Plant Ontology Browser Users Guide

Introduction

AmiGO is an HTML based application which allows users to browse, query and visualize data from any ontology in OBO format.  The AmiGO browser developed for GO has been modified for use on the Plant Ontology site.  AmiGO is an open source software available from the go-dev cvs repository at the Gene Ontology SourceForge site.

Browser Compatibility

AmiGO is compatible with most browser/operating systems that support Cascading Style Sheets (CSS) including:

• FireFox/Mozilla/Netscape 6 and up on Linux, Windows and Mac OS X.
• Internet Explorer on windows but NOT Mac OS X. IE on Mac OS X does not support CSS standards.
• Safari on Mac OS X.
• Konquerer on Linux.
• Opera on Linux, Windows and Mac OS X.

The Main Window

From the Plant Ontology (PO) browser main page you have options to do the following:

• Browse the ontologies and view terms
  
• Search for the ontologies and/or associated annotations
  
• Filter the annotations which are displayed in the browser.
• Perform an advanced search
• Get the data in another format
• Get data from a related website/database
• Request PO term
  

Browsing the ontologies.

Figure 1 

Plant Ontology (PO) browser

PO browser hompage (Figure 1) is accessed by clicking "Search/Browse Plant Ontologies" at the menu bar of the POC homepage.  Click "Browse" in Figure 1 to view the ontology tree structure, see Figure 1A.

Figure 1A

Ontology Tree Structure

The structure of the ontology is presented as a tree of terms (Figure 1A).  The top term or node is the highest level of the ontology.  Each term is identified by its ontology ID which has a PO (Plant Ontology) prefix that indicates the ontology domain and a seven digit number (e.g. PO:0009075). This identifier is unique for each term in the ontology.

The level of a term in the ontology is represented by its indentation within the tree.  In the Plant Ontology, plant structure (PO:0009011) is at the same level as plant growth and development (PO:0009012), these terms are siblings. Furthermore, the relationship of a term to its parent is represented by the icon immediately preceding the term ID.  Relationship types are: "part of", represented by the blue P icon; "is_a", represented by a grey I icon and "develops from", represented by a brown D icon.  In the plant ontology, both plant structure and plant growth and development have a 'is_a' relationship to the parent term (all:all).

Filter tree view

The ontology tree can be filtered by ontology type to limit the display to the selected ontology or ontologies; the default is to display all ontologies.  The number of annotations displayed next to each term can be filtered to show the annotations objects from the selected data sources.  Click "set filters" to set your display options; if no options are selected or you click "Remove all filters", PO browser will display all ontologies with full annotation counts.

Understanding term lines

Figure 2 

Each line in the tree contains one term and several pieces of information about the term and some associated functions.

Expanding/Closing term nodes: the term expand/close icon has three forms: a plus sign (+), a minus sign (-) and a period (.).  The plus (+) sign indicates that a term has children that are not shown in the current view.  The minus (-) sign indicates the term is selected and all of the children are shown in the view.  The period (.) indicates that the selected term has no children. You can use the expand/close icon to expand a node to see all the children, or collapse the node to just the parent term.

Term ID and Term name: the next two items are the term Id and the term name which are separated by a semicolon.  To see the full definition of a term, click on the term name to see the detailed term view.

The status of a term is indicated by color and font style.  If a term is selected in the tree, the name will be shown in bold font. 

Number of annotations: The next item is a number in parenthesis. This number represents the total number of annotations to that term.  This number can change depending on the search filters applied.  Click the number, a full list of annotation to this term and its children will be displayed, also the brief information of the annotation (Figure 2A).  The PO term is shown in large font at the top of the page.  Below the term, links are provided (by clicking the blue arrow) for direct access to the three subsections of the term details page: Term information, Term lineage and External reference. The type of annotations shown can also be specified using the 'View annotations' filter, by checking one of the options. 'All annotations' will display gene products annotated to the PO term or to any of its children; 'Direct annotations' will display only gene products annotated directly to the term. 

Figure 2A 

Browsing the tree

The expend/close icon is used for browsing through the tree structure.  If a term has children, you can 'drill down' by clicking on the plus sign selector next to the term.  Terms with no children have a period (.).  To close a node, click on the minus sign (-) to collapse the node and hide the children.

Search for the ontology and/or associated annotations (e.g gene products).

