVIEW
type: Class
subclass of: programming language

Lisp
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Lisp_(programming_language)

Lua
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Lua_(programming_language)

Maple
type: Class
subclass of: programming language

Mathematica
type: Class
subclass of: programming language

Pascal
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Pascal_(programming_language)

Perl
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Perl

PHP
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/PHP

Prolog
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Prolog

Python
type: Class
subclass of: programming language
definition: Python is a widely used general-purpose, high-level programming language. Its design philosophy emphasizes code readability, and its syntax allows programmers to express concepts in fewer lines of code than would be possible in languages such as C. The language provides constructs intended to enable clear programs on both a small and large scale.Python supports multiple programming paradigms, including object-oriented, imperative and functional programming or procedural styles.
definition source: http://dbpedia.org/resource/Python_(programming_language), accessed 27 November 2014.

REXX
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/REXX

Ruby
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Ruby_(programming_language)

SAS
type: Class
subclass of: programming language

Scala
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Scala_(programming_language)

Scheme
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Scheme_(programming_language)

Shell
type: Class
subclass of: programming language

Smalltalk
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Smalltalk

SQL
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/SQL

Turing
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Turing_(programming_language)

Verilog
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Verilog

VHDL
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/VHDL

Visual Basic
type: Class
subclass of: programming language
definition source: http://dbpedia.org/resource/Visual_Basic

DAVID
type: Class
subclass of: software
subclass of: Restriction
  on property: implements
  some values from: Gene-Set Enrichment Analysis
subclass of: Restriction
  on property: has interface
  some values from: SWO_5000002
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000051
subclass of: Restriction
  on property: has website homepage
  has value: http://david.abcc.ncifcrf.gov/
definition: DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a free online bioinformatics resource developed by the Laboratory of Immunopathogenesis and Bioinformatics (LIB). All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies, e.g. microarray and proteomics studies.
alternative term: DAVID Bioinformatics resource
alternative term: Database for Annotation, Visualization and Integrated Discovery
definition source: http://david.abcc.ncifcrf.gov/
creator: James Malone

MLXTRAN
type: Class
subclass of: programming language

PSI-BLAST
type: Class
subclass of: BLAST
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: SWO_3000067
    intersection of: Restriction
      on property: has format specification
      some values from: FASTA format
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: SWO_3000067
    intersection of: Restriction
      on property: has format specification
      some values from: GenBank format
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000052
subclass of: Restriction
  on property: has license
  some values from: SWO_1000061
definition: Position-Specific Iterated (PSI)-BLAST is the most sensitive BLAST program, making it useful for finding very distantly related proteins or new members of a protein family. Use PSI-BLAST when your standard protein-protein BLAST search either failed to find significant hits, or returned hits with descriptions such as "hypothetical protein" or "similar to...".
alternative term: Position-Specific Iterative
definition source: NIH BLAST homepage

NMTRAN
type: Class
subclass of: programming language

NONMEM
type: Class
subclass of: software with command line interface
subclass of: Restriction
  on property: implements
  some values from: SWO_4000004
subclass of: Restriction
  on property: is encoded in
  some values from: NMTRAN
subclass of: Restriction
  on property: has license
  some values from: SWO_1000002
subclass of: Restriction
  on property: has version
  has value: SWO_2000036

Entrez
type: Class
subclass of: search engine
subclass of: Restriction
  on property: has interface
  some values from: SWO_5000002
definition: The Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website.
alternative term: Entrez Global Query Cross-Database Search System
definition source: Ncbi Resource, C. (2012). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research 41 (Database issue): D8–D20. doi:10.1093/nar/gks1189. PMC 3531099.

web content search
type: Class
subclass of: Query and retrieval
definition: Web content search is the searching for information on the World Wide Web.
alternative term: website content search

search engine
type: Class
equivalent class: Class
  intersection of: software
  intersection of: Restriction
    on property: is executed in
    some values from: web content search
subclass of: software
subclass of: Restriction
  on property: is executed in
  some values from: web content search
definition: A search engine is a software system that is designed to search for information on the World Wide Web.
alternative term: web search engine

Weka
type: Class
subclass of: software
subclass of: Restriction
  on property: is encoded in
  some values from: Java
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000052
subclass of: Restriction
  on property: has license
  some values from: SWO_1000004
subclass of: Restriction
  on property: has website homepage
  has value: http://www.cs.waikato.ac.nz/~ml/weka/
definition: Weka (Waikato Environment for Knowledge Analysis) is a suite of machine learning software, originally intended for data mining tasks, written in Java and developed at the University of Waikato, New Zealand.
alternative term: Waikato Environment for Knowledge Analysis

PostgreSQL
type: Class
subclass of: software
subclass of: Restriction
  on property: is executed in
  some values from: data storage
subclass of: Restriction
  on property: has website homepage
  has value: http://www.postgresql.org/
definition: PostgreSQL, often simply Postgres, is an open source object-relational database management system (ORDBMS) with an emphasis on extensibility and standards compliance.
alternative term: Postgres

data storage
type: Class
subclass of: data transformation
definition: The storing of digital information. Often this is done for archiving and retrieval purposes.

Segway 1.2
type: Class
subclass of: software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000071
subclass of: Restriction
  on property: has specified data output
  some values from: SWO_3000073
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: BED format
subclass of: Restriction
  on property: implements
  some values from: SWO_4000005
subclass of: Restriction
  on property: is encoded in
  some values from: Class
    union of: Python 2.6
    union of: Python 2.7
subclass of: Restriction
  on property: is executed in
  some values from: Genome annotation
subclass of: Restriction
  on property: has license
  some values from: SWO_1000047
subclass of: Restriction
  on property: has version
  has value: SWO_2000037
definition: The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. Our method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling.
definition source: http://pmgenomics.ca/hoffmanlab/proj/segway/, accessed 27 November 2014.

Python 2.6
type: Class
subclass of: Python
subclass of: Restriction
  on property: has version
  has value: SWO_2000033
definition: Version 2.6 of the Python programming language.
definition source: Allyson Lister
creator: Allyson Lister

Python 2.7
type: Class
subclass of: Python
subclass of: Restriction
  on property: has version
  has value: SWO_2000034
definition: Version 2.7 of the Python programming language.
definition source: Allyson Lister
creator: Allyson Lister

Firth's bias reduction procedure
type: Class
subclass of: algorithm

Mac OS
type: Class
subclass of: operating system
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000017
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000017
definition: Mac OS is software which is used as the operating system for the Macintosh personal computer created by Apple Inc.
definition source: http://en.wikipedia.org/wiki/History_of_Mac_OS, accessed 25 March 2015.
creator: Allyson Lister

OS X
type: Class
subclass of: Mac OS
definition: OS X is a Mac OS operating system which succeeds the original Mac OS, which had been Apple's primary operating system since 1984. Unlike the earlier Macintosh operating system, OS X is a Unix-based operating system.
definition source: http://en.wikipedia.org/wiki/History_of_Mac_OS#OS_X, accessed 25 March 2015.
creator: Allyson Lister

iBioSim
type: Class
subclass of: software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SBML
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SBML
subclass of: Restriction
  on property: uses platform
  some values from: Linux
subclass of: Restriction
  on property: uses platform
  some values from: OS X
subclass of: Restriction
  on property: uses platform
  some values from: SWO_9000072
subclass of: Restriction
  on property: implements
  some values from: Markov Chain Monte Carlo
subclass of: Restriction
  on property: implements
  some values from: SWO_4000006
subclass of: Restriction
  on property: implements
  some values from: SWO_4000008
subclass of: Restriction
  on property: is executed in
  some values from: SWO_4000008
subclass of: Restriction
  on property: has license
  some values from: SWO_9000074
subclass of: Restriction
  on property: has license
  all values from: SWO_9000074
definition: iBioSim has been developed for the modeling, analysis, and design of genetic circuits. While iBioSim primarily targets models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed. iBioSim also includes modeling and visualization support for multi-cellular and spatial models as well.
definition source: http://www.async.ece.utah.edu/iBioSim/, accessed 25 March 2015.
creator: Allyson Lister

VCell
type: Class
subclass of: software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SBML
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SBML
subclass of: Restriction
  on property: uses platform
  some values from: Linux
subclass of: Restriction
  on property: uses platform
  some values from: OS X
subclass of: Restriction
  on property: uses platform
  some values from: SWO_9000072
subclass of: Restriction
  on property: implements
  some values from: SWO_4000006
subclass of: Restriction
  on property: implements
  some values from: SWO_4000009
subclass of: Restriction
  on property: implements
  some values from: SWO_4000010
subclass of: Restriction
  on property: is executed in
  some values from: Modelling and simulation
subclass of: Restriction
  on property: has license
  some values from: SWO_9000074
definition: VCell is a complete model building, editing and simulation environment. Includes spatial modeling capabilites, deterministic, stochastic, and hybrid algorithms. Parameter sensitivity analysis and parameter optimization. Desktop application and web-based environment. Bio- and math-based interfaces. Database and model sharing/publishing.
alternative term: Virtual Cell
definition source: http://sbml.org/SBML_Software_Guide/SBML_Software_Summary, accessed 26 March 2015.
creator: Allyson Lister
comment: The licensing issue is not clear. On the VCell wikipedia page, the source is described as having an MIT license (see http://en.wikipedia.org/wiki/Virtual_Cell, accessed 26 March 2015). However, the exact type of license is not mentioned on the VCell homepage (http://www.vcell.org), therefore I have not added the statement that the MIT license is the *only* license for VCell.

COBRA
type: Class
subclass of: software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SBML
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SBML
subclass of: Restriction
  on property: uses platform
  some values from: Linux
subclass of: Restriction
  on property: uses platform
  some values from: OS X
subclass of: Restriction
  on property: uses platform
  some values from: SWO_9000072
subclass of: Restriction
  on property: implements
  some values from: SWO_4000006
subclass of: Restriction
  on property: has license
  some values from: SWO_1000047
subclass of: Restriction
  on property: has license
  all values from: SWO_1000047
definition: COBRA (COnstraint-Based Reconstruction and Analysis Toolbox) includes implementations of many of the commonly used forms of constraint-based analysis such as FBA, gene deletions, flux variability analysis, sampling, and batch simulations together with tools to read in and manipulate constraint-based models.
alternative term: COnstraints Based Reconstruction and Analysis
creator: Allyson Lister

COBRApy
type: Class
subclass of: COBRA
subclass of: Restriction
  on property: is encoded in
  some values from: Python
subclass of: Restriction
  on property: is encoded in
  all values from: Python
definition: COBRA Toolbox is the version of the COBRA software for Python.
alternative term: COnstraints Based Reconstruction and Analysis for Python
creator: Allyson Lister

COBRA Toolbox
type: Class
subclass of: COBRA
subclass of: Restriction
  on property: is software for
  some values from: MATLAB
subclass of: Restriction
  on property: is software for
  all values from: MATLAB
definition: COBRA Toolbox is the version of the COBRA software for Matlab.
alternative term: COnstraints Based Reconstruction and Analysis Toolbox for MATLAB
creator: Allyson Lister

libSBML
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SBML
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SBML
subclass of: Restriction
  on property: uses platform
  some values from: Linux
subclass of: Restriction
  on property: uses platform
  some values from: OS X
subclass of: Restriction
  on property: uses platform
  some values from: SWO_9000072
subclass of: Restriction
  on property: is software for
  some values from: MATLAB
subclass of: Restriction
  on property: is encoded in
  some values from: Java
subclass of: Restriction
  on property: is encoded in
  some values from: C
subclass of: Restriction
  on property: is encoded in
  some values from: C Sharp
subclass of: Restriction
  on property: is encoded in
  some values from: C++
subclass of: Restriction
  on property: is encoded in
  some values from: Perl
subclass of: Restriction
  on property: is encoded in
  some values from: Python
subclass of: Restriction
  on property: is encoded in
  some values from: Ruby
subclass of: Restriction
  on property: is encoded in
  some values from: GNU Octave
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000054
subclass of: Restriction
  on property: has license
  some values from: SWO_9000080
subclass of: Restriction
  on property: has license
  all values from: SWO_9000080
definition: LibSBML is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It provides interfaces for C, C++, C#(.NET), Java, MATLAB, Octave, Perl, Python R and Ruby. LibSBML is available for free under LGPL terms in both source-code form and precompiled binaries for Windows, Mac OS X, and Linux.
definition source: http://sbml.org/SBML_Software_Guide/SBML_Software_Summary, accessed 27 March 2015.
creator: Allyson Lister

GNU Octave
type: Class
subclass of: programming language
definition: GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable.
definition source: https://www.gnu.org/software/octave/, accessed 27 March 2015.
creator: Allyson Lister

GWT
type: Class
subclass of: programming language

S language
type: Class
subclass of: programming language

Excel
type: Class
subclass of: programming language

GGtools
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: rda
definition: This package deals with hapmap SNP reports, GWAS, etc.
definition source: http://bioconductor.org/packages/2.4/bioc/html/GGtools.html
creator: Nandini Badarinarayan

GLAD
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)
definition: Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or lost) to each chromosomal regions identified.
definition source: http://bioconductor.org/packages/2.4/bioc/html/GLAD.html
creator: Nandini Badarinarayan

Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)
type: Class
subclass of: algorithm

GLEAMS software
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200012
definition: Microarray image quantification is performed using GLEAMS software
definition source: http://hmg.oxfordjournals.org/cgi/reprint/12/17/2145.pdf
creator: Nandini Badarinarayan

GMS
type: Class
subclass of: software
creator: Nandini Badarinarayan

GOstats
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene list
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Gene expression data
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: HTML report
    intersection of: Restriction
      on property: has format specification
      some values from: HTML
subclass of: Restriction
  on property: implements
  some values from: Hypergeometric probability
subclass of: Restriction
  on property: implements
  some values from: 't-test'
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations
definition source: http://bioconductor.org/packages/2.4/bioc/html/GOstats.html
creator: Nandini Badarinarayan

Gene Recommender algorithm
type: Class
subclass of: algorithm

GSEABase
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: XML
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
definition: This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).
definition source: http://bioconductor.org/packages/2.4/bioc/html/GSEABase.html
creator: Nandini Badarinarayan

GSEAlm
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Image
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: implements
  some values from: Gene-Set Enrichment Analysis
subclass of: Restriction
  on property: implements
  some values from: Linear modelling
subclass of: Restriction
  on property: is executed in
  some values from: gene expression analysis
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
definition: Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics.
definition source: http://bioconductor.org/packages/2.4/bioc/html/GSEAlm.html
creator: Nandini Badarinarayan

Gamma-Gamma hierarchical model
type: Class
subclass of: algorithm

Gaussian locally weighted regression
type: Class
subclass of: algorithm

Gene-Set Enrichment Analysis
type: Class
subclass of: algorithm

GeneData Expressionist Analyst v4.0.5
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000198
definition: Genedata Expressionist® is an enterprise solution that integrates, stores and analyzes transcriptomics, proteomics and metabolomics data as well as a wide variety of phenotypic data.
definition source: http://www.genedata.com/products/expressionist/overview.html
creator: Nandini Badarinarayan

Gene Pix
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000299
definition: GenePix is the industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and ease of use.
alternative term: Gene Pix
alternative term: Genepix
definition source: http://www.moleculardevices.com/pages/software/gn_genepix_pro.html
creator: Nandini Badarinarayan

GenePix 3.0.6
type: Class
subclass of: Gene Pix
creator: Nandini Badarinarayan

GenePix 4.1
type: Class
subclass of: Gene Pix
creator: Nandini Badarinarayan

GenePix 4100A
type: Class
subclass of: GenePix
alternative term: GenePix 4100A [Axon Instruments]
creator: Nandini Badarinarayan

GenePix 5.0.1
type: Class
subclass of: Gene Pix
creator: Nandini Badarinarayan

GenePix
type: Class
subclass of: Gene Pix
alternative term: GenePix [Axon Instruments]
creator: Nandini Badarinarayan

GenePix Pro
type: Class
subclass of: Gene Pix
creator: Nandini Badarinarayan

GenePix Pro 3
type: Class
subclass of: GenePix Pro
creator: Nandini Badarinarayan

GenePix Pro 5.0
type: Class
subclass of: GenePix Pro
creator: Nandini Badarinarayan

GenePix Pro 6.0
type: Class
subclass of: GenePix Pro
creator: Nandini Badarinarayan

GenePix Pro 6 [Axon Instruments]
type: Class
subclass of: GenePix Pro [Axon Instruments]
creator: Nandini Badarinarayan

GenePix Pro [Axon Instruments]
type: Class
subclass of: GenePix Pro
alternative term: Axon GenePix Pro
creator: Nandini Badarinarayan

GeneR
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: FASTA format
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene list
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
definition: Package manipulating nucleotidic sequences (Embl, Fasta, GenBank)
definition source: http://bioconductor.org/packages/2.4/bioc/html/GeneR.html
creator: Nandini Badarinarayan

GeneRegionScan
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Image
    intersection of: Restriction
      on property: has format specification
      some values from: CEL binary format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
definition: A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data
definition source: http://bioconductor.org/packages/2.4/bioc/html/GeneRegionScan.html
creator: Nandini Badarinarayan

GeneRfold
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000024
definition: Package manipulating sequences with fold routines
definition source: http://bioconductor.org/packages/2.4/bioc/html/GeneRfold.html
creator: Nandini Badarinarayan

GeneSelectMMD
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: MMD
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: Gene selection based on a mixture of marginal distributions
definition source: http://bioconductor.org/packages/2.4/bioc/html/GeneSelectMMD.html
creator: Nandini Badarinarayan

GeneSelector
type: Class
subclass of: R software
subclass of: Restriction
  on property: implements
  some values from: SAM
subclass of: Restriction
  on property: implements
  some values from: WilcEbam
subclass of: Restriction
  on property: implements
  some values from: Wilcoxon
subclass of: Restriction
  on property: implements
  some values from: Linear modelling
subclass of: Restriction
  on property: implements
  some values from: 't-test'
subclass of: Restriction
  on property: implements
  some values from: BaldiLongT
subclass of: Restriction
  on property: implements
  some values from: Bayesian Model
subclass of: Restriction
  on property: implements
  some values from: FoxDimmicT
definition: The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various featured ranking methods (currently 15). In addition, the stability of the findings can be taken in account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise.
definition source: http://bioconductor.org/packages/2.4/bioc/html/GeneSelector.html
creator: Nandini Badarinarayan

GeneSpring
type: Class
subclass of: Agilent Technologies Software
subclass of: R software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000743
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene list
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
definition: Set of functions and class definitions to be able to read and write GeneSpring specific data objects and covert them to BioConductor objects
definition source: http://bioconductor.org/packages/2.4/bioc/html/GeneSpring.html
creator: Nandini Badarinarayan

GeneSpringGX
type: Class
subclass of: GeneSpring
creator: Nandini Badarinarayan

GeneTac Analyser
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000036
definition: Genetic Analyzer is a multi-color fluorescence-based DNA analysis system with 16 capillaries operating in parallel, offers high-quality data and efficient sample processing
definition source: https://products.appliedbiosystems.com/ab/en/US/adirect/ab
creator: Nandini Badarinarayan

GeneTraffic
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
definition: Set of functions and class definitions to be able to read GeneTraffic specific data from a project summary zip file and covert them to BioConductor objects (for 1 color projects affy's ExpressionSet, for 2 color projects marray's marrayRaw)
definition source: http://bioconductor.org/packages/2.4/bioc/html/GeneTraffic.html
creator: Nandini Badarinarayan

GenePix Pro 4.0
type: Class
subclass of: GenePix Pro
alternative term: GenePix Pro v4.0 scanning software
alternative term: Genepix Pro 4.0
creator: Nandini Badarinarayan

GenePix Pro 3.0
type: Class
subclass of: GenePix Pro
alternative term: Genepix pro 3.0
creator: Nandini Badarinarayan

GeneticsBase
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: CSV data set
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: pedigree data file
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package (GeneticsBase) provides a foundation of efficient data structures and easy-to-use manipulation functions.
definition source: http://bioconductor.org/packages/2.4/bioc/html/GeneticsBase.html
creator: Nandini Badarinarayan

GeneticsDesign
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
definition: This package contains functions useful for designing genetics studies, including power and sample-size calculations.
definition source: http://bioconductor.org/packages/2.4/bioc/html/GeneticsDesign.html
creator: Nandini Badarinarayan

GeneticsPed
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: pedigree data file
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Mixed model equations
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable
definition source: http://bioconductor.org/packages/2.4/bioc/html/GeneticsPed.html
creator: Nandini Badarinarayan

GenomeGraphs
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
definition: Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system.
definition source: http://bioconductor.org/packages/2.4/bioc/html/GenomeGraphs.html
creator: Nandini Badarinarayan

GlobalAncova
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: ANCOVA
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values.
definition source: http://bioconductor.org/packages/2.4/bioc/html/GlobalAncova.html
creator: Nandini Badarinarayan

GOSemSim
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene list
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Clustered data set
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Semantic Similarity Measures
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
definition: Methods for estimating GO semantic similarities. Implemented five methods proposed by Resnik, Schlicker(Rel), Jiang, Lin and Wang respectively. Support five species: human, rat, mouse, fly, and yeast.
definition source: http://bioconductor.org/packages/2.4/bioc/html/GOSemSim.html
creator: Nandini Badarinarayan

GraphAT
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Clustered data set
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: k-means
definition: Functions and data used in Balasubramanian, et al. (2004)
definition source: http://bioconductor.org/packages/2.4/bioc/html/GraphAT.html
creator: Nandini Badarinarayan

GraphAlignment
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Bayesian Model
definition: Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores.
definition source: http://bioconductor.org/packages/2.4/bioc/html/GraphAlignment.html
creator: Nandini Badarinarayan

GridGrinder
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000211
definition: Software for microarray image analysis.
definition source: http://www.oxfordjournals.org/nar/webserver/summary/825
creator: Nandini Badarinarayan

Hexagon binning algorithm
type: Class
subclass of: algorithm

HELP
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: design file
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: pair file
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: RMA
    intersection of: k-nearest neighbour classification
subclass of: Restriction
  on property: is executed in
  some values from: data visualization
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000011
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
definition: The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications
definition source: http://bioconductor.org/packages/2.4/bioc/html/HELP.html
creator: Nandini Badarinarayan

HEM
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Heterogeneous Error Model (HEM)
subclass of: Restriction
  on property: implements
  some values from: Markov Chain Monte Carlo
subclass of: Restriction
  on property: implements
  some values from: Empirical Bayes rule
subclass of: Restriction
  on property: implements
  some values from: 'FDR'
definition: This package fits heterogeneous error models for analysis of microarray data
definition source: http://bioconductor.org/packages/2.4/bioc/html/HEM.html
creator: Nandini Badarinarayan

Heterogeneous Error Model (HEM)
type: Class
subclass of: algorithm

Hubert’s gamma
type: Class
subclass of: algorithm

Hidden Markov Model
type: Class
subclass of: algorithm

Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm
type: Class
subclass of: algorithm

Hidden Variable Dynamic Modelling HVDM)
type: Class
subclass of: algorithm
definition: Technique which predicts a given transcription factor activity and then uses this infor- mation to predict its targets.

