ACR Harmonized Data Model
LinkML Schema for ACR Harmonized Data.
URI: https://anvilproject.org/acr-harmonized-data-model
Name: acr-harmonized-data-model
Classes
| Class | Description |
|---|---|
| Thing | Highest Level Class |
| AccessControlledRecord | Element for which specific access control restrictions apply. |
| Aliquot | Specific tubes or details of a Sample. |
| BiospecimenCollection | Biospecimen Collection |
| Demographics | Basic participant demographics summary |
| Family | A group of individuals of some relation who are grouped together in the study. |
| FamilyMember | Designates a Subject as a member of a family with some specified role. |
| FamilyRelationship | A relationship between two Subjects. |
| File | File |
| Sample | Biospecimen data |
| SourceData | Reference to submitted data used to generate harmonized data. Applying the query_parameter(s) to the data_source.parameterized_query should return the specific data of interest. |
| Subject | This entity is the subject about which data or references are recorded. |
| SubjectAssertion | Assertion about a particular Subject. May include Conditions, Measurements, etc. |
| AccessPolicy | Describes the access required for a given element of data. |
| DataSource | Query configuration for specifying a source from which data are pulled. |
| FileMetadata | Metadata about the contents of the file. |
| Study | Study Meta Data |
Slots
| Slot | Description |
|---|---|
| access_policy_code | Access Policy Code |
| age_at_assertion | The age in decimal years of the Subject when the assertion was made. |
| age_at_collection | The age at which this biospecimen was collected in decimal years. |
| age_at_event | The age in decimal years of the Subject at the time point which the assertion describes, |
| age_at_last_vital_status | Age at last vital status in decimal years. |
| age_at_resolution | The age in decimal years of the Subject when the asserted state was resolved. |
| aliquots | Aliquot(s) from this Sample. |
| assertion_type | The semantic type of the resource, eg, Condition. |
| availablity_status | Can this Sample be requested for further analysis? |
| biospecimen_collection | Biospecimen Collection that generated this sample. |
| code | The structured term defining the meaning of the assertion. |
| concentration_number | What is the concentration of the analyte in the Aliquot? |
| concentration_unit | Units associated with the concentration of the analyte in the Aliquot? UCUM coding preferred (with curie, UCUM) |
| consanguinity | Is there known or suspected consanguinity in this study family? |
| data_access_type | Data Access Type |
| data_source | Defines the location of data and how to query it. |
| data_type | The type of data within this file. |
| date_of_birth | Date at which the individual was born. May be impacted by privacy rules described in date_of_birth_type. |
| date_of_birth_type | Privacy rule modification applied to date_of_birth. |
| description | Description |
| disease_limitation | Disease Use Limitations |
| display | The friendly display string of the coded term |
| drs_uri | DRS location to access the data. |
| ethnicity | Reported ethnicity as defined by the 1997 OMB directives. |
| ethnicity_display | The friendly display string of the coded term for Ethnicity |
| external_id | Other identifiers for this entity, eg, from the submitting study or in systems link dbGaP |
| family_description | Free title describing the study family, such as potential inheritance or details about consanguinity |
| family_member | The family member Subject who is the relationship "subject". |
| family_members | The Subjects who are included in this family and their roles. |
| family_relationships | Family relationships associated with this family. |
| family_role | The "role" of this individual in this family. Could include terms like "proband", "mother", etc. |
| family_study_focus | What is this study family investigating? EG, a specific condition. The code should be prefixed with a recognizable curie. |
| family_type | Describes the 'type' of study family, eg, trio. |
| file_metadata | Additional metadata about the contents of the file, eg, genome reference build. |
| filename | The name of the file. |
| format | The format of the file. |
| funding_source | Funding Source |
| google_data_project | The Google Data Project needed to query this snapshot in BigQuery. |
| has_access_policy | Which access policy applies to this element? |
| has_assertion | Which assertions are made about this Subject? |
| has_demographics | A demographic summary of the participant. |
| has_sample | Which samples were collected or processed for this Subject? |
| id | ID associated with a class |
| in_study | With which study is this class associated? |
| laterality | Laterality information for the site |
| method | The approach used to collect the biospecimen. |
| organism_type | Organism Type Label |
