Can I use this for identifier mapping?

Yes, the skill excels at converting identifiers between different biological databases, such as mapping UniProtKB AC-IDs to KEGG, Ensembl, or RefSeq.

Does it support sequence alignment and BLAST searches?

Yes, it provides programmatic interfaces for running BLAST searches and sequence alignments (like MUSCLE) through web services.

What biological databases are supported by this skill?

BioServices supports over 40 major bioinformatics databases, including UniProt for protein data, KEGG and Reactome for pathways, and ChEMBL and PubChem for chemical compounds.

How does it handle data formats like FASTA or XML?

The skill can retrieve data in various formats including FASTA, XML, and TSV, and is designed to integrate with tools like Pandas and BioPython for further processing.

Do I need individual API keys for all services?

Most services are public and do not require individual keys, though specific services like NCBI BLAST require an email address for rate-limiting and notification purposes.

Bioinformatics Services (BioServices)

Name: Bioinformatics Services (BioServices)
Author: Activer007

byActiver007

データサイエンスとML

Provides programmatic access to over 40 bioinformatics web services and databases for integrated biological data analysis.

概要

BioServices is a comprehensive Python-based skill that bridges the gap between biological research and programmatic data retrieval. It enables users to query major databases like UniProt, KEGG, and ChEMBL, perform complex identifier mapping, and automate sequence analysis workflows. It is particularly useful for researchers and developers building multi-database bioinformatics pipelines, allowing for the seamless integration of protein data, metabolic pathways, and chemical compound information within a single environment.

主な機能

Comprehensive metabolic pathway and gene function analysis
Seamless cross-database identifier mapping and conversion
0 GitHub stars
Automated sequence similarity searches via integrated NCBI BLAST
Protein-protein interaction data retrieval from PSICQUIC
Unified access to 40+ bioinformatics services (UniProt, KEGG, PDB, etc.)

ユースケース

Extracting and analyzing metabolic pathway networks for specific organisms
Mapping compound identifiers across chemical databases for drug discovery workflows
Automating multi-step protein characterization and functional annotation pipelines

概要

主な機能

Comprehensive metabolic pathway and gene function analysis
Seamless cross-database identifier mapping and conversion
0 GitHub stars
Automated sequence similarity searches via integrated NCBI BLAST
Protein-protein interaction data retrieval from PSICQUIC
Unified access to 40+ bioinformatics services (UniProt, KEGG, PDB, etc.)

ユースケース

Extracting and analyzing metabolic pathway networks for specific organisms
Mapping compound identifiers across chemical databases for drug discovery workflows
Automating multi-step protein characterization and functional annotation pipelines