Table of Contents
AmiGO is an HTML based application which allows the user to browse, query and visualize data from the Gene Ontology, or any ontology in OBO format. AmiGO can be accessed online at http://www.godatabase.org/cgi-bin/amigo/go.cgi. AmiGO is open source software and can be downloaded and installed as part of the go-dev cvs repository from the Gene Ontology sourceforge page.
AmiGO is compatible with most modern operating system/browser combinations with good CSS support, including:
Mozilla/Netscape 6 on Linux, Windows and Mas OS X.
IE on Windows, but NOT on Mac OS X. IE on Mac OS X does NOT support CSS standards.
Safari on Mac OS X.
Konqueror on Linux.
Opera on Linux, Windows and Mac OS X.
When you go to the URL of an AmiGO instantiation, you have the options of:
Browsing the ontology
Querying the ontology or associated gene products
Filtering which gene products are displayed
Going to the Advanced Query page
Getting the current page in a different format
Going to a related site
Returning to the top of the ontology
The HTML page may look slightly different and contain more or less page elements such as HTML forms.
When you go to the URL of an AmiGO instantiation, you are presented with a treeview of the top levels of the ontologies that have been loaded.
The structure of the ontology is presented as a tree of terms:
Each term is identified by its ontology ID followed by the name of the term. The level of a term is represented by it's indentation within the tree. In this case biological_process is a child of Gene_Ontology and a sibling of cellular_component. Furthermore, the relationship type of a term to its parent is represented by the icon immediately preceeding the term ID. In the case of the gene ontology, the relationship types are part_of, represented by the pink P icon and is_a, represented by a green I icon. So in this case we can say, "cellular_component is part_of the Gene_Ontology."
Each line in the tree contains one term and several piecse of information about that term.
Moving from left to right, the first piece of information about a term is the select/deselect icon. This will be either a +, a - or a dot (.). A + icon means that the term has children which are not shown in the current treeview. A - icon means that the term has been selected and all of its children are shown in the tree. Finally, a dot icon means that the term is not selected but that it does not have children.
The next item is an icon showing the relationship of that term to its parent, which was discussed above.
Next is the ID and name of the term seperated by a semicolon. To see the definition of a term, move your mouse pointer over the term name and let it sit for a second or two. The definition of the term should appear. Depending on your browser you may only see the first part of the definition. Clicking the term name brings you to the detailed term view for that term.
If a term is selected in the tree, the term name will be in bold. In the tree visualization example the term Gene_Ontology is selected. Now let's look at what happens when "biological_process" is selected by clicking on the selector icon (the + icon to the very left of the term):
As you can see, when biological_process is selected the term is bold-faced, indicating that it is a selected term in the current treeview. The plus icon is replaced with the minus icon, which can now be used to deselect it.
The next item is a number in parentheses. This number represents the number of gene products that are annotated to that term which are loaded in the current database and selected in the current view. This number can change based on the search filters the user selects. For instance, if a user opts to only look at gene products that have been annotated by flybase, the number will obviously be lower. For certain filters, the numbers of gene products associated to a term cannot be easily computed. In these cases, the number in the parentheses will be preceded by a less-than (<) symbol. Mousing over the number will give a short explanation of which filters are causing the uncertainty.
The final item in a term line is the round pie chart icon. Clicking this icon will create a helper window displaying a pie chart summary of the numbers of gene products associated to any selected descendants of this term in the tree. This will be discussed in detail in a later section.
As discussed above, the tree can be browsed by clicking on the select (+) and deselect (-) icons on the left side of term lines. This is what the intial tree will look like when we click on the select icon to the left of biological_process.
Notice that biological process is now shown in bold and its select icon has become a deselect icon. The other thing that has changed is that now all of the children of biological_process are shown in the tree. Notice that the children of biological_process all have is_a links to their parent. We can say that "behavior is_a biological process".
You can "drill down" deeper into the ontology by continuing to select terms. Alternatively you can deselect biological_process if you no longer wish to view it's descendants in the tree.
