BioData Catalyst Harmonized Model (bdchm)
This is the harmonized data model for use in the BioData Catalyst project.
URI: https://w3id.org/nhlbidatastage/bdchm
Name: bdchm
Classes
| Class | Description |
|---|---|
| Entity | Any resource that has its own identifier |
| BiologicProduct | A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. |
| BodySite | A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. |
| Condition | Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. |
| Consent | An entity that can be used to capture consent code and other relevant data about consent for a study. |
| Demography | Demographics about an individual or animal receiving care or other health-related services. |
| DimensionalObservation | A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. |
| DimensionalObservationSet | A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). |
| Document | A collection of information intented to be understood together as a whole, and codified in human-readable form. |
| Organization | A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. |
| Participant | A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject’s privacy. |
| Person | Administrative information about an individual or animal receiving care or other health-related services. |
| Quantity | A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. |
| Questionnaire | A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) |
| QuestionnaireItem | QuestionnaireItem defines a question or section within the Questionnaire |
| QuestionnaireResponse | QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) |
| ResearchStudy | A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. |
| Specimen | Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. |
| SpecimenContainer | A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) |
| SpecimenCreationActivity | The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). |
| SpecimenProcessingActivity | An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. |
| SpecimenQualityObservation | A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. |
| SpecimenQuantityObservation | A structured object that describes a single data item about the quantity of an entity, as generated through a point-in-time observation or measurement. |
| SpecimenStorageActivity | An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the |
| intrinsic physical nature of a specimen. | |
| SpecimenTransportActivity | An activity through which a specimen is transported between locations or organizations. |
| Substance | A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. |
| TimePoint | A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. |
| Visit | Events where Persons engage with the healthcare system for a duration of time. They are often also called “Encounters”. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) |
| Identifier | An Identifier is associated with a unique object or entity within a given system. |
| QuestionnaireResponseItem | QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) |
| QuestionnaireResponseValue | Single-valued answer to the question. (FHIR) |
| QuestionnaireResponseValueBoolean | Single-valued boolean answer to the question |
| QuestionnaireResponseValueDecimal | Single-valued decimal answer to the question |
| QuestionnaireResponseValueString | Single-valued string answer to the question |
| ResearchStudyCollection | A holder for ResearchStudy objects |
| TimePeriod | A period of time between a start and end time point. |
Slots
| Slot | Description |
|---|---|
| activity_type | The high-level type of creation activity |
| additive | A material substance added to the container (typically to support the primary... |
| age_at_condition_end | The Participant's age (expressed in days) when the condition was recorded as ... |
| age_at_condition_start | The Participant's age (expressed in days) when the condition was first record... |
| age_at_death | The age of an individual at the time of death, expressed in days since birth |
| age_at_enrollment | The age in days when the Participant enrolled on the ResearchStudy |
| age_at_response | The age (in days) of the Participant when the QuestionnaireResponse was captu... |
| age_at_visit_end | The age of the Participant (in days) at the end of the Visit |
| age_at_visit_start | The age of the Participant (in days) at the start of the Visit |
| alias | A secondary name for the organization such as a short name or abbreviation (e |
| analyte_type | For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), th... |
| associated_participant | A reference to the Participant that is associated with this record |
| associated_person | A reference to the Person that is associated with this record |
| associated_timepoint | A collection of timepoint observations that are relevant to research projects... |
| associated_visit | A reference to the Visit during which this QuestionnaireResponse was captured |
| breed | A label given to a group of animals homogeneous in appearance and other chara... |
| category | The general category of observation described |
| cause_of_death | Coded value indicating the circumstance or condition that results in the deat... |
| cellular_composition_type | A term describing the type of cell or cellular material comprising a specimen |
| code | Corresponding concept for this item in a terminology |
| collection_method_type | The type of method applied in collecting a sample from its original source |
| collection_site | The anatomic site from which a specimen was collected |
| condition_concept | The coded value for the presence of a disease or medical condition stated as ... |
