DH{}DataHunter

Dataset from Zenodo · Deutsch, David

Can we define "dark genome" using the number of research resources?

Open on Zenodo
License
CC BY 4.0commercial use allowedLicense text
This license allows commercial use. Usually you must credit the author; read the license for the exact terms.
Formats
PY, PNG, RES, SQL, CSV
Size
23 MB
Updated
Nov 18, 2025

Description

The dark genome, as defined by those genes that are understudied (Opera, 2019) have been defined to some extent by the Illuminating the Druggable Genome, IDG project (RRID:SCR 016924). One goal of this project is to encourage the study of genes that are likely to be important for precision medicine but are currently understudied. The KOMP project (RRID:SCR 005571) aims to knock out 8500 genes from mice, to deliver these mice and their associated phenotype data to the research community also to illuminate the dark genome. Pharos pharos.nih.gov (RRID:SCR 016258) provides a list of gene symbols and a ‘Tdark’ tag when genes are not sufficiently understood. We apply this convenient definition of darkness as a baseline. The RRID project works with antibody manufacturers, plasmid providers and animal stock centers and contains the largest freely available list of these key resources. We use the search for individual gene names in the RRID.site API as a proxy for the availability of tools. We do not know how well the presence of a knock out animal, the presence of data as defined by the IDG project, or the availability of tools like antibodies and plasmids impact the attention…

Description from Zenodo, shortened.

Files (19)

  • PYpostgres.py2.5 kB
  • PNGComparison of Dark Gene Counts Venn Diagrams.png361 kB
  • RESpapers_not_pharos_dark.res8.1 kB
  • RESpharos_not_drugs_dark.res502 byte
  • SQLpharos_dark_at_least_one_plasmid.sql304 byte
  • RESpapers_and_pharos_dark.res13 kB
  • PYgene_data_extraction.py3.9 kB
  • PYhypgeo.py3.4 kB
  • CSVgenes.csv21 MB
  • SQLpapers_not_pharos_dark.sql333 byte
  • RESpharos_dark_at_least_one_plasmid.res4 kB
  • CSVpharos.csv1.3 MB
  • PYenter_pharos_data.py558 byte
  • SQLpharos_not_papers_dark.sql514 byte
  • SQLpharos_not_drugs_dark.sql509 byte
  • SQLpapers_and_pharos_dark.sql305 byte
  • PYdgidb_raw.py1.7 kB
  • CSVpharos_dark.csv463 kB
  • RESpharos_not_papers_dark.res8 kB

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