Expression quantification:
  def: An instance of determination of a quantity representing the amount of a chemical target present in a given specimen or structure, typically by means of a specific chemical marking ensemble rendering this amount as an observable quantity (e.g. immunofluoresence at a specific wavelength).
  Quantity: A real (dimensionless) numerical value representing an amount with respect to some unit.
  Unit: For a 1-dimensional quantifiable/measurable property forming an abstract additive number system, i.e. exhibiting a natural addition operation, a unit is a choice of reference value for the property. Such a choice determines a correspondence between the possible values of the property and the standard 1-dimensional coordinate space, the (dimensionless) real numbers.
  Quantification method: The method by which marker presence is quantified. For example, averaging of raster image intensity values over an image mask.
  Discrete value: An information-theoretic entity representing one from among several pre-defined mutually exclusive values for some property. Often derived from a classification of a quantitative value using thresholds. Often one of two pre-defined values, positive and negative.
  Discretization method: The method by which the quantitative values of some property are cast into discrete values. For example, thresholding on the median over a collection.
  Histological structure:
    def: The histological structure which is the domain for the given expression quantification process.
    Histological structure:
      def: An instance of an anatomical entity identifiable in tissue sections. For example, a cell, a stromal region, or a subcellular compartment like a nucleus.
      Identifier: A symbol string meant to correspond to exactly one member of a collection. Generally not a linguistic name for verbalization in natural language speech or text.
      Anatomical entity: A part of a structural body pattern consistently observed across a class of organisms. For example cell, nucleus, cytoplasm, membrane, stroma, epithelium, liver.
  Target:
    def: The chemical species which is quantified by a given process.
    Chemical species:
      def: A class of chemical objects, or specific mixture of such objects, defined by structural criteria at the molecular length scale. For example, iron, sodium chloride, keratin, or mRNA molecule coded as the BCL2 gene.
      Identifier: A symbol string meant to correspond to exactly one member of a collection. Generally not a linguistic name for verbalization in natural language speech or text.
      Symbol: A symbol string representation of the chemical species, or possibly a gene class of closely-related species (for example, BCL2 for a certain DNA segment, the corresponding mRNA molecule, and the corresponding protein product).
      Name: A symbol string meant to correspond to exactly one member of a collection, and generally also intended to be capable of verbalization in natural language speech or text.
      Chemical structure class: A common higher taxon for chemical species, for example mRNA, DNA, protein, lipid, hydrocarbon. Often meant to aid in distinctions between species closely related in an information-theoretic sense, e.g. the distinction between the BCL2 gene's mRNA molecule, DNA segment, or protein product.
Histological structure identification:
  def: A specific instance of identification or delimitation of a histological structure in a slide by means of data measurements, e.g. imaging, resulting in a shape specification defined with respect to a plane coordinates reference system.
  Identification method: The method by which an annotator identifies or delimits histological structures, instances of an anatomical entity, in a histology slide. For example, manual marking on an image representation of the slide area, or a segmentation algorithm.
  Identification date: The time at which something happens. When represented by a string, the preferred format is ISO 8601-1:2019 (e.g. '1999-04-01' for April 1st in the year 1999), but this can also be represented as a timestamp or even a relative, ordinal value, so long as it is consistent across related records.
  Annotator: The person who identified a histological structure or operated software making such an identification.
  Histological structure: (ref)
  Data file:
    def: A concrete data artifact (byte string) whose contents represent the empirical-evidential component of a claim or claims about a given material entity.
    SHA256 hash: The SHA256 hash (Secure Hash Algorithm 2, 256-bit digest) of the contents of a given digital file.
    File name: The basename, i.e. without path information, for a file in some file system. A basename implicitly encoding information about the referents of file contents is not preferred; the SHA256 file hash is a reasonable choice of name convention which eschews implicit information (no SHA256 collisions are currently known).
    File format: A class of file content structures delimited by rough structural criteria. Often indicated with a file extension. For example, comma-separated values (CSV).
    Contents format: A documented reference specification for a given class of files which provides a way to parse the semantic meaning of specification-compliant files.
    Size: The number of bytes in the byte string contents of a given digital file.
    Source generation process:
      def: The measurement process which produced a given data file.
      Specimen data measurement process:
        def: A process in which a biospecimen is subject to measurement of some qualitative or quantitative feature, usually by means of some measurement apparatus, resulting in a data item or data items about the biospecimen.
        Identifier: A symbol string meant to correspond to exactly one member of a collection. Generally not a linguistic name for verbalization in natural language speech or text.
