1. INDRA Statements constructed from TRIPS NLP extractions, BioPAX, and BEL
INDRA Statements constructed from TRIPS NLP extractions, BioPAX, and BEL An identical INDRA Statement is constructed from three knowledge sources. A corresponding fragment of each source format (representing the phosphorylated state of MAP2K1 on S222) is highlighted in blue. Top left: A TRIPS EKB (see Box 1) graph is shown for the sentence “MAP2K1 that is phosphorylated on S218 and S222 phosphorylates MAPK1 at T185”. The main phosphorylation event has agent, affected, and site arguments, each of them referring to a term. The agent term resolves to a gene with name MAP2K1 and database references to UniProt and HGNC. The MAP2K1 term also refers to an additional event in which it is affected (yellow background). This additional event represents the phosphorylated state at two molecular sites: serine 218 and serine 222. The affected term associated with the main phosphorylation event is MAPK1 with its associated UniProt and HGNC references. Finally, the site argument of the main event is a molecular site resolving to threonine 185. Middle left: A BioPAX Biochemical Reaction is shown with unmodified MAPK1 on the left‐hand side and MAPK1 with a Sequence Modification Feature of phosphorylation at threonine 185 on the right‐hand side. Both the left‐ and the right‐hand sides use the same Cross Reference to a UniProt identifier. A Catalysis is associated with the Biochemical Reaction with MAP2K1 as the controller. MAP2K1 has two Sequence Modification Features: phosphorylation at serines 218 and 222. MAP2K1 also refers to a UniProt identifier via a Cross Reference. Two alternative visual representations of the same BioPAX Reaction are given in Appendix Fig S5. Bottom left: A graphical representation of a BEL statement is shown in which the subject is the Kinase Activity of the Protein Abundance of the modified MAP2K1 (with phosphorylations at serines 218 and 222). The object of the statement is the Protein Abundance of modified MAPK1 (phosphorylation at threonine 185) with the predicate being Directly Increases. Below the graphical representation, the statement is also given in BEL script format. Right: All example mechanisms from the three knowledge sources are constructed as the same INDRA Phosphorylation Statement with MAP2K1 as the enzyme (subject to modification conditions) and MAPK1 and the substrate. The Evidence associated with the INDRA Statement (not shown) constructed would be different for each knowledge source.
Benjamin M Gyori et al. Mol Syst Biol 2017;13:954
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