TY - GEN

T1 - Advanced data curation in GTRD database

T2 - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020

AU - Kulyashov, Mikhail A.

AU - Kolmykov, Semyon K.

AU - Yevshin, Ivan S.

AU - Kolpakov, Fedor A.

N1 - Funding Information: This work was supported by the Russian Science Foundation. (grant № 19-14-00295). Publisher Copyright: © 2020 IEEE. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2020/7

Y1 - 2020/7

N2 - 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.

AB - 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.

KW - database structure

KW - experiments annotation

KW - experiments comparison

KW - GTRD

UR - http://www.scopus.com/inward/record.url?scp=85094819427&partnerID=8YFLogxK

UR - https://www.elibrary.ru/item.asp?id=45218761

U2 - 10.1109/CSGB51356.2020.9214681

DO - 10.1109/CSGB51356.2020.9214681

M3 - Conference contribution

AN - SCOPUS:85094819427

T3 - Proceedings - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020

SP - 23

EP - 27

BT - Proceedings - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020

PB - Institute of Electrical and Electronics Engineers Inc.

Y2 - 6 July 2020 through 10 July 2020

ER -