        Specimen age: The amount of time between the inception of a given biospecimen (typically extraction) and the given event. Typically denominated in number of days.
        Date of measurement: The time at which something happens. When represented by a string, the preferred format is ISO 8601-1:2019 (e.g. '1999-04-01' for April 1st in the year 1999), but this can also be represented as a timestamp or even a relative, ordinal value, so long as it is consistent across related records.
        Specimen:
          def: The biospecimen analyzed by an analysis process, in case the subject is a biospecimen.
          Specimen collection process:
            def: A process in which a biospecimen is retrieved from its natural environment or host and placed under control for observation and analysis. Typically the process consists of extraction of a subspecimen from a whole organism, or from another subspecimen, at a specific site, preservation using a specific protocol, and storage together with similar specimens collected as part of a study.
            Specimen: The subspecimen extracted during a given biospecimen collection process.
            Source: The biospecimen from which a subspecimen was extracted during the given specimen collection process.
            Source site: The location on the source specimen from which a subspecimen is extracted.
            Source age: The amount of time between the inception of a given biospecimen (typically extraction) and the given event. Typically denominated in number of days.
            Extraction date: The time at which something happens. When represented by a string, the preferred format is ISO 8601-1:2019 (e.g. '1999-04-01' for April 1st in the year 1999), but this can also be represented as a timestamp or even a relative, ordinal value, so long as it is consistent across related records.
            Specimen collection study:
              def: An effort, generally undertaken by a group of collaborating participants, to collect biospecimens of a particular type for the purpose of eventual observation/measurement and analysis. Typically initiated and concluded at specific times, but may be ongoing.
              Name: A symbol string meant to correspond to exactly one member of a collection, and generally also intended to be capable of verbalization in natural language speech or text.
              Extraction method: The method by which subspecimens are extracted from a source specimen. For example, fine-needle aspiration.
              Preservation method: A method of treatment of a biospecimen intended to preserve the structure and chemical composition which were present at the time immediately prior to extraction.
              Storage location: The location of storage of biospecimens during the period after collection but before measurement or analysis.
              Inception date: The initial date of the continuant's existence.
              Conclusion date: The final date of the continuant's existence.
        Specimen measurement study:
          def: An effort, generally undertaken by a group of collaborating participants, to make data measurements on a collection of biological specimens. Typically initiated and concluded at specific times, provided that the specimen collection study is complete.
          Name: A symbol string meant to correspond to exactly one member of a collection, and generally also intended to be capable of verbalization in natural language speech or text.
          Assay: The plan design for the assessment of a subject or specimen for a specific feature. Usually the feature is quantitative. Usually the feature is also epistemologically elementary, as contrasted with assessments involving extensive reasoned judgement (as in a full-fledged diagnosis).
          Machine: A machine or tool used by an operator to make measurements of specific properties of subjects or specimens.
          Software: Software that runs on a computer linked to a measurement apparatus to control the measurement process or extract data results.
          Inception date: The initial date of the continuant's existence.
          Conclusion date: The final date of the continuant's existence.
  Shape file:
    def: A concrete data artifact representing a specific shape in the standard reference dimensionless coordinate space of a given dimension (the standard Euclidean space). For example, a representation of the unit circle in the coordinate plane, a closed polygon with specific enumerated vertices, or a single point.
    Identifier: A symbol string meant to correspond to exactly one member of a collection. Generally not a linguistic name for verbalization in natural language speech or text.
    Geometry specification file format: The documented file format for a given shape specification file.
    Base64 contents: The Base64-encoded ASCII character string serialization of the file contents byte string. The encoding is specified by RFC 4648.
  Plane coordinates reference system:
    def: A correspondence between a specific two-dimensional material or spatial area (or class of such areas under specific conditions) and the standard two-dimensional coordinate space, in the special case of intrinsically-flat areas and correspondences which preserve distances up to an overall scale. Such a correspondence is determined uniquely by (i) a correspondence between just one reference point on the source and target, (ii) an indication of the direction of the first coordinate axis on the referent, (iii) the choice of one of the two possible directions of the remaining, second coordinate axis direction on the referent, and (iv) a choice of length scale, or unit.
    Name: A symbol string meant to correspond to exactly one member of a collection, and generally also intended to be capable of verbalization in natural language speech or text.
    Reference point: The description of a single point, on the object or area of focus, which serves as a reference point for establishing an orthogonal (Euclidean similarity) coordinate system.
    Reference point coordinate 1: The intended first coordinate value of the coordinate-space point corresponding to the reference point. For orthogonal (Euclidean similarity) coordinate systems.
