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MetExplore offers great facilities to create new metabolic networks (BioSources), edit and manage them between several users.

Creation of private BioSources

Copy BioSources

You must first create an account and log in to be able to own private networks. When you are a new MetExplore user, the only networks available to you are public networks. These networks can not be modified. If you want to edit a public network, you must first copy it. To do this, select the BioSource that interests you. Then click on the "Duplicate" button in the "Selected BioSource" panel on the right side of the MetExplore interface.

Import BioSources

You can create a private BioSource by importing data from SBML, MetExplore xml or KEGG.

Create a BioSource from scratch

For creating a new BioSource from scratch, go in the "Network Curation" panel and click on "Create BioSource" to make visible a form where you can describe the BioSource you want to create.

Form for creating a BioSource from scratch

Edition of a BioSource

Add an element in a BioSource

You can add any component (compartment, pathway, reaction...) of a metabolic network by clicking on Add Element in the "Network curation" panel or by clicking on "Add" in the data grids. This will display a form when you will describe the new element.

Add an element in a BioSource

Best order for adding Biological elements

Since some biological elements are required for creating other ones, the best practice to add elements in a BioSource is the following one:

Create compartments
Create genes
Create gene products: requires genes and compartments
Create enzymatic complexes: requires gene products and compartments
Create metabolites: requires compartments
Create reactions: requires enzymatic complexes and metabolites
Create pathways: requires reactions

Choosing the right identifiers and names

The annotator must show particular care in the choice of names and identifiers. Before creation or curation begins, it is useful to establish a nomenclature to follow, especially when the BioSource is shared. For this, we can draw on the nomenclatures of existing models or databases. Even if annotatores are free to use their own rules, here is a list of the most used rules:

Any identifier must not contain space and must contain only alphanumeric characters or "_".
The names must not contain accentuations.
Metabolite identifers start by "M_" and ends with "_" the compartment id. Except the first letter, the identifier must be in lower case. Example: M_atp_c
Reactions start by "R_".
Proteins must be in upper case and genes in lower case.

Edition of compartments

Add a compartment

Click on "Add element" in the "Network Curation" panel and select "Compartment" or Click on "Add" in the toolbar of the Compartment grid. This will display a form in the Network Curation panel where you will describe the new compartment.

Add or Edit a compartment in a BioSource

Note that upper compartment, spatial dimensions, relative size, units and constant compartment size are facultative descriptors put here to be compliant with the SBML format that are not used in MetExplore. Once you have filled all the required fields, click on Save (you will stay in the Curation panel) or on "Save, and go back to the table" (you will be redirected to the Compartment table).

Edit a compartment

Select one or several compartments in the Compartment grid and click on "Edit". This will open one or several Edit forms in the Network Curation Panel.

Delete a compartment

For deleting a compartment, select it in the Compartment grid and click on "Delete". You can delete a compartment only if it is empty, i.e. it doesn't contain any metabolite. If it's not the case, filter the grids with the compartment selected and first delete all the metabolites contained in the compartment.

Edition of genes

Add a gene

Click on "Add element" in the "Network Curation" panel and select "Gene" or Click on "Add" in the toolbar of the Gene grid. This will display a form in the Network Curation panel where you will describe the new gene.

Add or Edit a gene in a BioSource.

Edit a gene

Select one or several gene products in the Gene grid and click on "Edit". This will open one or several Edit forms in the Network Curation Panel.

Delete a gene

For deleting a gene, select it in the Gene grid and click on "Delete".

Edition of proteins

Add a gene product

Click on "Add element" in the "Network Curation" panel and select "Gene Product" or Click on "Add" in the toolbar of the Gene Product grid. This will display a form in the Network Curation panel where you will describe the new gene product.

Add or Edit a gene product in a BioSource.

Selecting a compartment for a gene product is mandatory for being SBML compliant. Be careful that the gene protein localisation is the same than the enzymatic complex where it is involved.

Edit a gene product

Select one or several gene products in the Gene Product grid and click on "Edit". This will open one or several Edit forms in the Network Curation Panel.

Delete a gene product

For deleting a gene product, select it in the Gene Product grid and click on "Delete". This won't delete genes coding it.

Edition of enzymes

Add an enzymatic complex

Click on "Add element" in the "Network Curation" panel and select "Enzymatic Complex" or Click on "Add" in the toolbar of the Enzymatic Complex grid. This will display a form in the Network Curation panel where you will describe the new enzymatic complex.

Add or Edit an Enzymatic Complex in a BioSource.

Selecting a compartment for an enzyme is mandatory for being SBML compliant. Be careful that the enzyme localisation is the same than the reaction that it catalyses and the gene products composing it.

Edit an enzymatic complex

Select one or several enzymatic complexes in the Enzymatic complex grid and click on "Edit". This will open one or several Edit forms in the Network Curation Panel.

Delete an enzymatic complex

For deleting an enzymatic complex, select it in the Enzymatic Complex grid and click on "Delete". This won't delete gene products composing it.

