Cancer biomarker ontology (CBIO).
editor note
curator note
elucidation
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.
An account of the resource.
Description
A property to define the database an orthology dataset belongs to.
in database
http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation is an annotation property that is drawn from NCI_Thesaurus
An alternative label for a given entity such as a commonly used abbreviation or synonym.
A definition citation is a document, ontology class, person or organization from which the definition of the class is derived. It is used in the same sense as a citation in literature, in that the definition may have been derived from these sources or that this definition is related to these source.
The range of skos:altLabel is the class of RDF plain literals.
skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties.
alternative label
An alternative lexical label for a resource.
Acronyms, abbreviations, spelling variants, and irregular plural/singular forms may be included among the alternative labels for a concept. Mis-spelled terms are normally included as hidden labels (see skos:hiddenLabel).
definition
A statement or formal explanation of the meaning of a concept.
example
An example of the use of a concept.
note
A general note, for any purpose.
This property may be used directly, or as a super-property for more specific note types.
scope note
A note that helps to clarify the meaning and/or the use of a concept.
contained in
Connects a biological entity to its taxon of origin.
in taxon
'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
expressed in
g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.
highly expressed in
g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.
x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part.
ubiquitously expressed in
expresses
ubiquitously expresses
holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism
genomically related to
has anatomical entity
has expression or absence confidence level
has a developmental stage
has expression level characteristic
has an expression condition
has an experimental condition
has sequence unit
has strain
A sequence unit is absent (not expressed) in some expression condition (e.g. anatomical entity and/or developmental stage). Examples how to assign this property (at a high level of abstraction): GeneA "is absent in" Brain; GeneA "is abent in" adult stage.
Recommendation: prefer to instatiate 'absence of gene expression' and 'gene expression experiment condition' classes to represent Gene expression data. For example, rather than materializing this property at the data store level, it shoud be inferred by applying the logical rules: rule1- 'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?cond); rule2- 'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has a developmental stage'(?cond, ?stage), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?stage) rule3- 'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has strain'(?cond, ?strain), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?strain) rule4- 'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has anatomical entity'(?cond, ?anat), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?anat) These rules are currently defined in Genex ontology as a SWRL (Semantic Web Rule Language) rule. It can be tanslated into another semantic web language such as RIF.
is absent in
is not expressed in
A sequence unit (e.g. gene) is present (expressed) in some expression condition (e.g. anatomical entity and/or developmental stage). Examples how to assign this property (at a high level of abstraction): GeneA "is expressed in" Brain; GeneA "is expressed in" adult stage.
Recommendation: prefer to instatiate 'expressed gene' and 'gene expression experiment condition' classes to represent Gene expression data. For example, rather than materializing this property at the data store level, it shoud be inferred by applying the logical rules: - 'absence of gene expression'(?e),'has an expression condition'(?e, ?cond), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?cond); - 'absence of gene expression'?e),'has an expression condition'(?e, ?cond), 'has a developmental stage'(?cond, ?stage), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?stage) - 'absence of gene expression'(?e),'has an expression condition'(?e, ?cond), 'has strain'(?cond, ?strain), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?strain) - 'absence of gene expression'(?e),'has an expression condition'(?e, ?cond), 'has anatomical entity'(?cond, ?anat), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?anat) These rules are currently defined in Genex ontology as a SWRL (Semantic Web Rule Language) rule. It can be tanslated into another semantic web language such as RIF.
is expressed in
A resource that is replaced by this resource.
A relation between two objects, in which the first object contains information that is used to produce the second object.
encodes
has expression level score
expression score
A easy to remember identifier for a UniProtKB entry, but it is not a stable identifier and should not be used by programs to identify entries.
A rememberable string that can be used to find entries, not a stable identifier!
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
continuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
independent continuant
A part of a multicellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a multicellular organism with granularity above the level of a protein complex.
Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.
Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them.
Important for alignment with Darwin Core class "Organism".
Basic unit of graphs and trees
A population is a group of material entities consisting of individuals which share a particular characteristic such as inhabiting a particular region or area or ability to interbreed.
absence of gene expression
Not expressed gene
Not expressed sequence unit
An anatomical entity can be an organism part (e.g. brain, blood, liver and so on) or a material anatomical entity such as a cell.
Anatomical entity
All sequence units (e.g. Gene) that are expressed in some condition (e.g. organ and/or adult stage).
gene expression
expression
sequence unit expression
A sequence unit (e.g. Gene) is expressed in some expression condition (e.g. anatomical entity and/or developmental stage).
gene expression experiment condition
expression condition
sequence unit expression condition
Gene
A node of a tree whose leaf nodes are sequence units and whose internal nodes are clusters of homologs
Gene tree node
A living being, such as an animal, a plant, a bacterium, or a fungus., Any individual living (or previously living) being. Example: animal, human being. An organim can be associated to a taxon such as "Homo Sapiens", NCBI taxonomy identifier: 9606.
