Kpath Main Interface

The Kpath Main Interface is the main end-user interface that is divided into three important areas:

  1. The Quick Start. Where users can search a pathway or find out new relationships between components of a pathway.
  2. The Virtuoso Endpoint. Where users can access to the metabolic information stored in the SPARQL endpoint.
  3. The General Metabolism Map. Where a map with the main metabolisms is displayed and users can access to this information by clicking in each metabolism representations.

Quick Start

The Quick Start has three options that correspond to:

  1. View a pathway.
  2. Find relationships between pathway components.

View a pathway

A user can browse a given pathway according to several functionalities provided by the main interface:

  1. All pathways. In this option, users can select a pathway from a list which is provided.
  2. Browse by organism. This option allows users to select a pathway from a specific organism.
  3. Browse by name. A search box allows users to introduce a key-word (e.g. pentoses phosphate) and a list of pathways with these key-words is presented
  4. Browse the global map. A Roche metabolism map provided by ExPASy is displayed and the metabolites which participate in the pathway reaction(s) previously selected is/are highlighted.

Find relationships between pathway components

This option allows users to access to the relationship search by clicking the Go to Relationship Search button.

Virtuoso Endpoint

This option allows users to access to the SPARQL endpoint in which all integrated data is available. When the user accesses to the endpoint, a box with a default SPARQL query (which retrieves all classes included in the data) appears. In this box, the user can introduce an SPARQL query. The results of the query can be exported to standards such as N-triples, RDF (Resource Description framework), HTML, XML (Extensible Markup Language) etc.

Furthermore, we have included some examples of SPARQL queries which retrieve all the resources and their literal names. For example, when a user clicks on the Get all pathway names button, all the different pathways stored in the endpoint are retrieved ordered by name. Other parameterized SPARQL queries (non-defined SPARQL queries) have been also included in this link in which all the information is available at http://bioqueries.uma.es/endpoint/kpath.

General Metabolism Map

A user can access to every metabolism included in the Roche metabolism map (e.g., carbohydrate metabolism, lipid metabolism, nucleotide metabolism etc.). When a user clicks on a given metabolism, all those pathways that belong to this metabolism are filtered. Users can go to the kpath Browser and select a pathway from the list in which the pathways have been filtered or to the Roche global map where the metabolites involve in the pathway selected are highlighted.

Pathway Graphical Viewer

The Graphical Viewer is used to show all pathway components in a graphs composed by nodes (reactions, metabolites, enzymes and genes) and edges (relations between these components). The interface is composed by three different parts:

  1. The collapsible sidebar. Where the pathway information, graph manipulation actions and links to other places are located.
  2. The main graph area. Where the graph is drawn and can be interacted.
  3. The buttons bar. Where different buttons are located with different quick actions.

The collapsible sidebar

The collapsible sidebar has four sections that can be collapsed or expanded clicking on their names:

  1. Pathway information
  2. Components
  3. Style
  4. Related pathways

You can show or hide the collapsible bar clicking on the small tab placed on the top right of the collapsible bar.

Pathway information

The name, metabolism and organism of the pathways that are being showed in the graph is showed in this section. Some basic actions and links are provided too for each pathway.

  1. Pathway name. The name of the pathway that is being showed in the graph.
  2. Metabolism. The name of the metabolism from this pathway.
  3. Organism. The name of the organism of this pathway. There is a link called Change that makes an organism selectable list to appear. Using this list, the user can replace the pathway showed in the graph by the one from the selected organism. The user also can hide this list of organisms.
  4. Actions.
    • Highlight. Selects all the nodes from the graph that are part of this pathway. This option is useful to recognize which nodes are from one pathway when more than one is showed in the same graph. Also, when a group of nodes are selected, you can move all of them at once to separate the nodes from the graph according to the pathway they belong to.
    • Info. A new tab is opened with extra information from this pathway. This tab provides information like General information of the target pathway (e.g., name, organism and metabolism), the chemical reaction(s) which is/are involved in this pathway, the metabolism that this pathway belongs to and the pathways related.
    • Remove. This option is only showed when more than one pathway are included in the graph. It removes the selected pathway from the graph and from this list of pathways.
    • Export to file. Export the pathway and graph information from this pathway to a tabulated txt file.
  5. User icon. Showed only when the pathway is a custom one created by the Pathway Editor tool and saved in the user account.
  6. Star. Showed only when the pathway is NOT a custom one. It appears as a filled star if the user has marked this pathway as favourite. Otherwise, it will appear as an empty star. You can click on the empty star to mark this pathway as favourite to be stored in your favourite pathways list. Click on the filled star to delete this pathway from your favourite pathways list.

