KnoDE: Knowledge Development Environment

Building the Demo Server

nix-env -i leiningen git screen
git clone git@github.com:knocean/knode.git
Clone your desired project (for example, git@github.com:IEDB/ONTIE.git or git@github.com:knocean/knode-example.git)
Set up SSH keys using ssh-keygen (necessary for knode to push edits to the ontology)
Create a named screen session with screen -S knode
Load your ontology into knode state _(if you're setting up an ontology with a load.txt file, you can just do KNODE_PROJECT_DIR=<your project directory> lein run load. Otherwise, you'll need to pass in the project name and files in the proper order. For instance lein run load ONTIE ~/ONTIE/ontology/context.kn ~/ONTIE/ontology/external.tsv ~/ONTIE/ontology/predicates.tsv ~/ONTIE/ontology/index.tsv ~/ONTIE/ontology/templates.kn ~/ONTIE/ontology/ontie.kn)_
KNODE_SSH_PASSPHRASE=<your key passphrase> KNODE_PROJECT_DIR=<your project dir> lein run serve (the first time you run this, it will take a while because new JARs)

Configuration Files

You may provide a set of configuration options via an EDN file. By default, this can be knode.edn in the same directory that you run knode in. In this file, you may specify a number of configurators:

:project-name: name of the project
:project-dir: directory to house resources and knode.db file
:base-iri: base IRI for ontology (default http://ontology.iedb.org/ontology/ONTIE_)
:port: port to run the server on (default 3210)
:database-url: URL to database to store resources and states (default jdbc:sqlite:<absolute path>/knode.db)
:git-repo: path to git repository
:ssh-identity: SSH identity for git (default ~/.ssh/id_rsa)
:ssh-passphrase: SSH passphrase for git
:api-key
:write-file
:resources: see below

To run KnODE from a configuration file (replace knode.edn if necessary):

knode serve knode.edn

To view the configuration settings:

knode config knode.edn

Resources

To load resources from the configuration file (if you are using knode.edn, you do not need to specify the path):

knode load-config

Or:

knode load-config <path to edn>

Resources should be provided as a vector of individual resources. Each resource needs, minimally:

:idspace
:type

You may also include:

:label and/or :title
:description
:homepage

Valid types of resources are:

:local-file: include a :path or :paths to local resources
:obo-published-owl: use the :idspace to download an OBO published resource (must be the same as the OBO ID)
:direct-link: include a :url to point to the remote resource
:obo-github-repo: include a :repo pointing to a .git repository in the standard OBO directory layout

Example Config

{:project-name "ONTIE",
 :resources
 [{:idspace "ONTIE",
   :title "Ontology for Immune Epitopes",
   :description
   "ONTIE includes a range of terms to support the Immune Epitope Database.",
   :homepage "https://ontology.iedb.org",
   :type :local-file,
   :paths
   ["ontology/context.kn"
    "ontology/external.tsv"
    "ontology/predicates.tsv"
    "ontology/index.tsv"
    "ontology/templates.kn"
    "ontology/ontie.kn"]}
  {:idspace "OBI",
   :title "Ontology for Biomedical Investigations",
   :homepage "http://obi-ontology.org",
   :type :obo-published-owl}]}

License

Distributed under the BSD 3-Clause License.

knocean / knode