    Reference point coordinate 2: The intended second coordinate value of the coordinate-space point corresponding to the reference point. For orthogonal (Euclidean similarity) coordinate systems.
    Reference orientation: The description of the direction, on the object or area of interest, intended to correspond to the first coordinate positive axis, plus a description of the choice of which of the two orthogonal directions is intended to correspond to the second coordinate positive axis.
    Length unit: A representation (e.g. 10 micrometers) of the length unit intended to correspond to the displacement in the coordinate space by the value 1. For orthogonal (Euclidean similarity) coordinate systems.
Diagnosis:
  def: The concluding event of an assessor's determination of the presence or absence of a specific condition in a subject. Often the determination is made on the basis of consideration of multiple factors.
  Condition: The condition considered during a process of diagnosis.
  Result: The empirical claim about a subject supported by an act of diagnosis (often epistemologically complex and multi-factorial). May be 'positive' or 'negative' for disease presence, or an indication of disease subtype presence (e.g. 'triple-negative' for the disease 'breast cancer').
  Assessor: The person or agent who performs a given diagnosis.
  Date: The date on which a diagnosis was made.
  Date of evidence: For an evaluation of activity or condition based on evidential factors of consideration, the most recent known date of creation of the evidence. If this date is accurately known, events after this date cannot bias the evaluation. For example, for a diagnosis based on a blood sample, X-rays, and a biopsy, if the blood sample was taken last, then the date of this sample is the maximal date of evidence.
  Subject:
    def: A person, other organism, or biospecimen which is the subject of some study.
    Identifier: A symbol string meant to correspond to exactly one member of a collection. Generally not a linguistic name for verbalization in natural language speech or text.
    Species: A collection of organisms whose members are related by a sequence of tokogenies (ancestry/descent), and for which the collection is maximal subject to the constraint it that does not span any speciation boundaries, i.e. temporal boundaries formed by allopatric, parapatric, or sympatric speciation events (Wheeler and Meier, 'Species Concepts and Phylogenetic Theory'). For example, Homo sapiens (humans), or Mus musculus (mice).
    Sex: The class of reproductive compatibility to which a given organism belongs, in case its biological species admits such classes (gonochoric species). As indicated by observable phenotypic information. For example, male, female, or intersex.
    Birth date: The date of inception, in the case of a biological subject.
    Death date: The date of conclusion, in the case of a biological subject.
    Cause of death: The most significant causative factor in the death of a given subject. Often but not always pertinent to the study of which the subject is a part, in the case of disease studies.
Biological marking system:
  def: An ensemble consisting of an antibody and its target antigen, intended to be used to elicit a specific observable reaction which indicates (marks) antigen presence, often in tissue specimens but also in individual cells or other biospecimens. Developed or selected for use in a given study.
  Identifier: A symbol string meant to correspond to exactly one member of a collection. Generally not a linguistic name for verbalization in natural language speech or text.
  Antibody: The antibody used in the given marker/staining system.
  Marking mechanism: The mechanism by which the given marker system renders the target antigen observable.
  Chemical species: (ref)
  Specimen measurement study: (ref)
Histology assessment process:
  def: A specific instance of performance of an histology assay by an assessor at a specific time.
  Assay: The assessment (e.g. of a histology slide) for a specific feature. For example, tumor grading.
  Result: The empirical claim about a subject supported by an assay analyzing that subject. When the assay type is binary (present or not present), the assay result is just assertion or non-assertion of the claim corresponding to the assay type (for example, an assay for the presence of a specific disease). In this case a common convention for the values is 'positive' or 'negative'.
  Assessor: The person or agent who performs a given assay.
  Assessment date: The time at which something happens. When represented by a string, the preferred format is ISO 8601-1:2019 (e.g. '1999-04-01' for April 1st in the year 1999), but this can also be represented as a timestamp or even a relative, ordinal value, so long as it is consistent across related records.
  Specimen collection process: (ref)
Two-cohort feature association test:
  def: An application of a statistical test for association between a given specified feature on a sample set and assignment to one of two cohorts defined by selection criteria.
  Test: See OBI.
  p-value: See OBI.
  Diagnostic selection criterion: (ref)
  Feature specification:
    def: An information content entity using enumerated specifiers to describe one from among several possible feature derivations.
    Identifier: A symbol string meant to correspond to exactly one member of a collection. Generally not a linguistic name for verbalization in natural language speech or text.
    Derivation method: The plan for a computational or experimental process that results in associations of quantitative (or, sometimes, qualitative) values to elements of a sample set. Often the associations involve an aggregation over finer-grained samples to a coarsest level of granularity, and are dependent on enumerated specifiers, like an ordered tuple of genes or image channels.
