How does this help with metabolic pathway analysis?

It allows you to search for pathways by name or gene ID, parse KGML files, and extract protein interaction networks for specific organisms like humans or yeast.

Can I use this skill to map IDs between different databases?

Yes, BioServices excels at identifier mapping, allowing you to convert between UniProt, KEGG, Ensembl, and many others.

Which databases does the BioServices skill support?

It supports over 40 services, including major databases like UniProt, KEGG, ChEMBL, PubChem, PDB, and Reactome.

Does it support sequence alignment?

Yes, it provides programmatic access to NCBI BLAST and other tools for sequence similarity searches and alignments.

BioServices Bioinformatics

Name: BioServices Bioinformatics
Author: Zehong-Wang

byZehong-Wang

0•

Data Science & ML

Accesses over 40 bioinformatics web services and databases for biological data retrieval and analysis within Python workflows.

BioServices is a comprehensive Python interface for interacting with major bioinformatics platforms like UniProt, KEGG, ChEMBL, and NCBI. It enables researchers and developers to programmatically retrieve sequences, map identifiers across different databases, analyze metabolic pathways, and perform sequence alignments without needing to manually handle complex REST or SOAP protocols. This skill is ideal for building automated biological data pipelines, conducting cross-database queries, and integrating diverse biological resources into a unified analysis environment.

Key Features

01Advanced pathway discovery and protein-protein interaction mapping

020 GitHub stars

03Seamless identifier mapping between disparate biological data sources

04Simplified retrieval of chemical compound data and gene ontology terms

05Unified API for 40+ bioinformatics databases including UniProt and KEGG

06Automated sequence analysis with integrated BLAST and MUSCLE support

Use Cases

01Conducting large-scale metabolic pathway analysis for specific organisms

02Building automated pipelines for protein sequence annotation and structure retrieval

03Mapping gene or protein identifiers between different research databases at scale

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos bioservices

For use in Claude.ai and ChatGPT

Download Skill