Organism
Living being
Protein
protein or DNA sequence as a unit of comparison
Sequence unit
A region of the sequence of the gene
gene region
region of a gene
subgene
An element of a taxonomy for classifying life forms.
A database is a data store such as relational, hierarchical and graph databases.
database
An experimental factor in Array Express which are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This upper level class is really used to give a root class from which applications can rely on and not be tied to upper ontology classses which do change.
Concept naming convention is lower case natural naming with spaces, when necessary captials should be used, for example disease factor, HIV, breast carcinoma, Ewing's sarcoma
A developmental stage is spatiotemporal region encompassing some part of the life cycle of an organism, e.g. blastula stage
This branch will be replaced by, and if necessary merged with an Uberon import in future.
tissue, organ, system, sperm, blood or body location (arm).
The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm).
A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics.
strain
A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray.
An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs.
A confidence level representing a high trust in an evidence.
A confidence level representing a moderate trust in an evidence.
A confidence level representing an absence of trust in an evidence.
average expressed
medium expressed
g is highly expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background, e.g. all gene expressions taking into account a given gene expression condition.
highly expressed
over expressed
high expressed
g is lowly expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.
lowly expressed
under expressed
low expressed
x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x.
ubiquitously expressed
Examples of a Creator include a person, an organization, or a service. Typically, the name of a Creator should be used to indicate the entity.
An entity primarily responsible for making the resource.
Creator
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/creator) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
Recommended practice is to identify the resource by means of a string conforming to an identification system.
An unambiguous reference to the resource within a given context.
Identifier
A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/identifier) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.
This property is intended to be used with non-literal values. The described resource may be derived from the related resource in whole or in part. Best practice is to identify the related resource by means of a URI or a string conforming to a formal identification system.
A related resource from which the described resource is derived.
Source
This property is intended to be used with non-literal values. This property is an inverse property of Is Referenced By.
A related resource that is referenced, cited, or otherwise pointed to by the described resource.
References
This property is intended to be used with non-literal values. This property is an inverse property of References.
A related resource that references, cites, or otherwise points to the described resource.
Is Referenced By
Recommended practice is to identify the license document with a URI. If this is not possible or feasible, a literal value that identifies the license may be provided.
A legal document giving official permission to do something with the resource.
License
Recommended practice is to describe the date, date/time, or period of time as recommended for the property Date, of which this is a subproperty.
Date on which the resource was changed.
Date Modified
The statement may include a description of any changes successive custodians made to the resource.
A statement of any changes in ownership and custody of the resource since its creation that are significant for its authenticity, integrity, and interpretation.
Provenance
Any changes in ownership and custody of a resource since its creation that are significant for its authenticity, integrity, and interpretation.
Provenance Statement
Date of formal issuance of the resource.
Date Issued
Date of creation of the resource.
Date Created
Recommended practice is to identify the creator with a URI. If this is not possible or feasible, a literal value that identifies the creator may be provided.
An entity responsible for making the resource.
The term from <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> was adapted for the cancer biomarker data context. This provenance statement is asserted only for the case of modifications that include either deletion or replacement of class restrictions (e.g. quantifiers) and disjunction statements or property domain and ranges. Disjunction assertions are often removed for the sake of simplicity. This is because many of the dinjunctions and domain specificities are out of scope when actually structuring cancer biomarker data.
A name given to the resource.
Title
has member is a mereological relation between a collection and an item.
has member
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has part
An experimental factor which is a property or characteristic of some other entity. For example, the mouse has the colour white.
A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease.
A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role). For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease.
A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts.
A role played by the molecular entity or part thereof within a biological context.
A substance used as an indicator of a biological state.
A disease is a disposition that describes states of disease associated with a particular sample and/or organism.
A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease.
A disposition is an entity that causes a specific process or transformation in an entity in which it inheres, under specific circumstances and in conjunction with the laws of nature. For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease.
A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C.
Any disorder that features disrupted cell proliferation. Includes hyperplasia, neoplastic syndrome and isolated neoplasm diseases as well as precancerous conditions.
A pathological process with signs indicating it may become cancerous. Representative examples include leukoplakia, dysplastic nevus, actinic keratosis, xeroderma pigmentosum, and intraepithelial neoplasia.
Editor note: check classification. Also consider changing def, NCIT defines as disease. Also consider a grouping for this and paraneoplastic syndrome
Either an isolated neoplasm or a syndrome with neoplasm as a major feature.
A disorder either associated with an increased risk for malignant transformation (e.g., intraepithelial neoplasia, leukoplakia, dysplastic nevus, myelodysplastic syndrome) or that develops as a result of the presence of an existing malignant neoplasm (e.g., paraneoplastic syndrome).
An abnormal increase in the number of (otherwise normal) cells in an organ or a tissue with consequent enlargement.