Components

This section is useful to find a specific component in the pathway graphs (e.g. an enzyme with a specific EC number). Three selectable lists (one for enzymes, metabolites and genes, respectively) are provided. Select one element from one of the three lists and click its corresponding Find button. The node will appear selected and centered in the graph.

When more than one pathway is included in the Graph Viewer, some filter options will appear. You can use them to filter the elements that appear in the three lists. Using this filter, you can only show the nodes from every to one of the pathways that are checked below.

Style

In this section, you can modify the style (color and shape) of the nodes in the graph. For each type of node (metabolite, enzyme, gene or reaction) and edge (left, right, enzyme, gene) you can choose between a range of shapes and colours. When you have modified your preferences, click the Apply button to apply the selected style to the graph. Click the "Default" button to restore the default combination of colors and shapes.

Related pathways

In this section, there are links to related pathways to each one of the pathways that are being showed in the graph. Click one of them to browse to a new Pathway Graph Viewer window showing the selected pathway.

The main graph area

In this area, a graph composed by the components of the selected pathways is placed. You can manipulate the graph using the most common mouse actions.

  • Left click a node to select it.
  • Hold left click on a node to drag it and move it to a new position.
  • Hold left click on an empty place of the graph for more than one second until a grey circle appears to move the whole graph.
  • Hold left click and instantly move your cursor to make use of a rectangular area selection. Use this option to select and move a group of nodes.
  • Use your mouse wheel to zoom in or out the graph. If you are using a trackpad, you can use two fingers simultaneously and move them up or down to zoom in or out.
  • Right click on a node to make a contextual menu appear.

Contextual menu

This menu appears when right clicking on a node. The options in the menu will be different according to the type of the node.

  • Reactions
    1. Show reaction info. Open a new tab that shows all the information about the reaction. Each component of the reaction is a resource which points to more information about itself. For example, the chemical reaction includes enzymes and metabolites (reactives and products).
    2. Select all reaction components. Select and highlight all components of the reaction.
  • Metabolites
    1. Show metabolite info. Open a new tab that shows all the information about the metabolite. General information, related reactions and pathways to the target metabolite are shown.
    2. Select all related reactions. Select and highlight all reactions related to this metabolite.
  • Enzyme
    1. Show enzyme info. Open a new tab that shows all the information about the enzyme. General information and related elements such as pathways, reactions and genes to the enzyme are shown.
    2. Select all related reactions. Select and highlight all reactions related to this enzyme.
    3. Show genes in graph. Open a popup window when you can select genes related to this enzyme to be added as nodes in this graph. You should be careful to not add too many nodes to the graph depending on the capacity of your computer browser.
  • Gene
    1. Show gene info. Open a new tab that shows all the information about the gene. This information is related to general information and related elements such as pathways, reactions and enzymes.
    2. Select all related enzymes. Select and highlight all enzymes related to these genes.

The buttons bar

A set of buttons with useful actions are presented here.

  1. Compared/Mixed selector. Only showed when more than one pathway is included in the graph. If you select the Compared option, each component (enzyme, metabolite, ...) that appears in more than one pathway will be represented by different nodes that will be linked with a wide grey line. If you select the Mixed option, each repeated component will be placed in the graph as an unique node.
  2. Edit pathway graph. After selecting which pathway from the ones you are visualizing, you will be redirected to the Pathway Graph Editor tool with the selected pathway graph as an initial graph to work with.
  3. Add a new pathway to the graph. A new window will appear when clicking this button where you can select a new pathway to be included in the graph.
  4. Export graph to file. Export the pathway and graph information from all the pathways in the graph to a txt tabulated file.
  5. Fit graph to screen. Change the size and position of the graph to occupy the whole main graph area. This is useful when you have lost your position in the graph when zooming or moving the graph too much.
  6. Legend. Opens a small popup with the appearances of the nodes and edges of the graph.
  7. Help. Shows this help in a new tab.

