noctua

name	noctua
description	Use whenever you need to access the GO-CAM store (Noctua). This is accomplished via an API called barista.

About

Use for listing and searching models, create/read/update on models.

Command Line Client

This uses the noctua command line tool, which should have been installed when we ran uv sync

I recommend:

alias barista='uv run noctua barista'

You can get help at any time

barista --help

subcommands also have help

Tokens

Ask your the user to get a barista token. This should be on the test server:

http://noctua-dev.berkeleybop.org/workbench/noctua-landing-page/

Click "login"

The token should be in the environment

export BARISTA_TOKEN=<token>

or in .env

Read Access

To dump a model in minerva JSON:

barista export-model --model 646ff70100002557

This is the low-level triple representation used natively in Noctua

In gocam-yaml:

barista export-model --model 646ff70100002557 -f gocam-yaml

This is the structured version

Search and Browsing models

Most recent 50:

barista list-models --limit 50

All that reference a gene product

barista list-models --gp UniProtKB:Q14457

Search by title

barista list-models --title "immune"

More Information

Please see the /gocam-best-practice skill

Using the Barista Command-Line Tool

The barista command (alias for noctua barista) provides tools for model creation and editing.

Key Commands

Viewing Models

# Export model in Minerva JSON format
barista export-model --model <model-id>

# Export in GO-CAM YAML format
barista export-model --model <model-id> -f gocam-yaml

# List recent models
barista list-models --limit 50

# Search models by gene product
barista list-models --gp UniProtKB:Q14457

# Search models by title
barista list-models --title "immune"

Creating and Editing Models

# Create a new empty model
barista create-model

# Add an individual (molecular activity, BP, or CC)
barista add-individual --model <model-id> --class <GO-term> --assign <variable-name>

# Create a relationship between individuals
barista add-fact --model <model-id> \
  --subject <variable-or-id> \
  --object <variable-or-id> \
  --predicate <relation-id>

# Add evidence to support a relationship
barista add-fact-evidence --model <model-id> \
  --subject <variable-or-id> \
  --object <variable-or-id> \
  --evidence <evidence-code> \
  --reference <PMID>

Important Notes

• Commands use the test server by default; production requires the explicit --live flag
• Use variable names (via --assign) for readability when building complex models
• Production models with state="production" are protected against accidental deletion
• Always add evidence to support facts in models