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.
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
editor preferred label
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not.
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.
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.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative label
alternative term
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.
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
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).
definition source
Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
imported from
For external terms/classes, the ontology from which the term was imported
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
Person:Alan Ruttenberg
Add as annotation triples in the granting ontology
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
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.
is a defining property chain axiom where second argument is reflexive
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.
An entity responsible for making contributions to the content of the resource.
Contributor
The version in which a class or property has been made obsolete
Allyson Lister 14.9.22: Added as a temporary workaround with issues relating to equivalentClass axioms between IAO software and SWO software.
'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.
Alan Ruttenberg
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
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.
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/
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
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'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
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.
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'.
has_part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[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])
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
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
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])
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
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.
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.
is preceded by
preceded_by
precedes
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.
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
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.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
has_specified_input
see is_input_of example_of_usage
The inverse property of is_specified_input_of
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Alan Ruttenberg
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
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.
is_specified_input_of
has_specified_output
The inverse property of is_specified_output_of
is_manufactured_by
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)
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.
Liju Fan
has_make
has_manufacturer
is_specified_output_of
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.
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
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.
inheres in
this fragility inheres in this vase
this fragility is a characteristic of this vase
this red color inheres in this apple
this red color is a characteristic of this apple
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.
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
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
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.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
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
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.
bearer_of
is bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
Please see the official RO definition for the inverse of this property, 'has participant.'
has participant
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.
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
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.
a relation between a process and a continuant, in which the continuant is somehow involved in the process
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.
has_participant
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).
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).
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.
is concretized as
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).
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.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
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.
function_of
is function of
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.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
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.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
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.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
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.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
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.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
disposition of
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.
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.
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 negative regulatory component activity
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.
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 positive regulatory component activity
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
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.
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.
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.
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.
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.
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
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.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
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.
has component
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.
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
negatively regulates (process to process)
negatively regulates
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
positively regulates (process to process)
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
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.
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)".
capable of
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.
capable of part of
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.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
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.
has input
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.
has output
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.
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.
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
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.
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.
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
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.
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.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
characteristic of part of
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
a particular instances of akt-2 enables some instance of protein kinase activity
c enables p iff c is capable of p and c acts to execute p.
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.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
part of structure that is capable of
c involved_in p if and only if c enables some process p', and p' is part of p
involved in
enabled by
regulated by
negatively regulated by
positively regulated by
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
An entity A is the 'input of' another entity B if A was put into the system, entity or software represented by B.
input of
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.
An entity A is the 'output of' another entity B if it was produced as a result of the functioning of entity B.
output of
causally downstream of
immediately causally downstream of
p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
indirectly positively regulates
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
indirectly negatively regulates
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.
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 yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
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.
causally upstream of
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.
immediately causally upstream of
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.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
inverse of causally upstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
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
OWL does not allow defining object properties via a Union
involved in or involved in regulation of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
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.
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.
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.
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
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.
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.
directly negatively regulates activity of
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.
directly positively regulates activity of
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
A relationship between a material entity and a process where the material entity has some causal role that influences the process
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.
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
molecular interaction relation helper property
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).
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
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
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.
causal relation between material entity and a process
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
acts upstream of or within, positive effect
acts upstream of or within, negative effect
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
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
causally upstream of or within, negative effect
causally upstream of or within, positive effect
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.
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.
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
indirectly regulates
A diagnostic testing device utilizes a specimen.
X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
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.
See github ticket https://github.com/oborel/obo-relations/issues/497
device utilizes material
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.
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.
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.
AL 2023-03-05: Replaced by rdfs:comment as no longer within the EFO release files.
obsolete reason_for_obsolescence
AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs.
obsolete is developed by
The relationship between software and a software publisher.
This class can be entirely replaced with 'is published by', SWO_0004004. Please use SWO_0004004 instead.
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.
obsolete implements
obsolete is encoded in
'is version of' provides a link between a 'version name' and the entity with that version.
For further information, please see http://softwareontology.wordpress.com/2012/06/20/versioning-in-swo/
is version of
Cytoscape plugins would be linked to the Cytoscape application via uses software, while Microsoft Excel is linked to Microsoft Office via has_part.
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.
uses software
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.
is implemented by
The relationship between input data which is permitted to a piece of software.
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.
See also http://softwareontology.wordpress.com/2011/04/15/ins-and-outs-of-software/
The relationship between a piece of software and the data that it is possible to output.
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.
has specified data output
The relationship between a data and the software which can possibly take this data as input.
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 input of
The relationship between a data and the software which can possibly produce this data as output.
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.
is specified data output of
Microsoft version 2007 is directly preceded by Microsoft version 2003.
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.
'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.
directly followed by
'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.
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.
uses platform
is software for
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.
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.
The relationship between a software and software developer.
implements is the relationship between software and an algorithm that is defined for use within that software when executed.
Linking a type of software to its particular programming language.
Is encoded in is an "is about" relationship which describes the type of encoding used for the referenced class.
relationship between an entity and a version name or number
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.
Has format specification is a type of "is encoded in" relationship which specifically describes the relationship between data and a data format specification.
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.
'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.
Stores those object properties which are no longer appropriate for use within SWO.
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,
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.
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.
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.
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 license for
The format for BioPAX Manchester OWL syntax is an alternative format of the BioPAX RDF/XML format.
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.
is alternative format of
'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.
http://www.gnu.org/licenses/gpl-faq.html#WhatDoesCompatMean, accessed 12 June 2013.
is compatible license of
'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.
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.
The inverse property. 'part of', contains the full official RO 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.)
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".
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.
has documentation
The location from where the software can be downloaded.
has download location
The URL of the homepage for the resource this property is associated with.
The official date of release of software
A URL for a source of support information about software
An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc.
A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment.
Image, hybridisation or some other data arising from a study of gene expression, typically profiling or quantification.
Biological or biomedical data has been rendered into an image, typically for display on screen.
Groupings of gene expression profiles according to a clustering algorithm.
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.
Extensible Markup Language (XML) is a standard set of rules for encoding documents in a machine-readable form defined by the W3C.
OBO format is the text file format used by OBO-Edit, the open source, platform-independent application for viewing and editing ontologies.
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.
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.
PSI-MI format
Modified from http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012.
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.
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
Search or query a data resource and retrieve entries and / or annotation.
Annotate a genome sequence with terms from a controlled vocabulary.
Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models.
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.
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.
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.
AL 25.9.19: Already obsoleted in originating ontology (OntoDM) so added here so people could see the history of the term.
data visualization task is information processing objective achieved by a data visualization algorithm execution process.
A planned process that has specified output a software product and that involves the creation of source code.
Mathias Brochhausen
William R. Hogan
A planned process resulting in a software product involving the creation of source code.
software development
creating a data set
A planned process that has a data set as its specified output.
data set creation
dataset creation
dataset creating
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
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
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
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
continuant
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.
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
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
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])
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])
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])
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])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
An entity that has temporal parts and that happens, unfolds or develops through time.
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
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.
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.
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.
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])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
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])
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])
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])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(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]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
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])
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)
(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]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
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.
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])
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])
(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]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
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.
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])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(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]
(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]
realizable entity
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
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])
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])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(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]
quality
specifically dependent continuant
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
of one-sided specifically dependent continuants: the mass of this tomato
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.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
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])
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])
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.
(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]
(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]
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.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
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.
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.
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])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
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.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
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.
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])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
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.
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])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
material entity
Collection of random bacteria, a chair, dorsal surface of the body.
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
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.
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
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
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.
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.
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])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(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]
(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]
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.
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.
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.
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.
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
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.
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
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.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Melanie Courtot
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
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.
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."
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.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
Pour the contents of flask 1 into flask 2
A directive information entity that describes an action the bearer will take.
OBI Plan and Planned Process branch
action specification
datum label
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
GROUP: IAO
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
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
PERSON: Chris Stoeckert
GROUP: OBI
programming language
R, Perl, Java
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.
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.
person:Chris Stoeckert
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
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
PERSON: Jonathan Rees
data
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
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).
PERSON: James A. Overton
based on Oxford English Dictionary
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity.
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).
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.
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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.
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.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
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
directive information entity
dot plot
Dot plot of SSC-H and FSC-H.
A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
person:Allyson Lister
graph
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
PERSON: Lawrence Hunter
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
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.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
source code module
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.
A source code module is a directive information entity that specifies, using a programming language, some algorithm.
data format specification
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
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"
OBI branch derived
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
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.
image
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
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.
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.
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.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Clint Dowland
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 number
A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
material information bearer
A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
a brain
a hard drive
A material entity in which a concretization of an information content entity inheres.
histogram
A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
PERSON:Chris Stoeckert
PERSON:James Malone
heatmap
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.
dendrogram
Dendrograms are often used in computational biology to illustrate the clustering of genes.
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.
WEB: http://en.wikipedia.org/wiki/Dendrogram
scatter plot
Comparison of gene expression values in two samples can be displayed in a scatter plot
A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
scattergraph
WEB: http://en.wikipedia.org/wiki/Scatterplot
obsolescence reason specification
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.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
figure
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
diagram
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
A figure that expresses one or more propositions
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
denotator type
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.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Barry Smith, Werner Ceusters
planned process
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
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.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
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
a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
Person:Jennifer Fostel
OBI
regulator role
regulatory role
Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
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.
GROUP: Role branch
OBI, CDISC
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
Jackson Labs is an organization which provide mice as experimental material
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
Supplier role is a special kind of service, e.g. biobank
PERSON:Jennifer Fostel
material supplier role
A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels.
classified data set
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
material processing
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
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.
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.
specimen role
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
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.
regulatory agency
A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
material transformation objective
Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
Manufacturing implies reproducibility and responsibility AR
This includes a single scientist making a processed material for personal use.
manufacturing
is the objective to manufacture a material of a certain function (device)
manufacturing objective
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.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
A clustered data set is the output of a K means clustering data transformation
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.
data set with assigned discovered class labels
clustered data set
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
A planned process with the objective of collecting a specimen.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
class prediction data transformation
A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
supervised classification data transformation
PERSON: James Malone
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
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.
A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
decision tree building data transformation
A decision tree building data transformation is a data transformation that has objective decision tree induction.
a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
WEB: http://www.broadinstitute.org/cancer/software/genepattern/
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
k-nearest neighbors
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.
James Malone
CART
A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.
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
A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
A person or organization that has a manufacturer role
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
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
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.
A specimen that has been intentionally physically modified.
A tissue sample that has been sliced and stained for a histology study.
The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
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.
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.
Need to clarify if this is a document or a directive information entity (or what their connection is))
PERSON: Jessica Turner
Merriam-Webster
A value specification that is specifies one category out of a fixed number of nominal categories
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
collection of specimens
Blood cells collected from multiple donors over the course of a study.
A material entity that has two or more specimens as its parts.
Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
Person: Chris Stoeckert, Jie Zheng
histologic grade according to AJCC 7th edition
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
histologic grade according to the Fuhrman Nuclear Grading System
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
Histologic Grade (Fuhrman Nuclear Grading System)
A categorical value specification that is a histologic grade assigned to a ovarian tumor.
histologic grade for ovarian tumor according to a two-tier grading system
A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
histologic grade for ovarian tumor according to the World Health Organization
A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
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.
pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for lung according to AJCC 7th edition
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.
pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for kidney according to AJCC 7th edition
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.
pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for ovary according to AJCC 7th edition
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.
pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
pathologic lymph node stage for colon and rectum according to AJCC 7th edition
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.
pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pathologic lymph node stage for kidney according to AJCC 7th edition
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.
pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for ovary according to AJCC 7th edition
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.
pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
pathologic distant metastases stage for colon according to AJCC 7th edition
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.
M: colon distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for lung according to AJCC 7th edition
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.
M: lung distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for kidney according to AJCC 7th edition
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.
M: kidney distant Metastases (AJCC 7th Edition)
pathologic distant metastases stage for ovary according to AJCC 7th edition
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.
M: ovarian distant metastases (AJCC 7th Edition)
clinical tumor stage group according to AJCC 7th edition
A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
Clinical tumor stage group (AJCC 7th Edition)
International Federation of Gynecology and Obstetrics cervical cancer stage value specification
A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
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.
Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).
Eastern Cooperative Oncology Group score value specification
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.
A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
A person or organization that provides material supplies to other people or organizations.
organism
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
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.
WEB: http://en.wikipedia.org/wiki/Organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
leave one out cross validation method
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
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
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178
k-means clustering
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).
WEB: http://en.wikipedia.org/wiki/K-means
hierarchical clustering
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).
WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering
dimensionality reduction
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.
PERSON: Elisabetta Manduchi
principal components analysis dimensionality reduction
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.
pca data reduction
Generation of a heatmap from a microarray dataset
An planned process that creates images, diagrams or animations from the input data.
Tina Boussard
visualization
PERSON: Tina Boussard
Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding
data visualization
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
partitioning data transformation
A partitioning data transformation is a data transformation that has objective partitioning.
partitioning objective
A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
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.
class discovery data transformation
A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
unsupervised classification data transformation
class discovery objective
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.
discriminant analysis objective
unsupervised classification objective
class prediction objective
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.
supervised classification objective
cross validation objective
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.
rotation estimation objective
WEB: http://en.wikipedia.org/wiki/Cross_validation
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.
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
A unit which is a standard measure of the distance between two points.
A unit which is a standard measure of the amount of matter/energy of a physical object.
A unit which is a standard measure of the dimension in which events occur in sequence.