    Data analysis study:
      def: An effort, generally undertaken by a group of collaborating participants, to analyze data measurements.
      Name: A symbol string meant to correspond to exactly one member of a collection, and generally also intended to be capable of verbalization in natural language speech or text.
Cell phenotype criterion:
  def: A criterion which must be satisfied by a cell in order that it acquire the designation of a specific phenotype. Typically a suitable amount of membrane expression of a certain protein or other chemical species. The latter is often a Cluster of Differentiation (CD) protein, especially for immune cell phenotypes. The criteria used (and the phenotypes themselves) may depend on the specific data analysis study undertaken.
  Polarity: The value (typically positive or negative) stipulated by a given cell phenotype criterion.
  Cell phenotype:
    def: An in-principle observable character for a cell. Meant to be inclusive of potentially-transient cell states and more enduring cell types.
    Identifier: A symbol string meant to correspond to exactly one member of a collection. Generally not a linguistic name for verbalization in natural language speech or text.
    Symbol: A symbol string, not necessarily intended for verbalization in long-form speech or text, meant to summarize the intended meaning of a given cell phenotype. This is potentially an abbreviation of the full name.
    Name: A symbol string meant to correspond to exactly one member of a collection, and generally also intended to be capable of verbalization in natural language speech or text.
  Marker:
    def: The chemical species whose presence or absence is the substance of a given cell phenotype criterion.
    ref: Chemical species
  Data analysis study: (ref)
Quantitative feature value:
  def: An instance of quantification of a state or property of a subject which is carried out according to a given feature specification.
  Identifier: A symbol string meant to correspond to exactly one member of a collection. Generally not a linguistic name for verbalization in natural language speech or text.
  Subject: The entity that was subjected to the feature derivation or quantification process.
  Value: The quantity resulting from the quantification process.
  Feature:
    def: The specification for feature derivation which was used to carry out a given instance of quantification.
    ref: Feature specification
Research professional:
  def: A person who performs research or a service that directly supports a research activity.
  Full name: A full set of all personal names by which an individual is known and that can be recited as a word-group, with the understanding that, taken together, they all relate to that one individual.
  Surname: An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children.
  Given name: A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name.
  ORCID: A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistently identify oneself as a human researcher or contributor.
Study contact person:
  def: A person who has responsibility for receiving general queries regarding the conduct of a given study.
  Contact reference: An address for direction of communication, e.g. an email address, a mailing address, or a phone number.
  Research professional: (ref)
  Study:
    def: 'A planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).'
    Study specifier: A short name for the study meant mainly for human-readable reference which disambiguates against other studies in the context of a single database instance.
    Institution: The primary institution in which the investigation is carried out, which provides resources for the investigation, or which directs the conduct of the investigation.
Intervention:
  def: An activity that produces an effect, or that is intended to alter the course of a disease in a patient.
  Specifier: An identifier meant to be used in a limited context, for disambiguation between highly salient alternatives.
  Date: The date that a specific intervention was performed.
  Subject: (ref)
Author:
  def: A person who performed a substantial amount of the writing of a given publication, or otherwise performed investigation and related work responsible for the substance of the publication.
  Ordinality: The position of an author in the rank order of authors advertised by the publisher of a given publication, typically decided by the authors as an indication of level of contribution, but sometimes decided by other means (e.g. alphabetical order on names). Often the author in first position declare responsibility for communication regarding the work.
  Research professional: (ref)
  Publication:
    def: A document, i.e. a collection of information content entities intended to be understood together as a whole, which is the output of a publishing process and which is about an investigation.
    Title: A symbol string meant to correspond to exactly one member of a collection, and generally also intended to be capable of verbalization in natural language speech or text.
    Document type: See IAO.
    Publisher: The institution or organization which performs publication processes resulting in publications, i.e. which receives, accepts, and disseminates the document comprising the publications.
    Date of publication: The date on which the publication process was completed.
    Internet reference: A reference, typically a URL and often a DOI-formatted URL, that is issued by the publisher and refers to an at least partial digital representation of the publication.
    Study: (ref)
Feature specifier:
  def: A specifier that is an enumerated part of some feature specification.
  Specifier: An identifier meant to be used in a limited context, for disambiguation between highly salient alternatives.
  Ordinality: A data value that is an ordinal number, ie., a number that tells the position of something in a list.
  Feature specification: (ref)
Study component:
  def: A relation between a primary study and another study in which the latter is a component or part of the primary study.
  Primary study: The primary study of the component relation.
  Component study: The component study of the component relation.
