Command Line Interface
Aurelian provides a powerful command-line interface (CLI) for accessing its various agents and utilities. The CLI follows a consistent pattern that allows running agents in either direct query mode or interactive UI mode.
Usage Patterns
UI Mode
To start an agent in UI mode (interactive chat interface):
aurelian <agent-name> --ui
Example:
aurelian diagnosis --ui
This starts the Diagnosis agent with a chat interface where you can interactively ask questions.
Direct Query Mode
To run an agent with a direct query and get the response immediately:
aurelian <agent-name> "your query here"
Example:
aurelian diagnosis "Patient with hypotonia, seizures, and developmental delay"
This processes the query directly and prints the result to the console.
Common Options
All agent commands support these common options:
--model,-m: Specify the model to use for the agent--workdir,-w: Set the working directory (default: "workdir")--share/--no-share: Share the agent UI via public URL (default: no-share)--server-port,-p: Set the server port for UI mode (default: 7860)--ui/--no-ui: Force UI mode even with a query (default: no-ui)
Available Agents
Aurelian provides specialized agents for various scientific and biomedical tasks. Each agent can be accessed via its dedicated subcommand:
| Command | Description |
|---|---|
amigo |
Gene Ontology and gene product annotations |
biblio |
Bibliographic data and citations management |
checklist |
Paper evaluation against established checklists |
chemistry |
Chemical structure analysis |
datasheets |
Extract dataset metadata according to Datasheets for Datasets schema |
diagnosis |
Rare disease diagnosis using the Monarch Knowledge Base |
gocam |
Gene Ontology Causal Activity Models |
linkml |
Data modeling and schema validation |
literature |
Scientific publication analysis |
mapper |
Ontology mapping and term translation |
monarch |
Biomedical knowledge graph exploration |
phenopackets |
Standardized phenotype data in GA4GH format |
rag |
Retrieval-augmented generation for document collections |
robot |
Ontology operations and manipulations |
ubergraph |
SPARQL-based ontology queries |
Utility Commands
The CLI also provides several utility commands:
| Command | Description |
|---|---|
fulltext <pmid> |
Download full text for a PubMed article |
websearch <term> |
Search the web for a query term |
geturl <url> |
Retrieve content from a URL |
search-ontology <ontology> <term> |
Search an ontology for a term |
Full Command Reference
main
Main command for Aurelian.
Aurelian provides a collection of specialized agents for various scientific and biomedical tasks. Each agent can be run in either direct query mode or UI mode:
- Direct query mode: Run the agent with a query (e.g.,
aurelian diagnosis "patient with hypotonia"). - UI mode: Run the agent with
--uiflag to start a chat interface.
Some agents also provide utility commands for specific operations.
:param verbose: Verbosity while running. :param quiet: Boolean to be quiet or verbose.
Usage:
main [OPTIONS] COMMAND [ARGS]...
Options:
-v, --verbose
-q, --quiet TEXT
--version Show the version and exit.
--help Show this message and exit.
agent
NEW: Generic agent runner.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main agent [OPTIONS] [QUERY]...
Options:
-a, --agent TEXT The agent to use (if non-default).
-m, --model TEXT The model to use for the agent.
--use-cborg / --no-use-cborg Use CBORG as a model proxy (LBNL account
required). [default: no-use-cborg]
--share / --no-share Share the agent GradIO UI via URL. [default:
no-share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
-w, --workdir TEXT The working directory for the agent.
[default: workdir]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--run-evals / --no-run-evals Run the agent in evaluation mode. [default:
no-run-evals]
--help Show this message and exit.
amigo
Start the AmiGO Agent for Gene Ontology data exploration.
The AmiGO Agent provides access to the Gene Ontology (GO) and gene product annotations. It helps users explore gene functions and ontology relationships.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main amigo [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
aria
Start the Checklist UI (deprecated, use 'checklist' instead).
Usage:
main aria [OPTIONS]
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--help Show this message and exit.
biblio
Start the Biblio Agent for bibliographic data management.
The Biblio Agent helps organize and search bibliographic data and citations. It provides tools for searching a bibliography database, retrieving scientific publications, and accessing web content.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main biblio [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
checklist
Start the Checklist Agent for paper evaluation.
The Checklist Agent evaluates scientific papers against established checklists such as STREAMS, STORMS, and ARRIVE. It helps ensure that papers conform to relevant reporting guidelines and best practices.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main checklist [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
chemistry
Start the Chemistry Agent for chemical structure analysis.
The Chemistry Agent helps interpret and work with chemical structures, formulas, and related information.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main chemistry [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
datasheets
Start the Datasheets for Datasets (D4D) Agent.
