PharmSci is an Ontology for describing Pharmaceutical Science research. The aim of building ontology is to help Pharmaceutical Science researchers to find scientific research close to their work or their research topic. Ontology covers the study design for pharmaceutical science research which is a Clinical Study that includes experimental and non-experimental studies.
Zeynep Say, Said Fathalla, Sahar Vahdati, Jens Lehmann, Sören Auer
Creative Commons Attribution 3.0 (CC BY 3.0)
The :class property specifies the class a domain model refers to.
Class
The :datetime property specifies a system-generated datetime for an entity.
Datetime
The :example property specifies an example of an entity.
This property is similar to void:exampleResource. But see also skos:example.
Example
The :graph property specifies the full URI of any graph.
Graph
The :isNamedResource property marks whether an object resource is named or is unnamed (i.e. a blank node).
Is Named Resource
The :isRepeatable property marks whether a property can be repeated.
Is Repeatable
The :isVocabulary property marks whether a class is used for a controlled vocabulary.
Is Vocabulary
The :type property specifies the local name of the graph namespace used for instances of a class.
This property is used as a surrogate for the class name. There is a one-to-one relation between the class name and its associated graph, e.g. instances of the class :Subject are assigned to the subjects: graph.
Type
editor preferred label
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
example
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
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
example of usage
example of usage
definition
English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
DEFINITION
definition
definition
textual definition
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
IAO:0000116
uberon
editor_note
true
editor_note
IAO:0000116
uberon
editor_note
true
editor_note
editor note
editor note
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor
term editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
alternative term
alternative term
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
PERSON:Daniel Schober
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source
definition source
imported from
For external terms/classes, the ontology from which the term was imported
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
imported from
imported from
A property created to allow the source NICHD to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are the contributing source.
A11
Conceptual Entity
Has_NICHD_Parent
Has_NICHD_Parent
Has_NICHD_Parent
true
NHC0
code
code
code
The semantic type describes the sort of thing or category to which a concept belongs in the context of the UMLS semantic network.
P106
Conceptual Entity
Semantic Type
Semantic_Type
In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS.
Semantic_Type
Semantic_Type
Provides an alternative Preferred Name for use in some NCI systems.
P107
Conceptual Entity
Display Name
Display_Name
Display Name
Display_Name
Display_Name
The word or phrase that NCI uses by preference to refer to the concept.
P108
Conceptual Entity
Preferred Name
Preferred_Name
Preferred Name
Preferred Term
Preferred_Name
Preferred_Name
Concept Unique Identifiers, or CUIs, are concept numbers assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept.
P207
Conceptual Entity
UMLS CUI
UMLS_CUI
UMLS_CUI
UMLS_CUI
Contains a Concept Unique Identifier for those concepts that appear in NCI Metathesaurus but not in the NLM UMLS.
P208
Conceptual Entity
NCI Metathesaurus CUI
NCI_META_CUI
NCI_META_CUI
NCI_META_CUI
This property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake.
P322
Conceptual Entity
Contributing Source
Contributing_Source
Contributing_Source
Contributing_Source
English language definitions of what a source other than NCI means by the concept. These are limited to 1024 characters. They include information about the definition's source in a form that can easily be interpreted by software.
P325
Conceptual Entity
[source] Definition
ALT_DEFINITION
ALT_DEFINITION
ALT_DEFINITION
true
A retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding.
P366
Conceptual Entity
Legacy Concept Name
Legacy Concept Name
Legacy_Concept_Name
P371
Conceptual Entity
NICHD_Hierarchy_Term
NICHD
NICHD_Hierarchy_Term
NICHD_Hierarchy_Term
Design notes are notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept.
P98
Conceptual Entity
DesignNote
DesignNote
DesignNote
DesignNote
uberon
dc-contributor
true
dc-contributor
contributor
has_alternative_id
database_cross_reference
Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software.
FULL_SYN
Synonym with Source Data
has exact synonym
has_exact_synonym
has_obo_namespace
has_related_synonym
Used to associate the concept defining a particular terminology subset with concepts that belong to this subset.
Concept_In_Subset
in subset
in_subset
comment
label
notation
A notation, also known as classification code, is a string of characters such as "T58.5" or "303.4833" used to uniquely identify a concept within the scope of a given concept scheme.
By convention, skos:notation is used with a typed literal in the object position of the triple.
note
A general note, for any purpose.
This property may be used directly, or as a super-property for more specific note types.
Classify prov-o terms into three categories, including 'starting-point', 'qualifed', and 'extended'. This classification is used by the prov-o html document to gently introduce prov-o terms to its users.
Classify prov-o terms into six components according to prov-dm, including 'agents-responsibility', 'alternate', 'annotations', 'collections', 'derivations', and 'entities-activities'. This classification is used so that readers of prov-o specification can find its correspondence with the prov-dm specification.
A definition quoted from PROV-DM or PROV-CONSTRAINTS that describes the concept expressed with this OWL term.
A note by the OWL development team about how this term expresses the PROV-DM concept, or how it should be used in context of semantic web or linked data.
PROV-O does not define all property inverses. The directionalities defined in PROV-O should be given preference over those not defined. However, if users wish to name the inverse of a PROV-O property, the local name given by prov:inverse should be used.
The position that this OWL term should be listed within documentation. The scope of the documentation (e.g., among all terms, among terms within a prov:category, among properties applying to a particular class, etc.) is unspecified.
specializationOf
expanded
alternate
http://www.w3.org/TR/2012/WD-prov-dm-20120703/prov-constraints.html#prov-dm-constraints-fig
http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#prov-dm-constraints-fig
An entity that is a specialization of another shares all aspects of the latter, and additionally presents more specific aspects of the same thing as the latter. In particular, the lifetime of the entity being specialized contains that of any specialization. Examples of aspects include a time period, an abstraction, and a context associated with the entity.
http://www.w3.org/TR/2012/WD-prov-dm-20120703/prov-dm.html#term-specialization
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-specialization
generalizationOf
http://www.w3.org/TR/2012/WD-prov-dm-20120703/prov-n.html#expression-specialization
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-specialization
A revision is a derivation that revises an entity into a revised version.
wasRevisionOf
expanded
derivations
hadRevision
A homepage for some thing.
homepage
stable
Indicates the class of individuals that are a member of a Group
membershipClass
unstable
has marker
is substrate of
is marker of
stains
has perturbagen
has mode of action
has assay format
has detection method
has endpoint
has measure group
has assay stage
has target
has assay method
has specification
has assay kit
has curve fit specification
has percent response
has concentration
is perturbagen of
is assay method of
has inducer
is regulated by
has transcription factor
is measure group of
is related assay to
is assay format of
is endpoint of
is regulator of
is specification of
is target of
is detection method of
has manufacturer
has assay control
based on normalization
has measured entity
catalyzed by
has cell line
has form
involves biological process
has assay phase characteristic
is indicator of
encodes
is measured entity of
has quality
uses assay kit
has assay kit component
uses as substrate
has substrate
is binding site of
tagged with
has detected entity
is cell line of
has assay protocol
is assay protocol of
has associated disease
is associated disease of
has assay readout content
has assay readout content parametricity
has assay source
has assay title
has bioassay type
is bioassay type of
has assay readout type
has signal direction
has endpoint modifier
has phenotype
is phenotype of
is localized in
has concentration throughput
has repetition throughput
uses detection instrument
has assay footprint
silences
has gene symbol
is role of
is unit of
has unit
is detected by
has antibody source
recombinantly expressed in
has preparation method
has organism
has assay medium
has assay serum
is grown in
is transfected into
has role
reports
has binding site
has function
involves molecular function
phenotype 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.
has function in
http://www.obofoundry.org/ro/#OBO_REL:part_of
part of
has phenotype
has part
derives into
See also BFO_0001009
derives from
occurs in
bearer of
inheres in
contains process
X connected_to Y if and only if X and Y share a fiat boundary.
connected to
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
participates in
is derived from
detects phenotype
has indicator
is described by
quantifies
To give attention to or deal with a research or study.
addressesResearch
To look at or consider a statement carefully and in detail in order to explore and discover.
examinedBy
Determine evidence found in the study.
findEvidence
Kit used in Bioassay.
hasAssayKit
Stating methods used in Assay.
hasAssayMethod
Stating types of bioassay used in study.
hasBioAssayType
Cell Lines that are used as material in experimental study.
hasCellLine
Person who shows a definite pathological process having a characteristic set of signs and symptoms.
hasDisease
Drugs that are used as material in experimental study.
hasDrug
Study has a procedure done in order to discover or demonstrate some fact or general truth.
hasExperiment
An experiment has method is a way to solve a scientific task by executing a scientific experiment.
hasExperimentMethod
Experiment identifies the designed experiment involves the investigator assigning some or all conditions to subjects.
hasExperimentalSetting
Genes that are used as material in experimental study.
hasGene
Intervention or procedure is used in clinical study.
hasInterventionorProcedure
Experiment has materials are culture collections and chemicals used for executing of an experiment.
hasMaterial
Referencing a claim, focus, goal or hypothes is supported by the study findings and examined by the study experiment.
hasObjective
Outcome or results of experiment in the clinical study.
hasOutcome
Probes that are used as material in experimental study.
hasProbe
Reagents that are used as material in experimental study.
hasReagent
Clinical Study defines the study design for the trials and experiments, as well as observational studies in medical, clinical and other types of research involving human beings.
hasStudyDesign
Disease that has a therapeutic treatment.
hasTreatment
To observe or inquire into disease; examine systematically.
investigatesDisease
To observe or inquire into problem; examine systematically.
investigatesProblem
Patients are chosen as Clinical Trial for Clinical Study.
isClinicalTrial
Get, acquire, or secure specimen from patient.
obtainedFromPatient
To prove; to try a substance; to determine the chemical nature of a substance on Patient.
testOn
Method referencing a assay to carry out experiments for the purpose of testing the effect of a perturbing agent in a biological model system.
useBioAssay
Clinical study uses clinical data.
useClinicalData
Defining a period in a clinical study during which subjects receive therapeutic treatment.
useTreatment
has response value
has temperature value
has percent response value
has id value
has ID
has display info
has date
has purity value
has concentration value
has time value
has concentration-point number
has passage number
has cell count
This describes the number of repeats of an entity (e.g., artificial regulatory element, cDNA, etc.) present in a DNA construct.
has copy number
has sequence
A biosafety level is the level of biocontainment required to isolate hazardous biological agents in an enclosed facility. The levels of containment range from the lowest biosafety level of 1 to the highest at level 4.
The levels are as follows:
BSL1:
Suitable for work involving well-characterized agents not known to consistently cause disease in immunocompetent adult humans, and present minimal potential hazard to laboratory personnel and the environment (definition from CDC).
BSL2:
Suitable for work involving agents that pose moderate hazards to personnel and the environment. It differs from BSL-1 in that 1) laboratory personnel have specific training in handling pathogenic agents and are supervised by scientists competent in handling infectious agents and associated procedures; 2) access to the laboratory is restricted when work is being conducted; and 3) all procedures in which infectious aerosols or splashes may be created are conducted in BSCs or other physical containment equipment (definition from CDC).
