Can I convert identifiers between different databases?

Yes, one of the core capabilities is identifier mapping, allowing you to convert between UniProtKB, KEGG, Ensembl, RefSeq, and many other biological ID formats.

Does this skill support sequence alignment?

Yes, it includes wrappers for NCBI BLAST and MUSCLE, allowing you to run sequence similarity searches and alignments programmatically.

How does BioServices handle data formats like XML or JSON?

BioServices transparently handles both REST and SOAP protocols, providing the tools to parse results into Python-friendly formats like dictionaries, TSV, or XML.

What databases are supported by this skill?

BioServices provides access to over 40 services, including major repositories like UniProt, KEGG, ChEMBL, PubChem, Reactome, PDB, and QuickGO.

Bioinformatics Services (BioServices)

Name: Bioinformatics Services (BioServices)
Author: ovachiever

byovachiever

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Data Science & ML

Provides programmatic access to over 40 bioinformatics web services and databases for streamlined biological data retrieval and analysis.

About

The BioServices skill integrates a comprehensive Python framework into Claude Code, allowing for unified programmatic access to major biological databases such as UniProt, KEGG, ChEMBL, and PubChem. It simplifies complex bioinformatics workflows by providing tools for protein sequence analysis, metabolic pathway mapping, compound searches, and cross-database identifier conversion. This skill is particularly useful for researchers and computational biologists who need to automate data collection and integration from disparate biological resources within a single environment.

Key Features

Asynchronous execution and monitoring of NCBI BLAST sequence similarity searches.
Unified API access to 40+ bioinformatics services including UniProt, KEGG, and Reactome.
Detailed metabolic pathway discovery and protein-protein interaction network extraction.
Robust identifier mapping between diverse biological databases (e.g., KEGG to UniProt).
5 GitHub stars
Comprehensive chemical compound searching across ChEBI, ChEMBL, and PubChem.

Use Cases

Cross-referencing chemical compounds across multiple databases to aggregate property data.
Mapping gene lists to metabolic pathways to identify biological significance.
Automating the retrieval of protein sequences and functional annotations for batch analysis.

About

Key Features

Asynchronous execution and monitoring of NCBI BLAST sequence similarity searches.
Unified API access to 40+ bioinformatics services including UniProt, KEGG, and Reactome.
Detailed metabolic pathway discovery and protein-protein interaction network extraction.
Robust identifier mapping between diverse biological databases (e.g., KEGG to UniProt).
5 GitHub stars
Comprehensive chemical compound searching across ChEBI, ChEMBL, and PubChem.

Use Cases

Cross-referencing chemical compounds across multiple databases to aggregate property data.
Mapping gene lists to metabolic pathways to identify biological significance.
Automating the retrieval of protein sequences and functional annotations for batch analysis.