Two other things in this treeview are new. The term biological_process_unknown has a dot icon instead of an selector. This indicates that it has no children and thus is a leaf node. The term obsolete biological process is greyed out. Terms which are children of obsolete biological process are old terms that have been removed from the ontology. They are greyed out as a visual cue that they should no longer be considered current terms.
The onotlogy can be queried using the query form in the upper left of the screen.
AmiGO is queried by enetering a simple text string into the form. You can choose to search for either terms or gene products. By default, AmiGO will prepend and append wild cards to a search string, so the search string "transcription factor activity" will return both the exact match "transcription factor activity" and "RNA polymerase II transcription factor activity". The wild cards can be turned off by selecting the "Exact Match" field.
When you query for an ontology term, you will be presented with a list of "hits". Here are the results of a search for "transcriptional activator".
There are two hits, "transcriptional activator activity" and "zinc-mediated transcriptional activator activity". The name and definition of each term are presented. Clicking the term name brings you to the detailed term view for that term.
To the left of each term name are a select box and an icon representing an ontology tree. Clicking the icon will show you the tree view of that term's location in the ontology. You can see the location of both terms in the ontology by a) selecting them both using the checkboxes or b) clicking the "Check/Uncheck All" button and then clicking submit. This will show you a new ontology tree with both terms selected. You can add them as selected terms to a tree that you've already built by browsing or searching. To do this, select the terms you'd like to add, chang the option "Draw New Tree" to "Append to Tree", then click the submit button.
Here are the results of a query for the gene product bcat1.
The query for bcat1 hits the gene product whose symbol has the exact match "bcat1" from RGD (Rat Genome Database) as well as the gene product "T27I1.8" out of TIGR's (The Institute for Genomic Research) A. thaliana associations. Mousing over the abbreviations of the datasources will provide you with the full names when available. The reason for finding T27I1.8 is that it has a synonym of "bcat1". This can be seen in its gene product details page.
The terms that the gene products have been associated to are also shown, along with the abbreviation of the evidence code(s) for that association and the icon representing the treeview of that term. Mousing over the evidence code abbreviations will give you the full name.
Clicking the gene product symbol will bring you to the gene product details page for that gene product. Clicking the datasource name will bring you to the description of the gene product at that datasources website. Clicking the evidence code abbreviation will bring you to the source reference that the datasource used to make the association. Clicking a term name will bring you to a detailed term view of that term. Clicking a treeview icon in front of a term name will bring you to a treeview of that term.
The advanced queries link gives you several new options for querying the ontology.
There is still an input box for text queries and a choice to choose for terms or gene products. You can, however, enter multiple search strings seperated by newlines and AmiGO will return all hits to any of the search strings. Additionally, you can enter the name of a file which contains a newline seperated list of search terms. This could be useful for finding the results of automated analyses.
In this form, you have the option of selecting exactly which fields you'd like to search to find terms and gene products. When querying for terms you can query these fields:
Name and Synonym
Name and Definition
Ontology ID
External References
All Fields
When querying for gene products you can search on:
Name and Symbol
Full Gene Name
Sequence Accession
Gene Symbol
Synonyms
External references
Finally, when searching for gene products you can apply gene product filters.
The form on the lower lefthand side of the screen allows you to set filters for which gene products you'd like to see.
You can choose to view only gene products from a given species, gene products that have been annotated by a specific organization or gene products associated by a specific evidence code. In any given field, you may select more than one value by selecting one, then holding down your control key and selecting others.
When filters are turned on, this will be reflected in the gene product counts in the treeview. If specific information is not known about the number of gene product associations affected by a given filter, the number will be prepended by a less than (<) sign. Mousing over the number will give a short description of the filters in question.
Filters will also change the gene product associations that are displayed in the detailed term view .
Clicking the XML or Flat File links will bring you to an XML or GO Flat File representation of the tree that is currently selected.
Clicking the "permalink" will bring you to a URL that you can bookmark to save the currently selected tree. AmiGO keeps track of the tree you build with user sessions. If your session is inactive for more than two hours, your session will be lost along with a tree you've built. The permalink can save the tree indefinitely. Just add it to your bookmarks.