An abnormal increase in the number of cells in an organ or a tissue with consequent enlargement.
A broad classification for disorders in which the development of neoplasms typically occur in association with a characteristic set of signs or symptoms. These disorders may be inherited or acquired.
A group of signs, symptoms, and clinicopathological characteristics that may or may not have a genetic basis and collectively define an abnormal condition.
syndrome associated with disease or disorder
An characteristic of a disease in which the disease is not manifested as an isolated feature but has multiple distinct features.
An characteristic of a disease that varies depending on whether the disease appears as an isolated feature or whether the disease is a syndrome consisting of multiple features.
A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.
A disease or disorder is defined as rare in Europe when it affects fewer than 1 in 2000. A disease or disorder is defined as rare in the USA when it affects fewer than 200,000 Americans at any given time. Here we take the European definition to be consistent with Orphanet.
A quality is an entity that describes some aspect which is intrinsic to that particular object and is dependent on or more material entities in which it inheres in or is borne by. Example the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee
A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias.
NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS)
A malignant neoplasm in which new abnormal tissue grow by excessive cellular division and proliferation more rapidly than normal and continues to grow after the stimuli that initiated the new growth cease.
A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas.
A neoplasm which is characterized by the absence of morphologic features associated with malignancy (severe cytologic atypia, tumor cell necrosis, and high mitotic rate). Benign neoplasms remain confined to the original site of growth and do not metastasize to other anatomic sites.
Editor note: see https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues/14
An instrument is a device which provides a mechanical or electronic function.
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
occurrent
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
A processual entity that realizes a plan which is the concretization of a plan specification.
a clinical trial is a medical interventional study where participants are assigned prospectively to an intervention or interventions according to a protocol to evaluate the safety and efficacy of the intervention(s) on biomedical or other health related outcomes. The Interventions include but are not restricted to drugs, cells and other biological products, surgical procedures, radiologic procedures, devices, behavioral treatments, process-of-care changes, preventive care, etc.
clinical trial
A systematic, scientific investigation that can be either interventional or observational and involves human beings as research subjects. Human subject research can be either medical (clinical) research or non-medical (e.g., social science) research.
human subject study
Any interesting single amino-acid site on the sequence, that is not defined by another feature key. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids.
Description of a special region or site in a protein sequence.
Description of a resource on a specific topic.
Posttranslational modification of a residue.
Describes amino acid modifications, post pre- and post-translational.
Describes the occurrence of the attachment of a glycan (mono- or polysaccharide) to a residue of a protein.
Describes residues which are linked by an intra-chain disulfide bond. If the endpoints are identical, the disulfide bond is an interchain one.
Posttranslationally formed amino acid bonds.
Describes the occurrence of a non standard residue in the sequence record.
Indicates that the initiator methionine has been cleaved off and is not shown in the sequence.
Cleavage of the initiator methionine is one of the most common protein modifications and occurs co-translationally.
Authors report that sequence variants exist.
Amino acid(s) involved in the activity of an enzyme.
Binding site for any chemical group (co-enzyme, prosthetic group, etc.).
Although proteins can be modified pre-translationally (on the amino acid component of AMINO ACYL TRNA), co-translationally (during the process of GENETIC TRANSLATION), or after translation is completed (POST-TRANSLATIONAL PROTEIN PROCESSING), all protein modifications are generally referred to as PTMs, because a majority of them are made post-translationally, after the protein is folded. As a result, PTM here means a pre-, co- or post-translationally protein modification.
A probability is quantity of how likely it is that some event will occur.
Predictions for functional affect of variation on the protein reported by a tool such as PolyPhen-2 (e.g. benign, possibly damaging, or probably damaging) and NetNGlyc2.0, and the prediction probability to occur, if applicable.
It states the funtional impact prediction due to the fact of a variation in the protein sequence (e.g. caused by a mutation) reported by a tool such as PolyPhen-2 (e.g. benign, possibly damaging, or probably damaging) and NetNGlyc2.0 (e.g. gain, loss, no change).
It states a funtional impact prediction (i.e. a predicted effect of the protein variant, for example, due to mutation).
A biochemical or other measurement device developed to quantitate a biomarker. These tests can evaluate biomarkers for the detection and treatment of asymptomatic individuals (screening), establishing the presence and precise description of disease (diagnosis), estimating the risk or time to clinical outcomes (prognosis), identifying patient likelihood to benefit from certain therapies (predictive) or to experience therapy-related risks (pharmacogenomics), or treatment and post-treatment monitoring purposes (e.g., early detection and treatment of advancing disease or complications).
A relationship between a biomarker and a test by which the biomarker is used.
It states the disease target of a biomarker test or a differential gene expression analysis. The disease is defined by the controlled vocabulary: the Disease Ontology (DO). DO classes is therefore considered instances of efo:EFO_0000408 (EFO Disease class) by applying OWL 2 punning (see https://www.w3.org/TR/owl2-new-features/#F12:_Punning).
