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| This page gives some examples of advanced search usage in the [http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search AmiGO 2 beta]
| | = Introduction = |
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| == Example Pages == | |
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| * [http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/gene_product/PomBase:SPAC24B11.06c sty1 PomBase annotations]
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| ** See also [http://www.pombase.org/spombe/result/SPAC24B11.06c PomBase display]
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| * [http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/GO:0022008 neurogenesis]
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| * [http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/gene_product/MGI:MGI:1197518 Aatk mouse annotations]
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| * [http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/GO:0030517 negative regulation of axon extension]
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| == Annotations ==
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| For annotation queries, start at
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| http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search
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| The default tab is "annotation"
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| Note that in this tab, you are querying on a per-annotation basis
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| === Neurogenesis ===
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| Motivation: find Wnt family proteins involved in neurogenesis
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| # Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search
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| # Type '''neurogenesis''' into the filter box
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| # Use arrows to browse through results
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| # Filter by source - open "source" filter on left and select MGI
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| # Click on [http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/GO:0022008 neurogenesis] in one of the rows, taking you to the neurogenesis page
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| # Note that there are more results here - results include all descendants (isa, partof, regulates) of neurogenesis
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| # Open 'family' and select 'wnt related'
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| === Epithelia-related processes outside bilateria ===
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| 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.
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| # Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search - the starting point is all annotations
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| # 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
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| # Open "taxon" facet
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| # Select "-" next to bilateria
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| 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.
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| === Cell Cycle Phases (annotation extensions) ===
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| 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.
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| # Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search
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| # Select "PomBase" in "source" facet
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| # Open "annotation extension" facet
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| # Select "cell cycle phase" (should be near top)
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| # Explore different annotations
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| # Try a more specific phase in the extension facet - e.g. M phase
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| === Neuron-related processes (annotation extensions) ===
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| # Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search - the starting point is all annotations
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| # Open "annotation extension" facet
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| # Click "more"
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| # Search (e.g. ctrol+F in browser) for neuron and select "+"
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| # Explore deeper in neuron hierarchy via "extension" facet
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| == Gene Products ==
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| ''in progress''
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| For gene product queries, go to
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| http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search
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| And select "Gene/products" or follow this [http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search?golr_class=bbop_bio link].
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| === Limb Morphogenesis ===
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| # Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search - then select "gene products"
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| # Type "limb morphogenesis" in the filter field
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| # Open "involved in" and click "+" on "limb morphogenesis"
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| # ...
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| == Ontology ==
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| For ontology queries, go to
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| http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search
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| And select "Ontology" or follow this [http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search?golr_class=bbop_ont link].
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| Alternatively you can query from the main search bar: http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo
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| === neurogenesis ===
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| Motivation: explore neurogenesis
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| # Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo
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| # Type "neurogenesis"
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| # As you are typing, autocomplete should provide suggestions, with the desired term at the top
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| # Select '''neurogenesis'''
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| # This should take you here: http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/GO:0022008
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| From here you can:
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| # Explore annotations - use the facets on the left side to filter your search
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| # Explore neighboring terms - use "inferred tree view" for a compacted tree display
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| === Non-nuclear chromosomes ===
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| # Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search
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| # Select "Ontology" tab
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| # Open "source" facet
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| # Select 'cell component'
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| # Open part-of/involved in facet
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| # Select + chromosome
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| # In part-of/involved in facet, select "-" next to nucleus (negative filter)
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| === All obsolete terms in subsets ===
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| Motivation: ontology subset maintainers may wish to check if there are stale terms in subsets
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| # Start at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/search
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| # Select "Ontology" tab
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| # Open "subset" facet
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| # Select a GO slim - e.g. goslim_prok (note: some will be from other ontologies; use the "source" facet to eliminate these)
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| # Open "obsoletion" facet - you can see the distribution between obsolete / non-obsolete. Select "+" next to "true" (or "-" next to false)
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| Note you can also explore boolean combinations of slims - e.g. terms in both yeast and prok slim
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| | The core search facility for AmiGO 2. |
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| [[Category:Software]] | | [[Category:Software]] |
| [[Category:AmiGO_2_Manual]] | | [[Category:AmiGO_2_Manual]] |
| [[Category:AmiGO_2]] | | [[Category:AmiGO_2]] |