MultiPaths: a Python framework for analyzing multi-layer biological networks using diffusion algorithms.

Summary: High-throughput screening yields vast amounts of biological data which can be highly challenging to interpret. In response, knowledge-driven approaches emerged as possible solutions to analyze large datasets by leveraging prior knowledge of biomolecular interactions represented in the form of biological networks. Nonetheless, given their size and complexity, their manual investigation quickly becomes impractical.

PTSD Biomarker Database: deep dive metadatabase for PTSD biomarkers, visualizations and analysis tools.

The PTSD Biomarker Database (PTSDDB) is a database that provides a landscape view of physiological markers being studied as putative biomarkers in the current post-traumatic stress disorder (PTSD) literature to enable researchers to explore and compare findings quickly. The PTSDDB currently contains over 900 biomarkers and their relevant information from 109 original articles published from 1997 to 2017. Further, the curated content stored in this database is complemented by a web application consisting of multiple interactive visualizations that enable the investigation of biomarker knowledge in PTSD (e.

PathMe: merging and exploring mechanistic pathway knowledge.

Background: The complexity of representing biological systems is compounded by an ever-expanding body of knowledge emerging from multi-omics experiments. A number of pathway databases have facilitated pathway-centric approaches that assist in the interpretation of molecular signatures yielded by these experiments. However, the lack of interoperability between pathway databases has hindered the ability to harmonize these resources and to exploit their consolidated knowledge.

Erratum: Publisher Correction: ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases.

[This corrects the article DOI: 10.1038/s41540-018-0078-8.].

ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases.

Although pathways are widely used for the analysis and representation of biological systems, their lack of clear boundaries, their dispersion across numerous databases, and the lack of interoperability impedes the evaluation of the coverage, agreements, and discrepancies between them. Here, we present ComPath, an ecosystem that supports curation of pathway mappings between databases and fosters the exploration of pathway knowledge through several novel visualizations. We have curated mappings between three of the major pathway databases and present a case study focusing on Parkinson's disease that illustrates how ComPath can generate new biological insights by identifying pathway modules, clusters, and cross-talks with these mappings.