It relates an instrument to its manufacturer name.
It relates a biomarker test to its FDA (US Food and Drug Administration) submission identifier.
It assings clinical trials for a biomarker test device. If it is a FDA biomarker clinical, trials are represented with the following URI scheme https://clinicaltrials.gov/ct2/show/{trial id}.
The approved indication of a biomarker test.
It relates a biomarker test to its biomarker origin: multigene prediction, somatic mutation, or amplification.
It classifies a cancer by the type of tissue in which the cancer originates (histological type).
In the future this property might be replaced by an object property that assings, if exist, NCIT controlled vocabulary terms as instance values such as http://purl.obolibrary.org/obo/NCIT_C3224 (melanoma).
The specimen type for the biomarker test.
The platform method used by the biomarker test.
The number of genes that are members of a biomarker test.
It denotes the adoption evidence of a biomarker test.
It denotes the state of a biomarker test approval.
It states a specific study design for a biomarker test. A study design is a plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
A finding that has treatment or management implications for a patient's condition.
A cancer biomarker refers to a substance or process that is indicative of the presence of cancer in the body. A biomarker may be a molecule secreted by a tumor or a specific response of the body to the presence of cancer.
A segment of DNA with an identifiable physical location on a chromosome and whose inheritance can be followed. It is indeed an alteration in DNA that may indicate an increased risk of developing a specific disease or disorder.
A measurable DNA or RNA characteristic that is an indicator of normal biologic processes, pathogenic processes, and/or response to therapeutic or other intervention. The definition for a genomic biomarker is not limited to human samples. A genomic biomarker could, for example, reflect: the expression of a gene; the function of a gene; the regulation of a gene. A genomic biomarker can consist of one or more deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) characteristics. The definition for a genomic biomarker does not include the measurement and characterisation of proteins or low molecular weight metabolites. DNA characteristics include, but are not limited to: single nucleotide polymorphisms (SNPs); variability of short sequence repeats; DNA modification, e.g., methylation; insertions; deletions; copy number variation; cytogenetic rearrangements, e.g., translocations, duplications, deletions or inversions. RNA characteristics include, but are not limited to: RNA sequence; RNA expression levels; RNA processing, e.g., splicing and editing; microRNA levels (ICH Draft Consensus Guideline E15).
it provides key information about the dynamic nature of proteins, including functionality, post‐translational modifications, interaction with other biological molecules, and response to environmental factors. Proteomic biomarkers are often referred to those biomarkers discovered using technologies capable of analyzing many proteins simultaneously, such as protein microarray and mass spectrometry (MS).
Metabolomic biomarker refers to the systematic identification and quantification of the small molecule metabolic products (the metabolome) of a biological system (cell, tissue, organ, biological fluid, or organism) at a specific point in time that acts as a biomarker. Mass spectrometry and NMR spectroscopy are the techniques most often used for metabolome profiling. It can also enable diagnostic and prognostic prediction.
NCI defines a metabolic marker as follows: specific metabolic changes that characterize an organism's state of health or disease, or response to a particular therapeutic intervention, and helps make diagnosis more accurate or enable physicians to make diagnosis before symptoms appear and to track disease progression.
Any epigenetic mark or altered epigenetic mechanism that can be measured in the body fluids or tissues and that defines a disease (detection), predicts the outcome of diseases (prognostic) or response to a therapy (predictive), monitors treatment responses (therapy monitoring), or predicts risk of future disease development (risk). It is a dynamic biomarker which changes based on disease evolution and intra- or extra-environmental cellular conditions. Epigenetics is the study of heritable changes in gene expression that do not involve any alterations in the DNA sequence.
A form of gene expression that is indicative of a biological behavior such as a tumor or cancer.
it is a biomarker discovered from a simplified, semiquantitative, unbiased binary comparison between diseased and normal using biological samples for maximal detection of significant protein expression differences.
It relates a biomarker to the severity or presence of some disease state. The disease is defined with the controlled vocabulary: the Disease Ontology (DO). DO classes is therefore considered instances of efo:EFO_0000408 (EFO Disease class) by applying OWL 2 punning (see https://www.w3.org/TR/owl2-new-features/#F12:_Punning).
A biomarker composed of 2 or more single biomarkers
ALDH1A2 gene by itself is a specific biomarker for prostate cancer.
A biomarker that is composed of solely one marker (e.g. a unique gene).
It states which biomarkers composes a biomarker panel.
consist of
A biomarker panel that indicates some cancer disease.
A single biomarker that indicates some cancer disease.
It denotes whether biomarker has been accepted, curated or is under review.
The :BiomarkerState class provides a categorisation of the possible states a biomarker may have as a result of a quality evaluation process. For example, whether it has been Curated', 'Accepted' or 'Under review'. This categorisation is implemented as a SKOS vocabulary.
