Curation of data in cider
Information about disease-related interactions consists of three kinds of information.
- The central information is a structured interaction between two elements (e.g. protein A activates protein B). This is also known as subject-predicate-object structure. "Subjects" and "Objects" are linked/mapped to thesauri such as EntrezGene, KEGG, OMIM, miRBase, Gene Ontology, CORUM. If a term is not available in these vocabularies, we introduce suitable terms.
Additional information about conditions (Arg_Mod = mode) or locus (Arg_Loc) are also frequently presented.
- A textual comment allows to provide additional information about the experimental setup (e.g. concentration of a drug that was applied) and to present a more differentiated view than the structured information (e.g. the structured information is restricted to 'protein A increases_activity of protein B' whereas in the text we can specify that it is a 'significant' or a 'slight' increase of the protein activity).
- The general information consists of literature reference, organism, disease and if available tissue/cell line and gender. All information is linked to the PubMed content of the respective journal articles.
Information in CIDeR is given as entries and interactions. An entry comprises one or more result/-s (interactions) from one publication that was/were obtained under the same experimental conditions. A relation is part of an entry and describes an interaction between two elements (e.g. protein A increases_activity of protein B).