AL 2.10.2019: Incorrectly-formatted IRI. See also https://github.com/allysonlister/swo/issues/16
obsolete sequence feature format
AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information.
obsolete matlab software
obsolete 2-sample pooled t-test
obsolete 50-50 MANOVA
obsolete ABarray
obsolete 'ACME'
obsolete Algorithms for Calculating Microarray Enrichment
obsolete Affymetrix Expression Console
obsolete AIDA
obsolete Average log expression across arrays (ALE)
obsolete ALL/AML data set
obsolete AMDIS
obsolete ANCOVA
obsolete 'ANOVA'
obsolete AP-MS data
obsolete ARACNE algorithm
obsolete ARR
obsolete AWS algorithm
obsolete Absolute Expression Analysis
obsolete 'AffyCompatible'
obsolete 'AffyExpress'
obsolete Affymetrix GCOS v1.2
obsolete Affymetrix GeneChip Operating Software
obsolete Affymetrix Software
obsolete Agi4x44PreProcess
obsolete Agilent Feature Extraction 5.1.1
obsolete Agilent Feature Extraction software version 7.1
obsolete Agilent Feature Extraction software version 7.5
obsolete Agilent Feature Extraction software version A.5.1.1
obsolete Agilent Scan Control
obsolete Agilent Technologies Software
obsolete 'AnnotationDbi'
obsolete Applied Biosystems 1700 Expression Array System Software
obsolete ArrayGauge
obsolete ArrayNorm
obsolete 'ArrayTools'
obsolete ArrayVision
obsolete ArrayVision 6.0 (Imaging Research Inc.)
obsolete Array_vision_(Interfocus)
obsolete AtlasImage
obsolete Axon GenePix Pro 3
obsolete BAC
obsolete Binning clustering method
obsolete 'BCRANK'
Equivalence with EDAM term "BED" (format_3003).
obsolete BGL
obsolete 'BGmix'
obsolete BLAST
obsolete Iterative Bayesian Model Averaging (BMA)
obsolete Base-Pair-Distance Kernel
obsolete BPMAP
obsolete BRB-ArrayTools
obsolete 'BSgenome'
obsolete BZScan
obsolete BaldiLongT
obsolete BasReader 3.01
obsolete Bayesian Model
obsolete Beadstudio
obsolete 'BicARE'
obsolete 'BioMVCClass'
obsolete 'Biobase'
obsolete 'BiocCaseStudies'
obsolete BioConductor Software
obsolete 'Biostrings'
obsolete BlueFuse
obsolete 'BufferedMatrix'
obsolete 'BufferedMatrixMethods'
obsolete 'CALIB'
obsolete 'CAMERA'
obsolete CBS
obsolete CBS algorithm
obsolete CDF binary format
obsolete CEL binary format
obsolete 'CGHbase'
obsolete 'CGHcall'
obsolete 'CGHregions'
obsolete CHP binary format
obsolete CLR algorithm
obsolete 'CMA'
obsolete CMA
obsolete 'CORREP'
obsolete CRLMM algorithm
obsolete Continuous Wavelet Transform (CWT)-based peak detection algorithm
obsolete CARMAweb
obsolete Category analysis
obsolete Category
obsolete 'ChemmineR'
obsolete ChipReader 3.1
obsolete ChipSkipper
obsolete ChipSkipper V0.99
obsolete multiscan
obsolete affy
obsolete affycomp
obsolete PCMG
obsolete Feature Extraction Software
obsolete Chi-square
obsolete Annotation-Driven Clustering
obsolete distance calculation
obsolete R software
obsolete BCRANK
obsolete Cosmo
obsolete F test
obsolete MAGE-TAB inputting software
obsolete Text data set
obsolete CSV data set
obsolete Non-linear functional regression model
obsolete 'CoCiteStats'
obsolete CodeLink Expression Analysis Software
obsolete CodeLink Expression Scanning Software
obsolete Complex Estimation Algorithm
obsolete Cyber-T
obsolete 'DEDS'
obsolete 'DFP'
obsolete Discriminant Fuzzy Pattern Algorithm
obsolete DFW
obsolete Digital gene expression (DGE) datasets
obsolete 'DNAcopy'
obsolete 'DynDoc'
obsolete 'EBImage'
obsolete 'EBarrays'
obsolete Expectation-Maximization(EM) algorithm
obsolete Empirical Bayes rule
obsolete Expert 2100
This class had no definition, and seemed incorrectly placed as an algorithm, as from its name it seemed to only be an experimental method.
obsolete_FACS ( fluorescence-activated cell sorter)
obsolete FACS data
obsolete FARMS
Equivalence with EDAM term format_1929. Please use this term instead.
obsolete FC
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.
obsolete 'FDR'
obsolete Fixed effect model
obsolete Agilent Feature Extraction Software
obsolete Firth's bias reduction procedure
obsolete Fischer's Exact Test
obsolete FoxDimmicT
obsolete GACK
obsolete GASSCO method
obsolete GC-RMA Quantification
obsolete GEMTools 2.4
obsolete GEO data type
obsolete GEO Matrix Series format
obsolete GEOmetadb
obsolete GEOquery
obsolete GGBase
obsolete Gamma Gamma Model
obsolete GGtools
obsolete GLAD
obsolete Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)
obsolete GLEAMS software
obsolete GMS
obsolete GOstats
obsolete Gene Recommender algorithm
obsolete GSEABase
obsolete GSEAlm
obsolete Gamma-Gamma hierarchical model
obsolete Gaussian locally weighted regression
obsolete Gene-Set Enrichment Analysis
obsolete GeneData Expressionist Analyst v4.0.5
obsolete Gene Pix
obsolete GenePix 3.0.6
obsolete GenePix 4.1
obsolete GenePix 4100A
obsolete GenePix 5.0.1
obsolete GenePix
obsolete GenePix Pro
obsolete GenePix Pro 3
obsolete GenePix Pro 5.0
obsolete GenePix Pro 6.0
obsolete GenePix Pro 6 [Axon Instruments]
obsolete GenePix Pro [Axon Instruments]
obsolete GeneR
obsolete GeneRegionScan
obsolete GeneRfold
obsolete GeneSelectMMD
obsolete GeneSelector
obsolete GeneSpring
obsolete GeneSpringGX
obsolete GeneTac Analyser
obsolete GeneTraffic
obsolete GenePix Pro 4.0
obsolete GenePix Pro 3.0
obsolete GeneticsBase
obsolete GeneticsDesign
obsolete GeneticsPed
obsolete GenomeGraphs
obsolete GlobalAncova
obsolete GOSemSim
obsolete GraphAT
obsolete GraphAlignment
obsolete GridGrinder
obsolete Hexagon binning algorithm
obsolete HELP
obsolete HEM
obsolete Heterogeneous Error Model (HEM)
obsolete Hubert’s gamma
obsolete Hidden Markov Model
obsolete Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm
obsolete Hidden Variable Dynamic Modelling HVDM)
obsolete HaarSeg algorithm
obsolete Hardy-Weinberg equilibrium
obsolete Harshlight
obsolete Heatplus
obsolete HilbertVis
obsolete HilbertVisGUI
obsolete Hypergeometric probability
obsolete ICS-501 (version 2.3) Image Capture System
obsolete Iteratively ReWeighted Least Squares
obsolete IRanges
obsolete ITALICS
obsolete ILLUMINA data
obsolete ImaGene4.1 software
obsolete ImaGene 3.0
obsolete ImageQuant
obsolete ImageReader
obsolete ImaGene
obsolete Imagene v4.0
obsolete Initial microarray data processing (data filtering, local normalisation and quality control)
obsolete Jaccard’s index
obsolete Jaguar
obsolete KCsmart
obsolete KEGGSOAP
obsolete KEGGgraph
obsolete KGML
obsolete 'KLD'
obsolete Kolmogorov Smirnov rank-sum based algorithm
obsolete LBE
obsolete LC-MS data
obsolete LMGene
obsolete Locally Moderated Weighted-t (LMW) method
obsolete Lognormal Normal Model
obsolete Lognormal Normal with Modied Variance Model
obsolete LPE
obsolete LPEadj
obsolete publisher role
obsolete Langmuir Isotherm
obsolete Laplace mixture model
obsolete Library Search Algorithm
obsolete Loess algorithm
obsolete Logic regression
obsolete MAANOVA v1.2 package for MATLAB
obsolete Median Average Difference Algorithm
obsolete MANOR
obsolete MAQC data
obsolete MIcroarray Analysis Suite
obsolete MicroArraySuite 5.0
obsolete MATLAB language
obsolete MAVI Pro
obsolete Multivariate correlation estimator
obsolete Markov Chain Monte Carlo
obsolete MCR algorithm
obsolete MCRestimate
obsolete MEDME
obsolete 'MI'
obsolete Mutual information matrix (MIM)
obsolete MLInterfaces
obsolete MMD
obsolete MVCClass
obsolete Mahalanobis distance
obsolete MantelCorr
obsolete MassSpecWavelet
obsolete MeasurementError.cor
obsolete MergeMaid
obsolete Mfuzz
obsolete MiPP
obsolete Misclassification-Penalized Posteriors (MiPP)
obsolete MicroArraySuite 4.0
obsolete Mixed model equations
obsolete 'Needleman-Wunsch'
obsolete Nested Effects Models
obsolete Nonlinear Estimation by Iterative Partial Least Squares
obsolete OCplus
obsolete OLIN
obsolete OLINgui
obsolete Optiquant
obsolete OrderedList
obsolete OutlierD
obsolete Presence-Absence calls with Negative Probesets (PANP)
obsolete PAnnBuilder
obsolete Pearson correlation estimator
obsolete PCpheno
obsolete PGSEA
obsolete 'PLM'
obsolete PLPE
obsolete Probe level Locally moderated Weighted median-t (PLW) method
obsolete PPC algorithm
obsolete PROcess
obsolete Propagation of uncertainty in microarray analysis
obsolete Pathways 2.01 software
obsolete Power Law Global Error Model (PLGEM) analysis method
obsolete Probe Cell Analysis
obsolete PLIER (Probe Logarithmic Error Intensity Estimate) method
obsolete QuantArray scanner software
obsolete QuantArray, PackaardBiochip technologies
obsolete QuantArray version 2
obsolete Radial basis function
obsolete RBGL
obsolete R interface to boost graph library algorithm (RBGL)
obsolete RBioinf
obsolete Random effects model
obsolete Recursive Feature Elimination (RFE)
obsolete RLMM
obsolete Regression model
obsolete RMA
obsolete RMA+
obsolete RMA++
obsolete RMAExpress
obsolete RMAExpress 2.0
obsolete RMAExpress quantification
obsolete RMAGEML
obsolete RNAither
obsolete ROC
obsolete RWebServices
obsolete RankProd
obsolete RbcBook1
obsolete Rdbi
obsolete RdbiPgSQL
obsolete Rdisop
obsolete RefPlus
obsolete Resourcerer
obsolete Rgraphviz
obsolete Ringo
obsolete Rintact
obsolete Rmagpie
obsolete Rnw
obsolete Robust likelihood-based survival modeling
obsolete Rosetta Resolver
obsolete RpsiXML
obsolete Rredland
obsolete Rtreemix
obsolete Ruuid
obsolete S-Score algorithm
obsolete Serial Analysis of Gene Expression (SAGE)
obsolete SAGx
obsolete SAM
obsolete SAS/STAT Software, Version 8
obsolete SBMLR
obsolete SBMLR format
Identical to http://www.ebi.ac.uk/swo/data/SWO_3000037
'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'.
obsolete SDF format
obsolete SIM
obsolete SLGI
obsolete SLqPCR
obsolete SMAP
obsolete SNPRMA algorithm
obsolete SNPchip
obsolete SPIA
obsolete Semantic Similarity Measures
obsolete SSPA
obsolete SVDimpute algorithm
obsolete software developer role
Information processing is a process in which input information is analysed or transformed in order to produce information as output.
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.
obsolete software developer organization
obsolete software publisher organization
obsolete 50-50 MANOVA algorithm
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.
obsolete ArrayExpress Bioconductor
obsolete Gene list
obsolete Clustered data set
obsolete R data frame
obsolete R language
obsolete ScISI
obsolete ScanAlyze
obsolete ScanArray
obsolete ScanArray v3.1 software
obsolete scanning software
obsolete Scanning software G2565AA version A6.3.1
obsolete ShortRead
obsolete Signaling Pathway Impact Analysis (SPIA) algorithm
obsolete Silicon Genetics Genespring
obsolete Similarity score
obsolete 'Smith-Waterman'
obsolete Spot quantification
obsolete Spotfinder [TIGR]
obsolete Spotfire
obsolete TAS Software
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.
obsolete TargetSearch
obsolete Theodore Ts’o’s
obsolete TypeInfo
obsolete Variance-stabilizing transformation (VST) algorithm
obsolete VanillaICE
obsolete WilcEbam
obsolete Wilcoxon
obsolete XDE
obsolete XDotsReader
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.
obsolete Xba.CQV and Xba.regions
obsolete Array Comparative Genomic Hybridization
obsolete Acuity
obsolete affxparser
obsolete affyContam
obsolete affyImGUI
obsolete 'affyPLM'
obsolete affyPara
obsolete affyQCReport
obsolete affyTiling
obsolete 'affycoretools'
obsolete affyio
obsolete affypdnn
obsolete altcdfenvs
obsolete annaffy
obsolete 'annotate'
obsolete data annotation
obsolete annotationTools
obsolete Annotation data packages
obsolete 'apComplex'
obsolete aroma.light
obsolete arrayMvout
obsolete arrayQuality
obsolete arrayQualityMetrics
obsolete arrayWoRx 2.0
obsolete arrayWoRx
obsolete Associative T method
obsolete AvgNRRs
obsolete 'beadarray'
obsolete 'beadarraySNP'
obsolete 'betr'
obsolete bgafun
obsolete bgx
obsolete Bitmap object
obsolete bioDist
obsolete 'biocDatasets'
obsolete 'biocGraph'
obsolete 'biocViews'
obsolete biomaRT
obsolete Bootstrap
obsolete 'bridge'
obsolete cdt
obsolete 'cellHTS'
obsolete 'cellHTS2'
obsolete cghMCR
obsolete chamber slide format
obsolete cls
obsolete 'clusterStab'
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.
obsolete 'codelink'
obsolete dataset comparison
obsolete Concordance
obsolete convert
obsolete copa
obsolete cosmo
obsolete cosmoGUI
obsolete covdesc file
obsolete database creation
obsolete crlmm
obsolete ctc
obsolete dChip
obsolete daMA
obsolete .data
obsolete dcf
obsolete design file
obsolete 'diffGeneAnalysis'
obsolete 'domainsignatures'
obsolete 'dualKS'
obsolete dyebias
obsolete Dynamic programming algorithm
obsolete ecolitk
obsolete edd
obsolete 'edgeR'
obsolete exonmap
obsolete 'explorase'
obsolete 'externalVector'
obsolete f-test
obsolete factDesign
obsolete fbat
obsolete fdrame
obsolete flagme
obsolete flowClust
obsolete flowCore
obsolete flowFlowJo
obsolete flowQ
obsolete flowStats
obsolete flowUtils
obsolete flowViz
obsolete gaga
obsolete 'gaggle'
obsolete gcRMA quantification
obsolete gcrma
obsolete gct
obsolete 'genArise'
obsolete gene2pathway
obsolete geneRecommender
obsolete Gene array analysis algorithm
obsolete gene expression analysis
obsolete Gene expression dataset
obsolete genefilter
obsolete genemeta
obsolete geneplotter
obsolete genomeIntervals
obsolete Global test
obsolete globaltest
obsolete gmt format
obsolete goProfiles
obsolete goTools
obsolete gpls
obsolete gpr format
obsolete graph
obsolete gtr
obsolete gxl format
obsolete hexbin
obsolete Hierarchical clustering
obsolete hopach
obsolete HTML report
obsolete Hypergeometric enrichment
obsolete hypergraph
obsolete Icens
obsolete idiogram
obsolete impute
obsolete iterativeBMA
obsolete iterativeBMAsurv
obsolete Iterative local regression and model selection
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.
