How does this skill handle data formats?

It manages various formats including XML, JSON, and TSV, and integrates easily with Pandas for tabular data or BioPython for sequence analysis.

Which biological databases can I access with this skill?

You can access over 40 major services including UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO, and PDB.

Can I run sequence alignments using this skill?

Yes, BioServices includes wrappers for NCBI BLAST, allowing you to run similarity searches and retrieve results directly into your workflow.

Are there any requirements for using NCBI BLAST services?

Yes, NCBI requires a valid email address for their API usage policies when running asynchronous BLAST jobs.

Does BioServices support identifier mapping?

Yes, it provides robust tools to convert identifiers between different biological databases, such as mapping UniProt IDs to KEGG or Ensembl.

BioServices Bioinformatics Toolkit

Name: BioServices Bioinformatics Toolkit
Author: Microck

byMicrock

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数据科学与机器学习

Accesses and integrates over 40 bioinformatics web services and databases through a unified Python interface.

关于

BioServices is a comprehensive Python library that provides programmatic access to major biological databases, including UniProt, KEGG, and ChEMBL. It simplifies complex bioinformatics workflows by offering a unified API for tasks such as protein sequence retrieval, metabolic pathway analysis, chemical compound searches, and cross-database identifier mapping. This skill is essential for researchers and developers automating biological data pipelines, as it handles both REST and SOAP protocols transparently while ensuring consistent data handling across various biological domains.

主要功能

89 GitHub stars
Programmatic access to 40+ bioinformatics services including UniProt and KEGG
Automated metabolic pathway discovery and network extraction
Unified API for multi-database queries and identifier mapping
Transparent handling of REST and SOAP/WSDL communication protocols
Integrated sequence similarity searching via NCBI BLAST

使用场景

Building automated protein characterization and annotation pipelines
Mapping chemical identifiers across disparate drug and compound databases
Extracting and analyzing protein-protein interaction networks from pathways

关于

主要功能

89 GitHub stars
Programmatic access to 40+ bioinformatics services including UniProt and KEGG
Automated metabolic pathway discovery and network extraction
Unified API for multi-database queries and identifier mapping
Transparent handling of REST and SOAP/WSDL communication protocols
Integrated sequence similarity searching via NCBI BLAST

使用场景

Building automated protein characterization and annotation pipelines
Mapping chemical identifiers across disparate drug and compound databases
Extracting and analyzing protein-protein interaction networks from pathways