Why do we need Reactome?

Researchers have defined many biological pathways, represented in scientific literature, textbooks, or electronic databases, but...

  • The information is spread across many thousands of papers.
  • It is not easily accessible for computational reuse.
  • Scientific writing is highly subjective and nuanced.
  • Text mining has trouble identifying correct relationships.

 

A typical graphic from the scientific literature showing signal transduction pathways

Figure 9. A typical graphic from the scientific literature showing signal transduction pathways.

 

Pathway information is also contained in figures or diagrams, often associated with text in the scientific literature (see example in Figure 9). Even though a picture is an intuitive way to visualise a biological process or pathway, it is not computationally accessible, or interactive, or necessarily complete and accurate.

Moreover, there are problems associated with typical figures in scientific literature and textbooks:

  • They assume that the reader is familiar with the subject, so they leave out details.
  • The frequently promote a point of view, mixing established knowledge with hypotheses (models).
  • They rarely include citations to the supporting literature for all the represented interactions.
  • The may be out of date, or inaccurate, or controversial.

 

Reactome data consists of reactions and pathways based on information extracted from papers by people – biologists who are experts in their field – assisted by PhD-level curators who add structure to the information and place it in the database. This process optimises the details provided about each pathway, and makes the data accessible for computational data mining and re-use, in addition to browing by other people.

Reactome provides access to a curated, quality-assured slice of pathway information, available as diagrams and descriptions on the Reactome website and as downloadable pathways in standard formats such as BioPax and SBML.