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Glossary: Data source requirements for CDE semantic model.

This is a glossary that describes what are the data requirements for our Common data element semantic model. Its mandatory that column names used maintained so YARRRML file can recognize the data references. FAIR-in-a-box is prepared to cover this implementation and obtain RDF based on this data glossary.

Birthdate:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • value: ISO 8601 formatted date (not date time)
  • model: Birthdate
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • comments: Human readable comments of any kind related to this procedure

Birthyear:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • value: Year of birth defined as YYYY.
  • model: Birthyear
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • comments: Human readable comments of any kind related to this procedure

Deathdate:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • value: ISO 8601 formatted date of death (not date time), or age in which the patient died.
  • value_datatype: XSD datatype that defines value column type.
    • xsd:date in case you added date.
    • xsd:integer in case you added age.
  • model: Deathdate
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • comments: Human readable comments of any kind related to this procedure

First Confirmed Visit:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • value: ISO 8601 formatted date of first confirmed visit (not date time) or age in case you added the age of the first confirmed visit.
  • value_datatype: XSD datatype that defines value column type.
    • xsd:date in case you added date.
    • xsd:integer in case you added age.
  • model: First_visit
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • comments: Human readable comments of any kind related to this procedure

Symptoms onset:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • model: Symptom_onset
  • value: ISO 8601 formatted date of symptom onset (not date time) or age in case you added the age of symptom onset. This value represent the onset perceived by the patient, as a difference of the clinical encounter, defined as startdate.
  • value_datatype: XSD datatype that defines value column type.
    • xsd:date in case you added date.
    • xsd:integer in case you added age.
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • comments: Human readable comments of any kind related to this procedure

Sex:

Participation status:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • valueIRI: one of the following:
  • model: Status
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • age: (OPTIONAL) Patient age when this observation was taken, this age information can be both an addition or an alternative for start/end date information.
  • comments: Human readable comments of any kind related to this procedure

Symptoms or signs:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • valueIRI: IRI that defines clinical symptom or sign: For example Human Phenotype ontology (HPO) term represented with a full URL such as http://purl.obolibrary.org/obo/HP_0001251
  • model: Symptom
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • age: (OPTIONAL) Patient age when the patient started to perceive the symptoms.
  • comments: Human readable comments of any kind related to this procedure

Diagnosis:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • valueIRI: IRI that defines clinical condition as disease or disorder: Orphanet disease ontology (ORDO) represented with a full URL such as http://www.orpha.net/ORDO/Orphanet_199630
  • model: Diagnosis
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • age: (OPTIONAL) Patient age when this observation was taken, this age information can be both an addition or an alternative for start/end date information.
  • comments: Human readable comments of any kind related to this procedure

Genetic information:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • valueIRI: Genetic code constructed by appending the HGVS/HGNC/OMIM code, e.g. https://www.omim.org/entry/310200
  • value: (OPTIONAL) Human readable label that defines the genetic identifier. Example: HNGC:489
  • model: Genetic
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • age: (OPTIONAL) Patient age when this observation was taken, this age information can be both an addition or an alternative for start/end date information.
  • comments: Human readable comments of any kind related to this procedure

Consent for being contacted:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • value: Some label describing consent outcome
  • value_datatype: XSD datatype that defines value column type, for this case is xsd:string by default
  • model: Consent_contacted
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • age: (OPTIONAL) Patient age when this observation ocurred, this age information can be both an addition or an alternative for start/end date information.
  • comments: Human readable comments of any kind related to this procedure

Consent for Data (Re)Use Permission:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • value: Some label describing consent outcome
  • value_datatype: XSD datatype that defines value column type, for this case is xsd:string by default
  • model: Consent_used
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • age: (OPTIONAL) Patient age when this observation ocurred, this age information can be both an addition or an alternative for start/end date information.
  • comments: Human readable comments of any kind related to this procedure

Biobank:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • agent_id: Biobank Identifier as https://directory.bbmri-eric.eu/{biobank id}
  • value_datatype: XSD datatype that defines value column type, for this case is xsd:string by default
  • model: Biobank
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • age: (OPTIONAL) Patient age when this observation ocurred, this age information can be both an addition or an alternative for start/end date information.
  • comments: Human readable comments of any kind related to this procedure

Disability:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • process_type: Some child of http://purl.obolibrary.org/obo/NCIT_C20993 (research or clinical assessment tool)
  • value_datatype: XSD datatype that defines value column type, for this case is xsd:float by default, but depending on your score's datatype, it could be different.
  • value: the numeric score of the output from the test
  • model: Disability
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • age: (OPTIONAL) Patient age when this observation ocurred, this age information can be both an addition or an alternative for start/end date information.
  • comments: Human readable comments of any kind related to this procedure

