AmiGO 2 Manual: Search Examples

From GO Wiki
Jump to: navigation, search

This page gives some examples of advanced search usage in AmiGO 2.

Example Pages


Annotations

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

The default tab is "annotation"

Note that in this tab, you are querying on a per-annotation basis

Neurogenesis

Motivation: find Wnt family proteins involved in neurogenesis

  1. Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search
  2. Type neurogenesis into the filter box
  3. Use arrows to browse through results
  4. Filter by source - open "source" filter on left and select MGI
  5. Click on neurogenesis in one of the rows, taking you to the neurogenesis page
  6. Note that there are more results here - results include all descendants (isa, partof, regulates) of neurogenesis
  7. Open 'family' and select 'wnt related'


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.

Cell Cycle Phases (annotation extensions)

Motivation: The cell cycle phase terms may soon be separated from the main GO process hierarchy. Rather than annotating to these directly, they will be annotated to indirectly, through either pre-composed TG generated terms that use "during <phase>" as differentia, or as annotation extensions. We can see this now with many PomBase annotations.

  1. Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search
  2. Select "PomBase" in "source" facet
  3. Open "annotation extension" facet
  4. Select "cell cycle phase" (should be near top)
  5. Explore different annotations
  6. Try a more specific phase in the extension facet - e.g. M phase

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

in progress

For gene product queries, go to http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search And select "Gene/products" or follow this link.


Limb Morphogenesis

  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" or follow this link.

Alternatively you can query from the main search bar: http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo

neurogenesis

Motivation: explore neurogenesis

  1. Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo
  2. Type "neurogenesis"
  3. As you are typing, autocomplete should provide suggestions, with the desired term at the top
  4. Select neurogenesis
  5. This should take you here: http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/GO:0022008

From here you can:

  1. Explore annotations - use the facets on the left side to filter your search
  2. Explore neighboring terms - use "inferred tree view" for a compacted tree display

Non-nuclear chromosomes

  1. Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search
  2. Select "Ontology" tab
  3. Open "source" facet
  4. Select 'cell component'
  5. Open part-of/involved in facet
  6. Select + chromosome
  7. In part-of/involved in facet, select "-" next to nucleus (negative filter)

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