Software

Tools and data resources

  • The Duchenne and Becker Muscular Dystrophy rare disease structured review
    • A Knowledge graph for hypothesis generation. [GitHub::graph][GitHub::neo4j]
    • Authors: Núria Queralt-Rosinach
    • Funding: EU HORIZON 2020 BIND
  • COVID-19 Epidemiology and Monitoring Ontology
  • Rare Diseases specific FAIR Maturity Indicators
  • LUMC Clinical Ontology
  • COVID-19 synthetic patient cytokine knowledge graph
  • Measurements for Health Data research
    • Quantitative Trait model [GitHub]
    • Quantitative Trait Ontology [GitHub]
    • Integration into GA4GH Phenopackets standard [GitHub]
    • Authors: Núria Queralt Rosinach, Sue Bello, Robert Hoehndorf, Claus Weiland, Philipe Rocca-Serra, Paul Schofield
    • Publication: [pre-print]
  • The NGLY1 Deficiency rare disease structured review
    • A Knowledge graph for hypothesis generation. [GitHub::graph][GitHub::neo4j]
    • A Wikibase instance for community contribution “FAIR at source”. [GitHub]
    • A Python library for structured review creation and update. [GitHub]
    • Authors: Núria Queralt-Rosinach, Greg Stupp, Tong Shu Li, Michael Mayers, Maureen E Hoatlin, Matthew Might, Benjamin M Good, Andrew I Su
    • Publication: [pre-print][Database]
    • Funding: NCATS Biomedical Data Translator program 
  • Wikidata
    • NGLY1 deficiency phenotypic data [Wikidata][GitHub]
    • CIViC model 
    • Provenance model
    • Authors: Núria Queralt Rosinach, Andra Waagmeester, Greg Stupp, Elvira Mitraka, Sebastian Burgstaller-Muehlbacher, Tim Putman, M. Griffith, O. Griffith, Lynn Schriml, Benjamin Good, Andrew Su
    • Publication: [pre-print][Database]
    • Funding: National Institute of General Medical Sciences
  • disgenet2r R package
    • An R package to explore the molecular underpinnings of human diseases. [Bitbucket]
    • Authors: Alba Gutiérrez-Sacristán, Núria Queralt-Rosinach, Janet Piñero, Laura I. Furlong
    • Publication: —
    • Funding: MedBioinformatics
  • DisGeNET SPARQL endpoint and Faceted Browser [DisGeNET-RDF]
    • DisGeNET-RDF Linked Data can be explored and mined through two types of interfaces implemented: an SPARQL endpoint API and a Faceted Browser. [GitHub][GitHub::shex-shape]
    • Authors: Núria Queralt-Rosinach, Janet Piñero, Àlex Bravo, Laura I. Furlong
    • Publication: [Bioinformatics]
    • Funding: IMI – Open PHACTS
  • DisGeNET RDF Linked Dataset [datahub]
    • 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
    • Publication: [Bioinformatics]
    • Funding: IMI – Open PHACTS
  • DisGeNET Nanopublications Linked Dataset [Nanopub Server]
    • 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
    • Publication: [Semantic Web]
    • Funding: IMI – Open PHACTS
  • 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
    • Publication: [Database]
    • Funding: IMI – Open PHACTS
  • 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. [OWL]
    • 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
    • Publication: [J. Biomedical Semantics]
    • Funding: IMI – Open PHACTS
  • The BeFree System
    • It is a text mining tool to unlock the information contained in biomedical documents. [BeFree]
    • Authors: Àlex Bravo, Janet Piñero, Núria Queralt-Rosinach, Michael Rautschka, Laura I. Furlong
    • Publication: [BMC Bioinformatics]
    • Funding: IMI – eTOX
  • 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. [Private link for the consortium]
    • Authors: Ulrick Plesner, Olivier Taboureau, Núria Queralt-Rosinach, Montserrat Cases, Laura I. Furlong
    • Publication: —
    • Funding: IMI – eTOX
  • 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. [database-browser]
    • Authors: Àlex Bravo, Montserrat Cases, Núria Queralt-Rosinach, Ferran Sanz, Laura I. Furlong
    • Publication: [Big Data and Network Biology]
    • Funding: IMI – eTOX

Advertisement