| Definition | |
|---|---|
| Analysis process analysis_process |
Any act of analysis, broadly construed, of a subject. To include identification, observation, etc. (NCIT:C25391) |
| Anatomical entity 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. (UBERON:0001062) |
| Antibody antibody |
A molecule or other chemical species exhibiting reactivity with a specific target antigen. Especially when the antigen presence is temporally prior or naturally occurring, and the antibody presence is naturally-induced (as in an immune response) or is deliberately introduced (as in histological staining). |
| Assay assay |
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. (OBI:0000070) |
| Assay result assay_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'. (OBI:0001909) |
| Author author |
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. (IAO:0000442) |
| Author rank author_rank |
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. |
| Biological marking system biological_marking_system |
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. (OBI:0003146) |
| Biological species biological_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). |
| Biospecimen biospecimen |
A portion (or, more rarely, the whole) of an organism prepared to be an object of study, observation, measurement, or analysis. (OBI:0100051) |
| Biospecimen collection process biospecimen_collection_process |
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. (OBI:0000659) |
| Biospecimen collection study biospecimen_collection_study |
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. (OBI:0000471) |
| Biospecimen data measurement process biospecimen_data_measurement_process |
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. (OBI:0000070) |
| Biospecimen data measurement study biospecimen_data_measurement_study |
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. (OBI:0000471) |
| Biospecimen event biospecimen_event |
An event pertaining to a biospecimen. A time in the duration span of the biospecimen. |
| Biospecimen preservation method biospecimen_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. (NCIT:C64262) |
| Cell phenotype cell_phenotype |
An in-principle observable character for a cell. Meant to be inclusive of potentially-transient cell states and more enduring cell types. (CL:0000000PHENOTYPE) |
| Cell phenotype criterion cell_phenotype_criterion |
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. |
| Chemical species chemical_species |
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. (CHEBI:60003) |
| Chemical species structure class chemical_species_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. (FMA:63887) |
| Communication contact reference communication_contact_reference |
An address for direction of communication, e.g. an email address, a mailing address, or a phone number. (NCIT:C70806) |
| Condition condition |
An an-principle empirically diagnosable condition of a subject. (BFO:0000016) |
| Continuant continuant |
See BFO. (BFO:0000002) |
| Coordinate shape specification coordinate_shape_specification |
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. (PATO:0000052) |
| Data analysis study data_analysis_study |
An effort, generally undertaken by a group of collaborating participants, to analyze data measurements. (OBI:0200000) |
| Data file data_file |
A concrete data artifact (byte string) whose contents represent the empirical-evidential component of a claim or claims about a given material entity. (IAO:0000027) |
| Diagnosis assessor diagnosis_assessor |
The person or agent who performs a given diagnosis. (NCIT:C48206) |
| Diagnosis event diagnosis_event |
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. (OGMS:0000073) |
| Diagnosis result 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'). (OGMS:0000073) |
| Diagnostic selection criterion diagnostic_selection_criterion |
A criterion for cohort selection on the basis of a diagnosis result. (OBI:0001755) |
| Discrete value 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. (OBI:0001930) |
| Evaluation evaluation |
Systematic, objective appraisal of the significance, effectiveness, and impact of activities or condition according to specified objectives and criteria. (NCIT:C25214) |
| Event date event_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. |
| Family name family_name |
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. (IAO:0020017) |
| Feature derivation method feature_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. (OBI:0001028) |
| Feature specification feature_specification |
An information content entity using enumerated specifiers to describe one from among several possible feature derivations. (OBI:0001892) |
| Feature specifier feature_specifier |
A specifier that is an enumerated part of some feature specification. |
| File file |
A concrete data artifact consisting of a particular byte string. |
| File basename file_basename |
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 content structure specification file_content_structure_specification |
A documented reference specification for a given class of files which provides a way to parse the semantic meaning of specification-compliant files. (IAO:0000098) |
| File hash SHA256 file_hash_sha256 |
The SHA256 hash (Secure Hash Algorithm 2, 256-bit digest) of the contents of a given digital file. (NCIT:C68725) |
| File size file_size |
The number of bytes in the byte string contents of a given digital file. (NCIT:C171192) |
