BioKB

Please, provide a main entity and at least one relationship, target entity or type

Main entity:

Relationships:

Entity types:
Target entities:

Examples: NF2 or Asthma or ABCA1

Search bioentities
Search papers
Query Knowledge
Curate knowledge

Entity Search

First, start with a simple search on 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.

Simple Search
Advanced Search

Entity View

The search form will redirect you to the Entity View where you can start drilling down into the results of your 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. Please note that at the moment, it only considers the relationships appearing in the first page of each table.

Entity View

BioKB also allows searching for specific publications by title, DOI, PMC, or PUBMED ID.

The publication view will show the events extracted by BioKB pipeline, highlighting the entities tagged by the reflect engine. An event is a relationship between two bioentities.

Publication search
Publication view

Our knowledge base can also be queried via our SPARQL endpoint for complex and automated querying.

BioKC is the curation tool for BioKB, which benefits from the large knowledge base of text mined publications already available on this site. To access BioKC's functionality, simply register for and log into a BioKB user account.

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.

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  • 2021/02/08 Added publication search to browse BioKB pipeline results for specific articles.
  • 2020/10/03 BioKC pre-print is now available at BioRxiv.
  • 2020/09/04 Check BioKC demos at biokc.pages.uni.lu.
  • 2020/08/01 BioKC now supports identifiers.org.