AmiGO 2 Manual: Search

This page gives some examples of advanced queries in AmiGO 2

Annotations

For ontology queries, start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search

Epithelia-related processes outside bilateria

Motivation: epithelial cells are often regarded to be eumetazoan innovations. Here we use AmiGO 2 to explore this hypothesis and check for potential errorsin GO.

1. Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search - the starting point is all annotations
2. Type: epithel in the filter box to the left of the results. The results are very inclusive - anything that matches this string in any field, or descendent of term that matches this string. Approx ~10k annotations
3. Open "taxon" facet
4. Select "-" next to bilateria

Explore the results using the left and right arrows. At the time of writing there are some obvious erroroneus annotations - can you spot them? You can filter out the IEA using the "evidence" filter.

Neuron-related processes (annotation extensions)

1. Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search - the starting point is all annotations
2. Open "annotation extension" facet
3. Click "more"
4. Search (e.g. ctrol+F in browser) for neuron and select "+"
5. Explore deeper in neuron hierarchy via "extension" facet

Gene Products

1. Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search - then select "gene products"
2. Type "limb morphogenesis" in the filter field
3. Open "involved in" and click "+" on "limb morphogenesis"
4. ...

Ontology

For ontology queries, go to http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search And select "Ontology"

All obsolete terms in subsets

Motivation: ontology subset maintainers may wish to check if there are stale terms in subsets

1. Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search
2. Select "Ontology" tab
3. Open "subset" facet
4. Select a GO slim - e.g. goslim_prok (note: some will be from other ontologies; use the "source" facet to eliminate these)
5. Open "obsoletion" facet - you can see the distribution between obsolete / non-obsolete. Select "+" next to "true" (or "-" next to false)

Note you can also explore boolean combinations of slims - e.g. terms in both yeast and prok slim

Catgeory:AmiGO Catgeory:AmiGO 2