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Zhongwei Li
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skills/tooluniverse/references/domains.md
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skills/tooluniverse/references/domains.md
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# ToolUniverse Tool Domains and Categories
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## Overview
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ToolUniverse integrates 600+ scientific tools across multiple research domains. This document categorizes tools by scientific discipline and use case.
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## Major Scientific Domains
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### Bioinformatics
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**Sequence Analysis:**
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- Sequence alignment and comparison
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- Multiple sequence alignment (MSA)
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- BLAST and homology searches
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- Motif finding and pattern matching
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**Genomics:**
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- Gene expression analysis
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- RNA-seq data processing
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- Variant calling and annotation
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- Genome assembly and annotation
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- Copy number variation analysis
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**Functional Analysis:**
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- Gene Ontology (GO) enrichment
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- Pathway analysis (KEGG, Reactome)
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- Gene set enrichment analysis (GSEA)
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- Protein domain analysis
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**Example Tools:**
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- GEO data download and analysis
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- DESeq2 differential expression
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- KEGG pathway enrichment
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- UniProt sequence retrieval
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- VEP variant annotation
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### Cheminformatics
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**Molecular Descriptors:**
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- Chemical property calculation
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- Molecular fingerprints
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- SMILES/InChI conversion
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- 3D conformer generation
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**Drug Discovery:**
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- Virtual screening
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- Molecular docking
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- ADMET prediction
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- Drug-likeness assessment (Lipinski's Rule of Five)
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- Toxicity prediction
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**Chemical Databases:**
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- PubChem compound search
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- ChEMBL bioactivity data
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- ZINC compound libraries
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- DrugBank drug information
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**Example Tools:**
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- RDKit molecular descriptors
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- AutoDock molecular docking
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- ZINC library screening
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- ChEMBL target-compound associations
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### Structural Biology
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**Protein Structure:**
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- AlphaFold structure prediction
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- PDB structure retrieval
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- Structure alignment and comparison
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- Binding site prediction
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- Protein-protein interaction prediction
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**Structure Analysis:**
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- Secondary structure prediction
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- Solvent accessibility calculation
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- Structure quality assessment
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- Ramachandran plot analysis
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**Example Tools:**
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- AlphaFold structure prediction
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- PDB structure download
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- Fpocket binding site detection
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- DSSP secondary structure assignment
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### Proteomics
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**Protein Analysis:**
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- Mass spectrometry data analysis
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- Protein identification
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- Post-translational modification analysis
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- Protein quantification
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**Protein Databases:**
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- UniProt protein information
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- STRING protein interactions
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- IntAct interaction databases
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**Example Tools:**
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- UniProt data retrieval
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- STRING interaction networks
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- Mass spec peak analysis
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### Machine Learning
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**Model Types:**
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- Classification models
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- Regression models
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- Clustering algorithms
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- Neural networks
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- Deep learning models
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**Applications:**
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- Predictive modeling
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- Feature selection
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- Dimensionality reduction
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- Pattern recognition
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- Biomarker discovery
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**Example Tools:**
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- Scikit-learn models
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- TensorFlow/PyTorch models
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- XGBoost predictors
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- Random forest classifiers
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### Medical/Clinical
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**Disease Databases:**
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- OpenTargets disease-target associations
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- OMIM genetic disorders
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- ClinVar pathogenic variants
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- DisGeNET disease-gene associations
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**Clinical Data:**
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- Electronic health records analysis
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- Clinical trial data
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- Diagnostic tools
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- Treatment recommendations
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**Example Tools:**
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- OpenTargets disease queries
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- ClinVar variant classification
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- OMIM disease lookup
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- FDA drug approval data
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### Neuroscience
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**Brain Imaging:**
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- fMRI data analysis
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- Brain atlas mapping
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- Connectivity analysis
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- Neuroimaging pipelines
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**Neural Data:**
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- Electrophysiology analysis
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- Spike train analysis
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- Neural network simulation
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### Image Processing
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**Biomedical Imaging:**
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- Microscopy image analysis
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- Cell segmentation
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- Object detection
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- Image enhancement
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- Feature extraction
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**Image Analysis:**
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- ImageJ/Fiji tools
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- CellProfiler pipelines
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- Deep learning segmentation
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### Systems Biology
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**Network Analysis:**
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- Biological network construction
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- Network topology analysis
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- Module identification
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- Hub gene identification
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**Modeling:**
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- Systems biology models
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- Metabolic network modeling
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- Signaling pathway simulation
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## Tool Categories by Use Case
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### Literature and Knowledge
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**Literature Search:**
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- PubMed article search
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- Article summarization
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- Citation analysis
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- Knowledge extraction
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**Knowledge Bases:**
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- Ontology queries (GO, DO, HPO)
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- Database cross-referencing
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- Entity recognition
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### Data Access
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**Public Repositories:**
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- GEO (Gene Expression Omnibus)
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- SRA (Sequence Read Archive)
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- PDB (Protein Data Bank)
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- ChEMBL (Bioactivity database)
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**API Access:**
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- RESTful API clients
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- Database query tools
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- Batch data retrieval
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### Visualization
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**Plot Generation:**
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- Heatmaps
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- Volcano plots
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- Manhattan plots
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- Network graphs
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- Molecular structures
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### Utilities
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**Data Processing:**
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- Format conversion
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- Data normalization
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- Statistical analysis
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- Quality control
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**Workflow Management:**
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- Pipeline construction
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- Task orchestration
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- Result aggregation
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## Finding Tools by Domain
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Use domain-specific keywords with Tool_Finder:
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```python
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# Bioinformatics
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tools = tu.run({
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"name": "Tool_Finder_Keyword",
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"arguments": {"description": "RNA-seq genomics", "limit": 10}
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})
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# Cheminformatics
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tools = tu.run({
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"name": "Tool_Finder_Keyword",
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"arguments": {"description": "molecular docking SMILES", "limit": 10}
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})
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# Structural biology
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tools = tu.run({
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"name": "Tool_Finder_Keyword",
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"arguments": {"description": "protein structure PDB", "limit": 10}
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})
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# Clinical
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tools = tu.run({
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"name": "Tool_Finder_Keyword",
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"arguments": {"description": "disease clinical variants", "limit": 10}
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})
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```
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## Cross-Domain Applications
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Many scientific problems require tools from multiple domains:
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- **Precision Medicine**: Genomics + Clinical + Proteomics
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- **Drug Discovery**: Cheminformatics + Structural Biology + Machine Learning
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- **Cancer Research**: Genomics + Pathways + Literature
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- **Neurodegenerative Diseases**: Genomics + Proteomics + Imaging
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