HaarSeg algorithm
type: Class
subclass of: algorithm

Hardy-Weinberg equilibrium
type: Class
subclass of: algorithm

Harshlight
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Image
    intersection of: Restriction
      on property: has format specification
      some values from: CEL binary format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000024
subclass of: Restriction
  on property: implements
  some values from: RMA
subclass of: Restriction
  on property: implements
  some values from: 'MAS5'
definition: The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitue value as whole matrix to solve the memory problem.
definition source: http://bioconductor.org/packages/2.4/bioc/html/Harshlight.html
creator: Nandini Badarinarayan

Heatplus
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Heat map
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: is executed in
  some values from: data visualization
definition: Add an extra graphical display at the bottom of a heat map, indicating for each column a) whether it has one of several binary properties or not, and b) the value of a quantitative variable. A cutting threshold for the sample dendrogram can also be specified, and the resulting clustering of the columns is indicated by coloring both the dendrogram and the extra variable display.
definition source: http://bioconductor.org/packages/2.4/bioc/html/Heatplus.html
creator: Nandini Badarinarayan

HilbertVis
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: GFF
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: BED format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: is executed in
  some values from: data visualization
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
definition: Functions to visualize long vectors of integer data by means of Hilbert curves
definition source: http://bioconductor.org/packages/2.4/bioc/html/HilbertVis.html
creator: Nandini Badarinarayan

HilbertVisGUI
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: GFF
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: BED format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: is executed in
  some values from: data visualization
definition: An interactive tool to visualize long vectors of integer data by means of Hilbert curves
definition source: http://bioconductor.org/packages/2.4/bioc/html/HilbertVisGUI.html
creator: Nandini Badarinarayan

Hypergeometric probability
type: Class
subclass of: algorithm

ICS-501 (version 2.3) Image Capture System
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000204
creator: Nandini Badarinarayan

Iteratively ReWeighted Least Squares
type: Class
subclass of: algorithm

IRanges
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000016
definition: The IRanges class and its extensions are low-level containers for storing sets of integer ranges. A typical use of these containers in biology is for representing a set of chromosome regions. More specific extensions of the IRanges class will typically allow the storage of additional information attached to each chromosome region as well as a hierarchical relationship between these regions.
definition source: http://bioconductor.org/packages/2.4/bioc/html/IRanges.html
creator: Nandini Badarinarayan

ITALICS
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Image
    intersection of: Restriction
      on property: has format specification
      some values from: CEL binary format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)
subclass of: Restriction
  on property: implements
  some values from: HaarSeg algorithm
subclass of: Restriction
  on property: implements
  some values from: AWS algorithm
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
definition: A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set
definition source: http://bioconductor.org/packages/2.4/bioc/html/ITALICS.html
creator: Nandini Badarinarayan

ILLUMINA data
type: Class
subclass of: data item

ImaGene4.1 software
type: Class
subclass of: ImaGene
creator: Nandini Badarinarayan

ImaGene 3.0
type: Class
subclass of: ImaGene
creator: Nandini Badarinarayan

ImageQuant
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200013
definition: This is a general image analysis program used in the study of electrophoretic separations, dot blots, slot blots, microplate assays, TLC assays, and plaque assays. ImageQuant provides a point-and-click environment for fast analysis of qualitative and quantitative assays. With tools for accurate volume integration, ImageQuant generates accurate lane profiles even for curved or slanted lanes.
alternative term: ImageQuant (Molecular Dynamics)
definition source: http://www.research.bidmc.harvard.edu/AcademicIT/ImageQuant.asp
creator: Nandini Badarinarayan

ImageReader
type: Class
subclass of: software
creator: Nandini Badarinarayan

ImaGene
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200003
definition: ImaGene microarray image analysis software by biodiscovery for microarrays, protein arrays and CGH analysis.
alternative term: ImaGene [BioDiscovery]
alternative term: Imagene
definition source: http://www.biodiscovery.com/index/imagene
creator: Nandini Badarinarayan

Imagene v4.0
type: Class
subclass of: ImaGene
creator: Nandini Badarinarayan

Initial microarray data processing (data filtering, local normalisation and quality control)
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200001
definition: These scripts are for primer design and initial microarray data processing and are available as .zip files:
definition source: http://www.bahlerlab.info/resources/
creator: Nandini Badarinarayan

Jaccard’s index
type: Class
subclass of: algorithm

Jaguar
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200000
definition: Image analysis software
creator: Nandini Badarinarayan

KCsmart
type: Class
subclass of: software with image input
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: implements
  some values from: Gaussian locally weighted regression
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000011
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
definition: Multi sample aCGH analysis package using kernel convolution
definition source: http://bioconductor.org/packages/2.4/bioc/html/KCsmart.html
creator: Nandini Badarinarayan

KEGGSOAP
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene list
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
definition: A package that provides a client interface to the KEGG SOAP server
definition source: http://bioconductor.org/packages/2.4/bioc/html/KEGGSOAP.html
creator: Nandini Badarinarayan

KEGGgraph
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: KGML
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: R interface to boost graph library algorithm (RBGL)
definition: KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.
definition source: http://bioconductor.org/packages/2.4/bioc/html/KEGGgraph.html
creator: Nandini Badarinarayan

KGML
type: Class
subclass of: XML

'KLD'
type: Class
subclass of: algorithm

Kolmogorov Smirnov rank-sum based algorithm
type: Class
subclass of: algorithm
definition: KS measures how biased the ranks of a subset of items are among the ranks of the entire set

LBE
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: 'FDR'
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis.
definition source: http://bioconductor.org/packages/2.4/bioc/html/LBE.html
creator: Nandini Badarinarayan

LC-MS data
type: Class
subclass of: data item

LMGene
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Linear modelling
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
definition: LMGene package for analysis of microarray data using a linear model and glog data transformation in the R statistical package
definition source: http://bioconductor.org/packages/2.4/bioc/html/LMGene.html
creator: Nandini Badarinarayan

Locally Moderated Weighted-t (LMW) method
type: Class
subclass of: algorithm

Lognormal Normal Model
type: Class
subclass of: algorithm

Lognormal Normal with Modied Variance Model
type: Class
subclass of: algorithm

LPE
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Local-pooled-error
subclass of: Restriction
  on property: implements
  some values from: 'FDR'
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library.
definition source: http://bioconductor.org/packages/2.4/bioc/html/LPE.html
creator: Nandini Badarinarayan

LPEadj
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: Local-pooled-error
subclass of: Restriction
  on property: implements
  some values from: 'FDR'
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default the LPEadj uses the sample size based variance adjustment.
definition source: http://bioconductor.org/packages/2.4/bioc/html/LPEadj.html
creator: Nandini Badarinarayan

publisher role
type: Class
subclass of: role
definition: A publisher role is a role borne by an organization or individual in which they are responsible for making software available to a particular consumer group. Such organizations or individuals do need to be involved in the development of the software.
definition source: James Malone

Langmuir Isotherm
type: Class
subclass of: algorithm

Laplace mixture model
type: Class
subclass of: algorithm

Library Search Algorithm
type: Class
subclass of: algorithm

Loess algorithm
type: Class
subclass of: algorithm

Logic regression
type: Class
subclass of: algorithm

MAANOVA v1.2 package for MATLAB
type: Class
subclass of: software
definition: Tools for analyzing Micro Array experiments
definition source: http://cran.r-project.org/web/packages/maanova/index.html
creator: Nandini Badarinarayan

Median Average Difference Algorithm
type: Class
subclass of: algorithm

MANOR
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: implements
  some values from: Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)
subclass of: Restriction
  on property: implements
  some values from: HaarSeg algorithm
subclass of: Restriction
  on property: implements
  some values from: AWS algorithm
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: data visualization
    intersection of: SWO_7000015
definition: We propose importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments.
definition source: http://bioconductor.org/packages/2.4/bioc/html/MANOR.html
creator: Nandini Badarinarayan

MAQC data
type: Class
subclass of: data item

MIcroarray Analysis Suite
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200000
definition: Affymetrix® Microarray Suite (MAS) is the core software product in the Affymetrix Software System providing instrument control, data acquisition, and data analysis for the entire GeneChip® platform.
alternative term: Affymetrix MicroArraySuite
alternative term: MAS
definition source: http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf
creator: Nandini Badarinarayan

MicroArraySuite 5.0
type: Class
subclass of: MIcroarray Analysis Suite
alternative term: MAS 5.0 software
creator: Nandini Badarinarayan

MATLAB language
type: Class
subclass of: programming language

MAVI Pro
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000286
creator: Nandini Badarinarayan

Multivariate correlation estimator
type: Class
subclass of: algorithm

Markov Chain Monte Carlo
type: Class
subclass of: algorithm

MCR algorithm
type: Class
subclass of: algorithm
definition: minimum common regions (MCR) algorithm- Minimal common regions (MCRs) are dened as contiguous spans having at least a recurrence rate dened by a parameter (recurrence) across samples.

MCRestimate
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: ALL/AML data set
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
definition: This package includes a function for combining preprocessing and classification methods to calculate misclassification errors
definition source: http://bioconductor.org/packages/2.4/bioc/html/MCRestimate.html
creator: Nandini Badarinarayan

MEDME
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: GFF
definition: MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments
definition source: http://bioconductor.org/packages/2.4/bioc/html/MEDME.html
creator: Nandini Badarinarayan

'MI'
type: Class
subclass of: algorithm

Mutual information matrix (MIM)
type: Class
subclass of: data item

MLInterfaces
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: ALL/AML data set
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: implements
  some values from: k-nearest neighbour classification
definition: Uniform interfaces to machine learning code for data in Bioconductor containers
definition source: http://bioconductor.org/packages/2.4/bioc/html/MLInterfaces.html
creator: Nandini Badarinarayan

MMD
type: Class
subclass of: algorithm
definition: MMD describes the distributions of gene expression levels directly via the marginal distributions. It includes EM algorithm, FDR, it is the percentage of nondifferentially expressed genes among selected genes), false non-discovery rate (denoted as FNDR; it is the percentage of differentially expressed genes among unselected genes),false positive rate (denoted as FPR; it is the percentage of selected genes among nondifferentially expressed genes), and false negative rate (denoted as FNR; it is the percentage of un-selected genes among differentially expressed genes),

MVCClass
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: data visualization
definition: Creates classes used in model-view-controller (MVC) design
definition source: http://bioconductor.org/packages/2.4/bioc/html/MVCClass.html
creator: Nandini Badarinarayan

Mahalanobis distance
type: Class
subclass of: algorithm

MantelCorr
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Clustered data set
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: implements
  some values from: k-means
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data)
definition source: http://bioconductor.org/packages/2.4/bioc/html/MantelCorr.html
creator: Nandini Badarinarayan

MassSpecWavelet
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: Continuous Wavelet Transform (CWT)-based peak detection algorithm
definition: Processing Mass Spectrometry spectrum by using wavelet based algorithm
definition source: http://bioconductor.org/packages/2.4/bioc/html/MassSpecWavelet.html
creator: Nandini Badarinarayan

MeasurementError.cor
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Two-stage measurement error model
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
definition: Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation
definition source: http://bioconductor.org/packages/2.4/bioc/html/MeasurementError.cor.html
creator: Nandini Badarinarayan

MergeMaid
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene list
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: implements
  some values from: Logic regression
subclass of: Restriction
  on property: implements
  some values from: Regression model
definition: The functions in this R extension are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be 'list','matrix', or 'ExpressionSet'. The main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculate the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross-validate associations of gene expression data with survival.
definition source: http://bioconductor.org/packages/2.4/bioc/html/MergeMaid.html
creator: Nandini Badarinarayan

Mfuzz
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: implements
  some values from: OntoDM_000072
definition: Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)
definition source: http://bioconductor.org/packages/2.4/bioc/html/Mfuzz.html
creator: Nandini Badarinarayan

MiPP
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: ALL/AML data set
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Misclassification-Penalized Posteriors (MiPP)
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
definition: This package finds optimal sets of genes that seperate samples into two or more classes.
definition source: http://bioconductor.org/packages/2.4/bioc/html/MiPP.html
creator: Nandini Badarinarayan

Misclassification-Penalized Posteriors (MiPP)
type: Class
subclass of: algorithm

MicroArraySuite 4.0
type: Class
subclass of: MIcroarray Analysis Suite
creator: Nandini Badarinarayan

Mixed model equations
type: Class
subclass of: algorithm

'Needleman-Wunsch'
type: Class
subclass of: algorithm

Nested Effects Models
type: Class
subclass of: algorithm
definition: This includes exhaustive enumeration, triple-based inference,pairwise heuristic, module based inference, greedy hillclimbing

Nonlinear Estimation by Iterative Partial Least Squares
type: Class
subclass of: algorithm

OCplus
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression data
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: 'FDR'
definition: This package allows to characterize the operating characeristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes).
definition source: http://bioconductor.org/packages/2.4/bioc/html/OCplus.html
creator: Nandini Badarinarayan

OLIN
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression data
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: Iterative local regression and model selection
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000010
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
definition: Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data
definition source: http://bioconductor.org/packages/2.4/bioc/html/OLIN.html
creator: Nandini Badarinarayan

OLINgui
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression data
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: Iterative local regression and model selection
subclass of: Restriction
  on property: is executed in
  some values from: data visualization
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000011
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
definition: Graphical user interface for the OLIN package
definition source: http://bioconductor.org/packages/2.4/bioc/html/OLINgui.html
creator: Nandini Badarinarayan

Optiquant
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000325
definition: Computer software for image acquisition, analysis and reporting, for use in the life sciences
definition source: http://www.findownersearch.com/optiquant/7766418/
creator: Nandini Badarinarayan

OrderedList
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Gene list
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: implements
  some values from: Similarity score
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively.
definition source: http://bioconductor.org/packages/2.4/bioc/html/OrderedList.html
creator: Nandini Badarinarayan

OutlierD
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: LC-MS data
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Quantile regression techniques
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
definition: This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/OutlierD.html
creator: Nandini Badarinarayan

Presence-Absence calls with Negative Probesets (PANP)
type: Class
subclass of: algorithm

PAnnBuilder
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Annotation data packages
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
definition: Processing annotation data from public data repositories and building annoation data packages.
definition source: http://bioconductor.org/packages/2.4/bioc/html/PAnnBuilder.html
creator: Nandini Badarinarayan

Pearson correlation estimator
type: Class
subclass of: algorithm

PCpheno
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: Global test
subclass of: Restriction
  on property: implements
  some values from: Hypergeometric enrichment
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways.
definition source: http://bioconductor.org/packages/2.4/bioc/html/PCpheno.html
creator: Nandini Badarinarayan

PGSEA
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene list
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
definition: Parametric Analysis of Gene Set Enrichment
definition source: http://bioconductor.org/packages/2.4/bioc/html/PGSEA.html
creator: Nandini Badarinarayan

'PLM'
type: Class
subclass of: algorithm
definition: it is where we fit a model with probe level and chip level parameters on a probeset by probeset basis

PLPE
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: LC-MS data
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Statistical tests
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: This package performs tests for paired high-throughput data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/PLPE.html
creator: Nandini Badarinarayan

Probe level Locally moderated Weighted median-t (PLW) method
type: Class
subclass of: algorithm

PPC algorithm
type: Class
subclass of: algorithm

PROcess
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: CSV data set
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: k-nearest neighbour classification
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000011
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
definition: A package for processing protein mass spectrometry data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/PROcess.html
creator: Nandini Badarinarayan

Propagation of uncertainty in microarray analysis
type: Class
subclass of: algorithm
definition: Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting and data manipulation functions

Pathways 2.01 software
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000357
definition: The background intensity data from the spot quantification programs may be used to correct spot intensity. This software measures background globally as: BGLow (low background), BGAvg (Average background), BGRms (root mean square background).
definition source: http://maexplorer.sourceforge.net/MaeRefMan/hmaeDoc2.4.2.html
creator: Nandini Badarinarayan

Power Law Global Error Model (PLGEM) analysis method
type: Class
subclass of: algorithm

Probe Cell Analysis
type: Class
subclass of: MicroArraySuite 5.0
creator: Nandini Badarinarayan

PLIER (Probe Logarithmic Error Intensity Estimate) method
type: Class
subclass of: algorithm

QuantArray scanner software
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000325
definition: QuantArray® is a powerful microarray analysis software that enables researchers to easily and accurately visualize and quantitate gene expression data.
alternative term: QuantArray
definition source: http://las.perkinelmer.com/content/relatedmaterials/brochures/bro_quantarray.pdf
creator: Nandini Badarinarayan

QuantArray, PackaardBiochip technologies
type: Class
subclass of: QuantArray scanner software
creator: Nandini Badarinarayan

QuantArray version 2
type: Class
subclass of: QuantArray scanner software
creator: Nandini Badarinarayan

Radial basis function
type: Class
subclass of: algorithm

RBGL
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: gxl format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: BGL
subclass of: Restriction
  on property: is executed in
  some values from: data visualization
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
definition: A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.
definition source: http://bioconductor.org/packages/2.4/bioc/html/RBGL.html
creator: Nandini Badarinarayan

R interface to boost graph library algorithm (RBGL)
type: Class
subclass of: algorithm

RBioinf
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Image
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: Linear modelling
definition: Functions and datasets and examples to accompany the monograph R For Bioinformatics.
definition source: http://bioconductor.org/packages/2.4/bioc/html/RBioinf.html
creator: Nandini Badarinarayan

Random effects model
type: Class
subclass of: algorithm

Recursive Feature Elimination (RFE)
type: Class
subclass of: algorithm
definition: for the Support Vector Machine (SVM), as presented in [3] and the Nearest Shrunken Centroid (NSC)

RLMM
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      intersection of: Xba.CQV and Xba.regions
      intersection of: .raw files
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: implements
  some values from: Mahalanobis distance
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: A Genotype Calling Algorithm for Affymetrix SNP Arrays
definition source: http://bioconductor.org/packages/2.4/bioc/html/RLMM.html
creator: Nandini Badarinarayan

Regression model
type: Class
subclass of: algorithm

RMA
type: Class
subclass of: algorithm

RMA+
type: Class
subclass of: algorithm

RMA++
type: Class
subclass of: algorithm

RMAExpress
type: Class
subclass of: software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      all values from: Class
        union of: CEL binary format
        union of: CDF binary format
subclass of: Restriction
  on property: has specified data output
  some values from: Text data set
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000011
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
subclass of: Restriction
  on property: is developed by
  has value: SWO_0000440
definition: RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip® data using the Robust Multichip Average expression summary and to carry out quality assessment using probe-level metrics. It does not require R nor is it dependent on any component of the BioConductor project. If focuses on processing 3' IVT expression arrays, exon and WT gene arrays.
definition source: http://rmaexpress.bmbolstad.com/
creator: Nandini Badarinarayan

