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Protege 5.5 setup for Mondo Editors

(This was adopted from the Gene Ontology editors guide)

Operating System

These instructions are for Mac OS

Protege version

As of August 2019, Mondo editors are using Protege version 5.5.0

Download and install Protege

Increase memory in Protege

  1. Protege needs at least 4G of RAM to cope with Mondo, ideally use 12G or 16G if your machine can handle it.
  2. If running from Protege.app on a mac, open the /Applications/Protege-5.5.0/Protégé.app/Contents/info.plist file
  3. Below the line: -Xss16M
  4. Insert another line: -Xmx12G
  5. Note - if you have issues opening Protege, then reduce the memory, try 10G (or lower) instead.

Add ELK reasoner

These instructions are written for Mac users.

Install ELK 0.5

  • When downloaded, unzip and copy puli and elk jars (two .jar files) in the unpacked directory.

  • Paste these files in your Protege plugin directory, as described below. This can be done via one of two ways:

Approach 1

  1. Paste these files in your Protege plugin directory. This is in one of two locations:
    • ~/.Protege/plugins (note this is usually hidden from finder, but you can see it in the terminal) or
    • Go to Protege in Applications (Finder), right click, 'Show package contents' -> Java -> plugins
  2. Copy and paste the two files into the plugins directory
  3. Restart Protege. You should see ELK 0.5 installed in your Reasoner menu.

For a video showing how to install Elk on a Mac, click here

Approach 2

  1. In Terminal: open ~/.Protege, then click on plugins
  2. Click on plugins
  3. Copy and paste the two files into the plugins directory
  4. Restart Protege. You should see ELK 0.5 installed in your Reasoner menu.

Important: it seems Elk 0.5 does not work with all versions of Protege, in particular, 5.2 and below. These instructions were only tested with Protege 5.5.

### Remove the old Elk Reasoner It may be necessary to remove the old Elk reasoner.

  1. in your terminal, type: open ~/.Protege/
  2. go to plugins
  3. delete: org.semanticweb.elk.jar
  4. Restart Protege

Fix memory settings

  • Protege needs at least 4G of RAM to cope with Mondo, ideally use 12G or 16G if your machine can handle it.
  • If running from Protege.app on a mac, open the /Applications/Protege-5.5.0/Protégé.app/Contents/info.plist file
  • Below the line: <string>-Xss16M</string>
  • Insert another line: <string>-Xmx12G</string>

Note - if you have issues opening Protege, then reduce the memory, try 10G (or lower) instead.

Instructions for new Protege users

Obtaining your ID range

  • Curators and projects are assigned specific Mondo term ID ranges by senior editors.
  • These ID ranges are stored in the file: mondo-idranges.owl
  • NOTE: You should only use IDs within your range.

Setting ID range

  • Once you have your assigned ID range, you need to configure Protege so that your ID range is recorded in the Preferences menu. Protege does not read the mondo-idranges.owl file.
  • In the Protege menu, select Preferences. In the resulting pop-up window, click on the New Entities tab and set the values as described below.
  • In the Entity IRI section:
  • Start with: Specified IRI: http://purl.obolibrary.org/obo
  • Followed by /
  • End with: Select Auto-generated ID
  • In the Entity Label section:
  • Select Custom label
  • IRI http://www.w3.org/2000/01/rdf-schema#label
  • In the Auto-generated ID section:
  • Select Numeric (iterative)
  • Prefix: "MONDO_"
  • Suffix: leave this blank
  • Digit Count: "7"
  • Start and End: see mondo-idranges.owl. Only paste the number after the MONDO: prefix. Also, note that when you paste in your MONDO ID range, the number will automatically be converted to a standard number, e.g. pasting 0110001 will be converted to 110,001.)
  • Check the Remember last ID between Protege sessions box (Note: You want the ID to be remembered to prevent clashes when working in parallel on branches.)

NewEntities

User details

  1. User name Clcik Use supplied user name: add your name (ie nicolevasilevsky)
  2. Check Use Git user name when available
  3. Add ORCID. Add the ID number only, do not include https://, ie 0000-0001-5208-3432

UserDetails

Setting username and auto-adding creation date

  1. In the Protege menu, go to Preferences > New Entities Metadata tab
  2. Check Annotate new entities with creator (user) box
  3. Creator property Add http://www.geneontology.org/formats/oboInOwl#created_by
  4. Creator value Select Use ORCID
  5. Date property http://purl.org/dc/elements/1.1/date
  6. Date value format Select ISO-8601

NewEntitiesMetadata