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

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Mikhail A. Kulyashov¹, Semyon K. Kolmykov², Ivan S. Yevshin³, Fedor A. Kolpakov^4
1BIOSOFT.RU,LLC, Institute of Computational Technologies, SB RAS FRC Institute of Cytology and Genetics SB RAS, m.kulyashov@mail.ru
²BIOSOFT.RU,LLC, Institute of Computational Technologies, SB RAS FRC Institute of Cytology and Genetics SB RAS, kolmykovsk@gmail.com
³BIOSOFT.RU,LLC, Institute of Computational Technologies, SB RAS FRC Institute of Cytology and Genetics SB RAS, ivan@developmentontheedge.com
⁴BIOSOFT.RU,LLC, Institute of Computational Technologies, SB RAS FRC Institute of Cytology and Genetics SB RAS, fkolpakov@gmail.com

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 formalise 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.