Can I use this skill to convert gene or protein IDs?

Yes, it excels at identifier mapping between various databases like UniProtKB, KEGG, Ensembl, RefSeq, and chemical databases via UniChem.

Does it support sequence alignment tools like BLAST?

Yes, the skill provides programmatic methods to run NCBI BLAST jobs and other sequence alignment tools like MUSCLE.

How does BioServices handle different API protocols?

It transparently manages both REST and SOAP/WSDL protocols, providing a consistent, high-level Pythonic interface for all integrated services.

What databases are supported by the BioServices skill?

BioServices supports over 40 services, including UniProt, KEGG, ChEMBL, PubChem, PDB, Reactome, QuickGO, and BioMart.

Is an email address required for NCBI services?

Yes, many services like NCBI BLAST require a valid email address as a parameter to track usage and communicate about job status.

BioServices Bioinformatics Toolkit

Name: BioServices Bioinformatics Toolkit
Author: K-Dense-AI

byK-Dense-AI

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3,717

数据科学与机器学习

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

关于

BioServices is a comprehensive scientific skill that provides programmatic access to approximately 40 major bioinformatics databases, including UniProt, KEGG, ChEMBL, and PubChem. It simplifies complex biological research workflows by handling REST and SOAP/WSDL protocols transparently, allowing researchers to perform cross-database queries, map identifiers between different standards, and conduct pathway or sequence analysis directly within their coding environment without manually navigating multiple web interfaces.

主要功能

Unified programmatic access to 40+ bioinformatics databases
Automated biological pathway discovery and network extraction via KEGG
Integrated sequence analysis tools including NCBI BLAST and MUSCLE
Support for chemical compound searches across ChEBI and PubChem
Robust identifier mapping between UniProt, KEGG, Ensembl, and RefSeq
3,717 GitHub stars

使用场景

Mapping biological identifiers across multiple genomic and proteomic databases
Automating protein sequence retrieval and functional annotation workflows
Analyzing metabolic pathways and extracting protein-protein interaction networks

关于

主要功能

Unified programmatic access to 40+ bioinformatics databases
Automated biological pathway discovery and network extraction via KEGG
Integrated sequence analysis tools including NCBI BLAST and MUSCLE
Support for chemical compound searches across ChEBI and PubChem
Robust identifier mapping between UniProt, KEGG, Ensembl, and RefSeq
3,717 GitHub stars

使用场景

Mapping biological identifiers across multiple genomic and proteomic databases
Automating protein sequence retrieval and functional annotation workflows
Analyzing metabolic pathways and extracting protein-protein interaction networks