AmiGO Manual: Search

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Simple Searching with AmiGO

A simple search for GO terms or for gene products is available from the AmiGO home page or by entering text into the toolbar at the top of all pages in AmiGO. Enter one or more words into the query box and set the search type by selecting the terms or the gene or protein radio button. Examples of GO terms include DNA repair, protein kinase activity, or mitochondrion. Examples of genes or proteins include DMC1 or fuzzy onions.

If you know the name or ID of a GO term or the name or symbol of the gene product you are looking for, select the exact match checkbox to return items which fully match your query.

Click Submit Query to start the search.

Advanced Search

By default, the term search looks at GO term names, synonyms and GO IDs, and the gene product search looks at gene product names, symbols and synonyms. To search using other data, e.g. term definition or the database ID of a gene product, please use the Search link in the toolbar at the top of every page.

Entering your query

The Advanced Search allows you to query AmiGO with a little more flexibility than the standard search.

Search words or phrases can be entered into the text area or uploaded via a text file. All these words or phrases will be used to search AmiGO. The text box is used by default, so if search terms are entered in both text and upload a file, AmiGO will ignore the file.

If you want to search for GO terms which contain all three words, put the words on the same line. The search words do not need to be in the same order as they appear in the term name. This GO term search:

As1-a.png

would return the result:

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Gene product searches do need the words to be as they appear in the name or synonym.

To search for several alternative words or phrases, enter them on separate lines. For example, a GO term search query like this:

As1-c.png

would retrieve any terms containing the word "gluconeogenesis" or "regulation" or "positive".

Exact Match

To search for an exact word or phrase, select the "exact match" checkbox. If a list of terms or gene products is entered and the exact match option is selected, results will be returned if one or more of the search phrases produce a match. For example, the following gene product search:

As2-a.png

returns the results:

As2-b.png

as there is no gene product called 'willow' in the GO database.

Search fields

AmiGO can either search for GO terms or for gene products (genes, proteins, etc.). Pick the type of search by selecting the radio button next to "Terms" or "Gene Products".

To specify which data fields AmiGO should search, selecting one or more of the options in the search fields section. If you unselect all of the checkboxes, AmiGO will use the default search setting. For term searches, this is term names, synonyms and term IDs. For gene products, this is the gene symbol, name(s) and synonyms.

When searching for a gene product using its database ID or accession number, do not include the database prefix in your search terms. For example, enter FBgn0030028, rather than FB:FBgn0030028, and IPR009345 instead of Interpro:IPR009345.

Filtering

Term searches can be filtered by ontology to limit the results to the selected ontology or ontologies.

Gene product searches can be filtered by the species and by the database from which the gene product comes. You can also filter gene products by their associations, limiting the gene products shown to those which are annotated to terms in the selected ontology (or ontologies) with the chosen evidence code(s).

Multiple options can be selected in all the filters; select more than one option by control-clicking (apple-click on a Mac) the names.

This is a bit much for me...

If the Advanced Query form is too overwhelming, leaving all the settings on their defaults, entering your search phrase(s) and choosing either terms or gene or protein will perform a simple search. The standard search box can be accessed in the menu bar at the top of the page.