Extracting Functional Modules from Biological Pathways

Extracting Modules from Ontologies: Theory and Practice

The ability to extract meaningful fragments from an ontology is essential for ontology re-use. We propose a definition of a module that guarantees to completely capture the meaning of a given set of terms, i.e., to include all axioms relevant to the meaning of these terms, and study the problem of extracting minimally sized modules. We show that the problem of determining whether a subset of an...

Extracting Knowledge from Biological Descriptions

We describe a system which performs biological identification on the basis of natural language descriptions. The system parses texts containing large sets of biological descriptions in restricted natural language and constructs a knowledge base. The system can semi-automatically adapt to a text by extending its lexicon and perhaps its grammar. The constructed knowledge bases are used to perform...

Extracting active pathways from gene expression data

MOTIVATION A promising way to make sense out of gene expression profiles is to relate them to the activity of metabolic and signalling pathways. Each pathway usually involves many genes, such as enzymes, which can themselves participate in many pathways. The set of all known pathways can therefore be represented by a complex network of genes. Searching for regularities in the set of gene expres...

Extracting Biological Keywords from Scientific Text

Extracting meaning from biological imaging data

Biological imaging continues to improve, capturing continually longer-term, richer, and more complex data, penetrating deeper into live tissue. How do we gain insight into the dynamic processes of disease and development from terabytes of multidimensional image data? Here I describe a collaborative approach to extracting meaning from biological imaging data. The collaboration consists of teams ...