BSL3:
Suitable for clinical, diagnostic, teaching, research, or production facilities where work is performed with indigenous or exotic agents that may cause serious or potentially lethal disease through inhalation route exposure. Laboratory personnel must receive specific training in handling pathogenic and potentially lethal agents, and must be supervised by scientists competent in handling infectious agents and associated procedures. All procedures involving the manipulation of infectious materials must be conducted within BSCs, other physical containment devices, or by personnel wearing appropriate personal protective equipment (definition from CDC).
BSL4:
has biosafety level
pH approximates the negative logarithm (base 10) of the molar concentration of dissolved hydronium ions in a solution.
has assay pH value
It is the force per unit area applied in a direction perpendicular to the surface of an object in an assay.
has assay pressure value
It is the temperature at which the biological experiment was conducted.
has assay temperature value
It is the interval of time between the addition of a perturbagen, substrate or cell modification and the measurement of change, as observed by a detection method in the bioassay.
has incubation time value
The number of replicate measurements (repetitions) per concentration value used.
has repetition point-number
has wavelength value
is input data value of
has sequence position
The value (in conjunction with the signal direction) used to determine perturbagens of interest (hits.) Perturbagens with a readout value beyond the threshold in the direction of interest are considered active in the assay.
has activity threshold value
has recommended name
has value
reports assay measurment value
has assay design method
has assay supporting method
The reasons or causes of a condition or a fact of not achieving the desired end or ends.
failureReason
The ability of a drug or treatment to produce a specific result.
hasDrugEffects
Eligibility criteria for treatment studies often require that patients have a particular type and stage of disease.
hasEligibilityCriteria
Identification of Experimental results that are the set of facts and conclusions.
hasExperimentResult
A conclusion reached after examination or investigation.
hasFindings
The result of an alteration or change, as in nature, form, or quality.
hasMutationResult
The Gene that has overexpression which leads to the abundant target protein expression subsequently.
hasOverexpressionGene
Problem has the answer or the explanation for something.
hasProblemSolution
An idea is induced in or adopted by another without argument, command, or coercion.
hasSuggestion
A determination of the tissue place of proteins, genes.
hasTissueLocalization
A name that describes something.
hasTitle
A final product or end result of treatment.
treatmentOutcome
The :Abstract class represents a brief description of a scholarly work, usually author generated. Instances of :Abstract normally do not exist in isolation, but are linked to a :Document instance (of which they provide a summary).
Abstract
The :Agent class groups together all entities that can be the subject of an action. These can be single persons (:Person), or groups of people organised as a legal entity (:Organization).
Agent
The :AggregationEvent class groups together all events related to the construction of a publication.
Aggregation Event
The :Article class represents a scholarly work normally published as an item of a serial publication. In particular, this concept refers to the abstract notion of an article, rather than any of its realisations after it becomes embodied via a physical medium.
With reference to the FRBR model [http://www.ifla.org/publications/functional-requirements-for-bibliographic-records], an :Article can be mapped directly to the frbr:Expression concept. It is worth noting though that within the NPG core ontology we do not have any notion of a frbr:Work. Hence multiple versions of the same article (e.g. language translations, or revisions) are characterised as such simply by means of some relationship.
Article
The :ArticleType class represents the various kinds of publication which can be used to index and group content published by Macmillan Science and Education. The instances of :ArticleType are organised hierarchically using the SKOS vocabulary.
Article Type
The :Asset class groups together all physical entities which can be stored in digital systems.
Asset
The :Component class groups together all individuals that normally come into existence as part of a :Document.
Component
The :Concept class groups together all individuals which do not exist in the physical world (i.e. have no extension in spacetime).
Concept
The :Contributor class represents a document component detailing a contributor (personal or corporate) to the work being published. This class is disjoint from the :Agent class. Hence a :Contributor instance can be described as the name used to refer to a person or organisation in the context of a publication.
Contributor
The :Dataset class represents a collection of related sets of information modelled in a known way and stored in a computer system.
We are currently using this class for RDF datasets.
Dataset
The :Document class groups together all publications which were created to be distributed and consumed as individual, self-contained entities.
Document
The :Event class groups together events of varying granularity. Events differ from :Concept entities because they have an extension in time; they differ from :Asset entities because they do not have an extension in space.
Event
The :Graph class represents a collection of related sets of information modelled in RDF and organized as a named graph.
Each Graph instance is associated with instances of a particular class. For example, the 'npgg:articles' :Graph instance is a named graph which contains all the instances of the :Article class. The :Graph instances themselves are then used to describe the RDF graph, providing sometimes known as an RDF annotation. This may furnish various kinds of information about the RDF graph: provenance, rights, metrics, validation reports, etc.
Graph
The :Image class represents a graphical element within a publication.
Image
The :Item class represents the state of a document after this has been added to a :Collection by someone, at a specific time, and within a specific sequence.
Item
The :KnowledgeBase class represents a collection of related sets of information modelled in RDF and consisting of various objects, e.g. one or more graphs, other RDF datasets etc.
Differently from datasets, knowledge-bases refer to a composite dataset intended to be used as a consistent whole.
KnowledgeBase
The :Organization class represents an organised body of people normally having a legal status.
Organization
The :Person class represents a single person entity.
Person
The :Publication class groups together all individuals (or part of) created as the result of the publishing process. Note that we are not referring here to the physical artefacts, but just their abstract counterparts.
Publication
The :PublicationEvent class groups together events that happen within the publishing process, broadly conceived. For example, the submission of an article, or the acceptance of a paper.
Publication Event
The :PublicationState class groups together publish-state and review-state individuals.
Publication State
The :PublishEvent class represents events related to the publication of a document. This is intended in a strict sense, i.e. the time when a publication is made 'public'.
In order to differentiate these events further, the :PublishState vocabulary is used.
Publish Event
The :Publisher class represents organizations involved in the publishing business.
Publisher
The :ReviewEvent class models events related to the reviewing of a document (before its publication). In order to differentiate these events further, the :ReviewState vocabulary is used.
Review Event
The :Section class represents a part of a document.
Section
The :Serial class represents publications which appear in a new edition on a regular schedule. For example, a journal, a magazine or a blog. The :PublishEvent class is used to provide more details about the time, place and other contextual information relevant to when a new edition gets published.
Serial
The :SeverityLevel class represents a system status. The syslog standard (RFC 5424) for computer message logging is used to provide a reference set of states. This categorisation is implemented as a SKOS concept scheme.
Severity Level
The :Subject class represents a topic, field of study or research area which can be used to categorise the contents of a publication. The instances of :Subject are organised hierarchically using the SKOS vocabulary.
Subject
The :Summary class represents a brief description of a scholarly work, usually editorially generated.
Summary
The :SummaryType class represents an instance from a categorisation of types of :Summary. For example, 'Long Summary', 'Short Summary', etc. This categorisation is implemented as a SKOS concept scheme.
Summary Type
The :Thing class groups together all individuals used by Macmillan Science and Education within the NPG publishing world.
Thing
The :Type class groups together all domain-specific categorisations relevant to the NPG publishing world.
All of the :Type categorisations are implemented as self-contained reusable SKOS vocabularies (although not all of them are taxonomies in the strict sense of hierarchical vocabularies).
Type
The :Website class represents a site that maintains one or more pages on the Web.
Website
CHEBI:23888
drug
drugs
medicine
drug
CHEBI:33232
application
application
CHEBI:33893
reagent
reactif
reactivo
reagent
reagents
reagent
CHEBI:50406
probe
probe
CHEBI:52217
pharmaceutical
farmaco
medicament
pharmaceuticals
pharmaceutical
CLO:0000031
cell line
He, Tong-Chuan, et al., Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512.: "To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene".
Note that common usage in the literature is often of the form "a human colorectal cancer cell line", as seen above. But such references to studies in "a line" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'.
A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
In the spring of 2013, a working group comprised of domain experts and representatives from CLO, OBI, CL, and ReO worked to establish a consensus model and definitions of cultured cells across these efforts. This included a careful characterization of how the term 'cell line' should be defined and applied. Notes about this work and its outcomes can be found on the CLO wiki here:
http://code.google.com/p/clo-ontology/wiki/Cell_Lines
MB, SS, JZ, MAH, BP, CS, YH
The term 'line' is used when a culture has undergone an intentional experimental process to establish a more uniform and stable population of cells (see 'establishing cell line'). This will require one or more passages, but may involve additional selection processes. Through such passaging and/or selection processes, the resulting 'line' attains some level of genetic stability and compositional homogeneity which is typically absent in primary cultures. Because of their relative homogeneity, ‘lines’ are capable of being characterized and stably propagated over a period of time. A new *type* of cell line can be established not only through the passaging/selection of a primary culture, but also through experimental modifications of existing lines (e.g. immortalization, stable genetic modifications, drug selection for a resistant subset, etc.).
The definition provided here establishes the 'scale' of cell populations that qualify as cell lines - specifically those with a shared propagation history in culture. In this way, the 'cell line' class demarcates populations that represent what researchers actually use in the practice of science - e.g. as inputs to culturing, experimentation, and sharing. The definition is such that cell lines will exhibit important attributes. For example, they will have a relatively homogenous cell type composition as they have experienced similar selective pressures due to their continuous co-propagation. In addition, these populations can also be characterized by a passage number, again owing to their common passaging history. As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quiescent state for future use.
cell line
A disease that involving errors in metabolic processes of building or degradation of molecules.
ICD10CM:E88.9
ICD9CM:277.9
MESH:D008659
NCI:C3235
SNOMEDCT_US_2016_03_01:154733004
SNOMEDCT_US_2016_03_01:190961002
SNOMEDCT_US_2016_03_01:267456000
SNOMEDCT_US_2016_03_01:30390004
SNOMEDCT_US_2016_03_01:75934005
UMLS_CUI:C0025517
metabolic disease
disease_ontology
DOID:0014667
disease of metabolism
DOID:0014667
A disease that is the consequence of the presence of pathogenic microbial agents, including pathogenic viruses, pathogenic bacteria, fungi, protozoa, multicellular parasites, and aberrant proteins known as prions.
DOID:10115
DOID:11078
DOID:1304
DOID:1321
DOID:2040
DOID:2288
DOID:3099
DOID:4120
DOID:4620
DOID:5256
DOID:945
DOID:95
DOID:9532
DOID:9696
ICD9CM:079.0
UMLS_CUI:C0001485
infectious disease
disease_ontology
DOID:0050117
disease by infectious agent
DOID:0050117
An organ system cancer located_in the respiratory system that is characterized by uncontrolled cellular proliferation in the respiratory tract.
disease_ontology
DOID:0050615
respiratory system cancer
DOID:0050615
A cancer that is classified based on the organ it starts in.
snadendla
2011-06-13T03:28:33Z
MESH:D009371
disease_ontology
DOID:0050686
organ system cancer
DOID:0050686
A cancer that is classified by the type of cell from which it is derived.
snadendla
2011-06-13T03:28:50Z
disease_ontology
DOID:0050687
cell type cancer
DOID:0050687
A disease of cellular proliferation that results in abnormal growths in the body, which do not invade or destroy the surrounding tissue but, given enough time, will transform into a cancer.
lschriml
2011-05-11T12:18:41Z
disease_ontology
DOID:0060071
pre-malignant neoplasm
DOID:0060071
A disease of cellular proliferation that results in abnormal growths in the body which lack the ability to metastasize.
lschriml
2011-05-11T12:18:41Z
disease_ontology
DOID:0060072
benign neoplasm
DOID:0060072
An organ system cancer located_in the immune system that is characterized by uncontrolled cellular proliferation in organs of the immune system.
lschriml
2011-06-08T01:11:18Z
disease_ontology
DOID:0060083
immune system cancer
DOID:0060083
An organ system cancer located_in the muscular and skeletal organs and characterized by uncontrolled cellular proliferation of the musculoskeletal organs.
lschriml
2011-07-15T02:30:51Z
DOID:0060124
skeletal system cancer
disease_ontology
DOID:0060100
musculoskeletal system cancer
DOID:0060100
An organ system cancer that is located_in the skin, hair and nails.
lschriml
2011-07-27T02:31:34Z
disease_ontology
DOID:0060122
integumentary system cancer
DOID:0060122
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from precursor cells called blast cells.
disease_ontology
DOID:0070003
blastoma
DOID:0070003
A disease that has_material_basis_in a genetic abnormality, error with embryonic development, infection or compromised intrauterine environment.
disease_ontology
DOID:0080015
physical disorder
DOID:0080015
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from embryonic mesoderm.
