Data Files Used by the Data Model Loader
The information on this page is for the use of customers working with the DNAnexus xVantage team. Contact DNAnexus Sales for more information.
Overview
Phenotypic data must be delivered in a data model defined by the following files:
A data dictionary CSV file, named
data_dictionary.csvin this example.A data CSV file,
data.csv.A codings CSV file,
codings.csv.
Data Dictionary
Description: The data dictionary file describes data in the data file (*.data.csv) by file name and by column within the specified data file. The data dictionary lists the metadata for the input data.csv file and respective individual columns within the data file. This metadata includes human-readable field names, data types, data coding schemes, and the relationships between the data tables. The information supplied in the data dictionary guides the ingestion process.
Deliverable: The data_dictionary.csv file is similar in structure to a spreadsheet, where columns are defined in Table 1 in the Appendix below. Each row in the data dictionary file represents a field for which an entity, i.e. "patient", "sample", or "encounter," will have a value.
Note: all columns have to be present, however they can be left empty if there are no values for the corresponding entity:field combination. The example below does not include all columns, just enough to illustrate the general format. A complete template can be provided upon request.
Example data_dictionary.csv
data_dictionary.csventity | name | type | primary_key_type | coding_name | is_sparse_coding | referenced_entity_field | relationship | folder_path |
subject | subject_id | string | global | |||||
subject | first_name | string | ||||||
subject | last_name | string | ||||||
subject | birth_year | date | ||||||
encounter | encounter_id | string | local | |||||
encounter | subject_id | string | subject:subject_id | many_to_one | ||||
encounter | date | date | no | Encounter | ||||
encounter | height | float | no | Encounter>Measurements | ||||
encounter | weight | integer | no | Encounter>Measurements | ||||
encounter | sys_blood_pressure | integer | no | Encounter>Measurements |
Entity Dictionary
Description: The optional entity dictionary file describes entities that the data file represent (*.data.csv). The entity dictionary lists the metadata for each input data.csv. This metadata includes human-readable entity title, singular and plural labels, and a description. The information supplied in the entity dictionary provides additional contextualized information for the user.
Deliverable: The entity_dictionary.csv file is similar in structure to a spreadsheet, where columns are defined in Table 3 in the Appendix below. Each row in the entity dictionary file represents an entity for which data file and entries in the entity_dictionary.csv exist.
All columns have to be present, however they can be left empty if there are no values for the corresponding entity:field combination. The example below does not include all columns, just enough to illustrate the general format. A complete template can be provided upon request.
Example entity_dictionary.csv
entity_dictionary.csventity | entity_title | entity_label_singular | entity_label_plural | entity_description |
patient | Patient | Patient Record | Patient Records | The unique record for each patient participating in the clinical trial. |
clinical | Clinicals | Clinically supplied data at the patient level. | ||
encounter | Encounters | Encounter | Encounters | |
lab_test | Laboratory Tests | Lab Test | Lab Tests | Laboratory tests ordered during a patient's hospital visit |
Data Files
Description: Phenotypic data must be supplied in a CSV file.
Deliverable: The data.csv file is described in the data dictionary with its name. The data.csv file must be a flattened data structure (a table) with a header, columns and rows. The values must be of the following listed types: date, datetime, integer, float, or string.
Example subject data.csv
data.csvsubject_id | first_name | last_name | birth_year |
1 | Mom | Family | 1985 |
2 | Dad | Family | 1984 |
3 | Baby | Family | 2016 |
Codings
Description: The codings.csv file is a single file that contains information for coded values present in all the *.data.csv files. Often a meaning is designed for human consumption and codes are designed to optimize data storage and retrieval. For example, instead of storing the value “Acquired pure red cell aplasia [erythroblastopenia]” multiple times in a database, it is easier to code this as the shortened ICD10 code, “D60.” Data are stored as codes in the encoded fields. When retrieving a coded value, such as the ICD10 code "D60", from a database and displaying the value for consumption, the system converts this back to the full meaning, “Acquired pure red cell aplasia [erythroblastopenia],” so that the information is intelligible to the users.
Hierarchical Data: The codings file supports specification of a hierarchy. For example, ICD10 codes, A00 to B99, all point to the category, “Certain infectious and parasitic diseases”. The code, A31, points to “Other sepsis” and codes, A31.X, point to specific types of sepsis. Such a hierarchical structure can be defined in the codings.csv in the parent_code column (see example below).
