Advanced data curation in GTRD database: Hierarchical dictionaries of cell types and experimental factors

Mikhail A. Kulyashov, Semyon K. Kolmykov, Ivan S. Yevshin, Fedor A. Kolpakov

Research output: Chapter in Book/Report/Conference proceedingConference contributionResearchpeer-review

Abstract

GEO database contains a lot of different experiments about transcription regulation. Most part of such experiments (ChIP-seq, DNase-seq and Histone-ChIP-seq) for 9 species (Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae, Schizosaccharomyces pombe and Arabidopsis thaliana) were annotated and uniformly processed in GTRD database. Here we are describing the latest advances in these data annotations for GTRD database to formalize experimental data: hierarchical dictionaries of cell types and experimental factors. This approach helps us to integrate experimental data by cell lines (cell types and tissues) and experimental conditions as well as simplifies searching for relevant information for a user.

Original languageEnglish
Title of host publicationProceedings - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages23-27
Number of pages5
ISBN (Electronic)9781728195971
DOIs
Publication statusPublished - Jul 2020
Event2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020 - Novosibirsk, Russian Federation
Duration: 6 Jul 202010 Jul 2020

Publication series

NameProceedings - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020

Conference

Conference2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020
CountryRussian Federation
CityNovosibirsk
Period06.07.202010.07.2020

Keywords

  • database structure
  • experiments annotation
  • experiments comparison
  • GTRD

OECD FOS+WOS

  • 1.02 COMPUTER AND INFORMATION SCIENCES
  • 1.06 BIOLOGICAL SCIENCES
  • 3.01 BASIC MEDICAL RESEARCH
  • 3.03 HEALTH SCIENCES
  • 5.09 OTHER SOCIAL SCIENCES

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