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references/domains.md

ToolUniverse Tool Domains and Categories

Overview

ToolUniverse integrates 600+ scientific tools across multiple research domains. This document categorizes tools by scientific discipline and use case.

Major Scientific Domains

Bioinformatics

Sequence Analysis: - Sequence alignment and comparison - Multiple sequence alignment (MSA) - BLAST and homology searches - Motif finding and pattern matching

Genomics: - Gene expression analysis - RNA-seq data processing - Variant calling and annotation - Genome assembly and annotation - Copy number variation analysis

Functional Analysis: - Gene Ontology (GO) enrichment - Pathway analysis (KEGG, Reactome) - Gene set enrichment analysis (GSEA) - Protein domain analysis

Example Tools: - GEO data download and analysis - DESeq2 differential expression - KEGG pathway enrichment - UniProt sequence retrieval - VEP variant annotation

Cheminformatics

Molecular Descriptors: - Chemical property calculation - Molecular fingerprints - SMILES/InChI conversion - 3D conformer generation

Drug Discovery: - Virtual screening - Molecular docking - ADMET prediction - Drug-likeness assessment (Lipinski's Rule of Five) - Toxicity prediction

Chemical Databases: - PubChem compound search - ChEMBL bioactivity data - ZINC compound libraries - DrugBank drug information

Example Tools: - RDKit molecular descriptors - AutoDock molecular docking - ZINC library screening - ChEMBL target-compound associations

Structural Biology

Protein Structure: - AlphaFold structure prediction - PDB structure retrieval - Structure alignment and comparison - Binding site prediction - Protein-protein interaction prediction

Structure Analysis: - Secondary structure prediction - Solvent accessibility calculation - Structure quality assessment - Ramachandran plot analysis

Example Tools: - AlphaFold structure prediction - PDB structure download - Fpocket binding site detection - DSSP secondary structure assignment

Proteomics

Protein Analysis: - Mass spectrometry data analysis - Protein identification - Post-translational modification analysis - Protein quantification

Protein Databases: - UniProt protein information - STRING protein interactions - IntAct interaction databases

Example Tools: - UniProt data retrieval - STRING interaction networks - Mass spec peak analysis

Machine Learning

Model Types: - Classification models - Regression models - Clustering algorithms - Neural networks - Deep learning models

Applications: - Predictive modeling - Feature selection - Dimensionality reduction - Pattern recognition - Biomarker discovery

Example Tools: - Scikit-learn models - TensorFlow/PyTorch models - XGBoost predictors - Random forest classifiers

Medical/Clinical

Disease Databases: - OpenTargets disease-target associations - OMIM genetic disorders - ClinVar pathogenic variants - DisGeNET disease-gene associations

Clinical Data: - Electronic health records analysis - Clinical trial data - Diagnostic tools - Treatment recommendations

Example Tools: - OpenTargets disease queries - ClinVar variant classification - OMIM disease lookup - FDA drug approval data

Neuroscience

Brain Imaging: - fMRI data analysis - Brain atlas mapping - Connectivity analysis - Neuroimaging pipelines

Neural Data: - Electrophysiology analysis - Spike train analysis - Neural network simulation

Image Processing

Biomedical Imaging: - Microscopy image analysis - Cell segmentation - Object detection - Image enhancement - Feature extraction

Image Analysis: - ImageJ/Fiji tools - CellProfiler pipelines - Deep learning segmentation

Systems Biology

Network Analysis: - Biological network construction - Network topology analysis - Module identification - Hub gene identification

Modeling: - Systems biology models - Metabolic network modeling - Signaling pathway simulation

Tool Categories by Use Case

Literature and Knowledge

Literature Search: - PubMed article search - Article summarization - Citation analysis - Knowledge extraction

Knowledge Bases: - Ontology queries (GO, DO, HPO) - Database cross-referencing - Entity recognition

Data Access

Public Repositories: - GEO (Gene Expression Omnibus) - SRA (Sequence Read Archive) - PDB (Protein Data Bank) - ChEMBL (Bioactivity database)

API Access: - RESTful API clients - Database query tools - Batch data retrieval

Visualization

Plot Generation: - Heatmaps - Volcano plots - Manhattan plots - Network graphs - Molecular structures

Utilities

Data Processing: - Format conversion - Data normalization - Statistical analysis - Quality control

Workflow Management: - Pipeline construction - Task orchestration - Result aggregation

Finding Tools by Domain

Use domain-specific keywords with Tool_Finder:

# Bioinformatics
tools = tu.run({
    "name": "Tool_Finder_Keyword",
    "arguments": {"description": "RNA-seq genomics", "limit": 10}
})

# Cheminformatics
tools = tu.run({
    "name": "Tool_Finder_Keyword",
    "arguments": {"description": "molecular docking SMILES", "limit": 10}
})

# Structural biology
tools = tu.run({
    "name": "Tool_Finder_Keyword",
    "arguments": {"description": "protein structure PDB", "limit": 10}
})

# Clinical
tools = tu.run({
    "name": "Tool_Finder_Keyword",
    "arguments": {"description": "disease clinical variants", "limit": 10}
})

Cross-Domain Applications

Many scientific problems require tools from multiple domains:

  • Precision Medicine: Genomics + Clinical + Proteomics
  • Drug Discovery: Cheminformatics + Structural Biology + Machine Learning
  • Cancer Research: Genomics + Pathways + Literature
  • Neurodegenerative Diseases: Genomics + Proteomics + Imaging
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