Frequently Asked Questions (FAQs)

Table of Contents

1. General questions for Ontobat
2. Questions about Ontovert
3. Questions about Ontoload
4. Questions about RDF triple store
5. Questions about Lodbee
6. Questions about Lodquery
7. Questions about Ontostat
8. Questions about OntoCOG

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General questions for Ontobat:

What's Ontobat?

Ontobat is a a web-based Semantic Web tool to support ontology-based biological data query and analysis.

Questions about Ontovert:

What's Ontovert?

Ontovert is an Ontobat program that converts instance data from Excel or tab-delimited text format to ontology OWL or RDF/XML format.

Questions about Ontoload:

What's Ontoload?

Ontoload is an Ontobat program that automatically uploads OWL-formatted instance data into a RDF triple store.

Questions about our RDF triple store:

What's RDF triple store?

A RDF triple store is a type of database for the storage and retrieval of RDF triples. A RDF triple is a data entity composed of subject-predicate-object.

See more information here: http://en.wikipedia.org/wiki/Triplestore and http://en.wikipedia.org/wiki/Resource_Description_Framework.

Questions about Loadbee:

What's Loadbee?

Ontobeeis an Ontobat program that uses Ontobee-like technology to display experimental instance data used for Ontobat data visualization.

Questions about Lodquery:

What's Lodquery?

Lodquery is an Ontobat program that uses a SPARQL-based query program to query instance data stored in a SPARQL triple store(s).

Questions about Ontostat:

What's Ontostat?

Onotostat is an Ontobat program that targets for ontology-based LOD instance data analysis.

Questions about OntoCOG:

1. What's OntoCOG?

OntoCOG is an Ontobat program that targets for COG-based enrichment data analysis.

2. What's COG?

COG represents the Clusters of Orthologous Groups of proteins. It is a NCBI program that clusters proteins based on evolutionary orthology and functional clustering (http://www.ncbi.nlm.nih.gov/COG/).

3. What's the statistical method used in OntoCOG analysis?

The default statistical method used in OntoCOG is Fisher's exact test. Specifically, given a list of k COG annotated proteins with a total of t proteins from one organism. For a given COG category catA, there are q proteins within k and m proteins within t associated with it. The data will look like this in a 2×2 table:

	Given list	Not given list	Total
catA	q	m-q	M
non-catA	k-q	t-m-(k-q)	t-m
total	K	t-k	T

The COG enrichment analysis is to find out the statistical significance of the distribution of the data, particularly, the p-value to test whether COG category catA annotated protein q is enriched (unevenly distributed) among the given protein list t.