AmiGO Manual: Term Search

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Simple Term Search

The GO term search is available from the AmiGO home page or by clicking on the Search link in the toolbar at the top of all pages in AmiGO. Enter one or more words or a GO ID into the query box; the query terms do not need to be in order or exactly as they appear in a GO term name. AmiGO will search GO term names, IDs and synonyms, and will return any terms that contain all the words in the query.

If you know the GO ID or the name of the term you are looking for, select the exact match checkbox to return only terms which fully match your query.

Searching additional fields

By default, the term search looks at GO term names, synonyms and GO IDs. To search the definition, comments, database cross-references, or other term information, please use the Search option in the toolbar at the top of every page.

Search results

The results table lists the GO terms that match the query, sorted by term name, with the part(s) of the term that match the search term(s) highlighted in green. If the query match is in the term synonym(s), the matching synonym(s) will be displayed below the term name. If there is more than one matching synonym, the first synonym will be shown, followed by the text and x more; clicking on this text will display all the matching synonyms.

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Clicking on a term name brings you to the term details page for that GO term. Clicking on the [show def] link displays the definition of that term right below the term name on the search results page itself. Clicking on the [view associations] link opens the term associations page, displaying all the genes and gene products annotated to that term. Clicking on the name of the ontology (molecular function or cellular component or biological process) takes you to the documentation at the GO website on the scope and definition of these ontologies.

Terms displayed against a grey background are obsolete; the [show def] and [view associations] options are not available for obsolete terms. Some obsolete terms have comments advising annotators which terms would be suitable substitutes for annotation; if so, these are displayed in the term search results.

Filtering

Term searches can be filtered by ontology to limit the results to the selected ontology or ontologies. The default is to search all ontologies; select more than one ontology to display by control-clicking (apple-click on a Mac) the names and click Set filters. If no options are selected or you click Reset filters, AmiGO will display results from all ontologies.