Data Manager Reference

Database Manager

class pyctd.manager.database.DbManager(connection=None)

Implements functions to upload CTD files into a database. Preferred SQL Alchemy database is MySQL with pymysql.

Parameters:connection (str) – custom database connection SQL Alchemy string

db_import(urls=None, force_download=False)

Updates the CTD database

1. downloads all files from CTD
2. drops all tables in database
3. creates all tables in database
4. import all data from CTD files

Parameters:

• urls (iter[str]) – An iterable of URL strings
• force_download (bool) – force method to download

Returns:

SQL Alchemy model instance, populated with data from URL

Return type:

models.Namespace

classmethod download_urls(urls, force_download=False)

Downloads all CTD URLs that don’t exist

Parameters:

• urls (iter[str]) – iterable of URL of CTD
• force_download (bool) – force method to download

static get_column_names_from_file(file_path)

returns column names from CTD download file

Parameters:file_path (str) – path to CTD download file

static get_dtypes(sqlalchemy_model)

Parameters:sqlalchemy_model – Returns:

classmethod get_index_and_columns_order(columns_in_file_expected, columns_dict, file_path)

Parameters:

• columns_in_file_expected –
• columns_dict –
• file_path –

Returns:

classmethod get_index_of_column(column, file_path)

Get index of a specific column name in a CTD file

Parameters:

• column –
• file_path –

Returns:

int or None

classmethod get_path_to_file_from_url(url)

standard file path

Parameters:url (str) – CTD download URL

import_one_to_many(file_path, column_index, parent_table, column_in_one2many_table)

Parameters:

• file_path –
• column_index –
• parent_table –
• column_in_one2many_table –

Returns:

import_table(table)

import table by Table object

Parameters:table (manager.table_conf.Table) – Table object

import_table_in_db(file_path, use_columns_with_index, column_names_in_db, table)

Imports data from CTD file into database

Parameters:

• file_path (str) – path to file
• use_columns_with_index (list[int]) – list of column indices in file
• column_names_in_db (list[str]) – list of column names (have to fit to models except domain_id column name)
• table – manager.table.Table object

import_tables(only_tables=None, exclude_tables=None)

Imports all data in database tables

Parameters:

• only_tables (set[str]) – names of tables to be imported
• exclude_tables (set[str]) – names of tables to be excluded

mapper

returns a dictionary with keys of pyctd.manager.table_con.domains_to_map and pandas.DataFrame as values.

DataFrames column names:

• domain_id (represents the domain identifier of e.g. chemical)
• domain__id (represents the primary key in domain table)

Returns:dict of pandas DataFrames (keys:domain_name, values:DataFrame) Return type:dict of pandas.DataFrame

Database Models

Not all database models are documented here in order to keep the documentation simple. In general Query should be used to query the content of the database

SQLAlchemy database models in this module describes all tables the database and fits the description in the table_conf module

class pyctd.manager.models.Action(**kwargs)

Chemical–gene interaction types

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.ChemGeneIxn(**kwargs)

Chemical–gene interactions

reference:

• CTD Chemical–gene interactions

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.ChemGeneIxnGeneForm(**kwargs)

Gene forms of Chemical–gene interactions

reference:

• CTD Gene forms of Chemical–gene interactions

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.ChemGeneIxnInteractionAction(**kwargs)

Chemical–gene interactions actions

reference:

• CTD Chemical–gene interactions actions

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.ChemGeneIxnPubmed(**kwargs)

Chemical–gene interactions PubMed links

reference.

