Other than where specified, these are my notes from the IB07 Conference, and not expressions of opinion. Any errors are probably just due to my
own misunderstanding. 🙂
Most disease are multifactorial. Now we've reached a critical mass where we need to put all the information together, to understand the whole rather than the bits. This is the main aim of the Reactome database: to create a single, hand-curated model of human molecular biology, in pathway form.
There are three problems with the currently available biological information: data is lacking, the data that is out there is dispersed over a vast array of literature etc, and often the data is inapplicable (how do we discover what information is pertinent to us?). We extract the knowledge from the experts and insert it into Reactome via its data model. The core of Reactome is the mapping – they use external vocabularies, information etc. They map to proteins via UniProt and get further cross-references via this database. Other primary resources include GO and ChEBI. They also provide an API in both perl and java that can be used for querying and working with Reactome. There is also an online application called Reactome Mart.
How does Reactome represent its data? The better the way to describe biological structure, the better the method to describe biological activity. There is a physical entity class that can describe their state and what they are. What then followed was a very nice description of the data flow and the data model of Reactome, specifically how it deals with combinatorial explosion of possible complex types in a given pathway.
Even though they concentrate on human, they can use orthology information and create putative skeleton models for other organisms. They also have a tool called skypainter where you can paste in your favorite IDs and gene expression data, and then the Reactome pathways can be colored according to your data or IDs. All work and tools is freely available from the Reactome website.