Question: Determine GO hierarchy in a list of GO terms
0
gravatar for alessandrotestori7
14 months ago by
alessandrotestori7330 wrote:

Hi! I have a list of GO terms. I would like to know if in my list there are any child or ancestor terms of other GO terms in the list. Is there a tool to do this? Where can I alternatively download such a schema? Please let me know. Thanks, cheers.

gene ontology • 1.1k views
ADD COMMENTlink modified 14 months ago by Alex Reynolds27k • written 14 months ago by alessandrotestori7330

Your title should ideally be more descriptive. For example, "Determine GO hierarchy in a list of GO terms" is a lot more informative on what you're looking to do than just "GO (Gene Ontology)"

ADD REPLYlink written 14 months ago by RamRS20k

Thanks for your suggestion! I have now changed the title

ADD REPLYlink modified 14 months ago • written 14 months ago by alessandrotestori7330
1
gravatar for Alex Reynolds
14 months ago by
Alex Reynolds27k
Seattle, WA USA
Alex Reynolds27k wrote:

http://www.geneontology.org/faq/how-can-i-calculate-level-go-term

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.).

We do not pre-generate reports showing this. If you genuinely want this information you can perform SQL queries on our database to get it. See this example.

ADD COMMENTlink written 14 months ago by Alex Reynolds27k
1
gravatar for biofalconch
14 months ago by
biofalconch390
Mexico
biofalconch390 wrote:

Hi pal, there is a library call GO.db that can help you with this. For example, if you would like to find the children terms of the go term GO:0006412, you could use as.list(GOBPCHILDREN['GO:0006412']).

ADD COMMENTlink written 14 months ago by biofalconch390

Thanks! Is that a library in R?

ADD REPLYlink written 14 months ago by alessandrotestori7330
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