Collaborative workspaces for pathway curation

Funda Durupinar-Babur, Metin Can Siper, Ugur Dogrusoz, Istemi Bahceci, Ozgun Babur, Emek Demir

Research output: Contribution to journalConference articlepeer-review


We present a web based visual biocuration workspace, focusing on curating detailed mechanistic pathways. It was designed as a flexible platform where multiple humans, NLP and AI agents can collaborate in real-time on a common model using an event driven API. We will use this platform for exploring disruptive technologies that can scale up biocuration such as NLP, human-computer collaboration, crowd-sourcing, alternative publishing and gamification. As a first step, we are designing a pilot to include an author-curation step into the scientific publishing, where the authors of an article create formal pathway fragments representing their discovery- heavily assisted by computer agents. We envision that this "microcuration" use-case will create an excellent opportunity to integrate multiple NLP approaches and semi-automated curation.

Original languageEnglish (US)
JournalCEUR Workshop Proceedings
StatePublished - 2016
Event2016 Joint International Conference on Biological Ontology and BioCreative - Food, Nutrition, Health and Environment for the 9 Billion, ICBO-BioCreative 2016 - Corvallis, United States
Duration: Aug 1 2016Aug 4 2016


  • Biocuration
  • Pathways

ASJC Scopus subject areas

  • General Computer Science


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