Simple text search

The simple text search tool is located top right of the Home page. To search type a word, phrase or identifier in the search box. The search has an auto- complete function; if the text you wanted to use appears in the drop-down list, select it and results will be displayed. For other text click Search.

search box

Search results are presented in categories with grey headers, representing molecular entity or event types.

Below the header is a list of items from the named type that match your search terms. Matching words are highlighted in grey. Click on the name of an item to go to a page of details.

On the left side of the search results page are groups of check boxes. These can be used to change defaults and add filters. Check or uncheck boxes for types that you do/don’t want to see, e.g. if you want to see results for Mus musculus, under Species uncheck Homo sapiens and check Mus musculus. In the Type, Compartment and Reaction Type filter groups, select to only see results that fall into the selected category, e.g. to see only reactions, select Reaction in the Types filter group. To see only Reactions that occur in the cytosol, also select Cytosol in Compartments.

protein kinase results

Click on any of the results to go to a page of information about it. The contents of these Results Detail pages will depend on the type, but all have a section named ‘Locations in the PathwayBrowser’.

calmodulin details

This contains an expandable hierarchy that identifies the locations of the item in Reactome pathway diagrams. Click the plus symbol to open the hierarchy.

This hierarchy reflects the organisation of events in Reactome. ‘Top-level’ pathways representing a broad area of biology typically contain one or more levels of subpathways, becoming more specific with each level. The levels of the hierarchy are represented here by indentation; the most general pathways are closest to the left-hand edge of the screen, the most specific subpathways have the greatest indentation to the right. Note that some search result items (e.g. proteins) can be in more than one pathway, which may be in different broad areas of biology, resulting in representation in multiple hierarchies. Note that you can open all the hierarchy levels with a single click on the Expand all link, on the right side. Select any event name to open the corresponding Pathway Diagram. The diagram will open with an animation that shows you where the pathway is located in the Pathway Overview. If the selected item was an event it will be highlighted in blue in the Pathway Diagram. If it was a protein, all instances of it will be highlighted in pink.

In-Diagram Search (Searching in the Pathway Browser)

Searches can be performed within the Pathway Browser using the In-Diagram Search panel (top left corner of the Pathway Panel). When the Pathway Overview,  Diagram is Enhanced HIgh Level Diagram (EHLD) is displayed, all of Reactome is searched. 

In Diagram Start

Searching the Pathway Overview

In the example below, as the search term, ‘IL6’ has been entered. The search tool has predicted results that match this search term and displays a drop-down list of these matches. 

Overview Search

Note: the deep blue bar, which indicates that there are 23 results shown. Only the three results are clearly shown in the results window. To view additional results, move the cursor over the window and scroll down. Each result term has a symbol (to the left) representing the type of molecule or event it is. The first result, with a blue circle icon to the left of the name, represent matches to the IL6R protein, located in the plasma membrane. The second result, with a double-helix icon to the left, is the IL6R gene. The third result is a reaction, with icon showing above/below boxes on left connected by a right-pointing arrow to box on right, representing the binding of IL6 to IL6R. The Reactome stable identifier and cell compartment annotations are also provided for each molecule or event type that is displayed.

Overview Search Results Summary

In the following image, the recent search results are displayed at the bottom of the search results window. Clicking the "Clear History" button will remove the search terms from the history.

Overview Search History

In the next image, selecting an item in the Search Results Panel also causes a second drop-down Search Results Details Panel to appear. The additional annotations displayed include the molecule or event type, the Reactome stable identifier, an external reference database identifier, and the cell compartment. Clicking the "Filter" button (to the right of the search bar) will display options to filter the search results by molecule or event type, e.g. Pathway, Reaction, Complex, Protein, DNA Sequence, Set, etc. Selecting one or more of the filters will restrict the Search results viewed. Deselecting the filter(s) will alter the search results display. Selecting an item in the initial Search Results Panel causes the Overview to zoom and recentre, focusing on the region that represents pathways containing the selected item. This identifies the selected item and lists the pathways that contain the selected item. 

Overview Search Results Detailed

In the following image, moving the cursor over a pathway name (under the "Present in X pathway") will highlight the corresponding in the Overview, if it is visible in the viewport. The tooltip will display the name of the pathway.

Overview Search Results Selected

Clicking a pathway name (under the "Present in X pathway") in the Search Results Detail Panel will select the corresponding object in the Overview. If it is not visible, the Pathway Diagram will re-centre to show it. Double-click a pathway name in the Search Results Detail Panel or pressing the "GO >>>" button will open the corresponding Pathway Diagram. If you need to return to the Overview, you can use the browser back button. Note that in the image above, the Search Results Detail Panel extends beyond the limits of the Overview window, consequently some results are hidden. This explains why the results details title says Present in 3 pathways but only 2 are visible. To see all the matching pathways, click in the pathway list in the Search Results Detail Panel. 

In the following image, the "Flag" button in the Search Results Details Panel (to the right of IL6R) has been clicked and the events that contain the selected molecule are highlighted blue and the connected events are highlighted purple. Clicking the "Flag" button for a second time will remove the event highlighting.

Overview Search Results Highlighting

Searching a Pathway Diagram

In the example below, the search has identified IL6R and produced a dropdown list of matches. The first match is to a protein, as indicated by the icon on the left. The second match with the icon showing a double helix is a DNA sequence or gene. Note that if IL6R was represented in two cellular compartments in this diagram it would appear twice in this initial search result. The Reactome stable identifier and cell compartment annotations are also provided for each molecule or event type in the search results. Note: as the search term is entered, the search tool will predict results that match this search term and displays a drop-down list of these matches.