| File syntax format file_syntax_format |
A class of file content structures delimited by rough structural criteria. Often indicated with a file extension. For example, comma-separated values (CSV). (NCIT:C171252) |
| Given name 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. (IAO:0020016) |
| Histological structure histological_structure |
An instance of an anatomical entity identifiable in tissue sections. For example, a cell, a stromal region, or a subcellular compartment like a nucleus. (UBERON:0000061) |
| Histological structure identification method histological_structure_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. (OBI:0000272) |
| Histological structure identification process histological_structure_identification_process |
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. (NCIT:C80146) |
| Histology assay histology_assay |
The assessment (e.g. of a histology slide) for a specific feature. For example, tumor grading. (OBI:0001896) |
| Histology assessment process histology_assessment_process |
A specific instance of performance of an histology assay by an assessor at a specific time. (OBI:0600020) |
| Histology slide histology_slide |
A biological specimen together with a supporting substrate on which it is mounted. Typically for the purpose of microscopy analysis. (OBI:0400170) |
| Identifier 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. (OPMI:0000413) |
| Institution institution |
An established society, corporation, foundation or other organization founded and united for a specific purpose, e.g. for health-related research. (NCIT:C41206) |
| Intervention intervention |
An activity that produces an effect, or that is intended to alter the course of a disease in a patient. (NCIT:C25218) |
| Investigation investigation |
A planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). (OBI:0000066) |
| Measurement apparatus measurement_apparatus |
A machine or tool used by an operator to make measurements of specific properties of subjects or specimens. (OBI:0000832) |
| Measurement apparatus software measurement_apparatus_software |
Software that runs on a computer linked to a measurement apparatus to control the measurement process or extract data results. (IAO:0000010) |
| Measurement assay measurement_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). (OBI:0500000) |
| Method of marker discretization method_of_marker_discretization |
The method by which the quantitative values of some property are cast into discrete values. For example, thresholding on the median over a collection. (STATO:0000213) |
| Method of marker quantification method_of_marker_quantification |
The method by which marker presence is quantified. For example, averaging of raster image intensity values over an image mask. (STATO:0000039) |
| 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. (IAO:0000590) |
| Open researcher and contributor identifier open_researcher_and_contributor_identifier |
A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistently identify oneself as a human researcher or contributor. (IAO:0000708) |
| Ordinality ordinality |
A data value that is an ordinal number, ie., a number that tells the position of something in a list. (OBCS:0000196) |
| Personal full name personal_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. (GSSO:001755) |
| Phenotypic sex phenotypic_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. (PATO:0000047) |
| Plane coordinates reference system plane_coordinates_reference_system |
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. (STATO:0000010) |
| Publication publication |
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. (IAO:0000312) |
| Publisher publisher |
The institution or organization which performs publication processes resulting in publications, i.e. which receives, accepts, and disseminates the document comprising the publications. (SIO:000885) |
| Quantification of chemical target expression quantification_of_chemical_target_expression |
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). (OBI:0003142) |
| Quantitative feature derivation process quantitative_feature_derivation_process |
An instance of quantification of a state or property of a subject which is carried out according to a given feature specification. |
| Research professional research_professional |
A person who performs research or a service that directly supports a research activity. (OBI:0000202) |
| Specifier specifier |
An identifier meant to be used in a limited context, for disambiguation between highly salient alternatives. |
| Statistical test statistical_test |
See OBI. (OBI:0000673) |
| Study component study_component |
A relation between a primary study and another study in which the latter is a component or part of the primary study. (BFO:0000050) |
| Study contact person study_contact_person |
A person who has responsibility for receiving general queries regarding the conduct of a given study. (NCIT:C25461) |
| Study subject study_subject |
A person, other organism, or biospecimen which is the subject of some study. (OBI:0000097) |
| Subspecimen extraction method subspecimen_extraction_method |
The method by which subspecimens are extracted from a source specimen. For example, fine-needle aspiration. (OBI:0001882) |
| Two-cohort feature association test two_cohort_feature_association_test |
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. (STATO:0000279) |
| 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. (UO:0000000) |