Curation of data in HoPaCI
Information about pathogen-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. The distinction of the genes referring to pathogen or host can be made by their notation.
- If a term is not available in these vocabularies, we introduce suitable terms.
- 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, and if available tissue/cell line. All information is linked to the PubMed content of the respective journal articles.
Information in HoPaCI 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.
An interaction is part of an entry and describes an interaction between two elements (e.g. protein A increases_activity of protein B).