RMAExpress 2.0
type: Class
subclass of: RMAExpress
creator: Nandini Badarinarayan

RMAExpress quantification
type: Class
subclass of: RMAExpress
creator: Nandini Badarinarayan

RMAGEML
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: MAGE-ML
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package can be used to handle MAGEML documents in Bioconductor
definition source: http://bioconductor.org/packages/2.4/bioc/html/RMAGEML.html
creator: Nandini Badarinarayan

RNAither
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Text data set
subclass of: Restriction
  on property: has specified data output
  some values from: HTML report
subclass of: Restriction
  on property: implements
  some values from: Gene-Set Enrichment Analysis
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000015
    intersection of: SWO_7000017
definition: RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes
definition source: http://bioconductor.org/packages/2.4/bioc/html/RNAither.html
creator: Nandini Badarinarayan

ROC
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: utilities for ROC, with uarray focus
definition source: http://bioconductor.org/packages/2.4/bioc/html/ROC.html
creator: Nandini Badarinarayan

RWebServices
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      intersection of: R data frame
      intersection of: .data
      intersection of: SWO_3000034
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package provides mechanisms for automatic function prototyping and exposure of R functionality in a web services environment.
definition source: http://bioconductor.org/packages/2.4/bioc/html/RWebServices.html
creator: Nandini Badarinarayan

RankProd
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Rank product non-parametric method
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Rank Product method for identifying differentially expressed genes with application in meta-analysis
definition source: http://bioconductor.org/packages/2.4/bioc/html/RankProd.html
creator: Nandini Badarinarayan

RbcBook1
type: Class
subclass of: R software
definition: Support for Springer monograph on Bioconductor
definition source: http://bioconductor.org/packages/2.4/bioc/html/RbcBook1.html
creator: Nandini Badarinarayan

Rdbi
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Generic database methods
definition source: http://bioconductor.org/packages/2.4/bioc/html/Rdbi.html
creator: Nandini Badarinarayan

RdbiPgSQL
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Provides methods for accessing data stored in PostgreSQL tables.
definition source: http://bioconductor.org/packages/2.4/bioc/html/RdbiPgSQL.html
creator: Nandini Badarinarayan

Rdisop
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Decomposition of Isotopic Patterns
definition source: http://bioconductor.org/packages/2.4/bioc/html/Rdisop.html
creator: Nandini Badarinarayan

RefPlus
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000011
    intersection of: SWO_7000015
    intersection of: SWO_7000018
definition: The package contains functions for pre-processing Affymetrix data using the RMA+ and the RMA++ methods.
definition source: http://bioconductor.org/packages/2.4/bioc/html/RefPlus.html
creator: Nandini Badarinarayan

Resourcerer
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Annotation data packages
subclass of: Restriction
  on property: has specified data output
  some values from: Text data set
definition: This package allows user either to read an annotation data file from TIGR Resourcerer as a matrix or convert the file into a Bioconductor annotation data package using the AnnBuilder package.
definition source: http://bioconductor.org/packages/2.4/bioc/html/Resourcerer.html
creator: Nandini Badarinarayan

Rgraphviz
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Provides plotting capabilities for R graph objects
definition source: http://bioconductor.org/packages/2.4/bioc/html/Rgraphviz.html
creator: Nandini Badarinarayan

Ringo
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Text data set
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: GFF
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: data visualization
    intersection of: SWO_7000015
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
subclass of: Restriction
  on property: is specified data input of
  qualified cardinality: 2
  on class: Text data set
definition: The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects
definition source: http://bioconductor.org/packages/2.4/bioc/html/Ringo.html
creator: Nandini Badarinarayan

Rintact
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: XML
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: parse
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Queries and data structures for protein interactions
definition source: http://bioconductor.org/packages/2.4/bioc/html/Rintact.html
creator: Nandini Badarinarayan

Rmagpie
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Text data set
subclass of: Restriction
  on property: implements
  some values from: Recursive Feature Elimination (RFE)
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000013
definition: Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations.
definition source: http://bioconductor.org/packages/2.4/bioc/html/Rmagpie.html
creator: Nandini Badarinarayan

Rnw
type: Class
subclass of: Textual format

Robust likelihood-based survival modeling
type: Class
subclass of: algorithm

Rosetta Resolver
type: Class
subclass of: software
subclass of: Restriction
  on property: is developed by
  has value: SWO_0000366
definition: The Rosetta Resolver® system provides a central analysis center and repository for biologists, statisticians, and bioinformaticians for the evaluation of gene expression data from microarrays and qPCR studies.
definition source: http://www.rosettabio.com/products/resolver
creator: Nandini Badarinarayan

RpsiXML
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: XML
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: parse
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously.
definition source: http://bioconductor.org/packages/2.4/bioc/html/RpsiXML.html
creator: Nandini Badarinarayan

Rredland
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Text data set
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: interface to redland RDF utilities
definition source: http://bioconductor.org/packages/2.4/bioc/html/Rredland.html
creator: Nandini Badarinarayan

Rtreemix
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Text data set
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Class
    union of: Likelihood method
    union of: Sim method
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000016
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc.
definition source: http://bioconductor.org/packages/2.4/bioc/html/Rtreemix.html
creator: Nandini Badarinarayan

Ruuid
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Text data set
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Theodore Ts’o’s
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: A package to provide UUID values in R
definition source: http://bioconductor.org/packages/2.4/bioc/html/Ruuid.html
creator: Nandini Badarinarayan

S-Score algorithm
type: Class
subclass of: algorithm

Serial Analysis of Gene Expression (SAGE)
type: Class
subclass of: algorithm

SAGx
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: Linear modelling
    intersection of: 't-test'
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: A package for retrieval, preparation and analysis of data from the Affymetrix GeneChip. In particular the issue of identifying differentially expressed genes is addressed.
definition source: http://bioconductor.org/packages/2.4/bioc/html/SAGx.html
creator: Nandini Badarinarayan

SAM
type: Class
subclass of: algorithm
comment: Note: It is unclear from just the label what is meant by a SAM algorithm. It may or may not be related to the SAM sequence alignment software described by the class SWO_0000077 (Allyson Lister)

SAS/STAT Software, Version 8
type: Class
subclass of: software
subclass of: Restriction
  on property: is developed by
  has value: SWO_0000376
definition: Statistical Analysis with a number of procedures, providing statistical information such as analysis of variance, regression, multivariate analysis, and categorical data analysis.
definition source: http://en.wikipedia.org/wiki/SAS_System
creator: Nandini Badarinarayan

SBMLR
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: SBML
      union of: SBMLR format
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: SBML
      union of: SBMLR format
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package contains a systems biology markup language (SBML) interface and biochemical system analysis tools with illustrative examples.
definition source: http://bioconductor.org/packages/2.4/bioc/html/SBMLR.html
creator: Nandini Badarinarayan

SBMLR format
type: Class
subclass of: Textual format

SDF format
type: Class
subclass of: Textual format

SIM
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression data
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Heat map
    intersection of: Graph plot
    intersection of: Text data set
subclass of: Restriction
  on property: implements
  some values from: Global test
definition: Finds associations between DNA copy number and gene expression.
definition source: http://bioconductor.org/packages/2.4/bioc/html/SIM.html
creator: Nandini Badarinarayan

SLGI
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Annotation data packages
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: A variety of data files and functions for the analysis of genetic interactions
definition source: http://bioconductor.org/packages/2.4/bioc/html/SLGI.html
creator: Nandini Badarinarayan

SLqPCR
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
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      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000015
    intersection of: SWO_7000017
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH
definition source: http://bioconductor.org/packages/2.4/bioc/html/SLqPCR.html
creator: Nandini Badarinarayan

SMAP
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Hidden Markov Model
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: data visualization
    intersection of: SWO_7000017
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Functions and classes for DNA copy number profiling of array-CGH data
definition source: http://bioconductor.org/packages/2.4/bioc/html/SMAP.html
creator: Nandini Badarinarayan

SNPRMA algorithm
type: Class
subclass of: algorithm

SNPchip
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Text data set
subclass of: Restriction
  on property: implements
  some values from: Hidden Markov Model
subclass of: Restriction
  on property: is executed in
  some values from: Class
    union of: data visualization
    union of: data annotation
    union of: SWO_7000017
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package defines classes and functions for plotting copy number and genotype in high throughput SNP platforms such as Affymetrix and Illumina. In particular, SNPchip is a useful add-on to the oligo package for visualizing SNP-level estimates after pre-processing.
definition source: http://bioconductor.org/packages/2.4/bioc/html/SNPchip.html
creator: Nandini Badarinarayan

SPIA
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Signaling Pathway Impact Analysis (SPIA) algorithm
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000017
    intersection of: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.
definition source: http://bioconductor.org/packages/2.4/bioc/html/SPIA.html
creator: Nandini Badarinarayan

Semantic Similarity Measures
type: Class
subclass of: algorithm
definition: Semantic Similarity Measures- Four methods proposed by Resnik[Philip, 1999], Jiang[Jiang and Conrath, 1997], Lin[Lin, 1998] and Schlicker[Schlicker et al., 2006] respectively have presented to determine the semantic similarities of two GO terms based on the annotation statistics of their common ancestor terms. Wang [Wang et al., 2007] proposed a new method to measure the similarities based on the graph structure of GO.

SSPA
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: ALL/AML data set
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Sample size and power analysis for microarray data, where two groups are analysed.
definition source: http://bioconductor.org/packages/2.4/bioc/html/SSPA.html
creator: Nandini Badarinarayan

SVDimpute algorithm
type: Class
subclass of: algorithm

software developer role
type: Class
subclass of: role
definition: Software developer role is a role borne by an organization or individual in which they are responsible for authoring software.
definition source: James Malone

software developer organization
type: Class
equivalent class: Restriction
  on property: has_role
  some values from: software developer role
subclass of: organization
subclass of: Restriction
  on property: has_role
  some values from: software developer role
definition: An organization or legal entity (including single person) that is responsible for developing software. Developing includes aspects of design, coding and testing.

software publisher organization
type: Class
equivalent class: Restriction
  on property: has_role
  some values from: publisher role
subclass of: organization
subclass of: Restriction
  on property: has_role
  some values from: publisher role
definition: An organization or legal entity (including single person) that is responsible for publishing software. Publishing here includes tasks such as designing and producing physical products, technical customer support, licensing arrangements and marketing.

50-50 MANOVA algorithm
type: Class
subclass of: algorithm
definition: Classical multivariate analysis-of-variance tests perform poorly in cases with several highly correlated responses and the tests collapse when the number of responses exceeds the number of observations. This paper presents a new method which handles this problem. The dimensionality of the data is reduced by using principal component decompositions and the final tests are still based on the classical test statistics and their distributions. The methodology is illustrated with an example from the production of sausages with responses from near infrared reflectance spectroscopy. A closely related method for testing relationships in uniresponse regression with collinear explanatory variables is also presented. The new test, which is called the 50-50 F-test, uses the first k components to calculate SSMODEL. The next d components are not involved in SSERROR and they are called buffer components.
definition source: Langsrud, &Oslash. (2002), 50-50 Multivariate Analysis of Variance for Collinear Responses, The Statistician, 51, 305-317.

ArrayExpress Bioconductor
type: Class
subclass of: R software
subclass of: MAGE-TAB inputting software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200004
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000019
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000019
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: MAGE-TAB
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
definition: ArrayExpress Bioconductor package is software that read in MAGE-TAB format files from the ArrayExpress FTP site and converts them to R objects.
definition source: http://bioconductor.org/packages/2.4/bioc/html/ArrayExpress.html
creator: Nandini Badarinarayan

Gene list
type: Class
subclass of: data item

Clustered data set
type: Class
subclass of: data item

R data frame
type: Class
subclass of: Textual format

R language
type: Class
subclass of: programming language

ScISI
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: HTML report
    intersection of: Graph plot
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: data annotation
    intersection of: SWO_7000017
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Package to create In Silico Interactomes
definition source: http://bioconductor.org/packages/2.4/bioc/html/ScISI.html
creator: Nandini Badarinarayan

ScanAlyze
type: Class
subclass of: software
subclass of: Restriction
  on property: is developed by
  has value: SWO_0000431
definition: Processes fluorescent images of microarrays
definition source: http://smd.stanford.edu/resources/restech.shtml
creator: Nandini Badarinarayan

ScanArray
type: Class
subclass of: software
subclass of: Restriction
  on property: is developed by
  has value: SWO_0000325
definition: ScanArray Express provides superior spot finding and quantization algorithm. This combined with template adjustment features drives excellence in analysis performance.
alternative term: ScanArray Express
alternative term: ScanArray Express [PerkinElmer]
definition source: http://las.perkinelmer.com/Catalog/ProductInfoPage.htm
creator: Nandini Badarinarayan

ScanArray v3.1 software
type: Class
subclass of: ScanArray
alternative term: ScanArray version 3.1
creator: Nandini Badarinarayan

scanning software
type: Class
subclass of: software
creator: Nandini Badarinarayan

Scanning software G2565AA version A6.3.1
type: Class
subclass of: scanning software
subclass of: Restriction
  on property: is developed by
  has value: SWO_0000033
definition: High resolution scanning with pixel sizes of 2, 3, 5, and 10 microns enables users to scan a range of array types from ultra-high density commercial arrays as well as low-density home-brew arrays.Low level detection resulting from optimized precision optics, broad dynamic range, minimal spectral cross talk allowing users to detect weak features, achieve rapid, accurate and dependable results
definition source: http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/dnamicroarrayscanner/pages/default.aspx
creator: Nandini Badarinarayan

ShortRead
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Text data set
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Base classes, functions, and methods for representation of high-throughput, short-read sequencing data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/ShortRead.html
creator: Nandini Badarinarayan

Signaling Pathway Impact Analysis (SPIA) algorithm
type: Class
subclass of: algorithm

Silicon Genetics Genespring
type: Class
subclass of: software
subclass of: Restriction
  on property: is developed by
  has value: SWO_0000033
definition: The GeneSpring-R integration package will allow you to expand the capability of GeneSpring by integrating R programs seamlessly into GeneSpring. With the integration package you will be able to use the power of R and BioConductor scripts in GeneSpring's rich graphical environment
alternative term: SiliconGenetics GeneSpring
definition source: http://www.silicongenetics.com/cgi/SiG.cgi/Support/gs_r_int.smf
creator: Nandini Badarinarayan

Similarity score
type: Class
subclass of: algorithm

'Smith-Waterman'
type: Class
subclass of: algorithm

Spot quantification
type: Class
subclass of: software
creator: Nandini Badarinarayan

Spotfinder [TIGR]
type: Class
subclass of: software
subclass of: Restriction
  on property: is developed by
  has value: SWO_0000244
subclass of: Restriction
  on property: is developed by
  has value: SWO_1200008
definition: TIGR Spotfinder was designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression
definition source: http://www.tm4.org/contributors.html
creator: Nandini Badarinarayan

Spotfire
type: Class
subclass of: software
subclass of: Restriction
  on property: is developed by
  has value: SWO_0000433
definition: Spotfire’s interactive, visual capabilities for data analysis empower individuals to easily see trends, patterns outliers and unanticipated relationships in data with unprecedented speed and adaptability.
definition source: http://spotfire.tibco.com/Products/Info.aspx
creator: Nandini Badarinarayan

TAS Software
type: Class
subclass of: Affymetrix Software
subclass of: Restriction
  on property: is published by
  has value: SWO_1200000
definition: Tiling Analysis Software (TAS) is a freely downloadable tool for analysis, with which one can perform a simulation to assess the likelihood that an observed probe overlap region is different from the expected overlap with no enrichment from binding, and can derive an interval overlap report and/or computation of summary statistics.
definition source: http://dmaf.biochem.uci.edu/affymetrix_analysis_software.html
creator: Nandini Badarinarayan

TargetSearch
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Text data set
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      all values from: SWO_3000015
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: Library Search Algorithm
    intersection of: PPC algorithm
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This packages provides a targeted pre-processing method for GC-MS data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/TargetSearch.html
creator: Nandini Badarinarayan

Theodore Ts’o’s
type: Class
subclass of: algorithm

TypeInfo
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    union of: Gene expression dataset
    union of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: A prototype for a mechanism for specifying the types of parameters and the return value for an R function. This is meta-information that can be used to generate stubs for servers and various interfaces to these functions
definition source: http://bioconductor.org/packages/2.4/bioc/html/TypeInfo.html
creator: Nandini Badarinarayan

Variance-stabilizing transformation (VST) algorithm
type: Class
subclass of: algorithm

VanillaICE
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Hidden Markov Model
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays
definition source: http://bioconductor.org/packages/2.4/bioc/html/VanillaICE.html
creator: Nandini Badarinarayan

WilcEbam
type: Class
subclass of: algorithm

Wilcoxon
type: Class
subclass of: algorithm

XDE
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: Markov Chain Monte Carlo
    intersection of: Bayesian Model
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000013
    intersection of: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
definition source: http://bioconductor.org/packages/2.4/bioc/html/XDE.html
creator: Nandini Badarinarayan

XDotsReader
type: Class
subclass of: software
subclass of: Restriction
  on property: is developed by
  has value: SWO_1200006
definition: Analysis Software for Integrated Image Analysis for Spot Detection , Position and Quantification
definition source: http://www.cose.fr/us_dots.html
creator: Nandini Badarinarayan

Xba.CQV and Xba.regions
type: Class
subclass of: data format specification

Array Comparative Genomic Hybridization
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: CSV data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: sproc
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: Hidden Markov Model
subclass of: Restriction
  on property: implements
  some values from: 't-test'
subclass of: Restriction
  on property: implements
  some values from: 'FDR'
definition: The aCGH package functions for reading data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.
definition source: http://bioconductor.org/packages/2.4/bioc/html/aCGH.html
creator: Nandini Badarinarayan

Acuity
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000299
definition: Acuity is the complete enterprise microarray informatics platform for microarray data storage, data filtering and data analysis. It analysis tools for quality, visualizations for discovery and Data Management for Security.
definition source: http://www.bio-medicine.org/
creator: Nandini Badarinarayan

affxparser
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: SWO_3000060
subclass of: Restriction
  on property: has specified data output
  some values from: Text data set
subclass of: Restriction
  on property: is executed in
  some values from: parse
subclass of: Restriction
  on property: has specified data input
  all values from: SWO_3000060
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: affxparser is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK.
definition source: http://bioconductor.org/packages/2.4/bioc/html/affxparser.html
creator: Nandini Badarinarayan

affyContam
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: CEL binary format
      union of: SWO_3000059
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: CEL binary format
      union of: SWO_3000059
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: affyContam is software which provides the in silico creation of quality problems in CEL-level data to help evaluate performance of quality metrics. In essence, it creates structured corruption within CEL data to demonstrate QA effectiveness.
definition source: http://bioconductor.org/packages/2.4/bioc/html/affyContam.html (access unknown); http://www.bioconductor.org/packages/2.12/bioc/vignettes/affyContam/inst/doc/affyContam.pdf, accessed 22 May 2013.
creator: Allyson Lister
creator: Nandini Badarinarayan

affyImGUI
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: implements
  some values from: Class
    union of: 'PLM'
    union of: RMA
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: A Graphical User Interface for affy analysis using the limma Microarray package
definition source: http://bioconductor.org/packages/2.4/bioc/html/affylmGUI.html
creator: Nandini Badarinarayan
comment: Removed the links to specified data inputs, as this software is a GUI wrapper for another package, and it is this package which takes the inputs. (Allyson Lister 22/05/2013)

'affyPLM'
type: Class
subclass of: affypdnn
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: 'PLM'
    intersection of: RMA
    intersection of: M-estimation regression
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000010
    intersection of: SWO_7000015
definition: A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.
definition source: http://bioconductor.org/packages/2.4/bioc/html/affyPLM.html
creator: Nandini Badarinarayan

affyPara
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: CEL binary format
      union of: SWO_3000059
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000005
    intersection of: SWO_7000010
    intersection of: SWO_7000015
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/affyPara.html
creator: Nandini Badarinarayan

affyQCReport
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    some values from: Class
      union of: CEL binary format
      union of: SWO_3000059
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000015
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object.
definition source: http://bioconductor.org/packages/2.4/bioc/html/affyQCReport.html
creator: Nandini Badarinarayan

affyTiling
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      intersection of: CEL binary format
      intersection of: BPMAP
subclass of: Restriction
  on property: has specified data output
  some values from: CSV data set
subclass of: Restriction
  on property: implements
  some values from: RMA
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000010
    intersection of: SWO_7000015
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package provides easy, fast functions for the extraction and annotation of individual probes from Affymetrix tiling arrays.
definition source: http://bioconductor.org/packages/2.4/bioc/html/AffyTiling.html
creator: Nandini Badarinarayan

