BioDati Studio

Powering Network Biology

for Biology, Drug R&D, Disease Foundations, Personalized Medicine

Overview

Demo

Uses

By providing our users with an interactive and easy to use platform, we allow them to focus on what is really important: the science.

  • Causal Reasoning
  • Systems Biology
  • Biomarker Discovery
  • Target Validation
  • Toxicology
  • Drug Safety
  • Microbiome Analysis

Features



Biological Networks

Build, view and share networks using a standard language BEL in an open-standard format JGF. Fully searchable network database, find networks by network nodes, attributes and associated metadata. Easy import and export of networks.

API-Driven

BioDati Studio is fully API-driven providing access to all functionality and documented using Swagger/OAS. This makes it easy to connect into analytics pipeline or your own platforms.

Knowledge Distillation

Condenses papers and databases into a contexualized and highly relevant biological relationships. BEL compresses biological literature into a highly readable and relatable format.

Open Standards-based

BEL (Biological Expression Language) is an open standard that represents biology from molecular to species-level scale which captures causal and non-causal relationships in biology with experimental context.

Biology Integration

You can load BioDati Studio with your own BEL Nanopubs, public BEL Nanopubs and databases licensed from Qiagen Ingenuity and Clarivate Analytics or BEL curation companies.

EdgeStore

All curated biological knowledge gets converted into a graph database for searching pathways and other biology relationships for use in building networks or knowledge-driven analytics.

components



BEL

Biological Expression Language (BEL) is an open standard language for representing scientific findings in the life sciences in a computable form. BEL is designed to represent scientific findings by capturing causal and correlative relationships in context, where context can include information about the biological and experimental system in which the relationships were observed, the supporting publications cited, and the curation process used.

Nanopubs

Nanopubs are the smallest unit of BEL knowledge. It is composed of BEL assertion(s), source citation, experimental context, other annotations, and associated metadata. Nanopubs are stored in a database with powerful text and data searching functionality. BioDati Studio provides the most advanced BEL Nanopub editor available to create and edit Nanopubs.

Edges

The database of edges created from curated biology (BEL Nanopubs) is used as a source of edges for network building (filterable by species, disease context, experimental conditions, …). You can select a set of edges to insert into a new network or add to an existing network. For example, find all human edges, 2 steps out from the protein AKT1 derived from an experiment using lung epithelial tissue.

Networks

Networks created from BEL edges represent specific biological systems and/or states. An example network could represent all known biological knowledge for a particular mechanism, such as apoptosis in humans, where each edge in the network is contextualized by edge metadata from one or more BEL Nanopubs.

Focus Areas



Biologists

  • Understand large-scale data experiments
  • World's largest possible collection of biological knowledge.
  • Map your experimental data onto your personal knowledgebase
  • Create customized networks

bioPharma

  • Faster cycle times to integrate research results into treatments
  • Enhance drug target evaluation
  • Better model organism vs human biology analysis
  • Understand toxicity and adverse event findings

Disease Foundations

  • Build and share a comprehensive disease knowledge base
  • Drive new disease hypothesis generation and evaluation
  • Distribute disease knowledge faster and further
  • Convert knowledge into cures

Academia

  • Extend biological knowledge and share it
  • Publish new knowledge as Nanopubs
  • Share and collaborate using network-based hypothesis
  • Easily collaborate with other labs - integrate knowledgebases