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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Data Science & ML

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

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.

Key Features

01Metabolic pathway discovery and protein interaction network extraction

02Automated protein sequence retrieval and functional annotation

03Unified access to 40+ bioinformatics databases including UniProt, KEGG, and ChEMBL

04Cross-database identifier mapping and batch conversion utilities

05Programmatic execution of BLAST searches and sequence alignments

0681 GitHub stars

Use Cases

01Mapping UniProt protein identifiers to KEGG metabolic pathways for gene expression analysis

02Integrating sequence alignment jobs with protein-protein interaction data in a single pipeline

03Automating batch retrieval of compound structures and properties from PubChem and ChEBI

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add microck/ordinary-claude-skills bioservices

For use in Claude.ai and ChatGPT

Download Skill