• CTD Chemical–gene interactions PubMed links

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.ChemGoEnriched(**kwargs)

Chemical–GO enriched associations

reference:

• CTD Chemical–GO enriched associations

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.ChemPathwayEnriched(**kwargs)

Chemical–pathway enriched associations

reference:

• CTD Chemical–pathway enriched associations

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.Chemical(**kwargs)

Chemical vocabulary

reference:

• CTD Help: Chemicals

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.ChemicalDisease(**kwargs)

Chemical–disease associations

reference:

• CTD Chemical–disease associations

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.ChemicalDiseaseOmim(**kwargs)

Online Mendelian Inheritance in Man (OMIM) mappings to Chemical–disease associations

reference:

• CTD OMIM

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.ChemicalDiseasePubmedid(**kwargs)

PubMed Literature references to Chemical–disease associations

reference:

• CTD PubMed

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.ChemicalDrugbank(**kwargs)

DrugBank identifiers to Chemical vocabulary

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.ChemicalParentid(**kwargs)

Parent IDs of Chemical vocabulary

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.ChemicalParenttreenumber(**kwargs)

Parent tree numbers of Chemical vocabulary

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.ChemicalSynonym(**kwargs)

Synonymy to Chemical vocabulary

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.ChemicalTreenumber(**kwargs)

Tree numbers of Chemical vocabulary

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.Disease(**kwargs)

Disease vocabulary (MEDIC)

reference:

• CTD Disease vocabulary (MEDIC); structure
• CTD description disease

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

definition

definition of disease (str)

disease_id

MeSH or OMIM identifier (str)

disease_name

Disease name (str)

parent_ids

identifiers of the parent terms; ‘|’-delimited list

parent_tree_numbers

identifiers of the parent nodes; ‘|’-delimited list

tree_numbers

identifiers of the disease’s nodes; ‘|’-delimited list

class pyctd.manager.models.DiseaseAltdiseaseid(**kwargs)

Alternative disease identifiers to Disease vocabulary (MEDIC)

reference:

• CTD Disease (alternative identifier)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.DiseasePathway(**kwargs)

Disease–pathway associations

reference:

• CTD Disease–pathway associations

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.DiseaseSlimmapping(**kwargs)

MEDIC-Slim mappings to Disease vocabulary (MEDIC)

reference:

• CTD MEDIC-Slim mappings

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.DiseaseSynonym(**kwargs)

Synonyms to Disease vocabulary (MEDIC)

reference:

• CTD Disease synonym

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.ExposureEvent(**kwargs)

Exposure–event associations

reference:

• CTD Exposure–event associations

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.Gene(**kwargs)

Gene vocabulary

reference:

• CTD Gene
• CTD Help: Genes
• UniProt accession numbers

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

alt_gene_ids

list of alternative NCBI Gene identifiers

biogrid_ids

list of BioGRID identifier

gene_id

NCBI Gene identifier

gene_name

gene name

gene_symbol

gene_symbol”“”

pharmgkb_ids

list of PharmGKB identifiers

synonyms

list of synonyms

uniprot_ids

UniProt accession number

class pyctd.manager.models.GeneAltGeneId(**kwargs)

Alternative gene identifiers to Gene vocabulary

reference:

• CTD alternative NCBI Gene identifiers

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.GeneBiogrid(**kwargs)

BioGRID mappings to Gene vocabulary

reference:

• CTD BioGRID
• BioGRID

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.GeneDisease(**kwargs)

Gene–disease associations

reference:

• CTD Gene–disease associations

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.GeneDiseaseOmim(**kwargs)

Online Mendelian Inheritance in Man (OMIM) mappings to Gene–disease associations

reference:

• CTD OMIM mappings to Gene–disease associations

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.GeneDiseasePubmed(**kwargs)

PubMed references to Gene–disease associations

reference:

• CTD PubMed references to Gene–disease associations

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.GenePathway(**kwargs)

Gene–pathway associations

reference:

• CTD Gene–pathway associations

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.GenePharmgkb(**kwargs)

PharmGKB mapping to Gene vocabulary

reference:

• CTD PharmGKBIDs
• PharmGKB

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.GeneSynonym(**kwargs)

Synonyms to Gene vocabulary

reference:

• CTD Synonyms

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.GeneUniprot(**kwargs)

UniProt mappings to Gene vocabulary

reference:

• CTD UniProt
• UniProt

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyctd.manager.models.Pathway(**kwargs)

Pathway vocabulary

CTD link

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

pyctd.manager.models.foreign_key_to(table_name)

Creates a standard foreign key to a table in the database

Parameters:table_name (str) – name of the table without TABLE_PREFIX Returns:foreign key column Return type:sqlalchemy.Column