Protege5 5 setup for GO Eds
Which Protege version
As of July 2019, the Protégé version GO Ontology Editors are using is Protege 5.5.0.
Get this from protege.stanford.edu
Protege needs at least 4G of RAM to cope with the GO. Make sure your machine can handle this. Many current editors have 16G of RAM.
to be confirmed - Jim ?
If you need to increase your memory settings, the info.plist file now has an Xss option which specifies the stack size. This is set by specifying the following -Xmx argument for the java, for e.g. for 6G, specify -Xmx6000M. How to set this varies with the OS and Protege version. If launching from ./run.command, edit run.command to jre/bin/java -Xmx6000M. If running from Protege_n.app on a mac, you need to find and edit the -Xmx entry in an XML file called info.plist under Protege_n.app/.
Protege has a highly configurable layout and a plugin architecture. You can control which components are visible from the window menu. Selecting something from the view menu allows you to create a new subwindow in a tab with the component of your choice - just move the target icon to the location you want and click.
As many plugins come with the standard download, the default layout may be intimidating, but can easily be simplified: The following tabs are sufficient for GO work:
ask David: ontograph or obo graph ?
The OntoGraph plugin allows to view a GO term and its relations to other terms.
- Both children and parents can be viewed.
- All relations are shown (or at least, many, see screenshot).
- Double click on the
+sign in the top left corner of each box to expand that part of the ontology.
- Mouse over the arrow on an edge to view details about the relation.
- The icon representing logical definitions (LD; ≡) is shown on edges that have inferences based on LDs.
- If terms have logical definitions, those are shown with the icon representing LDs (≡).
The following plugins should be installed from the Protégé menus: File>Check for plugins>
This directory structure for P5 is Protege-5.1.0.app/Contents/Java/plugins/. To see the directory structure so that you can drag and drop files, you'll need to control-click/right click on the app icon, then select 'Show Package Contents' and drill down to the directory you want. Note there are two plugins folders. Make sure you use the correct one.
(In P5, the latest ELK can be found using File>Check for Plugins)
ELK OWL reasoner Make sure you choose a version appropriate to your Protege version.
(In P5, the OBO Annotation plugin can be found using File>Check for Plugins) Have this view show up by going to the Entities tab, selecting Window>Views>OBO Views>OBO Annotation. Drag the black circle that appears to the area where you want it and click. The panel will appear.
OBO Annotation – add and edit terms more easily
NEED TO CHECK THIS
OBO Graph View Component – For all you hairball fans - this plugin displays an OBO-style connected graph of classification (is_a) and other relationship types. (Be careful what you wish for).
To make this a tab:
- Window > Create New Tab
- Window > Views > Ontology Views > OBO Graph View Component
- Take the black circle, put into the Tab you just created and click within it.
Obsoletion plugin - Once installed, you should see an "obsolete" option in your Edit menu. NEED TO CHECK THIS
- Curators and projects are assigned specific GO term ID ranges by senior editors.
- These ID ranges are stored in the file: go-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 go-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 follows.
- Set the values as follows.
- In the Entity IRI box: #* Start with: Specified IRI: http://purl.obolibrary.org/obo
- Followed by: /
- End with: Auto-generated ID
- In the Entity Label section:
- Same as label renderer:IRI: http://www.w3.org/2000/01/rdf-schema#label
- In the Auto-generated ID section:
- Prefix: "GO"
- Suffix: leave this blank
- Digit Count "7"
- Start: see [go-idranges.owl](https://github.com/geneontology/go-ontology/blob/master/src/ontology/go-idranges.owl). Only paste the number after the GO: prefix. Also, note that when you paste in your GO ID range, the number will automatically be converted to a standard number, e.g. pasting 0110001 will be converted to 110,001.)
- End: see [go-idranges.owl](https://github.com/geneontology/go-ontology/blob/master/src/ontology/go-idranges.owl)
- Remember last ID between Protege sessions: ALWAYS CHECK THIS
- (Note: You want the ID to be remembered to prevent clashes when working in parallel on branches.)
WARNING: The ID generator in Protege doesn't overwrite existing IRIs, but it can't cope with the OBO alt_id system - where losing IDs following a merge are stored in annotation properties This system is problematic for OWL translations as it leads to the loss or IRIs. Without IRIs, this ID generator doesn't know about the IDs and will stomp on them if they fall in the specified ID range. Until this is fixed,
We plan to move to a system in which obsolete classes with these IRIs are created for all alt_ids on OBO to OWL translation.
Setting username and auto-adding creation date
- In the Protege menu, select Preferences >New Entities Metadata tab
- Click on: Annotate new entities with creator (user)
- Creator property: Add http://www.geneontology.org/formats/oboInOwl#created_by
- Creator value: Use username
- Check: Annotate new entities with creation date and time.
- Date property: Add http://www.geneontology.org/formats/oboInOwl#creation_date
- Check: ISO-8601
Configuring User details
- In the Protege menu, select Preferences >User details
- Select 'User name', and use the supplied user name; that is, your GOC identity.
(The default settings may be fine, but details are included for reference)
Protege allows users to set the annotation property to be used for rendering OWL entities (classes, object properties, annotation properties, individuals) in graphs, trees and text etc. This should be set to rdfs:label, as follows:
Background on rendering. All entities in OWL are identified by an IRI. This includes annotation properties such as label. In the absence of an annotation to annotation property specified as suitable for rendering, the short form of this IRI (the bit following a '#' or a '/') is used.
Last reviewed: June 7, 2018