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.
obsolete k-cores
obsolete k-means
obsolete k-nearest neighbour classification
obsolete keggorth
obsolete lapmix
obsolete Likelihood method
obsolete limma
obsolete limmaGUI
obsolete Linear modelling
obsolete lma
obsolete Local-pooled-error
obsolete log file
obsolete logicFS
obsolete logicFS dataset
obsolete logitT
obsolete Logit-t algorithm
obsolete lumi
obsolete maCorrPlot
obsolete maDB
obsolete maSigPro
obsolete maanova
obsolete macat
obsolete made4
obsolete maigesPack
obsolete makePlatformDesign
obsolete makecdfenv
obsolete marray
obsolete 'MAS5'
obsolete mas5 format
obsolete matchprobes
obsolete mdqc
obsolete M-estimation regression
obsolete metaArray
obsolete Meta data
obsolete metahdep
obsolete miRNApath
obsolete microRNA
obsolete minet
obsolete mrnet algorithm
obsolete Multinomial probit regression with Gaussian Process priors
obsolete Multiple testing
obsolete Multivariate t mixture models
obsolete multtest
obsolete Negative binomial distribution
obsolete nem
obsolete Neural networks models
obsolete nnNorm
obsolete nudge
obsolete occugene
obsolete oligo
obsolete oligoClasses
obsolete OMICS data
obsolete oneChannelGUI
obsolete ontoTools
obsolete pair file
obsolete pamr
obsolete panp
obsolete parody
obsolete parse
obsolete pathRender
obsolete pcaMethods
obsolete pcot2
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.
obsolete pdInfoBuilder
obsolete pdmclass
obsolete pedigree data file
obsolete pgUtils
obsolete pickgene
obsolete pkgDepTools
obsolete plgem
obsolete plier
obsolete Graph plot
obsolete plw
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.
obsolete Position weight matrix (PWM )
obsolete ppiStats
obsolete prada
obsolete preprocessCore
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.
obsolete puma
obsolete qPCR data
obsolete qpcrNorm
obsolete qpgraph
obsolete Quantile normalization
obsolete Quantile regression techniques
obsolete quantsmooth
obsolete qvalue
obsolete rHVDM
obsolete rMAT
obsolete rama
obsolete Rank-invariant set normalization
obsolete Rank product non-parametric method
obsolete .raw files
obsolete rbsurv
obsolete rda
obsolete reb
obsolete rflowcyt
obsolete .rma format
obsolete rsbml
obsolete rtracklayer
obsolete safe
obsolete sagenhaft
obsolete seqLogo
obsolete sigPathway
obsolete siggenes
obsolete Sim method
obsolete simpleaffy
obsolete simulatorAPMS
obsolete sizepower
obsolete xmapbridge
obsolete snapCGH
obsolete snpMatrix
obsolete spikeLI
obsolete spkTools
obsolete splicegear
obsolete splots
obsolete spotSegmentation
obsolete sproc
obsolete sqlite
obsolete sscore
obsolete ssize
obsolete stam
obsolete Statistical tests
obsolete stepNorm
obsolete 't-test'
obsolete tilingArray
obsolete timecourse
obsolete tkWidgets
obsolete topGO
obsolete tspair
obsolete twilight
obsolete Two-stage measurement error model
obsolete vbmp
AL 25.9.19: Redundant with http://purl.obolibrary.org/obo/OBI_0200111
obsolete data visualization
obsolete vsn
obsolete weaver
obsolete webbioc
obsolete widgetTools
obsolete xcms
obsolete xps
obsolete yaqcaffy
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.
Modified in parts from https://en.wikipedia.org/wiki/Software
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.
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.
Modified from http://en.wikipedia.org/wiki/Software_license
licence
AL 18.9.2019: This class is identical (based on its definition) with OBI 'data transformation' and is no longer required.
Microsoft Excel 2007 is a spreadsheet editing and viewing tool.
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
OmniOutliner is commercial outlining software for Mac OS X produced by The Omni Group
Racket is a Scheme-based language interpreter and programming environment
IntelliJ IDEA is a commercial Java IDE for developing software.
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.
http://sbml.org/SBML_Software_Guide/SBML_Software_Summary, accessed 24 March 2015.
Microsoft Excel 2003 is a spreadsheet editing and viewing tool.
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.
Adobe Illustrator is a graphics editor for creating and editing vector graphics.
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.
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
This package provides user interface and database connection code for annotation data packages using SQLite data storage.
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.
Applied Biosystems 1700 Expression Array System Software
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.
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.
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.
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.
The C++ version of the command line BLAST+ tool made by the NCBI. (See also http://www.ncbi.nlm.nih.gov/books/NBK1763)
BLAST+ 2.2.26
This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments
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
Multiple alignment program for nucleic acid or protein sequences.
http://www.clustal.org/, Accessed 13 June 2012.
Clustal
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.
http://www.clustal.org/omega/, Accessed 13 June 2012
Clustal Omega
ClustalW
ClustalX
Clustal Omega 1.1
ClustalW 2.1
ClustalX 2.1
EBI Clustal W2 Web Tool
EBI Clustal Omega Web Tool
MUSCLE
EBI Muscle Web Tool
MUSCLE 3.8.31
Drive5 MUSCLE
TCoffee
TCoffee is a multiple sequence alignment program with a number of different modes.
CRG TCoffee
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.
EBI TCoffee Web Tool
Aligns RNA sequences using predicted secondary structures by accessing the RCoffee mode of the underlying TCoffee software.
http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012
CRG RCoffee Web Tool
Performs an alignment of DNA, RNA or Proteins with the standard TCoffee mode.
CRG TCoffee Web Tool
Aligns DNA, RNA or Proteins by combining the output of popular aligners and by accessing the MCoffee mode of the underlying TCoffee software.
CRG MCoffee Web Tool
Aligns protein sequences using structural information by accessing the 3DCoffee/Expresso mode of the underlying TCoffee software.
CRG Expresso Web Tool
Aligns distantly related proteins using homology extension (slow and accurate) by accessing the PSICoffee mode of the underlying TCoffee software.
CRG PSICoffee Web Tool
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.
CRG TCoffee 9.02.r1228
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.
Data analysis software which performs a variety of statistical, summarising, analytical and visualization tasks.
SPSS
SPSS 20.0
Sequence Alignment and Modeling System, a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis.
http://bioinformatics.org/wiki/SAM, Accessed 19 June 2012.
Sequence Alignment and Modeling System
SAM 3.5
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.
http://www.cytoscape.org/what_is_cytoscape.html, Accessed June 20, 2012.
Cytoscape
Cytoscape 2.8
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)"
Plugin
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.
http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html, accessed 22 May 2013.
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)
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
Gene Expression Atlas at EBI R statistics package
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.
http://dbpedia.org/resource/Python_(programming_language), accessed 27 November 2014.
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.
Database for Annotation, Visualization and Integrated Discovery
MLXTRAN
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...".
NMTRAN
NONMEM
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.
Entrez Global Query Cross-Database Search System
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 is the searching for information on the World Wide Web.
A search engine is a software system that is designed to search for information on the World Wide Web.
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.
Waikato Environment for Knowledge Analysis
PostgreSQL, often simply Postgres, is an open source object-relational database management system (ORDBMS) with an emphasis on extensibility and standards compliance.
The storing of digital information. Often this is done for archiving and retrieval purposes.
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.
http://pmgenomics.ca/hoffmanlab/proj/segway/, accessed 27 November 2014.
Segway 1.2
Version 2.6 of the Python programming language.
Python 2.6
Version 2.7 of the Python programming language.
Python 2.7
Mac OS is software which is used as the operating system for the Macintosh personal computer created by Apple Inc.
http://en.wikipedia.org/wiki/History_of_Mac_OS, accessed 25 March 2015.
Mac OS
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.
http://en.wikipedia.org/wiki/History_of_Mac_OS#OS_X, accessed 25 March 2015.
OS X
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.
http://www.async.ece.utah.edu/iBioSim/, accessed 25 March 2015.
iBioSim
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.
http://sbml.org/SBML_Software_Guide/SBML_Software_Summary, accessed 26 March 2015.
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.
VCell
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.
COnstraints Based Reconstruction and Analysis
COBRA
COBRA Toolbox is the version of the COBRA software for Python.
COnstraints Based Reconstruction and Analysis for Python
COBRApy
COBRA Toolbox is the version of the COBRA software for Matlab.
COnstraints Based Reconstruction and Analysis Toolbox for MATLAB
COBRA Toolbox
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.
http://sbml.org/SBML_Software_Guide/SBML_Software_Summary, accessed 27 March 2015.
libSBML
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.
https://www.gnu.org/software/octave/, accessed 27 March 2015.
GNU Octave
GWT
S language
Excel
This package deals with hapmap SNP reports, GWAS, etc.
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.
Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)
Microarray image quantification is performed using GLEAMS software
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
This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).
Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics.
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.
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.
Package manipulating nucleotidic sequences (Embl, Fasta, GenBank)
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
Package manipulating sequences with fold routines
Gene selection based on a mixture of marginal distributions
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.
Set of functions and class definitions to be able to read and write GeneSpring specific data objects and covert them to BioConductor objects
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
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)
This package (GeneticsBase) provides a foundation of efficient data structures and easy-to-use manipulation functions.
This package contains functions useful for designing genetics studies, including power and sample-size calculations.
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
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.
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.
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.
Functions and data used in Balasubramanian, et al. (2004)
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.
The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications
This package fits heterogeneous error models for analysis of microarray data
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm
Technique which predicts a given transcription factor activity and then uses this infor- mation to predict its targets.
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.
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.
Functions to visualize long vectors of integer data by means of Hilbert curves
An interactive tool to visualize long vectors of integer data by means of Hilbert curves
ICS-501 (version 2.3) Image Capture System
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.
A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set
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.
ImaGene microarray image analysis software by biodiscovery for microarrays, protein arrays and CGH analysis.
These scripts are for primer design and initial microarray data processing and are available as .zip files:
Initial microarray data processing (data filtering, local normalisation and quality control)
Multi sample aCGH analysis package using kernel convolution
A package that provides a client interface to the KEGG SOAP server
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.
KS measures how biased the ranks of a subset of items are among the ranks of the entire set
Kolmogorov Smirnov rank-sum based algorithm
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.
LMGene package for analysis of microarray data using a linear model and glog data transformation in the R statistical package
Locally Moderated Weighted-t (LMW) method
Lognormal Normal with Modied Variance Model
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.
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.
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.
Tools for analyzing Micro Array experiments
We propose importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments.
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.
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.
This package includes a function for combining preprocessing and classification methods to calculate misclassification errors
MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments
Uniform interfaces to machine learning code for data in Bioconductor containers
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),
Creates classes used in model-view-controller (MVC) design
Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data)
Processing Mass Spectrometry spectrum by using wavelet based algorithm
Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation
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.
Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)
This package finds optimal sets of genes that seperate samples into two or more classes.
Misclassification-Penalized Posteriors (MiPP)
This includes exhaustive enumeration, triple-based inference,pairwise heuristic, module based inference, greedy hillclimbing
Nonlinear Estimation by Iterative Partial Least Squares
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).
Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data
Graphical user interface for the OLIN package
Computer software for image acquisition, analysis and reporting, for use in the life sciences
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.
This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data.
Presence-Absence calls with Negative Probesets (PANP)
Processing annotation data from public data repositories and building annoation data packages.
Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways.
Parametric Analysis of Gene Set Enrichment
it is where we fit a model with probe level and chip level parameters on a probeset by probeset basis
This package performs tests for paired high-throughput data.
Probe level Locally moderated Weighted median-t (PLW) method
A package for processing protein mass spectrometry data.
Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting and data manipulation functions
Propagation of uncertainty in microarray analysis
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).
Power Law Global Error Model (PLGEM) analysis method
PLIER (Probe Logarithmic Error Intensity Estimate) method
QuantArray® is a powerful microarray analysis software that enables researchers to easily and accurately visualize and quantitate gene expression data.
QuantArray, PackaardBiochip technologies
A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.
R interface to boost graph library algorithm (RBGL)
Functions and datasets and examples to accompany the monograph R For Bioinformatics.
for the Support Vector Machine (SVM), as presented in [3] and the Nearest Shrunken Centroid (NSC)
A Genotype Calling Algorithm for Affymetrix SNP Arrays
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.
This package can be used to handle MAGEML documents in Bioconductor
RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes
This package provides mechanisms for automatic function prototyping and exposure of R functionality in a web services environment.
Rank Product method for identifying differentially expressed genes with application in meta-analysis
Support for Springer monograph on Bioconductor
Provides methods for accessing data stored in PostgreSQL tables.
The package contains functions for pre-processing Affymetrix data using the RMA+ and the RMA++ methods.
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.
Provides plotting capabilities for R graph objects
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
Queries and data structures for protein interactions
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.
Robust likelihood-based survival modeling
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.
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.
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.
Serial Analysis of Gene Expression (SAGE)
A package for retrieval, preparation and analysis of data from the Affymetrix GeneChip. In particular the issue of identifying differentially expressed genes is addressed.
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)
Statistical Analysis with a number of procedures, providing statistical information such as analysis of variance, regression, multivariate analysis, and categorical data analysis.
This package contains a systems biology markup language (SBML) interface and biochemical system analysis tools with illustrative examples.
Finds associations between DNA copy number and gene expression.
A variety of data files and functions for the analysis of genetic interactions
Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH
Functions and classes for DNA copy number profiling of array-CGH data
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.
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.
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.
Sample size and power analysis for microarray data, where two groups are analysed.
Software developer role is a role borne by an organization or individual in which they are responsible for authoring software.
An organization or legal entity (including single person) that is responsible for developing software. Developing includes aspects of design, coding and testing.
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.
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.
Langsrud, &Oslash. (2002), 50-50 Multivariate Analysis of Variance for Collinear Responses, The Statistician, 51, 305-317.
ArrayExpress Bioconductor package is software that read in MAGE-TAB format files from the ArrayExpress FTP site and converts them to R objects.
Package to create In Silico Interactomes
Processes fluorescent images of microarrays
ScanArray Express provides superior spot finding and quantization algorithm. This combined with template adjustment features drives excellence in analysis performance.
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
Scanning software G2565AA version A6.3.1
Base classes, functions, and methods for representation of high-throughput, short-read sequencing data.
Signaling Pathway Impact Analysis (SPIA) algorithm
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
TIGR Spotfinder was designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression
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.
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.
This packages provides a targeted pre-processing method for GC-MS data.
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
Variance-stabilizing transformation (VST) algorithm
Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
Analysis Software for Integrated Image Analysis for Spot Detection , Position and Quantification
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.
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.
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.
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.
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.
A Graphical User Interface for affy analysis using the limma Microarray package
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)
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.
The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data.
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.
This package provides easy, fast functions for the extraction and annotation of individual probes from Affymetrix tiling arrays.
Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see
Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.
The package contains functions to perform the PDNN method described by Li Zhang et al.
altcdfenvs is a software package for alternative CDF environments (aka probeset mappings) and contains convenience data structures and functions to handle cdfenvs.
http://www.bioconductor.org/packages/release/bioc/html/altcdfenvs.html, accessed May 28 2013.
This package functions for handling data from Bioconductor Affymetrix annotation data packages.Allows searching biological metadata using various criteria.
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).
This package functions to estimate a bipartite graph of protein complex membership using AP-MS data.
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.
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
This package functions for performing print-run and array level quality assessment.
This package generates a quality metrics report on ExpressionSet, NChannelSet, AffyBatch or BeadLevelList objects containing microarray data with one or two channels.
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.
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.
Importing data from Illumina SNP experiments and performing copy number calculations and reports.
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.
http://www.bioconductor.org/packages/2.12/bioc/html/betr.html, accessed 28 May 2013.
BGAfun is a method to identify specifity determining residues in protein families
Bayesian integrated analysis of Affymetrix GeneChips
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.
Synthetic datasets to a) demonstrate the usage of bioconductor packages, b) write unit tests, while keeping dependencies and ressources usage minimal.
This package provides examples and code that make use of the different graph related packages produced by Bioconductor.
Categorized views of R package repositories
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.
The bridge package consists of several functions for testing for dierential expression among mul- tiple samples
Bioconductor package concerned with analysis of cell-based RNA interference screens
Analysis of cell-based RNA interference screens
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.
Categorical (e.g tumor vs normal) class file format
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.
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.
Define coerce methods for microarray data objects.
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.
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.
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.
An objective in which the aim is to create a new database instance.
Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 6.0.
Tools for export and import classification trees and clusters to other programs
Analysis and visualization of gene expression and SNP microarrays
This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data.
Find significantly enriched gene classifications in a list of functionally undescribed genes based on their InterPro domain structure.
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.
Gene-specific dye-bias correction of two-color microarray data using the GASSCO method
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.
This package provides tools for evaluating cohort distributions of gene expression levels
Estimation and Testing for Differential Expression in Multiple Digital Gene Expression Libraries.
