P0324
Knowledge.Bio: A Web Application for Collaboratively Building and Exploring Networks of Biological Relationships

Richard Michael Bruskiewich , STAR Informatics / Delphinai Corporation, Port Moody, BC, Canada
Kenneth Casimir Huellas-Bruskiewicz , Simon Fraser University, Burnaby, BC, Canada
Chandan Kumar Mishra , Simon Fraser University, Burnaby, BC, Canada
Farzin Ahmed , Simon Fraser University, Burnaby, BC, Canada
Yinglun Colin Qiao , Simon Fraser University, Burnaby, BC, Canada
Jarielle D Lim , Simon Fraser University, Burnaby, BC, Canada
Lance Hannestad , Simon Fraser University, Burnaby, BC, Canada
Rudy Kong Tin Lun , Simon Fraser University, Burnaby, BC, Canada
Benjamin M Good , The Scripps Research Institute, La Jolla, CA
Knowledge.Bio (Bruskiewich et al., 2016) is an open source web resource to enhance access and interpretation of networks of concepts and relationships derived from text mining or curated public resources. Each edge in these networks is linked to underlying evidence (e.g. an abstract in PubMed), which may be accessed within the context of the application. Along the way, users construct their own graphical map of related concepts which can be exported and shared either locally as a file on a user's computer, or remotely within an indexed map library.

The initial research literature knowledge base of Knowledge.Bio is drawn from the Semantic Medline Database (https://skr3.nlm.nih.gov/SemMed/; Kilicoglu et al., 2012) and the Implicitome (Hettne et al., 2016), two complementary resources derived from text mining of NCBI Pubmed abstracts. Additional cross-linkages are provided to external biological databases via integration with WikiData (https://www.wikidata.org; Burgstaller-Muehlbacher 2016). In addition, Knowledge.Bio data loading protocols allow additional concept and relationship data to be loaded from other data sources.

Availability and Implementation: hosted at http://knowledge.bio/; open source code available at http://bitbucket.org/sulab/kb2/.

Contact: richard@plantinformatics.com

References:

Bruskiewich, RM, et al. (2016) Knowledge.Bio: A Web application for exploring, building and sharing webs of biomedical relationships mined from PubMed.doi: http://dx.doi.org/10.1101/055525

Burgstaller-Muehlbacher, Sebastian, et al. (2016) "Wikidata as a semantic framework for the Gene Wiki initiative." Database 2016 : baw015.

Hettne, KM, et al. (2016) The Implicitome: A Resource for Rationalizing Gene-Disease Associations.PLoS ONE 11(2): e0149621. doi:10.1371/journal.pone.0149621

Kilicoglu, H, et al. (2012) SemMedDB: a PubMed-scale repository of biomedical semantic predications.Bioinformatics, 28(23), 3158-60.

Handouts
  • PAG-XXV-Knowledge-Bio-final.pdf (1.7 MB)
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