A state to assign the biomarker status under review (i.e. being evaluated). After the reviewing process, the status can change into curated or accepted, for example.
It indicates that a curation process was performed by a curator for accuracy checks and compliance with a set of requirements to confirm the veracity of an assertion, i.e. statement. The statement which has been assessed for accuracy by domain experts.
The Early Detection Research Network (EDRN) implemented a nationally recognized research schema designed to bring forward into clinical practice verifiably effective cancer biomarkers. The network established a roadmap and standards for research that minimizes chance, bias and over-fitting, based on a protocol driven, five-phase approach.
Preclinical Exploratory – Exploratory studies to identify potentially useful biomarkers
Clinical Assay and Validation – Studies to determine the capacity of biomarkers to distinguish between people with cancer and those without.
Retrospective Longitudinal – Determine how well biomarkers detect preclinical disease by testing the markers against specimens collected longitudinally from research cohorts.
Prospective Screening – Identify the extent and characteristics of disease detected by the test and determine the false referral rate.
Cancer Control – Evaluate both the role of the biomarkers for detection of cancer and the overall impact of screening on the population through large-scale population studies.
It states one of the 5 phases of a biomarker research as defined by Early Detection Research Network (EDRN).
It states the phase of a research or a trial such as a biomarker research phase.
Cancer differential gene expression analysis to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between normal (i.e. healthy) and cancer cells. Identify from molecular sequence analysis (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different or not between two sample groups.
The logarithm (to base 2) of the fold change from normal expression to tumor expression. Fold change is equivalent to the expression level of a gene in cancer divided by the expression level of a gene in the same kind of tissue but a healthy one.
P-value for statistical significance of the reported change, computed directly by DESeq2. DESeq2 is a tool to verify the change of expression of genes between two samples.
P-value adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate (FDR).
Trends are considered significant when FDR adjusted p-value < 0.05
Gene expression trend. Possible values are normal (no change), increased (up) and decreased (down).
The amount of patients with increased gene expression.
The amount of patients with decreased gene expression.
The amount of patients with no change in terms of gene expression.
The amount of patients with no coverage.
The total number of patients with data for the study.
This property relates a sequence unit such as a gene to a biological concept explicilty defined in its range.
is a sequence unit related to
A gene alteration due to mutation that causes or predisposes an individual to a specific disease. It depicts mutation positions and functional annotations.
A sequence variation that deviates from a canonical or reference sequence.
The nucleotide or amino acid in a sequence before modification.
The nucleotide or amino acid in a sequence after modification.
A structure found in the nucleus of human cells that is comprised of a strand of linearized double-stranded DNA plus proteins that package the DNA in a condensed coil form and regulate chromosomal function. [def-source: NCI]
One of the bodies in the cell nucleus that is the bearer of genes, has the form of a delicate chromatin filament during interphase, contracts to form a compact cylinder segmented into two arms by the centromere during metaphase and anaphase stages of cell division, and is capable of reproducing its physical and chemical structure through successive cell divisions. [def-source: NCI]
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. Nucleobases are used to represent intances of nucleotides. Nucleobases, also known as nitrogenous bases or often simply bases, are nitrogen-containing biological compounds that form nucleosides, which in turn are components of nucleotides. A set of five nitrogenous bases is used in the construction of nucleotides, which in turn build up nucleic acids like DNA and RNA. These nitrogenous bases are adenine (A), uracil (U), guanine (G), thymine (T), and cytosine (C).
A carboxylic acid containing one or more amino groups.
It indicates the presence of an undertermined amino acid
A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
partially characterised change in DNA sequence
An alpha-amino acid that consists of propionic acid bearing an amino substituent at position 2.
A sulfur-containing amino acid that is propanoic acid with an amino group at position 2 and a sulfanyl group at position 3.
An alpha-amino acid that consists of succinic acid bearing a single alpha-amino substituent
An alpha-amino acid that is glutaric acid bearing a single amino substituent at position 2.
An aromatic amino acid that is alanine in which one of the methyl hydrogens is substituted by a phenyl group.
The simplest (and the only achiral) proteinogenic amino acid, with a hydrogen atom as its side chain.
The L-enantiomer of the amino acid histidine.
(2S)-2-amino-3-(1H-imidazol-4-yl)propanoic acid
(S)-alpha-Amino-1H-imidazole-4-propionic acid
(S)-alpha-amino-1H-Imidazole-4-propanoic acid
A diamino acid that is caproic (hexanoic) acid bearing two amino substituents at positions 2 and 6.
A branched-chain amino acid that consists of glycine in which one of the hydrogens attached to the alpha-carbon is substituted by an isobutyl group.
A sulfur-containing amino acid that is butyric acid bearing an amino substituent at position 2 and a methylthio substituent at position 4.
alpha-amino-gamma-methylmercaptobutyric acid
An alpha-amino acid in which one of the hydrogens attached to the alpha-carbon of glycine is substituted by a 2-amino-2-oxoethyl group.