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.
This package explores and analyzes *omics data with R and GGobi
Basic class definitions and generics for external pointer based vector objects for R. A simple in-memory implementation is also provided
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.
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
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
Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data
Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed
This package provides S4 data structures and basic functions to deal with flow cytometry data.
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.
This package provides quality control and quality assessment tools for flow cytometry data.
This package contains methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package.
This package provides utilities for flow cytometry data.
Provides visualization tools for flow cytometry data
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).
This package contains functions connecting R with the Gaggle
Bioconductor package concerned with background adjustment using sequence information
Allyson Lister
Background adjustment using sequence information
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.
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.
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.
Some basic functions for filtering genes
A collection of meta-analysis tools for analysing high throughput experimental data
Some basic functions for plotting genetic data
Tools for operation on genomic intervals.
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.
Testing whether sets of genes (e.g. KEGG pathways of GO terms) are significantly associated with a clinical variable of interest.
The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'.
Wraper functions for description/comparison of oligo ID list using Gene Ontology database
Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.
A package that implements some simple graph handling capabilities.
Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods.
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).
A package that implements some simple capabilities for representing and manipulating hypergraphs.
Many functions for computing the NPMLE for censored and truncated data.
A package for plotting genomic data by chromosomal location
Imputation for microarray data (currently KNN only)
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).
The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data.
Iterative local regression and model selection
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.
Data analysis, linear models and differential expression for microarray data.
A Graphical User Interface for the limma Microarray package
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.
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.
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.
Graphically displays correlation in microarray data that is due to insufficient normalization
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.
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.
Analysis of N-dye Micro Array experiment using mixed model effect. Containing anlysis of variance, permutation and bootstrap, cluster and consensus tree.
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'.
Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4.
This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data
makePlatformDesign creates the Platform Design environments (PDenvs) required by oligo.
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.
Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.
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.
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.
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
Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies
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.
microRNA is a software package which provides data resources for microRNAs and various functions for manipulating them.
http://bioconductor.org/packages/2.4/bioc/html/microRNA.html, accessed 28 May 2013.
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.
Multinomial probit regression with Gaussian Process priors
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.
Resampling-based multiple hypothesis testing
Nested Effects Models to reconstruct phenotypic hierarchies
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.
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)
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.
A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
This package contains class definitions, validity checks, and initialization methods for classes used by the oligo package.
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.
tools for working with ontologies and graphs
Some functions for sample classification in microarrays
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.
Routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics
build graphs from pathway databases, render them by Rgraphviz
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.
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.
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.
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.
Functions for creating PostgreSQL database tables, with auto incrementing primary keys, selection of foreign keys to allow referencial integrity and a logging mechanism.
Functions to Analyze Microarray (Gene Expression) Data.
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.
PLGEM is useful for detecting differential expression in microarray and proteomics datasets.
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.
Probe level Locally moderated Weighted median-t (PLW) and Locally Moderated Weighted-t (LMW).
Tools for the analysis of protein interaction data.
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).
A library of core preprocessing routines
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.
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.
Reverse engineering of molecular regulatory networks with qp-graphs
Quantile smoothing and genomic visualization of array data
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.
R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.
The rama package consists of several functions for robust estimation of two color microarray intensities with replicates
This package selects genes associated with survival.
A set of functions to dentify regional expression biases
Statistical tools and data structures for analytic flow cytometry
R interface to genome browsers and their annotation tracks
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.
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
seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo
Conducts pathway analysis by calculating the NT_k and NE_k statistics
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).
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
Functions to computationally simulate the AP-MS technology based on wet-lab data.
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.
xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format.
Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays.
Implements classes and methods for large-scale SNP association studies
Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
The package contains functions that can be used to compare expression measures on different array platforms.
A set of tools to work with alternative splicing
The splots package provides the plotScreen function for the visualization of for high-throughput assays in microtitre plate or chamber slide format.
Spot segmentation via model-based clustering and gridding for blocks within microarray slides
This package contains an implementation of the S-Score algorithm
Functions for computing and displaying sample size information for gene expression arrays.
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.
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.
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.
Stepwise normalization functions for cDNA microarray data.
Transcript mapping with high-density oligonucleotide tiling arrays
Functions for data analysis and graphical displays for developmental microarray time course data.
Widgets to provide user interfaces. tcltk should have been installed for the widgets to run.
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.
Top Scoring Pairs for Microarray Classification
Estimation of local false discovery rate
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.
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
This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included.
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.
This packages contains tools to support the construction of tcltk widgets
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.
Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.
50-50 Manova is software in which the 50-50 MANOVA algorithm is implemented.
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.
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.
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.
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.
Algorithms for Calculating Microarray Enrichment
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
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.
Average log expression across arrays (ALE)
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 or Analysis of Variance is a hypothesis testing algorithm which a variable is partitioned into components attributable to different sources of variation.
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.
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.
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.
Preprocessing of Agilent 4x44 array data
Agilent Feature Extraction software version 7.1
Agilent Feature Extraction software version 7.5
Agilent Feature Extraction software version A.5.1.1
Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search
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
Bayesian models for differential gene expression
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.
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.
Allyson Lister: added 'achieves objective' axioms for pairwise and multiple sequence alignment classes.
Iterative Bayesian Model Averaging (BMA)
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.
http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/bpmap.html, accessed 22 May 2013.
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.
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
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.
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).
BeadStudio Software is a modular analysis tool for genotyping, gene expression, and methylation applications
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
Creates classes used in model-view-controller (MVC) design that uses Biobase
Functions that are needed by many other packages or which replace R functions
Software and data to support the case studies.
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.
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)
Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or set of sequences.
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.
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.
This package involves microarray Data related methods that utlize BufferedMatrix objects
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.
Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, EIC correlation based tagging of unknown adducts and fragments
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.
http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cdf.html, accessed 22 May 2013.
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.
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.
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)
Multivariate correlation estimation and statistical inference.
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
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.
A collection of tools for performing category analysis.
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.
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.
ChipSkipper - an integrated tool for analysis, evaluation and quantitation of DNA micro-array data
ChipSkipper Microarray Data Evaluation Software
A multiscan is an R package for combining multiple scans
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.
The affycomp package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.
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.
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.
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments.
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 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
non-linear functional regression model with both additive and multiplicative error terms
A collection of software tools for dealing with co-citation data.
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.
Slides are scanned using CodeLink Expression Scanning Software
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.
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.
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.
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'
Segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number
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.
EBarrays provides tools for the analysis of replicated/unreplicated microarray data.
Exper 2100 offers powerful data evaluation tools for all available assays, automatic and manual integration, smear analysis and many assay-specific tools.
FACS data is data which describes flow cytometry data sets.
http://www.bioconductor.org/packages/2.12/bioc/vignettes/prada/inst/doc/fcs3.html, accessed 29 May 2013.
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
Feature Extraction Software [Agilent Technologies]
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.
Single-user desktop software package for analyzing microarray data from multiple microarray platforms.
GC-RMA Quantification (Stratagene ArrayAssist Expression Software)
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.
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.
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.
This package is an infrastructure for dealing with hapmap SNP reports, GWAS, etc.
Computer software for the analysis and comparison of Atlas™ nylon and plastic arrays.
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.
Contains functions and classes that are needed by arrayCGH packages.
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.
Dimension Reduction for Array CGH Data with Minimal Information Loss
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.
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.
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.
A set of functions to create and interact with dynamic documents and vignettes.
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.
AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/15
bcbio
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.
AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/12
shinyNGS
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.
AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/13
Seurat
GraphPad Prism is a commercial scientific 2D graphing and statistics software available for both Windows and Macintosh computers.
AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/14
Graphpad Prism
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.
Salmon
StavroX software identifies cross-linked peptides.
AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/35
ProteomicsTools software suite contains a bunch of tools used in proteomics research, including identification, result parsing, quantification, and modification.
AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/34
Chromeleon software provides full integration of Thermo Scientific gas chromatography (GC-MS/MS), liquid chromatography (LC-MS/MS), and ion chromatography (IC-MS) instruments.
AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/32
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
AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/31
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.
AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/30
SupernovoTM is a unique, hands-free solution for end-to-end de novo sequencing of monoclonal antibodies (mAbs), enabling high throughput protein discovery.
AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/29
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.
AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/28
HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/27
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.
AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/26
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.
AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/25
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/24
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.
AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/23
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/22
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.
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.
Modified by Allyson Lister from http://creativecommons.org/tag/attribution
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.
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.
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.
A Number of installations clause is a license clause which may limit the number of installations a particular licensee may peform.
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.
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.
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.
No restrictions on derivatives is a derivatives clause which places no rules or restrictions on how derivative software is created.
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.
Derivatives not allowed clauses are derivatives clauses which state that derivative resources are never allowed using the licensed resource.
Derivative code same license is a restrictive derivatives clause where derivative software must be released under the same license.
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.
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.
Platform restricted is a platform clause which places restrictions on which platform the licensed resource may be installed on.
Platform unrestrictred is a platform clause which does not place any restrictions on which type of platform the resource may be licensed for.
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.
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.
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.
A Number of users unrestricted clause is a number of users clause which does not restrict the number of users of the licensed resource.
Time for use restricted is a time clause which places restrictions on the length of time the licensed resource may be used.
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 is a usage clause which places no restrictions on how the licensed resource may be used.
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.
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 is a usage restricted clause which restricts the use of the licensed resource to academic licensees only.
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.
The mode of interaction with a piece of software.
AL 2.10.2019: Incorrectly-formatted IRI. See also https://github.com/allysonlister/swo/issues/18
obsolete software before Microsoft 2007
A stochastic algorithm for population pharmacology modeling
SAEM
A Dynamic Bayesian Network model is a Bayesian Network which relates variables to each other over adjacent time steps.
http://en.wikipedia.org/wiki/Dynamic_Bayesian_network, accessed 27 November 2014.
dynamic Bayesian network model
In mathematics, an ordinary differential equation or ODE is an equation containing a function of one independent variable and its derivatives. The term "ordinary" is used in contrast with the term partial differential equation which may be with respect to more than one independent variable.
Ordinary Differential Equation Algorithm
http://en.wikipedia.org/wiki/Ordinary_differential_equation, accessed 25 March 2015.
ODE Algorithm
Gillespie's Stochastic Simulation Algorithm is an algorithm which generates a statistically correct trajectory (possible solution) of a stochastic equation. It can be used to simulate chemical or biochemical systems of reactions efficiently and accurately using limited computational power. The algorithm is particularly useful for simulating reactions within cells where the number of reagents typically number in the tens of molecules (or less). Mathematically, it is a variety of a dynamic Monte Carlo method and similar to the kinetic Monte Carlo methods. It is used heavily in computational systems biology
http://en.wikipedia.org/wiki/Gillespie_algorithm, accessed 25 March 2015.
Gillespie's Stochastic Simulation Algorithm
Monte Carlo is a discrete stochastic simulation algorithm and an estimation procedure algorithm. If it is necessary to know the average value of some random variable and its distribution can not be stated, and if it is possible to take samples from the distribution, we can estimate it by taking the samples, independently, and averaging them. If there are sufficiently enough samples, then the law of large numbers says the average must be close to the true value. The central limit theorem says that the average has a Gaussian distribution around the true value.
http://en.wikipedia.org/wiki/Stochastic_simulation#Monte_Carlo_simulation, accessed 25 March 2015, and http://www.async.ece.utah.edu/iBioSim/docs/iBioSim.html, accessed 25 March 2015.
Monte Carlo
Differential Algebraic equations (DAEs) are a general form of (systems of) differential equations for vector–valued functions in one independent variable. In practical terms, the distinction between DAEs and ODEs is often that the solution of a DAE system depends on the derivatives of the input signal and not just the signal itself as in the case of ODEs.
Differential Algebraic Equation Algorithm
http://en.wikipedia.org/wiki/Differential_algebraic_equation, accessed 26 March 2015.
A partial differential equation (PDE) is a differential equation that contains unknown multivariable functions and their partial derivatives. This is in contrast to ordinary differential equations, which deal with functions of a single variable and their derivatives.
http://en.wikipedia.org/wiki/Partial_differential_equation, accessed 26 March 2015.
PDE Algorithm
A spreadsheet data format is one in which data is organised into a matrix (or matrices) of columns and rows to form cells in which values are entered.
A spreadsheet data format designed for Microsoft Excel.
A spreadsheet data format in which the structure of the data is described using XML, such as column and row headers and cell identity.
Equivalence with EDAM http://edamontology.org/format_2332, please use that instead.
"Resource Description Framework (RDF) format." [http://edamontology.org]
The Resource Description Framework (RDF) is a general-purpose language for representing information in the Web.
Data in RDF format can be serialised into XML, textual, or binary format.
Merged with now-obsolete EDAM class 'RDF' http://edamontology.org/format_2376 by Allyson Lister.
A serialisation of RDF into an XML format.
DWG ("drawing") is a binary file format used for storing two and three dimensional design data and metadata
DXF (Drawing Interchange Format, or Drawing Exchange Format) is a CAD data file format developed by Autodesk for enabling data interoperability between AutoCAD and other programs.
The BMP File Format is a Raster graphics image file format used to store bitmap digital images, independently of the display device (such as a graphics adapter).
Computer Graphics Metafile (CGM) is a free and open international standard file format for 2D vector graphics, raster graphics, and text, and is defined by ISO/IEC 8632.
PDF is an open standard for document exchange.
TIFF is a flexible, adaptable file format for handling images and data within a single file, by including the header tags (size, definition, image-data arrangement, applied image compression) defining the image's geometry.
JPEG is a lossy file format for storing images
PNG is a bitmapped image format and video codec that employs lossless data compression.
The Graphics Interchange Format (GIF) is a bitmap image format. The format supports up to 8 bits per pixel thus allowing a single image to reference a palette of up to 256 distinct colors. The colors are chosen from the 24-bit RGB color space. It also supports animations and allows a separate palette of 256 colors for each frame. The color limitation makes the GIF format unsuitable for reproducing color photographs and other images with continuous color, but it is well-suited for simpler images such as graphics or logos with solid areas of color. [wikipedia]
A raster image is a format for representing a rectangular grid of dots (pixels) which contains information on the specific colour of each pixel.
A vector image is a collection of connected lines and curves that produce objects. This geometric description enables the image to be displayed without loss at any size rendering.
PostScript is a format used for describing documents.
tex is a format for documents written in the document markup language and document preparation system LaTeX.
A format specification for data used or produced by outliner software
A proprietary format for documents created and edited using OmniOutliner outliner software,
OPML (Outline Processor Markup Language) is an XML format for outlines
JPEG 2000 is a compression standard enabling both lossless and lossy storage. The compression methods used are different from the ones in standard JFIF/JPEG; they improve quality and compression ratios, but also require more computational power to process. [wikipedia]
A file format for word processing documents for Microsoft Word.
A source code file format which is specified to be used with the Java programming language.
A format in which a .java file has been compiled into bytecode using a Java compiler and which is specified to be executed using the Java virtual machine.
An XML-based file format for use with the COPASI software.
AL 17.9.2019: The EDAM CopasiML (format_3239) was used elsewhere in SWO and therefore this class was no longer required.
Equivalence with the EDAM SBML class format_2585.
The Web Ontology Language (OWL) in XML serialization
Web Ontology Language version 2 in XML Serialization
Equivalence with EDAM http://edamontology.org/format_2330, please use that class instead.
Tab delimited file format is a plain text file format where each field value of a record is separated from the next by a tab stop character.
http://en.wikipedia.org/wiki/Tab-separated_values, accessed 6 June 2013.