Edition of metabolites

Add a metabolite

Click on "Add element" in the "Network Curation" panel and select "Metabolite" or Click on "Add" in the toolbar of the Metabolite grid. This will display a form in the Network Curation panel where you will describe the new metabolite.

Add or Edit a metabolite in a BioSource. Here the fields have been automatically completed from the KEGG identifier C00001 (water).

Auto-completion from KEGG or Chebi identifier

If you have a valid KEGG or Chebi identifier for the metabolite that you want to add, put it in the corresponding field and click on "Auto-complete", this will fill the form with values from KEGG or Chebi.

Define steady-state boundaries for flux analyses

By checking "Set Boundary Condition to True", the metabolite will be considered as external metabolite in flux analyses. This means that it won't be considered in the steady-state assumption.

Define a metabolite as a side compound

A metabolite defined as a Side Compound can be easiliy filtered for lightening network visualisation.

Edit a metabolite

Select one or several metabolites in the Metabolite grid and click on "Edit". This will open one or several Edit forms in the Network Curation Panel.

Delete a metabolite

For deleting a metabolite, select it in the Metabolite grid and click on "Delete".

Edition of reactions

Add a reaction

Click on "Add element" in the "Network Curation" panel and select "Reaction" or Click on "Add" in the toolbar of the Reaction grid. This will display a form in the Network Curation panel where you will describe the new reaction.

Add or Edit a reaction in a BioSource

Add substrates and products

Select a metabolite, change its stoichiometric coefficient and indicate if it's a substrate or a product. When the metabolic network is huge, it's often difficult to select a metabolite in the box. To facilitate the selection, first filter the Metabolite grid: the Metabolite box in the Reaction form will contain only the metabolites that appear in the filtered Metabolite grid.

Fields used in SBML export

The following fields are retrieved in the resulting file after exporting a BioSource in SBML format and are not used in MetExplore analyses:

Constant coeff for metabolite participant
Kinetic law

Fields used in MetExplore xml export

The following fields are retrieved in the resulting file after exporting a BioSource in MetExplore xml format and are not used in MetExplore analyses:

Side compound for metabolite participant. This indicates that this metabolite is a side compound only for this reaction and not a side compound for all the reactions.
Spontaneous reaction
Generic reaction
Hole reaction

Confidence level

A confidence level set from Thiele and Palsson, 2010 can be set.

Edit a reaction

Select one or several reactions in the Reaction grid and click on "Edit". This will open one or several Edit forms in the Network Curation Panel.

Delete a reaction

For deleting a reaction, select it in the Reaction grid and click on "Delete". This won't delete the metabolites involved in the reaction.

Edition of pathways

Add a pathway

Click on "Add element" in the "Network Curation" panel and select "Pathway" or Click on "Add" in the toolbar of the Pathway grid. This will display a form in the Network Curation panel where you will describe the new pathway.

Add or Edit a pathway in a BioSource

Edit a pathway

Select one or several pathways in the Pathway grid and click on "Edit". This will open one or several Edit forms in the Network Curation Panel.

Delete a pathway

Select one or several pathways in the Pathway grid and click on "Delete". This will delete only the pathway as a classifier but not the reactions classified into this pathway.

Multi-user management of private BioSources

The annotation of a metabolic network often requires the intervention of several collaborators. It is interesting that they can have several roles: from the consultation role to the addition and editing of network components. Today, metabolic reconstruction projects can apply to several close species or belonging to the same ecosystem. It is therefore important to be able to manage several networks in the same way, from the point of view of access rights as well as the centralization of information. Being able to generate the history of each BioSource also makes easy to monitor curation. Finally, a metabolic reconstruction project requires a fine organization that must be shared by all collaborators. It is for these reasons that we integrated in MetExplore the concept of a project grouping several BioSources. Collaborators added to a project will have different rights that will apply equally to all BioSources in the project. The history of all the actions performed on the BioSources of the same project can be displayed. Finally, a shared list TODO system facilitates the organization of the reconstruction. For testing Project functionalities without creating a new project, logout if you are logged and click on "Demo" in the User Profile panel.

For sharing a private BioSource between several users without creating a project, go in the "Selected BioSource" panel at the right of the MetExplore interface, and click on the Share button. Then fill the form with user e-mails or MetExplore user names. Be careful, sharing a BioSource without creating a Project means that this BioSource is modifiable, removable by all the users that have the access to this BioSource. For critical BioSources, we recommend going through the creation of a project for finely managing the read-write rights of the collaborators.

Share a BioSource between several users

Easy data checking by votes

The objective of the Votes is to propose a tool to those who would not dare to modify the database, or who do not have the right, to give their opinion on biological component of the metabolic network. Also, the idea is to be able to easily gather the opinions of several people for each component of the metabolic network and to facilitate the organization of manual correction of the metabolic network.

