Research

Research Interests

I am a postdoc researcher at the Integrative Biomedical Informatics Group (IBI), Research Programme on Biomedical Informatics (GRIB) in the Hospital del Mar Medical Research Institute (IMIM) and the Department of Experimental and Health Sciences of the Universitat Pompeu Fabra.

My research interests are in developing semantic web resources and tools to leverage the biomedical big data for health care and translational research. The myriad of multiomics data, clinical findings, and basic research knowledge need to be integrated to get a full picture that helps to understand the biology and pathophysiology of human systems. By using semantic web technologies from RDF to ontologies, and the linked data approach, i tackled the data and knowledge integration problems arising from bridging the gap between biology and medicine. In particular, my methodological work lies in applying these technologies for:

  • data management, data modeling, and data integration.
  • working on semantic technologies for knowledge representation, data interoperability and computational reasoning.
  • the design and development of interoperable bioinformatic tools and services to analyse and understand pathophysiological mechanisms that elicit diseases.
  • knowledge discovery based on evidence:
    • developing semantic web tools harnessing the web of linked data for data analysis and knowledge discovery.
    • working on metadata description to enhance discovery in science based on evidence, and to foster a better data science.

My applied research interests include work on gene-disease associations in common, complex and rare diseases:

  • to understand the molecular mechanisms that lead to abnormal phenotypes, disease conditions or drug toxicity for drug discovery, therapy development and toxicology.
  • to study networks of bioentities to understand biology from a systems biology approach.

I received my PhD in Quantum Chemistry from Rovira i Virgili University in May 2010 under the direction of Dr. Rosa Caballol Lorenzo and Dr. Coen de Graaf. I received my MSc in Bioinformatics for Health Sciences from the Pompeu Fabra University in June 2008. My Bachelors degree is from Rovira i Virgili University in Chemistry. For high school, I graduated from the Institut Salvador Vilaseca.

Scientific Tools and Resources

  • disgenet2r R package
    • An R package to explore the molecular underpinnings of human diseases.
    • Authors: Alba Gutiérrez-Sacristán, Núria Queralt-Rosinach, Janet Piñero, Laura I. Furlong
  • DisGeNET RDF Linked Dataset
    • Linked Dataset in RDF is an alternative way to access the DisGeNET data and provides new opportunities for data integration, querying and integrating DisGeNET data to other external RDF datasets. The RDF version of DisGeNET has been developed in the context of the Open PHACTS project to provide disease relevant information to the knowledge base on pharmacological data.
    • Authors: Núria Queralt-Rosinach, Janet Piñero, Àlex Bravo, Laura I. Furlong
  • DisGeNET Nanopublications Linked Dataset
    • Linked Dataset implemented in combination of the nanopublication approach [nanopub.org] and the Trusty URIs technique [PDF]. Nanopublications are a new way of publishing structured data that allows the tracking of provenance along with the scientific statement. The Trusty URIs is a novel technique to make resources in the Web immutable and verifiable, and to ensure the unambiguity of the data linking in the (semantic) Web.
    • Authors: Núria Queralt-Rosinach, Tobias Kuhn, Christine Chichester, Michel Dumontier, Ferran Sanz, Laura I. Furlong
  • DisGeNET Discovery Platform
    • Discovery platform integrating information on gene-disease associations from several public data sources and the literature (Piñero et al., 2015 ). The current version (DisGeNET v3.0) contains 429,111 associations, between 17,181 genes and 14,619 diseases, disorders and clinical or abnormal human phenotypes.
    • Authors: Janet Piñero, Núria Queralt-Rosinach, Àlex Bravo, Jordi Deu-Pons, Anna Bauer-Mehren, Martin Baron, Ferran Sanz, Laura I. Furlong
  • The Semanticscience Integrated Ontology
    • OWL ontology that provides a simple, integrated ontology of types and relations for rich description of objects, processes and their attributes.
    • Authors: Michel Dumontier, Christopher JO Baker, Joachim Baran, Alison Callahan, Leonid Chepelev, José Cruz-Toledo, Nicholas R Del Rio, Geraint Duck, Laura I Furlong, Nichealla Keath, Dana Klassen, James P McCusker, Núria Queralt-Rosinach, Matthias Samwald, Natalia Villanueva-Rosales, Mark D Wilkinson, Robert Hoehndorf
  • The BeFree System
    • It is a text mining tool to unlock the information contained in biomedical documents.
    • Authors: Àlex Bravo, Janet Piñero, Núria Queralt-Rosinach, Michael Rautschka, Laura I. Furlong
  • Tox-PPI network
    • Network visualization tool for the exploration of putative molecular mechanisms underlying drug toxicity events. It facilitates the navigation through the protein-protein interaction (PPI) networks expanded with pharmacological and toxicological data available in the public domain.
    • Authors: Ulrick Plesner, Olivier Taboureau, Núria Queralt-Rosinach, Montserrat Cases, Laura I. Furlong
  • Disease-related biomarker database
    • A database of of 131,012 disease-biomarker associations between 2,803 genes and 2,751 diseases extracted by text mining.
    • Authors: Àlex Bravo, Montserrat Cases, Núria Queralt-Rosinach, Ferran Sanz, Laura I. Furlong

Conferences/Workshops/BYODs/Hackathons

Biomedicine
Chemistry
  • IV Trobada de Joves Investigadors dels Països Catalans 2006, Lleida (Spain), [Talk]
  • Electronic Structure: Principles and Applications (ESPA) 2004, Valladolid (Spain), [Poster]
  • International Conference of Quantum Chemistry (ICQC) 2003, Bönn (Germany), [Poster]
  • Electronic Structure: Principles and Applications (ESPA) 2002, Sevilla (Spain), [Poster]

Scientific European Projects

  • MedBioinformatics
    1. Outcomes:
      • D4.3 – Report on the development of the trait-based diseasome
    2. Activities:
      • My main objective is the development of systems medicine tools (Disease Biomarker Browser, Disease Trajectory Comorbidity Browser) able to mine, integrate, filter, prioritise, analyse and visualise relevant health data and scientific knowledge (WP4).
  • Open PHACTS
    1. Outcomes:
    2. Activities:
      • My main objective is the implementation of DisGeNET in the Open PHACTS Discovery Platform.
      • My activities are attending teleconferences, following up the advance of the technical part of the platform, attending community workshops among others.
    3. My research outcomes embedded in this project here.
  • eTOX
    1. Outcomes:
    2. Activities:
      • My activities are attending teleconferences, following up the advance of the technical part of the project, attending community workshops among others.
      • Developing resources and tools for unraveling the toxicity mechanisms of drugs and the extraction of disease biomarkers.

Research Profiles