Pyrrolidine in which the pro-S hydrogen at position 2 is substituted by a carboxylic acid group. L-Proline is the only one of the twenty DNA-encoded amino acids which has a secondary amino group alpha to the carboxyl group. It is an essential component of collagen and is important for proper functioning of joints and tendons. It also helps maintain and strengthen heart muscles.
An optically active form of glutamine having L-configuration.
An L-alpha-amino acid that is the L-isomer of arginine.
(2S)-2-amino-5-(carbamimidamido)pentanoic acid
(S)-alpha-Amino-beta-hydroxypropionic acid
An optically active form of threonine having L-configuration.
An alpha-amino acid that is alanine bearing an indol-3-yl substituent at position 3.
alpha-Amino-beta-(3-indolyl)-propionic acid
An alpha-amino acid that is phenylalanine bearing a hydroxy substituent at position 4 on the phenyl ring.
2-Amino-3-(p-hydroxyphenyl)propionic acid
2-amino-3-(4-hydroxyphenyl)propanoic acid
A nucleotide is a nucleoside phosphate resulting from the condensation of the 3 or 5 hydroxy group of a nucleoside with phosphoric acid.
That part of DNA or RNA that may be involved in pairing.
A common and naturally occurring pyrimidine nucleobase in which the pyrimidine ring is substituted with two oxo groups at positions 2 and 4. Found in RNA, it base pairs with adenine and replaces thymine during DNA transcription.
A 2-aminopurine carrying a 6-oxo substituent.
The parent compound of the 6-aminopurines, composed of a purine having an amino group at C-6.
An aminopyrimidine that is pyrimidin-2-one having the amino group located at position 4.
A pyrimidine nucleobase that is uracil in which the hydrogen at position 5 is replaced by a methyl group.
A relation between two objects, in which the first object is produced from the information contained in the second object.
is encoded by
A probability measure is quantity of how likely it is that some event will occur.
probability measure
A stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation.
stop codon
A quality that has a value that is increased compared to normal or average.
increased
A quality that has a value that is decreased compared to normal or average.
decreased
A quality that has a value that is normal or average.
normal
A quality that has a value that is outside normal or average.
abnormal
A chromosome is a molecular complex of circular or linear DNA and bound proteins.
chromosome
PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6.
A information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts.
2010-01-31 Philippe Rocca-Serra: restriction now changed to be the output of a digital curation process + reflected in example of usage and reference
curated information
PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. "After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)"
A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level.
FDR adjusted p-value
p-value
PMID:19696660 in contrast to the in-vivo data AT-III increased significantly from 113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2).
A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
WEB: http://en.wikipedia.org/wiki/P-value
Fold change is a number describing how much a quantity changes going from an initial to a final value or one condition to another condition
Alejandra Gonzalez-Beltran
Philippe Rocca-Serra
fold change
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
An object property that specifies that a party governs the approval of a resource.
References to which parties approve an entity.
A super-property of governance properties: 'approves', 'gives concurrence for', 'reviews' and 'witness to'.
A pointer to who is responsible for the governance of some entity of interest. This is a two-way reference with the inverse property 'governs'.
Image is a class for figures, pictures, logos, and icons of various kinds
The property 'vaem:image' points to an image using a URL.
Height is typically used to specify an image's height attribute.
A property to reference an image that is used as a logo.
A short description, typically used on a table or a figure.
Width is typically used to specify an image's width attribute.
The Early Detection Research Network (EDRN), an initatve of the National Cancer Institute (NCI), brings together dozens of institutions to help accelerate the translation of biomarker information into clinical applications and to evaluate new ways of testng cancer in its earliest stages and for cancer risk.
The Food and Drug Administration (FDA) is an agency within the U.S. Department of Health and Human Services. It consists of the Office of the Commissioner and four directorates overseeing the core functions of the agency: Medical Products and Tobacco, Foods and Veterinary Medicine, Global Regulatory Operations and Policy, and Operations.
A gene alteration that causes or predisposes an individual to a specific disease.
Prediction of the probable course and outcome of a disease.
The likely outcome or course of a disease; the chance of recovery or recurrence.
An extrapolation of given data into the future.
The investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms; also, the scientific determination of any kind; the concise results of such an investigation.
The process of identifying a disease, such as cancer, from its signs and symptoms.
An estimated probability that one or more adverse event(s) will occur as a result of exposure to an actual or potential hazardous situation or chemical.
A process used to estimate the risk that a certain event will happen. In medicine, this may include a person's risk of having a child with a certain condition or disease, such as cancer. It may also be used to estimate the risk of carrying a certain gene mutation (change), or of having an adverse event (unexpected medical problem) in response to certain types of drugs or other substances. A risk assessment may be done by collecting information about a person's age, sex, personal and family medical history, ethnic background, lifestyle, and other factors and using statistics tools to calculate risk.
