Knowledge Graph & Search - See More Features

Unify knowledge and unlock the full potential in your data


Every scientist should benefit from Knowledge Graphs and have access to its advanced Search and insights

Knowledge Graphs integrate data by describing entities and their relationships. These allow logical inference for retrieving implicit knowledge rather than only allowing queries requesting explicit knowledge. Knowledge Graphs are crucial for advanced search, machine learning, and for uncovering patterns & correlations.

Empowers every user to search & collaborate across their personal Knowledge Graph, automatically integrating every result, sample, comparison, and much more

Search for any gene, pathway, disease, or drug to find matching showcases, projects, experiment, collaboration space and more

Unify knowledge and empower greater insight across organizations with Enterprise Knowledge Graphs

ROSALIND Enterprise Knowledge Graph provides secure, private, and highly scalable Knowledge Graph functionality for teams & Enterprise customers. This unlocks the full potential of Search and enables organizations to achieve the greatest value from their research investments by empowering every authorized scientist to search, explore and collaborate on every available dataset

Every dataset and record is automatically added and available, including public data and private signatures

SSO integration with Active Directory permissions provides discrete authorization for sensitive data collections, such as clinical trials

Achieving ROI on research projects requires FAIR data access

Search globally, access instantly

Search for any gene, pathway, disease, drug or term. Search for anything that describes your Projects, Experiments, Comparisons, Filters, Meta-Analyses, Collaboration Spaces and more.

Don't worry about spelling adalimumab, ROSALIND uses fuzzy logic to find the best search results.

Graph powers every search and interpretation with hybrid search providing valuable insights for each query

Focus on your results even when your favorite pathway doesn't show up

Within any experiment, search over 300,000 terms and pathways to find the ones that most closely match your research focus and observe the gene expression directly in your experiment.

Find any pathway or term from the integrated knowledge bases

Each search result includes Graph insights on the comparisons, samples and attributes of each experiment

Everything you need to know when you're looking for it

Hybrid search broadly queries the knowledge management system to provide context and insights as query results including significance, genes up and downregulated, descriptions, locations and storage hierarchy, as well as related and similar results.

Inspect pathway source knowledge bases and each of the genes contained in each

Search results in the context of your experiment

Explore search results within your experiments to see focused insights on gene expression and pathway significance from any knowledge base

Aggregate pathways of interest in one concise view with custom plots

Click on the pathway magnifier to inspect pathway details across Search results

Dive deeper into Search results with detailed pathway exploration

Inspect pathways and terms from Search to see genes in term, up and downregulated genes as well as p-values

Click on table headers to adjust sorting

Toggle plot types to see interactive heatmaps and bar plots

Click download to access aggregated knowledge base records

Graph Search
Enterprise Graph
Global Results
Gene Nodes
Hybrid Search
Analyze Results
Pathway Exploration
View More

An Interactive Data Ecosystem

Unlocking FAIR Data Access & the Enterprise Knowledge Graph


The ROSALIND Knowledge Graph unifies knowledge and accelerates every aspect of ROSALIND, enabling advanced intelligence and powerful Search. Every analysis evaluates over 100 million relationships across 300,000 gene signatures and terms from the 50+ ROSALIND Knowledge Bases.

ROSALIND organizes data into a knowledge graph that enables semantic search and AI applications. Each new analysis is integrated into the knowledge graph thus connecting it to past analyses and enabling deeper comparisons. Knowledge graphs can be limited to individual users or expanded to cover all users within an organization via Enterprise SSO and permissions-based access. ROSALIND makes the knowledge graph accessible to users via a simple search box and can enable expanded access to machine learning tools via API.



A knowledge graph integrates collections of data and information by describing entities and their relationships. Knowledge Graphs allow logical inference for retrieving implicit knowledge rather than only allowing queries requesting explicit knowledge. Knowledge Graphs are crucial for advanced search and machine learning, and are being used for uncovering patterns and new relationships in ROSALIND.

1 - Knowledge Graph Stock


  • Personal Knowledge Graph empowers every user to rapidly search & explore relationships across datasets
  • Enterprise Knowledge Graph unifies knowledge across the Enterprise, transforming FAIR access
  • Evaluates 100 Million relationships across 300,000 pathways and terms
  • Accelerates every analysis across 50+ Knowledge Bases
  • Enables powerful machine learning analysis, using public & private algorithms
  • Discover more with custom algorithms and private data integration to extend the Knowledge Graph
  • Integrates every sample, comparison, filter, meta-analysis, and experiment.

