How do I handle different output formats like XML or TSV?

BioServices is designed to work with Python's data ecosystem; it can return parsed dictionaries, and it integrates well with Pandas for tabular data and BioPython for sequence objects.

What biological databases does this skill support?

BioServices supports programmatic access to over 40 major services, including UniProt for protein data, KEGG and Reactome for pathway analysis, and PubChem, ChEBI, and ChEMBL for chemical compounds.

Can I perform cross-database identifier mapping?

Yes, the skill includes specialized methods for mapping IDs between databases, such as converting UniProt accessions to KEGG IDs or using UniChem for chemical identifier cross-referencing.

Does it support sequence analysis tools like BLAST?

Yes, the skill provides programmatic access to NCBI BLAST and alignment tools like MUSCLE, allowing you to submit sequences, monitor job status, and retrieve results.

Bioinformatics Services (BioServices)

Name: Bioinformatics Services (BioServices)
Author: Microck

byMicrock

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データサイエンスとML

Accesses over 40 bioinformatics web services and databases through a unified Python interface for biological data retrieval and analysis.

概要

BioServices provides a comprehensive Python wrapper for interacting with major biological databases and tools, including UniProt, KEGG, ChEMBL, and PubChem. It streamlines complex bioinformatics workflows by offering a unified API for querying protein sequences, mapping identifiers across disparate platforms, performing metabolic pathway analysis, and executing sequence similarity searches like BLAST. This skill is ideal for researchers and developers who need to integrate data from diverse biological resources into automated pipelines without managing individual REST or SOAP protocol complexities.

主な機能

Metabolic pathway discovery and protein interaction network extraction
Automated protein sequence retrieval and functional annotation
Unified access to 40+ bioinformatics databases including UniProt, KEGG, and ChEMBL
Cross-database identifier mapping and batch conversion utilities
Programmatic execution of BLAST searches and sequence alignments
81 GitHub stars

ユースケース

Mapping UniProt protein identifiers to KEGG metabolic pathways for gene expression analysis
Integrating sequence alignment jobs with protein-protein interaction data in a single pipeline
Automating batch retrieval of compound structures and properties from PubChem and ChEBI

概要

主な機能

Metabolic pathway discovery and protein interaction network extraction
Automated protein sequence retrieval and functional annotation
Unified access to 40+ bioinformatics databases including UniProt, KEGG, and ChEMBL
Cross-database identifier mapping and batch conversion utilities
Programmatic execution of BLAST searches and sequence alignments
81 GitHub stars

ユースケース

Mapping UniProt protein identifiers to KEGG metabolic pathways for gene expression analysis
Integrating sequence alignment jobs with protein-protein interaction data in a single pipeline
Automating batch retrieval of compound structures and properties from PubChem and ChEBI