DOID:3936
ICD10CM:C49
ICD9CM:171
ICD9CM:171.9
SNOMEDCT_US_2016_03_01:187985009
SNOMEDCT_US_2016_03_01:93765001
UMLS_CUI:C0153519
connective and soft tissue neoplasm
tumor of soft tissue and skeleton
disease_ontology
DOID:1115
sarcoma
DOID:1115
DOID:11934
An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx.
MESH:D006258
NCI:C3077
SNOMEDCT_US_2016_03_01:255055008
UMLS_CUI:C0018671
head and neck neoplasm
head and neck tumours
head/neck neoplasm
tumor of head and neck (disorder)
disease_ontology
DOID:11934
head and neck cancer
DOID:11934
A disease that is characterized by abnormally rapid cell division.
DOID:0000818
cell process disease
neoplasm
disease_ontology
DOID:14566
disease of cellular proliferation
DOID:14566
A disease that involves a psychological or behavioral pattern generally associated with subjective distress or disability that occurs in an individual, and which are not a part of normal development or culture.
ICD10CM:F99
ICD10CM:F99-F99
MESH:D001523
NCI:C2893
SNOMEDCT_US_2016_03_01:154843007
SNOMEDCT_US_2016_03_01:154971002
SNOMEDCT_US_2016_03_01:154972009
SNOMEDCT_US_2016_03_01:154980002
SNOMEDCT_US_2016_03_01:192637001
SNOMEDCT_US_2016_03_01:192639003
SNOMEDCT_US_2016_03_01:74732009
UMLS_CUI:C0004936
disease_ontology
DOID:150
disease of mental health
DOID:150
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from two germinal layers of tissue.
DOID:1905
MESH:D018198
NCI:C3729
NCI:C6930
SNOMEDCT_US_2016_03_01:189802003
SNOMEDCT_US_2016_03_01:8145008
UMLS_CUI:C0206625
UMLS_CUI:C1368354
malignant mixed cancer
malignant mixed neoplasm
mixed tumor
mixed tumor, malignant (morphologic abnormality)
mixed tumor, malignant, NOS (morphologic abnormality)
disease_ontology
malignant mixed tumor
mixed neoplasm
DOID:154
mixed cell type cancer
DOID:154
DOID:162
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
ICD10CM:C80
ICD10CM:C80.1
ICD9CM:199
MESH:D009369
NCI:C9305
SNOMEDCT_US_2016_03_01:154432008
SNOMEDCT_US_2016_03_01:154433003
SNOMEDCT_US_2016_03_01:154577008
SNOMEDCT_US_2016_03_01:187597000
SNOMEDCT_US_2016_03_01:188475001
SNOMEDCT_US_2016_03_01:188482002
SNOMEDCT_US_2016_03_01:190150006
SNOMEDCT_US_2016_03_01:269513004
SNOMEDCT_US_2016_03_01:269623003
SNOMEDCT_US_2016_03_01:269626006
SNOMEDCT_US_2016_03_01:269634000
SNOMEDCT_US_2016_03_01:363346000
SNOMEDCT_US_2016_03_01:38807002
UMLS_CUI:C0006826
malignant neoplasm
malignant tumor
primary cancer
disease_ontology
DOID:162
Updating out dated UMLS CUI.
cancer
DOID:162
An organ system cancer located_in endocrine system that is characterized by uncontrolled cellular proliferation of the hormone producing glands of the endocrine system.
DOID:10009
ICD10CM:C75.9
ICD9CM:194.9
MESH:D004701
NCI:C3010
NCI:C3575
SNOMEDCT_US_2016_03_01:127015005
SNOMEDCT_US_2016_03_01:190140005
SNOMEDCT_US_2016_03_01:363347009
SNOMEDCT_US_2016_03_01:371982006
SNOMEDCT_US_2016_03_01:387922007
SNOMEDCT_US_2016_03_01:387927001
SNOMEDCT_US_2016_03_01:93780007
UMLS_CUI:C0014132
UMLS_CUI:C0153658
Endocrine tumor
endocrine neoplasm
malignant Endocrine tumor
malignant neoplasm of endocrine gland
malignant tumour of endocrine gland
neoplasm of endocrine gland (disorder)
neoplasm of endocrine system (disorder)
disease_ontology
DOID:170
endocrine gland cancer
DOID:170
An organ system cancer that is located in the peritoneum.
ICD10CM:C48.1
ICD9CM:158.8
SNOMEDCT_US_2016_03_01:187808008
SNOMEDCT_US_2016_03_01:187816004
UMLS_CUI:C0153466
disease_ontology
cancer of peritoneum
peritoneal neoplasm
DOID:1725
peritoneum cancer
DOID:1725
An organ system cancer that located_in the heart and blood vessels.
NCI:C4784
UMLS_CUI:C0497243
Cardiovascular tumors
cardiovascular neoplasm
disease_ontology
DOID:176
cardiovascular cancer
DOID:176
A cell type cancer that has_material_basis_in mesothelial tissue.
DOID:4487
DOID:6965
DOID:7434
MESH:C562839
NCI:C27926
NCI:C4456
NCI:C7865
NCI:C8420
OMIM:156240
SNOMEDCT_US_2016_03_01:62064005
UMLS_CUI:C0278752
UMLS_CUI:C0345967
UMLS_CUI:C0392400
UMLS_CUI:C1332338
Diffuse malignant Mesothelioma
advanced malignant mesothelioma
asbestos-related malignant mesothelioma
malignant tumor of Mesothelium
disease_ontology
DOID:1790
OMIM mapping confirmed by DO. [SN].
malignant mesothelioma
DOID:1790
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from melanocytes which are found in skin, the bowel and the eye.
EFO:0000756
KEGG:05218
MESH:D008545
NCI:C3224
SNOMEDCT_US_2016_03_01:154501005
SNOMEDCT_US_2016_03_01:189749008
SNOMEDCT_US_2016_03_01:2092003
SNOMEDCT_US_2016_03_01:269503007
SNOMEDCT_US_2016_03_01:269577007
SNOMEDCT_US_2016_03_01:372244006
UMLS_CUI:C0025202
Naevocarcinoma
malignant melanoma
disease_ontology
DOID:1909
melanoma
DOID:1909
An organ system cancer that is manifested in the reproductive organs.
DOID:1900
NCI:C3674
UMLS_CUI:C0178830
Reproductive tumor
malignant reproductive system neoplasm
disease_ontology
cancer of reproductive system
DOID:193
reproductive organ cancer
DOID:193
A disease comprised of a group of signs and symptoms that occur together and characterize a particular abnormality.
MESH:D013577
NCI:C28193
SNOMEDCT_US_2016_03_01:64572001
UMLS_CUI:C0039082
disease_ontology
DOID:225
syndrome
DOID:225
MESH:D005729
NCI:C3049
NCI:C6934
SNOMEDCT_US_2016_03_01:116371000119107
SNOMEDCT_US_2016_03_01:128919000
SNOMEDCT_US_2016_03_01:189929007
SNOMEDCT_US_2016_03_01:53801007
UMLS_CUI:C0017075
disease_ontology
DOID:2426
gangliocytoma
DOID:2426
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from germ cells.
DOID:2157
MESH:D009373
NCI:C3708
SNOMEDCT_US_2016_03_01:115233005
SNOMEDCT_US_2016_03_01:189839002
SNOMEDCT_US_2016_03_01:189854008
SNOMEDCT_US_2016_03_01:28307001
SNOMEDCT_US_2016_03_01:302853003
SNOMEDCT_US_2016_03_01:402878003
UMLS_CUI:C0205851
malignant tumor of the germ cell
disease_ontology
germ cell neoplasm
germ cell tumour
DOID:2994
germ cell cancer
DOID:2994
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
DOID:2428
DOID:6570
CSP:2000-1867
MESH:D002277
MESH:D009375
NCI:C2916
NCI:C3709
SNOMEDCT_US_2016_03_01:118285006
SNOMEDCT_US_2016_03_01:134207000
SNOMEDCT_US_2016_03_01:154433003
SNOMEDCT_US_2016_03_01:188083002
SNOMEDCT_US_2016_03_01:189546004
SNOMEDCT_US_2016_03_01:189549006
SNOMEDCT_US_2016_03_01:189559007
SNOMEDCT_US_2016_03_01:269513004
SNOMEDCT_US_2016_03_01:68453008
SNOMEDCT_US_2016_03_01:71298006
UMLS_CUI:C0007097
UMLS_CUI:C0553707
UMLS_CUI:C1368683
epithelioma
malignant Epithelioma
disease_ontology
DOID:305
carcinoma
DOID:305
A cell type cancer that has_material_basis_in glial cells and is located_in brain or located_in spine.
DOID:2627
KEGG:05214
MESH:D005910
NCI:C3059
NCI:C4822
OMIM:137800
OMIM:607248
OMIM:613030
OMIM:613031
OMIM:613032
OMIM:613033
ORDO:182067
SNOMEDCT_US_2016_03_01:115240006
SNOMEDCT_US_2016_03_01:189908003
SNOMEDCT_US_2016_03_01:189909006
SNOMEDCT_US_2016_03_01:189926000
SNOMEDCT_US_2016_03_01:269505000
SNOMEDCT_US_2016_03_01:393564001
SNOMEDCT_US_2016_03_01:416500007
SNOMEDCT_US_2016_03_01:74532006
UMLS_CUI:C0017638
UMLS_CUI:C0555198
Neuroglial tumor
glial cell tumor
glioma, malignant
malignant Neuroglial tumor
disease_ontology
DOID:3070
Xref MGI.
OMIM mapping confirmed by DO. [SN].
malignant glioma
DOID:3070
An organ system cancer located_in the nervous system that affects the central or peripheral nervous system.
DOID:1193
DOID:3195
DOID:4695
ICD9CM:192
ICD9CM:192.9
MESH:D009380
NCI:C35562
SNOMEDCT_US_2016_03_01:188306000
UMLS_CUI:C0027665
UMLS_CUI:C0153643
UMLS_CUI:C1334956
malignant neoplasm of nervous system
neoplasm of nervous system (disorder)
nervous system neoplasm
neural neoplasm
neural tumor
tumor of the nervous system
disease_ontology
DOID:3093
nervous system cancer
DOID:3093
An organ system cancer located_in gastrointestinal tract that is manifested in organs of the gastrointestinal system.
DOID:4945
DOID:8377
ICD10CM:C26.9
ICD9CM:239.0
MESH:D004067
MESH:D005770
NCI:C3052
NCI:C4890
SNOMEDCT_US_2016_03_01:126768004
SNOMEDCT_US_2016_03_01:128348002
SNOMEDCT_US_2016_03_01:128415001
SNOMEDCT_US_2016_03_01:189527000
SNOMEDCT_US_2016_03_01:276806006
SNOMEDCT_US_2016_03_01:367543008
SNOMEDCT_US_2016_03_01:428905002
SNOMEDCT_US_2016_03_01:93811007
UMLS_CUI:C0012243
UMLS_CUI:C0017185
UMLS_CUI:C0685938
GI tumor
digestive system cancer
gastrointestinal tract cancer
disease_ontology
DOID:3119
gastrointestinal system cancer
DOID:3119
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from embryonic connective tissue that is capable of developing into connective tissue, such as bone, and cartilage, the lymphatic system, and the circulatory system.
DOID:1630
NCI:C6587
NCI:C7059
UMLS_CUI:C1332517
UMLS_CUI:C1334699
benign miscellaneous mesenchymal tumor
mesenchymal tumor
disease_ontology
DOID:3350
mesenchymal cell neoplasm
DOID:3350
An organ system cancer that is located_in the kidneys, ureteres, bladder or urethra.
ICD10CM:C68.9
ICD9CM:189.9
SNOMEDCT_US_2016_03_01:190132004
SNOMEDCT_US_2016_03_01:448233000
UMLS_CUI:C0348371
disease_ontology
DOID:3996
urinary system cancer
DOID:3996
DOID:4
A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
MESH:D004194
NCI:C2991
SNOMEDCT_US_2016_03_01:64572001
UMLS_CUI:C0012634
disease_ontology
DOID:4
disease
DOID:4
An organ system cancer located_in the thoracic cavity that develops in the different types of cells within the lungs, as well as less common cancers of the esophagus, the trachea, or the chest wall.
DOID:3937
ICD10CM:C76.1
ICD9CM:195.1
MESH:D013899
NCI:C3406
NCI:C3576
SNOMEDCT_US_2016_03_01:188361007
SNOMEDCT_US_2016_03_01:188365003
SNOMEDCT_US_2016_03_01:255058005
UMLS_CUI:C0039981
UMLS_CUI:C0153661
Thoracic tumor
thorax cancer
thorax neoplasm
tumor of thorax
disease_ontology
DOID:5093
thoracic cancer
DOID:5093
An organ system cancer located_in the retroperitoneal space that is manifested in retroperitoneal space in the abdominal cavity behind the peritoneum.
DOID:12340
DOID:9860
ICD10CM:C48
ICD10CM:C48.0
ICD9CM:158
ICD9CM:158.0
MESH:D012186
NCI:C3357
NCI:C3537
SNOMEDCT_US_2016_03_01:126872008
SNOMEDCT_US_2016_03_01:187801002
SNOMEDCT_US_2016_03_01:187805006
SNOMEDCT_US_2016_03_01:187817008
SNOMEDCT_US_2016_03_01:254617008
SNOMEDCT_US_2016_03_01:359767009
SNOMEDCT_US_2016_03_01:359770008
SNOMEDCT_US_2016_03_01:363420003
SNOMEDCT_US_2016_03_01:94092006
UMLS_CUI:C0035358
UMLS_CUI:C0153464
UMLS_CUI:C0153465
malignant neoplasm of retroperitoneum and peritoneum
malignant neoplasm of retroperitoneum and peritoneum NOS (disorder)
malignant tumor of peritoneum and retroperitoneum
malignant tumor of peritoneum and retroperitoneum (disorder)
neoplasm of retroperitoneum
neoplasm of the retroperitoneum
retroperitoneal neoplasm
tumor of retroperitoneum (disorder)
disease_ontology
malignant neoplasm of retroperitoneum
malignant retroperitoneal cancer
DOID:5875
retroperitoneal cancer
DOID:5875
A disease that has_material_basis_in genetic variations in the human genome.
MESH:D030342
NCI:C3101
SNOMEDCT_US_2016_03_01:264530000
SNOMEDCT_US_2016_03_01:32895009
UMLS_CUI:C0019247
disease_ontology
DOID:630
genetic disease
DOID:630
A disease that manifests in a defined anatomical structure.
DOID:1
DOID:2
DOID:5
DOID:71
DOID:72
DOID:8
disease_ontology
DOID:7
disease of anatomical entity
DOID:7
NCIT:C15206
Research conducted with human subjects or on material of human origin in which an investigator directly interacts with human subjects; includes development of new technologies, study of mechanisms of human diseases, therapy, clinical trials, epidemiologic, behavior, and health services research.
C15206
Research Activity
Clinical Study
C0008972
CDISC
CDISC-GLOSS
FDA
A clinical study involves research using human volunteers (also called participants) that is intended to add to medical knowledge. There are two main types of clinical studies: clinical trials (also called interventional studies) and observational studies. [ClinicalTrials.gov] See also clinical trial.
A clinical study involves research using human volunteers (also called participants) that is intended to add to medical knowledge. There are two main types of clinical studies: clinical trials (also called interventional studies) and observational studies. [ClinicalTrials.gov] See also clinical trial. (CDISC Glossary)
Clinical_Study
CLINICAL STUDY
Clinical Research
Clinical Studies
Clinical Study
Study
clinical study
Clinical Study
NCIT:C15320
A plan detailing how a study will be performed in order to represent the phenomenon under examination, to answer the research questions that have been asked, and defining the methods of data analysis. Study design is driven by research hypothesis being posed, study subject/population/sample available, logistics/resources: technology, support, networking, collaborative support, etc.
C15320
Research Activity
Study Design
C0035171
CDISC
CDISC-GLOSS
A plan detailing how a study will be performed in order to represent the phenomenon under examination, to answer the research questions that have been asked, and informing the statistical approach.
Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. specific design elements (e.g., crossover, parallel, dose-escalation) [Modified from Pocock, Clinical Trials: a Practical approach] See Trial Design Model. See also, arm, epoch, and visit.
Study_Design
Experiment Design
Experimental Design
Research Design
Study Design
study design
Study Design
NCIT:C15429
Systematic investigation into a subject in order to discover facts, establish or revise a theory, or develop a plan of action based on the facts discovered.
C15429
Research Activity
Research Activity
C0242481
A scientific study of nature that sometimes includes processes involved in health and disease. For example, clinical trials are research studies that involve people. These studies may be related to new ways to screen, prevent, diagnose, and treat disease. They may also study certain outcomes and certain groups of people by looking at data collected in the past or future.
Research_Activity
Research
Research Activity
research study
Research Activity
NCIT:C15632
The use of synthetic or naturally-occurring chemicals for the treatment of diseases.
C15632
Therapeutic or Preventive Procedure
Chemotherapy
Chemotherapy
C0392920
CTRP
Non-systemic chemotherapy treatment (e.g., intra-peritoneal, intra-cavitary, intra-thecal), or chemotherapy not described by Chemotherapy Single Agent Systemic or Multi-Agent Systemic.
Treatment with anticancer drugs.
Chemotherapy
Although this term is used to describe any therapy involving the use of chemical-based agents, it is particularly used to refer to the use of chemical-based agents to treat cancer. Antineoplastic chemotherapy works by arresting or killing the growth and spread of cancer cells. Chemotherapy may also include agents that enhance immune function or alter hormonal activity.
Chemo
Chemotherapy
Chemotherapy (NOS)
Chemotherapy, Cancer, General
chemotherapy
Chemotherapy
NCIT:C15783
Data obtained through patient examination or treatment.
C15783
Idea or Concept
Clinical Data
C1516606
CDISC-GLOSS
Data pertaining to the medical well-being or status of a patient. Category also includes clinical reports and individual patient data (IPD) as defined in the EMA Policy 0070 Implementation Guide. [http://www.ema.eoropa.eu/docs/en_GB/document_library/REPORT/2014/10/WC500174378.PDF]
Clinical_Data
Clinical Data
clinical data
Clinical Data
NCIT:C16203
Any specific activity undertaken during the course of a clinical study or research protocol.
C16203
Activity
Clinical or Research Activity
C1516654
Clinical_or_Research_Activity
Clinical or Research Activity
Clinical or Research Activity
NCIT:C16612
A functional unit of heredity which occupies a specific position on a particular chromosome and serves as the template for a product that contributes to a phenotype or a biological function.
C16612
Gene or Genome
Gene
C0017337
CDISC
A functional unit of heredity which occupies a specific position on a particular chromosome and serves as the template for a product that contributes to a phenotype or a biological function. (NCI)
The functional and physical unit of heredity passed from parent to offspring. Genes are pieces of DNA, and most genes contain the information for making a specific protein.
Gene
The gene as a functional unit consists of a discrete segment of a giant DNA molecule containing the purine (adenine and guanine) and pyrimidine (cytosine and thymine) bases in the ordered and correct sequence that encodes a specific functional product (i.e., a protein or RNA molecule).
GENE
Gene
Genes
gene
Gene
NCIT:C16960
A person who receives medical attention, care, or treatment, or who is registered with medical professional or institution with the purpose to receive medical care when necessary.
C16960
Patient or Disabled Group
Patient
C0030705
CDISC-GLOSS
FDA
A patient is the subject of observations.
Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Although often used interchangeably as a synonym for subject, a healthy volunteer is not a patient.
Patient
LAY USER/PATIENT
PATIENT
PT
Patient
Patients
patient
Patient
NCIT:C18020
Any procedure or test to diagnose a disease or disorder.
C18020
Diagnostic Procedure
Diagnostic Procedure
Diagnostic Procedure
C0430022
CTRP
NICHD
A specific test or series of steps done to help diagnose a disease or condition. Mammograms and colonscopies are examples of diagnostic procedures.
Diagnostic_Procedure
Diagnostic Procedure
Diagnostic Method
Diagnostic Procedure
Diagnostic Technique
Diagnostic Test
diagnostic procedure
diagnostic technique
Diagnostic Procedure
NCIT:C20181
An organizational header for concepts representing mostly abstract entities.
C20181
Classification
Conceptual Entity
C1254372
Conceptual_Entities
Conceptual Entity
Conceptual Entity
NCIT:C20189
A distinguishing quality or prominent aspect of a person, object, action, process, or substance.
C20189
Conceptual Entity
Property or Attribute
C1514495
NICHD
Properties_or_Attributes
Property or Attribute
Property or Attribute
Property or Attribute
NCIT:C20200
The result of an action.
C20200
Finding
Outcome
C1274040
BRIDG
CDISC
CDISC-GLOSS
1. events or experiences that clinicians or investigators examining the impact of an intervention or exposure measure because they believe such events or experiences may be influenced by the intervention or exposure. 2. (SDTM) The result of carrying out a mathematical or statistical procedure. NOTE: 1. such events and experiences are called clinical outcomes independently of whether they are part of the original question/protocol of the investigation. [1. Guyatt, G., Schunemann H., Dept. epidemiology & statistics, McMaster University-personal communication] See also variable; outcome can be a result of analysis; outcome is more general than endpoint in that it does not necessarily relate to a planned objective of the study.outcome. The measureable characteristic (clinical outcome assessment, biomarker) that is influenced or affected by an individual's baseline state or an intervention as in a clinical trial or other exposure. [BEST Resource]
A specific result or effect that can be measured. Examples of outcomes include decreased pain, reduced tumor size, and improvement of disease.
Outcome
OUT
Outcome
Result
outcome
result
Outcome
NCIT:C25190
A human being.
C25190
Human
Person
C0027361
BRIDG
NICHD
A human being.
Person
Person
Individual
Person
Person
NCIT:C25214
Systematic, objective appraisal of the significance, effectiveness, and impact of activities or condition according to specified objectives and criteria.
C25214
Activity
Evaluation
Evaluation
C0220825
CTRP
NICHD
Evaluation
Evaluation Procedure
Evaluate
Evaluated
Evaluation
Evaluation Procedure
Evaluation
NCIT:C25218
An activity that produces an effect, or that is intended to alter the course of a disease in a patient or population. This is a general term that encompasses the medical, social, behavioral, and environmental acts that can have preventive, therapeutic, or palliative effects.
C25218
Health Care Activity
Intervention or Procedure
C0184661
CDISC-GLOSS
NICHD
In medicine, a treatment or action taken to prevent or treat disease, or improve health in other ways.
The drug, device, therapy, or process under investigation in a clinical study that is believed to have an effect on outcomes of interest in a study (e.g., health-related quality of life, efficacy, safety, pharmacoeconomics). See also: test articles; devices; drug product; medicinal product; combination product.
Procedure
Intervention or Procedure
Intervention
Intervention Strategies
Intervention or Procedure
Interventional
Procedure
intervention
interventionDescription
Intervention or Procedure
NCIT:C25294
Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting.
C25294
Laboratory Procedure
Laboratory Procedure
Laboratory Procedure
C0022885
CTRP
NICHD
A medical procedure that involves testing a sample of blood, urine, or other substance from the body. Tests can help determine a diagnosis, plan treatment, check to see if treatment is working, or monitor the disease over time.
Test
Laboratory Procedure
Lab Test
Lab Tests
Laboratory Procedure
Laboratory Test
Test
Tests
laboratory test
Laboratory Procedure
NCIT:C25474
A collection or single item of factual information, derived from measurement or research, from which conclusions may be drawn.
C25474
Idea or Concept
Data
C1511726
CDISC-GLOSS
Representations of facts, concepts, or instructions in a manner suitable for communication, interpretation, or processing by humans or by automated means. [FDA]
Data
Data
Data Point
Datum
data
Data
NCIT:C27993
A term that helps define and render another concept unique.
C27993
Qualitative Concept
General Qualifier
C1517500
General_Modifier
General Modifier
General Qualifier
General Qualifiers
General Qualifier
NCIT:C28020
A difficulty, disorder, or condition needing resolution.
C28020
Phenomenon or Process
Problem
C0033213
Problem
Issue
Problem
Problem
NCIT:C3367
Clinical, laboratory or molecular evidence, or absence of evidence of disease.
C3367
Finding
Finding
C1285578
CDISC-GLOSS
NICHD
A meaningful interpretation of data or observations resulting from planned evaluations. Compare to conclusion, hypothesis.
Finding
Finding
Finding
Observable Entity
finding
Finding
NCIT:C36295
C36295
Finding
Other Finding
C1335151
Header_Concept
Other_Finding
Other Finding
Other Finding
NCIT:C41009
A term that helps define and render a concept unique.
C41009
Conceptual Entity
Qualifier
C1514623
Qualifier
Modifier
Qualifier
Qualifier
NCIT:C42729
The act of appraisal, evaluation, or analysis.
C42729
Activity
Review
C1552617
Review
Review
Review
NCIT:C43431
An active process; excludes processes and mechanisms which fulfill biological functions.
C43431
Activity
Activity
C0441655
BRIDG
Any action that can, in the context of a study or a post-marketing investigation, be defined, planned, scheduled or performed. EXAMPLE(S): surgical procedure, laboratory test, administration of a drug.
Activity
Activity
General activity
Activity
NCIT:C43583
Knowledge on which to base belief.
C43583
Idea or Concept
Evidence
C0332120
Evidence
Evidence
Evidence
NCIT:C47955
A way of doing something; how a result is obtained or an end is achieved.
C47955
Conceptual Entity
Means
C1704970
Means
Means
Means
NCIT:C48187
The tangible substance that goes into the makeup of a physical object.
C48187
Substance
Material
C0520510
BRIDG
A physical substance. EXAMPLE(S): drug, device, specimen
Material
Material
Material
NCIT:C48191
Knowledge derived from study, experience, or instruction that has been gathered or received by communication.
C48191
Conceptual Entity
Information
CL448704
Information
Info
Information
Information
NCIT:C48674
Refers to in vitro testing or in vivo animal testing before clinical trials in humans are to be carried out.
C48674
Qualitative Concept
Preclinical
C1709630
Preclinical
Pre-clinical
Preclinical
Preclinical
NCIT:C49155
A goal or aim to be accomplished or attained.
C49155
Idea or Concept
Objective
C0018017
Objective
Objective
Objective
NCIT:C49236
An action or administration of therapeutic agents to produce an effect that is intended to alter or stop a pathologic process.
C49236
Therapeutic or Preventive Procedure
Therapeutic Procedure
Therapeutic Procedure
C0087111
CDISC-GLOSS
CTRP
NICHD
See intervention.
Treatment.
Therapeutic_Procedure
Therapeutic Procedure
TREAT
TX
Therapeutic Interventions
Therapeutic Method
Therapeutic Procedure
Therapeutic Technique
Therapy
Treatment
therapeutic intervention
therapy
Therapeutic Procedure
NCIT:C63536
A detailed examination, analysis, or critical inspection of a subject designed to discover facts about it.
C63536
Research Activity
Study
C0947630
Study
Study
Study
NCIT:C7057
A condition that is relevant to human neoplasms and non-neoplastic disorders. This includes observations, test results, history and other concepts relevant to the characterization of human pathologic conditions.
C7057
Conceptual Entity
Disease, Disorder or Finding
C1511989
Diseases_Disorders_and_Findings
Disease, Disorder or Finding
Disease, Disorder or Finding
NCIT:C70742
Subject to a process with the aim of readying for some purpose, improving, or remedying a condition.
C70742
Activity
Treat
CL448901
CDISC
Any action or process to improve or remedy a syndrome, disease, or condition.
Treat
Treat
Treated
Treatment
Treat
NCIT:C71104
A research study that prospectively assigns human participants or groups of humans to one or more health-related interventions to evaluate the effects on health outcomes.
C71104
Research Activity
Clinical Trial
C0008976
CDISC
CDISC-GLOSS
1) A research investigation involving human subjects that is designed to answer specific questions about the safety and efficacy of a biomedical intervention (drug, treatment, device) or new ways of using a known drug, treatment, or device). 2) A research study in which one or more human subjects are prospectively assigned to one or more interventions (which may include placebo or other control) to evaluate the effects of those interventions on health-related biomedical or behavioral outcomes.(1. modified from ICH E6 Glossary, Directive 2001/20/EC. 2. NIH revised definition 2015) (CDISC Glossary)
A research investigation involving human subjects that is designed to answer specific questions about the safety and efficacy of a biomedical intervention (drug, treatment, device) or new ways of using a known drug, treatment, or device). NOTE: NIH Office of Science Policy further specifies that a clinical trial is a type of research study that prospectively assigns subjects to interventions, and the EU clinical trial regulations set forth 3 specific conditions, any one of which qualifies a study as a clinical trial. These conditions include applying diagnostic or monitoring procedures not used in normal clinical practice to subjects. [after ICH E6 [R2], EU CTR 2014] See also clinical study, clinical investigation.
A type of research study that tests how well new medical approaches work in people. These studies test new methods of screening, prevention, diagnosis, or treatment of a disease.
Clinical_Trial_Generic
Clinical Trial
Clinical Trials
Clinical Trials, Unspecified
Trial
clinical trial
Clinical Trial
NCIT:C71460
A means, manner of procedure, or systematic course of actions that have to be performed in order to accomplish a particular goal.
C71460
Conceptual Entity
Method
C0025663
Method
Method
Method
NCIT:C74299
Exertion or effort directed to produce or accomplish something.
C74299
Activity
Work
C0043227
Work
Labor
Toil
Work
Work
NCIT:C78166
The administration of a substance in order to assess for a response.
C78166
Activity
Challenge
C0805586
Challenge
Challenge
Challenge
sio:Entity
Every thing is an entity.
core
entity
sio:Experiment
An experiment is an investigation that has the goal of verifying, falsifying, or establishing the validity of a hypothesis.
study
experiment
sio:HeterogeneousSubstance
A heterogeneous substance is a chemical substance that is composed of more than one different kind of component.
heterogeneous substance
sio:Investigation
investigation is the process of carrying out a plan or procedure so as to discover facts or information about the object of study.
study
investigation
sio:MaterialEntity
A material entity is a physical entity that is spatially extended, exists as a whole at any point in time and has mass.
core
material entity
sio:Object
An object is an entity that is wholly identifiable at any instant of time during which it exists.
core
object
sio:Procedure
A procedure is a process that attempts to achieve one or more objectives by following an established set of actions.
procedure
sio:Process
A process is an entity that is identifiable only through the unfolding of time, has temporal parts, and unless otherwise specified/predicted, cannot be identified from any instant of time in which it exists.
core
process+
process
sio:Sample
A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use.
sample
sio:Specimen
A specimen is a portion of material for use in testing, examination, or study.
specimen
bao:BAO_0000008
Categorization of bioassays based on the property or process that the assay is interrogating, e.g. ADMET, functional, etc.
bioassay type
1
bao:BAO_0000015
A set of instructions, methodology, operations, required reagents, instruments to carry out experiments for the purpose of testing the effect of a perturbing agent in a biological model system, measuring one or multiple effect(s) of the agent facilitated by an assay design method translate the perturbation into a detectable signal to arrive at one or multiple endpoint(s) that quantify or qualify the extent of the perturbation. Bioassay is described by multiple bioassay components: assay format, biology (biological participants in various role and processes), design method, physical detection method / technology, screened entity, and endpoint. Bioassay includes one or multiple measure groups to describe panel, profiling, multiparametric (or multiplexed) assays (assays that measure more than one effect of the perturbagen on the system that is screened).
bioassay
bao:BAO_0000248
The title of the kit/biologicals used in the assay.
assay kit
bao:BAO_0002753
assay method component
bao:BAO_0002927
disease
bao:BAO_0002929
role
bao:BAO_0003028
The methods required to perform typical screening assay. These include the assay design methods (to generate a detectable signal) and assay supporting methods. Assay methods include laboratory methods. Computational methods are not currently categorized as assay methods, although some may also be used to process the assay measurement results.
assay method
bao:BAO_0003112
assay bioassay component
bao:BAO_0003113
assay format component
bao:BAO_0003114
assay biology component
bao:BAO_0020005
experimental setting
bao:BAO_0020006
ex vivo
bao:BAO_0020007
in silico
bao:BAO_0020008
in vitro
bao:BAO_0020009
in vivo
prov:Agent
Agent
starting-point
agents-responsibility
An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-Agent
prov:Organization
Organization
expanded
agents-responsibility
An organization is a social or legal institution such as a company, society, etc.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-types
prov:Person
Person
expanded
agents-responsibility
Person agents are people.
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-types
prov:SoftwareAgent
SoftwareAgent
expanded
agents-responsibility
A software agent is running software.
http://www.w3.org/TR/2012/WD-prov-dm-20120703/prov-dm.html#term-agent
http://www.w3.org/TR/2013/REC-prov-dm-20130430/#term-agent
http://www.w3.org/TR/2012/WD-prov-dm-20120703/prov-n.html#expression-types
http://www.w3.org/TR/2013/REC-prov-n-20130430/#expression-types
An agent (eg. person, group, software or physical artifact).
Agent
stable
A class of Agents.
Group
stable
An organization.
Organization
stable
A person.
Person
stable
electric charge < 0
electric charge = -1
electric charge > 0
Electric Charge = +1
electric charge = 0
2012-06-14
DCMI Metadata Terms - other
2008-01-14
A book, article, or other documentary resource.
Bibliographic Resource
2000-07-11
2008-01-14
The set of regions in space defined by their geographic coordinates according to the DCMI Box Encoding Scheme.
DCMI Box
2000-07-11
2012-06-14
The set of classes specified by the DCMI Type Vocabulary, used to categorize the nature or genre of the resource.
DCMI Type Vocabulary
2000-07-11
2008-01-14
The set of conceptual resources specified by the Dewey Decimal Classification.
DDC
2008-01-14
A rate at which something recurs.
Frequency
2000-07-11
2008-01-14
The set of media types specified by the Internet Assigned Numbers Authority.
IMT
2000-07-11
2008-01-14
The set of codes listed in ISO 3166-1 for the representation of names of countries.
ISO 3166
2000-07-11
2008-01-14
The three-letter alphabetic codes listed in ISO639-2 for the representation of names of languages.
ISO 639-2
2008-01-14
The set of three-letter codes listed in ISO 639-3 for the representation of names of languages.
ISO 639-3
2000-07-11
2008-01-14
The set of conceptual resources specified by the Library of Congress Classification.
LCC
2000-07-11
2008-01-14
The set of labeled concepts specified by the Library of Congress Subject Headings.
LCSH
2008-01-14
A legal document giving official permission to do something with a Resource.
License Document
Examples include written, spoken, sign, and computer languages.
2008-01-14
A system of signs, symbols, sounds, gestures, or rules used in communication.
Linguistic System
2000-07-11
2008-01-14
The set of labeled concepts specified by the Medical Subject Headings.
MeSH
2008-01-14
A method by which resources are added to a collection.
Method of Accrual
2008-01-14
A process that is used to engender knowledge, attitudes, and skills.
Method of Instruction
2005-06-13
2008-01-14
The set of conceptual resources specified by the National Library of Medicine Classification.
NLM
2000-07-11
2008-01-14
The set of time intervals defined by their limits according to the DCMI Period Encoding Scheme.
DCMI Period
2008-01-14
A material thing.
Physical Resource
2000-07-11
2008-01-14
The set of points in space defined by their geographic coordinates according to the DCMI Point Encoding Scheme.
DCMI Point
2008-01-14
A plan or course of action by an authority, intended to influence and determine decisions, actions, and other matters.
Policy
2008-01-14
A statement of any changes in ownership and custody of a resource since its creation that are significant for its authenticity, integrity, and interpretation.
Provenance Statement
2000-07-11
2008-01-14
The set of tags, constructed according to RFC 1766, for the identification of languages.
RFC 1766
RFC 3066 has been obsoleted by RFC 4646.
2002-07-13
2008-01-14
The set of tags constructed according to RFC 3066 for the identification of languages.
RFC 3066
RFC 4646 obsoletes RFC 3066.
2008-01-14
The set of tags constructed according to RFC 4646 for the identification of languages.
RFC 4646
RFC 5646 obsoletes RFC 4646.
2010-10-11
The set of tags constructed according to RFC 5646 for the identification of languages.
RFC 5646
2008-01-14
A statement about the intellectual property rights (IPR) held in or over a Resource, a legal document giving official permission to do something with a resource, or a statement about access rights.
Rights Statement
2008-01-14
A basis for comparison; a reference point against which other things can be evaluated.
Standard
2000-07-11
2008-01-14
The set of places specified by the Getty Thesaurus of Geographic Names.
TGN
2000-07-11
2008-01-14
The set of conceptual resources specified by the Universal Decimal Classification.
UDC
2000-07-11
2008-01-14
The set of identifiers constructed according to the generic syntax for Uniform Resource Identifiers as specified by the Internet Engineering Task Force.
URI
2000-07-11
2008-01-14
The set of dates and times constructed according to the W3C Date and Time Formats Specification.
W3C-DTF
An alternative name for the resource.
The distinction between titles and alternative titles is application-specific.
2000-07-11
2010-10-11
An alternative name for the resource.
Alternative Title
Recommended practice is to include sufficient bibliographic detail to identify the resource as unambiguously as possible.
2003-02-15
2008-01-14
A bibliographic reference for the resource.
Bibliographic Citation
Examples of a Contributor include a person, an organization, or a service.
2008-01-14
2010-10-11
An entity responsible for making contributions to the resource.
Contributor
Spatial topic and spatial applicability may be a named place or a location specified by its geographic coordinates. Temporal topic may be a named period, date, or date range. A jurisdiction may be a named administrative entity or a geographic place to which the resource applies. Recommended best practice is to use a controlled vocabulary such as the Thesaurus of Geographic Names [TGN]. Where appropriate, named places or time periods can be used in preference to numeric identifiers such as sets of coordinates or date ranges.
2008-01-14
2008-01-14
The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant.
Coverage
2000-07-11
2008-01-14
A related resource that is included either physically or logically in the described resource.
Has Part
This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration.
Recommended best practice is to identify the resource by means of a string conforming to a formal identification system.
2008-01-14
2008-01-14
An unambiguous reference to the resource within a given context.
Identifier
2000-07-11
2008-01-14
A related resource in which the described resource is physically or logically included.
Is Part Of
This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration.
2000-07-11
2008-01-14
A related resource that references, cites, or otherwise points to the described resource.
Is Referenced By
This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration.
Changes in version imply substantive changes in content rather than differences in format.
2000-07-11
2008-01-14
A related resource of which the described resource is a version, edition, or adaptation.
Is Version Of
This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration.
Recommended best practice is to use a controlled vocabulary such as RFC 4646 [RFC4646].
2008-01-14
2008-01-14
A language of the resource.
Language
2000-07-11
2008-01-14
A related resource that is referenced, cited, or otherwise pointed to by the described resource.
References
This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration.
Recommended best practice is to identify the related resource by means of a string conforming to a formal identification system.
2008-01-14
2008-01-14
A related resource.
Relation
This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration.
Typically, the subject will be represented using keywords, key phrases, or classification codes. Recommended best practice is to use a controlled vocabulary.
2008-01-14
2012-06-14
The topic of the resource.
Subject
This term is intended to be used with non-literal values as defined in the DCMI Abstract Model (http://dublincore.org/documents/abstract-model/). As of December 2007, the DCMI Usage Board is seeking a way to express this intention with a formal range declaration.
Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMITYPE]. To describe the file format, physical medium, or dimensions of the resource, use the Format element.
2008-01-14
2008-01-14
The nature or genre of the resource.
Type
This document is published by the Provenance Working Group (http://www.w3.org/2011/prov/wiki/Main_Page).
If you wish to make comments regarding this document, please send them to public-prov-comments@w3.org (subscribe public-prov-comments-request@w3.org, archives http://lists.w3.org/
Archives/Public/public-prov-comments/). All feedback is welcome.
W3C PROVenance Interchange
prov:EmptyCollection
EmptyCollection
expanded
collections
An empty collection is a collection without members.
A. T. Fojo
ABCA2
ABC_genes
ABC_transporters_and_in_vitro_MDR_materials
ABC transporters as multidrug resistance mechanisms
2005
One of the major problems related with anticancer chemotherapy is resistance against anticancer drugs. The ATP-binding cassette (ABC) transporters are a family of transporter proteins that are responsible for drug resistance and a low bioavailability of drugs by pumping a variety of drugs out cells at the expense of ATP hydrolysis. One strategy for reversal of the resistance of tumor cells
expressing ABC transporters is combined use of anticancer drugs with chemosensitizers. In this review, the physiological functions and structures of ABC transporters, and the development of chemosensitizers are described focusing on well-known proteins including P-glycoprotein, multidrug resistance associated protein, and breast cancer resistance protein.
ABC transporters as multidrug resistance mechanisms and the
development of chemosensitizers for their reversal
MULTIDRUG RESISTANCE IN CANCER
ABC transporters in human cancers
ADE
ALL
AML
AML experiments
AML experiments material
AML_sample
Arun k. Rishi
1998
MCF-7yAdrVp is a multidrug-resistant human
breast cancer subline that displays an ATP-dependent
reduction in the intracellular accumulation of anthracycline
anticancer drugs in the absence of overexpression of known
multidrug resistance transporters such as P glycoprotein or
the multidrug resistance protein. RNA fingerprinting led to
the identification of a 2.4-kb mRNA that is overexpressed in
MCF-7yAdrVp cells relative to parental MCF-7 cells. The
mRNA encodes a 663-aa member of the ATP-binding cassette
superfamily of transporters that we term breast cancer resistance
protein (BCRP). Enforced expression of the full-length
BCRP cDNA in MCF-7 breast cancer cells confers resistance
to mitoxantrone, doxorubicin, and daunorubicin, reduces
daunorubicin accumulation and retention, and causes an
ATP-dependent enhancement of the efflux of rhodamine 123
in the cloned transfected cells. BCRP is a xenobiotic transporter
that appears to play a major role in the multidrug
resistance phenotype of MCF-7yAdrVp human breast cancer
cells.
A multidrug resistance transporter from human MCF-7 breast cancer cells
Accumulation_Bioassay
Actinomycin_D
Acute_lymphoblastic_leukemia
Adrenocortical_Cancer
Advanced_and_recurrent_breast_cancer_sample
Analysis_of_leukemic_blast_MDR_function
Anthracyclines-doxorubucin_daunorubicin_epirubicin
Anthranilic-acid-based_drug
AssayKit
AssayMethod
Transport assays
Assay with Human Cancer Cells materials
Asuka Mizutani
BBR3390
BCRP
BH3_profiling
BH3_profiling_method
Bevacizumab
Blast populations in the two bioassays
P-gp accumulation ratio, P-gp efflux ratio, percent unimpeded efflux for total MDR activity, percent efflux in the presence of zosuquidar, and percent inhibition of efflux by zosuquidar
Bone_marrow_aspirates
Bortezomib
Branimir I. Sikic
Breast Cancer
Breast_cancer_samples
CAVE
CCL_127__PC12
CI1033
CML
Caitriona Holohan
Vinca alkaloid, doxorubicin, or actinomycin D might not be effective in the therapy of pheochromocytoma.
Cancer_chemotherapy_doxorubicin_vinblastine
2003
Resistance to chemotherapy and molecularly targeted therapies is a major
problem facing current cancer research. The mechanisms of resistance to ‘classical’ cytotoxic
chemotherapeutics and to therapies that are designed to be selective for specific molecular
targets share many features, such as alterations in the drug target, activation of prosurvival
pathways and ineffective induction of cell death. With the increasing arsenal of anticancer
agents, improving preclinical models and the advent of powerful high-throughput screening
techniques, there are now unprecedented opportunities to understand and overcome drug
resistance through the clinical assessment of rational therapeutic drug combinations and the
use of predictive biomarkers to enable patient stratification.
Cancer drug resistance: an evolving paradigm
Carboplatin
Catherine Booth Genthe
Cetuximab
Chemotherapy that included vincristine and
daunomycin
Chemotherapy
Chemotherapy mdr1
Chemotherapy_with_targeted_inhibitors_of_Pgp-mediated_drug_transport
Cheol Hee Choi
Clonogenic_survival_assays
Colchicine
Colerectal_cancer
Colon Cancer
Colerectal_cancer
Colon_carcinoma
Competitive Inhibition Assay
Crizotinib
Cyclosporine
Cytarabine
D. G. Poplack
D. J. Slamon
Douglas D. Ross
Daniel B. Longley
Dasatinib
Daunomycin
Daunorubicin
Delta_RNA_Fingerprinting_kit
Deoxycytidine 5
The most common of these mechanisms, one that relies on drug efflux from cancer cells mediated by ATP-binding cassette (ABC) transporters.
Describe_various_approaches_to_combating_multidrug-resistant_cancer
DiOC2
2018
Background Little is known about the affinity and stability of
99mTc-labeled 2-methoxyisobutylisonitrile (99mTc-MIBI) and
tetrofosmin (99mTc-TF) for imaging of multiple drug resistance
transporters in cancer. We examined the affinity of 99mTc-labeled
compounds for these transporters and their stability.
Methods 99mTc-MIBI and 99mTc-TF were incubated in vesicles
expressing P-glycoprotein (MDR1), multidrug resistanceassociated
protein (MRP)1–4, or breast cancer resistance protein
with and without verapamil (MDR1 inhibitor) or MK-
571 (MRP inhibitor). Time activity curves of 99mTc-labeled
compounds were established using SK-N-SH neuroblastoma,
SK-MEL-28 melanoma, and PC-3 prostate adenocarcinoma
cell lines, and transporter expression of multiple drug resistance
was measured in these cells. The stability was evaluated.
Results In vesicles, 99mTc-labeled compounds had affinity for
MDR1 and MRP1. 99mTc-TF had additional affinity for
MRP2 and MRP3. In SK-N-SH cells expressing MDR1 and
MRP1, MK-571 produced the highest uptake of both 99mTclabeled
compounds. 99mTc-MIBI uptake with inhibitors was
higher than 99mTc-TF uptake with inhibitors. 99mTc-TF was
taken up more in SK-MEL-28 cells expressing MRP1 and
MRP2 than PC-3 cells expressing MRP1 and MRP3. 99mTc-
MIBI was metabolized, whereas 99mTc-TF had high stability.
Conclusion 99mTc-MIBI is exported via MDR1 and MRP1
(MRP1 > MDR1) at greater levels and more quickly compared
to 99mTc-TF, which is exported via MDR1 and MRP1–3
(MRP1 > MDR1; MRP1, 2 >MRP3). Because 99mTc-MIBI
is metabolized, clinical imaging for monitoring MDR and
shorter examination times may be possible with an earlier scanning
time on late phase imaging. 99mTc-TF has high stability.
Different Efflux Transporter Aff inity and Metabolism of 99mTc-2-Methoxyisobutylisonitrile and 99mTc-Tetrofosmin for Multidrug Resistance Monitoring in Cancer
There was increased intracellular
accumulation of doxorubicin as was evidenced using
confocal microscopy and reduced toxicity compared to the
free (unencapsulated) doxorubicin.
Differential_inhibition_of_various_transporters_by_two_structurally_similar_MDR_modulators
Doxorubicin
Drosophila_white_gene
Dubin-Johnson syndrome
Liver, kidney, intestine, adrenal glands, pancreas, lung, ovary
Drug_Resistance
Targeting multidrug resistance in cancer
Drug_efflux_from_cancer_cells_mediated_by_ATP-binding_cassette_ABC_transporters
Cellular mechanisms of multidrug resistance and ATP-binding cassette (ABC) transporters
Drug_resistance_and_its_role_in_clinical_oncology
EasternBlotting
Eastern_Blot_Analysis
Efflux_Bioassay
Elisabeth Paietta
Endogenous_and_exogenous_substrates_for_ABC_transporters
Epirubicin
Etoposide
2019
Background: Multidrug resistance (MDR) transporter proteins such as P-glycoprotein (P-gp) efflux a variety
of chemotherapeutic drugs from acute myeloid leukemia (AML) blasts leading to clinical drug resistance.
Methods: This study examined heterogeneity of MDR functional efflux by AML blasts using two flow cytometry
bioassays. Bone marrow specimens (N = 50) from elderly patients with newly diagnosed AML were analyzed
for CD34+ blasts with MDR efflux function. Efflux was measured with a fluorescent dye (DiOC2) as a
surrogate for oncology drugs that are substrates for MDR efflux. P-gp-mediated efflux was differentiated from
non-P-gp MDR activities using zosuquidar, a highly selective P-gp modulator. The bioassays included a
zosuquidar-dependent DiOC2 accumulation bioassay that measured only P-gp. The second method, termed the
efflux bioassay, could detect P-gp and other non-P-gp efflux depending on bioassay culture conditions.
Results: Sixty-two percent of the specimens were considered positive for blasts with P-gp function, and
26% of such P-gp-positive specimens also exhibited zosuquidar-resistant (i.e., non-P-gp) MDR efflux activity;
37% of P-gp-negative AML blast specimens displayed zosuquidar-resistant MDR function in the efflux
bioassay.
Conclusions: These results confirm the heterogeneous nature of MDR efflux pumps in AML blasts, and provide
support for the hypothesis that non-P-gp MDR contributed to negative
Evidence of a Role for Functional Heterogeneity in
Multidrug Resistance Transporters in Clinical Trials of
P-Glycoprotein Modulation in Acute Myeloid Leukemia
Evidence of a Role for Functional Heterogeneity in Multidrug Resistance Transporters in Clinical Trials of P-Glycoprotein Modulation in Acute Myeloid Leukemia
ExperimentalStudy
Experimental Study
Assay with Human Cancer Cells
Expression of a multidrug-resistance gene in human tumors and tissues
Some cases of colon cancer, increased expression of the mdr1 gene might be involved in the intrinsic resistance of these tumors to chemotherapeutic agents.
Expression_of_a_multidrug-resistance_gene
1987
The identification and cloning of a segment of
a human multidrug resistance gene (mdrl) was reported
recently. To examine the molecular basis of one type of
multidrug resistance, we have prepared RNA from human
tumors and normal tissues and measured their content of mdrl
RNA. We find that the mdrl gene is expressed at a very high
level in the adrenal gland; at a high level in the kidney; at
intermediate levels in the lung, liver, lower jejunum, colon, and
rectum; and at low levels in many other tissues. The mdrl gene
is also expressed in several human tumors, including many but
not all tumors derived from the adrenal gland and the colon.
In addition, increased expression was detected in a few tumors
at the time of relapse following initial chemotherapy. Although
controlled clinical studies will be required, our results suggest
that measurement of mdrl RNA may prove to
Expression of a multidrug-resistance gene in human tumors and tissues
Flavopiridol
Fluorochrome-labeled_anti-CD_antibodies
Fluorouracil
Functional_Assay
Functional_Bioassay
PGP expression increased after therapy and was associated with a greater likelihood of treatment failure.
Toxicity
Functions_of_ABC_transporters_in_Chemotherapy
Gastrointestinal_stromal_tumour_GIST_cell_lines
Gefitinib
Growth_inhibition_assays
HTB_10_HTB_11_HTB_38
Head_and_neck_cancer
High-risk_MDS_sample
IL-2
Iamivudine
Idarubicine
Idarubicinol
Identification_of_the_BCRP_gene-Functional_configuration_of_BCRP
Ifosfamide
Imatinib
Immunosuppressant_cyclosporin_A
Indolocarbazole
KB-3-1
KB-3-1_KB-8-5_KB-V1
KB-8-5
Leukaemia
Leukotriene_C4
Since expression of the mdrl gene is responsible for multidrug resistance in tissue culture systems, we measured levels of mdrl mRNA in normal human tissues and in untreated and treated human cancers.
Levels_of_mdrl_mRNA
Lung_cancer
Lymphoma
MCF-7_human_breast_carcinoma_cells
MDR2
MRP1
MRP2
MRP3
MRP4
MRP5
MRP6
MRP7
MRP8
Macmillan Magazines Ltd
Mechanisms_that_enable_the_survival_of_cancer_cells_during_drug_treatment
Melanoma
Melanoma_cell_line
Methotrexate
Mitomycin_C
Mitoxantrone
Multidrug Resistance
Multidrug_Resistance_Monitoring_in_Cancer
Multidrug resistance (MDR) in cancer Mechanisms, reversal using modulators of MDR and the role of MDR modulators in influencing the pharmacokinetics of anticancer drugs
Multidrug_resistance-MDR_in_cancer_Mechanisms
Multidrug_resistance_MDR_efflux_pumps_capable_of_eliminating_chemotherapeutic_drugs_from_tumor_cells
Multidrug resistance (MDR) efflux pumps capable of
eliminating chemotherapeutic drugs from tumor cells
contribute to clinical drug resistance in acute myeloid
leukemia (AML) and other cancers.
2000
In recent years, there has been an increased understanding of P-glycoprotein (P-GP)-mediated pharmacokinetic interactions. In addition, its role in modifying the bioavailability of orally administered drugs via induction or inhibition has been also been demonstrated in various studies. This overview presents a background on some of the commonly documented mechanisms of multidrug resistance (MDR),
reversal using modulators of MDR, followed by a discussion on the functional aspects of P-GP in the context of the pharmacokinetic interactions when multiple agents are coadministered. While adverse pharmacokinetic interactions have been documented with first and second generation MDR modulators, certain newer agents of the third generation class of compounds have been less susceptible in
eliciting pharmacokinetic interactions. Although the review focuses on P-GP and the pharmacology of MDR reversal using MDR modulators, relevance of these drug transport proteins in the context of pharmacokinetic implications (drug absorption, distribution, clearance, and interactions) will also be discussed.
Multidrug resistance (MDR) in cancer Mechanisms, reversal using modulators of MDR and the role of MDR modulators in influencing the pharmacokinetics of anticancer drugs
2003
Observations of functional adenosine triphosphate (ATP)-
dependent drug efflux in certain multidrug-resistant
cancer cell lines without overexpression of P-glycoprotein
or multidrug resistance protein (MRP) family members
suggested the existence of another ATP-binding cassette
(ABC) transporter capable of causing cancer drug
resistance. In one such cell line (MCF-7/AdrVp), the
overexpression of a novel member of the G subfamily of
ABC transporters was found. The new transporter was
termed the breast cancer resistance protein (BCRP),
because of its identification in MCF-7 human breast
carcinoma cells. BCRP is a 655 amino-acid polypeptide,
formally designated as ABCG2. Like all members of the
ABC G (white) subfamily, BCRP is a half transporter.
Transfection and enforced overexpression of BCRP in
drug-sensitive MCF-7 or MDA-MB-231 cells recapitulates
the drug-resistance phenotype of MCF-7/AdrVp
cells, consistent with current evidence suggesting that
functional BCRP is a homodimer. BCRP maps to
chromosome 4q22, downstream from a TATA-less
promoter. The spectrum of anticancer drugs effluxed by
BCRP includes mitoxantrone, camptothecin-derived and
indolocarbazole topoisomerase I inhibitors, methotrexate,
flavopiridol, and quinazoline ErbB1 inhibitors. Transport
of anthracyclines is variable and appears to depend on the
presence of a BCRP mutation at codon 482. Potent and
specific inhibitors of BCRP are now being developed,
opening the door to clinical applications of BCRP
inhibition. Owing to tissue localization in the placenta,
bile canaliculi, colon, small bowel, and brain microvessel
endothelium, BCRP may play a role in protecting the
organism from potentially harmful xenobiotics. BCRP
expression has also been demonstrated in pluripotential
‘side population’ stem cells, responsible for the characteristic
ability of these cells to exclude Hoechst 33342 dye,
and possibly for the maintenance of the stem cell
phenotype. Studies are emerging on the role of BCRP
expression in drug resistance in clinical cancers. More
prospective studies are needed, preferably combining
BCRP protein or mRNA quantification with functional
assays, in order to determine the contribution of BCRP to
drug resistance in human cancers.
Multidrug resistance mediated by the breast cancer resistance protein BCRP (ABCG2)
Multiple_chemotherapeutic_agents
Myeloma
NSCLC
NSCLC_cell_lines
NSCLC_sample
Nature Publishing Group
Neck_squamous_cell_carcinoma_cell_lines
Neuroblastoma
Neuroblastoma_Cell
Neuroepithelioma
Nilotinib
Non-P-gp_MDR_contributed_to_negative_results_with_zosuquidar
Non-P-gp MDR contributed to negative results with zosuquidar in AML trials
like ECOG-ACRIN E3999
Non_Smallcell_Lung_Cancer
Northern_analysis_of_the_expression_of_BCRP_mRNA
Observational Study
Ovarian_cancer
The focus of this review is P-GP-mediated MDR, a general overview of the underlying mechanisms and types of drug resistance is presented in the context of the overall MDR phenomenon.
P-GP-mediated_MDR_a_General_overview_of_the_underlying_mechanisms_and_types_of_drug_resistance
P-Glycoprotein Modulation in AML
PC-3 prostate adenocarcinoma
Paclitaxel
Pancreatic_cancer
Pancreatic_cancer_cell_lines
Patient_with_adrenocortical_cancer_and_breast_cancer
Peripheral_blood_lymphocytes
Phase_III_clinical_trials_with_ABC_transporter_inhibitors
Phase_II_clinical_trials_in_patients
Pheochromocytoma
Podophyllotoxin
Podophyllotoxin-etoposide_teniposide
Poor-risk_acute_leukaemia_samples
Prazocin
Proc. Nati. Acad. Sci. USA
RNA_Fingerprinting
ROLE_OF_ATP-DEPENDENT_TRANSPORTERS_in_chemotherapy_and_A_surrogate_assay_for_PGP_inhibition
RT-PCR_assay
Refractory_AML_high-risk_MDS_sample
Relapsed_and_refractory_AML_sample
Renal_cell_cancer
Review Study
Rhabdomyosarcoma
Role_of_P-GP_in_MDR
SK-MEL-28 melanoma
SK-N-SH neuroblastoma
Sarcoma
Small_Cell_Lung_Cancer
Southern_Blot_Analysis
Sulforhodamine-B_cytotoxicity_assay
Surrogate_Assay
Taxenes-paclitaxel_docetaxel
Teniopside
Testicular_cancer
The_new_transporter_was_termed_the_breast_cancer_resistance_protein_BCRP
The new transporter was
termed the breast cancer resistance protein (BCRP),
because of its identification in MCF-7 human breast
carcinoma cells.
The_physiological_functions_and_structures_of_ABC_transporters
The_physiological_functions_and_structures_of_ABC_transporters_and_development_of_chemosensitizers
The physiological functions and structures of ABC transporters, and
development of chemosensitizers are described focusing
on well-known proteins including Pgp, MRP, and BCRP.
Topotecan
Trastuzumab
VAD
Vemurafenib
Verapamil
Vesicle Assay
Vesicle_transport_experiments
Vincristine
Vindesine
Western_Blot_Analysis
Zidovudine
Zosuquidar
50 AML specimens for MDR function
using zosuquidar, a P-gp-selective modulator, and two
ex vivo leukemic blast bioassays confirms the heterogeneous
nature of MDR efflux pump function by AML
blasts. Moreover, it supports the supposition that function
of multiple transporters could have circumvented
or obscured efficacy of P-gp modulators in AML clinical
trials like E3999 with zosuquidar.
Zosuquidar_AML_experiments
anti-CD34-APC
antibody-mediated_cytolysis_experiment
cDNA
Each well was pre-incubated with 1 mL incubation medium for 10 min
identify_and_overcome_underlying_mechanisms_of_resistance
this Review focuses on the mechanisms that enable the survival of cancer
cells during drug treatment and on current research
efforts to identify and overcome underlying mechanisms
of resistance to both standard chemotherapeutic agents
and molecularly targeted therapies.
inhibitors_NB-506_J-107088
MDR1
Expression of mdr1 in Tumors from Untreated and Treated Patients
mdr1_gene_expression
mdr1 mRNA experiment materials
mdr1 mRNA in normal human tissues and in untreated and treated human cancers.
multidrug_resistance_to_cancer_cells
The cells were incubated for 5 min with 99mTc-MIBI or 99mTc-TF in the presence of inhibitor
topoisomerase_I
useDrug
useGene
useProbe
useReagent
Specimen that are used as material in experimental study.
useSpecimen
10_patients_with_acute_lymphocytic_leukemia
50_patients_with_newly_diagnosed_AML
795-bp_cDNA
99mTc-labeled compounds in a human-derived cancer cell line
99mTc-labeled_compounds_were_exported_via_MRP2–4_and_BCRP
We examinedwhether 99mTc-labeled compounds were
exported via MRP2–4 and BCRP and whether these compounds
had affinity for these transporters including MDR1
and MRP1 in cancer cells.
The hypothesis that an ATPdependent xenobiotic transporter may contribute significantly to the multidrug-resistance phenotype of MCF-7yAdrVp cells.
ATP_dependent_xenobiotic_transporter_may_contribute_significantly_to_the_MCF-7/AdrVp_cells
Jan Wijnholds
Marcel Kool
Piet Borst
Raymond Evers
A Family of Drug Transporters: the Multidrug Resistance-Associated Proteins
BCRP_substrate/inhibitors
CAV/EP
CD34+_Leukemic_Blasts
CD56+
Colon carcinoma cell lines (WIDR and LS-174)
Comparative_CD34+_blast_responses_were_examined
A multidrug resistance transporter from human MCF-7 breast cancer cells
The presence of the phosphopantetheine attachment site on BCRP suggests
that BCRP may be part of a multiprotein complex.
Differentially_overexpressed_in_MCF-7/AdrVp_cells_compared_with_MCF-7_cells
MCF-7/AdrVp is a multidrug-resistant human
breast cancer subline that displays an ATP-dependent
reduction in the intracellular accumulation of anthracycline
anticancer drugs in the absence of overexpression of known
multidrug resistance transporters such as P glycoprotein or
the multidrug resistance protein.
ERBB2_amplified_breast_cancer_cell_lines
99mTc-99mTc take of MIBI or -TF was examined in ATP solution with verapamil
K562/R7 leukemia
Sensitivity of selected MCF-7 sublines to antineoplastic agents determined by sulforhodamine-B cytotoxicity assay (21). Experiments such as those
displayed in Figure 4D were used to obtain the LC50. For each drug and cell type, the table displays the median LC50 and range of LC50 measurements
(nM), the number of experimental determinations of LC50 that were performed (N), and the resistance factor (RF). The RF was calculated by
dividing the median LC50 for a given drug against a transfected cell line by the median LC50 of that drug against nontransfected MCF-7yW cells.
For each drug tested, the LC50 for the BCRP-transfected cells was examined for statistically significant difference from the LC50 of MCF-7yW or
MCF-7ypcDNA3 by the Mann–Whitney test, using MINITAB statistical software MINITAB release 8 extended, Minitab, State College, PA) and a 95%
confidence interval. The values of P for the statistically significant differences are as follows Mitoxantrone: MCF-7yW vs. MCF-7yBCRPclone6,
P 5 0.0107, MCF-7yW vs. MCF-7yBCRPclone8, P 5 0.0058, MCF-7ypcDNA3 vs. MCF-71BCRPclone6, P 5 0.0142, MCF-7ypcDNA3 vs.
MCF-7yBCRPclone8, P 5 0.0081; daunorubicin: MCF-7yW vs. MCF-7yBCRPclone6, P 5 0.0107, MCF-7yW vs. MCF-7yBCRPclone8, P 5
0.0058, MCF-7ypcDNA3 vs. MCF-7yBCRPclone6, P 5 0.0195, MCF-7ypcDNA3 vs. MCF-7yBCRPclone8, P 5 0.0163; doxorubicin: MCF-7yW
vs. MCF-7yBCRPclone6, P 5 0.0373, MCF-7yW vs. MCF-7yBCRPclone8, P 5 0.02, MCF-7ypcDNA3 vs. MCF-7yBCRPclone8, P 5 0.0304;
cis-platin: MCF-7yW vs. MCF-7yBCRPclone19, P 5 0.0497.
MCF-7/AdrVp_comparison
2002
Chemotherapeutics are the most effective treatment for metastatic tumours. However, the ability of cancer cells to become simultaneously resistant to different drugs — a trait known as multidrug resistance — remains a significant impediment to successful chemotherapy. Three decades of multidrug-resistance research have identified a myriad of ways in which cancer cells can elude chemotherapy, and it has become apparent that resistance exists against every effective drug, even our newest agents. Therefore, the ability to predict and circumvent drug
resistance is likely to improve chemotherapy.
MULTIDRUG RESISTANCE IN CANCER: ROLE OF ATP-DEPENDENT TRANSPORTERS
PGP/MDR1
RNA Extraction, Electrophoresis, and Blot Analysis
neuroblastoma cell lines (HTB 10, HTB 11, and CCL 127)
2008-01-14
Agent Class
2012-06-14
A group of agents.
Examples of Agent Class include groups seen as classes, such as students, women, charities, lecturers.
Abstract
2008-01-14
2000-07-11
A summary of the resource.
An entity primarily responsible for making the resource.
2010-10-11
2008-01-14
Creator
Examples of a Creator include a person, an organization, or a service.
2008-01-14
Description
An account of the resource.
2008-01-14
Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.
2010-10-11
2008-01-14
Publisher
Examples of a Publisher include a person, an organization, or a service.
An entity responsible for making the resource available.
An entity responsible for making the resource available.
A name given to the resource.
Title
A name given to the resource.
2008-01-14
2010-10-11
EasternBlotting
The eastern blot is a biochemical technique used to analyze protein post translational modifications (PTM) including the addition of lipids, phosphates, and glycoconjugates.
The eastern blot is a biochemical technique used to analyze protein post translational modifications (PTM) including the addition of lipids, phosphates, and glycoconjugates.
useDrug
Drugs that are used as material in experimental study.
Specimen that are used as material in experimental study.
useSpecimen