bioservices

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.

1.49x

Quality

86%

Does it follow best practices?

Impact

91%

1.49x

Average score across 3 eval scenarios

Securityby

Passed

No known issues

Evaluation results

86%

40%

Compound Database Cross-Reference Tool

Cross-database compound mapping

Criteria

Without context

With context

KEGG compound search

100%

KEGG entry retrieval

100%

ChEBI parsing from KEGG

100%

UniChem for ChEMBL

Error handling per compound

60%

80%

Graceful missing values

100%

CSV output file

100%

Verbose suppression

100%

KEGG cpd prefix handling

100%

Summary output

100%

Protein Identifier Harmonization Pipeline

Batch protein identifier conversion

Criteria

Without context

With context

UniProtKB_AC-ID source code

100%

KEGG target database code

100%

Ensembl target database code

100%

Comma-separated batch query

100%

Batch chunking

100%

Rate-limiting delay

100%

Error handling per batch

100%

Missing mapping placeholder

100%

CSV output structure

100%

Progress and summary reporting

100%

Organism specificity

100%

87%

41%

Signaling Pathway Interaction Network Builder

KEGG pathway network extraction

Criteria

Without context

With context

KEGG organism setting

100%

Organism code format

50%

83%

Pathway keyword search

100%

parse_kgml_pathway usage

pathway2sif usage

100%

NetworkX graph construction

100%

GML export

100%

CSV interaction output

100%

Error handling

62%

100%

Verbose suppression

100%

Network summary file

100%

Repository: K-Dense-AI/claude-scientific-skills
Commit: b58ad7e

Evaluated: 27 days ago
Agent: Claude Code
Model: Claude Sonnet 4.6

Table of Contents

Compound Database Cross-Reference Tool Protein Identifier Harmonization Pipeline Signaling Pathway Interaction Network Builder

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