The ontology can be queried using the search options available in the menu bar at the top of all pages in the PO browser.

Figure 3

The database query works by entering a query string into the text input box and selecting the type of search to perform (exact/inexact) and data type to search for.  The default option is a search for " Ontology" terms, meaning a search for the term 'leaf' will retrieve all ontology terms containing the word 'leaf'.

Querying for ontology terms

The text string used for queries treats each word in the string as a complete phrase. A search for the term "juvenile leaf" will find terms containing the string "juvenile leaf" rather than "juvenile" OR "leaf".  For the broadest search use a simple term and the contains option. In addition to searching the term names, the term search also searches alternative names, such as synonyms, which are stored in the database.  For example, a search for the term 'panicle' which is the name of the inflorescence in rice, will return the term 'inflorescence' because panicle is a synonym for this term.

1. Enter the term you are searching for into the text input box.
2. Select "Ontology" as the data type to search for.  This is the default selected option.
3. If you know the exact term you are looking for, choose the "Exact Match" option.
4. Click 'Submit Query'.

The results that match your query are shown in a list (Figure 4).  If no results are found, check your spelling or try using simpler terms (leaf vs. juvenile leaf).  If you do not find a term in the PO, you can suggest a new term by clicking on the "Request PO term" link in the menu bar at the top of the browser window.

Term search filters

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 ontology names and click "Set filters".  If no options are selected or you click "Reset filters", PO browser will display results from all ontologies.

Figure 4 

Click on the name of the term to display the term detail view (Figure 9). To the right of the term are [show def] and [view annotations].  Click [show def] , the definition of the selected term will appear under the term; click [view annotations], a list of annotations to the selected term and its childrem will be shown (Figure 4A).  The PO term is shown in large font at the top of the page.  Below the term, links are provided (by clicking the blue arrow) for direct access to the three subsections of the term details page: Term information, Term lineage and External reference. The type of annotations shown can also be specified. "All annotations" will display gene products annotated to the PO term or to any of its children; "direct annotations" will display only gene products annotated directly to the term.

For genes or gene products which have GO annotations in GO database, a external link "GO" will appear at the last column of individual annotation, clicking "GO" will open the corresponding GO gene product details page (for example, GO associations to Arabidopsis ABI4 gene)

Figure 4A  

Querying for Annotations (e.g gene products)

The Plant Ontology Browser allows you to search for "Annotations" (e.g gene products or other object types) associated to ontology terms in the database (Figure 5). The PO Browser will search annotation object names, symbols and synonyms, and will return any annotations that contain the query word or phrase.

Figure 5 

1. Enter the name (symbolic or full name ) of the annotation object such as "endosperm".
2. Choose the "Annotations" option.
3. If you know the exact name or symbol of the annotation object, select an 'Exact Match' checkbox, otherwise the search will be a 'contains' search.
4. Click "Submit Query".

The query for annotation object names containing the word "endosperm" is shown in Figure 6.

Figure 6 

The Query Summary, shown in the top box lists the search parameters, data filtering options selected and number of results returned. The main results section lists all of the annotations that matched your query and the species where the annotations are derived from.  Clicking on a annotation object name brings you to the  annotation object details page (Figure10).

Annotations Overview and filters

To the left of each row of the table is a check box which can be used for selecting multiple names on the list and to get an "annotations overview" to a set of annotations (Figure 6A).  The result can be filtered by "evidence code" and "ontology" to limit the terms shown to those select filters.

Figure 6A

Filtering annotations (gene products) which are displayed in the browser

The Plant Ontology Browser has four filters which you can use to filter the list of annotations (gene products) displayed in the browser or included in search results (Figure 6). The default option does not use any filters for retrieving associated data. The filters can be set when performing an advanced database search, or when viewing the ontology tree or term details. One or more filters can be set; the corresponding results will meet the criteria set by ALL the filters in combination.

Using the species filter

The species filter allows you to restrict the display of annotated data in the browser display or search results to one or more species. This feature is useful if you want to find annotations to a specific organism (say Zea mays) or a set of organisms.  For example, say you wanted to take advantage of maize-rice synteny for identifying candidate genes in maize. Given a phenotype in maize, are there mutants in rice with similar phenotypes.

1. Select one or more species to filter.  To select multiple species, hold down the CTRL key (PC) or APPLE key (Mac) while selecting with the mouse.
2. Click 'Set Filters'.

