To address this task, we manually annotated reaction-document pairs with the relevance of the documents to each reaction (Section 3.1).
We used PathBuilder (36), a pathway annotation tool developed by our group, to annotate reactions in TSLP signaling.
An extensive search of published literature was carried out in PubMed to annotate reactions involved in the TSLP signaling pathway.
However, the organelles in Recon 1 usually have values below the reference line, due mainly to a higher difficulty to annotate reactions specific to an organelle.
Therefore, MEMOSys supports annotating reactions, metabolites, genes and compartments with references to external databases using the 'minimum information requested in the annotation of biochemical models' (MIRIAM) (31) notation.
We maintain three annotation tables for BioModels Database models: (a) Annotating models with organisms from the NCBI organism taxonomy, (b) Annotating models with Gene Ontology (GO) terms, (c) Annotating reactions in models with EC (Enzyme Commission) numbers.
The database contains chemical structures of xenobiotic biotransformations with substrate atoms annotated as reaction centra, the resulting product formed, and the catalyzing enzyme, type of experiment, and literature references.
CPDB has also annotated each reaction of a signaling network with the above mentioned PPI databases.
The reaction is annotated with the reaction direction and if it is reversible or not.
Recon 1 is a comprehensive map of all the known annotated metabolic reactions of human cells, containing 1496 genes, 3402 intracellular reactions, and 2785 metabolites.
Furthermore, only 27.7% of all 55,488 MCS are fully annotated, enzymatic reactions.
