Knowledge Graph & Search

ROSALIND's Knowledge Graph & Search is a semantic data discovery layer built into the ROSALIND bioinformatics platform, designed to unify and accelerate access to genomic insights for scientists across pharma, biotech, and academic research. By organizing every analysis, sample, comparison, and experiment into an interconnected knowledge graph, ROSALIND enables researchers to retrieve implicit relationships and patterns across their data — without requiring expertise in bioinformatics, programming, or biostatistics.

Every analysis performed in ROSALIND evaluates over 100 million relationships across 300,000 gene signatures and terms drawn from 50+ ROSALIND Knowledge Bases. The result is a continuously growing, intelligent data ecosystem that connects past and present analyses, enabling deeper comparisons and accelerating discovery at every stage of research.

Core Knowledge Graph Capabilities

• Personal Knowledge Graph empowers every user to rapidly search and explore relationships across their own datasets
• Enterprise Knowledge Graph unifies knowledge across an entire organization, transforming FAIR (Findable, Accessible, Interoperable, Reusable) data access
• Evaluates 100 million relationships across 300,000 pathways and terms
• Accelerates analyses across 50+ integrated Knowledge Bases
• Enables powerful machine learning analysis using both public and private algorithms
• Supports custom algorithms and private data integration to extend the Knowledge Graph
• Automatically integrates every sample, comparison, filter, meta-analysis, gene list, and experiment

Search Functionality

• Users can search for any gene, pathway, disease, drug, or descriptive term via a simple search box in the ROSALIND header menu
• Search returns results globally and contextually, linking directly to datasets or displaying statistical significance and gene-level details within any experiment
• Searchable objects include Projects, Experiments, Comparisons, Filters, Meta-Analyses, Collaboration Spaces, and Gene Lists
• Example queries include finding all COVID-related items and public data experiments, locating related pathways with p-Adjust significance and up/down gene expression counts, and identifying gene expression levels and significance within a specific experiment
• Enterprise users can be granted permissions for search functionality that spans the entire organization

Enterprise Knowledge Graph & FAIR Data Management

• Team and Enterprise Subscriptions unlock the Institutional Knowledge Graph, enabling authorized scientists to search, explore, and collaborate with unified intelligence across the organization
• Knowledge graphs can be scoped to individual users or expanded organization-wide via Enterprise SSO and permissions-based access control
• IT departments can define detailed policies to administer and restrict sharing, enabling teamwork without compromising corporate security
• All data transmissions and storage are encrypted, and an access-control architecture ensures only authenticated, permissioned users can access shared datasets
• Space owners can delete Spaces and remove experiments, meta-analyses, or participants at any time; participants can remove their own contributions or leave a Space at any time
• All changes within a Space are reported on an activity feed for full transparency

Platform Highlights

• Designed for scientists, allowing focus on biology and science without requiring bioinformatics or programming knowledge
• Supports advanced analyses including contamination detection, covariate correction, batch correction, and multi-omic analyses
• Clean, intuitive user interface enables rapid onboarding with minimal training
• Rich, interactive, publication-ready data visualizations for exploring experiment results
• Pathway interpretation built in for biological context
• Accepts input from FASTQ files or processed counts data (raw or normalized)
• Built-in pipelines leverage industry-standard, widely published bioinformatics tools

ROSALIND Knowledge Graph & Search is accessible via web interface and API, with API integration supporting production informatics workflows and Single Sign-On (SSO) for enterprise environments. The platform is available under Enterprise, Professional, and Academic subscription tiers, and is also licensed to Service Providers, CROs, and Academic Core Labs.