Obsoleted after the version 0.4 release.
SIF stands for Simple Interaction Format, and is a text format invented for Cytoscape. If the file contains any tab characters, then tabs are used to delimit the fields and spaces are considered part of the name. If the file contains no tabs, then any spaces are delimiters that separate names (and names cannot contain spaces).
http://wiki.cytoscape.org/GettingStarted and http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats, accessed 20 June 2012
SIF
GML stands for Graph Markup Language, and is a standard network file format; supported by multiple generic network software packages
http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012
GML
XGMML stands for eXtensible Graph Markup and Modelling Language, and it is a XML standard; similar to but preferred over GML.
XGMML
A type of data which defines interactions between items in the file. This can be simple pairwise interactions or more complex ones. Used to provide a class of data for software requiring specific types of interaction data as input.
Interaction data
A knowledge representation role is a role borne by a data format which utilizes formalisms to make complex systems easier to design and build. Knowledge representation is the field of artificial intelligence devoted to representing information about the world in a form that a computer system can utilize to solve complex tasks.
Modified from http://en.wikipedia.org/wiki/Knowledge_representation, accessed 10 February 2014
AL 6.9.22: This has been moved from 'role' and used to be called 'knowledge representation role'. The issue in its former placement is to do with the domain and range of role. Bcause this class is intended as a role for a data format, it means that we use it for various children of IAO data format specification (http://purl.obolibrary.org/obo/IAO_0000098). has_role is an RO property with a domain of independent continuant, and data format specification is an ICE (a generically dependent continuant). This means we cannot use has_role for this class. Therefore, we have moved the class out of role and updated the label, and are now using 'characteristic of'/'has characteristic' instead. We may wish to refine the placement of this class in future.
Knowledge representation
AL 6.9.22: I would prefer to use the updated RO label 'has characteristic', but for some reason Protege only allows the use of the label RO deems older, 'bearer of'
BioPAX RDF/XML format
BioPAX Manchester OWL Syntax format
The CDF ASCII format is an ASCII data format specification created by Affymetrix similar to the Windows INI format. This 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.
CDF ASCII format
BAR is a binary data format specification created by Affymetrix where the data is stored in big-endian format. The format of the file is a header section followed by sequences sections (one section per sequence defined). The BAR file contains one and two sample analysis results (signal and p-values) from the tiling array software.
http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/bar.html, accessed 22 May 2013.
BAR
CEL ASCII format is ASCII data format specification created by Affymetrix similar to the Windows INI 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.
CEL ASCII format
Affymetrix-compliant data is data produced in a format compatible with Affymetrix software. This is a defined class where other data classes will be inferred to be members if they have a data format specification which has been published by Affymetrix.
Affymetrix-compliant data
The flow cytometry data file standard provides the specifications needed to completely describe flow cytometry data sets within the confines of the file containing the experimental data. The principal goal of the Standard is to provide a uniform file format allowing files created by one type of acquisition hardware and software to be analyzed by another type.
http://www.bioconductor.org/packages/2.12/bioc/vignettes/prada/inst/doc/fcs3.html, accessed May 29. 2013.
Data File Standard for Flow Cytometry
FCS3.0 is version 3.0 of the Data File Standard for Flow Cytometry. It contains a mechanism for handling data sets of 100 megabytes and larger, support for UNICODE text for keyword values, support for cyclic redundancy check (CRC) validation for each data set, a requirement for the inclusion of information describing the method of signal amplification and increased support for the inclusion of time as a measurement parameter.
FCS3.0
NONMEM data format
A nucleic acid sequence that indicate the order of nucleotides within some DNA.
DNA nucleotide sequence
Data about primary biological sequence information, such as DNA neucleotide sequences.
Data which contains information about amino acid sequences of proteins.
Nucleotide-nucleotide BLAST (blastn) is a type of BLAST software that takes a given DNA query and returns the most similar DNA sequences from the DNA database that the user specifies.
Tabix indexes a TAB-delimited genome position file and creates an index file when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally.
Genomedata provides a way to store and access large-scale functional genomics data in a format which is both space-efficient and allows efficient random-access. Genomedata archives are implemented as one or more HDF5 files, either as single files or as directory archives. HDF5 archives are self describing, like XML, but may also contain more complex structures such contain binary data.
http://pmgenomics.ca/hoffmanlab/proj/genomedata/doc/1.3.5/genomedata.html and http://www.hdfgroup.org/why_hdf/, accessed 27 November 2014.
genomedata format
The bedGraph format is a line-oriented text file format. Bedgraph data are preceeded by a track definition line, which adds a number of options for controlling the default display of this track. Following the track definition line are the track data in four column BED format. The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data. This track type is similar to the wiggle (WIG) format, but unlike the wiggle format, data exported in the bedGraph format are preserved in their original state.
http://genome.ucsc.edu/goldenpath/help/bedgraph.html, accessed December 3, 2014.
BedGraph
GMTK parameter data is a type of data which contains the various parameter files required by GMTK to define a dynamic Bayesian network.
http://noble.gs.washington.edu/proj/philius/README, accessed 3 December 2014.
GMTK parameter data
MathML 2.0 is an XML format which is a low-level specification for describing mathematics as a basis for machine to machine communication. It is a W3C Recommendation and was released on 21 Feb 2001. A product of the W3C Math working group, it provides a much needed foundation for the inclusion of mathematical expressions in Web pages.
FieldML is an XML-based language for describing time-varying and spatially-varying fields. The aims of the language design process are to keep the language concise, consistent, intuitive and flexible.
FieldML
WKn is a collective name for a spreadsheet format created for Lotus 1-2-3.
http://support.sas.com/documentation/cdl/en/acpcref/63184/HTML/default/viewer.htm#a003103772.htm and http://en.wikipedia.org/wiki/Lotus_1-2-3, accessed 3 December 2014.
Please note that this is a collective class for all versions of the WKn format, and the specific version required should be created as necessary and placed as a child of this class.
WKn
.gz
.zip
audio format
RIFF
.bw
.csv
.mgf
.mysql
.sql
A Web User interface is a Graphical User Interface which is loaded and run via a Web browser rather than within the user's operating system.
web user interface
A Desktop Graphical User interface is a Graphical User Interface which is loaded and run within the user's operating system rather than via a Web browser.
desktop graphical user interface
A SOAP service is a Web service which provides a standard, extensible, composable framework for packaging and exchanging XML messages. The service may expose an arbitrary, application-specific set of operations.
Modified from http://en.wikipedia.org/wiki/SOAP, accessed 6 June 2013; modified from http://www.w3.org/TR/ws-arch, accessed 6 June 2013.
SOAP service
A REST service is a Web service in which the primary purpose of the service is to manipulate XML representations of Web resources using a uniform set of "stateless" operations. RESTful APIs do not require XML-based web service protocols (SOAP and WSDL) to support their light-weight interfaces.
Modified from http://www.w3.org/TR/ws-arch, accessed 6 June 2013, Modified from http://en.wikipedia.org/wiki/Web_service, accessed 6 June 2013.
REST service
A web service in which calls invoked return JSON.
A web service is a software interface which works as a method of communication between two electronic devices over the World Wide Web and which is provided at a particular network address. There are two major classes of Web services: REST-compliant Web services, and arbitrary (or application-specific) Web services.
Modified from http://www.w3.org/TR/ws-arch/, accessed 6 June 2013; Modified from http://en.wikipedia.org/wiki/Web_service, accessed 6 June 2013.
A Graphical user interface is a type of software interface that allows users to interact with electronic devices using images rather than text commands. A GUI represents the information and actions available to a user through graphical icons and visual indicators such as secondary notation, as opposed to text-based interfaces, typed command labels or text navigation.
https://en.wikipedia.org/wiki/Graphical_user_interface, accessed 6 June 2013.
A command-line interface is a means of interacting with a computer program where the user (or client) issues commands to the program in the form of successive lines of text (command lines).
http://en.wikipedia.org/wiki/Command-line_interface, accessed 25 November 2014.
An application programming interface is a set of routines, protocols, and tools for building software applications. An API expresses a software component in terms of its operations, inputs, outputs, and underlying types. An API defines functionalities that are independent of their respective implementations, which allows definitions and implementations to vary without compromising each other. The API specifies how software components should interact.
http://en.wikipedia.org/wiki/Application_programming_interface, accessed 25 November 2014.
Distribution clauses are license clauses which state the requirements on how the licensed resource is redistributed. The license for a resource may or may not allow the redistribution of that resource. If it is allowed, such usage may be restricted in a variety of ways.
Distribution restricted is a distribution clause which places restrictions on how the licensed resource may be distributed by third parties. These restrictions may be complete, e.g. no further redistribution, or partial.
Distribution unrestricted is a distribution clause which states that the licensed resource can be redistributed by a third party in whatever manner that party wishes.
Derivatives allowed clauses are derivatives clauses which state that derivative resources are allowed using the licensed resource. Even when allowed, such a clause may or may not restrict the usage of the licensed resource in a variety of ways.
This is a free software license under the definition of "free" by the GNU Project, and is compatible with version 3 of the GNU GPL.
http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013.
The Academic Free License is a free software license under the definition of "free" by the GNU Project, is not copyleft, and is incompatible with the GNU GPL.
http://directory.fsf.org/wiki/License:AFLv3, accessed 12 June 2013; http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013
This is the original BSD license with the advertising clause and another clause removed. (It is also sometimes called the “2-clause BSD license”.) It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL.
License without restrictions on derivatives
A licensed is a free license according to GNU if the users have the four essential freedoms: The freedom to run the program, for any purpose (freedom 0). The freedom to study how the program works, and change it so it does your computing as you wish (freedom 1). Access to the source code is a precondition for this. The freedom to redistribute copies so you can help your neighbor (freedom 2). The freedom to distribute copies of your modified versions to others (freedom 3). By doing this you can give the whole community a chance to benefit from your changes. Access to the source code is a precondition for this. A program is free software if users have all of these freedoms. Thus, you should be free to redistribute copies, either with or without modifications, either gratis or charging a fee for distribution, to anyone anywhere. Being free to do these things means (among other things) that you do not have to ask or pay for permission to do so. “Free software” does not mean “noncommercial”. A free program must be available for commercial use, commercial development, and commercial distribution. Commercial development of free software is no longer unusual; such free commercial software is very important. You may have paid money to get copies of free software, or you may have obtained copies at no charge. But regardless of how you got your copies, you always have the freedom to copy and change the software, even to sell copies.
http://www.gnu.org/philosophy/free-sw.html, accessed 12 June 2013.
Allyson Lister: This class defines those licenses which are free licenses, but which may or may not be compatible with any version of the GNU GPL.
GNU GPL Compatible License Type is a GNU Project Free License Type which is also compatible with one or more versions of the GNU GPL
Modified from http://www.gnu.org/copyleft/copyleft.html, accessed 12 June 2013.
Copyleft is a derivative code same license clause which says that anyone who redistributes the software, with or without changes, must pass along the freedom to further copy and change it. In other words, it requires that all derivative code uses the same license, but further limits the type of license to one which gives everyone the rights to use, modify, and redistribute the program's code, or any program derived from it, but only if the distribution terms are unchanged. To copyleft a program, you first state that it is copyrighted; then the distribution terms described above are added. This makes copyleft a legal instrument ensuring that the code and the freedoms become legally inseparable.
Copyleft
The GNU GPL v3 is the latest version of the GNU GPL: a free software license, and a copyleft license. Please note that GPLv3 is not compatible with GPLv2 by itself. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. When this is the case, you can use the code under GPLv3 to make the desired combination.
https://www.gnu.org/licenses/license-list.html, accessed on 23 June 2016.
GNU GPL v3
The GNU GPL v2 is an earlier version of the GNU GPL: a free software license, and a copyleft license. Please note that GPLv2 is, by itself, not compatible with GPLv3. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. When this is the case, you can use the code under GPLv3 to make the desired combination.
https://www.gnu.org/licenses/license-list.html, accessed 23 June 2016.
GNU GPL v2
CC0 is a public domain dedication from Creative Commons. A work released under CC0 is dedicated to the public domain to the fullest extent permitted by law. If that is not possible for any reason, CC0 also provides a lax, permissive license as a fallback. Both public domain works and the lax license provided by CC0 are compatible with the GNU GPL.
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
CC BY 2.0 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software.
Creative Commons Attribution 2.0 Generic (CC BY 2.0)
Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013 and 28 June 2016; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013.
CC BY 2.0
Attribution required is an attribution clause which states that attribution of the type specified in the license must be provided whenever the resource is used.
Attribution required
CC BY-SA 2.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL.
Creative Commons Attribution-Sharealike 2.0 Generic
Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013.
LPPL v1.3 is a free software license (by the defintion of the GNU Project), with less stringent requirements on distribution than LPPL 1.2. It is still incompatible with the GPL because some modified versions must include a copy of or pointer to an unmodified version.Software projects other than LaTeX rarely use it.
Latex Project Public License v1.3c
Modified from http://en.wikipedia.org/wiki/LaTeX_Project_Public_License, accessed 12 June 2013; modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013.
LPPL v1.2 is a free software license (by the defintion of the GNU Project), This license is an incomplete statement of the distribution terms for LaTeX. While it is a free software license, it is incompatible with the GPL because it has many requirements that are not in the GPL. Software projects other than LaTeX rarely use it.
Latex Project Public License v1.2
LPPL v1.2
MPL v2.0 a free software license as defined by the GNU Project. Section 3.3 provides indirect compatibility between this license and the GNU GPL version 2.0, the GNU LGPL version 2.1, the GNU AGPL version 3.0, and all later versions of those licenses. The MPL allows covered source code to be mixed with other files under a different, even proprietary license. However, code files licensed under the MPL must remain under the MPL and freely available in source form.
http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; http://en.wikipedia.org/wiki/Mozilla_Public_License, accessed 12 June 2013.
MPL v2.0
The Artistic License v 2.0 is a free software license by the definition of the GNU Project and compatible with the GPL thanks to the relicensing option in section 4(c)(ii) (as compared with the Artistic License 1.0).
Purchase cost is a license clause which states whether there is a cost involved with a particular usage or licensing of a resource.
In some ways, purchase cost is similar to the already-extant usage clause hierarchy, which includes restricted and unrestricted usage. However, a usage limitation is not necessarily due to whether or not something costs money: even if the usage is academic only, it could still be either free or non-free. A license could have multiple usage clauses, e.g. academic only when free, and unrestricted if a fee is paid. Purchase cost was created which, together with a usage clause, defines both limitations and cost.
Free is a type of purchase cost clause which, when applied, means that there is no cost for the users of the resource to which the license is attached. This clause can be combined with other clauses (such as usage clauses) to specify that only certain usages are free.
This class refers only to the cost of the resource, not to the definition of "free software" as provided by the GNU Project and which is commonly used to describe software that respects users' freedom and community (http://www.gnu.org/philosophy/free-sw.html).
Not Free is a type of purchase cost clause which, when applied, means that there is a cost for the users of the resource to which the license is attached. This clause can be combined with other clauses (such as usage clauses) to specify that only certain usages incur a purchase cost.
A license which allows any form of usage of the artifact.
free to use license
The CC BY 4.0 license is a Creative Commons license. This is a non-copyleft free license that is good for art and entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. People are free to: Share — copy and redistribute the material in any medium or format; Adapt — remix, transform, and build upon the material for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. But they must conform to the following terms: Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. No additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.