Use of a device, marker, or other means for the purpose of detecting the presence of a tumor early in its development.
The constitutional or inborn state disposing to a disease, group of diseases, or metabolic or structural anomaly.
The National Cancer Institute (NCI) reference terminology and ontology. NCI Thesaurus (NCIt) provides controlled terminology for clinical care, translational and basic research, public dissemination of information and associated administrative activities. NCIt is updated monthly to support precise coding of data based on the most recent developments in the cancer and biomedical research community. NCIt has rich textual and formal logic descriptions of biomedical concepts, including full text definitions, synonyms, a true is_a taxonomic structure, polyhierarchy, inferred partonomy, and other features that make it suitable for supporting accurate human understanding and complex computer processing. NCIt has been produced by NCI Enterprise Vocabulary Services (EVS) since 1997, and adopted since then for use by numerous federal agencies, standards development and research organizations.
In statistics, a number that expresses the probability that the result of a given experiment or study could have occurred purely by chance. This number can be a margin of error or it can indicate a confidence level.
A structure found in the nucleus of human cells that is comprised of a strand of linearized double-stranded DNA plus proteins that package the DNA in a condensed coil form and regulate chromosomal function.
Normal human somatic cells have 23 pairs of chromosomes.
The designation for each member of the largest human autosomal chromosome pair. Chromosome 1 spans about 247 million nucleotide base pairs and represents about 8% of the total DNA in normal diploid cells.
The designation for each member of the second largest human autosomal chromosome pair. Chromosome 2 spans more than 237 million base pairs and represents almost 8% of the total DNA in normal diploid cells.
The designation for each member of the third largest human autosomal chromosome pair. Chromosome 3 spans almost 200 million base pairs and represents about 6.5% of the total DNA in normal diploid cells.
The designation for each member of the fourth largest human autosomal chromosome pair. Chromosome 4 spans more than 186 million base pairs and represents between 6 and 6.5% of the total DNA in normal diploid cells.
The designation for each member of the fifth largest human autosomal chromosome pair. Chromosome 5 spans about 181 million base pairs and represents almost 6% of the total DNA in normal diploid cells.
The designation for each member of the sixth largest human autosomal chromosome pair. Chromosome 6 spans more than 170 million base pairs and represents between 5.5 and 6% of the total DNA in normal diploid cells.
The designation for each member of the seventh largest human autosomal chromosome pair. Chromosome 7 spans more than 158 million base pairs and represents between 5 and 5.5% of the total DNA in normal diploid cells.
The designation for each member of the eighth largest human autosomal chromosome pair. Chromosome 8 spans about 145 million base pairs and represents between 4.5 and 5.0% of the total DNA in normal diploid cells.
The designation for each member of the ninth largest human autosomal chromosome pair. Chromosome 9 spans about 145 million base pairs of nucleic acids and represents between 4 and 4.5% of the total DNA in normal diploid cells.
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.
The designation for each member of the tenth largest human autosomal chromosome pair. Chromosome 10 spans about 135 million base pairs and represents between 4 and 4.5% of the total DNA in normal diploid cells.
The designation for each member of the eleventh largest human autosomal chromosome pair. Chromosome 11 spans about 134.5 million base pairs and represents between 4 and 4.5% of the total DNA in normal diploid cells.
The designation for each member of the twelfth largest human autosomal chromosome pair. Chromosome 12 spans about 143 million base pairs and represents between 4 and 4.5% of the total DNA in normal diploid cells.
The designation for each member of the thirteenth largest human autosomal chromosome pair. Chromosome 13 spans about 113 million base pairs and represents between 3.5 and 4% of the total DNA in normal diploid cells.
The designation for each member of the fourteenth largest human autosomal chromosome pair. Chromosome 14 spans about 105 million base pairs and represents between 3 and 3.5% of the total DNA in normal diploid cells.
The designation for each member of the fifteenth largest human autosomal chromosome pair. Chromosome 15 spans about 106 million base pairs and represents between 3 and 3.5% of the total DNA in normal diploid cells.
The designation for each member of the sixteenth largest human autosomal chromosome pair. Chromosome 16 spans about 90 million base pairs and represents just under 3% of the total DNA in normal diploid cells.
The designation for each member of the seventeenth largest human autosomal chromosome pair. Chromosome 17 spans more than 81 million base pairs and represents between 2.5 and 3% of the total DNA in normal diploid cells.
The designation for each member of the eighteenth largest human autosomal chromosome pair. Chromosome 18 spans about 76 million base pairs and represents about 2.5% of the total DNA in normal diploid cells.
The designation for each member of the nineteenth largest human autosomal chromosome pair. Chromosome 19 spans more than 63 million base pairs and represents between 2 and 2.5% of the total DNA in normal diploid cells.
