INFORMATION SUPPORT OF RESEARCH ON TRANSCRIPTIONAL REGULATORY MECHANISMS: AN ONTOLOGICAL APPROACH
By now, a huge body of experimental data on gene transcription regulation has been accumulated. Transcription is controlled by a great number of proteins acting at various steps of the process; thus, a diversity of regulatory mechanisms can be realized. This paper presents approaches to building kno...
Saved in:
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2014-12-01
|
| Series: | Вавиловский журнал генетики и селекции |
| Subjects: | |
| Online Access: | https://vavilov.elpub.ru/jour/article/view/71 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832575299437461504 |
|---|---|
| author | N. L. Podkolodnyy E. V. Ignatieva O. A. Podkolodnaya N. A. Kolchanov |
| author_facet | N. L. Podkolodnyy E. V. Ignatieva O. A. Podkolodnaya N. A. Kolchanov |
| author_sort | N. L. Podkolodnyy |
| collection | DOAJ |
| description | By now, a huge body of experimental data on gene transcription regulation has been accumulated. Transcription is controlled by a great number of proteins acting at various steps of the process; thus, a diversity of regulatory mechanisms can be realized. This paper presents approaches to building knowledge domain ontology, formalized description of the mechanisms of transcriptional regulation and the development of methods for integration of heterogeneous information on the features of the regulation of gene expression on this base. The pilot version of the knowledge base on the transcriptional regulation of eukaryotic genes includes: (1) description of basic terms related to transcription regulation and relationships between them; (2) hierarchical classification of transcription regulators; (3) classification of phases and steps of transcription; (4) a database of transcriptional regulators of three mammalian species (human, mouse, and rat); and (5) dictionaries for molecular processes involved in transcriptional regulation. The knowledge base is designed for information support of computer analysis of transcriptional regulatory mechanisms. Approaches to reconstruction of eukaryotic transcriptional regulatory mechanisms with the new knowledge base are presented. |
| format | Article |
| id | doaj-art-689e125c3db144f79ae73a69d77e7f03 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2014-12-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-689e125c3db144f79ae73a69d77e7f032025-02-01T09:57:59ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592014-12-01164/174275555INFORMATION SUPPORT OF RESEARCH ON TRANSCRIPTIONAL REGULATORY MECHANISMS: AN ONTOLOGICAL APPROACHN. L. Podkolodnyy0E. V. Ignatieva1O. A. Podkolodnaya2N. A. Kolchanov3Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Institute of Computational Mathematics and Mathematical Geophysics, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk National Research State University, Novosibirsk, Russia National Research Centre «Kurchatov Institute», Moscow, RussiaBy now, a huge body of experimental data on gene transcription regulation has been accumulated. Transcription is controlled by a great number of proteins acting at various steps of the process; thus, a diversity of regulatory mechanisms can be realized. This paper presents approaches to building knowledge domain ontology, formalized description of the mechanisms of transcriptional regulation and the development of methods for integration of heterogeneous information on the features of the regulation of gene expression on this base. The pilot version of the knowledge base on the transcriptional regulation of eukaryotic genes includes: (1) description of basic terms related to transcription regulation and relationships between them; (2) hierarchical classification of transcription regulators; (3) classification of phases and steps of transcription; (4) a database of transcriptional regulators of three mammalian species (human, mouse, and rat); and (5) dictionaries for molecular processes involved in transcriptional regulation. The knowledge base is designed for information support of computer analysis of transcriptional regulatory mechanisms. Approaches to reconstruction of eukaryotic transcriptional regulatory mechanisms with the new knowledge base are presented.https://vavilov.elpub.ru/jour/article/view/71bioinformaticstranscription regulationknowledge base systemsontology |
| spellingShingle | N. L. Podkolodnyy E. V. Ignatieva O. A. Podkolodnaya N. A. Kolchanov INFORMATION SUPPORT OF RESEARCH ON TRANSCRIPTIONAL REGULATORY MECHANISMS: AN ONTOLOGICAL APPROACH Вавиловский журнал генетики и селекции bioinformatics transcription regulation knowledge base systems ontology |
| title | INFORMATION SUPPORT OF RESEARCH ON TRANSCRIPTIONAL REGULATORY MECHANISMS: AN ONTOLOGICAL APPROACH |
| title_full | INFORMATION SUPPORT OF RESEARCH ON TRANSCRIPTIONAL REGULATORY MECHANISMS: AN ONTOLOGICAL APPROACH |
| title_fullStr | INFORMATION SUPPORT OF RESEARCH ON TRANSCRIPTIONAL REGULATORY MECHANISMS: AN ONTOLOGICAL APPROACH |
| title_full_unstemmed | INFORMATION SUPPORT OF RESEARCH ON TRANSCRIPTIONAL REGULATORY MECHANISMS: AN ONTOLOGICAL APPROACH |
| title_short | INFORMATION SUPPORT OF RESEARCH ON TRANSCRIPTIONAL REGULATORY MECHANISMS: AN ONTOLOGICAL APPROACH |
| title_sort | information support of research on transcriptional regulatory mechanisms an ontological approach |
| topic | bioinformatics transcription regulation knowledge base systems ontology |
| url | https://vavilov.elpub.ru/jour/article/view/71 |
| work_keys_str_mv | AT nlpodkolodnyy informationsupportofresearchontranscriptionalregulatorymechanismsanontologicalapproach AT evignatieva informationsupportofresearchontranscriptionalregulatorymechanismsanontologicalapproach AT oapodkolodnaya informationsupportofresearchontranscriptionalregulatorymechanismsanontologicalapproach AT nakolchanov informationsupportofresearchontranscriptionalregulatorymechanismsanontologicalapproach |