The Votes panel is included in the information window of any component in a private metabolic network. This information window is displayed after clicking on the icon in the data grids. A color code has been decided for all the views representing the votes. Thus, the green corresponds to the vote "The object exists in this organism and is correct". Yellow corresponds to the vote "The object exists in this organism but contains some errors". Finally, the red corresponds to the vote "The object does not exist in this organism". The first tab of this panel allows the user to vote. The second tab summarizes the votes of all users.

Votes panel for a reaction

The "Details" button lets know who voted for what.

Details of a vote

In the corresponding grid, the button "Curation Votes" allows to add a column, "Votes summary", which summarizes the votes of all the objects of the grid, allowing to classify them of those who have the more votes to those who have it less. This column represents the summarized votes for each biological component, in the form of a multicolored bar. This bar takes the color corresponging to the vote, and the width of each rectangle of the bar is proportional to the corresponding number of voters, indicated inside. If the user clicks on one of these graphs, the information window of the corresponding object opens with the Votes panel open.

Column resuming the votes of the annotators

Comments on reactions

For facilitating the curation of a BioSource, each annotator can add comments on reactions. For visualising and adding comments, open the reaction information window by clicking on the icon in the Reaction grid. A file can be uploaded to complete a comment.

Add a comment for a reaction

User panel

The User panel is thought of as a personal portal in MetExplore. So from this panel, the user has access to a summary of the work done or to be done in the Projects to which hebelongs. Thus, at the top of the panel appears the TODO List of actions done or to be done. In the bottom of the User Panel, different tabs are present:

The list of Projects to which the user belongs
The list of private BioSources to which the user has access.
The history of any change to BioSources that the user has access.

At the top of the panel is the name of the logged in user, next to a button to disconnect and down a button to edit his personal information.

MetExplore User Panel

Project panel

The purpose of the Project panel is to concentrate within the same interface all the information about the Project and the work done or to be done for this Project. For a better user experience, the structure of this panel is built in the same way as the User Panel. Thus, we find at the top the TODO List over the entire width. At the bottom, we found these tabs:

List of BioSources associated with the Project
Project Comments List
History of all changes applied to Project BioSources
Project description
Project users

In the header is displayed the title of the project, next to a button to close it and below the date of creation of the Project and a button to modify the details of the Project, if the user is a owner. The latter opens a form pre-filled with the data origins of the Project.

MetExplore Project Panel

The rights that can be assigned to each collaborator of a project are as follows.

MetExplore project user rights

History panel

It's important when working on metabolic reconstruction, as for many of scientific work, to keep track of what we do. Adding a history allows here to easily view all the changes that are made to a BioSource or to one of its components. This can also facilitate the work when publishing the metabolic reconstruction.

History panel

The history panel displays all the actions done in all BioSources to which the user has access. When loading the interface, the history displays only the entries associated with the connected user through a filter. Just click on "All" in the bottom toolbar to display those of all collaborators associated with the user. The "Personal" button is used to return to the initial state. For each entry, the history displays its date, the user who performed the action, the associated Project if there is one, the associated BioSource and a description of the action taken. To have more information about this action, just click on the icon of the corresponding line, in last column. The details are displayed in a new window. In the case of an addition of an object, one can see the details of the new object. In the case of the deletion of an object, one can see the details of the object that was deleted. Finally, in the case of updating an object, the window shows the old version at the top, on a red background, and the new version at the bottom, on a green background. The changed fields appear on a yellow background.

Detail of a modification from the History panel.

When loading the interface, the history displays the entries since the date of the most recent entry found in the database, up to 15 days before that date. It is possible to change the start and end dates directly in the present date fields in the toolbar at the bottom of the grid. As soon as these dates are modified, the history is reloaded. It is also possible to navigate through the history keeping the specified date range in the fields. This is done through the arrows on the bottom toolbar, on both sides of the fields of date. The one on the left makes it possible to visualize the older entries, and the one on the right the more recent entries.

TODO panel

The TODO List includes all the actions made or to be done by all users for all Projects to which the connected user participates.

By default, the TODO List only displays the actions associated with the connected user. But it is possible to view all actions of all his/her collaborators by clicking on the button "All" at the bottom of the grid. To see only user's actions, click on "Personal". Each action has a description, an associated Project, an associated user, a deadline and a status. Status can be: not started, in progress, done or canceled. If the deadline of an action is in less than five days (or past), and that the status is not completed or canceled, the action appears on a red background for indicate that it must be completed soon. To change the status of one or more actions, simply select them and click on the desired status button, at the top of the toolbar to the right of the grid. To add a new TODO item, a button is present in the toolbar on the right. By clicking on it, a form is displayed allowing to indicate the information of the action to be added. The connected user is placed by default when opening the form, and the list of users will update based on the selected project. To edit an action, the user must double click on it. The form is then displayed, pre-populated with the original values of the action. To delete one or more TODO items, the user selects them and click on the corresponding button in the toolbar on the right. The modification or deletion of an action is only possible if it is its own action or if it is an owner of the associated Project.

Form to add a TODO item

Create and curate metabolic networks