AmiGO 2 Manual: Search: Difference between revisions

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This page gives some examples of advanced queries in the [http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search AmiGO 2 beta]
This page gives some examples of advanced search usage in the [http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search AmiGO 2 beta]


== Annotations ==
== Annotations ==

Revision as of 17:11, 31 March 2013

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

Annotations

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

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.

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

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"

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