This is our vision: a cell biologist asks a biological question to a modeling tool (e.g. Virtual Cell). The modeling tool then retrieves biological knowledge from the web about pathways (e.g. Pathway Commons, BioCyc), proteins (e.g. UniProt), genes (e.g. KEGG, Entrez), metabolites (e.g. ChEBI) and kinetic data (e.g. SABIO-RK, SGMP).
Then, the modeling tool builds and annotates the model, simulates it, and comes back with the answer the biologist wanted.
In recent years, we have been edging closer to realizing this vision through the proliferation of biological knowledge available on the web and the development of standards to encode this knowledge in machine-readable form (e.g. BioPAX, SBML, see also COMBINE). This web site is dedicated to fill in the gaps and build the final bridge through technical solutions such as SBPAX3, UOME and DRIMD.
Systems Biology Pathway Exchange (SBPAX) is an ontology and data format designed to store and organize systems biological knowledge data and data related to quantitative modeling. The latest version, SBPAX3 , can be used as an extension to BioPAX Level 3 and has been proposed as part of BioPAX Level 4. SBPAX allows the use of relevant vocabularies such as the Systems Biology Ontology (SBO).
To specify units of measurements, SBPAX uses Units of Measurement Expressions (UOME) , which provides ways to reference vocabularies such as the Unit Ontology as well as ways to derive units from other units. It also includes a long list of predefined units.
To turn human-readable data base web pages into a machine-readable interface without changing its appearance, add a few attributes to the HTML by using Data Retrieval Interface Microdata (DRIMD) .
To download SBPAX3, UOME or sample data, visit the download page.