Deliverable: The codings.csv file must have columns as defined in Table 2 of the Appendix. Each categorical field in your data will need to have an associated entry in the codings.csv file. The same coding_name value must be used in the respective data_dictionary.csv field to match each field with its respective codes.
Example codings.csv file
codings.csv filecoding_name | code | meaning | parent_code | display_order |
blood_pressure | -1 | Did not measure | 1 | |
blood_pressure | -2 | Measurement failed | 2 | |
t_f_na | 1 | True | ||
t_f_na | 2 | False | ||
t_f_na | 3 | Not Applicable | ||
reason_discontinued_treatment | 1 | Pain subsided | ||
reason_discontinued_treatment | 2 | Lost medication | ||
reason_discontinued_treatment | 3 | Forgot | ||
allergies | a | Environment | 1 | |
allergies | b | Food | 2 | |
allergies | c | Medicine | 3 |
Appendix
Table 1: Data Dictionary File Description (data_dictionary.csv)
data_dictionary.csv)Column | Possible values* | Description |
entity | /^[a-zA-Z][a-zA-Z_0-9]*$/ max length 256 characters | Required: The name of the entity associated with the current field. For example, "subject" or "sample" or encounter. Note: An entity is a logical table in a dataset (i.e. patients, prescriptions, lab tests). Datasets must contain exactly one main entity (denoted using the primary_key_type column below), which is used as the primary entry point to a dataset, and for which cohorts are to be built. Beyond the main entity, datasets may contain additional entities linked to the main entity using relationships such as one-to-one or one-to-many. |
name | /^[a-zA-Z][a-zA-Z_0-9]*$/ max length 2000 characters | Required: The name of the current field. No two fields, within an entity, may have the same name. |
type | date datetime integer float string | Required: The type of the raw data as given to the system. Type "date" is a timepoint with day granularity in ISO 8601 date format. Type "datetime" is a timepoint with millisecond granularity in ISO 8601 datetime format. Type "integer" is an integer number with 64-bit signed integer precision. Type "float" is a floating-point number with 64-bit (double) floating-point precision. When given as a fractional number, values to the right of the decimal point are supported up to 15 digits. Type "string" is a string. There may be one, and only one, “type” for each entity:field. |
coding_name | /r"[\w+-]+"/ max length 256 characters | This column denotes whether the current field is codified. For example a gender field could have type set to "integer" and be codified with a coding where 0 means "female" and 1 means "male". If coding_name is not empty, it must match the coding_name field in the |
description | Any character except /^[*'|"]*$/ (or left empty) | A human readable description of the field that will be displayed to users in the Apollo Cohort Browser. |
folder_path | /^[a-zA-Z_0-9][ ][a-zA-Z_0-9][>]*$/ (or left empty) max length 2000 characters | Fields may be displayed in user defined groups, with the strict purpose of visualizing data in a browser. This field will display in the browser as a series of folders and is the method to group entity:name pairs in a hierarchical manner. This then appears as a kind of table of contents for the data in the UI to make it easier to find data fields of interest. The value should be comprised of a single folder name (e.g. “Online follow-up”) or nested folders separated by the carrot symbol “>” (e.g. "Online follow-up > Mental health > Anxiety"). Each folder name must be separated by ">". If empty, the field will not be accessible within the browser. However, folder_path must be empty where primary_key_type is “local” and where reference_entity_field is not empty. Also, folder_path should be empty for any non-supported data types (e.g., free-text strings) as they can still be imported into the dataset, just not displayed in the Cohort Browser. |
is_multi_select | yes (or left empty) | If you are using a coding_name and the field is multi-select, then enter “yes” in this column. Multi-select fields contains potentially multiple values originating from answering a multiple-choice question (i.e. subject may choose "select all that apply" on a questionnaire). This is only applicable to codified fields. Thus, for "is_multi_select" to be set to "yes", it requires the "coding_name" to also be present. In the |
is_sparse_coding | yes (or left empty) | Set this field to the value “yes” if the coding name field is sparsely codified. The meaning of sparsely codified field depends on the "type".
