Gene ontology level

Question

[Sudhir Jadhao]

I have done denovo transcriptome assembly and I have done annotation by doing blastx with NRDB.(I have saved result in tabular format). I have fetched gene ontology of genes from UniProtKB/Swiss-Prot.

But I dont know their Gene Ontology level.

Can anyone please help me to get Gene Ontology level for assembled transcript.

[Lluís R.]

What do you mean by "Gene Ontology level" ? if they are in the first level after Biological Process ontology, or in a second, or in ...?

[Medhat]

GO terms do not occupy strict fixed levels in the hierarchy. Because GO is structured as a graph, terms would appear at different 'levels' if different paths were followed through the graph. This is especially true if one mixes the different relations used to connect terms. Thus it is more proper to ask: "what is the maximum depth of such and such a term" (or minimum, average, etc.).

Source

If you genuinely want this information you can perform SQL queries on our database to get it. See this example.

Answer 1

[LLTommy]

The easiest way of getting a quick impression where your term is sitting, in my opinion, is to head over to the ontology lookup service. Find the Gene Ontology and browse through it or search for your term directly in the interface. It offers a tree view as well as a graphview. Having said that, I assume here that you have a number of terms that you can check manually and not 100s of them - in which cause we'd need a more automatic/programmatic approach.

Answer 2

[Sudhir Jadhao]

Thank you guys for replay. My problem is solved in DAVID