The D4D Agent extracts structured metadata from dataset documentation according to the Datasheets for Datasets schema. It can analyze both web pages and PDF documents describing datasets.
Run with a URL for direct mode or with --ui for interactive chat mode.
Usage:
main datasheets [OPTIONS] [URL]
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
diagnosis
Start the Diagnosis Agent for rare disease diagnosis.
The Diagnosis Agent assists in diagnosing rare diseases by leveraging the Monarch Knowledge Base. It helps clinical geneticists evaluate potential conditions based on patient phenotypes.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main diagnosis [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
draw
Start the Draw Agent for creating SVG drawings.
The Draw Agent creates SVG drawings based on text descriptions and provides feedback on drawing quality from an art critic judge. It helps generate visual representations from textual descriptions with a focus on clarity and simplicity.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main draw [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
fulltext
Download full text for a PubMed article.
Usage:
main fulltext [OPTIONS] PMID
Options:
--help Show this message and exit.
gene
Start the Gene Agent for retrieving gene descriptions.
The Gene Agent retrieves descriptions for gene identifiers using the UniProt API. It can process a single gene or a list of genes and returns detailed information about gene function, products, and associations.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main gene [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
geturl
Retrieve content from a URL.
Usage:
main geturl [OPTIONS] URL
Options:
--help Show this message and exit.
github
Start the GitHub Agent for repository interaction.
The GitHub Agent provides a natural language interface for interacting with GitHub repositories. It can list/view pull requests and issues, find connections between PRs and issues, search code, clone repositories, and examine commit history.
Requires GitHub CLI (gh) to be installed and authenticated.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main github [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
goann
Start the GO Annotation Review Agent for evaluating GO annotations.
The GO Annotation Review Agent helps review GO annotations for accuracy and proper evidence. It can evaluate annotations based on evidence codes, identify potential over-annotations, and ensure compliance with GO guidelines, particularly for transcription factors.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main goann [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
--use-cborg / --no-use-cborg Use CBORG as a model proxy (LBNL account
required). [default: no-use-cborg]
-w, --workdir TEXT The working directory for the agent.
[default: workdir]
--share / --no-share Share the agent GradIO UI via URL. [default:
no-share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
gocam
Start the GO-CAM Agent for gene ontology causal activity models.
The GO-CAM Agent helps create and analyze Gene Ontology Causal Activity Models, which describe biological systems as molecular activities connected by causal relationships.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main gocam [OPTIONS] [QUERY]...
Options:
-a, --agent TEXT The agent to use (if non-default).
-m, --model TEXT The model to use for the agent.
--use-cborg / --no-use-cborg Use CBORG as a model proxy (LBNL account
required). [default: no-use-cborg]
--share / --no-share Share the agent GradIO UI via URL. [default:
no-share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
linkml
Start the LinkML Agent for data modeling and schema validation.
The LinkML Agent helps create and validate data models and schemas using the Linked data Modeling Language (LinkML). It can assist in generating schemas, validating data against schemas, and modeling domain knowledge.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main linkml [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
literature
Start the Literature Agent for scientific publication analysis.
The Literature Agent provides tools for analyzing scientific publications, extracting key information, and answering questions about research articles.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main literature [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
mapper
Start the Ontology Mapper Agent for mapping between ontologies.
The Ontology Mapper Agent helps translate terms between different ontologies and vocabularies. It can find equivalent concepts across ontologies and explain relationships.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main mapper [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
-i, --ontologies TEXT Comma-separated list of ontologies to use for the
agent.
--help Show this message and exit.
monarch
Start the Monarch Agent for biomedical knowledge exploration.
The Monarch Agent provides access to relationships between genes, diseases, phenotypes, and other biomedical entities through the Monarch Knowledge Base.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main monarch [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
paperqa
PaperQA management commands for indexing and querying documents.
PaperQA supports PDF, TXT, HTML, and Markdown files in all operations.
Examples: # Index documents in a directory aurelian paperqa index -d /path/to/papers
# Ask a question about indexed papers
aurelian paperqa ask "What is the role of tau protein in Alzheimer's?" -d /path/to/papers
# List indexed papers
aurelian paperqa list -d /path/to/papers
# Run with increased verbosity
aurelian paperqa --verbose index -d /path/to/papers
# Add documents through the agent
# (Using these commands in chat modes like Gradio or MCP)
"Add the paper from /path/to/paper.pdf"
"Add all papers from the directory /path/to/papers/"
Usage:
main paperqa [OPTIONS] COMMAND [ARGS]...