| other_family_member | The family member Subject for the relationship "object". |
| parameterized_query | A parameterized query that contains the primary key fields and can be used to select specific rows. This should be formatted according to (https://cloud.google.com/bigquery/docs/parameterized-queries)[BigQuery instructions], including using named parameters. |
| parent_sample | Sample from which this sample is derived |
| parent_study_id | Parent Study ID |
| principal_investigator | Principal Investigator |
| processing | Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded this distinct sample |
| quantity_number | The total quantity of the specimen |
| quantity_units | The structured term defining the units of the quantity. |
| query_parameter | One or more query parameters used to select the specific row. It will leverage the parameterized_query defined by a data_source. This should be formatted according to (https://cloud.google.com/bigquery/docs/parameterized-queries)[BigQuery instructions], specifically the bq CLI version with named parameters, ie, " |
| race | Reported race as defined by the 1997 OMB directives. |
| race_display | The friendly display string of the coded term(s) for Race |
| relationship_code | Code definting the relationship predicate. Relationship of the "Family Member" to the "Other Family Member" (i.e. mother, father, etc). Code must be from the HL7 FamilyMember ValueSet |
| sample | The Samples(s) used to generate data in this file. |
| sample_type | Type of material of which this Sample is comprised |
| sex | Sex of the individual |
| sex_display | The friendly display string of the coded term for Sex |
| site | The location of the specimen collection. |
| size | Size of the file, in Bytes. |
| snapshot_dataset | The Dataset within BigQuery where the table can be queried. |
| snapshot_id | The Terra Data Repository Snapshot ID. |
| source_data | The sources from which this assertion was derived |
| spatial_qualifier | Any spatial/location qualifiers |
| storage_method | Sample storage method, eg, Frozen or with additives |
| study_title | Study Title |
| subject | The Subject(s) which this file describes. |
| subject_type | Type of entity this record represents |
| table | The table in the dataset that contains the row of interest. |
| value_code | The structured term defining the value of the assertion. |
| value_display | The friendly display string of the coded term for the value of the assertion. |
| value_number | The numeric value of the assertion. |
| value_units | The structured term defining the units of the value. |
| value_units_display | The friendly display string of units of the value. |
| vital_status | Vital Status |
| website | Website |
Enumerations
| Enumeration | Description |
|---|---|
| EDAMDataTypes | Data types from the EDAM ontology. |
| EDAMFormats | Data formats from the EDAM ontology. |
| EnumAccessCode | Type of research use case allowed |
| EnumAccessType | Type of access controls applied |
| EnumAssertionType | Provides options to describe the expressed semantics of a condition. |
| EnumAvailabilityStatus | Is the Thing available for use? |
| EnumConditionAssertion | Enumerations for Condition Assertion |
| EnumConditionCode | Recommended ontologies include: SNOMED_CT, HP, OMIM and ORPHA, prefixed with those curies SNOMED : https://bioregistry.io/registry/snomedct HP : https://bioregistry.io/registry/hp OMIM : https://bioregistry.io/registry/omim ORPHA : https://bioregistry.io/registry/orphanet |
| EnumConsanguinityAssertion | Asserts known or suspected consanguinity in this study family |
| EnumDateOfBirthType | Privacy rules that may modify a date value. |
| EnumEthnicity | OMB Codes describing Hispanic or Latino ethnicity. |
| EnumFamilyType | Enumerations describing research family type |
| EnumLaterality | Laterality information for the site |
| EnumRace | OMB Codes describing race. |
| EnumSampleCollectionMethod | The approach used to collect the biospecimen. Recommend ontology: LOINC. |
| EnumSex | Terms describing an individual's sex. |
| EnumSite | The location of the specimen collection. Recommended ontology: SNOMED Body Site |
| EnumSpatialQualifiers | Any spatial/location qualifiers. |
| EnumSubjectType | Types of entities |
| EnumVitalStatus | Is the entity living? |
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 specification |
| 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. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. |
| Jsonpointer | A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. |
| 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. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. |
| String | A character string |
| Time | A time object represents a (local) time of day, independent of any particular day |
| Uri | a complete URI |
| Uriorcurie | a URI or a CURIE |
Subsets
| Subset | Description |
|---|---|