Data from: The implicitome: a resource for rationalizing gene-disease associations

Hettne KM, Thompson M, van Haagen HHHBM, van der Horst E, Kaliyaperumal R, Mina E, Tatum Z, Laros JFJ, van Mulligen EM, Schuemie M, Aten E, Li TS, Bruskiewich R, Good BM, Su AI, Kors JA, den Dunnen J, van Ommen G, Roos M, 't Hoen PAC, Mons B, Schultes EA

Date Published: March 10, 2016

DOI: http://dx.doi.org/10.5061/dryad.gn219

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title PMID list
Downloaded 21 times
Description list of PMIDs used to create concept profiles; gzipped file, one PMID per line
Download Restricted1980tillnow.PMIDs.gz (39.24 Mb)
Details View File Details
Title Medline concept index
Downloaded 42 times
Description Concept index of Medline articles as specified in http://dx.doi.org/10.5061/dryad.gn219/1
Download Medline1980till17Jul2014_UMLS2010ABHomolo..._6.zip (4.622 Gb)
Download README.txt (173 bytes)
Details View File Details
Title Overview of software packages
Downloaded 43 times
Description Software packages used for the various analyses and figures. Links are clickable and point to the repository for that code or data.
Download Copy of Gene-disease paper - code overview.pdf (1.102 Mb)
Details View File Details
Title Explicit associations (co-occurrence) nanopublications
Downloaded 24 times
Description Set of 7,858,449 nanopublications, each of which asserts a single gene-disease co-occurrence and the PubMed ID of the abstract in which they co-occur
Download gd-coocc.nq.gz (975.5 Mb)
Details View File Details
Title All associations as nanopublications
Downloaded 21 times
Description The complete set of all ~204 million associations (explicit and implicit) as nanopublications. Each nanopublication asserts an association between a gene and a disease concept and the percentile rank of the match score.
Download gda-np.nq.gz (29.22 Gb)
Details View File Details
Title All associations as CSV
Downloaded 38 times
Description All ~204 million associations (explicit and implicit) listed as a CSV text file. Note that concept pairs are specified by concept ID and its first label according to our thesaurus.
Download README.txt (228 bytes)
Download matchscores.release.csv.gz (7.009 Gb)
Details View File Details
Title Pre-compiled software dependencies
Downloaded 10 times
Description Collection of JAR files containing the dependencies for generating concept profiles and match scores. Source code is also available in our github repository.
Download libraries.zip (19.47 Mb)
Details View File Details
Title https://github.com/BiosemanticsDotOrg/GeneDiseasePaper
Description Source code for generating and analyzing concept profiles is available from Github under a AGPLV3.0 license: https://github.com/BiosemanticsDotOrg/GeneDiseasePaper
Download //github.com/BiosemanticsDotOrg/GeneDiseasePaper (0 bytes)
Details View File Details

When using this data, please cite the original publication:

Hettne KM, Thompson M, van Haagen HHHBM, van der Horst E, Kaliyaperumal R, Mina E, Tatum Z, Laros JFJ, van Mulligen EM, Schuemie M, Aten E, Li TS, Bruskiewich R, Good BM, Su AI, Kors JA, den Dunnen J, van Ommen G, Roos M, 't Hoen PAC, Mons B, Schultes EA (2016) The implicitome: a resource for rationalizing gene-disease associations. PLOS ONE 11(2): e0149621. http://dx.doi.org/10.1371/journal.pone.0149621

Additionally, please cite the Dryad data package:

Hettne KM, Thompson M, van Haagen HHHBM, van der Horst E, Kaliyaperumal R, Mina E, Tatum Z, Laros JFJ, van Mulligen EM, Schuemie M, Aten E, Li TS, Bruskiewich R, Good BM, Su AI, Kors JA, den Dunnen J, van Ommen G, Roos M, 't Hoen PAC, Mons B, Schultes EA (2016) Data from: The implicitome: a resource for rationalizing gene-disease associations. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.gn219
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: