alzabo

A schema management and documentation tool for graph-shaped knowledge sources. Example.

Alzabo defines a a simple schema format for graph databases or other storage formats. It's semantically close to RDF.

Core:

• Defines an .edn schema format, with semantics similar to RDF.
• Tool to generate HTML documentation from Alzabo schemas
• A Clojurescript applet to do autocompletion over Alzabo schemas (appears as part of HTML doc)

Import:

• Tool to convert the CANDEL schema into Alzabo schema
• Tool to convert OpenAPI YAML format into Alzabo schemas
• Tool to convert GraphQL format into Alzabo schema

Export:

• Tool to generate Datomic schemas from Alzabo format

Schema Generation:

• Tool to generate arbitrary domain schemas

Schema format

See documentation

Credits & License

Originally developed by Mike Travers at the Parker Institute for Cancer Immunotherapy as part of the CANDEL project.

Released under Apache 2.0 License.

Installation

To generate documentation, you need graphviz installed. On the Mac, you can do this with

$ brew install graphviz

Usage

Install as local library

lein with-profile library, prod install

Publish on Clojars

From a real terminal (not Emacs)

lein deploy clojars

You will need to supply credentials (user name and authentication token).

Commands

You can run these commands with lein run <config> <cmd>.

$ lein run <config> documentation 

Generates documentation from the given Alzabo schema file.

$ lein run <config> datomic 

Generates a Datomic schema from the given Alzabo schema file.

$ lein run <config> server

Opens the generated documentation in browser..

Use as a library

Add dependency `[hyperphor/alzabo ]

Example

(ns ...
  (:require [hyperphor.alzabo.schema :as schema]
            [hyperphor.alzabo.datomic :as datomic]
			[hyperphor.alzabo.html :as html]))

;; read in a schema file
(let [schema (schema/read-schema <schema.edn>)]

  ;; write out a Datomic schema
  (datomic/write-schema schema "datomic-schema.edn")

  ;; generate documentation 
  (html/schema->html schema "public/schema" {}))

Schema Generation

Alzabo can generate a complete domain ontology for you using an LLM.:

export OPENAI_API_KEY=<your OpenAI key>
lein repl
(full-demo "model rocketry" "rockets")  ; or use your favorint doamin

History

• 1.0.0 Initial open source release, as org.parkerici/alzabo
• 1.0.1 Renamed to org.candelbio/alzabo; mods for use as a library, OpenAPI import
• 1.1.0 GitHub Pages deployment of generated documentation
• 1.2.1 GraphQL import, config-driven categories/colors, misc CANDEL/Ganymede integration work
• 1.2.2 Replace clj-http with hato; LLM-based schema/entity generation
• 1.3.0 Incorporate into PICI/okc; renamed to com.hyperphor/alzabo
• 1.3.1 Turn off schema validation which is broken
• 1.3.2 Use ellum, revamp html gen for easier library use
• 1.3.3 output-path as a param to html gen, deprecate config-based paths
• 1.3.4 Only generate edge labels where there's a need
• 1.3.5 Make edge labels plural-aware, upgrade deps
• 1.3.6 Fix Entities section rendering blank for single-category schemas