There are detailed pages for both terms and gene products. These pages generally are displayed in a small helper window that is created when you click on the name of a term or gene product. The helper window allows you to keep a tree that you've been browsing in the main window while exploring interesting terms and gene products in further depth.
The detailed term page is linked to from the term names in the main tree view, from term names in the term and gene product query results and from term names in the gene product details page.
The top of the page shows the name of the term. Following that are the terms Accession, Synonyms and Definition.
The next section is the Term Lineage. This section shows tha DAG view of a term very much like in the main treeview but without the select/deselect icons. Next to the Term Lineage header is a link to the graphical view of the term
The nest section shows the "External References" of a term. These links represent the same or related concepts in other databases such as interpro.
The rest of the page is taken up by gene product associations.
The header of this section is one of two things:
Direct Gene Product Associations
These are gene products which have been associated directly to the selected term.
All Gene Product Associations
These are gene products which have been associated to the selected term OR any of its descendents. Note that the number of gene products displayed in this view should be equal to the number in parentheses following the term name in the tree view.
The selector to the right of this header can be used to toggle between viewing direct associations and all associations. When viewing all options AmiGO can display them all as one long list or broken down by the terms that they are directly associated to when the "All Associations with Terms" option is selected.
Following the header and toggle is a greyed section where gene product filters can be set.
Finally, the table of gene products is displayed. The first column has the gene product name linked to its gene product details page. The second column has the datasource who provided the gene product association linked to the representation of that gene product on that datasource's website. To see the full name of a datasource, just mouseover it. The next column is the evidence code for that association. Clicking the evidence code abbreviation will bring you to the source reference that the datasource used to make the association. To see the full name of an evidence code, just mouseover it. Certain evidence codes have a "with" field. For example, ISS (Inferred by Sequence Similarity) evidence codes are inferred by sequence similarity "with" another sequence. The with field links to a representation of a sequence used in making that association. The last column in the table has the gene product's full name when available.
When the checkboxes to the left of gene product symbols are selected, AmiGO will take you to the gene product details page for the selected gene products or to a fasta file of the gene product sequences for gene products which have sequences available.
The Gene Product details page is linked to from gene product queries and from term detail pages.
The header of the page displays the gene product symbol.
Following this, the gene product's full name, synonyms and datasource provider are displayed. The datasource provider links to the gene products page at the providers website. Mousing over the abbreviation will display the providers full name.
Next is a list of terms that the selected gene product has been associated to. The first column is the evidence code for that association. Clicking the evidence code abbreviation will bring you to the source reference that the datasource used to make the association. To see the full name of an evidence code, just mouseover it. The second column has the term name and a treeview icon. Clicking the term name will bring you to the detailed term view for the specified term. Clicking the treeview icon will replace the tree in the main window with the treeview for the specified term. Multiple terms may be selected to replace or append to the main treeview.
Following the list of terms is a fasta representation of the sequence of the gene product when available.
The other pages are the pie chart summaries of gene associations and "box and stick" DAG views of term graphs. These pages are drawn in the "helper window".
Pie chart summaries can be reached by clicking the pie chart icon to the right of selected terms in the main treeview. The pie chart will display a summary of gene products associated to the selected term and ALL OF ITS DESCENDANTS WHO'VE BEEN SELECTED. The number of selected products is limited to the same constraints as in other pages when filters are used.
The header displays the name of the selected term.
Next is a pie chart that shows the relative numbers of gene products that have been associated to that term and all of its selected descendants.
The last item in the page is a table summarizing these results. The first column displays the names of the selected term and all of its selected descendents. The first row is titled "ALL " followed by the selected term name. This is the total number of gene products associated to the selected term and any of its descendents, selected or otherwise. The second column shows the number of gene products associated to the term in that row. The last column shows this number as a percentage of the number in the first row (the total number of gene products associated to the selected term and any of its descendents, selected or otherwise).
The graphical view for a term is linked to from that term's detail page.
The header displays the name of the selected term.
The bottom portion of the page displays the actual "boxes and sticks" view of that terms DAG view.
The form in the greyed out section of the window allows you to select the display options for the DAG view, including the color of the boxes, the color of the text and the orientation of the digram layout.