INOH (Integrating Network Objects with Hierarchies) is a pathway database of model organisms including human, mouse, rat and others. In INOH, the term pathway refers to higher order functional knowledge such as relationships among multiple bio-molecules that constitute signal transduction pathways or biological events in general. As most part of this knowledge resides in scientific articles, the database focuses on curating and encoding textual k...
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INOH (Integrating Network Objects with Hierarchies) is a pathway database of model organisms including human, mouse, rat and others. In INOH, the term pathway refers to higher order functional knowledge such as relationships among multiple bio-molecules that constitute signal transduction pathways or biological events in general. As most part of this knowledge resides in scientific articles, the database focuses on curating and encoding textual knowledge into a machine-processable form.
The system contains a number of unique features to encode this type of knowledge. Biological terms such as protein names typically represent abstract, conceptual molecules that are used for unspecified organisms. Biologists interpret the name as a specific instance of protein using background knowledge. For example, the term "MAP-kinase" indicates ERK1 of a human, JNK1 of a mouse, p38alpha of a rat, etc.
These abstract names are collected from the literature and are organized into an ontology to annotate abstract objects in pathways. In addition, each term has links to database such as SWISS-PROT and Gene Ontology (GO).
The system provides pathway information as a composite of biological events, since functional knowledge is usually described as a set of fragmented processes. Each event is annotated with entries of a event ontology, which also has links to GO.
