How to Explore BioKB and Curate Facts with BioKC

BioKC is the curation tool for BioKB which benefits from the large knowledge base of text mined publications already available on this site.

On top of the home page you will find a link to login or register.

After registration, a group will be created for you in which you can start creating your own facts and populate them.

Entity Search

First, start with a simple search in the home page. You will be redirected to the entity view.

For more advanced searches, try the advanced search form. You will also be redirected to the entity view, but this time the results will be filtered with your search choices.


Entity View

Search form will redirect us to the Entity View where we can start drilling down the results of our search.

Entity view consist of 3 sections: Co-occurrences, Relationships and Visualization.

Co-occurrences

This section shows entities appearing together with the searched entity.

Relationships

This section shows relationships from extracted sentence events in which the searched entity appears. Contrary to Co-occurrences, relationships have directionality, either incoming or outgoing, and a relationship type.

Visualization

The graph shows the combined network of incoming and outgoing relationships. However, for now it only considers the relationships appearing in the first page of each table.

The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model

BioKC stores facts in a data model similar to SBML and allows exporting a fact in SBML format.


Excerpt from: Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

E + S k off k on E S k cat E + P

In this example, the model has the identifier EnzymaticReaction. The model contains one compartment (with identifier cytosol), four species (with identifiers ESPS, and E), and two reactions (veq and vcat).

The elements in the listOfReactants and listOfProducts in each reaction refer to the names of elements listed in the listOfSpecies.

The correspondences between the various elements is explicitly stated by the speciesReference elements.

The model also features local parameter definitions in each reaction. In this case, the three parameters (kon, koff, kcat) all have unique identifiers and they could also have just as easily been declared global parameters in the model.

Local parameters frequently become more useful in larger models, where it may become tedious to assign unique identifiers for all the different parameters.


From the curator's perspective, BioKC only handles the following elements.

For now Species, Compartment, Reaction, SpeciesReference, ModifierSpeciesReference and some parts of Model are supported.

The whole SBML specification can be found in their website http://sbml.org/.


Species

A pool of entities of the same species type located in a specific compartment.


Compartment

A well-stirred container of a particular type and finite size where SBML species may be located. Every species in a model must be located in a compartment.


Reaction

A statement describing some transformation, transport or binding process that can change the amount of one or more species.

For example, a reaction may describe how certain entities (reactants) are transformed into certain other entities (products). Reactions have associated kinetic rate expressions describing how quickly they take place. In SBML, the rate expressions can be arbitrary mathematical functions.

A reaction represents any transformation, transport or binding process, typically a chemical reaction, that can change the quantity of one or more species. In SBML, a reaction is defined primarily in terms of the participating reactants and products (and their corresponding stoichiometries), along with optional modifier species, an optional rate at which the reaction takes place, and optional parameters.

These various parts of a reaction are recorded in the SBML Reaction object class and other supporting data classes, defined in figure.

The lists of reactants, products and modifiers. The species participating as reactants, products, and/or modifiers in a reaction are declared using lists of SpeciesReference and/or ModifierSpeciesReference instances stored in listOfReactants, listOfProductsand listOfModifiers.


Model

Only one instance of a Model object is allowed per instance of an SBML.

Model serves as a container for components of classes FunctionDefinition, UnitDefinition, CompartmentType, SpeciesType, Compartment, Species, Parameter, InitialAssignment, Rule, Constraint, Reaction and Event.

Instances of the classes are placed inside instances of classes ListOfFunctionDefinitions, ListOfUnitDefinitions, ListOfCompartmentTypes, ListOfSpeciesTypes, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfInitialAssignments, ListOfRules, ListOfConstraints, ListOfReactions, and ListOfEvents.

The “list” classes are defined in the Figure. All of the lists are optional, but if a given list container is present within the model, the list must not be empty; that is, it must have length one or more.

A fact is similar to SBML model. It contains Species, Compartments and Reactions. Each fact belongs to a single group of facts, in which users can have different roles.

We call the process of building the fact, curation. Only the users with the role curator can curate the model.

We can collect sentences found in BioKB and assign them to different parts of the fact model. We call this process Annotation. It is also possible to add custom sentences. Only the users with the role annotator can annotate the model.

Example of a fact as seen in the Fact view page.

What does it mean to play a Fact?

Also Annotator's Mode and Curator's Mode


In order to modify the different parts of the fact, two modes can be enabled. Annotator's mode and Curator's mode. The access to this modes is restricted by the user group roles.

Users with annotation permission can start the annotation mode in order to assign evidence from BioKB to different parts of the fact model.

Users with curation permission can start the curation mode to modify the different elements that compose the fact model. Curators can add and modify Species, Compartments, Reactions as well as remove them from the fact model.

⚠️ Important ! A warning will be prompt if another user is already curating or annotating a fact. It is recommended that only one user curates/annotates the fact at the same time. However, nothing stops you from having multiple users curating/annotating the fact at the same time. Keep in mind that curation from multiple users might produce undesired and inconsistent results.

Curators and Annotators can play a fact in different modes depending on their roles.

While on Annotation Mode, sentences found in BioKB can be assigned to different parts of the model.
While on Annotation Mode, a box on the top right corner will indicate this mode is enabled. Information regarding the annotations will be shown in this menu. This menu will be available as you browse BioKB.

Similarly, the Curator's Box will be shown while the fact is being curated. Both menus allow the user to stop the annotation/curation process.

Roles provide allow for different sets of actions. The roles are assigned per group of facts. Therefore, each user can have different set of roles for each group of facts

Reader

  • Read only access to facts.

Annotator

  • Permission to annotate the facts.

Curator

  • Permission to change the elements that compose a fact.

Manager

  • Administrators of the group.
  • Can delete facts.