Pathway Graphical Editor

With this tool, you can edit the components of a pathway to create a custom one. You can later view the custom pathway created and compare it with the existing real pathways.

WARNING! In order to save a modified custom pathway, you have to be logged in as a registered user before starting to modify the pathway. Otherwise, you won't be able to save your modified version of the pathway.

The Graphical Editor interface is composed by three different parts:

  1. The collapsible sidebar. Where the pathway name and some other graph manipulation actions are located.
  2. The main graph area. Where the graph is drawn and can be interacted and modified.
  3. The buttons bar. Where different buttons are located with different quick actions.

The collapsible sidebar

The collapsible sidebar has three sections that can be collapsed or expanded clicking in their names:

  1. Pathway graph
  2. Components
  3. Style

You can show or hide the collapsible bar clicking on the small tab placed on the top right of the collapsible bar.

Pathway graph

An input text is shown with the name of the pathway. You can edit this name now, or later when you are going to save your pathway. Click the Save button when you want to finish the modifications and save your pathway. If you can't see a save button, it means you are not logged in and you won't be able to save your pathway after modifying it.

After clicking the Save button, a popup window will appear where you can enter the name of the pathway. You can select one organism and one metabolism for your custom pathway before saving it.

Components

This section is useful to find a specific component in the pathway graphs. Two selectable lists (one for enzymes and another for metabolites) are provided. Select one element from one of the two lists and click its corresponding Find button. The node will appear selected and centered in the graph.

Style

In this section, you can modify the style (color and shape) of the nodes in the graph. For each type of node (metabolite, enzyme, gene or reaction) and edge (left, right, enzyme, gene) you can choose between a range of shapes and colors. When you have modified your preferences, click the Apply button to apply the selected style to the graph. Click the "Default" button to restore the default combination of colors and shapes.

The main graph area

In this area, a graph composed by the components of the pathway to edit is placed. You can manipulate the graph using the most common mouse actions.

  • Left click a node to select it.
  • Hold left click on a node to drag and move it to a new position.
  • Hold left click on an empty place of the graph for more than one second until a grey circle appears to move the whole graph.
  • Hold left click and instantly move your cursor to make use of a rectangular area selection. Use this option to select and move a group of nodes.
  • Use your mouse wheel to zoom in or out the graph. If you are using a trackpad, you can use two fingers simultaneously and move them up or down to zoom in or out.
  • Right click on a node, edge or on an empty space in the graph to make a contextual menu appear.

Contextual menu

This menu appears when right clicking on a node or on an empty space in the graph. The options in the menu will be different according to where you right-clicked.

You right clicked on...

  • ...a reaction
    1. Show reaction info. Open a new tab that shows all the information about the reaction components such as enzymes and metabolites (reactives and products).
    2. Edit reaction. Opens the reaction editor window.
    3. Delete reaction node. Remove this node from the graph.
  • ...a metabolite
    1. Show metabolite info. Open a new tab that shows all the information related to the metabolite such as general information (e.g. formula, mass, name and synonyms), the related pathways and reactions.
    2. Delete metabolite node. Remove this node from the graph.
  • ...an enzyme
    1. Show enzyme info. Open a new tab that shows all the information related to the enzyme such as general information (e.g. E.C. number), related pathways, reactions and genes.
    2. Delete enzyme node. Remove this node from the graph.
  • ...an edge
    1. Delete right/left/enzyme relation. Remove this edge from the graph.
  • ...an empty space
    1. Add reaction. Open the Add new reaction window where you can introduce a new enzyme stored in the kpath> database or an enzyme that already exists in the pathway to edit.
    2. Add enzyme. Open the Add new enzyme window where a number of 10, 25, 50 and 100 entries can be shown. Also, the user can look for a specific enzyme by entering a key-word in the search box.
    3. Add metabolite. Open the Add new metabolite window where a number of 10, 25, 50 and 100 entries can be shown. Also, the user can look for a specific metabolite by entering a key-word in the search box.

The buttons bar

A set of buttons with useful actions are presented here.

