OmniBar
Context-aware command surface — search databases, ask the assistant, query tables, navigate the canvas, and capture findings from a single interface
The OmniBar is the primary interaction surface in the Omics-OS Cloud workspace. It combines database search, an AI assistant, and workspace actions into a single keyboard-driven overlay. Press Cmd+Space (or Ctrl+Space) to open it anywhere on the canvas.
Three Modes
The OmniBar operates in three modes. Tab behavior depends on context: if you have typed text matching a tag, Tab selects that tag. If the input is empty and no tag is selected, Tab switches to Assist mode.
| Mode | What It Does | Activated By |
|---|---|---|
| Search | Tag-scoped federated search across 8 biological databases and workspace | Default when opened |
| Assist | AI assistant with workspace context, table queries, and canvas navigation | Press Tab, or type a natural language question |
| Act | Ticket and finding capture flow | Triggered by assistant or classification |
Opening the OmniBar
| Entry Point | How |
|---|---|
| Global shortcut | Cmd+Space (macOS) or Ctrl+Space (Windows/Linux) |
| Canvas node | Right-click a node → assistant opens with that node as context |
| Canvas edge | Click an edge → opens with source/target context |
| Footer toolbar | Click Search in the canvas footer |
The OmniBar adapts its context based on how it was opened:
- Cockpit — General workspace context, no focused node
- Component — Opened from a specific node; injects node label, type, table schema, and selection narrative
- Edge — Opened from a canvas edge; injects source and target node labels
Search Mode
Tag-Based Search
Select a tag to scope your search, then type your query. This prevents ambiguity (e.g., "TP53" could be a gene, protein, or literature search).
Open the OmniBar
Press Cmd+Space on the canvas.
Select a tag
Type a few letters (e.g., prot) and press Tab to select the Protein tag.
Search
Type your query (e.g., TP53). Results appear in real-time with 300ms debounce.
Select a result
Press Enter or click a result. A canvas node appears automatically.
Database Tags (8)
| Tag | Source | Creates | Example Queries |
|---|---|---|---|
| Protein | UniProt (reviewed) | 3D structure (Mol*) or InfoCard | TP53, P04637, insulin receptor |
| Gene | NCBI Gene (human-first) | Gene InfoCard | BRCA1, EGFR, HER2/neu |
| Structure | RCSB PDB | 3D structure (Mol* viewer) | ribosome, 1CRN, kinase |
| Literature | PubMed | Citation InfoCard | CRISPR, "single cell sequencing" |
| Compound | PubChem | Compound InfoCard | aspirin, imatinib |
| Dataset | NCBI GEO | Dataset InfoCard | single cell RNA, PBMC scRNA |
| Pathway | KEGG Pathways | Interactive pathway map | glycolysis, MAPK, mTOR |
| Sequence | NCBI Nucleotide | Circular/linear genome map | pUC19, SARS-CoV-2 |
Entity facets: Protein and Gene tags have sub-badges after selection. Protein offers Structure, Sequence, Info, and Pathways facets. Gene offers Info, Literature, and Pathways.
Workspace Tags (3)
| Tag | Searches | Action |
|---|---|---|
| File | Visualization files (.pdb, .cif, .bam, .vcf, .gbk) | Opens as viewer node |
| Plot | Plots from current session | Materializes or scrolls to plot |
| Session | All user sessions | Switches to selected session |
Action Tags (2)
| Tag | Action |
|---|---|
| Lobster | Opens chat with query pre-filled |
| Command | Executes a slash command (/help, /status, /tokens) |
Assist Mode
Press Tab to switch to Assist mode. The OmniBar becomes a context-aware AI assistant powered by PI — the shared assistant core that runs across all Omics-OS surfaces.
Enter sends your question. Cmd+Enter sends in deep mode (more thorough reasoning). Shift+Enter promotes to full chat panel.
The assistant knows:
- What node you have focused (label, type, table schema)
- What datasets are loaded in your session
- Your canvas layout and recent actions
- Your selection narrative (if you selected data points)
Assistant Tools
| Tool | What It Does |
|---|---|
| table_query | Runs SQL against a focused DataTable via DuckDB-WASM in the browser. Table is always named obs. Returns up to 50 rows. |
| focus_node | Scrolls the canvas viewport to a specific node by ID |
| submit_record | Captures a finding (stored with ontology triplets) or opens a ticket composer |
| search_database | Searches biological databases without leaving assist mode |
| update_memory | Stores a durable preference or fact for future sessions |
The assistant is designed for quick interactions (max 5 turns). For deeper analysis, it promotes to the full Lobster chat panel.
Debug
Type <context> in assist mode to copy the full system prompt and registered tools to your clipboard — useful for understanding what the assistant sees.
Act Mode
Act mode activates when the assistant classifies your input as a report (bug, feature, feedback) or when you trigger submit_record with type=ticket.
The flow:
- Classifying — Assistant determines report category
- Reporting — Ticket Composer opens with pre-filled context
- Submitting — Report is sent
- Submitted — Confirmation (auto-dismisses after 5s)
Canvas Nodes
Each search result creates a node on the canvas:
| Source | Node Type | Interactive |
|---|---|---|
| Protein (PDB match) | MolstarNode (1200x800) | Rotate, zoom, measure, restyle |
| Protein (no PDB) | InfoCard (400x300) | UniProt link |
| Gene | InfoCard (400x300) | NCBI link |
| Structure | MolstarNode (1200x800) | Full Mol* controls |
| Literature | InfoCard (400x300) | PubMed link |
| Compound | InfoCard (400x300) | PubChem link |
| Dataset | InfoCard (400x300) | GEO link |
| Pathway | PathwayNode (1200x800) | Click entities, zoom, layout |
| Sequence | CgviewNode (800x800) | Zoom, rotate, features |
All nodes auto-position to avoid overlaps.
Keyboard Reference
No tag selected (Search mode):
| Key | Action |
|---|---|
| Type text | Fuzzy-matches tag suggestions |
| Tab | Select tag / switch to Assist mode |
| Enter | Select highlighted tag or result |
| Arrow Up/Down | Navigate suggestions |
| Escape | Close OmniBar |
Tag selected:
| Key | Action |
|---|---|
| Type text | Searches the selected database |
| Enter | Execute highlighted result |
| Backspace (empty) | Clear tag, return to tag selection |
| Escape | First: clear tag. Second: close |
Assist mode:
| Key | Action |
|---|---|
| Enter | Send message (quick mode) |
| Cmd+Enter | Send message (deep mode) |
| Shift+Enter | Promote to full Lobster chat |
| Tab | Switch back to Search mode |
| Escape | Close OmniBar |
Troubleshooting
OmniBar does not open — The canvas must have focus. Click on the canvas background first, then press Cmd+Space. The shortcut is disabled inside chat input fields and text editors.
table_query returns no results — A DataTable node must be focused (selected) on the canvas. The SQL runs against the focused table only. The table is always named obs in queries.
No results found in search — Try alternative names or accession IDs. Use P04637 instead of TP53 for exact UniProt match. Quoted phrases enable exact-match in Literature.