| condition_provenance | A value representing the provenance of the Condition record |
| condition_status | A value indicating whether the medical condition described in this record is ... |
| consent_code | Data Use Restrictions that are used to indicate permissions/restrictions for ... |
| consents | Data Use Restrictions that are used to indicate permissions/restrictions for ... |
| contained_in | A physical container in which a specimen is presently held or attached - as ... |
| container | A container in which the specimen is held or affixed during its storage |
| container_number | Informal number by which the container is referenced or identified (e |
| container_type | The kind of the container |
| copyright | Textual description of any use and/or publishing restrictions |
| copyright_label | Copyright holder and year(s) |
| creation_activity | The activity through which a specimen was created, by removing material from ... |
| date_ended | The date when the research project ended |
| date_started | The date when the research project began |
| date_time | An explicitly specified timepoint described in terms of a date and optionally... |
| derivation_method_type | The type of method applied to derive a new specimen from an existing one |
| derived_product | A 'living' biologically active product that was derived from the specimen (e |
| description | A free text field to capture additional info/explanation about the research s... |
| description_shortened | An abbreviated description of a research program, project, or study |
| dimensional_measures | Observations about the current physical dimensions of an object (e |
| document_type | The high-level type of the document (e |
| duration | The length of time over which the activity was performed |
| entries | |
| ethnicity | An individual's self-described social and cultural grouping, specifically whe... |
| event_type | An event that occurred at the point in time specified by this TimePoint |
| focus | The entity that the report is primarily about |
| growth_rate | When the specimen an actively growing model system, such as a cell or tissue ... |
| has_questionnaire_item | A reference to the QuestionnaireItem that this QuestionnaireResponseItem resp... |
| id | The 'logical' identifier of the entity within the system of record |
| identity | A 'business' identifier or accession number for the entity, typically as prov... |
| index_time_point | Another TimePoint from which this point is offset |
| index_timepoint | The text term used to describe the reference or anchor date used for date obf... |
| items | A collection of QuestionnaireItem objects which encapsulate the question bein... |
| language | The language(s) in which questions are presented |
| member_of_research_study | A reference to the Study(s) of which this Participant is a member |
| method_type | A type of method used in generating the Observation result |
| name | An unabridged name of a research program, project, or study |
| name_shortened | An abbreviated name of a research program, project, or study |
| observation_type | The specific type of observation made - i |
| observations | A set of one or more more atomic observations that are conceptually or logica... |
| offset_from_index | A quantity of time that, together with the index date or event, can be used t... |
| organization_type | The type of the organization (e |
| originating_site | The Organization through which a subject was enrolled on a ResearchStudy |
| parent_container | A larger container of which this container is a part (e |
| parent_specimen | An existing specimen from which the specimen of interest was directly derived... |
| part_of | A reference to a parent ResearchStudy (e |
| passage_number | When the specimen an actively growing model system, such as a cell or tissue ... |
| performed_by | The organization or group that performed the activity |
| period_end | When a period of time ended |
| period_start | When a period of time started |
| principal_investigator | The investigator or investigators leading a project |
| processing_activity | An activity that modifies the physical structure, composition, or state of a ... |
| product_type | The high level type of model system (e |
| publisher | Name of the publisher/steward (organization or individual) of this Questionna... |
| qualifier | A qualifier that further refines or specifies the location of the body site -... |
| quality_measure | An observation about characteristics of a specimen that are indicative of its... |
| quantity_collected | The quantity of material in the specimen as originally collected from its ori... |
| quantity_measure | An observation related to the present quantity of a specimen - e |
| race | An arbitrary classification of a taxonomic group that is a division of a spec... |
| related_document | A reference to an external document that is about or related to the specimen ... |
| relationship_to_participant | A value indicating the relationship between the Participant to which the Cond... |
| research_project_type | The 'type' of ResearchStudy represented (e |
| response_value | |
| role | A role played by the substance in a particular application (e |
| section_location | The location in a parent specimen from which a section/portion was excised (e |
| sex | The biologic character or quality that distinguishes male and female from one... |
| site | A term describing any site in the body |
| source_material_type | The general kind of material from which the specimen was derived |
| source_participant | A specific Subject from which the specimen was directly or indirectly derived |
| species | The scientific binomial name for the species of the Person (e |