'affycoretools'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    union of: Rnw
    union of: Text data set
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: HTML report
    intersection of: Graph plot
    intersection of: Text data set
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: RMA
    intersection of: 'FDR'
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see
definition source: http://bioconductor.org/packages/2.4/bioc/html/affycoretools.html
creator: Nandini Badarinarayan

affyio
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: CEL binary format
      union of: CDF binary format
      union of: SWO_3000057
      union of: SWO_3000059
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: CEL binary format
      union of: CDF binary format
      union of: SWO_3000057
      union of: SWO_3000059
subclass of: Restriction
  on property: is executed in
  some values from: parse
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.
definition source: http://bioconductor.org/packages/2.4/bioc/html/affyio.html
creator: Nandini Badarinarayan

affypdnn
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: The package contains functions to perform the PDNN method described by Li Zhang et al.
definition source: http://bioconductor.org/packages/2.4/bioc/html/affypdnn.html
creator: Nandini Badarinarayan

altcdfenvs
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: FASTA format
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: altcdfenvs is a software package for alternative CDF environments (aka probeset mappings) and contains convenience data structures and functions to handle cdfenvs.
definition source: http://www.bioconductor.org/packages/release/bioc/html/altcdfenvs.html, accessed May 28 2013.
creator: Allyson Lister
creator: Nandini Badarinarayan

annaffy
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: HTML report
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package functions for handling data from Bioconductor Affymetrix annotation data packages.Allows searching biological metadata using various criteria.
definition source: http://bioconductor.org/packages/2.4/bioc/html/annaffy.html
creator: Nandini Badarinarayan

'annotate'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: CSV data set
subclass of: Restriction
  on property: has specified data output
  some values from: HTML report
definition: Using R enviroments for annotation.
definition source: http://bioconductor.org/packages/2.4/bioc/html/annotate.html
creator: Nandini Badarinarayan

data annotation
type: Class
subclass of: data transformation

annotationTools
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: CSV data set
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: data annotation
    intersection of: gene expression analysis
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files).
definition source: http://bioconductor.org/packages/2.4/bioc/html/annotationTools.html
creator: Nandini Badarinarayan

Annotation data packages
type: Class
subclass of: data item

'apComplex'
type: Class
subclass of: R software
subclass of: Restriction
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subclass of: Restriction
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subclass of: Restriction
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definition: This package functions to estimate a bipartite graph of protein complex membership using AP-MS data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/apComplex.html
creator: Nandini Badarinarayan

aroma.light
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definition: This package functions as methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.
definition source: http://bioconductor.org/packages/2.4/bioc/html/aroma.light.html
creator: Nandini Badarinarayan

arrayMvout
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definition: This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate
definition source: http://bioconductor.org/packages/2.4/bioc/html/arrayMvout.html
creator: Nandini Badarinarayan

arrayQuality
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    intersection of: HTML report
    intersection of: Graph plot
definition: This package functions for performing print-run and array level quality assessment.
definition source: http://bioconductor.org/packages/2.4/bioc/html/arrayQuality.html
creator: Nandini Badarinarayan

arrayQualityMetrics
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definition: This package generates a quality metrics report on ExpressionSet, NChannelSet, AffyBatch or BeadLevelList objects containing microarray data with one or two channels.
definition source: http://bioconductor.org/packages/2.4/bioc/html/arrayQualityMetrics.html
creator: Nandini Badarinarayan

arrayWoRx 2.0
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subclass of: arrayWoRx
creator: Nandini Badarinarayan

arrayWoRx
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definition: Applied Precision MicroArray Scanner Model arrayWoRx Comprehensive system that fully automates the image capture and quantitation of microarrays. by integrating Slid handling, fluorescent microscopy, and sophisticated spot scan and analysis software the systems detects and measures the fluorescence intensity at each of the specified elements in a microarray. The intensity data can be presented as image data, graphical representation, or as numerical data.
definition source: http://www.hitechtrader.com/detail.cfm
creator: Nandini Badarinarayan

Associative T method
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subclass of: algorithm

AvgNRRs
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subclass of: algorithm

'beadarray'
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definition: The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.
definition source: http://bioconductor.org/packages/2.4/bioc/html/beadarray.html
creator: Nandini Badarinarayan

'beadarraySNP'
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definition: Importing data from Illumina SNP experiments and performing copy number calculations and reports.
definition source: http://bioconductor.org/packages/2.4/bioc/html/beadarraySNP.html
creator: Nandini Badarinarayan

'betr'
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definition: betr is a software package which implements the BETR (Bayesian Estimation of Temporal Regulation) algorithm to identify differentially expressed genes in microarray time-course data.
definition source: http://www.bioconductor.org/packages/2.12/bioc/html/betr.html, accessed 28 May 2013.
creator: Allyson Lister
creator: Nandini Badarinarayan

bgafun
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definition: BGAfun is a method to identify specifity determining residues in protein families
definition source: http://bioconductor.org/packages/2.4/bioc/html/bgafun.html
creator: Nandini Badarinarayan

bgx
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definition: Bayesian integrated analysis of Affymetrix GeneChips
definition source: http://bioconductor.org/packages/2.4/bioc/html/bgx.html
creator: Nandini Badarinarayan

Bitmap object
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subclass of: data item

bioDist
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definition: The bioDist package contains some distance functions that have been shown to be useful in a number of dierent biological or bioinformatic problems. The return values are typically instances of the S3 class dist.
definition source: http://bioconductor.org/packages/2.4/bioc/html/bioDist.html
creator: Nandini Badarinarayan

'biocDatasets'
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subclass of: R software
definition: Synthetic datasets to a) demonstrate the usage of bioconductor packages, b) write unit tests, while keeping dependencies and ressources usage minimal.
definition source: http://bioconductor.org/packages/2.4/bioc/html/biocDatasets.html
creator: Nandini Badarinarayan

'biocGraph'
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    intersection of: HTML report
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definition: This package provides examples and code that make use of the different graph related packages produced by Bioconductor.
definition source: http://bioconductor.org/packages/2.4/bioc/html/biocGraph.html
creator: Nandini Badarinarayan

'biocViews'
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definition: Categorized views of R package repositories
definition source: http://bioconductor.org/packages/2.4/bioc/html/biocViews.html
creator: Nandini Badarinarayan

biomaRT
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definition: The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries.
definition source: http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html
creator: Nandini Badarinarayan

Bootstrap
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subclass of: algorithm

'bridge'
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    intersection of: Markov Chain Monte Carlo
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definition: The bridge package consists of several functions for testing for dierential expression among mul- tiple samples
definition source: http://bioconductor.org/packages/2.4/bioc/html/bridge.html
creator: Nandini Badarinarayan

cdt
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subclass of: SWO_3000046

'cellHTS'
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definition: Bioconductor package concerned with analysis of cell-based RNA interference screens
creator: Nandini Badarinarayan

Axiom
annotated source: 'cellHTS'
annotated property: definition
annotated target: Bioconductor package concerned with analysis of cell-based RNA interference screens
definition source: http://bioconductor.org/packages/2.4/bioc/html/cellHTS.html

'cellHTS2'
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    intersection of: data annotation
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definition: Analysis of cell-based RNA interference screens
definition source: http://bioconductor.org/packages/2.4/bioc/html/cellHTS2.html
creator: Nandini Badarinarayan

cghMCR
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  some values from: SWO_7000015
subclass of: Restriction
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definition: Based on the algothrim proposed by Dr. Lynda Chin's lab, this package provides functions that identify chromosome regions that show gains/losses commonly observed across different samples profiled using arrayCGH platform.
definition source: http://bioconductor.org/packages/2.4/bioc/html/cghMCR.html
creator: Nandini Badarinarayan

chamber slide format
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subclass of: data format specification

cls
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subclass of: Textual format
definition: Categorical (e.g tumor vs normal) class file format
definition source: http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#CLS:_Categorical_.28e.g_tumor_vs_normal.29_class_file_format_.28.2A.cls.29

'clusterStab'
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  some values from: Gene list
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definition: This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters.
definition source: http://bioconductor.org/packages/2.4/bioc/html/clusterStab.html
creator: Nandini Badarinarayan

'codelink'
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definition: This packages allow reading into R of Codelink bioarray data exported as text from the Codelink software. Also includes some functions to ease the manipulation and pre-processing of data, such in background correction and normalization.
definition source: http://bioconductor.org/packages/2.4/bioc/html/codelink.html
creator: Nandini Badarinarayan

dataset comparison
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subclass of: data transformation

Concordance
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convert
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definition: Define coerce methods for microarray data objects.
definition source: http://bioconductor.org/packages/2.4/bioc/html/convert.html
creator: Nandini Badarinarayan

copa
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definition: COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles.
definition source: http://bioconductor.org/packages/2.4/bioc/html/copa.html
creator: Nandini Badarinarayan

cosmo
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  some values from: gene expression analysis
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definition: cosmo searches a set of unaligned DNA sequences for a shared motif that may, for example, represent a common transcription factor binding site. The algorithm is similar to MEME, but also allows the user to specify a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may include bounds on the information content across certain regions of the unknown motif, for example, and can often be formulated on the basis of prior knowledge about the structure of the transcription factor in question. The unknown motif width, the distribution of motif occurrences (OOPS, ZOOPS, or TCM), as well as the appropriate constraint set can be selected data-adaptively.
definition source: http://bioconductor.org/packages/2.4/bioc/html/cosmo.html
creator: Nandini Badarinarayan

cosmoGUI
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definition: cosmoGUI allows the user to interactively define constraint sets that can be used by the cosmo package to supervise the search for shared motifs in a set of DNA sequences. The constraints can be either adapted from a set of commonly used templates or defined from scratch.
definition source: http://bioconductor.org/packages/2.4/bioc/html/cosmoGUI.html
creator: Nandini Badarinarayan

covdesc file
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subclass of: data format specification

database creation
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subclass of: data transformation
definition: An objective in which the aim is to create a new database instance.
definition source: PERSON: James Malone
creator: James Malone

crlmm
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definition: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 6.0.
definition source: http://bioconductor.org/packages/2.4/bioc/html/crlmm.html
creator: Nandini Badarinarayan

ctc
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definition: Tools for export and import classification trees and clusters to other programs
definition source: http://bioconductor.org/packages/2.4/bioc/html/ctc.html
creator: Nandini Badarinarayan

dChip
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definition: Analysis and visualization of gene expression and SNP microarrays
definition source: http://www.bioinformatics.org/dchip/
creator: Nandini Badarinarayan

daMA
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definition: This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/daMA.html
creator: Nandini Badarinarayan

.data
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subclass of: data format specification

dcf
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alternative term: debian control file format

design file
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subclass of: data format specification

'diffGeneAnalysis'
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    intersection of: Graph plot
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definition: Analyze microarray data
definition source: http://bioconductor.org/packages/2.4/bioc/html/diffGeneAnalysis.html
creator: Nandini Badarinarayan

'domainsignatures'
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definition: Find significantly enriched gene classifications in a list of functionally undescribed genes based on their InterPro domain structure.
definition source: http://bioconductor.org/packages/2.4/bioc/html/domainsignatures.html
creator: Nandini Badarinarayan

'dualKS'
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definition: This package implements a Kolmogorov Smirnov rank-sum based algorithm for training and classification of gene expression data sets. One of the chief strengths of this approach is that it is amenable to the "multiclass" problem. That is, it can discriminate between more than 2 classes.
definition source: http://bioconductor.org/packages/2.4/bioc/html/dualKS.html
creator: Nandini Badarinarayan

dyebias
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definition: Gene-specific dye-bias correction of two-color microarray data using the GASSCO method
definition source: http://bioconductor.org/packages/2.4/bioc/html/dyebias.html
creator: Nandini Badarinarayan

Dynamic programming algorithm
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subclass of: algorithm

ecolitk
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Meta data
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids.
definition source: http://bioconductor.org/packages/2.4/bioc/html/ecolitk.html
creator: Nandini Badarinarayan

edd
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
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  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000017
    intersection of: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package provides tools for evaluating cohort distributions of gene expression levels
definition source: http://bioconductor.org/packages/2.4/bioc/html/edd.html
creator: Nandini Badarinarayan

'edgeR'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Digital gene expression (DGE) datasets
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Text data set
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: Negative binomial distribution
    intersection of: Empirical Bayes rule
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: Estimation and Testing for Differential Expression in Multiple Digital Gene Expression Libraries.
definition source: http://bioconductor.org/packages/2.4/bioc/html/edgeR.html
creator: Nandini Badarinarayan

exonmap
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: covdesc file
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: CEL binary format
      union of: CDF binary format
      union of: SWO_3000057
      union of: SWO_3000059
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: RMA
    intersection of: 'FDR'
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package provides fine grained annotation of Affymetrix exon arrays, including mappings between the array probes and probesets and the Ensembl exons, transcripts and genes they target.
definition source: http://bioconductor.org/packages/2.4/bioc/html/exonmap.html
creator: Nandini Badarinarayan

'explorase'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: CSV data set
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Text data set
subclass of: Restriction
  on property: implements
  some values from: Linear modelling
definition: This package explores and analyzes *omics data with R and GGobi
definition source: http://bioconductor.org/packages/2.4/bioc/html/explorase.html
creator: Nandini Badarinarayan

'externalVector'
type: Class
subclass of: R software
definition: Basic class definitions and generics for external pointer based vector objects for R. A simple in-memory implementation is also provided
definition source: http://bioconductor.org/packages/2.4/bioc/html/externalVector.html
creator: Nandini Badarinarayan

f-test
type: Class
subclass of: algorithm

factDesign
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: CEL binary format
      union of: SWO_3000059
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Heat map
    intersection of: Graph plot
    intersection of: Text data set
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: RMA
    intersection of: Linear modelling
    intersection of: 'ANOVA'
    intersection of: 'FDR'
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection.
definition source: http://bioconductor.org/packages/2.4/bioc/html/factDesign.html
creator: Nandini Badarinarayan

fbat
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: pedigree data file
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: Hardy-Weinberg equilibrium
    intersection of: Markov Chain Monte Carlo
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package implements a broad class of Family Based Association Tests for genetids data, with adjustments for population admixture using the code from the 'FBAT' software program
definition source: http://bioconductor.org/packages/2.4/bioc/html/fbat.html
creator: Nandini Badarinarayan

fdrame
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: 'ANOVA'
    intersection of: 'FDR'
subclass of: Restriction
  on property: is executed in
  some values from: gene expression analysis
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma
definition source: http://bioconductor.org/packages/2.4/bioc/html/fdrame.html
creator: Nandini Badarinarayan

flagme
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: CDF binary format
      union of: SWO_3000057
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: Dynamic programming algorithm
    intersection of: AMDIS
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data
definition source: http://bioconductor.org/packages/2.4/bioc/html/flagme.html
creator: Nandini Badarinarayan

flowClust
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: R data frame
      union of: SWO_3000061
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: Multivariate t mixture models
    intersection of: Bayesian Model
    intersection of: Expectation-Maximization(EM) algorithm
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed
definition source: http://bioconductor.org/packages/2.4/bioc/html/flowClust.html
creator: Nandini Badarinarayan

flowCore
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: R data frame
      union of: SWO_3000061
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package provides S4 data structures and basic functions to deal with flow cytometry data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/flowCore.html
creator: Nandini Badarinarayan

flowFlowJo
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: XML
subclass of: Restriction
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  some values from: Restriction
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    all values from: SWO_3000061
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: parse
    intersection of: SWO_7000017
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the "FlowJo Workspace". This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm.
definition source: http://bioconductor.org/packages/2.4/bioc/html/flowFlowJo.html
creator: Nandini Badarinarayan

flowQ
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: SWO_3000061
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: HTML report
    intersection of: Graph plot
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package provides quality control and quality assessment tools for flow cytometry data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/flowQ.html
creator: Nandini Badarinarayan

flowStats
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: SWO_3000061
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package contains methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package.
definition source: http://bioconductor.org/packages/2.4/bioc/html/flowStats.html
creator: Nandini Badarinarayan

flowUtils
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: SWO_3000061
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: XML
subclass of: Restriction
  on property: is executed in
  some values from: parse
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package provides utilities for flow cytometry data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/flowUtils.html
creator: Nandini Badarinarayan

flowViz
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: SWO_3000061
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Text data set
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Provides visualization tools for flow cytometry data
definition source: http://bioconductor.org/packages/2.4/bioc/html/flowViz.html
creator: Nandini Badarinarayan

gaga
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: Gamma-Gamma hierarchical model
    intersection of: 'FDR'
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000017
    intersection of: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package fits Rossell's generalizations of the Gamma-Gamma hierarchical model for microarray data analysis, which substantially improve the quality of the fit at a low computational cost. The model can be fit via empirical Bayes (Expectation-Maximization and Simulated Annealing) and fully Bayesian techniques (Gibbs and Metropolis-Hastings posterior sampling).
definition source: http://bioconductor.org/packages/2.4/bioc/html/gaga.html
creator: Nandini Badarinarayan

'gaggle'
type: Class
subclass of: R software
definition: This package contains functions connecting R with the Gaggle
definition source: http://bioconductor.org/packages/2.4/bioc/html/gaggle.html
creator: Nandini Badarinarayan

gcRMA quantification
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200004
definition: Bioconductor package concerned with background adjustment using sequence information
Contributor: Allyson Lister
creator: Nandini Badarinarayan

Axiom
annotated source: gcRMA quantification
annotated property: definition
annotated target: Bioconductor package concerned with background adjustment using sequence information
definition source: http://www.bioconductor.org/packages/2.3/bioc/html/gcrma.html

gcrma
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: CEL binary format
      union of: SWO_3000059
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: RMA
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000010
    intersection of: SWO_7000015
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Background adjustment using sequence information
definition source: http://bioconductor.org/packages/2.4/bioc/html/gcrma.html
creator: Nandini Badarinarayan

gct
type: Class
subclass of: SWO_3000046
definition: Gene Cluster Text file format
definition source: http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GCT:_Gene_Cluster_Text_file_format_.28.2A.gct.29

'genArise'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Text data set
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000010
    intersection of: SWO_7000015
    intersection of: SWO_7000018
definition: genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.
definition source: http://bioconductor.org/packages/2.4/bioc/html/genArise.html
creator: Nandini Badarinarayan

gene2pathway
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene list
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Hierarchical clustering
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: The package takes a list of genes and predicts to which KEGG pathway each gene maps to. This is done by looking at the InterPro domains of each gene. Each prediction is assigned a confidence score. The package also allows to predict connected component membership of genes within signaling pathways. Separate models for each organism supported by KEGG can be trained.
definition source: http://bioconductor.org/packages/2.4/bioc/html/gene2pathway.html
creator: Nandini Badarinarayan

geneRecommender
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene list
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
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subclass of: Restriction
  on property: implements
  some values from: Gene Recommender algorithm
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000015
    intersection of: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions.
definition source: http://bioconductor.org/packages/2.4/bioc/html/geneRecommender.html
creator: Nandini Badarinarayan

Gene array analysis algorithm
type: Class
subclass of: algorithm

gene expression analysis
type: Class
subclass of: data transformation

Gene expression dataset
type: Class
subclass of: data item

genefilter
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: k-nearest neighbour classification
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Some basic functions for filtering genes
definition source: http://bioconductor.org/packages/2.4/bioc/html/genefilter.html
creator: Nandini Badarinarayan

genemeta
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression data
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: 't-test'
    intersection of: 'FDR'
    intersection of: Class
      union of: Random effects model
      union of: Fixed effect model
definition: A collection of meta-analysis tools for analysing high throughput experimental data
definition: http://bioconductor.org/packages/2.4/bioc/html/GeneMeta.html
definition source: http://bioconductor.org/packages/2.4/bioc/html/GeneMeta.html
creator: Nandini Badarinarayan

geneplotter
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
definition: Some basic functions for plotting genetic data
definition source: http://bioconductor.org/packages/2.4/bioc/html/geneplotter.html
creator: Nandini Badarinarayan

genomeIntervals
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      intersection of: GFF
      intersection of: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Tools for operation on genomic intervals.
definition source: http://bioconductor.org/packages/2.4/bioc/html/genomeIntervals.html
creator: Nandini Badarinarayan

Global test
type: Class
subclass of: algorithm
definition: global test allows the unit of analysis of the microarray experiment to be shifted from the single gene level to the pathway level, where a ‘pathway’ may be any set of genes, e.g. chosen using the Gene Ontology database or from earlier experiments.