|
linkout | Compliant URL (or left empty) | A URL for linking to additional information. |
primary_key_type | global local | This column denotes whether the current field is a primary key for the entity, and whether that entity is the main entity. If the current field is the primary key for the entity, and the entity is the main entity, this column should contain the value "global". If the current field is the primary key for the entity but the entity is not the main entity, this column should contain the value "local". There must be exactly one "global" primary_key_type per dataset. If a field is a primary key, the values must be NOT NULL and UNIQUE. |
referenced_entity_field | entity_name:field_name (or left empty) | If the field is a foreign key that references a field in another entity (e.g., a patient_id field present in the prescriptions entity), then the corresponding reference_entity_field must contain this mapping as the entity_name:field_name. For example: if there is a patient_id field in the prescription entity that maps to the id field in the patients entity, then the corresponding referenced_entity_field is patients:id). If referenced_entity_field is not blank for a given field, then the relationship field must also contain a value. Every entity in the data dictionary should be referenced or reference another entity (all entities linked). |
relationship | one_to_one many_to_one (or left empty) | This describes the relationship between two entities (tables). If, for the specified field, the entity has many rows that map back to a column (i.e. field) in another table, then the relationship is a "many_to_one" relationship for the field. For example, assume there are two entities, subject and encounter. Each subject may have multiple encounters. The relationship of the encounter_id field to the subject_id field in the If relationship is not blank for a given field, then the referenced_entity_field field must also contain a value. |
title | /^[a-zA-Z_0-9][ ][a-zA-Z_0-9]*$/ (or left empty) max length 2000 characters | A human readable title for name (column name) which will be displayed to users in the Apollo Cohort Browser as the field name. |
units | /^[a-zA-Z][a-zA-Z_0-9]*$/ (or left empty) | For the end user to understand the data, it is necessary to specify the unit of measurement. For example, for a temperature field the unit may be "Celsius", "Fahrenheit", "Kelvin", or anything else one prefers. The units will display in the metadata for the field and in any corresponding charts. |
* A value is required unless specified as "or left empty."
Table 2: Codings File Description (codings.csv)
codings.csv)Column | Possible values* | Description |
coding_name | /r"[\w+-]+"/ max length 256 characters | The name of the set of codes referenced when a field is codified. This column cannot be empty. |
code | Unique for a specific coding_name | Specifies the code for the respective code:meaning pair. |
meaning | Any non-empty string. max length 2000 characters | Specifies the value each code should take on, for a given grouping of codes, grouped by the coding_name field. |
parent_code | An existing code in the coding_name set | The hierarchical structure to a coding group may be maintained by specifying parent codes within the grouping |
display_order | A non-zero, non-negative integer (or left empty) | The order for how values are displayed may be retained by directly specifying the order. Note: use this to control the order of values list-type charts (non-hierarchical) and bar graphs. |
Table 3: Entity Dictionary File Description (entity_dictionary.csv)
entity_dictionary.csv)Column | Possible values* | Description |
entity | /^[a-zA-Z][a-zA-Z_0-9]*$/ max length 256 characters | A machine-readable entity name. Values here must be reflected in the entity column of the main data dictionary and the data files (<entity>.csv). For example "subject" or "sample " or "encounter". Note: An entity is a logical table in a dataset (i.e. patients, prescriptions, lab tests).
|
entity_title | /^[a-zA-Z_0-9][ ][a-zA-Z_0-9]*$/ max length 2000 characters | A human-readable title for the value in the entity field. We suggest that the entity_title should be a sensible and informative value, such that it is easy to quickly discern general content of the entity.
This title is used in forming existential cohort filter statement and is available in the data flyouts in the cohort browser. |
entity_label_singular | Any non-empty string. max length 2000 characters | A human-readable entity label in singular grammatical number, like "Lab test". This should often be a value that makes sense in the singular format and is descriptive of the entity.
The singular label is used in the tiles on the cohort browser when a value = 1, -1. |
entity_label_plural | Any non-empty string. max length 2000 characters | A human-readable entity label in plural grammatical number, like "Lab tests" . This should often be the plural version of the entity_label_singular (or entity_title if singular label is blank).
The plural label is used in the tiles on the cohort browser when a value not equal to 1 (e.g. 0 or >1). |
entity_description | Any character except /^['|"]/$/ (or left empty) | A human-readable description of the field. This can describe details about the entity, how it is tracked, any additional information a person may need to know about the entity. Description is exposed to the user in the entity tooltip on the cohort browser. |
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