Abstract
The complexity of biomolecular interactions and influences is a major obstacle to their comprehension and elucidation. Visualizing knowledge of biomolecular interactions increases comprehension and facilitates the development of new hypotheses. The rapidly changing landscape of high-content experimental results also presents a challenge for the maintenance of comprehensive knowledgebases. Distributing the responsibility for maintenance of a knowledgebase to a community of subject matter experts is an effective strategy for large, complex and rapidly changing knowledgebases. Cognoscente serves these needs by building visualizations for queries of biomolecular interactions on demand, by managing the complexity of those visualizations, and by crowdsourcing to promote the incorporation of current knowledge from the literature.
Highlights
The complexity of biomolecular interactions and influences is a major obstacle to their comprehension and elucidation
Comprehension of the complexity of this corpus of knowledge will be facilitated by effective visualizations of the corresponding biomolecular interaction networks
Cognoscente was motivated by the need to (1) update the knowledgebase of biomolecular interactions at the user level, and (2) flexibly visualize multi-molecule query results for heterogeneous interaction types across different orthologs
Summary
The complexity of biomolecular interactions and influences is a major obstacle to their comprehension and elucidation. Distributing the responsibility for maintenance of a knowledgebase to a community of subject matter experts is an effective strategy for large, complex and rapidly changing knowledgebases Cognoscente serves these needs by building visualizations for queries of biomolecular interactions on demand, by managing the complexity of those visualizations, and by crowdsourcing to promote the incorporation of current knowledge from the literature. Cognoscente was motivated by the need to (1) update the knowledgebase of biomolecular interactions at the user level, and (2) flexibly visualize multi-molecule query results for heterogeneous interaction types across different orthologs. Satisfying these needs provides a strong foundation for developing new hypotheses about regulatory and metabolic pathway topologies. The current weaknesses of Cognoscente relative to these other tools are (1) that it does not fully support web service interactions with the database, (2) it does not fully support small molecule interactants, and (3) it does not score interactions to Planned feature
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