globaltest
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
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subclass of: Restriction
  on property: implements
  some values from: globaltest
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Testing whether sets of genes (e.g. KEGG pathways of GO terms) are significantly associated with a clinical variable of interest.
definition source: http://bioconductor.org/packages/2.4/bioc/html/globaltest.html
creator: Nandini Badarinarayan

gmt format
type: Class
subclass of: data format specification

goProfiles
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene list
subclass of: Restriction
  on property: has specified data output
  some values from: Image
subclass of: Restriction
  on property: implements
  some values from: Gene-Set Enrichment Analysis
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: data visualization
    intersection of: SWO_7000017
    intersection of: SWO_7000018
definition: The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'.
definition source: http://bioconductor.org/packages/2.4/bioc/html/goProfiles.html
creator: Nandini Badarinarayan

goTools
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene list
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: dataset comparison
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Wraper functions for description/comparison of oligo ID list using Gene Ontology database
definition source: http://bioconductor.org/packages/2.4/bioc/html/goTools.html
creator: Nandini Badarinarayan

gpls
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subclass of: R software
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  on property: has specified data input
  some values from: Restriction
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subclass of: Restriction
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  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Iteratively ReWeighted Least Squares
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.
definition source: http://bioconductor.org/packages/2.4/bioc/html/gpls.html
creator: Nandini Badarinarayan

gpr format
type: Class
subclass of: SWO_3000046
alternative term: GenePix Pro Results file format

graph
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subclass of: R software
subclass of: Restriction
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  some values from: R interface to boost graph library algorithm (RBGL)
subclass of: Restriction
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    intersection of: distance calculation
    intersection of: SWO_7000017
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: A package that implements some simple graph handling capabilities.
definition source: http://bioconductor.org/packages/2.4/bioc/html/graph.html
creator: Nandini Badarinarayan

gtr
type: Class
subclass of: SWO_3000046

gxl format
type: Class
subclass of: XML

hexbin
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subclass of: R software
subclass of: Restriction
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subclass of: Restriction
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subclass of: Restriction
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  some values from: Hexagon binning algorithm
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: data visualization
    intersection of: SWO_7000015
subclass of: Restriction
  on property: is published by
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definition: Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods.
definition source: http://bioconductor.org/packages/2.4/bioc/html/hexbin.html
creator: Nandini Badarinarayan

Hierarchical clustering
type: Class
subclass of: algorithm

hopach
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression data
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Image
    intersection of: Graph plot
subclass of: Restriction
  on property: implements
  some values from: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: data visualization
    intersection of: distance calculation
    intersection of: SWO_7000005
    intersection of: SWO_7000016
    intersection of: SWO_7000018
definition: The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering).
definition source: http://bioconductor.org/packages/2.4/bioc/html/hopach.html
creator: Nandini Badarinarayan

HTML report
type: Class
subclass of: data item
subclass of: Restriction
  on property: is encoded in
  some values from: HTML

Hypergeometric enrichment
type: Class
subclass of: algorithm

hypergraph
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
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  some values from: Graph plot
subclass of: Restriction
  on property: implements
  some values from: k-cores
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: A package that implements some simple capabilities for representing and manipulating hypergraphs.
definition source: http://bioconductor.org/packages/2.4/bioc/html/hypergraph.html
creator: Nandini Badarinarayan

Icens
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
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subclass of: Restriction
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    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
definition: Many functions for computing the NPMLE for censored and truncated data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/Icens.html
creator: Nandini Badarinarayan

idiogram
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
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  some values from: Class
    intersection of: Image
    intersection of: Graph plot
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: A package for plotting genomic data by chromosomal location
definition source: http://bioconductor.org/packages/2.4/bioc/html/idiogram.html
creator: Nandini Badarinarayan

impute
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Gene expression dataset
subclass of: Restriction
  on property: implements
  some values from: k-nearest neighbour classification
definition: Imputation for microarray data (currently KNN only)
definition source: http://bioconductor.org/packages/2.4/bioc/html/impute.html
creator: Nandini Badarinarayan

iterativeBMA
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Image
    intersection of: Graph plot
subclass of: Restriction
  on property: implements
  some values from: Iterative Bayesian Model Averaging (BMA)
definition: The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402).
definition source: http://bioconductor.org/packages/2.4/bioc/html/iterativeBMA.html
creator: Nandini Badarinarayan

iterativeBMAsurv
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
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subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: implements
  some values from: Iterative Bayesian Model Averaging (BMA)
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/iterativeBMAsurv.html
creator: Nandini Badarinarayan

Iterative local regression and model selection
type: Class
subclass of: algorithm

k-cores
type: Class
subclass of: algorithm

k-means
type: Class
subclass of: algorithm

k-nearest neighbour classification
type: Class
subclass of: algorithm

keggorth
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Test package for a pathway 'ontology'
definition source: http://bioconductor.org/packages/2.4/bioc/html/keggorth.html
creator: Nandini Badarinarayan

lapmix
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
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    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
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  on property: implements
  some values from: Laplace mixture model
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: lapmix is a software package for the identification of differentially expressed genes. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes.
definition source: http://bioconductor.org/packages/2.4/bioc/html/lapmix.html
creator: Allyson Lister
creator: Nandini Badarinarayan

Likelihood method
type: Class
subclass of: algorithm

limma
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
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    intersection of: Text data set
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      on property: has format specification
      all values from: SWO_3000016
subclass of: Restriction
  on property: implements
  some values from: Linear modelling
subclass of: Restriction
  on property: is developed by
  has value: SWO_0000443
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Data analysis, linear models and differential expression for microarray data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/limma.html
creator: Nandini Badarinarayan

limmaGUI
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
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    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      all values from: SWO_3000016
subclass of: Restriction
  on property: implements
  some values from: Linear modelling
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: A Graphical User Interface for the limma Microarray package
definition source: http://bioconductor.org/packages/2.4/bioc/html/limmaGUI.html
creator: Nandini Badarinarayan

Linear modelling
type: Class
subclass of: algorithm

lma
type: Class
subclass of: binary format

Local-pooled-error
type: Class
subclass of: algorithm

log file
type: Class
subclass of: data format specification

logicFS
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: logicFS dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Logic regression
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification.
definition source: http://bioconductor.org/packages/2.4/bioc/html/logicFS.html
creator: Nandini Badarinarayan

logicFS dataset
type: Class
subclass of: data format specification

logitT
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: CEL binary format
      union of: SWO_3000059
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
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  some values from: Class
    intersection of: Logit-t algorithm
    intersection of: 't-test'
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: The logitT library implements the Logit-t algorithm introduced in --A high performance test of differential gene expression for oligonucleotide arrays-- by William J Lemon, Sandya Liyanarachchi and Ming You for use with Affymetrix data stored in an AffyBatch object in R.
definition source: http://bioconductor.org/packages/2.4/bioc/html/logitT.html
creator: Nandini Badarinarayan

Logit-t algorithm
type: Class
subclass of: algorithm

lumi
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Text data set
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Variance-stabilizing transformation (VST) algorithm
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level.
definition source: http://bioconductor.org/packages/2.4/bioc/html/lumi.html
creator: Nandini Badarinarayan

maCorrPlot
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: mas5 format
      union of: .rma format
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: data visualization
    intersection of: SWO_7000011
    intersection of: SWO_7000015
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Graphically displays correlation in microarray data that is due to insufficient normalization
definition source: http://bioconductor.org/packages/2.4/bioc/html/maCorrPlot.html
creator: Nandini Badarinarayan

maDB
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression data
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: data visualization
    intersection of: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: maDB allows to create a simple microarray database to store microarray experiments and annotation data into it. Affymetrix GeneChip expression values as well as values from two color microarrays can be stored into the database. Whole experiments or subsets from a experiment (or also values for a subset of genes in a subset of microarrays) can be fetched back to R. Additionally maDB provides different utility functions for the microarray data analysis like functions to draw MA plots or volcano plots with the data points color coded according to the local point density or functions that allow a replicate handling of miroarrays.
definition source: http://bioconductor.org/packages/2.4/bioc/html/maDB.html
creator: Nandini Badarinarayan

maSigPro
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Heat map
    intersection of: Gene list
    intersection of: Graph plot
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: Regression model
    intersection of: 'FDR'
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments.
definition source: http://bioconductor.org/packages/2.4/bioc/html/maSigPro.html
creator: Nandini Badarinarayan

maanova
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    union of: R data frame
    union of: Text data set
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Text data set
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: Bootstrap
    intersection of: 'ANOVA'
    intersection of: F test
    intersection of: 'FDR'
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000017
    intersection of: SWO_7000018
definition: Analysis of N-dye Micro Array experiment using mixed model effect. Containing anlysis of variance, permutation and bootstrap, cluster and consensus tree.
definition source: http://bioconductor.org/packages/2.4/bioc/html/maanova.html
creator: Nandini Badarinarayan

macat
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Text data set
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: HTML report
    intersection of: Graph plot
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: Radial basis function
    intersection of: k-nearest neighbour classification
    intersection of: Base-Pair-Distance Kernel
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: data visualization
    intersection of: distance calculation
    intersection of: SWO_7000017
    intersection of: SWO_7000018
definition: This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. MACAT is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia (Yeoh et al.Cancer Cell 2002), which is provided in the library 'stjudem'.
creator: Nandini Badarinarayan

made4
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Hierarchical clustering
    intersection of: Graph plot
subclass of: Restriction
  on property: implements
  some values from: OntoDM_000072
definition: Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4.
definition source: http://bioconductor.org/packages/2.4/bioc/html/made4.html
creator: Nandini Badarinarayan

maigesPack
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Image
    intersection of: Clustered data set
    intersection of: HTML report
    intersection of: Graph plot
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: 't-test'
    intersection of: 'ANOVA'
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000015
    intersection of: SWO_7000017
    intersection of: SWO_7000018
definition: This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data
definition source: http://bioconductor.org/packages/2.4/bioc/html/maigesPack.html
creator: Nandini Badarinarayan

makePlatformDesign
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: FASTA format
      union of: CDF binary format
      union of: SWO_3000057
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: makePlatformDesign creates the Platform Design environments (PDenvs) required by oligo.
definition source: http://bioconductor.org/packages/2.4/bioc/html/makePlatformDesign.html
creator: Nandini Badarinarayan

makecdfenv
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: CDF binary format
      union of: SWO_3000057
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment.
definition source: http://bioconductor.org/packages/2.4/bioc/html/makecdfenv.html
creator: Nandini Badarinarayan

marray
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Text data set
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    union of: Graph plot
    union of: Class
      intersection of: Text data set
      intersection of: Restriction
        on property: has format specification
        all values from: gpr format
subclass of: Restriction
  on property: implements
  some values from: Linear modelling
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.
definition source: http://bioconductor.org/packages/2.4/bioc/html/marray.html
creator: Nandini Badarinarayan

'MAS5'
type: Class
subclass of: algorithm

mas5 format
type: Class
subclass of: Textual format

matchprobes
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Class
      union of: CEL binary format
      union of: R data frame
      union of: SWO_3000059
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: CDF binary format
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Basic infrastructure for using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment. For general work with genomic sequences, this package is inadequate. Please refer to the Biostrings package for that.
definition source: http://bioconductor.org/packages/2.4/bioc/html/matchprobes.html
creator: Nandini Badarinarayan

mdqc
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Text data set
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: Multivariate correlation estimator
    intersection of: OntoDM_000072
definition: MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.
definition source: http://bioconductor.org/packages/2.4/bioc/html/mdqc.html
creator: Nandini Badarinarayan

M-estimation regression
type: Class
subclass of: algorithm

metaArray
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Markov Chain Monte Carlo
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: 1) Data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) 2) Combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform
definition source: http://bioconductor.org/packages/2.4/bioc/html/metaArray.html
creator: Nandini Badarinarayan

Meta data
type: Class
subclass of: data item

metahdep
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subclass of: R software
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  on property: has specified data input
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subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
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subclass of: Restriction
  on property: implements
  some values from: Bayesian Model
subclass of: Restriction
  on property: is published by
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definition: Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies
definition source: http://bioconductor.org/packages/2.4/bioc/html/metahdep.html
creator: Nandini Badarinarayan

miRNApath
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
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subclass of: Restriction
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    intersection of: Heat map
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      on property: has format specification
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subclass of: Restriction
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  some values from: gene expression analysis
subclass of: Restriction
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definition: This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes.
definition source: http://bioconductor.org/packages/2.4/bioc/html/miRNApath.html
creator: Nandini Badarinarayan

microRNA
type: Class
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    on property: has format specification
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subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: microRNA is a software package which provides data resources for microRNAs and various functions for manipulating them.
definition source: http://bioconductor.org/packages/2.4/bioc/html/microRNA.html, accessed 28 May 2013.
creator: Allyson Lister
creator: Nandini Badarinarayan

minet
type: Class
subclass of: R software
subclass of: Restriction
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  some values from: Gene expression data
subclass of: Restriction
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    intersection of: Mutual information matrix (MIM)
    intersection of: Graph plot
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    intersection of: mrnet algorithm
    intersection of: ARACNE algorithm
    intersection of: CLR algorithm
subclass of: Restriction
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  some values from: SWO_7000017
definition: This package implements various algorithms for inferring mutual information networks from data. All the algorithms compute the mutual information matrix in order to infer a network. Several mutual information estimators are implemented.
definition source: http://bioconductor.org/packages/2.4/bioc/html/minet.html
creator: Nandini Badarinarayan

mrnet algorithm
type: Class
subclass of: algorithm

Multinomial probit regression with Gaussian Process priors
type: Class
subclass of: algorithm

Multiple testing
type: Class
subclass of: algorithm
definition: multiple testing which includes controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included.

Multivariate t mixture models
type: Class
subclass of: algorithm

multtest
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subclass of: R software
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subclass of: Restriction
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subclass of: Restriction
  on property: is executed in
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subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Resampling-based multiple hypothesis testing
definition source: http://bioconductor.org/packages/2.4/bioc/html/multtest.html
creator: Nandini Badarinarayan

Negative binomial distribution
type: Class
subclass of: algorithm

nem
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subclass of: R software
subclass of: Restriction
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subclass of: Restriction
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subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000015
    intersection of: SWO_7000016
    intersection of: SWO_7000018
definition: Nested Effects Models to reconstruct phenotypic hierarchies
definition source: http://bioconductor.org/packages/2.4/bioc/html/nem.html
creator: Nandini Badarinarayan

Neural networks models
type: Class
subclass of: algorithm

nnNorm
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subclass of: R software
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    union of: Image
    union of: Graph plot
    union of: Restriction
      on property: has format specification
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subclass of: Restriction
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subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.
definition source: http://bioconductor.org/packages/2.4/bioc/html/nnNorm.html
creator: Nandini Badarinarayan

nudge
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subclass of: Restriction
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  some values from: Expectation-Maximization(EM) algorithm
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample)
definition source: http://bioconductor.org/packages/2.4/bioc/html/nudge.html
creator: Nandini Badarinarayan

occugene
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subclass of: Restriction
  on property: implements
  some values from: Markov Chain Monte Carlo
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries.
definition source: http://bioconductor.org/packages/2.4/bioc/html/occugene.html
creator: Nandini Badarinarayan

oligo
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      union of: CEL binary format
      union of: SWO_3000059
subclass of: Restriction
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  some values from: Class
    intersection of: SNPRMA algorithm
    intersection of: CRLMM algorithm
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
definition source: http://bioconductor.org/packages/2.4/bioc/html/oligo.html
creator: Nandini Badarinarayan

oligoClasses
type: Class
subclass of: R software
definition: This package contains class definitions, validity checks, and initialization methods for classes used by the oligo package.
definition source: http://bioconductor.org/packages/2.4/bioc/html/oligoClasses.html
creator: Nandini Badarinarayan

OMICS data
type: Class
subclass of: data item

oneChannelGUI
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subclass of: R software
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    union of: Gene expression dataset
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        union of: CEL binary format
        union of: GEO Matrix Series format
        union of: SWO_3000059
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    intersection of: Graph plot
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    intersection of: Restriction
      on property: has format specification
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    intersection of: RMA
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    intersection of: data visualization
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subclass of: Restriction
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definition: This package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. This library provides a graphical interface allowing QC, filtering, statistical validation, and alternative splicing analysis.
definition source: http://bioconductor.org/packages/2.4/bioc/html/oneChannelGUI.html
creator: Nandini Badarinarayan

ontoTools
type: Class
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subclass of: R software
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  some values from: Restriction
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subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: tools for working with ontologies and graphs
definition source: http://bioconductor.org/packages/2.4/bioc/html/ontoTools.html
creator: Nandini Badarinarayan

pair file
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subclass of: data format specification

pamr
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  on property: is executed in
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subclass of: Restriction
  on property: is published by
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definition: Some functions for sample classification in microarrays
definition source: http://bioconductor.org/packages/2.4/bioc/html/pamr.html
creator: Nandini Badarinarayan

panp
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    intersection of: Gene expression dataset
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        union of: CEL binary format
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    intersection of: Graph plot
    intersection of: CSV data set
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  on property: implements
  some values from: Presence-Absence calls with Negative Probesets (PANP)
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    intersection of: gene expression analysis
    intersection of: SWO_7000017
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.
definition source: http://bioconductor.org/packages/2.4/bioc/html/panp.html
creator: Nandini Badarinarayan

parody
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subclass of: R software
subclass of: Restriction
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  some values from: Restriction
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    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
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subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics
definition source: http://bioconductor.org/packages/2.4/bioc/html/parody.html
creator: Nandini Badarinarayan

parse
type: Class
subclass of: data transformation

pathRender
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subclass of: R software
subclass of: Restriction
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subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: data visualization
    intersection of: SWO_7000018
definition: build graphs from pathway databases, render them by Rgraphviz
definition source: http://bioconductor.org/packages/2.4/bioc/html/pathRender.html
creator: Nandini Badarinarayan

pcaMethods
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    intersection of: Nonlinear Estimation by Iterative Partial Least Squares
    intersection of: SVDimpute algorithm
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    intersection of: data visualization
    intersection of: SWO_7000013
subclass of: Restriction
  on property: is published by
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definition: A cluster based method for missing value estimationn is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided.
definition source: http://bioconductor.org/packages/2.4/bioc/html/pcaMethods.html
creator: Nandini Badarinarayan

pcot2
type: Class
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  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
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subclass of: Restriction
  on property: implements
  some values from: 'FDR'
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: PCOT2 is a permutation-based method for investigating changes in the activity of multi-gene networks. It utilizes inter-gene correlation information to detect significant alterations in gene network activities. Currently it can be applied to two-sample comparisons.
definition source: http://bioconductor.org/packages/2.4/bioc/html/pcot2.html
creator: Nandini Badarinarayan

pdInfoBuilder
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    intersection of: Text data set
    intersection of: CSV data set
    intersection of: Restriction
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        union of: CDF binary format
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subclass of: Restriction
  on property: is executed in
  some values from: data annotation
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.
definition source: http://bioconductor.org/packages/2.4/bioc/html/pdInfoBuilder.html
creator: Nandini Badarinarayan

pdmclass
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subclass of: BioConductor Software
subclass of: R software
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    intersection of: Graph plot
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  some values from: SWO_7000017
subclass of: Restriction
  on property: is published by
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definition: This package can be used to classify microarray data using one of three penalized regression methods; partial least squares, principal components regression, or ridge regression.
definition source: http://bioconductor.org/packages/2.4/bioc/html/pdmclass.html
creator: Nandini Badarinarayan

pedigree data file
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subclass of: data format specification

pgUtils
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subclass of: Restriction
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subclass of: Restriction
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definition: Functions for creating PostgreSQL database tables, with auto incrementing primary keys, selection of foreign keys to allow referencial integrity and a logging mechanism.
definition source: http://bioconductor.org/packages/2.4/bioc/html/pgUtils.html
creator: Nandini Badarinarayan

pickgene
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    intersection of: Median Average Difference Algorithm
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subclass of: Restriction
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definition: Functions to Analyze Microarray (Gene Expression) Data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/pickgene.html
creator: Nandini Badarinarayan

pkgDepTools
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subclass of: Restriction
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subclass of: Restriction
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definition: This package provides tools for computing and analyzing dependency relationships among R packages. It provides tools for building a graph-based representation of the dependencies among all packages in a list of CRAN-style package repositories. There are also utilities for computing installation order of a given package. If the RCurl package is available, an estimate of the download size required to install a given package and its dependencies can be obtained.
definition source: http://bioconductor.org/packages/2.4/bioc/html/pkgDepTools.html
creator: Nandini Badarinarayan

plgem
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subclass of: R software
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    intersection of: Graph plot
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    intersection of: SWO_7000017
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subclass of: Restriction
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  has value: SWO_1200004
definition: PLGEM is useful for detecting differential expression in microarray and proteomics datasets.
definition source: http://bioconductor.org/packages/2.4/bioc/html/plgem.html
creator: Nandini Badarinarayan

plier
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subclass of: R software
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subclass of: Restriction
  on property: has specified data output
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subclass of: Restriction
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  some values from: PLIER (Probe Logarithmic Error Intensity Estimate) method
definition: The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values.
definition source: http://bioconductor.org/packages/2.4/bioc/html/plier.html
creator: Nandini Badarinarayan

Graph plot
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subclass of: data item

plw
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      union of: CEL binary format
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    intersection of: Locally Moderated Weighted-t (LMW) method
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definition: Probe level Locally moderated Weighted median-t (PLW) and Locally Moderated Weighted-t (LMW).
definition source: http://bioconductor.org/packages/2.4/bioc/html/plw.html
creator: Nandini Badarinarayan