Creative Commons Attribution 4.0 International (CC BY 4.0)
http://creativecommons.org/licenses/by/4.0/ accessed June 22, 2016; https://www.gnu.org/licenses/license-list.html, accessed on June 28, 2016.
Allyson Lister: The only restriction on derivatives is that of the attribution requirement.
CC BY 4.0
Attribution not required is an attribution clause which states that no attribution need be provided whenever the resource is used.
Attribution not required
CC BY 2.0 UK is a UK-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software.
Creative Commons Attribution 2.0 UK: England & Wales (CC BY 2.0 UK)
Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050.
CC BY 2.0 UK
This is the latest version of the LGPL: a free software license, but not a strong copyleft license, because it permits linking with nonfree modules. It is compatible with GPLv3. It is therefore recommend for special circumstances only. Please note that LGPLv3 is not compatible with GPLv2 by itself. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. When this is the case, you can use the code under GPLv3 to make the desired combination.
GNU Lesser General Public License (LGPL) version 3
GNU AGPL
This is a free software, copyleft license. Its terms effectively consist of the terms of GPLv3, with an additional paragraph in section 13 to allow users who interact with the licensed software over a network to receive the source for that program. It is recommended that developers consider using the GNU AGPL for any software which will commonly be run over a network.
GNU Affero General Public License (AGPL) version 3
GNU AGPL v3
This is the previous version of the LGPL: a free software license, but not a strong copyleft license, because it permits linking with nonfree modules. It is compatible with GPLv2 and GPLv3. We generally recommend the latest version of the LGPL, for special circumstances only.
GNU Lesser General Public License (LGPL) version 2.1
https://www.gnu.org/licenses/license-list.html, accessed 28 June 2016.
GNU LGPL v2.1
CC BY 2.1 JP is a Japan-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software.
Creative Commons Attribution 2.1 Japan (CC BY 2.1 JP)
CC BY 2.5 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software.
Creative Commons Attribution 2.5 Generic (CC BY 2.5)
CC BY 2.5
CC BY 3.0 AU is an Australia-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software.
Creative Commons Attribution 3.0 Australia (CC BY 3.0 AU)
CC BY 3.0 AU
CC BY 3.0 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software.
Creative Commons Attribution 3.0 Unported (CC BY 3.0)
CC BY 3.0
CC BY 3.0 US is a US-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software.
Creative Commons Attribution 3.0 United States (CC BY 3.0 US)
CC BY 3.0 US
CC BY-ND 3.0 is a nonfree license, as there are restrictions on distributing modified versions. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. This license is generally used for documentation.
Creative Commons Attribution-NoDerivs 3.0 Unported (CC BY-ND 3.0)
https://www.gnu.org/licenses/license-list.html accessed 29 June 2016; https://creativecommons.org/licenses/by-nd/3.0/ accessed 29 June 2016.
CC BY-ND 3.0
CC BY-ND 4.0 is a nonfree license, as there are restrictions on distributing modified versions. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. This license is generally used for documentation.
Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
CC BY-ND 4.0
CC BY-NC 3.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, use the work for non-commercial purposes, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible.
Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)
https://www.gnu.org/licenses/license-list.html accessed 29 June 2016.
CC BY-NC 3.0
CC BY-NC 4.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, use the work for non-commercial purposes, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible.
Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
CC BY-NC-ND 3.0 is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material.
Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)
CC BY-NC-ND 3.0
CC BY-NC-ND 2.5 is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material.
Creative Commons Attribution-NonCommercial-NoDerivs 2.5 Generic (CC BY-NC-ND 2.5)
CC BY-NC-ND 2.5
CC BY-NC-ND 2.5 CH is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material.
Creative Commons Attribution-NonCommercial-NoDerivs 2.5 Switzerland (CC BY-NC-ND 2.5 CH)
CC BY-NC-ND 2.5 CH
CC BY-NC-ND 4.0 is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material.
Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International (CC BY-NC-ND 4.0)
CC BY-NC-ND 4.0
CC BY-NC-SA 2.5 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible.
Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Generic (CC BY-NC-SA 2.5)
CC BY-NC-SA 2.5
CC BY-NC-SA 3.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible.
Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)
CC BY-NC-SA 3.0
CC BY-NC-SA 3.0 US is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible.
Creative Commons Attribution-NonCommercial-ShareAlike 3.0 United States (CC BY-NC-SA 3.0 US)
CC BY-NC-SA 3.0 US
CC BY-NC-SA 2.5 IN is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible.
Creative Commons Attribution-NonCommercial-ShareAlike 2.5 India (CC BY-NC-SA 2.5 IN)
CC BY-NC-SA 2.5 IN
CC BY-NC-SA 4.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible.
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
CC BY-NC-SA 4.0
CC BY-SA 2.1 JP is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL.
Creative Commons Attribution-Sharealike 2.1 Japan
CC BY-SA 3.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL.
Creative Commons Attribution-Sharealike 3.0 Unported
CC BY-SA 3.0
CC BY-SA 3.0 US is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL.
Creative Commons Attribution-Sharealike 3.0 United States
CC BY-SA 3.0 US
CC BY-SA 4.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL.
Creative Commons Attribution-Sharealike 4.0 International
CC BY-SA 4.0
Open Data Commons
The ODbL v1.0 allows a user of the databases to share, create and adapt the database. You must attribute any public use of the database, or works produced from the database. For redistribution of the database or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original database. If you publicly use any adapted version of this database, or works produced from an adapted database, you must also offer that adapted database under the ODbL. If you redistribute the database, or an adapted version of it, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures.
http://opendatacommons.org/licenses/odbl/summary/, accessed 5 July 2016.
ODbL v1.0
The DbCL v1.0 allows a user of the database contents to share, create and adapt the contents. You must attribute any public use of the contents, or works produced from them. For redistribution or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original. If you publicly use any adapted version, or works produced from an adapted version, you must also offer it under the DbCL. If you redistribute the contents, or an adapted version of them, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures. Users of the DbCL must comply with the ODbL v1.0.
ODC Database Contents License (DbCL) v1.0
http://opendatacommons.org/licenses/odbl/summary/, accessed 5 July 2016; http://opendatacommons.org/licenses/dbcl/1.0/, accessed 5 July 2016.
DbCL v1.0
The EMBLEM ELM Academic LIcense was developed as the license for the ELM (Eukaryotic Linear Motif) resource. Non-commerical use is allowed under this license, an additional commercial license is also available. This license makes the Licensed Software available free of charge for the licensee, which is a non-profit educational, academic and/or research institution. The software can only be used for academic research projects. This explicitly excludes projects which charge a fee, or projects that are done in collaboration with a third party that is funding the research in whole or in part in exchange for commercial rights on the results and/or possible delay in publication of any relevant results to the academic community. The user and any research assistants, co-workers or other workers who may use the Software agree to not grant licenses on any software that includes the Licensed Software, alone or integrated into other software, to third parties. Modification of the Licensed Software code is prohibited without the prior written consent of EMBLEM.
http://elm.eu.org/media/Elm_academic_license.pdf, accessed 6 July 2017; http://elm.eu.org/infos/about.html accessed 6 July 2016.
EMBLEM ELM Academic License
The FlowRepository Open Access Terms of Use license allows any individual to access the licensed product (originally the Flow Cytometry Data Repository) for any purpose. There are no restrictions on the use or redistribution of the data associated with this license, though it makes the statement that some data covered may also be included under more restrictive licensing.
http://flowrepository.org/terms_of_service, accessed 6 July 2016.
FlowRepository Open Access Terms of Use
The ODbL v1.0 allows a user of the databases to share, create and adapt the database. You must attribute any public use of the database, or works produced from the database. For redistribution of the database or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original database. If you redistribute the database, or an adapted version of it, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures.
Open Data Commons Attribution License (ODC-By) v1.0
http://opendatacommons.org/licenses/by/summary/, accessed 6 July 2016.
ODC-By v1.0
The ODC Public Domain Dedication and Licence is a document intended to allow you to freely share, modify, and use this work for any purpose and without any restrictions. This licence is intended for use on databases or their contents (“data”), either together or individually. The goal is to eliminate restrictions held by the original creator of the data and database on the use of it by others. Rightsholders will not be able to “dual license” their work by releasing the same work under different licences. This is because they have allowed anyone to use the work in whatever way they choose. Rightsholders therefore can’t re-license it under copyright or database rights on different terms because they have nothing left to license.
ODC Public Domain Dedication and Licence
http://opendatacommons.org/licenses/pddl/1.0/, accessed 7 July 2016.
PDDL v1.0
This is the original BSD license, modified by removal of the advertising clause. It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. This license is sometimes referred to as the 3-clause BSD license. According to the GNU Project, the modified BSD license is not bad, as lax permissive licenses go, though the Apache 2.0 license is preferable. However, it is risky to recommend use of “the BSD license”, even for special cases such as small programs, because confusion could easily occur and lead to use of the flawed original BSD license. To avoid this risk, you can suggest the X11 license instead. The X11 license and the modified BSD license are more or less equivalent. According to the GNU project, the Apache 2.0 license is better for substantial programs, since it prevents patent treachery.
1.6 (expected version number, after 1.5)
This class is a duplicate of http://www.ebi.ac.uk/swo/license/SWO_9000085.
obsolete_Modified BSD License
A vendor-specific license is a license which was, at least originally, created by a specific organization to be used just on the resources created within that organization. This is a hierarchy of convenience rather than of shared philosophy. Many of the licenses have since been taken up by other groups whose licensing requirements matched those of the originating organization.
Vendor-specific License
The NIDA NIH Data Access Policy specifies under what legal requirements NIDA NIH data may be accessed. Researchers may gain access to clinical data, genetic analysis data, and DNA by obtaining formal approval from the NIDA Genetic Data Access Request Committee.
NIDA NIH Data Access Policy
The Addgene Terms of Use specifies under what legal requirements Addgene data may be accessed. Data is available for use for non-commercial purposes, but users must get express written consent of Addgene to exploit the data for commercial purposes. All copyright, trademark and other proprietary notices must be retained on the data. As consent must be aquired for commercial use, this license only allows non-commercial use (a separate agreement must be entered into for commercial use).
https://www.addgene.org/terms-of-use/, accessed 7 July 2016
Addgene Terms of Use
The CAS Information Use Policy specifies under what legal requirements CAS Information may be accessed. Attribution to ACS must be included whenever creating derivatives or redistributing data covered under this license.Each User is permitted to download and retain a maximum of 5,000 Records and a maximum of 5,000 Molfiles at any given time for personal use or to share within a Project team for the life of the Project. There are also limits on how long records may be stored with the licensee, and how records may be linked.
http://www.cas.org/legal/infopolicy accessed 7 July 2016.
The created contents and works provided under this license by CellFinder are subject to the German copyright law. Third-party contributions are marked as such. Reproduction, adaptation, dissemination and any kind of exploitation outside the limits of the copyright require the written consent of the author or creator. Downloads and copies of these pages are only permitted for private, non-commercial use. The operators of these pages aim to observe the copyright of others or will refer to their own or license-free works.
http://cellfinder.de/contact/disclaimer/, accessed 7 July 2016.
CellFinder Copyright
The LINCS Data Policy is a license which allows redistribution and derivative works as long as the original data is attributed correctly. All investigators are encouraged, to publish results based on LINCS data. These results may include, but would not be limited to, integrating LINCS data with data from other sources. LINCS data are released with the sole restriction that they must be correctly cited so that others can establish provenance and access the original data; the correct citation will be released with each data set and will comprise either a PMID/PMCID reference or a unique LINCS identifier.
http://www.lincsproject.org/data/data-release-policy/, accessed 7 July 2016.
LINCS Data Policy
The GeneNetwork Conditions of Use describes the data licensing for the resource covered. Commercial and non-commercial use is allowed, though attribution is requested via either acknowledgement or co-authorship. Further restrictions on the bulk download of as-yet unpublished data is also described. (While mentioned in the document, software licensing is not the focus of this conditions of use and therefore is not modelled here.)
http://www.genenetwork.org/conditionsofUse.html, accessed 7 July 2016.
GeneNetwork Conditions of Use
The GMD Academic License is a vendor-specific license which allows the access and use of the licensed data for non-commercial purposes, as long as the appropriate attribution is used and copyright notices retained. A separate license agreement is required for commercial users and as such, they are not covered by this license. Without written consent by the GMD, no part of the GMD - in its original or in any way processed or reformatted form - may be re-distributed in any way.
Golm Metabolome Database Academic License
http://gmd.mpimp-golm.mpg.de/termsconditions.aspx, accessed 7 July 2016.
GMD Academic License
The GeneProf Academic License is a vendor-specific license which allows the access and use of the licensed resource for non-commercial purposes.
http://www.geneprof.org/GeneProf/terms_and_conditions.jsp, accessed 7 July 2016.
GeneProf Academic License
The European Medicines Agency Copyright states that the Agency is the owner of copyright and other intellectual property rights for documents and other content published on their website. Information and documents made available on the Agency's webpages are public and may be reproduced and/or distributed, totally or in part, irrespective of the means and/or the formats used, for non-commercial and commercial purposes, provided that the Agency is always acknowledged as the source of the material. Such acknowledgement must be included in each copy of the material. Citations may be made from such material without prior permission, provided the source is always acknowledged. The above-mentioned permissions do not apply to content supplied by third parties. Therefore, for documents where the copyright vests in a third party, permission for reproduction must be obtained from this copyright holder.
http://www.ema.europa.eu/ema/index.jsp?curl=pages/regulation/general/general_content_000178.jsp, accessed 12 July 2016.
European Medicines Agency Copyright
miRTaBase Data License is a simple vendor license which allows academic users to make use of the data for free.
http://mirtarbase.mbc.nctu.edu.tw/cache/download/LICENSE, accessed 12 July 2016
miRTaBase Data License
GBIF Data Sharing Agreement is a simple vendor license which allows all users to make use of the data for free, as long as the source of the data is properly attributed.
http://www.gbif.org/terms/licences/data-sharing, accessed 12 July 2016
GBIF Data Sharing Agreement
IUPAC/InChI-Trust InChI Licence No. 1.0 is a vendor license which allows all users to make use of the resource, including the source code, for free, as long as its source is properly attributed. It is broadly compatible with the GNU GPL v3 and v2 in that it states in the license that you can change the license from this one to the GNU GPL if you wish.
IUPAC/InChI-Trust Licence for the International Chemical Identifier (InChI) Software version 1.04
http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/LICENCE.pdf, accessed 12 July 2016
IUPAC/InChI-Trust InChI Licence No. 1.0
The Labome copyright makes the contents of their resource freely available for browsing. Any redistribution or reproduction of part or all of the contents in any form is prohibited other than the following: you may print or download to a local hard disk extracts for your use only, with a daily limit of 50 webpages; and you may copy the content to individual third parties for their use, but only if you acknowledge the website as the source of the material. You may not, except with our express written permission, distribute or commercially exploit the content.
http://www.labome.com/about/copyright.html, accessed 12 July 2016.
Labome Copyright
The CTD Legal Notice and Terms of Data Use specifies under what legal requirements the CTD data may be accessed. Data is available for use for non-commercial purposes as long as the data is properly attributed, but users must get express written consent of CTD to exploit the data for commercial purposes. As consent must be aquired for commercial use, this license only allows non-commercial use (a separate agreement must be entered into for commercial use). Additionally,You must notify CTD and describe your use of their data. For quality control purposes, you must provide CTD with periodic access to your publication of their data.
