{"version":"desci-nodes-0.2.0","components":[{"id":"root","name":"root","type":{".pdf":"pdf"},"payload":{"cid":"bafybeibxffgjeyd3objtxh4tpslonqczkz6sao3husfzsjzrwistazproe","path":"root"}},{"id":"7f256e5c-b7b9-489a-a5a9-a0c24446a0c5","name":"Implicitome_Publication.pdf","type":"pdf","payload":{"cid":"bafybeigngh65477q3kwqgyoa3kp6k6ip7x4s66w2lqlkvrbn2djnopfhhq","path":"root/Implicitome_Publication.pdf","title":"Manuscript","doi":["10.1371/journal.pone.0149621"]},"starred":true,"subtype":"manuscript"}],"authors":[{"name":"Kristina Hettne","role":"Author","organizations":[{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0000-0002-4182-7560"},{"name":"Mark Thompson","role":"Author","organizations":[{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0000-0002-7633-1442"},{"name":"Herman H. H. B. M. van Haagen","role":"Author","organizations":[{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0009-0009-5295-1741"},{"name":"Eelke van der Horst","role":"Author","organizations":[{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0000-0002-8777-5612"},{"name":"Rajaram Kaliyaperumal","role":"Author","organizations":[{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0000-0002-1215-167X"},{"name":"Eleni Mina","role":"Author","organizations":[{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0000-0002-8972-9206"},{"name":"Zuotian Tatum","role":"Author","organizations":[{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0000-0001-8874-7720"},{"name":"Jeroen F. J. Laros","role":"Author","organizations":[{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0000-0002-8715-7371"},{"name":"Erik M. van Mulligen","role":"Author","organizations":[{"name":"Erasmus MC","id":"https://ror.org/018906e22"},{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0000-0003-1377-9386"},{"name":"Martijn J. Schuemie","role":"Author","organizations":[{"name":"Erasmus MC","id":"https://ror.org/018906e22"}],"orcid":"0000-0002-0817-5361"},{"name":"Emmelien Aten","role":"Author","organizations":[{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0009-0000-5086-1595"},{"name":"Tong Shu Li","role":"Author","organizations":[{"name":"Scripps Research Institute","id":"https://ror.org/02dxx6824"}]},{"name":"Richard Bruskiewich","role":"Author","orcid":"0000-0002-4447-5978"},{"name":"Benjamin M. Good","role":"Author","organizations":[{"name":"Scripps Research Institute","id":"https://ror.org/02dxx6824"}],"orcid":"0000-0002-7334-7852"},{"name":"Andrew I. Su","role":"Author","organizations":[{"name":"Scripps Research Institute","id":"https://ror.org/02dxx6824"}],"orcid":"0000-0002-9859-4104"},{"name":"Jan A. Kors","role":"Author","organizations":[{"name":"Erasmus MC","id":"https://ror.org/018906e22"}],"orcid":"0000-0002-4929-026X"},{"name":"Johan T. den Dunnen","role":"Author","organizations":[{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0000-0003-4526-298X"},{"name":"Gert‐Jan B. van Ommen","role":"Author","organizations":[{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0000-0002-8603-218X"},{"name":"Marco Roos","role":"Author","organizations":[{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0000-0002-8691-772X"},{"name":"Peter A.C. ’t Hoen","role":"Author","organizations":[{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0000-0003-4450-3112"},{"name":"Barend Mons","role":"Author","organizations":[{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0000-0003-3934-0072"},{"name":"Erik Schultes","role":"Author","organizations":[{"name":"Leiden University Medical Center","id":"https://ror.org/05xvt9f17"}],"orcid":"0000-0001-8888-635X"}],"title":"The Implicitome: A Resource for Rationalizing Gene-Disease Associations","defaultLicense":"CC BY","researchFields":[],"description":"High-throughput experimental methods such as medical sequencing and genome-wide association studies (GWAS) identify increasingly large numbers of potential relations between genetic variants and diseases. Both biological complexity (millions of potential gene-disease associations) and the accelerating rate of data production necessitate computational approaches to prioritize and rationalize potential gene-disease relations. Here, we use concept profile technology to expose from the biomedical literature both explicitly stated gene-disease relations (the explicitome) and a much larger set of implied gene-disease associations (the implicitome). Implicit relations are largely unknown to, or are even unintended by the original authors, but they vastly extend the reach of existing biomedical knowledge for identification and interpretation of gene-disease associations. The implicitome can be used in conjunction with experimental data resources to rationalize both known and novel associations. We demonstrate the usefulness of the implicitome by rationalizing known and novel gene-disease associations, including those from GWAS. To facilitate the re-use of implicit gene-disease associations, we publish our data in compliance with FAIR Data Publishing recommendations [https://www.force11.org/group/fairgroup] using nanopublications. An online tool (http://knowledge.bio) is available to explore established and potential gene-disease associations in the context of other biomedical relations.","dpid":{"prefix":"beta","id":"261"}}