Is BioServices suitable for drug discovery workflows?

Absolutely. It integrates compound searches from ChEMBL and PubChem with pathway analysis from KEGG, making it ideal for identifying molecular targets.

Can BioServices help with cross-database ID mapping?

Yes, it is highly optimized for mapping identifiers between sources like UniProt, KEGG, Ensembl, PDB, and RefSeq using tools like UniChem.

Does this skill support sequence analysis tasks?

Yes, it can run BLAST searches, perform sequence alignments with MUSCLE, and retrieve FASTA or XML records for protein and genomic sequences.

How does BioServices handle different data formats?

It transparently parses diverse formats including XML, JSON, and TSV, allowing users to manipulate results as Python dictionaries or Pandas DataFrames.

Which biological databases can I access with this skill?

BioServices provides access to over 40 major services including UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO, and NCBI BLAST.

BioServices Bioinformatics Tool

Name: BioServices Bioinformatics Tool
Author: jimmc414

byjimmc414

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324

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Data Science & ML

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

BioServices is a powerful Claude Code skill designed for bioinformatics research and computational biology. It offers a unified Python interface to interact with approximately 40 major biological databases and services, including UniProt, KEGG, ChEMBL, and NCBI. This skill simplifies complex workflows such as cross-database identifier mapping, metabolic pathway discovery, protein-protein interaction mining, and asynchronous sequence similarity searches (BLAST). By abstracting REST and SOAP protocols, it enables Claude to function as an autonomous AI scientist capable of integrating disparate biological data sources into cohesive discovery pipelines.

Key Features

01Asynchronous sequence similarity searching via NCBI BLAST and alignment tools

02324 GitHub stars

03Metabolic pathway discovery and KGML interaction network extraction

04Automated cross-database identifier mapping (e.g., KEGG ID to UniProt AC)

05Unified API access to 40+ bioinformatics services like UniProt, KEGG, and ChEMBL

06Comprehensive chemical compound searching across PubChem, ChEBI, and UniChem

Use Cases

01Mapping identifiers across multiple biological databases to integrate heterogeneous datasets

02Retrieving protein sequences and functional annotations for comparative genomics

03Extracting metabolic pathway interactions to identify potential drug targets or biomarkers

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add jimmc414/kosmos bioservices

For use in Claude.ai and ChatGPT