Figure 7 

Using the data source filter

This portion allows you to restrict the display of annotated data by contributing database.  It functions similarly to the species filter by limiting the associated data types in the ontology and term detail views as well as in searches.

Using the evidence code filter

The evidence code filter is a very useful option that allows you to restrict the display of associated data based on the quality of evidence supporting the annotation.  The default option is set to 'All Curator Approved'.  Curator approved means the association of a term to a data object is based on evidence that was evaluated by a trained biologist. This default option excludes annotations based on electronic unsupervised methods.

Using the ontology filter

You can also filter the annotations objects by "ontology" association, limiting the anntations shown to those which are annotated to terms in the selected ontology (or ontologies).

Performing an advanced search

The "Advanced Search" features are accessible by clicking on the 'Advanced Search' link at the menu bar of the PO browser toolbar.  These options allow you to query the Plant Ontology with a little more flexibility than standard search.

Figure 8 

Entering your query:  in the text input box you can enter a single word as with the Basic Query; you can also enter multiple terms separated by new lines (carriage returns) and the PO browser will search for hits to each of these terms.  Alternatively, you can upload a file of terms where each term is on a single line.  The terms must all be of the same type.  Choose 'Terms' or 'Gene Products' to search one or the other of these fields.  You can also enter phrases into the text box, entire phrase will be used to search the Plant Ontology.

1. Enter the term(s) in the text input box or upload a file of query terms.
2. To search for an exact word or phrase, select the "exact match" checkbox.
   
3. Choose the term type to search, the choices are "Terms" or "Annotations". To specify which data fields the PO browser should search, selecting one or more of the options in the "search field" section.
   
4. Set the filtering options for annotation search; multiple options can be selected in all the filters; select more than one option by control-clicking (apple-click on a Mac) the names.
   
5. Click "Submit Query"

When searching for terms, the types of terms you can search for are:

• Term Name and Synonym.
• Term Name and Definition.
• Ontology ID: e.g. PO:0009074
• All of the above fields

When searching for annotations, the options are:

• Annotation objects Full Name and Symbolic Name
• Full Gene Name
• Gene Symbol
• Synonyms (Gene Name aliases)

Getting the data in another format

XML or Flat File: Clicking on either of these links will bring you to a new page with a different representation of a selected ontology tree.  This option is useful if you want to parse the tree using either the XML or GO flat file format.  Some browsers (such as Safari) do not display XML properly.

Permalinks: Clicking on this option creates a new page with a new URL which you can use to bookmark the currently selected tree.  The PO browser tracks the tree you build in your 'user session'. After 2 hours if inactivity, the session will expire along with any trees you have built. To save the tree indefinitely, add the URL from the Permalink to your browsers bookmarks file.

Detail Windows

There are detail pages for ontology terms and annotations (gene products) that are in the PO database.  These pages are displayed in new browser windows when you click on the name of a term or an annotation , and also allows you to view a tree that you have been browsing in the main window open, while exploring interesting terms and annotations in depth.

Ontology term details

Overview of "Term Details"

The term detail page displays information associated with the PO term.  The PO term is shown in large font at the top of the term details page (Figure 9).  Below the term, links are provided (by clicking the blue arrow) for direct access to the three subsections of the term details page: Term information, Term lineage and External reference.  The Term annotations is a hyperlink to a page listing all the annotations that are associated with the PO term (Figure 2A, 4A).

Figure 9 

Term Information

"Term Information" displays a list of fields with the PO term which includes "Accession", "Ontology", "Synonyms", "Definition" and "Comment".  The accession is a unique identifier for the PO term in the PO database, this is always in the format PO:xxxxxxx (a seven digit number).  Synonyms are alternative names for the term, in PO, synonyms may include more specific instances of a term, for example, a cyme is a specific type of inflorescence and is included as a synonym for the term inflorescence.  The definition is an explanation of what the term means, the origin of the definition is indicated in [ ] after "source:".  A wide variety of additional information related to the term is added in the "comment" section, this may include noteworthy biological information related to the term, suggestion for database curators to help them choose the most appropriate term or historical information on the term.

Term Lineage

The next section on the detail page is the Term Lineage.  This section shows the tree view (actually a directed acyclic graph or DAG) of the term, i.e the term in relation to other terms in the ontology.  The term can be viewed in the context of either 'Term ancestors' or 'Term parents, siblings and children' by checking the preferred checkbox then clicking 'Set filters'. The view will change accordingly. Viewing the Term ancestor is the default view.