Body measurement:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • valueIRI: Child of Personal Attribute: http://purl.obolibrary.org/obo/NCIT_C19332
  • value: Resulting value from this observation
  • value_datatype: XSD datatype that defines value column type, for this case is xsd:float by default, but depending on your score's datatype, it could be different.
  • unit_type: Child of UO:unit http://purl.obolibrary.org/obo/UO_0000000
  • model: Body_measurement
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • age: (OPTIONAL) Patient age when this observation ocurred, this age information can be both an addition or an alternative for start/end date information.
  • comments: Human readable comments of any kind related to this procedure

Laboratory measurement:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • input_type: Material input represented as Child of Anatomic, Structure, System, or Substance http://purl.obolibrary.org/obo/NCIT_C12219 (ex: obo:Urine)
  • value: Resulting value from this analysis
  • value_datatype: XSD datatype that defines value column type, for this case is xsd:float by default, but depending on your score's datatype, it could be different.
  • target_type: Compound being measured in the sample. Child of Drug, Food, Chemical or Biomedical Material http://purl.obolibrary.org/obo/NCIT_C1908 (ex: obo:Creatinine http://purl.obolibrary.org/obo/NCIT_C399)
  • unit_type: Child of UO:unit http://purl.obolibrary.org/obo/UO_0000000
  • model: Lab_measurement
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • age: (OPTIONAL) Patient age when this observation ocurred, this age information can be both an addition or an alternative for start/end date information.
  • comments: Human readable comments of any kind related to this procedure

Imaging:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • process_type: child of Imaging technique http://purl.obolibrary.org/obo/NCIT_C17369 (example: obo:Digital X-Ray http://purl.obolibrary.org/obo/NCIT_C18001)
  • target_type: Child of Anatomic Structure, System, or Substance http://purl.obolibrary.org/obo/NCIT_C12219 (ex: obo:Palmar Region http://purl.obolibrary.org/obo/NCIT_C33252)
  • valueIRI: Preferably a URI-based GUID of the file (must be a GUID system compatible with RDF Resource identifiers)
  • model: Imaging
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • age: (OPTIONAL) Patient age when this observation ocurred, this age information can be both an addition or an alternative for start/end date information.
  • comments: Human readable comments of any kind related to this procedure

Medications and Therapies:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • route_type: Child of Route of Administration http://purl.obolibrary.org/obo/NCIT_C38114 (example: obo:Sublingual Route of Administration http://purl.obolibrary.org/obo/NCIT_C38300 )
  • value: Dose value prescribe to the patient
  • value_datatype: XSD datatype that defines value column type, for this case is xsd:float by default, but depending on your score's datatype, it could be different.
  • unit_type: Child of UO:unit http://purl.obolibrary.org/obo/UO_0000000
  • frequency_type: Child of obo:Temporal Qualifier http://purl.obolibrary.org/obo/NCIT_C21514 (ex: obo:Per Day)
  • frequency_value: Frequency value prescribe to the patient
  • agent_id: ATC URI-code for drugs components. (example: https://www.whocc.no/atc_ddd_index/?code=A07EA01)
  • model: Medications
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • age: (OPTIONAL) Patient age when this observation ocurred, this age information can be both an addition or an alternative for start/end date information.
  • comments: Human readable comments of any kind related to this procedure

Interventions:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • process_type: Child of Intervention or Procedure http://purl.obolibrary.org/obo/NCIT_C25218 (ex: obo:Tumor Resection http://purl.obolibrary.org/obo/NCIT_C164212)
  • target_type: (RECOMMENDED) Child of Anatomic Structure, System, or Substance
  • agent_id: (IN CASE OF ANY) ATC URI-code for drugs components. (example: https://www.whocc.no/atc_ddd_index/?code=A07EA01)
  • route_type: (IN CASE OF ANY) Child of Route of Administration http://purl.obolibrary.org/obo/NCIT_C38114 (example: obo:Sublingual Route of Administration http://purl.obolibrary.org/obo/NCIT_C38300 ) or obo:Material (example: obo: Tumor Tissue http://purl.obolibrary.org/obo/NCIT_C18009)
  • model: Intervention
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • age: (OPTIONAL) Patient age when this observation ocurred, this age information can be both an addition or an alternative for start/end date information.
  • comments: Human readable comments of any kind related to this procedure

Clinical trials:

  • pid: Patient unique identifier
  • context_id: (OPTIONAL) Contextual identifier in case you want to relate several data elements under a common context (ex: certain diagnosis/phenotype relationship or some elements under same visit occurrence)
  • agent_id: GUID for this medical center where this clinical trial is taking place.
  • valueIRI: IRI that defines clinical condition as disease or disorder: Orphanet disease ontology (ORDO) represented with a full URL such as http://www.orpha.net/ORDO/Orphanet_199630- model: Clinical_trial
  • startdate: (OPTIONAL) ISO 8601 formatted start date of observation
  • enddate: (OPTIONAL) ISO 8601 formatted enddate of observation in case it is different from startdate.
  • age: (OPTIONAL) Patient age when this observation ocurred, this age information can be both an addition or an alternative for start/end date information.
  • comments: Human readable comments of any kind related to this procedure