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Create your CSV file
In order to create a functional CSV file for your patient data for implementing CARE-SM. A set of column names are required to be populated in a CSV file. We recommend first to create an empty CSV file with all these column names on it. The required column names are:
model: Tagname used by CARE-SM toolkit to recognize which data element is being represented.pid: individual identifier, in the form of a patient identifier.value: Numerical or Lexical data value of this data entry.value_datatype: XSD data type of thevaluecolumn name.valueIRI: IRI-based value of this data entry.activity: IRI-based ontological class that describes the patient's specific description related to the clinical procedure.unit: IRI-based ontological class that describes the unit ofvaluemeasurement.input: IRI-based ontological class that describes the input of the patient procedure.target:IRI-based ontological class that describes the target of the patient procedure.protocol_id: IRI-based identifier that is used the define the protocol identifier.frequency_type: IRI-based ontological class that describes the frequency ofvaluepresence.frequency_value: Numerical value associated with thefrequency_typeagent: GUID used to describe any agent that participates in the data entrystartdate: the start date of the observation processenddate: the end date of the observation processage: the age of the patient at time of observationcomments: free-text commentsevent_id: a method for grouping observations together (explained elsewhere... one day!)
Very few of this column names are present at all (or most) of the cases, but it's not mandatory to provide all columns that exists in the CSV file, but it's forbidden to use other columns that the named above. Each data element requires a subset of these columns to be filled, and the rest are 'null'.
This is an example of an empty CSV file with the proper columns names:
model,pid,event_id,value,age,value_datatype,valueIRI,activity,unit,input,target,protocol_id,frequency_type,frequency_value,agent,startdate,enddate,comments ,,,,,,,,,,,,,,,,, -
Rename the CSV file as
preCARE.csv. CARE-SM will recognize the name as the proper tagname and perform the quality control on it usingCARE-SM Toolkit. This is why it's mandatory to create a single file because this is the one file it's going to be executed. -
Populate your patient data elements
Every data element requires a concrete set of column names to be populated. This is because not every clinical entry contains the same type of information.(e.g. a laboratory measurement needs to specify the targeting molecule to analyze, but a diagnosis assessment doesn't require defining any target).
This is a glossary of every data requirement documentation:-
Medical history and participation status:
- Birthdate - Patient date of birth.
- Birthyear - Year in which a person was born.
- Deathdate - Patient date of death.
- First confirmed visit - Patient first contact with specialized center.
- Participation status - Patient healthcare participation status.
- Symptoms onset - Patient signs/symptoms onset.
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Demographic and questionnaire/PROMs representations:
- Sex - Patient sex at birth.
- Education level - Patient scholar level code measured by ISCED.
- Disability - Patient disability score/assessment.
- Questionnaire - Generic questionnaire representation for any clinical question/PROM.
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Conditions and findings assesments:
- Diagnosis - Patient disease diagnosis.
- Symptom/phenotype assessment - Patient symptom/phenotype assessment.
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Clinical and molecular measurements:
- Laboratory measurement - Patient laboratory measurements.
- Body measurement - Patient physical measurement of the body.
- Medical imaging - Patient medical imaging data.
- Genetic variant - Genetic variant assessment.
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Treatment-related assesments:
- Medication - Patient drug administration based on a prescription.
- Surgical intervention - Therapeutical interventation related to a surgerical procedure.
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Research sample availability and consent:
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Clinical trials:
- Clinical trial - patient participation in clinical trial.
This is an example of functional `preCARE.csv` file that can be used with CARE-SM Toolkit, both for `FAIR-in-a-box` software or Standalone implementation:model,pid,event_id,value,age,value_datatype,valueIRI,activity,unit,input,target,intensity,protocol_id,frequency_type,frequency_value,agent,route,startdate,enddate,comments Diagnosis,30056,,,,,http://www.orpha.net/ORDO/Orphanet_93552,,,,,,,,,,,2006-01-19,,Find more complete exemplar cases at
exemplar_datafolder. -
This column is UNUSED for this case.
This column is filled in IN CASE OF ANY.
This column colored is REQUIRED for this case.
Here you can find the list of data elements and the columns required to be defined. Those that are optional, feel free to add them. If not, leave them empty.
This data element can be queried (for counting anonymized patient information) by Beacon API created for CARE-SM, for more information, click here
valuestartdate.integer) used for relating several of this data elements under the same visit occurrence event.
This data element can be queried (for counting anonymized patient information) by Beacon API created for CARE-SM, for more information, click here
integer) used for relating several of this data elements under the same visit occurrence event.
valuestartdate.agecolumn. Patient age when this observation was taken, this age information can be both an addition or an alternative forvalue/startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
valueand/oragecolumn (preferablyvalue)valuestartdate.value/startdate/enddateinformation. It's required to add at least one the following:valueand/oragecolumn (preferablyvalue). Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
This data element can be queried (for counting anonymized patient information) by Beacon API created for CARE-SM, for more information, click here
- http://purl.obolibrary.org/obo/NCIT_C16576 (Female) ;
- http://purl.obolibrary.org/obo/NCIT_C20197 (Male);
- http://purl.obolibrary.org/obo/NCIT_C124294 (Undetermined) ;
- http://purl.obolibrary.org/obo/NCIT_C17998 (Unknown, use this for foetal undetermined)
startdate.integer) used for relating several of these data elements under the same visit occurrence event.
- http://semanticscience.org/resource/SIO_010059 (dead)
- http://semanticscience.org/resource/SIO_010058 (alive)
- http://purl.obolibrary.org/obo/NCIT_C70740 (lost to follow-up)
- http://purl.obolibrary.org/obo/NCIT_C124784 (refused to participate)
startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of this data elements under the same visit occurrence event.
startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
This data element can be queried (for counting anonymized patient information) by Beacon API created for CARE-SM, for more information, click here
startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
This data element can be queried (for counting anonymized patient information) by Beacon API created for CARE-SM, for more information, click here
startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
This data element can be queried (for counting anonymized patient information) by Beacon API created for CARE-SM, for more information, click here
startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
This data element can be queried (for counting anonymized patient information) by Beacon API created for CARE-SM, for more information, click here
startdate/enddate/agefor defining when this observation was registered).valuecolumn.xsd:datefor date orxsd:integerfor age. (xsd:float is not included as an option because fractional ages are not accepted by CARE-SM Toolkit).startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
valuecolumn type, e.g.xsd:floatpor a decimal score.startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
valuecolumn type, e.g.xsd:floatpor a decimal score.startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of this data elements under the same visit occurrence event.
valuecolumn type, e.g.xsd:floatorxsd:integerfor numerical values. In case of none,xsd:floatwill be added by default.startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
valuecolumn type, e.g.xsd:floatorxsd:integerfor numerical values. In case of none,xsd:floatwill be added by default.startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
valuecolumn type, e.g.xsd:floatorxsd:integerfor numerical values.startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
startdate.value/startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.
startdate.startdate/enddateinformation. Its units are fractional years, so it accepts any decimal figure for age. E.g. 33.75 years.integer) used for relating several of these data elements under the same visit occurrence event.