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Updated: Apr 26, 2026

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

Semantic Web repositories for genomics data using the eXframe platform.

Emily Merrill¹, Stéphane Corlosquet¹, Paolo Ciccarese²

¹Massachusetts General Hospital, Partners Research Building, 65 Landsdowne St, Cambridge, MA, 02139, USA.

Journal of Biomedical Semantics

|August 6, 2014

Summary

This summary is machine-generated.

The eXframe platform now publishes Semantic Web data for genomics experiments, enabling easier integration and reuse of research findings. This facilitates interoperability with the broader biomedical knowledge base.

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Area of Science:

Genomics
Bioinformatics
Semantic Web technologies

Background:

Genomics data and databases have grown significantly due to affordable assay technologies.
Sample annotation is increasingly common but rarely available as Linked Data.
Lack of machine-readable, standardized formats hinders large-scale data reuse and integration.

Purpose of the Study:

To develop a reusable framework for creating online genomics experiment repositories.
To enable the publication of Semantic Web data from genomics experiments.
To address challenges in data integration and reuse within the genomics domain.

Main Methods:

Developed the second generation of the eXframe platform.
Created an experiment model covering provenance, citations, assays, biomaterials, and data.
Mapped model elements to established biomedical ontologies and produced Resource Description Framework (RDF) data.
Indexed RDF data in an RDF store with a SPARQL endpoint.

Main Results:

The eXframe platform now publishes Semantic Web data.
An experiment model was created and mapped to biomedical ontologies.
RDF data is automatically generated and indexed for SPARQL queries.

Conclusions:

Open-source eXframe software allows institutions to create Semantic Web repositories.
Enables integration of genomics data with heterogeneous resources.
Facilitates interoperability with the Semantic Web of biomedical knowledge.