Frequently Asked Questions (FAQs)
Table of Contents
- General questions for Ontobat
- Questions about Ontovert
- Questions about Ontoload
- Questions about RDF triple store
- Questions about Lodbee
- Questions about Lodquery
- Questions about Ontostat
- Questions about OntoCOG
General questions for Ontobat:
Ontobat is a a web-based Semantic Web tool to support ontology-based biological data query and analysis.
Questions about 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:
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:
Ontobeeis an Ontobat program that uses Ontobee-like technology to display experimental instance data used for Ontobat data visualization.
Questions about 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:
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:
Not given list
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.