The goal of the module is to provide a unified(-ish) interface to different biological databases. The module has interfaces the following databases:
- Uniprot: This is a database of protein sequences and annotations. The module provides a way to search for proteins and their respective annotations. The entirety of the Uniprot database can be searched using the module, including variation isoforms and mutagenesis endpoints. These are then integrated into a single dictionary that can be used to access the data.
- NCBI: This is a database of nucleotide sequences and annotations. The module provides a way to search for all of the NCBI databases, including nucleotide sequences, protein sequences, gene annotations, and more. While you can search pubmed using this module, the literature module is better suited for that purpose (see below).
- Ensembl: This is a database of genomic sequences and annotations. The module provides a way to search for gene variants mapping between different coordinates systems, and more. The module also provides a way to search for genes and their annotations, annotate variants, query cross-references from different databases and more.
- stringdb: This is a database of protein-protein interactions. The module provides a way to search for protein-protein interactions. Additionally you can use the Biogrid and IntAct endpoints under others to perform similar queries.
- reactome: Reactome is a comprehensive database of biolgicla reaction, proteins and pathways. You can query many of the endpoints using this submodule
- rnacentral: RnaCentral the non-coding RNA sequence database, this is different from the NCBI genes in that it is dedicated to non-coding sequences.
- BioGrid: Biogrid is a biomedical interaction repository that contains information about protein-protein and protein-chemical interactions that are mostly manually curated at different levels. You will need a free API key to be able to use this module. You can obtain one here
- IntAct: Simlar to BioGrid this database contains interaction data. You can query this database to arbitrary depth to obtain information about different biological complexes and much more.
- AlphaGenome: AlphaGenome is a server running the latest alphagenome models for variant, sequence and genomic interval consequence/feature predictions.
You can see detailed usage examples for each of these publicly available databases in their respective documentation. Not every database provides a robus api to query, nor their documentaion is exhaustive or even well prepared. We are a small team and we are trying to generate as many resources as we can while being mindful or the work that is required to achieve the highest yield in the shortest amount of time.