DH{}DataHunter

Dataset de Zenodo · Deutsch, David

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

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Licencia
CC BY 4.0uso comercial permitidoTexto de la licencia
Esta licencia permite el uso comercial. Normalmente hay que citar al autor; consulta la licencia para ver las condiciones exactas.
Formatos
PY, PNG, RES, SQL, CSV
Tamaño
23 MB
Actualizado
18 nov 2025

Descripción

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…

Descripción de Zenodo, abreviada.

Archivos (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 B
  • SQLpharos_dark_at_least_one_plasmid.sql304 B
  • RESpapers_and_pharos_dark.res13 kB
  • PYgene_data_extraction.py3,9 kB
  • PYhypgeo.py3,4 kB
  • CSVgenes.csv21 MB
  • SQLpapers_not_pharos_dark.sql333 B
  • RESpharos_dark_at_least_one_plasmid.res4 kB
  • CSVpharos.csv1,3 MB
  • PYenter_pharos_data.py558 B
  • SQLpharos_not_papers_dark.sql514 B
  • SQLpharos_not_drugs_dark.sql509 B
  • SQLpapers_and_pharos_dark.sql305 B
  • PYdgidb_raw.py1,7 kB
  • CSVpharos_dark.csv463 kB
  • RESpharos_not_papers_dark.res8 kB

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