Comparative Toxicogenomics Database Legal Notice and Terms of Use
http://ctdbase.org/about/legal.jsp, accessed 12 July 2016
CTD Legal Notice and Terms of Data Use
LOINC RELMA Terms of Use is a vendor license which allows all users to make use of the data for free, as long as the source of the data is properly attributed. An unlimited number of copies of the licensed material may be used.
https://loinc.org/terms-of-use/, accessed 12 July 2016
LOINC RELMA Terms of Use
MIACA Full Copyright is a vendor-specific license which allows the document it references to be copied and furnished to others, and derivative works that comment on or otherwise explain it or assist in its implementation may be prepared, copied, published and distributed, in whole or in part, without restriction of any kind, provided that the above copyright notice and this paragraph are included on all such copies and derivative works. However, this document itself may not be modified in any way, such as by removing the copyright notice or references to the MIACA Standards Initiative or other organizations, except as needed for the purpose of developing MIACA Standards Initiative Recommendations in which case the procedures for copyrights defined in the MIACA Document process must be followed, or as required to translate it into languages other than English.
http://miaca.sourceforge.net/copyrightNotice.txt, accessed 12 July 2016
MIACA Full Copyright
The ORCID MIT-style license is identical to the MIT License, except for the addition of the following two clauses: 1. "The above license does not apply to the branding or the "look and feel" of the websites located at the orcid.org URL even if elements thereof are contained in the Software."; 2. "Except to provide the copyright notice required above or as allowed under ORCID Inc.'s Trademark Use Policy (available at http://orcid.org, under "Policies"), you may not use the name of ORCID, Inc., ORCID, its marks and logo, to advertise, promote or suggest any affiliation with or endorsement by ORCID, Inc. in connection with your use of the Software.". The MIT License is is a lax, permissive non-copyleft free software license, compatible with the GNU GPL.
https://github.com/ORCID/ORCID-Source/blob/master/LICENSE.md, accessed 12 July 2016; https://www.gnu.org/licenses/license-list.html, accessed 28 June 2016.
ORCID MIT-Style License (MIT)
The NIH Genomic Data Sharing Policy specifies under what legal requirements NIH genomic data may be accessed. Access to human data is through a tiered model involving unrestricted- and controlled-data access mechanisms. Requests for controlled-access data are reviewed by NIH Data Access Committees (DACs).
NIH Genomic Data Sharing Policy
The Facebase Data Access Policy specifies under what legal requirements Facebase data may be accessed. Non-sensitive data is available for use for all purposes and usages. As consent must be aquired for sensitive (or closed) data, this license only covers the use of the open data (a separate agreement must be entered into for restricted access data).
https://www.facebase.org/methods/policies/, accessed 12 July 2016
Facebase Data Access Policy
The ORCID Terms of Use is a vendor-specific license for describing how the data in the ORCID resource may be used. ORCID data can be sublicensed, reproduced, stored, transmitted, distributed, publicly performed and publicly displayed for non-commercial and commercial uses.
http://orcid.org/content/orcid-terms-use, accessed 12 July 2016
ORCID Terms of Use
The PPDB Academic Licens specifies under what legal requirements PPDB data may be accessed. Data is available for use for non-commercial purposes, but users must get express written consent of PPDB to exploit the data for commercial purposes. The resource will be used for teaching or not-for-profit research purposes only. The resource will not be further distributed to others. The recipient agrees to acknowledge the source of the material in any publication reporting its use. As consent must be aquired for commercial use, this license only allows non-commercial use (a separate agreement must be entered into for commercial use).
Plant Promoter Database Academic License
http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi, accessed 12 July 2016
PPDB Academic License
The SciCrunch Terms and Conditions specifies under what legal requirements SciCrunch data may be accessed. Broadly speaking, the site conforms, both for data and for the site documents themselves, to the CC BY 3.0 license. However, particular details for this resource (other than attribution requirements) are unclear.
https://neuinfo.org/page/terms, accessed 12 July 2016.
SciCrunch Terms and Conditions
The ProDom Commercial License is a vendor-specific license which allows the access and use of the licensed data for commercial purposes for a fee. Non-commercial use does not require licensing or a fee, and is covered by a separate license.
http://prodom.prabi.fr/prodom/current/html/downcom.php, accessed 12 July 2016.
ProDom Commercial License
The SBGN Open License with Attribution is a very simple statement of openness for the SBGN standard and related resources available on its website. No one—not the principal investigators, nor the SBGN Editors, nor the members of the SBGN Scientific Committee, nor the funding agencies or anyone else—owns SBGN; it is a free and open community effort that extends beyond any single group, and they view themselves only as organizers and fellow developers.
Systems Biology Graphical Notation Open License with Attribution
http://www.sbgn.org/About, accessed 12July 2016.
SBGN Open License with Attribution
The NLM Open License with Attribution is a vendor-specific license which is similar to public domain, but which requests attribution. Government information at NLM Web sites is in the public domain. Public domain information may be freely distributed and copied, but it is requested that in any subsequent use the National Library of Medicine (NLM) be given appropriate acknowledgement. When using NLM Web sites, you may encounter documents, illustrations, photographs, or other information resources contributed or licensed by private individuals, companies, or organizations that may be protected by U.S. and foreign copyright laws. Transmission or reproduction of protected items beyond that allowed by fair use as defined in the copyright laws requires the written permission of the copyright owners. Specific NLM Web sites containing protected information provide additional notification of conditions associated with its use.
National Library of Medicine Open License with Attribution
https://www.nlm.nih.gov/copyright.html, accessed 12 July 2016.
NLM Open License with Attribution
The RegenBase Terms of Use is a vendor-specific license which requires attribution and which does not meet the requirements for open source code, as there is a statement saying that the user will NOT translate, reverse engineer, decompile or disassemble the SYSTEM, or disclose the SYSTEM or any underlying information or technology to any third party.
http://regenbase.org/terms-of-use.html, accessed 12 July 2016
RegenBase Terms of Use
The SABIO-RK Non-Commercial Purpose License covers use of the Database for Non-Commercial Purpose only, and appropriate attribution must be given. Non-Commercial Purpose means the use of the Database solely for internal non-commercial research and academic purposes. As consent must be aquired for commercial use, a separate agreement must be entered into for commercial use and is not covered here.
http://sabiork.h-its.org/layouts/content/termscondition.gsp, accessed 13 July 2016
SABIO-RK Non-Commercial Purpose License
The Terms of Use for EMBL-EBI Services reflect EMBL-EBI’s commitment to OpenScience through its mission to provide freely available online services, databases and software relating to data contributed from life science experiments to the largest possible community. They impose no additional constraints on the use of the contributed data than those provided by the data owner. EMBL-EBI expects attribution (e.g. in publications, services or products) for any of its online services, databases or software in accordance with good scientific practice. The expected attribution will be indicated on the appropriate web page.
http://www.ebi.ac.uk/about/terms-of-use, accessed 13 July 2016.
Terms of Use for EMBL-EBI Services
The UCUM Terms of Use is a vendor-specific license which allows the resource it references to be used for commercial or non-commercial purposes without restriction of any kind, provided that appropriate attribution is given. However, the resource itself may not be modified in any way. Users may make and distribute an unlimited number of copies of the Licensed Materials. Each copy thereof must include the Copyright Notice and License.
The Unified Code for Units of Measure Terms of Use
http://unitsofmeasure.org/trac/wiki/TermsOfUse, accessed 13 July 2016
UCUM Terms of Use
The UMLS Metathesaurus License is a vendor-specific license which allows redistribution (as part of a larger computer application) as long as the original data is attributed correctly and a summary of data use provided each year. There is no cost to use the service, and may be used both commercially and non-commercially. Users must inform the resource if it is redistributed within a computer application.
https://uts.nlm.nih.gov/license.html, accessed 13 July 2016.
UMLS Metathesaurus License
The MHAS Data Policy is a vendor-specific license which requires that users attribute the data properly. The data is accessible free of charge to all commercial and non-commercial users.
http://www.mhasweb.org/Data.aspx, accessed 13 July 2016.
MHAS Data Policy
The ALFRED Copyright is a vendor-specific license which states that the resource is freely available to the scientific community for statistical analysis, the only condition being that attribution is required.
https://alfred.med.yale.edu/alfred/fullcopyrightpage.asp, accessed 13 July 2016.
ALFRED Copyright
Commercial use only is a usage restricted clause which restricts the use of the licensed resource only to licensees who are commercial entites.
Allyson Lister: Some licenses are expressly written for their commercial users. In such cases, a vendor will normally have multiple licenses, one for non-commercial use and one for commercial use.
Commercial use only
Fee-Based Commercial License is a license which, among its license clauses, states that commercial entities may use the resource for a fee.
Allyson Lister: This is a convenience class which combines multiple license clauses to create a defined class, such that any license type which meets the requirements will be inferred to fall into this category.
Fee-Based Commercial License
The BRENDA License is a vendor-specific license which allows access to the official website and its data free of charge. Any inclusion of BRENDA components into other data bases, or redistribution of BRENDA requires a license. To obtain commercial in-house versions please contact our distributor Biobase GmbH ( http://www.biobase-international.com). In-house versions for academic users are available from Enzymeta GmbH (http://www.enzymeta.de). The copyright of the printed version is held by Springer publishers. Users of the website may retrieve a copy of the data but must not alter the BRENDA data or charge money for a copy of it, and must not distribute any BRENDA data without prior permission of the copyright holder. As there are separate licenses for in-house versions of BRENDA, please note that this license only describes the website-accessible version of BRENDA.
http://www.brenda-enzymes.org/copy.php, accessed 13 July 2016.
BRENDA License
The TCGA Data Use Certification is a vendor-specific license which specifies the certification which must be officially agreed to before data may be accessed. There are a number of requirements in this license including attribution, non-transferability, annual progress updates, and a number of security measures.
The Cancer Genome Atlas Data Use Certification
http://cancergenome.nih.gov/pdfs/Data_Use_Certv082014, accessed 13 July 2016
TCGA Data Use Certification
Non-Commercial No-Fee License is a license which, among its license clauses, states that non-commercial entities may use the resource without a purchase or usage cost.
Non-Commercial No-Fee License
DrugBank is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes (including internal use) requires a license. We ask that users who download significant portions of the database cite the DrugBank paper in any resulting publications. As consent must be aquired for commercial use, this license only describes the non-commercial aspects of data usage (a separate agreement must be entered into for commercial use).
http://www.drugbank.ca/about, accessed 13 July 2016
DrugBank Academic License
The UCSC Genome Browser Commercial Software License is a vendor-specific license which allows the access and use of the licensed data for commercial purposes under specific restrictions for a fee. The licensee shall not have the right to create Derivative Works of the Licensed Products, and the Licensee shall not have the right to sublicense, sell, transfer, or assign the Licensed Products. Non-commercial use does not require licensing or a fee, and is covered by a separate license.
http://genome.cse.ucsc.edu/license/gblicense.pdf, accessed 13 July 2016.
UCSC Genome Browser Commercial Software License
Permission required for commercial use is a clause which restricts the use of the licensed resource only to licensees who are commercial entites which have received explicit permission in the manner stipulated by the resource.
Permission required for commercial use
Permission required for derivative work is a clause which restricts the production of derivative work based on the licensed resource only to licensees who have received explicit permission in the manner stipulated by the resource.
Permission required for derivative work
Data are to be used only for purposes of research and education. Commercial use is prohibited without written permission from Xenbase. The contributor(s) of unpublished data should be explicitly acknowledged in any publication that incorporates, or is based in part or entirely on these data. Xenbase should be explicitly acknowledged when data used in any publication, has been in part or solely derived from analysis of data from this website. As consent must be aquired for commercial use, this license only describes the non-commercial aspects of data usage (a separate agreement must be entered into for commercial use).
http://www.xenbase.org/other/static/aboutXenbase.jsp, accessed 13 July 2016
Xenbase Academic Conditions of Use
The RIKEN copyright is a vendor-specific license which states that all text, photographs, diagrams, and other materials on their website are copyrighted by RIKEN unless explicitly specified otherwise on the website. It is prohibited to use, reproduce, or modify any of the material without RIKEN's permission.
http://www.riken.jp/en/terms/, accessed 14 July 2016
RIKEN Copyright
The Design Science License is a license intended to be a general "copyleft" that can be applied to any kind of work that has protection under copyright. This license states those certain conditions under which a work published under its terms may be copied, distributed, and modified. Unlike other open source licenses, the DSL was intended to be used on any type of copyrightable work, including documentation and source code. It was the first "generalized copyleft" license. This is a free and copyleft license meant for general data. THe GNU Project does not recommend it for software or documentation, since it is incompatible with the GNU GPL and with the GNU FDL; however, they consider it appropriate for other kinds of data. The DSL was written by Michael Stutz. The DSL came out in the 1990s, before the formation of the Creative Commons. According to Wikipedia, once the Creative Commons arrived, Stutz considered the DSL experiment "over" and no longer recommended its use.
https://www.gnu.org/licenses/dsl.html, accessed 13 July 2016; https://www.gnu.org/licenses/license-list.html, accessed 13 July 2016; https://en.wikipedia.org/wiki/Design_science_license, accessed 13 July 2016.
Design Science License
The University of Concordia Terms of Use is a vendor-specific license which states that no document appearing on this website or any other website owned, operated or controlled by Concordia may be copied, sold, reproduced, republished, downloaded, posted, transmitted or distributed by any means with the exception of downloading or printing the contents of the site for personal, non-commercial use. This use must bear in mind that Concordia reserves its copyright and its rights to exclusivity over the material.
http://www.concordia.ca/web/terms.html, accessed 14 July 2016
University of Concordia Terms of Use
All OME formats and software are freely available, and all OMERO and Bio-Formats source code is available under GNU public "copyleft" licenses or through commercial license from Glencoe Software. FLIMfit is also now available under a GNU public "copyleft" license. For questions about the GNU license refer to the Frequently Asked Questions about the GNU Licenses page. Bio-Formats - under the terms of the GNU public "copyleft" license, any software package linking to Bio-Formats, either directly or indirectly, cannot be distributed unless its source code is also made available under the terms of the GPL. Some components which provide reader and writer implementations for open file formats, are released under a more permissive BSD-2 license which enables non-GPL third party software. For a complete list of which file formats are included in the BSD license, see the BSD column of the supported formats table. Developers of non-GPL software wishing to leverage Bio-Formats components not covered by the BSD license may purchase a commercial license from Glencoe Software; please contact them at bioformats@glencoesoftware.com to discuss your requirements. The core OME Model Schema files (.XSD) use the Creative Commons Attribution 4.0 International License, and as such you are free to share or adapt them as long as you attribute the OME consortium as follows; "This work is derived in part from the OME specification. Copyright (C) 2002-2016 Open Microscopy Environment". See further information about using OME-XML in your work. This website is also covered by the Creative Commons Attribution 4.0 International License - you are free to share or adapt content as long as you credit the Open Microscopy Environment. The exception to this is the screenshots and videos which can only be used for non-commercial purposes, see Attributions below.
http://www.openmicroscopy.org/site/about/licensing-attribution/licensing, accessed on 23 June 2016.
OME Software Conditons of Use
The ImmPort Conditions of Use is a vendor-specific license which allows the use of ImmPort data for any legal purpose except for those prohibited elsewhere in this agreement. There are very few prohibitions, and no requirement for attribution.
https://aspera-immport.niaid.nih.gov:9443/displayAgreement, accessed 14 July 2016
ImmPort Conditions of Use
Distribution with notices is a distribution clause in which distribution is unrestricted, except that all distributions must retain certain licence information (e.g., copyright notices).