  1. Fit graph to screen. Change the size and position of the graph to occupy the whole main graph area. This is useful when you have lost your position in the graph when zooming or moving the graph too much.
  2. Legend. Opens a small popup with the appearances of the nodes and edges of the graph.
  3. Redraw graph. Recalculates the position of the nodes in the graph. Useful after adding or deleting some nodes.
  4. Add new element. Shows a menu with the following three options:
    • Add new Metabolite. Open the Add new metabolite window.
    • Add new Enzyme. Open the Add new enzyme window.
    • Add new Empty Reaction. Open the Add new reaction window.
  5. Save edited pathway. Opens a popup window where you can enter the name that your pathway will have. You can select one organism and one metabolism for your custom pathway before saving it..
  6. Help. Shows this help in a new tab.

Relationship Search

With this tool, you can search for relations between pairs of elements within a maximum distance.

WARNING! The execution may need some minutes (or even hours) depending on the amount of components introduced as inputs and the maximum distance allowed between them. However, it is possible to recover partial results when some of them have been obtained and let the tool continue working to recover extra results later.

The Relationship Search interface is composed by three different parts:

  1. The collapsible sidebar. Where the input and output are located.
  2. The main graph area. Where the graph with the relations is drawn.
  3. The buttons bar. Where different buttons are located with different quick actions.

The collapsible sidebar

The collapsible sidebar has two sections that can be collapsed or expanded clicking in their names:

  1. Input
  2. Output

You can show or hide the collapsible bar clicking on the small tab placed on the top right of the collapsible bar.

Input

The input section has the following components:

  1. Organism. A selectable list that restricts the relationship search to only one organism or to all of them.
  2. List of added inputs. Each element in the list shows its type (enzyme, metabolite or gene), its name, an Info link (which opens a new tab with the element information) and a X button that removes the element from the input list.
  3. Find button. Button that starts the search. It will be disabled if there are less than two inputs added or if another search is being executed now.
  4. Add gene button. Button that opens the Add new gene window. In this window, you can select a gene to be added as an input to the relationship search.
  5. Add metabolite button. Button that opens the Add new metabolite window. In this window, you can select a metabolite to be added as an input to the relationship search.
  6. Add enzyme button. Button that opens the Add new enzyme window. In this window, you can select an enzyme to be added as an input to the relationship search.
  7. Load from file button. Button that opens the Load inputs from file window. In this window, you can upload a txt file that includes names of genes, metabolites or enzymes to add as inputs.
  8. Advanced options. Submenu that includes more options to be applied in the relationship search.
Advanced options

In the advanced options subsection, you can select the maximum distance allowed between two pairs of inputs. The distance is considered the number of edges between two nodes in the graph.

It is possible to filter the type of nodes that will be processed when you are looking for relationships. The nodes that appear in the relations retrieved would have to be the same type (e.g. organism, gene, pathway, reaction, enzyme and metabolite) than the ones checked out.

Outputs

In this section there are two parts:

  • Inputs: Here, the list of inputs used in the Relationship search appears. You can use the magnifying glass button to highlight the corresponding node in the graph.
  • Relations: Here, it appears a set of numbered buttons to highlight every relation found between the pairs of inputs. An Export to file button is also provided to export all information about the executed Relationship search into a tabulated txt file with BioPax terminology, RDF, N-Triples and TURTLE.

The main graph area

In this area, after execute a Relationship Search, a graph composed by the relations found is displayed. You can manipulate the graph using the most common mouse actions.

  • Left click a node to select it.
  • Hold left click on a node to drag and move it to a new position.
  • Hold left click on an empty place of the graph for more than one second until a grey circle appears to move the whole graph.
  • Hold left click and instantly move your cursor to make use of a rectangular area selection. Use this option to select and move a group of nodes.
  • Use your mouse wheel to zoom in or out the graph. If you are using a trackpad, you can use two fingers simultaneously and move them up or down to zoom in or out.
  • Right click on a node, edge or on an empty space in the graph to make a contextual menu appear.

Contextual menu

This menu appears when right clicking on a node in the graph. For all type of nodes, it will appear an option to show the corresponding node information in a new browser tab.

The buttons bar

A set of buttons with useful actions are presented here.

  1. Export graph to file. Export the pathway and graph information from all the pathways in the graph to a txt tabulated file.
  2. Fit graph to screen. Change the size and position of the graph to occupy the main graph area. This is useful when you have lost your position in the graph when zooming or moving the graph too much.
  3. Legend. Opens a small popup with the appearances of the nodes and edges of the graph.
  4. Help. Shows this help in a new tab.