“ROSALIND is extremely easy to use and share results with other colleagues. Our scientists are able lookup results instantly without consulting our bioinformaticians.”


Long Do
Sr. Manager, Informatics at Samumed LLC


Every user has access to search and collaborate across their own personal Knowledge Graph, which automatically integrates every sample, comparison, filter, gene list, meta-analysis, and experiment that the user has access to. Enterprise users can be granted permissions for search functionality that cuts across the entire organization.

Users can search for any gene, pathway, disease, drug, or term as well as any descriptive text that may describe any Project, Experiment, Comparison, Filter, Meta-Analysis, Collaboration Space, or Gene List. ROSALIND Search returns the results globally and contextually, linking directly to datasets or showing the statistical significance and gene-level details within any experiment.


  • Find all COVID-related items including the COVID-19 Research Community Showcase and many shared public data experiments.
  • Find all related pathways with significance (p-Adjust) and quantity of genes expressed up and down within an experiment.
  • Find genes and the associated expression levels and significance within an experiment. Globally, find all related search items.

To search, select the magnifying glass from the ROSALIND header menu and enter a query in the search box.


Team and Enterprise Subscriptions unlock the Institutional Knowledge Graph, empowering authorized scientists to search, explore and collaborate with the Unified Intelligence of all insights across the organization. To learn more, please contact

ROSALIND secures all information and every Space by encrypting all data transmissions and data storage. Using an access-control system architecture ensures that access is only granted to authenticated users with permissions to a shared dataset. Only Space owners have the ability to delete Spaces they create and may also remove any experiment, meta-analysis, or participant at any time. Each participant has the ability to remove their own experiments and meta-analyses or to leave a Space. All changes within a Space are reported on the activity feed.

IT departments may define detailed policies to administer and restrict sharing such that teamwork is enabled without compromising corporate security policies. Learn more about Enterprise Subscriptions by contacting sales.



ROSALIND is designed for the Scientist, so you can focus on the biology and science without having to invest months and months trying to learn bioinformatics, programming or biostatistics


Capable of performing advanced analyses including contamination detection, covariate correction, batch correction and multi-omic analyses


Utilizing a clean, intuitive and immersive user interface, Scientists new to the platform ramp quickly with little training to focus on discovery


Explore experiment results in high-quality, publiction-ready, interactive diagrams and plots


ROSALIND is designed for the Scientist, so you can focus on the biology and science without having to invest months and months trying to learn bioinformatics, programming or biostatistics


Start new experiments by importing FASTQ files from sequencing, or counts (raw or normalized)


Built-in pipelines are tuned to utilize industry standard, widely published bioinformatics tools. For more information, review the ROSALIND specifications and method section


Every communication and data transfer on ROSALIND is encrypted and secured. Multiple layers of data protection ensure availability


faqPerson cube2b

Is a subscription required to join a Space?


A subscription is not required to accept an invite and join a Space. However, all users must have a ROSALIND account to join a Space.

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Can I share an experiment in more than one Space?


Yes, an experiment may be shared in any number of spaces to enable collaboration across multiple groups. Consistency, and security are preserved for the experiment within every space that it is included.

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How do I register for a ROSALIND account?


ROSALIND accounts can be setup by clicking New User on the login page, or by completing a Trial Request. To learn more about Subscriptions, visit the Product Comparison.

faqPerson cube2b

Can I remove my experiment or meta-analysis from a Space?


Any participant can remove an experiment or meta-analysis that they have shared within a Space at anytime. Doing so immediately removes access to the shared resource.

faqPerson cube2b

How do I create a new Space and begin sharing an experiment?


Any user with a ROSALIND account can create a collaboration Space. Users may only add experiments and meta-analyses that they own, including public data experiments they have imported.

faqPerson cube2b

Can I leave a Space and remove myself from the collaboration?


Any participant can leave a Space at anytime. Doing so removes their access and will require a new invite to join the collaborative Space again. Only the owner of a Space or an Enterprise Administrator may remove participants.

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What can I do if I’m invited to a collaboration Space?


After joining a Space, every user can view and explore the shared experiments and meta-analyses, including all of the applicable pathway intepretation. ROSALIND Scientists, Directors and Explorers can add new filters to change cut-offs, or add new comparions and meta-analyses.

faqPerson cube2b

Can the API be used to add experiments to a Space?


Yes, API integration enables production informatics teams to centrally process and distribute results within Spaces to each program or project team requesting an analysis. This is a best practice among pharma R&D teams. API integration also includes Single-Sign-On (SSO) support. Contact sales to learn more

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