From 26d4fde324e1d1ace173203c64d5ba29c876e21c Mon Sep 17 00:00:00 2001 From: Vinayak Agarwal Date: Sun, 26 Oct 2025 18:52:50 -0700 Subject: [PATCH] Updated skill descrtipotions to resolve possible conflicts in their use --- scientific-databases/kegg-database/SKILL.md | 2 +- scientific-databases/pubmed-database/SKILL.md | 2 +- scientific-databases/uniprot-database/SKILL.md | 2 +- scientific-packages/biopython/SKILL.md | 2 +- scientific-packages/bioservices/SKILL.md | 2 +- scientific-packages/datamol/SKILL.md | 2 +- scientific-packages/gget/SKILL.md | 2 +- scientific-packages/rdkit/SKILL.md | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/scientific-databases/kegg-database/SKILL.md b/scientific-databases/kegg-database/SKILL.md index e301232..9a96cf0 100644 --- a/scientific-databases/kegg-database/SKILL.md +++ b/scientific-databases/kegg-database/SKILL.md @@ -1,6 +1,6 @@ --- name: kegg-database -description: "Query KEGG REST API for pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion, compound structures, for systems biology and enrichment analysis." +description: "Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control." --- # KEGG Database diff --git a/scientific-databases/pubmed-database/SKILL.md b/scientific-databases/pubmed-database/SKILL.md index a0c4de6..b79ae77 100644 --- a/scientific-databases/pubmed-database/SKILL.md +++ b/scientific-databases/pubmed-database/SKILL.md @@ -1,6 +1,6 @@ --- name: pubmed-database -description: "Search PubMed biomedical literature. Advanced queries with Boolean/MeSH/field tags, E-utilities API access, batch processing, citation management, for literature review and systematic analysis." +description: "Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations." --- # PubMed Database diff --git a/scientific-databases/uniprot-database/SKILL.md b/scientific-databases/uniprot-database/SKILL.md index 86e42bb..bf389f6 100644 --- a/scientific-databases/uniprot-database/SKILL.md +++ b/scientific-databases/uniprot-database/SKILL.md @@ -1,6 +1,6 @@ --- name: uniprot-database -description: "Query UniProt protein database REST API. Search proteins by name/gene/accession, retrieve sequences (FASTA), annotations, ID mapping, Swiss-Prot/TrEMBL, GO terms, for protein analysis." +description: "Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control." --- # UniProt Database diff --git a/scientific-packages/biopython/SKILL.md b/scientific-packages/biopython/SKILL.md index 930c466..863149b 100644 --- a/scientific-packages/biopython/SKILL.md +++ b/scientific-packages/biopython/SKILL.md @@ -1,6 +1,6 @@ --- name: biopython -description: "Toolkit for computational molecular biology. Manipulate sequences, parse biological file formats (FASTA, GenBank, FASTQ, PDB), access NCBI databases, run BLAST, analyze structures, build phylogenetic trees, for bioinformatics workflows." +description: "Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database." --- # Biopython: Computational Molecular Biology in Python diff --git a/scientific-packages/bioservices/SKILL.md b/scientific-packages/bioservices/SKILL.md index 98bb93e..4205490 100644 --- a/scientific-packages/bioservices/SKILL.md +++ b/scientific-packages/bioservices/SKILL.md @@ -1,6 +1,6 @@ --- name: bioservices -description: "Access 40+ bio web services (UniProt, KEGG, ChEMBL, PubChem, BLAST, QuickGO, Reactome). Retrieve data, map IDs, pathway analysis, for multi-database integration workflows." +description: "Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database)." --- # BioServices diff --git a/scientific-packages/datamol/SKILL.md b/scientific-packages/datamol/SKILL.md index 4313dd5..be4bc92 100644 --- a/scientific-packages/datamol/SKILL.md +++ b/scientific-packages/datamol/SKILL.md @@ -1,6 +1,6 @@ --- name: datamol -description: "Pythonic RDKit wrapper for cheminformatics. SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing, for drug discovery workflows." +description: "Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly." --- # Datamol Cheminformatics Skill diff --git a/scientific-packages/gget/SKILL.md b/scientific-packages/gget/SKILL.md index 8c8d861..b5ef2a3 100644 --- a/scientific-packages/gget/SKILL.md +++ b/scientific-packages/gget/SKILL.md @@ -1,6 +1,6 @@ --- name: gget -description: "Bioinformatics query toolkit. Gene info (Ensembl/UniProt), BLAST, AlphaFold, ARCHS4 expression, Enrichr, OpenTargets, COSMIC, genome downloads, CLI/Python, for rapid database queries." +description: "CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices." --- # gget diff --git a/scientific-packages/rdkit/SKILL.md b/scientific-packages/rdkit/SKILL.md index a3005fc..0326db7 100644 --- a/scientific-packages/rdkit/SKILL.md +++ b/scientific-packages/rdkit/SKILL.md @@ -1,6 +1,6 @@ --- name: rdkit -description: "Cheminformatics toolkit for molecules. Parse SMILES/SDF, calculate descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, for drug discovery." +description: "Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms." --- # RDKit Cheminformatics Toolkit