Position weight matrix (PWM )
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subclass of: algorithm

ppiStats
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subclass of: R software
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subclass of: Restriction
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definition: Tools for the analysis of protein interaction data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/ppiStats.html
creator: Nandini Badarinarayan

prada
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subclass of: R software
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    intersection of: FACS data
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subclass of: Restriction
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definition: Tools for analysing and navigating data from high-throughput phenotyping experiments based on cellular assays and fluorescent detection (flow cytometry (FACS), high-content screening microscopy).
definition source: http://bioconductor.org/packages/2.4/bioc/html/prada.html
creator: Nandini Badarinarayan

preprocessCore
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definition: A library of core preprocessing routines
definition source: http://bioconductor.org/packages/2.4/bioc/html/preprocessCore.html
creator: Nandini Badarinarayan

puma
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definition: Most analyses of Affymetrix GeneChip data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods.
definition source: http://bioconductor.org/packages/2.4/bioc/html/puma.html
creator: Nandini Badarinarayan

qPCR data
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subclass of: data item

qpcrNorm
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    intersection of: Quantile normalization
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subclass of: Restriction
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definition: The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available.
definition source: http://bioconductor.org/packages/2.4/bioc/html/qpcrNorm.html
creator: Nandini Badarinarayan

qpgraph
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subclass of: Restriction
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definition: Reverse engineering of molecular regulatory networks with qp-graphs
definition source: http://bioconductor.org/packages/2.4/bioc/html/qpgraph.html
creator: Nandini Badarinarayan

Quantile normalization
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subclass of: algorithm

Quantile regression techniques
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quantsmooth
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definition: Quantile smoothing and genomic visualization of array data
definition source: http://bioconductor.org/packages/2.4/bioc/html/quantsmooth.html
creator: Nandini Badarinarayan

qvalue
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subclass of: Restriction
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definition: This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant.
definition source: http://bioconductor.org/packages/2.4/bioc/html/qvalue.html
creator: Nandini Badarinarayan

rHVDM
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definition: Hidden Variable Dynamic Modeling
definition: http://bioconductor.org/packages/2.4/bioc/html/rHVDM.html
creator: Nandini Badarinarayan

rMAT
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definition: R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/rMAT.html
creator: Nandini Badarinarayan

rama
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subclass of: Restriction
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definition: The rama package consists of several functions for robust estimation of two color microarray intensities with replicates
definition source: http://bioconductor.org/packages/2.4/bioc/html/rama.html
creator: Nandini Badarinarayan

Rank-invariant set normalization
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Rank product non-parametric method
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subclass of: algorithm

.raw files
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rbsurv
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definition: This package selects genes associated with survival.
definition source: http://bioconductor.org/packages/2.4/bioc/html/rbsurv.html
creator: Nandini Badarinarayan

rda
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subclass of: Textual format

reb
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definition: A set of functions to dentify regional expression biases
definition source: http://bioconductor.org/packages/2.4/bioc/html/reb.html
creator: Nandini Badarinarayan

rflowcyt
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subclass of: Restriction
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  has value: SWO_1200004
definition: Statistical tools and data structures for analytic flow cytometry
definition source: http://bioconductor.org/packages/2.4/bioc/html/rflowcyt.html
creator: Nandini Badarinarayan

.rma format
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subclass of: SWO_3000079

rsbml
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definition: R support for SBML, using libsbml
definition source: http://bioconductor.org/packages/2.4/bioc/html/rsbml.html
creator: Nandini Badarinarayan

rtracklayer
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definition: R interface to genome browsers and their annotation tracks
definition source: http://bioconductor.org/packages/2.4/bioc/html/rtracklayer.html
creator: Nandini Badarinarayan

safe
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subclass of: Restriction
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subclass of: Restriction
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definition: SAFE is a resampling-based method for testing functional categories is gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions.
definition source: http://bioconductor.org/packages/2.4/bioc/html/safe.html
creator: Nandini Badarinarayan

sagenhaft
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definition: This package implements several functions useful for analysis of SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison
definition source: http://bioconductor.org/packages/2.4/bioc/html/sagenhaft.html
creator: Nandini Badarinarayan

seqLogo
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  some values from: Position weight matrix (PWM )
subclass of: Restriction
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definition: seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo
definition source: http://bioconductor.org/packages/2.4/bioc/html/seqLogo.html
creator: Nandini Badarinarayan

sigPathway
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    intersection of: HTML report
    intersection of: Graph plot
definition: Conducts pathway analysis by calculating the NT_k and NE_k statistics
definition source: http://bioconductor.org/packages/2.4/bioc/html/sigPathway.html
creator: Nandini Badarinarayan

siggenes
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    intersection of: SAM
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definition: Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).
definition source: http://bioconductor.org/packages/2.4/bioc/html/siggenes.html
creator: Nandini Badarinarayan

Sim method
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subclass of: algorithm

simpleaffy
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      intersection of: CEL binary format
      intersection of: covdesc file
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definition: Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures
definition source: http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html
creator: Nandini Badarinarayan

simulatorAPMS
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    intersection of: Graph plot
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subclass of: Restriction
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definition: Functions to computationally simulate the AP-MS technology based on wet-lab data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/simulatorAPMS.html
creator: Nandini Badarinarayan

sizepower
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definition: This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations.
definition source: http://bioconductor.org/packages/2.4/bioc/html/sizepower.html
creator: Nandini Badarinarayan

xmapbridge
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definition: xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format.
definition source: http://bioconductor.org/packages/2.4/bioc/html/xmapbridge.html
creator: Nandini Badarinarayan

snapCGH
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subclass of: Restriction
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definition: Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays.
definition source: http://bioconductor.org/packages/2.4/bioc/html/snapCGH.html
creator: Nandini Badarinarayan

snpMatrix
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definition: Implements classes and methods for large-scale SNP association studies
definition source: http://bioconductor.org/packages/2.4/bioc/html/snpMatrix.html
creator: Nandini Badarinarayan

spikeLI
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definition: Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
definition source: http://bioconductor.org/packages/2.4/bioc/html/spikeLI.html
creator: Nandini Badarinarayan

spkTools
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    intersection of: Average log expression across arrays (ALE)
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definition: The package contains functions that can be used to compare expression measures on different array platforms.
definition source: http://bioconductor.org/packages/2.4/bioc/html/spkTools.html
creator: Nandini Badarinarayan

splicegear
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definition: A set of tools to work with alternative splicing
definition source: http://bioconductor.org/packages/2.4/bioc/html/splicegear.html
creator: Nandini Badarinarayan

splots
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definition: The splots package provides the plotScreen function for the visualization of for high-throughput assays in microtitre plate or chamber slide format.
definition source: http://bioconductor.org/packages/2.4/bioc/html/splots.html
creator: Nandini Badarinarayan

spotSegmentation
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definition: Spot segmentation via model-based clustering and gridding for blocks within microarray slides
definition source: http://bioconductor.org/packages/2.4/bioc/html/spotSegmentation.html
creator: Nandini Badarinarayan

sproc
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sqlite
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sscore
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definition: This package contains an implementation of the S-Score algorithm
definition source: http://bioconductor.org/packages/2.4/bioc/html/sscore.html
creator: Nandini Badarinarayan

ssize
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definition: Functions for computing and displaying sample size information for gene expression arrays.
definition source: http://bioconductor.org/packages/2.4/bioc/html/ssize.html
creator: Nandini Badarinarayan

stam
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    intersection of: data annotation
    intersection of: SWO_7000013
definition: The stam package performs a biologically structured classification of microarray profiles according to clinical phenotypes. GO terms are used to link classification results to biological aspects.
definition source: http://bioconductor.org/packages/2.4/bioc/html/stam.html
creator: Nandini Badarinarayan

Statistical tests
type: Class
subclass of: algorithm
definition: A statistical test is an algorithm for making quantitative decisions to determine which outcomes of a study would lead to a rejection of the null hypothesis for a pre-specified level of significance.
definition source: Modified from http://en.wikipedia.org/wiki/Statistical_test, accessed 9 May 2013; http://www.itl.nist.gov/div898/handbook/prc/section1/prc13.htm, accessed 9 May 2013.

stepNorm
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression data
subclass of: Restriction
  on property: has specified data output
  some values from: Gene expression data
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
definition: Stepwise normalization functions for cDNA microarray data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/stepNorm.html
creator: Nandini Badarinarayan

't-test'
type: Class
subclass of: algorithm

tilingArray
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: CEL binary format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: data visualization
    intersection of: SWO_7000011
    intersection of: SWO_7000015
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Transcript mapping with high-density oligonucleotide tiling arrays
definition source: http://bioconductor.org/packages/2.4/bioc/html/tilingArray.html
creator: Nandini Badarinarayan

timecourse
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: CEL binary format
subclass of: Restriction
  on property: implements
  some values from: RMA
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Functions for data analysis and graphical displays for developmental microarray time course data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/timecourse.html
creator: Nandini Badarinarayan

tkWidgets
type: Class
subclass of: R software
definition source: Widgets to provide user interfaces. tcltk should have been installed for the widgets to run.
definition source: http://bioconductor.org/packages/2.4/bioc/html/tkWidgets.html
creator: Nandini Badarinarayan

topGO
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene list
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Kolmogorov Smirnov rank-sum based algorithm
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.
definition source: http://bioconductor.org/packages/2.4/bioc/html/topGO.html
creator: Nandini Badarinarayan

tspair
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000013
    intersection of: SWO_7000017
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Top Scoring Pairs for Microarray Classification
definition source: http://bioconductor.org/packages/2.4/bioc/html/tspair.html
creator: Nandini Badarinarayan

twilight
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: Pearson correlation estimator
    intersection of: 't-test'
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Estimation of local false discovery rate
definition source: http://bioconductor.org/packages/2.4/bioc/html/twilight.html
creator: Nandini Badarinarayan

Two-stage measurement error model
type: Class
subclass of: algorithm

vbmp
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      all values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Multinomial probit regression with Gaussian Process priors
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000013
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination.
definition source: http://bioconductor.org/packages/2.4/bioc/html/vbmp.html
creator: Nandini Badarinarayan

vsn
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000010
    intersection of: SWO_7000015
    intersection of: SWO_7000018
definition: The package implements a method for normalising microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references
definition source: http://bioconductor.org/packages/2.4/bioc/html/vsn.html
creator: Nandini Badarinarayan

weaver
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: Rnw
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: Rnw
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included.
definition source: http://bioconductor.org/packages/2.4/bioc/html/weaver.html
creator: Nandini Badarinarayan

webbioc
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: CEL binary format
subclass of: Restriction
  on property: has specified data output
  some values from: HTML report
subclass of: Restriction
  on property: implements
  some values from: Multiple testing
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users.
definition source: http://bioconductor.org/packages/2.4/bioc/html/webbioc.html
creator: Nandini Badarinarayan

widgetTools
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Text data set
definition: This packages contains tools to support the construction of tcltk widgets
definition source: http://bioconductor.org/packages/2.4/bioc/html/widgetTools.html
creator: Nandini Badarinarayan

xcms
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: LC-MS data
subclass of: Restriction
  on property: has specified data output
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, and mzData files. Preprocesses data for high-throughput, untargeted analyte profiling.
definition source: http://bioconductor.org/packages/2.4/bioc/html/xcms.html
creator: Nandini Badarinarayan

xps
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: CEL binary format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Text data set
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: RMA
    intersection of: 'MAS5'
    intersection of: DFW
    intersection of: FARMS
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
definition source: http://bioconductor.org/packages/2.4/bioc/html/xps.html
creator: Nandini Badarinarayan

yaqcaffy
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Gene expression dataset
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
definition: Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.
definition source: http://bioconductor.org/packages/2.4/bioc/html/yaqcaffy.html
creator: Nandini Badarinarayan

2-sample pooled t-test
type: Class
subclass of: algorithm

50-50 MANOVA
type: Class
subclass of: R software
subclass of: matlab software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000290
subclass of: Restriction
  on property: implements
  some values from: 50-50 MANOVA algorithm
definition: 50-50 Manova is software in which the 50-50 MANOVA algorithm is implemented.
definition: General linear modeling of fixed-effects models with multiple responses is performed. The function calculates 50-50 MANOVA p-values, ordinary univariate p-values and adjusted p-values using rotation testing.
definition source: http://rss.acs.unt.edu/Rdoc/library/ffmanova/html/ffmanova.html
creator: Nandini Badarinarayan

ABarray
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: CSV data set
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Image
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: CSV data set
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: implements
  some values from: Local-pooled-error
subclass of: Restriction
  on property: implements
  some values from: 't-test'
subclass of: Restriction
  on property: implements
  some values from: 'ANOVA'
subclass of: Restriction
  on property: implements
  some values from: 'FDR'
subclass of: Restriction
  on property: is executed in
  some values from: gene expression analysis
definition: The ABarray is designed to work with Applied Biosystems whole genome microarray platform, as well as any other platform whose data can be tranformed into expression data matrix.
definition source: http://www.bioconductor.org/packages/2.4/bioc/html/ABarray.html
creator: Nandini Badarinarayan

'ACME'
type: Class
subclass of: algorithm
definition: The ACME algorithm is quite straightforward. Using a user-dened quantile of the data,called the threshold, any probes in the data that are above that threshold are considered positive probes. A p-value is then assigned to each probe.

Algorithms for Calculating Microarray Enrichment
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: Algorithms for Calculating Microarray Enrichment
    intersection of: Chi-square
definition: ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.
definition source: http://bioconductor.org/packages/2.4/bioc/html/ACME.html
creator: Nandini Badarinarayan

Affymetrix Expression Console
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200000
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200000
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Image
    intersection of: Restriction
      on property: has format specification
      some values from: CEL binary format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: CHP binary format
subclass of: Restriction
  on property: implements
  some values from: PLIER (Probe Logarithmic Error Intensity Estimate) method
subclass of: Restriction
  on property: implements
  some values from: RMA
subclass of: Restriction
  on property: implements
  some values from: 'MAS5'
definition: Expression Console™ software supports probe set summarization and CHP file generation for 3' expression (e.g., GeneChip® Human Genome U133 Plus 2.0 Array), gene-level (e.g., GeneChip® Human Gene 1.0 ST array) and exon-level arrays (e.g., GeneChip® Human Exon 1.0 ST Array). The Expression Console workflow provides the user with a choice of the more commonly used probe set summarization algorithms
definition source: http://www.affymetrix.com/
creator: Nandini Badarinarayan

AIDA
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000351
definition source: AIDA is a modular software package for evaluation and documentation of images that were obtained with digital devices such as CCD cameras, flat bed scanners, or BAS / FLA- scanners from Fuji. Additionally, AIDA allows the loading of loading a variety of images in other image formats (e.g.: TIFF, JPEG, Bmp, gel). AIDA can control all scanning devices offering a TWAIN compatible driver.
definition source: http://www.raytest.de/index2.html
creator: Nandini Badarinarayan

Average log expression across arrays (ALE)
type: Class
subclass of: algorithm

ALL/AML data set
type: Class
subclass of: data item

AMDIS
type: Class
subclass of: algorithm

ANCOVA
type: Class
subclass of: algorithm
definition: The ANCOVA global test is a test for the association between expression values and clinical entities. The test is carried out by comparison of linear models via the extra sum of squares principle. If the mean expression level for at least one gene diers between corresponding models the global null hypothesis, which is the intersection of all single gene null hypotheses, is violated. FDR

'ANOVA'
type: Class
subclass of: algorithm
definition: ANOVA or Analysis of Variance is a hypothesis testing algorithm which a variable is partitioned into components attributable to different sources of variation.
alternative term: ANNOVA

AP-MS data
type: Class
subclass of: data item

ARACNE algorithm
type: Class
subclass of: algorithm

ARR
type: Class
subclass of: XML

AWS algorithm
type: Class
subclass of: algorithm

Absolute Expression Analysis
type: Class
subclass of: MicroArraySuite 4.0
creator: Nandini Badarinarayan

Absolute Expression Analysis
type: Class
subclass of: MicroArraySuite 5.0
creator: Nandini Badarinarayan

'AffyCompatible'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: CSV data set
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: MAGE-TAB
subclass of: Restriction
  on property: is executed in
  some values from: parse
definition: The AffyCompatible package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.
definition source: http://bioconductor.org/packages/2.4/bioc/html/AffyCompatible.html
creator: Nandini Badarinarayan

'AffyExpress'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Image
    intersection of: Restriction
      on property: has format specification
      some values from: CEL binary format
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: HTML report
    intersection of: Restriction
      on property: has format specification
      some values from: HTML
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: implements
  some values from: 'ANOVA'
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000010
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/AffyExpress.html
creator: Nandini Badarinarayan

Affymetrix GCOS v1.2
type: Class
subclass of: Affymetrix GeneChip Operating Software
creator: Nandini Badarinarayan

Affymetrix GeneChip Operating Software
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200000
definition: The Affymetrix GeneChip Operating Software (GCOS) is an operating system software that controls Affymetrix instruments, acquires data, and executes gene expression analysis. In addition, GCOS contains an embedded database that manages both experiment information and data.
alternative term: Affymetrix GCOS software
alternative term: GCOS software
alternative term: GeneChip Operating Software
definition source: http://www.affymetrix.com
creator: Nandini Badarinarayan

Affymetrix Software
type: Class
equivalent class: Class
  intersection of: software
  intersection of: Restriction
    on property: is published by
    has value: SWO_1200000
subclass of: software
creator: Nandini Badarinarayan

Agi4x44PreProcess
type: Class
subclass of: software with image input
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Heat map
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: cls
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: gct
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: HTML report
    intersection of: Restriction
      on property: has format specification
      some values from: HTML
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: implements
  some values from: Loess algorithm
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000010
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: Preprocessing of Agilent 4x44 array data
definition source: http://bioconductor.org/packages/2.4/bioc/html/Agi4x44PreProcess.html
creator: Nandini Badarinarayan

Agilent Feature Extraction 5.1.1
type: Class
subclass of: Agilent Feature Extraction Software
creator: Nandini Badarinarayan

Agilent Feature Extraction software version 7.1
type: Class
subclass of: Agilent Feature Extraction Software
creator: Nandini Badarinarayan

Agilent Feature Extraction software version 7.5
type: Class
subclass of: Agilent Feature Extraction Software
creator: Nandini Badarinarayan

Agilent Feature Extraction software version A.5.1.1
type: Class
subclass of: Agilent Feature Extraction Software
creator: Nandini Badarinarayan

ArrayVision 6.0 (Imaging Research Inc.)
type: Class
subclass of: ArrayVision
creator: Nandini Badarinarayan

'BCRANK'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: FASTA format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: 'BCRANK'
definition: Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search
definition source: http://bioconductor.org/packages/2.4/bioc/html/BCRANK.html
creator: Nandini Badarinarayan

BGL
type: Class
subclass of: algorithm
definition: BGL implements Depth First Search, Breadth First Search,Dijkstra's, Bellman Ford's and DAG,Johnson's and Floyd Warshall's.Kruskal's algorithm and Prim's algorithm Cuthill-McKee's algorithm Minimum degree Ordering

'BGmix'
type: Class
subclass of: R software
subclass of: Restriction
  on property: implements
  some values from: Markov Chain Monte Carlo
subclass of: Restriction
  on property: implements
  some values from: Bayesian Model
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: Bayesian models for differential gene expression
definition source: http://bioconductor.org/packages/2.4/bioc/html/BGmix.html
creator: Nandini Badarinarayan

BLAST
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000303
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000056
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000303
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: SWO_3000066
    intersection of: Restriction
      on property: has format specification
      some values from: FASTA format
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: SWO_3000066
    intersection of: Restriction
      on property: has format specification
      some values from: GenBank format
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000003
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000004
definition: BLAST, or Basic Local Alignment Search Tool in full, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
definition: The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
definition source: http://blast.ncbi.nlm.nih.gov/Blast.cgi
Contributor: Allyson Lister: added 'achieves objective' axioms for pairwise and multiple sequence alignment classes.
creator: James Malone
creator: Nandini Badarinarayan

Iterative Bayesian Model Averaging (BMA)
type: Class
subclass of: algorithm

Base-Pair-Distance Kernel
type: Class
subclass of: algorithm

BPMAP
type: Class
subclass of: binary format
subclass of: Restriction
  on property: is published by
  has value: SWO_1200000
definition: BPMAP is a binary data format specification created by Affymetrix where the data is stored in big-endian format. The BPMAP format contains information relating to the design of the Affymetrix tiling arrays.
definition source: http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/bpmap.html, accessed 22 May 2013.
creator: Allyson Lister

BRB-ArrayTools
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200005
definition: BRB-ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data. It was developed by professional statisticians experienced in the analysis of microarray data and involved in the development of improved methods for the design and analysis of microarray based experiments. The system incorporates a variety of powerful analytic and visualization tools developed specifically for microarray data analysis.
definition source: http://linus.nci.nih.gov/BRB-ArrayTools.html
creator: Nandini Badarinarayan