| specimen_order | A numeric value that represents the sequential order of this creation activit... |
| specimen_type | The high-level type of the specimen, based on its derivation provenance (i |
| sponsor | An entity that is responsible for the initiation, management, and/or financin... |
| storage_activity | An activity that results in the storage or maintenance of a specimen in a par... |
| study_arm | The arm(s) of the study on which the Participant is enrolled |
| substance_quantity | The quantity of substance this instance stands for |
| substance_type | The specific type of the substance - at as granular a level as possible |
| system | The system or namespace that defines the identifier |
| text | Name for group or question text |
| title | Name for this Questionnaire (human friendly) |
| transport_activity | An activity through which the specimen is transported between locations |
| transport_destination | An organization (facility, site, lab, etc) to which the specimen is delivered... |
| transport_origin | An organization (facility, site, lab, etc) from which the specimen was transp... |
| type | |
| unit | A coded or free text (in the |
| url | A URL address for a resource that provides information about a research progr... |
| valid_from | The point in time from which the consent record is valid |
| valid_to | The point in time after which the consent record is invalid |
| value | A general slot to hold a value |
| value_concept | A coded value representing a quantity (e |
| value_decimal | An amount, in the given units (if specified) |
| value_quantity | The result of the observation, encoded as a free-text Quantity |
| version | The identifier that is used to identify this version of the questionnaire whe... |
| visit_category | A value representing the kind (or category) of visit, like inpatient or outpa... |
| visit_provenance | A value representing the provenance of the visit record, or where the record ... |
| vital_status | Coded value indicating the state or condition of being living or deceased; al... |
| year_of_birth | Numeric value to represent the calendar year in which an individual was born |
| year_of_death | Numeric value to represent the calendar year in which an individual died |
Enumerations
| Enumeration | Description |
|---|---|
| AnalyteTypeEnum | |
| CellularOrganismSpeciesEnum | A constrained set of enumerative values containing the NCBITaxon values for c... |
| ConditionConceptEnum | A constrained set of enumerative values containing both the MONDO values for ... |
| ConditionProvenanceEnum | A constrained set of enumerative values containing the OMOP values for visit ... |
| ConditionStatusEnum | A constrained set of enumerative values indicating whether a Condition is pre... |
| DataUseEnum | A constrained set of enumerative values drawn from the Data Use Ontology (DUO... |
| EthnicityEnum | A constrained set of enumerative values containing the United States Office o... |
| HpoPhenotypicAbnormalityEnum | A constrained set of enumerative values containing the HPO values for phenoty... |
| MondoHumanDiseaseEnum | A constrained set of enumerative values containing the MONDO values for human... |
| RaceEnum | A constrained set of enumerative values containing the United States Office o... |
| SectionLocationEnum | The location in a parent specimen from which a section/portion was excised |
| SexEnum | A constrained set of enumerative values containing the OMOP values for sex |
| SourceMaterialTypeEnum | |
| SpecimenCollectionMethodType | |
| SpecimenCreationActivityTypeEnum | The high-level type of activity through which the specimen was generated (i |
| SpecimenProcessingActivityTypeEnum | The high-level type of processing activity performed |
| SpecimenQualityObservationMethodEnum | A type of method used in determining the quantity of a specimen |
| SpecimenQualityObservationTypeEnum | Types of measurements that reflect the quality of a specimen or its suitabili... |
| SpecimenQuantityObservationTypeEnum | Measures related to the quantity of a specimen or analyte it currently contai... |
| SpecimenTypeEnum | A high-level type of specimen, based on its derivation provenance (i |
| VertebrateBreedEnum | A constrained set of enumerative values containing the VBO values for vertebr... |
| VisitCategoryEnum | A constrained set of enumerative values containing the OMOP values for visit ... |
| VisitProvenanceEnum | A constrained set of enumerative values containing the OMOP values for visit ... |
| VitalStatusEnum | A constrained set of enumerative values containing the OMOP values for vital ... |
Types
| Type | Description |
|---|---|
| Boolean | A binary (true or false) value |
| Curie | a compact URI |
| Date | a date (year, month and day) in an idealized calendar |
| DateOrDatetime | Either a date or a datetime |
| Datetime | The combination of a date and time |
| Decimal | A real number with arbitrary precision that conforms to the xsd:decimal speci... |
| Double | A real number that conforms to the xsd:double specification |
| Float | A real number that conforms to the xsd:float specification |
| Integer | An integer |
| Jsonpath | A string encoding a JSON Path |
| Jsonpointer | A string encoding a JSON Pointer |
| Ncname | Prefix part of CURIE |
| Nodeidentifier | A URI, CURIE or BNODE that represents a node in a model |
| Objectidentifier | A URI or CURIE that represents an object in the model |
| Sparqlpath | A string encoding a SPARQL Property Path |
| String | A character string |
| Time | A time object represents a (local) time of day, independent of any particular... |
| Uri | a complete URI |
| Uriorcurie | a URI or a CURIE |
Subsets
| Subset | Description |
|---|---|