PGxLOD

Welcome on PGxLOD

About expand_less

PGxLOD is intended to host pharmacogenomic knowledge that the PractiKPharma project will extract from various sources such as the literature and Electronic Health Records.

PGxLOD uses the PGxO ontology. A full description of the motivation, implementation and instantiation of PGxO and PGxLOD is available in [1].

Citing PGxLOD expand_less

When citing PGxO/PGxLOD, please use the following reference:
Monnin, P., Legrand, J., Husson, G., Ringot, P., Tchechmedjiev, A., Jonquet, C., Napoli, A., & Coulet, A. (2019). PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison. BMC bioinformatics, 20(Suppl 4), 139. [link] 

							
@Article{Monnin2019,
	author="Monnin, Pierre
	and Legrand, Jo{\"e}l
	and Husson, Graziella
	and Ringot, Patrice
	and Tchechmedjiev, Andon
	and Jonquet, Cl{\'e}ment
	and Napoli, Amedeo
	and Coulet, Adrien",
	title="PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances,
	enabling further comparison",
	journal="BMC Bioinformatics",
	year="2019",
	month="Apr",
	day="18",
	volume="20-S",
	number="4",
	pages="139",
	issn="1471-2105",
	doi="10.1186/s12859-019-2693-9",
	url="https://doi.org/10.1186/s12859-019-2693-9"
}

Integrated data sets expand_less

Integration methods and generated mappings are described in [1,2]. The main ontology used, PGxO, and the encoding for provenance metadata are described in [1,3]. The integrated data sets are:

Statistics expand_less

Examples of SPARQL queries expand_less

Counting instances of pgxo:Gene

SELECT COUNT(DISTINCT ?entity)
WHERE
{
    ?entity a <http://pgxo.loria.fr/Gene>
}

Getting the graph around CYP2D6 wih a length ≤ 4

CONSTRUCT
{
    <http://bio2rdf.org/clinvar:CYP2D6> ?p1 ?o1.
    ?o1 ?p2 ?o2 .
    ?o2 ?p3 ?o3 .
    ?o3 ?p4 ?o4 .
}
WHERE
{
    <http://bio2rdf.org/clinvar:CYP2D6> ?p1 ?o1 .
    OPTIONAL
    {
        ?o1 ?p2 ?o2 .
        OPTIONAL
        {
            ?o2 ?p3 ?o3 .
            OPTIONAL
            {
              ?o3 ?p4 ?o4 .
            }
        }
    }
}

References expand_less

  1. Monnin, P., Legrand, J., Husson, G., Ringot, P., Tchechmedjiev, A., Jonquet, C., Napoli, A., & Coulet, A. (2019). PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison. BMC bioinformatics, 20(Suppl 4), 139. [link]
  2. Dalleau, K., Marzougui, Y., Da Silva, S., Ringot, P., Ndiaye, N. C., & Coulet, A. (2017). Learning from biomedical linked data to suggest valid pharmacogenes. Journal of biomedical semantics, 8(1), 16. [link]
  3. Monnin, P., Jonquet, C., Legrand, J., Napoli, A., & Coulet, A. (2017, October). PGxO: A very lite ontology to reconcile pharmacogenomic knowledge units. In Methods, tools & platforms for Personalized Medicine in the Big Data Era. [link]
  4. Landrum, M. J., Lee, J. M., Benson, M., Brown, G. R., Chao, C., Chitipiralla, S., ... & Karapetyan, K. (2017). ClinVar: improving access to variant interpretations and supporting evidence. Nucleic acids research, 46(D1), D1062-D1067.
  5. Wishart, D. S., Knox, C., Guo, A. C., Cheng, D., Shrivastava, S., Tzur, D., ... & Hassanali, M. (2007). DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic acids research, 36(suppl_1), D901-D906.
  6. Kuhn, M., Campillos, M., Letunic, I., Jensen, L. J., & Bork, P. (2010). A side effect resource to capture phenotypic effects of drugs. Molecular systems biology, 6(1), 343.
  7. Kuhn, M., Letunic, I., Jensen, L. J., & Bork, P. (2015). The SIDER database of drugs and side effects. Nucleic acids research, 44(D1), D1075-D1079.
  8. Bauer-Mehren, A., Rautschka, M., Sanz, F., & Furlong, L. I. (2010). DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene–disease networks. Bioinformatics, 26(22), 2924-2926.
  9. Bauer-Mehren, A., Bundschus, M., Rautschka, M., Mayer, M. A., Sanz, F., & Furlong, L. I. (2011). Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases. PloS one, 6(6), e20284.
  10. Pinero, J., Queralt-Rosinach, N., Bravo, A., Deu-Pons, J., Bauer-Mehren, A., Baron, M., Sanz F., & Furlong, L. I. (2015). DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. Database, 2015.
  11. Queralt-Rosinach, N., Kuhn, T., Chichester, C., Dumontier, M., Sanz, F., & Furlong, L. I. (2016). Publishing DisGeNET as nanopublications. Semantic Web, 7(5), 519-528.
  12. Queralt-Rosinach, N., Pinero, J., Bravo, À., Sanz, F., & Furlong, L. I. (2016). DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases. Bioinformatics, 32(14), 2236-2238.
  13. Whirl‐Carrillo, M., McDonagh, E. M., Hebert, J. M., Gong, L., Sangkuhl, K., Thorn, C. F., Altman, R. B., & Klein, T. E. (2012). Pharmacogenomics knowledge for personalized medicine. Clinical Pharmacology & Therapeutics, 92(4), 414-417.
  14. Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., King, B. L., McMorran, R., Wiegers, J., Wiegers, T. C., Mattingly, C. J. (2016). The comparative toxicogenomics database: update 2017. Nucleic acids research, 45(D1), D972-D978.

Privacy policy expand_less

Who we are

We are a group of researchers part of the Loria, the "Lorraine Research Laboratory in Computer Science and its Applications" which is a research unit (UMR 7503), common to CNRS, Inria Nancy-Grand Est, and the University of Lorraine. PGxLOD is an output of the PractiKPharma project, founded by the French National Research Agency (ANR).

This website is hosted by the Loria.

What follows concerns users of this website.

What personal data we collect on this site and why we collect them

Cookies

We do not use cookies.

Analytics

We keep the connection logs (including the user IP address, the visited URL which may contain the SPARQL query from the SPARQL endpoint or the URL of the described entity from the Faceted Browser) for approximately 13 months (including backups).

We need to keep this information for legal and security reasons and we want to measure usage statistics for this service.

Who we share your data with

We do not share your data with others.

How long we retain your data

Connection logs are kept for approximately 13 months.

What rights you have over your data

Users of this site do not have an account.

We cannot remove your connections out of our system due to legal and security reasons. They disappear completely after approximately 13 months.

Your contact information

pgxlod-contact-at-inria.fr (replace -at- by @)

Third-party tools expand_less

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