How does it handle identifier mapping?

It leverages services like UniProt and UniChem to convert biological identifiers between different databases, such as mapping KEGG gene IDs to UniProt accessions.

Can I use this for sequence alignment?

Yes, the skill supports sequence analysis tasks including running BLAST searches and alignments via services like NCBIblast.

Does it support metabolic pathway analysis?

Yes, it provides specialized tools for KEGG and Reactome to search pathways, extract KGML data, and convert pathway information into Simple Interaction Format (SIF).

What is the primary purpose of the BioServices skill?

BioServices provides a unified Python interface to programmatically interact with over 40 major bioinformatics web services, allowing for complex multi-database workflows.

What databases are supported for compound searches?

The skill supports major chemical databases including ChEBI, ChEMBL, PubChem, and KEGG Compound.

BioServices Bioinformatics

Name: BioServices Bioinformatics
Author: Microck

byMicrock

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Data Science & ML

Provides a unified Python interface for accessing over 40 major bioinformatics web services and databases including UniProt, KEGG, and ChEMBL.

About

BioServices is a comprehensive Claude Code skill that streamlines complex bioinformatics workflows by providing programmatic access to a vast network of biological databases. It enables developers and researchers to perform cross-database queries, map identifiers between disparate systems, analyze metabolic pathways, and run sequence alignments without manually navigating individual REST or SOAP APIs. This skill is particularly valuable for building integrated data pipelines that require data from multiple sources like UniProt for proteins, KEGG for pathways, and PubChem for chemicals, handling both protocol transparency and data parsing.

Key Features

Advanced pathway analysis and protein-protein interaction network extraction
Unified access to 40+ bioinformatics services via a single Python API
Programmatic execution of BLAST searches and sequence alignments
Integrated compound database searching across ChEBI, ChEMBL, and PubChem
Automated identifier mapping between databases like UniProt, Ensembl, and KEGG
81 GitHub stars

Use Cases

Cross-referencing protein identifiers and metabolic pathways for genomic research
Building automated pipelines for multi-database biological data retrieval and normalization
Mapping chemical compounds across disparate drug and molecule databases

About

Key Features

Advanced pathway analysis and protein-protein interaction network extraction
Unified access to 40+ bioinformatics services via a single Python API
Programmatic execution of BLAST searches and sequence alignments
Integrated compound database searching across ChEBI, ChEMBL, and PubChem
Automated identifier mapping between databases like UniProt, Ensembl, and KEGG
81 GitHub stars

Use Cases

Cross-referencing protein identifiers and metabolic pathways for genomic research
Building automated pipelines for multi-database biological data retrieval and normalization
Mapping chemical compounds across disparate drug and molecule databases