'BSgenome'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: FASTA format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: dcf
definition: This document describes the process of forging a BSgenome data package. It is intended for Bioconductor users who want to make a new BSgenome data package
definition source: http://bioconductor.org/packages/2.4/bioc/html/BSgenome.html
creator: Nandini Badarinarayan

BZScan
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000436
definition: BZScan is a free java tool for automatic quantification of DNA microarrays with radioactive labeling. BZScan provides saturation, overshining, and background noise correction, it also gives quality control measures. It can work either in a fully automatic "batch mode" or at different levels of manual operation.
definition source: http://tagc.univ-mrs.fr/bioinformatics/bzscan/
creator: Nandini Badarinarayan

BaldiLongT
type: Class
subclass of: algorithm

BasReader 3.01
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000351
definition: This program may be used to read out image data from all scanners of the FujiFilm BAS series (BAS1000, BAS1500, BAS1800, BAS2000, BAS2500, BAS3000, BAS5000) and the FujiFilm FLA scanners (FLA-2000, FLA-3000).
definition source: http://www.rubion.rub.de/labor/pdf/BASREAD.pdf
creator: Nandini Badarinarayan

Bayesian Model
type: Class
subclass of: algorithm

Beadstudio
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000232
definition: BeadStudio Software is a modular analysis tool for genotyping, gene expression, and methylation applications
definition source: http://www.illumina.com/pages.ilmn
creator: Nandini Badarinarayan

'BicARE'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: HTML report
    intersection of: Restriction
      on property: has format specification
      some values from: HTML
definition: This package is dedicated to biclustering analysis which allows to discover sets of genes that have the same expression pattern accross a set of samples
definition source: http://bioconductor.org/packages/2.4/bioc/html/BicARE.html
creator: Nandini Badarinarayan

'BioMVCClass'
type: Class
subclass of: R software
definition: Creates classes used in model-view-controller (MVC) design that uses Biobase
Contributor: Allyson Lister
creator: Nandini Badarinarayan

Axiom
annotated source: 'BioMVCClass'
annotated property: definition
annotated target: Creates classes used in model-view-controller (MVC) design that uses Biobase
definition source: http://bioconductor.org/packages/2.4/bioc/html/BioMVCClass.html

'Biobase'
type: Class
subclass of: R software
definition: Functions that are needed by many other packages or which replace R functions
definition source: http://bioconductor.org/packages/2.4/bioc/html/Biobase.html
creator: Nandini Badarinarayan

'BiocCaseStudies'
type: Class
subclass of: R software
definition: Software and data to support the case studies.
definition source: http://bioconductor.org/packages/2.4/bioc/html/BiocCaseStudies.html
creator: Nandini Badarinarayan

BioConductor Software
type: Class
equivalent class: Class
  intersection of: software
  intersection of: Restriction
    on property: is published by
    has value: SWO_1200004
subclass of: software
subclass of: Restriction
  on property: is executed in
  some values from: SWO_4000014
definition: Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data. Bioconductor is based primarily on the R programming language, but does contain contributions in other programming languages.
definition: http://www.bioconductor.org/overview
alternative term: Bioconductor
creator: Nandini Badarinarayan
comment: This is a defined class which will be populated if a piece of software identifies itself as having the value 'Bioconductor' for the 'is published by' property. (Allyson Lister)

'Biostrings'
type: Class
subclass of: R software
subclass of: Restriction
  on property: implements
  some values from: 'Needleman-Wunsch'
subclass of: Restriction
  on property: implements
  some values from: 'Smith-Waterman'
definition: Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or set of sequences.
definition source: http://bioconductor.org/packages/2.4/bioc/html/Biostrings.html
creator: Nandini Badarinarayan

BlueFuse
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000492
definition: BlueFuse for Microarrays is a powerful software solution for the analysis of microarray expression and arrayCGH experiments. Operation is simple and fully automated, saving time, removing operator error and subjectivity and ensuring experimental reproducibility.
alternative term: BlueFuse [BlueGnome]
definition source: http://www.cambridgebluegnome.com/bluefuse.htm
creator: Nandini Badarinarayan

'BufferedMatrix'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000015
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Image
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
definition: This package creates a tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/BufferedMatrix.html
creator: Nandini Badarinarayan

'BufferedMatrixMethods'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression data
    intersection of: Restriction
      on property: has format specification
      some values from: CEL binary format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Gene expression data
    intersection of: Restriction
      on property: has format specification
      some values from: CEL binary format
definition: This package involves microarray Data related methods that utlize BufferedMatrix objects
definition source: http://bioconductor.org/packages/2.4/bioc/html/BufferedMatrixMethods.html
creator: Nandini Badarinarayan

'CALIB'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estiamted from external control spikes.
definition source: http://bioconductor.org/packages/2.4/bioc/html/CALIB.html
creator: Nandini Badarinarayan

'CAMERA'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: LC-MS data
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: CSV data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: is executed in
  some values from: data annotation
definition: Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, EIC correlation based tagging of unknown adducts and fragments
creator: Nandini Badarinarayan

CDF binary format
type: Class
subclass of: binary format
subclass of: Restriction
  on property: is published by
  has value: SWO_1200000
definition: The CDF binary format is a binary data format specification created by Affymetrix was created for faster access and smaller file size in comparison to the CDF ASCII format. The values in the file are stored in little-endian format. CDF binary format describes the layout for an Affymetrix GeneChip array. An array may contain Expression, Genotyping, CustomSeq, Copy Number and/or Tag probe sets. All probe set names within an array are unique. Multiple copies of a probe set may exist on a single array as long as each copy has a unique name.
definition source: http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cdf.html, accessed 22 May 2013.
comment: It is unclear whether, originally, this format was intended to be the ASCII or binary version of the CDF format. As such, this class has been renamed as the binary format, and a new class created (CDF ASCII format) to make both options available.

'CMA'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: 'CMA'
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
definition: This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment.
definition source: http://bioconductor.org/packages/2.4/bioc/html/CMA.html
creator: Nandini Badarinarayan

CMA
type: Class
subclass of: algorithm
definition: CMA- it implements k-fold cross validation, MCMC cross validation, bootstrap and (t.test or welch.test or wilcox.test or f.test or kruskal.test or One-step Recursive Feature Elimination or random forest variable importance measure or lasso or elastic net or componentwise boosting)

'CORREP'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: OMICS data
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: Multivariate correlation estimation and statistical inference.
definition source: http://bioconductor.org/packages/2.4/bioc/html/CORREP.html
creator: Nandini Badarinarayan

CRLMM algorithm
type: Class
subclass of: algorithm
definition: This algorithm offers improved confidence scores, quality scores for SNP’s and batches, higher accuracy on different datasets and better performance.

Continuous Wavelet Transform (CWT)-based peak detection algorithm
type: Class
subclass of: algorithm

CARMAweb
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000242
definition: CARMAweb allows the analysis of Affymetrix GeneChip, ABI microarrays and two color microarrays. The analysis includes normalization and data preprocessing, detection for differentially expressed genes, cluster analysis and GO analysis. All calculations (except the cluster analysis) are performed in R using functions provided by the BioConductor packages.
alternative term: CarmaWEB
definition source: https://carmaweb.genome.tugraz.at/carma/
creator: Nandini Badarinarayan

Category analysis
type: Class
subclass of: algorithm

Category
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    all values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Heat map
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: Category analysis
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: A collection of tools for performing category analysis.
definition source: http://bioconductor.org/packages/2.4/bioc/html/Category.html
creator: Nandini Badarinarayan

'ChemmineR'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SDF format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Image
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: HTML report
    intersection of: Restriction
      on property: has format specification
      some values from: HTML
subclass of: Restriction
  on property: implements
  some values from: Binning clustering method
subclass of: Restriction
  on property: is executed in
  some values from: distance calculation
definition: ChemMineR is an open source compound mining framework. It contains functions for atom descriptor calculation, structure similarity searching, clustering of compound libraries and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is integrated with the online ChemMine environment and allows bidirectional communications between the two services.
definition source: http://bioconductor.org/packages/2.4/bioc/html/ChemmineR.html
creator: Nandini Badarinarayan

ChipReader 3.1
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200002
definition: Versarray ChipReader systems are highly sensitive laser confocal systems designed for rapid imaging of microarrays. These are advanced scanners that meet your expectations, differentiating between a spot response and background level, and optimizing the signal on the bottom as well as the top end of the range for increased sensitivity. Results with versarray chipreader systems have a low background, enhanced weak signal detection, and virtually no photobleaching for a long dye lifetime.
alternative term: VersArray ChipReader
definition source: http://www.bio-medicine.org/
creator: Nandini Badarinarayan

ChipSkipper
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200009
definition: ChipSkipper - an integrated tool for analysis, evaluation and quantitation of DNA micro-array data
alternative term: ChipSkipper Microarray Data Evaluation Software
alternative term: ChipSkipper [EMBL]
definition source: http://angiogenesis.dkfz.de/software/chipskipper/index.htm
creator: Nandini Badarinarayan

ChipSkipper V0.99
type: Class
subclass of: ChipSkipper
creator: Nandini Badarinarayan

multiscan
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    union of: Text data set
    union of: CSV data set
subclass of: Restriction
  on property: has specified data output
  some values from: Graph plot
subclass of: Restriction
  on property: implements
  some values from: Non-linear functional regression model
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: A multiscan is an R package for combining multiple scans
definition source: http://bioconductor.org/packages/2.4/bioc/html/multiscan.html
creator: Nandini Badarinarayan

affy
type: Class
subclass of: BioConductor Software
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Restriction
    on property: has format specification
    some values from: Class
      union of: CEL binary format
      union of: CDF binary format
      union of: SWO_3000057
      union of: SWO_3000059
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Image
    intersection of: Graph plot
    intersection of: Text data set
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: RMA
    intersection of: 'MAS5'
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: SWO_7000011
    intersection of: SWO_7000015
    intersection of: SWO_7000018
subclass of: Restriction
  on property: is published by
  has value: SWO_1200004
definition: The affy package contains functions for exploratory oligonucleotide array analysis. The dependance to tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
definition source: http://bioconductor.org/packages/2.4/bioc/html/affy.html
creator: Nandini Badarinarayan

affycomp
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: CSV data set
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Text data set
subclass of: Restriction
  on property: implements
  some values from: Class
    intersection of: RMA
    intersection of: 'MAS5'
subclass of: Restriction
  on property: is executed in
  some values from: Class
    intersection of: dataset comparison
    intersection of: SWO_7000010
definition: The affycomp package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.
definition source: http://bioconductor.org/packages/2.4/bioc/html/affycomp.html
creator: Nandini Badarinarayan

PCMG
type: Class
subclass of: algorithm
definition: PCMG- a bipartite graph in which one set of nodes represents proteins, the other set represents complexes, and an edge from a protein node to a complex node represents membership of the protein in that complex.

Feature Extraction Software
type: Class
subclass of: Affymetrix GeneChip Operating Software
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000019
creator: Nandini Badarinarayan

Chi-square
type: Class
subclass of: algorithm

Annotation-Driven Clustering
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Image
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
subclass of: Restriction
  on property: implements
  some values from: k-means
subclass of: Restriction
  on property: implements
  some values from: 'FDR'
definition: adSplit implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.
definition source: http://bioconductor.org/packages/2.4/bioc/html/adSplit.html
creator: Nandini Badarinarayan

distance calculation
type: Class
subclass of: data transformation

R software
type: Class
equivalent class: Restriction
  on property: is encoded in
  some values from: R language
subclass of: software
subclass of: Restriction
  on property: is encoded in
  some values from: R language
definition: Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments.
definition source: http://www.stat.berkeley.edu/users/terry/zarray/Software/smacode.html
creator: Nandini Badarinarayan

BCRANK
type: Class
subclass of: algorithm
definition: BCRANK is a method that takes a ranked list of genomic regions as input and outputs short DNA sequences that are overrepresented in some part of the list.

Cosmo
type: Class
subclass of: algorithm
definition: cosmo allows the user to target the motif search by specifying a set of constraints that the unknown position weight matrix must satisfy. The algorithm is based on a probabilistic model that describes the DNA sequences of interest through a two- component multinomial mixture model with estimates of the position weight matrix entries obtained by maximizing the observed data likelihood over the smaller parameter space corresponding to the imposed constraints. It includes methods such as Probabilistic models and one-occurrence-per-sequence and zero-or-one-occurrence-per-sequence and two-component mixture

F test
type: Class
subclass of: algorithm

MAGE-TAB inputting software
type: Class
equivalent class: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: MAGE-TAB
subclass of: software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: MAGE-TAB
creator: Nandini Badarinarayan

Text data set
type: Class
subclass of: data item

CSV data set
type: Class
subclass of: data item

Non-linear functional regression model
type: Class
subclass of: algorithm
definition: non-linear functional regression model with both additive and multiplicative error terms

'CoCiteStats'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene list
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: implements
  some values from: Hubert’s gamma
subclass of: Restriction
  on property: implements
  some values from: Jaccard’s index
subclass of: Restriction
  on property: implements
  some values from: Concordance
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
definition: A collection of software tools for dealing with co-citation data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/CoCiteStats.html
creator: Nandini Badarinarayan

CodeLink Expression Analysis Software
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000302
definition: This software has a series of analytical tools to address the manufacturing, detection and data analysis components of a microarray experiment. Together, these tools help optimize performance in an expression profiling study.
definition source: http://www.pubmedcentral.nih.gov/articlerender.fcgi
creator: Nandini Badarinarayan

CodeLink Expression Scanning Software
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000302
definition: Slides are scanned using CodeLink Expression Scanning Software
creator: Nandini Badarinarayan

Complex Estimation Algorithm
type: Class
subclass of: algorithm

Cyber-T
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000439
definition: Cyber-T may be used to statistically determine what the probability is that a specific gene is differentially expressed by determining an associated p-value statistic.
definition source: http://dmaf.biochem.uci.edu/affymetrix_analysis_software.html
creator: Nandini Badarinarayan

'DEDS'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression dataset
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: SAM
subclass of: Restriction
  on property: implements
  some values from: 't-test'
subclass of: Restriction
  on property: implements
  some values from: FC
subclass of: Restriction
  on property: implements
  some values from: 'FDR'
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.
definition source: http://bioconductor.org/packages/2.4/bioc/html/DEDS.html
creator: Nandini Badarinarayan

'DFP'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: CSV data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Discriminant Fuzzy Pattern Algorithm
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: This package provides a supervised technique able to identify differentially expressed genes. The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values.
definition source: http://bioconductor.org/packages/2.4/bioc/html/DFP.html
creator: Nandini Badarinarayan

Discriminant Fuzzy Pattern Algorithm
type: Class
subclass of: algorithm
definition: A DFP version of a FP (fuzzy pattern) only includes those genes that can serve to differentiate it from the rest of the patterns.This algorithm is based on the discretization of float values (gene expression values) stored in an ExpressionSet object into labels combining 'Low', 'Medium' and 'High'

DFW
type: Class
subclass of: algorithm

Digital gene expression (DGE) datasets
type: Class
subclass of: data item

'DNAcopy'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
definition: Segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number
definition source: http://bioconductor.org/packages/2.4/bioc/html/DNAcopy.html
creator: Nandini Badarinarayan

'EBImage'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Image
    intersection of: Restriction
      on property: has format specification
      some values from: CEL binary format
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Image
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000008
definition: EBImage is an R package which provides general purpose functionality for the reading, writing, processing and analysis of images. Furthermore, in the context of microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors.
definition source: http://bioconductor.org/packages/2.4/bioc/html/EBImage.html
creator: Nandini Badarinarayan

'EBarrays'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Gene expression data
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Clustered data set
    intersection of: Restriction
      on property: has format specification
      some values from: data format specification
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: Lognormal Normal Model
subclass of: Restriction
  on property: implements
  some values from: Lognormal Normal with Modied Variance Model
subclass of: Restriction
  on property: implements
  some values from: Empirical Bayes rule
subclass of: Restriction
  on property: implements
  some values from: Gamma Gamma Model
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000018
definition: EBarrays provides tools for the analysis of replicated/unreplicated microarray data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/EBarrays.html
creator: Nandini Badarinarayan

Expectation-Maximization(EM) algorithm
type: Class
subclass of: algorithm

Empirical Bayes rule
type: Class
subclass of: algorithm

Expert 2100
type: Class
subclass of: Agilent Technologies Software
definition: Exper 2100 offers powerful data evaluation tools for all available assays, automatic and manual integration, smear analysis and many assay-specific tools.
definition source: http://www.chem.agilent.com/en-US/products/instruments/lab-on-a-chip/2100expertsoftware/pages/default.aspx
creator: Nandini Badarinarayan

FACS data
type: Class
subclass of: data item
definition: FACS data is data which describes flow cytometry data sets.
definition source: http://www.bioconductor.org/packages/2.12/bioc/vignettes/prada/inst/doc/fcs3.html, accessed 29 May 2013.
creator: Allyson Lister

FARMS
type: Class
subclass of: algorithm

FC
type: Class
subclass of: algorithm

'FDR'
type: Class
subclass of: algorithm

Fixed effect model
type: Class
subclass of: algorithm

Agilent Feature Extraction Software
type: Class
subclass of: Agilent Technologies Software
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000019
definition: The software automatically finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences. Application-specific QC reports summarize results and provide an at-a-glance quality assessment
alternative term: Feature Extraction Software
alternative term: Feature Extraction Software [Agilent Technologies]
alternative term: Feature Extraction software
definition source: http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/featureextractionsoftware/pages/default.aspx
creator: Nandini Badarinarayan

Fischer's Exact Test
type: Class
subclass of: algorithm

GACK
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000003
definition: Dynamically chooses cutoffs for grouping into present/divergent genes based on the shape of the distribution. More resistant to variation in hybridization data than CCACK.
definition source: http://falkow.stanford.edu/whatwedo/software/software.html
creator: Nandini Badarinarayan

GASSCO method
type: Class
subclass of: algorithm

GC-RMA Quantification
type: Class
subclass of: Agilent Technologies Software
definition: Single-user desktop software package for analyzing microarray data from multiple microarray platforms.
alternative term: GC-RMA Quantification (Stratagene ArrayAssist Expression Software)
definition source: http://www.biocompare.com/ProductDetails/475470/ArrayAssist-Expression-Software-(1-year-academic-license).html
creator: Nandini Badarinarayan

GEMTools 2.4
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_0000240
definition: Incyte GEMTools software is an enterprise solution for managing gene expression data using the SQL Server and Oracle relational databases. It was one of the first integrated software packages designed with an easy-to-use interface to help scientist track and analyze the vast amounts of gene expression data generated from microarray experiments. GEMTools can be used quantify and graphically display your gene expression data. Incyte Genomics relied on the GEMTools for internal operations and to track each well, probe, cDNA target, and other components of GEM arrays through ordering, fabrication, image analysis, and final data delivery.
definition source: http://www.baymedia.com/gemtools/
creator: Nandini Badarinarayan

GEO data type
type: Class
subclass of: data item

GEOmetadb
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
definition: The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata.
definition source: http://bioconductor.org/packages/2.4/bioc/html/GEOmetadb.html
creator: Nandini Badarinarayan

GEOquery
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
definition: The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of these data, it is only natural to want to apply BioConductor tools to these data.
definition source: http://bioconductor.org/packages/2.4/bioc/html/GEOquery.html
creator: Nandini Badarinarayan

GGBase
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: Text data set
    intersection of: Restriction
      on property: has format specification
      some values from: Textual format
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: rda
definition: This package is an infrastructure for dealing with hapmap SNP reports, GWAS, etc.
definition source: http://bioconductor.org/packages/2.4/bioc/html/GGBase.html
creator: Nandini Badarinarayan

Gamma Gamma Model
type: Class
subclass of: algorithm

matlab software
type: Class
equivalent class: Restriction
  on property: is encoded in
  some values from: MATLAB language
subclass of: software
subclass of: Restriction
  on property: is encoded in
  some values from: MATLAB language

AtlasImage
type: Class
subclass of: software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_1200007
definition: Computer software for the analysis and comparison of Atlas™ nylon and plastic arrays.
definition source: http://www.clontech.com/images/pacs/634650-PA27475.pdf
creator: Nandini Badarinarayan

CBS
type: Class
subclass of: algorithm
definition: The circular binary segmentation (CBS) algorithm divides the genome into regions of equal copy number . The algorithm tests for change-points using a maximal t-statistic with a permutation reference distribution to obtain the corresponding p-value. The number of computations required for the maximal test statistic is O(N^2),where N is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster algorithm.

