INDRA-IPM: interactive pathway modeling using natural language with automated assembly

Petar V Todorov; Benjamin M Gyori; John A Bachman; Peter K Sorger

doi:10.1093/bioinformatics/btz289

INDRA-IPM: interactive pathway modeling using natural language with automated assembly

Bioinformatics. 2019 Nov 1;35(21):4501-4503. doi: 10.1093/bioinformatics/btz289.

Authors

Petar V Todorov¹, Benjamin M Gyori¹, John A Bachman¹, Peter K Sorger¹

Affiliation

¹ Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.

Abstract

Summary: INDRA-IPM (Interactive Pathway Map) is a web-based pathway map modeling tool that combines natural language processing with automated model assembly and visualization. INDRA-IPM contextualizes models with expression data and exports them to standard formats.

Availability and implementation: INDRA-IPM is available at: http://pathwaymap.indra.bio. Source code is available at http://github.com/sorgerlab/indra_pathway_map. The underlying web service API is available at http://api.indra.bio:8000.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Computers*
Natural Language Processing
Software*

Grants and funding

P50 GM107618/GM/NIGMS NIH HHS/United States