Although not shown below, when a new search is performed, the recent search results are displayed at the bottom of the search results window. Clicking the "Clear History" button will remove the search terms from the history.

In Diagram Search

The deep blue highlighted bar, which indicates that there are 3 results shown in "This diagram". Only the two results are clearly shown in the results window. To view additional results, move the cursor over the window and scroll down. Each result term has a symbol (to the left) representing the type of molecule or event it is. The first result, with a blue circle icon to the left of the name, represent matches to the IL6R protein, located in the plasma membrane. The second result, with a double-helix icon to the left, is the IL6R gene. The Reactome stable identifier and cell compartment annotations are also provided for each molecule or event type that is displayed.

In the next image, clicking the "Filter" button (to the right of the search bar) will display options to filter the search results by molecule or event type, e.g. Pathway, Reaction, Complex, Protein, DNA Sequence, Set, etc. Selecting one or more of the filters will restrict the Search results viewed. Deselecting the filter(s) will alter the search results display.

In Diagram Search Filter

In the next image, selecting an item in the Search Results Panel also causes a second drop-down Search Results Details Panel to appear. The at the top of the Detials Panel, additional annotations are displayed that include the molecule or event type, the Reactome stable identifier, an external reference database identifier (if applicable), and the cell compartment. Additonal annotations are listed below describing the involvement of the protein within complexes, sets and reactions within the diagram. Selecting names in the Search Results Detail Panel will select the corresponding object in the Pathway Diagram. If it is not visible, the Pathway Diagram will re-centre to show it.

In this example query, clicking the "Flag" button in the Search Results Details Panel (to the right of IL6R) will highlight all (15) the objects in the diagram that contain IL6R. Clicking the "Flag" button for a second time (or the "X" button toward the bottom of the pathway viewport) will remove the object highlighting. To see all the matches, it is necessary to resize the Pathway Diagram panel.

In Diagram Search Entity This Diagram

In the following image, selecting the second item in the Search Results Panel (IL6 binds IL6R) causes a second drop-down Search Results Details Panel to appear. The at the top of the Detials Panel, additional annotations are displayed that include the event type, the Reactome stable identifier, and the cell compartment. Additonal annotations are listed below describing the involvement of the reaction within the diagram, and participants of the reaction. Selecting names in the Search Results Detail Panel will select the corresponding object in the Pathway Diagram. If it is not visible, the Pathway Diagram will re-centre to show it. in this image, the IL6 binds IL6R reaction is blue highlighed.

In Diagram Search Event This Diagram

In the next image, clicking the "All diagram" tab will present a different set of results when selecting an item in the Search Results Panel. As before, at the top of the Detials Panel, additional annotations are displayed that include the molecule or event type, the Reactome stable identifier, an external reference database identifier (if applicable), and the cell compartment. Instead of displaying ojects within the current displayed pathway, the pathways not shown in the pathway viewport that contain the search term are displayed.

In Diagram Search Gene All Diagrams

Selecting the hyperlinked pathway name in the Search Results Detail Panel ("Present in n pathway diagram") will open the new pathway diagram in the Pathway Browser and select the corresponding object in new diagram.

In Diagram Search Gene Set All Diagrams

Searching a Enhanced HIgh Level Diagram (EHLD)

In the example below, the search has identified IL6R and produced a dropdown list of matches. The first match is to a protein, as indicated by the icon on the left. The second match with the icon showing a double helix is a DNA sequence or gene. Note that if IL6R was represented in two cellular compartments in this diagram it would appear twice in this initial search result. The Reactome stable identifier and cell compartment annotations are also provided for each molecule or event type in the search results. Note: as the search term is entered, the search tool will predict results that match this search term and displays a drop-down list of these matches.

Although not shown below, when a new search is performed, the recent search results are displayed at the bottom of the search results window. Clicking the "Clear History" button will remove the search terms from the history.

EHLD Search

The deep blue highlighted bar, which indicates that there are 23 results shown in "This diagram" and 30 results shown in "All diagrams". Only the two results are clearly shown in the results window. To view additional results, move the cursor over the window and scroll down. Each result term has a symbol (to the left) representing the type of molecule or event it is. The first result, with a blue circle icon to the left of the name, represent matches to the IL6R protein, located in the plasma membrane. The second result, with a double-helix icon to the left, is the IL6R gene. The Reactome stable identifier and cell compartment annotations are also provided for each molecule or event type that is displayed.

In the following image, selecting the first item in the Search Results Panel (IL6R) causes a second drop-down Search Results Details Panel to appear. The at the top of the Detials Panel, additional annotations are displayed that include the moelcule or event type, the Reactome stable identifier, and the cell compartment. Additonal annotations are listed below describing the involvement of the object within the EHLD. Selecting pathway names in the Search Results Detail Panel will select the corresponding object in the EHLD. If it is not visible, the EHLD will re-centre to show it in the

EHLD Search Results Detailed

Getting Started

Search Exercises

This exercise encourages you to find information via the menu bar and Search

  1. What’s the latest news item on the Reactome Home page?
  2. How many human proteins are represented in Reactome?
  3. What’s the first item listed that will be included in the next release?
  4. Is VAV2 in Reactome?
  5. How many reactions involve VAV2?
  6. Are there any complexes that include VAV2?
  7. Is CRB2 in Reactome?