Python API for accessing a locally hosted DGIdb v5 database. Currently supported searches will return individual interaction data for drugs or genes, category annotations for genes, or information for drugs.
THIS REPO HAS MIGRATED TO: https://github.com/GenomicMedLab/dgipy
dgidb.py must be imported from dgidb first:
from dgidb import dgidb
dgidb.py sends a pre-defined graphql query with user determined parameters to dgidb v5. Response objects are built into a dataframe using Pandas and returned to the user for readability, ease of use. Users can skip dataframe generation and instead receive the response object by setting use_pandas=False for most search functions.
Currently supported searches:
dgidb.get_drug(terms, use_pandas=True)
dgidb.get_categories(terms, use_pandas=True)
dgidb.get_interactions(terms, search='genes', use_pandas=True)
dgidb.get_interactions(terms, search='drugs', use_pandas=True)
Search terms support list or string format inputs (e.g. terms=['BRAF','ABL1'] or terms='BRAF'). Interaction searches default to genes but can also accept drugs if search='drugs'.
Example usage:
genes = ['BRAF','ABL1','BCR','PDGFRA']
drugs = ['IMATINIB','OLARATUMAB','DASATINIB','NELOTINIB']
gene_interactions = dgidb.get_interactions(genes)
gene_categories = dgidb.get_categories(genes)
drug_interactions = dgidb.get_interactions(drugs,search='drugs')
drug_information = dgidb.get_drug(drugs)
interaction_response_object = dgidb.get_interactions(genes, use_pandas=False)
graph_app.py must be imported from dgidb first:
from dgidb import graph_app
To generate and run the app, run the following command:
app = graph_app.generate_app()
if __name__ == '__main__':
app.run_server()
Once the server is running, The dash app can be viewed at its default URL 'http://127.0.0.1:8050/'
This app displays a visual network of drug-gene interactions (queried using dgidb.py), with selectable nodes and edges for user interactivity. Users can query genes, which will allow the network to show all drugs connected to the said genes. Additionally, the network will reveal drugs that two genes share. Drugs that are only connected to one gene are considered "single-degree drugs", while drugs that are connected to two genes are considered "multi-degree drugs". The unique colorations for single-degree drugs, multi-degree drugs, and genes can be viewed in the graph legend on the right side.
The main network graph on the left provides many options to view and interact with the graph: Zooming in/out of the graph, panning the graph, reseting the graph perspective, etc. Alongside these options, the user can hover over nodes to reveal their name, and select them by clicking on the node. Users can also select edges (lines between nodes), by hovering on the center of an edge and clicking (just like nodes). Selected Nodes/Edges will appear on the right-side info box under "Selected Node/Edge:".
The "Genes Dropdown Display" provides a dropdown menu listing every available queryable gene. Multiple genes can be selected to create larger networks. Specific Genes can also be typed to narrow down search results in the dropdown menu list.
The "Neighbors Dropdown Display" provides a dropdown menu listing every neighbor for a selected node. This also allows users to select edges between two nodes without utilizing the graph. Only when selecting a node (drug/gene) will a dropdown display neigbors. An edge has no neighbors, and therefore will not display anything.
As previously mentioned, "Selected Node/Edge" will update when a node or edge is selected on the graph by the user. "Selected Edge Info" will update when either 1) the user selects an edge directly from the graph, or 2) the user selects a node (drug/gene) and uses the "Neighbors Dropdown Display" to select an neighbor to view an edge.
- Implement metadata support (i.e. get_source)
- Implement support for live dgidb (pending v5 launch date)
- Notebooks for analysis purposes