Tutorials

  1. - Setting up SVN and file access
  2. How to checkout OBI from SVN and edit it
  3. How to get sourceforge access
  4. How to reason with OBI
  5. Opening OBI with Protege 4 - DO NOT EDIT IN 4
  6. OBI release process
  7. Obsoleting terms in OBI
  8. Editing Instances

OBI Tutorial from ICBO conference

Contents

SVN

see http://obi-ontology.org/page/General_introduction#SVN

Checkout

A) Install latest Protege 3.4.1 version from http://protege.stanford.edu/download/registered.html

B) Install an svn client. For windows, we recommend http://tortoisesvn.tigris.org/ for Mac try SmartSVN http://www.syntevo.com/smartsvn/index.html

C) Using the svn client, check out http://obi.svn.sourceforge.net/svnroot/obi/trunk/src/ontology (If you want to commit changes back to the repository, you will need to use https: instead of http:, and will need a sourceforge password for obi.)

D) Go to the directory: ontology\branches

  • we made some changes 8 Oct 09. There is a new OBI file which gives a widget to help adding annotation properties and curation status etc. These instructions have been updated

download obi.owl, obi-edit.owl and the .template extension files. Rename the obi-edit.pprj.template file to obi-edit.pprj, and obi-edit.repository.template -> obi.edit.repository

E) open the obi-edit.pprj file in protege 3.4.1 (double clicking works on windows)

This will give you access to the obi.owl merged file plus annotation assistance widgets.

You must select the obi.owl as the active ontology by clicking on the meta data tab, select obi.owl. If you don't do this edits will not propagate to the correct file obi.owl

Pencil icon should be active, if not go to OWL tab, ontology repositories and deselect read only for the relevant file, pencil icon now should be active

When new classes are created, they will display as URLs in the class view until they are assigned an rdfs:label. Add the label as usual - rdfs:label should is listed in the annotation properties.

F)If you are editing OBI we are now working with a merged file rather than a series of branch files therefore:

  • You MUST edit in 3.4.1
  • Do an SVN update of your local repository prior to editing
  • Send email to the devel list before checking out, after checking in
  • Keep edits short
  • launch the file using the obi-edit.pprj by clicking on it - you will find on editing that the obi.owl file has been updated and the obi-edit.owl, which imports this file has also been updated. You can edit the obi.owl file in 3.4.1. - launch by clicking on obi.pprj - but you won't get the widget assistance. You want this, it's handy.

Sourceforge

1. First, you need to have a sourceforge.net account. If you do not have one, register at sourceforge: https://sourceforge.net/account/registration/ .

2. Second, email one of the OBI sourceforge administrators listed OBI sourceforge site. Alternatively, email the obi developer mailing list (obi-devel@lists.sourceforge.net). You will very likely be issued the right to access OBI sourceforge. This will allow you to make changes in OBI sourceforge.


Reasoning

google doc explaining a diagnotics application

Authors: Melanie Courtot, Alan Ruttenberg - Alan's google group page and Helen Parkinson.

The aim is to detect problems with the OWL file that cause OBI to reason slowly. Some use of axioms prevents this. The application described provides some support for detecting and visualising these cases and some usage examples are included here. It's bleeding edge, contact Alan for details on usage, or see the google doc link above.

Protege4

  • Protege 3.4 is the recommended editor for OBI. However you may find that you are not able to classify OBI with its Pellet default reasoner. Instead using Protege 4 with the Pellet 2 reasoner is working. Do NOT edit with Protege 4, only view and classify the ontology. Edits must be made in 3.4.
  • Installing Protege 4: choose the installer that "includes Java VM", and when the installer asks, choose to install a VM for protege rather than using the installed default.
  • Opening OBI with protege 4.

You cannot click on the .pprj file in this case. Instead check out OBI from the SVN to a local copy (see instructions above). We recommend you have a local sandbox directory so you can edit a local copy without accidentally checking back in your local copy to the OBI SVN.

  1. Start protege 4
  1. 29/9/09 - changes have been made to stop importing IAO obsolete terms
  2. Therefore do a fresh checkout, add a new line to the .repository file ../external/iao/iao-main.owl?forceReadOnly=true
  3. You may need to assign Protege more memory. Details here http://protegewiki.stanford.edu/index.php/Setting_Heap_Size. Then start Protege 4
  4. Choose open owl ontology
  5. Select obi.owl from your local copy of OBI obi\obi\trunk\src\ontology\branches - this is an OBI owl file with the imports present locally so you should not need to resolve these manually.
  6. When tested on 12 Aug 09 protege-dc failed to import, this can be imported locally by selecting the appropriate OWL protege-dc.owl file from your local copy of OBI - obi\obi\trunk\src\ontology\external
  7. To get the class labels rather than the OBI ids to display select 'preferences' from the 'file' menu (protege menu on mac), Choose the renderer tab. Choose 'render entitities using annotation values' and OK.
  8. You should now be able to see OBI class labels rather than ids.
  9. Ensure everything is being loaded locally, rather than from the web - check menu 'File' 'Loaded Ontology Sources' Everything should be loaded from files, so add to "ontology libraries" 3 local directories branches, external, external/iao
  10. Click on the classes tab to see OBI classes and you are ready to classify
  11. Choose 'Reasoner', FACT++ is the default reasoner, however download Pellet 2, choose file, preferences, click the plugin tab, select Pellet 2, and it will be available after a Protege restart. Once you select Pellet then classification will start.
  12. This should be 2-4 minutes depending on the machine you are running on
  13. After the ONTIE merge Aug 2009, Pellet 2 classifies in a couple of minutes.
  14. A new tab will appear - 'inferred hierarchy' - enjoy.

Release

The current OBI release process is documented here You may need to request edit privs to this document

We are considering to move OBI release using JAVA based program. Here are discussion about it.

Obsoletion

Step by step:

Checkout a fresh update of OBI, open in 3.4.1

1. remove child classes to sensible parent., drag and drop one by one

2. add reason for deprecation property

3. add replacement term property

4. add prefix to rdfs label obsolete_

5. remove from existing parent class

6. add OBOinOWLObsolete parent class

7. remove logical definition

8. save

9. open and reason over in p4, check consistency

10. if OK check in as a new file with an svn log

Instances

To edit OBI instances e.g. for the investigation use case

1. Click on the obi.pprj file - this will open the OWL file in 3.4.1 and will render all properties etc with rdfs labels

2. Click on the meta data tab, select the instances file e.g. Investigation-use-case.owl

3. Pencil icon should be active, if not go to OWL tab, ontology repositories and deselect read only for the relevant file. If you need to add a class then you'll be editing the obi.owl so repeat the process for selecting the active ontology but select the obi.owl file.

4. Navigate to the instances tab. Instances for a given class are shown, unless click on owl thing when all are shown. Choose the class you want instances for and add these

4. To add an instance - click on the diamond with a plus - this will add instances for the selected class. Add rdfs labels, definitions, restrictions etc.

5. Save and reason over in p4 before committing, if you've edited classes and instances commit both the obi.owl and investigation-use-case.owl

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