AmiGO help Advanced Search

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

Entering your query

Your search text can be entered into the text area or you can upload a text file which AmiGO will use to query the database. You can upload a file of GO terms or gene product names or IDs. Select the appropriate 'Search Type' by clicking the radio button for GO terms or Gene products. AmiGO uses the text box by default, so if you enter both text and upload a file, AmiGO will ignore the file.

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

  • cytokinesis
  • buoyancy
  • apoptosis

would retrieve all terms containing 'cytokinesis' OR 'buoyancy' OR 'apoptosis'. If you want to search for terms which contain all three words, put the terms on the same line:

  • cytokinesis buoyancy apoptosis

(although I can't guarantee you will get any results with that query!). For term searches, the search words do not need to be in the same order as they appear in the term name. Gene product searches do need the words to be as they appear in the name or synonym. [Should this be changed?]

To search for an exact word or phrase, tick the 'exact match' box. If you enter a list of terms or gene products and use the exact match option, results will be returned if one or more of the search phrases produce a match. For example, the following gene product search:

  • buffy
  • angel
  • willow
  • spike

returns the results

  • buffy
  • angel
  • spike

(there is no gene product called 'willow' at present).

Search fields

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

You can specify which fields you want AmiGO to search for your query word(s) in by 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 name and synonyms, and for gene products, this is symbol, name(s) and synonyms.

If you want to search for a gene product using its database ID or accession number, you don't need to include the database prefix in your search terms. For example, you should enter FBgn0030028, rather than FB:FBgn0030028 for a flybase ID and IPR009345 instead of Interpro:IPR009345. Examples of gene product names, Database IDs are provided below-

Gene products can also be searched using their corresponding Uniprot or NCBI_RefSeq IDs, provided a mapping of the database ID to these IDs were provided to the GO consortium by the contributing database group. Also, since AmiGO displays only manually curated annotations, if a gene product has only IEA annotations, then the Uniprot or NCBI_RefSeq IDS for those gene products are not available for searching. Table below lists gene_product name, corresponding database ID and Uniprot or NCBI IDs for some databases.

Database GeneProduct Name Database ID Corresponding UniprotID Corresponding NCBI_RefSeq ID
SGD ASK1 S000001535 NP_012872
FlyBase Corp FBgn0030028 Q9W3G9
MGI Mbd4 MGI:1333850 Q9Z2D7
ZFIN xrcc5 ZDB-GENE-041008-108 Q5FY48
TAIR AT2G07681.1 Gene:3696217 NP_565344



Filtering the results

You can limit term searches by selecting one or more of the ontologies in the ontology filter.

Gene product searches can be filtered by the species and the database from which the gene product comes. You can also filter gene products by their association data, using the ontology and evidence code filters. These will limit your results to those gene products associated to terms in the selected ontology (or ontologies) that are annotated with the chosen evidence code(s). All the filters allow you to pick one or more of the options, and will default to 'all' if no options are selected.

Submit

Click 'Submit' to perform the search.

Oh no, this is all too much for me...

Leaving all the settings on their defaults, entering your search phrase(s) and choosing either 'terms' or 'gene products' will perform a simple search. You can also access the standard search box in the menu bar at the top of the page if the query form is too overwhelming!