The designation for each member of the third smallest human autosomal chromosome pair. Chromosome 20 spans around 63 million base pairs and represents between 2 and 2.5% of the total DNA in normal diploid cells.
The designation for each member of the second smallest human autosomal chromosome pair. Chromosome 21 spans around 47 million nucleotides and represents about 1.5% of the total DNA in normal diploid cells.
The designation for each member of the smallest human autosomal chromosome pair. Chromosome 22 spans about 49 million base pairs and represents between 1.5 and 2% of the total DNA in normal diploid cells.
The sex chromosome that is present in both sexes: singly in males and doubly in females.
The y-shaped sex chromosome. In mammals, its presence or absence determines male or female sex.
A companion diagnosis is a diagnostic test that provides essential information for the safe and effective use of a corresponding drug or biological product. The test helps a health care professional determine whether a particular therapeutic product’s benefits to patients will outweigh any potential serious side effects or risks.
This term should be suggested as part of the NCI thesaurus.
has broader match
If 'concept A has-broad-match concept B' then the set of resources properly indexed against concept A is a subset of the set of resources properly indexed against concept B.
skos:broadMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes.
Broader concepts are typically rendered as parents in a concept hierarchy (tree).
has broader
Relates a concept to a concept that is more general in meaning.
By convention, skos:broader is only used to assert an immediate (i.e. direct) hierarchical link between two conceptual resources.
has broader transitive
skos:broaderTransitive is a transitive superproperty of skos:broader.
By convention, skos:broaderTransitive is not used to make assertions. Rather, the properties can be used to draw inferences about the transitive closure of the hierarchical relation, which is useful e.g. when implementing a simple query expansion algorithm in a search application.
has close match
skos:closeMatch is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, skos:closeMatch is not declared to be a transitive property.
skos:exactMatch is disjoint with each of the properties skos:broadMatch and skos:relatedMatch.
has exact match
skos:exactMatch is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch.
These concept mapping relations mirror semantic relations, and the data model defined below is similar (with the exception of skos:exactMatch) to the data model defined for semantic relations. A distinct vocabulary is provided for concept mapping relations, to provide a convenient way to differentiate links within a concept scheme from links between concept schemes. However, this pattern of usage is not a formal requirement of the SKOS data model, and relies on informal definitions of best practice.
is in mapping relation with
Relates two concepts coming, by convention, from different schemes, and that have comparable meanings
has narrower match
If 'concept A has-narrow-match concept B' then the set of resources properly indexed against concept A is a superset of the set of resources properly indexed against concept B.
skos:narrowMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes.
Narrower concepts are typically rendered as children in a concept hierarchy (tree).
has narrower
Relates a concept to a concept that is more specific in meaning.
has narrower transitive
skos:narrowerTransitive is a transitive superproperty of skos:narrower.
By convention, skos:narrowerTransitive is not used to make assertions. Rather, the properties can be used to draw inferences about the transitive closure of the hierarchical relation, which is useful e.g. when implementing a simple query expansion algorithm in a search application.
skos:related is disjoint with skos:broaderTransitive
has related
Relates a concept to a concept with which there is an associative semantic relationship.
has related match
skos:relatedMatch is used to state an associative mapping link between two conceptual resources in different concept schemes.
is in semantic relation with
Links a concept to a concept related by meaning.
This property should not be used directly, but as a super-property for all properties denoting a relationship of meaning between concepts.
Concept Scheme
A set of concepts, optionally including statements about semantic relationships between those concepts.
Thesauri, classification schemes, subject heading lists, taxonomies, 'folksonomies', and other types of controlled vocabulary are all examples of concept schemes. Concept schemes are also embedded in glossaries and terminologies.
A concept scheme may be defined to include concepts from different sources.
is in scheme
Relates a resource (for example a concept) to a concept scheme in which it is included.
A concept may be a member of more than one concept scheme.
Concept
An idea or notion; a unit of thought.
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 :Document class groups together all publications which were created to be distributed and consumed as individual, self-contained entities.
Document
The :Component class groups together all individuals that normally come into existence as part of a :Document.
Component
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 :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 :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 :Concept class groups together all individuals which do not exist in the physical world (i.e. have no extension in spacetime).
The :Thing class groups together all individuals used by Macmillan Science and Education within the NPG publishing world.
Thing
A sub property of instrument. An object used (but not consumed) when performing instructions or a direction.
The object that helped the agent perform the action. e.g. John wrote a book with a pen.
An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle
has_exact_synonym
A relation between a class and an alias term.
Note that this should be a super-property of hasRelatedSynonym, hasExactSynonym etc; however, we cannot state this and remain in OWL-DL
has_synonym
has_dbxref
An alias in which the alias is related the primary class name, but not necessarily broader or narrower. Example: cytochrome bc1 complex is a related synonym of ubiquinol-cytochrome-c reductase activity; virulence is a related synonym of pathogenesis
has_related_synonym