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Welcome to the almanac-browser wiki!
The following tables describe the structure of the database underlying the Molecular Almanac Browser. See the Vertabelo website for an editable graphical representation of the database. Note that Vertabelo is used to generate the db_scripts/db_create.sql
and db_scripts/db_drop.sql
files which are in turn used by create_db.sh
to create the Almanac SQLite database and fill it with spreadsheet data.
- Assertion
- Assertion_To_Source
- Source
- Feature_Set
- Feature
- Feature_Attribute
- Feature_Definition
- Feature_Attribute_Definition
- Version
Holds all information related to a specific assertion made by a Source document.
Column | Type | Key/Nullable | Description |
---|---|---|---|
assertion_id |
integer |
PK | |
created_on |
text |
Date this assertion was created, as a UNIX timestamp. | |
last_updated |
text |
Date this assertion was last modified, as a UNIX timestamp. | |
disease |
text |
N | Name of the disease this assertion relates to, as specified by the user adding the assertion. |
oncotree_term |
text |
N | Standardized OncoTree descriptor of the referenced disease state. |
oncotree_code |
text |
N | Short format of standardized OncoTree descriptor of the referenced disease state. |
stage |
integer |
N | Specific stage number of the disease this assertion references, if applicable. |
therapy_name |
text |
N | Name of therapy referenced by this assertion. |
therapy_sensitivity |
boolean |
N | If True , this assertion describes a scenario in which the patient's disease state may be responsive to the referenced therapy. |
therapy_resistance |
boolean |
N | If True , this assertion describes a scenario in which the patient's disease state may be resistant to the referenced therapy. |
predictive_implication |
text |
N | "Confidence level" of this assertion; must be one of Inferential , Preclinical , Clinical , Guideline , FDA-Approved . |
favorable_prognosis |
boolean |
N | If True , this assertion describes a scenario in which the patient is predicted to experience a less severe disease (somatic variants) or be less likely to acquire the disease (germline variants). If False , this assertion describes a scenario in which the patient is predicted to experience a more severe disease (somatic variants) or to be more likely to acquire the disease (germline variants). |
description |
text |
N | User-provided text describing the assertion in a human-readable format; often explains how the linked source(s) relate to the assertion. |
validated |
boolean |
Describes whether a user-submitted assertion has been validated by an admin. If True , the assertion is validated and should appear in the Almanac. If False , the assertion has not yet been validated and should be hidden. |
|
submitted_by |
text |
Email address of user that submitted the alteration. |
Association table linking Assertion
and Source
in a many-to-many relationship.
Column | Type | Key/Nullable | Description |
---|---|---|---|
ats_id |
integer |
PK | ID for this Assertion_To_Source relationship. |
assertion_id |
integer |
FK | Foreign key referencing Assertion.assertion_id . |
source_id |
integer |
FK | Foreign key referencing Source.source_id . |
Describes a source document describing the information in one or multiple Assertion
s.
Column | Type | Key/Nullable | Description |
---|---|---|---|
source_id |
integer |
PK | ID for this source. |
source_type |
text |
String describing the type of source (e.g., Journal , Guideline , etc.). |
|
cite_text |
text |
Formal citation string for this source (ideally in AMA format). | |
doi |
text |
N | DOI for this source (do not use DOI URLs - only the DOI itself). |
Association table linking Assertion
and Feature
in a one-to-many relationship (one assertion may have many features grouped together as a feature set).
Column | Type | Key/Nullable | Description |
---|---|---|---|
feature_set_id |
integer |
PK | ID for this feature set. |
assertion_id |
integer |
FK | Foreign key referencing Assertion.assertion_id . |
Describes a single molecular feature associated with a given assertion (e.g., Somatic Variant
or Mutational Burden
). Instantiates one of the feature definitions given in the Feature_Definition
table.
Column | Type | Key/Nullable | Description |
---|---|---|---|
feature_id |
integer |
PK | ID for this feature. |
feature_set_id |
integer |
FK | Foreign key referencing Feature_Set.feature_set_id for the feature set this feature belongs to. |
feature_def_id |
integer |
FK | Foreign key referencing Feature_Definition.feature_def_id for the feature definition this feature instantiates. |
Describes a single attribute associated with a molecular feature. E.g., the Somatic Variant
feature has the variant_type
, gene
, and protein_change
attributes, each of which is described by a separate Feature_Attribute
row for the given Assertion
. Instantiates one of the attribute definitions given in the Feature_Attribute_Definition
table.
Column | Type | Key/Nullable | Description |
---|---|---|---|
attribute_id |
integer |
PK | ID for this attribute. |
feature_id |
integer |
FK | Foreign key referencing Feature.feature_id for the feature of which this attribute is a member. |
attribute_def_id |
integer |
FK | Foreign key referencing Feature_Attribute_Definition for the attribute definition this attribute instantiates. |
Provides a user-defined definition for a given feature (e.g., Somatic Variant
or Mutational Burden
). All features linked to a given assertion must reference a single feature definition described in this table.
Column | Type | Key/Nullable | Description |
---|---|---|---|
feature_def_id |
integer |
PK | ID for this feature definition. |
name |
text |
"Programmatic" name of this feature (e.g., "somatic_variant"). | |
readable_name |
text |
Human-readable name for display to users (e.g., "Somatic Variant"). | |
is_germline |
boolean |
If True , this feature applies to germline data; otherwise applies to somatic data. |
Provides a user-defined definition of a single attribute (e.g., the gene
or protein_change
attributes within the Somatic Variant feature. All attributes linked to a given feature must reference a single attribute definition given in this table.
Column | Type | Key/Nullable | Description |
---|---|---|---|
attribute_def_id |
integer |
PK | ID for this attribute definition. |
feature_def_id |
integer |
FK | Foreign key referencing Feature_Definition.feature_def_id for the feature definition this attribute definition is defined under. |
name |
text |
"Programmatic" name of this feature (e.g., "protein_change"). | |
readable_name |
text |
Human-readable name for display to users (e.g., "Protein Change"). | |
type |
text |
Type of data that is stored in this attribute; may be used by the Browser to classify certain attributes or decide how to display them. May hold any value, but the Browser explicitly recognized text , integer , and gene at this time. |
Contains the version number of the underlying Almanac database from which the Browser is pulling information. Versioning follows the Semantic Versioning guidelines.
Column | Type | Key/Nullable | Description |
---|---|---|---|
major |
integer |
PK | Incremented when major changes are made to the database such that the Almanac Browser itself must be modified to continue reading data from the database (e.g., changes in the structure of the database). |
minor |
integer |
Incremented when data is added to the database without requiring modification of the Almanac Browser to use the database (e.g., adding new assertions). | |
patch |
integer |
Incremented after bug fixing (e.g., fixing a typo in an entered assertion). |