Options:
-v, --verbose Increase verbosity level (-v for INFO, -vv for DEBUG)
-q, --quiet Suppress non-error output
--help Show this message and exit.
ask
Ask a question about the indexed documents.
This command searches the indexed documents for information relevant to the provided query and generates an AI-powered answer with references. Make sure to run the 'index' command first to create an index.
Example: aurelian paperqa ask "What are the key findings on tau proteins?" -d ~/research/papers
Usage:
main paperqa ask [OPTIONS] QUERY
Options:
-d, --directory TEXT Paper directory containing indexed documents
[required]
--help Show this message and exit.
index
Index documents for search and querying.
This command scans the specified directory for documents (PDF, TXT, HTML, MD) and creates a searchable index for them. The index is stored in the .pqa subdirectory of the specified directory.
Example: aurelian paperqa index -d ~/research/papers
Usage:
main paperqa index [OPTIONS]
Options:
-d, --directory TEXT Paper directory containing PDF, TXT, HTML, and MD
files to index [required]
--help Show this message and exit.
list
List documents in the directory and their indexing status.
This command displays all documents (PDF, TXT, HTML, MD) in the specified directory and shows which ones have been indexed. Use this to verify that your documents are properly recognized and indexed.
Example: aurelian paperqa list -d ~/research/papers
Usage:
main paperqa list [OPTIONS]
Options:
-d, --directory TEXT Paper directory containing documents [required]
--help Show this message and exit.
perplexity
Search the web for a query term, with citations.
Usage:
main perplexity [OPTIONS] TERM
Options:
--help Show this message and exit.
phenopackets
Start the Phenopackets Agent for standardized phenotype data.
The Phenopackets Agent helps work with GA4GH Phenopackets, a standard format for sharing disease and phenotype information for genomic medicine.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main phenopackets [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
rag
Start the RAG Agent for document retrieval and generation.
The RAG (Retrieval-Augmented Generation) Agent provides a natural language interface for exploring and searching document collections. It uses RAG techniques to combine search capabilities with generative AI.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main rag [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default:
no-share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
-d, --db-path TEXT The path to the database.
-c, --collection-name TEXT The name of the collection.
--help Show this message and exit.
robot
Start the ROBOT Agent for ontology operations.
The ROBOT Agent provides natural language access to ontology operations and manipulations using the ROBOT tool. It can create, modify, and analyze ontologies through a chat interface.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main robot [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
search-ontology
Search the ontology for the given query term.
Also has side effect of indexing. You may want to pre-index before starting an individual UI.
Usage:
main search-ontology [OPTIONS] ONTOLOGY TERM
Options:
-l, --limit INTEGER Number of results to return. [default: 10]
--help Show this message and exit.
talisman
Start the Talisman Agent for advanced gene analysis.
The Talisman Agent retrieves descriptions for gene identifiers using UniProt and NCBI Entrez. It can process a single gene, protein ID, or a list of genes and returns detailed information. It also can analyze relationships between multiple genes to identify functional connections.
Run with --list and --taxon options for direct mode or with --ui for interactive chat mode. The taxon/species parameter is required to provide proper context for gene analysis.
Examples: aurelian talisman --list "TP53" --taxon "Homo sapiens" aurelian talisman --list "TP53, MDM2" --taxon "Homo sapiens" aurelian talisman --list "DVUA0001, DVUA0002" --taxon "Desulfovibrio vulgaris"
Usage:
main talisman [OPTIONS] [QUERY]...
Options:
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
-l, --list TEXT Comma-separated list of gene identifiers
-t, --taxon TEXT Species/taxon the genes belong to (e.g., 'Homo
sapiens', 'Desulfovibrio vulgaris') [required]
--help Show this message and exit.
ubergraph
Start the UberGraph Agent for SPARQL-based ontology queries.
The UberGraph Agent provides a natural language interface to query ontologies using SPARQL through the UberGraph endpoint. It helps users formulate and execute SPARQL queries without needing to know the full SPARQL syntax.
Run with a query for direct mode or with --ui for interactive chat mode.
Usage:
main ubergraph [OPTIONS] [QUERY]...
Options:
-m, --model TEXT The model to use for the agent.
-w, --workdir TEXT The working directory for the agent. [default:
workdir]
--share / --no-share Share the agent GradIO UI via URL. [default: no-
share]
-p, --server-port INTEGER The port to run the UI server on. [default:
7860]
--ui / --no-ui Start the agent in UI mode instead of direct
query mode. [default: no-ui]
--help Show this message and exit.
websearch
Search the web for a query term.
Usage:
main websearch [OPTIONS] TERM
Options:
--help Show this message and exit.