The number in parenthesis represents the total number of annotations to that term.  Click the number, a full list of annotation to this term and its children will be displayed, also the brief information of the annotation (Figure 4A).

The number of annotations displayed next to each term can be filtered to show the annotations objects from the selected data sources.  Click "set filters" to set your display options; if no options are selected or you click "Remove all filters", PO browser will display all ontologies with full annotation counts.

Next to the term lineage is a link to a graphical view of the term.  View in tree browser links back to the main term browser (Figure 1A) for further browsing. 

External References

This section show cross reference between the PO term and external references.  The number of external database entries mapping to the PO term is shown in brackets after the database abbreviation.  A ist of database identifiers can be viewed by clicking on the (+) icon; where direct links to the database entries are provided (if available).

Annotations (Gene Product) Details

The Annotation (Gene Product) Detail pages are linked from the Annotations Search  Results page (Figure 6) and Term Annotations page (Figure 4A).  Each contributing database (datasource) submits information about the symbolic name, full name and aliases for each annotation object.  A typical annotation object page has the following information.

Figure 10 

Annotation Details Information

The information section displays the following data associated with the annotation object: Name, the common name of the gene or gene products; Type, the feature or sequence type of the gene or gene product; Species, the species from which the annotation comes, the species name is hyperlinked to the NCBI Taxonomy Browser; Synonyms, other names for the annotations; Database, the data source that provided the annotations to POC and hyperlinked to the corresponding detail page in the contributing database.  Sequence, currentlly this function is not available in the PO database.

Term Annotations

Any annotation object can be annotated to one or more terms in the PO database.  A table of the PO terms that the selected gene or gene products has been associated is displayed here.  The "Qualifier" column is used for flags that modify the interpretation of an annotation, allowable values are " not", "contributes_to", and "colocalizes_with", more information is in GO annotation guide.  Clicking the "Term" name will display the "term details page" (Figure 9), clicking the [view annotations] will display the "term annotations page" (Figure 4A), all the gene or gene products annotated to the term.  "Ontology" denotes the ontology that the term belongs to, clicking on the ontology name will display the PO documentation on that ontology (e.g plant structure).  The "Evidence" which can be used to assay the strength of the assertion, mouse over the evidence code to see the full name of an evidence code,  clicking the selected evidence code will display the evidence code documentation page.  Clicking the "Reference" hyperlink will display the reference used to make the association.  "Assigned by" shows the database or group that made the annotations, if this is different to the database from which the annotation comes, it will state that data were submitted "via" another data source.

Term annotations filter

Term annotations can be filtered by "ontology" and "evidence code" to limit the results.  Multiple options can be selected in all filters.

Using the links out to contributing databases

There are several places where you can find "Data Source" links to related databases or websites to find additional information about a gene or term.

Data Source links

The "term detail pages" (Figure 9) and "annotation detail pages" (Figure 10) include hyperlinks to data detail pages from the contributing database.  The data source listed in this field (e.g. TAIR, Gramene or MaizeGDB) is a hyperlink.  Click on this link to view the databases detail page for the gene, phenotype, allele or other data type.  For each database, the detail pages will provide as much information as they have available about the data type such as sequences, map locations, stock ordering, etc.  For example, if you were interested in using the rice sequence to identify candidate genes for a maize mutation you could search for mutants in rice with a similar phenotype (using PO anatomy terms), then use Gramene's comparative map tool (CMAP) to locate the syntenic region in rice and maize.

Generating Pie Charts

If a PO term is fully expanded (i.e all its children PO terms are displayed), a pie chart icon will appear at the end of the line (Figure 11A). 

Figure 11A 

Clicking on the pie chart icon will generate a pie chart showing the distribution of annotations associated with that PO term and its children (Figure 11).

Figure 11 

Graphical Ontology Views

A graphical view of each term and its lineage is linked from the term detail page. The header displays the name of the selected term.  The remainder of the page displays a box and stick diagram of the term lineage where each term in the lineage is contained in a box and terms are connected to each other by lines.  The arrowheads indicate the direction of the graph and are labeled with the relationship type between the term and its parent.  The control panel below the term name can be used to change the layout of the graphical view and color of the text and term boxes.

Figure 12