CBS algorithm
type: Class
subclass of: algorithm

'CGHbase'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000005
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
definition: Contains functions and classes that are needed by arrayCGH packages.
definition source: http://bioconductor.org/packages/2.4/bioc/html/CGHbase.html
creator: Nandini Badarinarayan

'CGHcall'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: CBS algorithm
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000005
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000015
subclass of: Restriction
  on property: is executed in
  some values from: SWO_7000017
definition: Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.
definition source: http://bioconductor.org/packages/2.4/bioc/html/CGHcall.html
creator: Nandini Badarinarayan

'CGHregions'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: Graph plot
    intersection of: Restriction
      on property: has format specification
      some values from: R data frame
subclass of: Restriction
  on property: implements
  some values from: CBS algorithm
definition: Dimension Reduction for Array CGH Data with Minimal Information Loss
definition source: http://bioconductor.org/packages/2.4/bioc/html/CGHregions.html
creator: Nandini Badarinarayan

CHP binary format
type: Class
subclass of: binary format
subclass of: Restriction
  on property: is published by
  has value: SWO_1200000
definition: CHP binary format is a binary data format specification created by Affymetrix, stored in little-endian format and used to store expression, resequencing and genotyping results from algorithms implemented in the GCOS 1.2, 1.3 and 1.4 and BRLMM Analysis Tool software applications.
definition source: http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/chp.html, http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/chp-xda.html, accessed 22 May 2013.
creator: Allyson Lister
comment: As this is a child of Binary format, it is assumed that this class is intended to represent the binary form of this format. As described in the definition sources, there are other formats for CHP available.

CLR algorithm
type: Class
subclass of: algorithm

'DynDoc'
type: Class
subclass of: R software
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: Rnw
definition: A set of functions to create and interact with dynamic documents and vignettes.
definition source: http://bioconductor.org/packages/2.4/bioc/html/DynDoc.html
creator: Nandini Badarinarayan

FoxDimmicT
type: Class
subclass of: algorithm

GEO Matrix Series format
type: Class
subclass of: Textual format

software before Microsoft 2007
type: Class
equivalent class: Class
  intersection of: software
  intersection of: Restriction
    on property: has version
    some values from: Class
      intersection of: version name
      intersection of: Restriction
        on property: followed by
        has value: SWO_2000007
subclass of: software
subclass of: Restriction
  on property: has version
  some values from: Class
    intersection of: version name
    intersection of: Restriction
      on property: followed by
      has value: SWO_2000007

bcbio
type: Class
subclass of: software
subclass of: Restriction
  on property: has website homepage
  has value: https://github.com/bcbio/bcbio-nextgen
definition: bcbio provides a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.
Contributor: https://github.com/drmarkreuter
creator: Allyson Lister
comment: AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/15

Axiom
annotated source: bcbio
annotated property: definition
annotated target: bcbio provides a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.
definition source: https://github.com/bcbio/bcbio-nextgen

shinyNGS
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_1000070
subclass of: Restriction
  on property: has website homepage
  has value: https://github.com/pinin4fjords/shinyngs
definition: Shinyngs is an R package designed to facilitate downstream analysis of RNA-seq and similar expression data with various exploratory plots and data mining tools.
Contributor: https://github.com/drmarkreuter
creator: Allyson Lister
comment: AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/12

Axiom
annotated source: shinyNGS
annotated property: definition
annotated target: Shinyngs is an R package designed to facilitate downstream analysis of RNA-seq and similar expression data with various exploratory plots and data mining tools.
definition source: https://github.com/pinin4fjords/shinyngs

Seurat
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_1000046
subclass of: Restriction
  on property: has website homepage
  has value: https://satijalab.org/seurat/
definition: Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.
Contributor: https://github.com/drmarkreuter
creator: Allyson Lister
comment: AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/13

Axiom
annotated source: Seurat
annotated property: definition
annotated target: Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.
definition source: https://satijalab.org/seurat/

Graphpad Prism
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_1000002
subclass of: Restriction
  on property: has website homepage
  has value: https://www.graphpad.com/scientific-software/prism/
definition: GraphPad Prism is a commercial scientific 2D graphing and statistics software available for both Windows and Macintosh computers.
Contributor: https://github.com/drmarkreuter
creator: Allyson Lister
comment: AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/14

Axiom
annotated source: Graphpad Prism
annotated property: definition
annotated target: GraphPad Prism is a commercial scientific 2D graphing and statistics software available for both Windows and Macintosh computers.
definition source: https://github.com/drmarkreuter

Salmon
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_1000046
subclass of: Restriction
  on property: has website homepage
  has value: https://combine-lab.github.io/salmon/
definition: Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the concept of quasi-mapping with a two-phase inference procedure) to provide accurate expression estimates very quickly (i.e. wicked-fast) and while using little memory. Salmon performs its inference using an expressive and realistic model of RNA-seq data that takes into account experimental attributes and biases commonly observed in real RNA-seq data.
Contributor: https://github.com/drmarkreuter
creator: Allyson Lister
comment: AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/15

Axiom
annotated source: Salmon
annotated property: definition
annotated target: Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the concept of quasi-mapping with a two-phase inference procedure) to provide accurate expression estimates very quickly (i.e. wicked-fast) and while using little memory. Salmon performs its inference using an expressive and realistic model of RNA-seq data that takes into account experimental attributes and biases commonly observed in real RNA-seq data.
definition source: https://combine-lab.github.io/salmon/

Stavrox
type: Class
subclass of: software
subclass of: Restriction
  on property: has website homepage
  has value: http://www.stavrox.com
definition: StavroX software identifies cross-linked peptides.
term editor: Allyson Lister
Contributor: Allyson Lister
Contributor: Mark Reuter
creator: Allyson Lister
creator: Mark Reuter
comment: AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/35

Axiom
annotated source: Stavrox
annotated property: definition
annotated target: StavroX software identifies cross-linked peptides.
definition source: Mark Reuter

ProteomicsTools
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_1000046
subclass of: Restriction
  on property: has website homepage
  has value: https://github.com/shengqh/RCPA.Tools/wiki
definition: ProteomicsTools software suite contains a bunch of tools used in proteomics research, including identification, result parsing, quantification, and modification.
term editor: Allyson Lister
Contributor: Allyson Lister
Contributor: Mark Reuter
creator: Allyson Lister
creator: Mark Reuter
comment: AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/34

Axiom
annotated source: ProteomicsTools
annotated property: definition
annotated target: ProteomicsTools software suite contains a bunch of tools used in proteomics research, including identification, result parsing, quantification, and modification.
definition source: https://github.com/shengqh/RCPA.Tools

Chromeleon
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_1000002
subclass of: Restriction
  on property: has website homepage
  has value: https://www.thermofisher.com/order/catalog/product/CHROMELEON7#/CHROMELEON7
definition: Chromeleon software provides full integration of Thermo Scientific gas chromatography (GC-MS/MS), liquid chromatography (LC-MS/MS), and ion chromatography (IC-MS) instruments.
term editor: Allyson Lister
Contributor: Allyson Lister
Contributor: Mark Reuter
creator: Allyson Lister
creator: Mark Reuter
comment: AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/32

Axiom
annotated source: Chromeleon
annotated property: definition
annotated target: Chromeleon software provides full integration of Thermo Scientific gas chromatography (GC-MS/MS), liquid chromatography (LC-MS/MS), and ion chromatography (IC-MS) instruments.
definition source: https://www.thermofisher.com/order/catalog/product/CHROMELEON7#/CHROMELEON7

AnalyzerPro
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_1000002
subclass of: Restriction
  on property: has website homepage
  has value: https://www.spectralworks.com/products/analyzerpro/
definition: AnalyzerPro​ is a productivity software application for both low and high resolution LC-MS and GC-MS data with support for multiple vendors’ data. This comprehensive post-processing utility provides optimized workflows for sample-to-sample comparison, target component analysis, quantitation and library searching for data generated from any LC-MS and GC-MS platform
term editor: Allyson Lister
Contributor: Allyson Lister
Contributor: Mark Reuter
creator: Allyson Lister
creator: Mark Reuter
comment: AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/31

Axiom
annotated source: AnalyzerPro
annotated property: definition
annotated target: AnalyzerPro​ is a productivity software application for both low and high resolution LC-MS and GC-MS data with support for multiple vendors’ data. This comprehensive post-processing utility provides optimized workflows for sample-to-sample comparison, target component analysis, quantitation and library searching for data generated from any LC-MS and GC-MS platform
definition source: https://www.spectralworks.com/products/analyzerpro/

SWATH Software
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_1000002
subclass of: Restriction
  on property: has website homepage
  has value: https://sciex.com/technology/swath-acquisition
definition: SWATH is the only data independent acquisition (DIA) technique that allows comprehensive detection and quantitation of virtually every detectable compound in a sample (MS/MSALL). This provides confidence in your quantitative results and virtually eliminates the risk of missing a critical component. SWATH Acquisition strategy can only be achieved through the power and speed of SCIEX TripleTOF® and QTOF technology.
term editor: Allyson Lister
Contributor: Allyson Lister
Contributor: Mark Reuter
creator: Allyson Lister
creator: Mark Reuter
comment: AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/30

Axiom
annotated source: SWATH Software
annotated property: definition
annotated target: SWATH is the only data independent acquisition (DIA) technique that allows comprehensive detection and quantitation of virtually every detectable compound in a sample (MS/MSALL). This provides confidence in your quantitative results and virtually eliminates the risk of missing a critical component. SWATH Acquisition strategy can only be achieved through the power and speed of SCIEX TripleTOF® and QTOF technology.
definition source: https://sciex.com/technology/swath-acquisition

Supernovo
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_1000002
subclass of: Restriction
  on property: has website homepage
  has value: https://www.proteinmetrics.com/products/supernovo/
definition: SupernovoTM is a unique, hands-free solution for end-to-end de novo sequencing of monoclonal antibodies (mAbs), enabling high throughput protein discovery.
term editor: Allyson Lister
Contributor: Allyson Lister
Contributor: Mark Reuter
creator: Allyson Lister
creator: Mark Reuter
comment: AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/29

Axiom
annotated source: Supernovo
annotated property: definition
annotated target: SupernovoTM is a unique, hands-free solution for end-to-end de novo sequencing of monoclonal antibodies (mAbs), enabling high throughput protein discovery.
definition source: https://www.proteinmetrics.com/products/supernovo/

PEAKS DB
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_1000002
subclass of: Restriction
  on property: has website homepage
  has value: http://www.bioinfor.com/peaksdb/
definition: Protein Identification Software including an LC-MS/MS search engine, modification search and PTM profiling, sequence variant search, integration with de novo sequencing, and support for all types of fragment ions.
term editor: Allyson Lister
Contributor: Allyson Lister
Contributor: Mark Reuter
creator: Allyson Lister
creator: Mark Reuter
comment: AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/28

Axiom
annotated source: PEAKS DB
annotated property: definition
annotated target: Protein Identification Software including an LC-MS/MS search engine, modification search and PTM profiling, sequence variant search, integration with de novo sequencing, and support for all types of fragment ions.
definition source: Mark Reuter

HTSeq
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_1000046
subclass of: Restriction
  on property: has website homepage
  has value: https://htseq.readthedocs.io/en/release_0.11.1/
definition: HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
term editor: Allyson Lister
Contributor: Allyson Lister
Contributor: Mark Reuter
creator: Allyson Lister
creator: Mark Reuter
comment: AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/27

Axiom
annotated source: HTSeq
annotated property: definition
annotated target: HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
definition source: https://htseq.readthedocs.io/en/release_0.11.1/overview.html

RNA-SeQC
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_9000085
subclass of: Restriction
  on property: has website homepage
  has value: https://github.com/broadinstitute/rnaseqc
definition: RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis.
term editor: Allyson Lister
Contributor: Allyson Lister
Contributor: Mark Reuter
creator: Allyson Lister
creator: Mark Reuter
comment: AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/26

Axiom
annotated source: RNA-SeQC
annotated property: definition
annotated target: RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis.
definition source: Mark Reuter

RSeQC
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_1000046
subclass of: Restriction
  on property: has website homepage
  has value: http://rseqc.sourceforge.net/
definition: RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.
term editor: Allyson Lister
Contributor: Allyson Lister
Contributor: Mark Reuter
creator: Allyson Lister
creator: Mark Reuter
comment: AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/25

Axiom
annotated source: RSeQC
annotated property: definition
annotated target: RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.
definition source: http://rseqc.sourceforge.net/

SAMtools
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_9000074
subclass of: Restriction
  on property: has website homepage
  has value: https://github.com/samtools/samtools
definition: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
term editor: Allyson Lister
Contributor: Allyson Lister
Contributor: Mark Reuter
creator: Allyson Lister
creator: Mark Reuter
comment: AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/24

Axiom
annotated source: SAMtools
annotated property: definition
annotated target: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
definition source: Mark Reuter

FastQC
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_1000047
subclass of: Restriction
  on property: has website homepage
  has value: https://github.com/s-andrews/FastQC
definition: FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
term editor: Allyson Lister
Contributor: Allyson Lister
Contributor: Mark Reuter
creator: Allyson Lister
creator: Mark Reuter
comment: AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/23

Axiom
annotated source: FastQC
annotated property: definition
annotated target: FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
definition source: Mark Reuter

CutAdapt
type: Class
subclass of: software
subclass of: Restriction
  on property: has license
  some values from: SWO_9000074
subclass of: Restriction
  on property: has website homepage
  has value: https://cutadapt.readthedocs.io/en/stable/
definition: Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
term editor: Allyson Lister
Contributor: Allyson Lister
Contributor: Mark Reuter
creator: Allyson Lister
creator: Mark Reuter
comment: AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/22

Axiom
annotated source: CutAdapt
annotated property: definition
annotated target: Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
definition source: https://cutadapt.readthedocs.io/en/stable/

clause
type: Class
subclass of: information content entity
definition: A licence clause is a component of a licence which defines some aspect of a restriction or conversely permission in how something corresponding to a licence may be legally redistributed, partially redistrubed, extended, modified or otherwise used in some way.
creator: James Malone
label: licence clause

Attribution clause
type: Class
subclass of: clause
definition: An Attribution clause is a license clause intended to provide a specified level of recognition of the licensor as the copyright holder of the work. This can take many forms, including the requirement to preserve any copyright notice, attribution statements and the URL (link) to the original work. The attribution requirement thus serves the dual purpose of ensuring that the publisher receives appropriate credit, and that provenance information is kept intact. There are varying strengths of these clauses, from licensors requesting not to be attributed at all to requiring attribution for all uses of the resource.
definition source: Modified by Allyson Lister from http://creativecommons.org/tag/attribution

Derivatives clause
type: Class
subclass of: clause
definition: Derivatives clauses are license clauses which state what requirements on derivative resource, if any, are attached to a license. The license for a resource may or may not allow the creation of new resources derived from it. If it is allowed, such usage may be restricted in a variety of ways.
definition source: Allyson Lister

Source code clause
type: Class
subclass of: clause
definition: A source code clause is a license clause which states the restrictions placed on the source code for the licensed software, if any. The license for a piece of software may or may not allow access to the source code. If such access is allowed, usage may be restricted in a variety of ways.
definition source: Allyson Lister

Platform clause
type: Class
subclass of: clause
definition: A Platform clause is a license clause which states the platform restrictions for the licensed resource, if any. The license for a resource may or may not allow the use of any platform. If it is allowed, such usage may be restricted in a variety of ways.
definition source: Allyson Lister

Number of installations clause
type: Class
subclass of: clause
definition: A Number of installations clause is a license clause which may limit the number of installations a particular licensee may peform.
definition source: Allyson Lister

Number of users clause
type: Class
subclass of: clause
definition: A Number of users clause is a license clause which may limit the number of users a particular licensee may allow to use the resource.
definition source: Allyson Lister

Time clause
type: Class
subclass of: clause
definition: A time clause is a license clause which states the restrictions placed on the length of time the licensed resource may be used, if any. The license for a resource may or may not allow access to the resource for an unlimited time. If such access is allowed, usage may be restricted in a variety of ways.
definition source: Allyson Lister

Usage clause
type: Class
subclass of: clause
definition: A usage clause is a license clause which states the restrictions placed on how the licensed resource may be used. The license for a resource may restrict how the licensee may use the software. If such access is allowed, usage may be restricted in a variety of ways.
definition source: Allyson Lister

No restrictions on derivatives
type: Class
subclass of: SWO_10000038
disjoint with: Restrictions on derivative software
definition: No restrictions on derivatives is a derivatives clause which places no rules or restrictions on how derivative software is created.
definition source: Allyson Lister

Restrictions on derivative software
type: Class
subclass of: SWO_10000038
definition: Restrictions on derivative software is a derivatives clause which allows the creation of derivatives but which also places some kind of restriction on how derivative software may be created.
definition source: Allyson Lister

Derivatives not allowed
type: Class
subclass of: Derivatives clause
disjoint with: SWO_10000038
definition: Derivatives not allowed clauses are derivatives clauses which state that derivative resources are never allowed using the licensed resource.
definition source: Allyson Lister

derivative code same license
type: Class
subclass of: Restrictions on derivative software
definition: Derivative code same license is a restrictive derivatives clause where derivative software must be released under the same license.
definition source: Allyson Lister

Source code available
type: Class
subclass of: Source code clause
disjoint with: Source code unavailable
definition: A source code available clause is a source code clause which states that the source code for the licensed software is available to the licensee. However, usage of the source code may or may not be restricted in a variety of ways.
definition source: Allyson Lister

Source code unavailable
type: Class
subclass of: Source code clause
definition: A source code unavailable clause is a source code clause which states that the source code for the licensed software is not available to the licensee.
definition source: Allyson Lister

Platform restricted
type: Class
subclass of: Platform clause
disjoint with: Platform unrestricted
definition: Platform restricted is a platform clause which places restrictions on which platform the licensed resource may be installed on.
definition source: Allyson Lister

Platform unrestricted
type: Class
subclass of: Platform clause
definition: Platform unrestrictred is a platform clause which does not place any restrictions on which type of platform the resource may be licensed for.
definition source: Allyson Lister

Number of installations restricted
type: Class
subclass of: Number of installations clause
disjoint with: Number of installations unrestricted
definition: A Number of installations restricted clause is a number of installations clause which restricts the number of times the resource may be installed by any given licensee.
definition source: Allyson Lister

Number of installations unrestricted
type: Class
subclass of: Number of installations clause
definition: A Number of installations unrestricted clause is a number of installations clause which does not restrict the number of times the resource may be installed by any given licensee.
definition source: Allyson Lister

Number of users restricted
type: Class
subclass of: Number of users clause
disjoint with: Number of users unrestricted
definition: A Number of users restricted clause is a number of users clause which restricts the number of users the resource may have for a particular licensee. This may be number of total users, or number of concurrent users.
definition source: Allyson Lister

Number of users unrestricted
type: Class
subclass of: Number of users clause
definition: A Number of users unrestricted clause is a number of users clause which does not restrict the number of users of the licensed resource.
definition source: Allyson Lister

Time for use restricted
type: Class
subclass of: Time clause
disjoint with: Time for use unrestricted
definition: Time for use restricted is a time clause which places restrictions on the length of time the licensed resource may be used.
definition source: Allyson Lister

Time for use unrestricted
type: Class
subclass of: Time clause
definition: Time for use unrestrictred is a time clause which does not place any restrictions on the length of time the resource may be licensed for.

Usage unrestricted
type: Class
subclass of: Usage clause
disjoint with: Usage restricted
definition: Usage unrestricted is a usage clause which places no restrictions on how the licensed resource may be used.
definition source: Allyson Lister

Usage restricted
type: Class
subclass of: Usage clause
definition: Usage restricted is a usage clause which places restrictions on how the licensed resource may be used. These restrictions will vary according to the individual license.
definition source: Allyson Lister

Non-commercial use only
type: Class
subclass of: Usage restricted
definition: Non-commercial use only is a usage restricted clause which restricts the use of the licensed resource only to licensees who are not commercial entites.

Academic use only
type: Class
subclass of: Usage restricted
definition: Academic use only is a usage restricted clause which restricts the use of the licensed resource to academic licensees only.
definition source: Allyson Lister

derivative code linked same license
type: Class
subclass of: Restrictions on derivative software
definition: Derivative code linked same license is a restrictive derivatives clause where code may only be linked to in derivative software that is released under the same license.
definition source: Allyson Lister

software interface
type: Class
subclass of: information content entity
definition: The mode of interaction with a piece of software.

Microsoft Excel
type: Class
subclass of: Microsoft developed software
subclass of: Restriction
  on property: output of
  some values from: Class
    intersection of: SWO_9000055
    intersection of: Restriction
      on property: has participant
      has value: SWO_9000001
subclass of: Restriction
  on property: has specified data input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000002
subclass of: Restriction
  on property: has specified data output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: has format specification
      some values from: SWO_3000002
subclass of: Restriction
  on property: has interface
  some values from: SWO_9000052
subclass of: Restriction
  on property: is executed in
  some values from: SWO_4000001
subclass of: Restriction
  on property: has license
  some values from: SWO_1000002

Microsoft Excel for Windows 2010
type: Class
subclass of: Microsoft Excel