This is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. It is sometimes ambiguously referred to as the MIT License. For substantial programs it is better to use the Apache 2.0 license since it blocks patent treachery.
The GNU Lesser General Public License (LGPL) is a free software license published by the Free Software Foundation (FSF). The license allows developers and companies to use and integrate LGPL software into their own (even proprietary) software without being required by the terms of a strong copyleft license to release the source code of their own software-parts. The license requires that only the LGPL software-parts be modifiable by end-users via source code availability.
http://en.wikipedia.org/wiki/GNU_Lesser_General_Public_License, accessed 27 March 2015.
The Artistic License v1.0 is not considered a free software license by the definition of the GNU Project because it is too vague; some passages are "too clever for their own good", and their meaning is not clear. The GNU Project recommends that it is not used except as part of the disjunctive license of Perl.
http://www.gnu.org/licenses/license-list.html, accessed 13 June 2013.
The Eclipse Public License is similar to the Common Public License. This is a free software license. Unfortunately, its weak copyleft and choice of law clause make it incompatible with the GNU GPL. The only change is that the EPL removes the broader patent retaliation language regarding patent infringement suits specifically against Contributors to the EPL'd program.
The Modified BSD is a software license based on he original FreeBSD license, modified by removal of the advertising clause. It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. This license is sometimes referred to as the 3-clause BSD license. According to the GNU Project, the modified BSD license is not bad, as lax permissive licenses go, though the Apache 2.0 license is preferable. However, it is risky to recommend use of “the BSD license”, even for special cases such as small programs, because confusion could easily occur and lead to use of the flawed original BSD license. To avoid this risk, you can suggest the X11 license instead. The X11 license and the modified BSD license are more or less equivalent. According to the GNU project, the Apache 2.0 license is better for substantial programs, since it prevents patent treachery.
http://www.gnu.org/licenses/license-list.html, accessed June 12, 2013.
OPL v1.0 is not a free software license according to the definition of the GNU Project because it requires sending every published modified version to a specific initial developer.
Development status is an information content entity which indicates the maturity of a software entity within the context of the software life cycle.
Alpha is a development status which is applied to software by the developer/publisher during initial development and testing. Software designated alpha is commonly unstable and prone to crashing. It may or may not be released publicly.
Modified from http://en.wikipedia.org/wiki/Software_release_life_cycle, accessed 11 June 2013.
Beta is a development status which is generally applied to software by the developer/publisher once the majority of features have been implemented, but when the software may still contain bugs or cause crashes or data loss. Software designated beta is often released publicly, either on a general release or to a specific subset of users called beta testers.
A release candidate (RC) is a beta version with potential to be a final product, which is ready to release unless significant bugs emerge.
http://en.wikipedia.org/wiki/Software_release_life_cycle#Release_candidate, accessed 22 October 2014.
Live is a development status which is applied to software that has been designated as suitable for production environments by the developer/publisher. If a non-free product, software at this stage is available for purchase
Allyson Lister, Jon Ison, and Modified from http://en.wikipedia.org/wiki/Software_release_life_cycle, accessed 11 June 2013.
Sofware is no longer being supplied by the developers/publishers
An updated version of the software is available.
The first release of a piece of software. A first release does not imply any particular levels of maturity other than is this is the first instance of this software to be considered released.
The latest release of a piece of software. This does not imply any levels of maturity other than indicating this is the most recent release.
Software has developers actively maintaining it (fixing bugs)
AL 24.9.2019: Duplicate of http://www.ebi.ac.uk/swo/organization/SWO_9000056
obsolete software development
simulation and analysis of biochemical networks
Manage Laboratory information such is commonly performed by LIMS software.
the objective of performing the actions of an operation system such as managing the software running a computer and the interactions with the system resources and hardware.
Text editing is the objective of editing plain text files.
Renders a file in such a way that its contents can be understood by users.
AL 18.9.2019: Redundant with EDAM 'Modelling and simulation'.
sequence alignment
multiple sequence alignment
pairwise sequence alignment
An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
A correction is where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself.
A background correction is where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation.
An error correction is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself.
curve fitting is a data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints.
A normalization is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons.
A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image.
The process of publishing software. Typically this process involves a software publisher performing acts such as licensing, marketing, publicising and/or providing support for a product.
The process of developing software, typically involving the design, implementation and testing of software.
AL 24.9.19: Merged the now-obsolete http://www.ebi.ac.uk/swo/objective/SWO_4000007 into this class as they were describing the same concept. See also https://github.com/allysonlister/swo/issues/2
A ensemble of generalizations specification is a generalization specification and denotes a type of generalization that is produced by a ensemble algorithm. This algorithm produces a set of generalizations at its output.
A data mining algorithm is an algorithm that has as its objective a data mining task and outputs as a result a generalization specified by a generalization specification.
Clustering algorithm is a data mining algorithm that solves a clustering task and as a result produces a clustering.
A patten specification is a single generalization specification and denotes a pattern P on type T which is a boolean funtion on objects of type T.
Estimating the (Joint) Probability Distribution. A set of data (of type T) is often assumed to be a sample taken from a population according to a probability distribution. A probability distribution/density function assigns a non-negative probability/density to each object of type T. Probably the most general data mining task (Hand et al. 2001) is the task of estimating the (joint) probability distribution D over type T from a set of data items or a sample drawn from that distribution. As mentioned above, in the most typical case we would have T = Tuple(T1, . . ., Tk), where each of T1, . . ., Tk is Boolean, Discrete(S) or Real. We talk about the joint probability distribution to emphasize the difference to the marginal distributions of each of the variables of type T1, . . ., Tk: the joint distribution captures the interactions among the variables. Representing multi-variate distributions is a non-trivial task. Two approaches are commonly used in data mining. In the density-based clustering paradigm, mixtures of multi-variate Gaussian distributions are typically considered (Hand et al. 2001). Probabilistic graphical models, most notably Bayesian networks, represent graphically the (in)dependencies between the variables: Learning their structure and parameters is an important approach to the problem of estimating the joint probability distribution.
probability distribution estimation task
the task of pattern discovery is to find all local patterns from a given pattern language that satisfy the required conditions. A prototypical instantiation of this task is the task of finding frequent itemsets (sets of items, such as {bread, butter}), which are often found together in a transaction (e.g., a market basket) (Aggrawal et al 1993). The condition that a pattern (itemset) has to satisfy in this case is to appear in (hold true for) a sufficiently high proportion (called support and denoted by s) of the transactions in the input dataset. With the increasing interest in mining complex data, mining frequent patterns is also considered for structured data. We can thus talk about mining frequent subsequences or mining frequent subgraphs in sequence or graph data. We can consider as frequency the multiple occurrences of a pattern in a single data structure (e.g., sequence or graph) or the single occurrences of a pattern in multiple data structures.
A data mining task is an objective specification that specifies the objective that a data mining algorithm needs to achieve when executed on a dataset to produce as output a generalization.
Clustering specification is a single generalization specification is a generalization specification and denotes a type of generalization that models the mapping of a set of objects S of type T from S to a set of natural numbers {1,...K}. This generalization is obtained by appliing a clustering algorithm on a set of data.
Predictive modeling algorithm is a data mining algorithm that solves a predictive modeling task and as a result produces a predictive model.
Pattern discovery algorithm is a data mining algorithm that solves a pattern discovery task and as a result produces a set of patterns.
A predictive model M for types Td, Tc specifies a function that takes an object of type Td and returns one of type Tc, i.e., has the signature m :: Td → Tc. Most often, predictive modelling is concerned with classification, where Tc would be Boolean (for binary classification) or Discrete(S) (for multi-class classification), or regression, where Tc would be Real. In our case, we allow both Td (description) and Tc (class/target) to be arbitrarily complex data types.
Predictive model specification is a single generalization specification and denotes a type of generalization that represents a mapping taking objects of type Td and returns objects of type To.
Learning a (Probabilistic) Predictive Model. In this task, we are given a dataset that consists of examples of the form (d, c), where each d is of type Td and each c is of type Tc. We will refer to d as the description and c as the class or target. To learn a predictive model means to find a mapping from the description to the target, m :: Td → Tc, that fits the data closely. This means that the observed target values and the target values predicted by the model, i.e., c and ˆc = m(d), have to match closely.
probability distribution estimation algorithm
Clustering. Clustering in general is concerned with grouping objects into classes of similar objects (Kaufman and Rousseeuw 1990). Given a set of examples (object descriptions), the task of clustering is to partition these examples into subsets, called clusters.
A probability distribution D on type T specifies a mapping from objects of type T to non-negative Reals, i.e., has the signature d :: T → R0+. For uncountably infinite types, probability densities are used instead. The sum of all probabilities (the integral of the probability densities) over T is constrained to amount to one.
A probability distribution specification is a single generalization specification and denotes a type of generalization that is a mapping from objects of type T to non-negative reals. This generalization is an output of a probability distribution estimation algorithm.
Examples of such generalization types are: decision trees, desicion rules, neural networks, frequent itemsets, clusters etc.
A single generalization specification is a generalization specification and denotes a type of generalization that is produced by a single generalization data mining algorithm. This algorithm produces only one generalization at its output.
Ensemble algorithms are algorithms that generate an ensemble when executed on a dataset. The ensemble algorithms include a specification of single generalization algorithms which are executed in oreder to produce the single generalizations that compose the ensemble. Examples of ensemble algorithms include bagging, boosting, stacking, random forests, random subspaces,bagging of random subspaces etc. For example, bagging of decision trees algorithm includes the specification of a bagging algorithm and having a decision tree algorithm for generating the base models composing the ensemble.
single generalization algorithms are data mining algorithms that given a dataset on input produce a generalization at the output.
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
universal
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Transformation-ML
Transformation-ML file describing parameter transformations used in a GvHD experiment.
Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf)
person:Jennifer Fostel
ACS
d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/)
XML
RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document
XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/)
RDF
A FOAF file, a SKOS file, an OWL file.
RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/)
zip
MagicDraw MDZIP archive, Java JAR file.
zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)
tar
Example.tar file.
tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)
FCS
d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/)
Compensation-ML
compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment
Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf)
Gating-ML
foogate.xml, Gating-ML file describing gates used in a GvHD experiment.
Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/)
OWL
OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file.
OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/)
An organization which supplies technology, tools and protocols for use in high throughput applications
GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation.
GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation.
GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations.
GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations.
GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation.
GenePattern module HierarchicalClustering
GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation.
GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation.
GenePattern HeatMapViewer data visualization
The GenePattern process of generating Heat Maps from clustered data.
GenePattern HierarchicalClusteringViewer data visualization
The GenePattern process of generating hierarchical clustering visualization from clustered data.
A GenePattern software module which is used to generate a heatmap view of data.
GenePattern module HierarchicalClusteringViewer
A GenePattern software module which is used to generate a view of data that has been hierarchically clustered.
The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
Advanced Instruments Inc. (AI Companies)
An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing.
An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution.
An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules.
An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.
A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria).
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus).
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s).
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s).
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed.
A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma.
A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential.
A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0).
3: symptomatic in bed more than 50% of the day but not bed ridden
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden.
2: symptomatic but in bed less than 50% of the day
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day.
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden.
An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic.
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory.
A Karnofsky score vaue specification indicating that a patient is asymptomatic.
A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory.
60-70: symptomatic but in bed less than 50% of the day
A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day.
40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden.
An organization that is developing and selling nanopore sequencing products and is based in the UK.
An organization that manufactures mosquito traps and other mosquito control products.
The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
A length unit which is equal to one thousandth of a meter or 10^[-3] m.
A length unit which is equal to one millionth of a meter or 10^[-6] m.
A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
A length unit which is equal to 10 [-10] m.
A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
A mass unit which is equal to one millionth of a gram or 10^[-6] g.
A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
A mass unit which is equal to 10^[-12] g.
A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
A time unit which is equal to 60 seconds.
A time unit which is equal to 3600 seconds or 60 minutes.
A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
A substance unit equal to a millionth of a mol or 10^[-6] mol.
A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.
A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
A unit of molarity which is equal to 10^[-12] M.
A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.
A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L.
A volume unit which is equal to one millionth of a liter or 10^[-6] L.
A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.
A volume unit which is equal to 10^[-12] L.
A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.
A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius.
A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
A concentration unit which a measure of viable bacterial numbers in a given volume.
A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.
A rate unit which is equal to one over one nanomolar second.
A rate unit which is equal to one over one molar second.
A rate unit which is equal to one over one nanomolar.
A rate unit which is equal to one over one molar.
A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.
AL 5.4.23: We believe this was erroneously created some time ago and therefore are obsoleting it with no recommended alternative individual.
obsolete Affymetrix
obsolete Agilent Technologies
obsolete Applied Biosystems
obsolete Applied Precision Life Science
obsolete Bahler Lab
obsolete Bio-Rad Laboratories
obsolete Bio Discovery
obsolete Bioconductor
obsolete Biometric Research Branch
obsolete COSE
obsolete Clontech Laboratories
obsolete Dana-Farber Cancer Institute and Harvard School of Public Health
obsolete EMBL
obsolete Fujifilm
obsolete GE Healthcare Life Sciences
obsolete Genedata
obsolete Genicon Sciences
obsolete Grid grinder
obsolete Havard School of Public Health
obsolete Illumina
obsolete Incyte Genomics
obsolete Institute for Genomics and Bioinformatics Graz University of Technology
obsolete J. Craig Venter Institute
obsolete MWG Biotech
obsolete Matforsk
MathWorks (SWO_0000291 and SWO_9000002), SWO_9000002 was retained, whileSWO_0000291 became an instance of obsolete class. Please use SWO_9000002 instead.
obsolete Molecular Devices
obsolete Molecular Neuroscience Core
obsolete Molecular Dynamics
obsolete Motorola Life Sciences
obsolete NIH
obsolete PerkinElmer
obsolete Raytest
obsolete Research Genetics
obsolete Rosetta Biosoftware
obsolete SAS Institute Inc.
obsolete Speed Berkeley Research Group
obsolete obsolete_Stanford University
obsolete TIBCO Software Inc
obsolete Technological Advances for Genomics and Clinics
obsolete UC Irvine
obsolete University Of California
obsolete Walter and Eliza Hall Institute
obsolete Cambridge Bluegnome
obsolete Strand Life Sciences
Institute for Genomics and Bioinformatics Graz University of Technology
Stanford University (SWO_0000431 and SWO_9000003). SWO_9000003 was retained, while SWO_0000431 became an instance of obsolete class. Please use SWO_9000003 instead.
Technological Advances for Genomics and Clinics, France
Dana-Farber Cancer Institute and Harvard School of Public Health
Molecular Neuroscience Core, Center for Behavioral Neuroscience, Atlanta
FCS Data Standard Version 3.0
An undefined, or ill-defined, group of people. May be used, for example, to denote software development as being done by 'the community', with contributions by many individuals, but no over-arching organisation.
Drive5
Conway Institute UCD Dublin
Centre for Genomic Regulation (CRG) of Barcelona
IBM
AL 8.10.2019: References https://github.com/allysonlister/swo/issues/19
Uppsala Molekylmekaniska HB
UC Santa Cruz Computational Biology Group
BLAST+ version 2.2.26
ClustalW version 2.1
ClustalX version 2.1
Clustal Omega version 1.1
MUSCLE version 3.8.31
CRG TCoffee version 9.02.r1228
Python version 2.6
Python version 2.7
Segway version 1.2
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X