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[go-software] GO Help request

Chris Mungall cjmungall at lbl.gov
Tue Apr 3 13:27:40 PDT 2012


> 
> 
> Email: mkim95 at gatech.edu
> Name: Software (from Mijung)
> Text: Hi,
> 
> I'm a PhD student in Georgia Tech CS and doing research on testing ontology-driven database systems in a software testing research group. I think the GO system is a great benchmark for our research and would like to ask a couple of questions about the testing process of the GO database as follows:

Thanks for your interest. Just for background before we start, I assume by "GO database" you mean the MySQL instance, which is 

> 1. How do you test your system with respect to the GO ontology?
> e.g., what do you do to the database when some changes are made in the GO ontology?

The database is created from scratch at period intervals. The ontology source is managed in a VCS rather than in the database.

> Do you update the database (in addition to the "termdb" table) in terms of the changes in the ontology?

The database is created fresh each time, using the latest version of the ontology. We don't store full audit trails in the database.

> If so, how do you test such updates in the database?

The database build scripts are implemented in perl and use a standard perl testing framework, but I don't think this is what you're asking.

There are a variety of tests that are performed both on the ontologies themselves, and on the contributed annotations, but these all happen upstream of the database loading.

For example, we run OWL reasoners within a Jenkins continuous integration environment - see:

	https://douroucouli.wordpress.com/2012/02/16/ontologies-and-continuous-integration/

There are also a battery of tests that are executed to check the contents of annotations:

	http://www.geneontology.org/GO.annotation_qc.shtml

> 2. What kind of test cases do you use for testing your system (database)? Are they all queries or code or combination of both?

See above

> Can you give an example of test cases that are related to the GO ontology?

Is this the kind of thing you have in mind?

	http://www.biomedcentral.com/1471-2105/11/530

> How do you get the test cases? Are they generated automatically or created manually or semi-automatically?

I suppose all tests (whether they are at the level of software infrastructure or semantic content of the ontologies and annotations) are generated manually and executed automatically.

> It's a big list of questions. Hope I am not bugging you too much. Thank you for you time.

You're welcome, hope this helps.

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