AmiGO 2 Manual: Search: Difference between revisions
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Revision as of 16:50, 3 April 2013
This page gives some examples of advanced search usage in the AmiGO 2 beta
Example Pages
- sty1 PomBase annotations
- See also PomBase display
- neurogenesis
- Aatk mouse annotations
- negative regulation of axon extension
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
- Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search
- Type neurogenesis into the filter box
- Use arrows to browse through results
- Filter by source - open "source" filter on left and select MGI
- Click on neurogenesis in one of the rows, taking you to the neurogenesis page
- Note that there are more results here - results include all descendants (isa, partof, regulates) of neurogenesis
- Open 'family' and select 'wnt related'
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.
- Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search - the starting point is all annotations
- 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
- Open "taxon" facet
- 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.
- Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search
- Select "PomBase" in "source" facet
- Open "annotation extension" facet
- Select "cell cycle phase" (should be near top)
- Explore different annotations
- Try a more specific phase in the extension facet - e.g. M phase
- Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search - the starting point is all annotations
- Open "annotation extension" facet
- Click "more"
- Search (e.g. ctrol+F in browser) for neuron and select "+"
- 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
- Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search - then select "gene products"
- Type "limb morphogenesis" in the filter field
- Open "involved in" and click "+" on "limb morphogenesis"
- ...
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
- Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo
- Type "neurogenesis"
- As you are typing, autocomplete should provide suggestions, with the desired term at the top
- Select neurogenesis
- This should take you here: http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/GO:0022008
From here you can:
- Explore annotations - use the facets on the left side to filter your search
- Explore neighboring terms - use "inferred tree view" for a compacted tree display
Non-nuclear chromosomes
- Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search
- Select "Ontology" tab
- Open "source" facet
- Select 'cell component'
- Open part-of/involved in facet
- Select + chromosome
- 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
- Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search
- Select "Ontology" tab
- Open "subset" facet
- Select a GO slim - e.g. goslim_prok (note: some will be from other ontologies; use the "source" facet to eliminate these)
- 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