Integrated relational database of human protein-protein interactions
Аутори
Jošić, BojanaKovačević, Jovana
Perović, Vladimir
Veljković, Nevena
Остала ауторства
Morić, IvanaĐorđević, Valentina
Конференцијски прилог (Објављена верзија)
,
© 2023 Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
Метаподаци
Приказ свих података о документуАпстракт
Protein-protein interactions’ data are stored in various publicly available databases of
different types and formats. In this work, a new database for protein-protein interactions
is created by integrating data from multiple existing databases. This task is not trivial
since different databases use distinct gene or protein identifiers for protein annotation.
Additionally, they use different methods to determine interaction scores, and the
interactions are obtained through diverse experimental or predictive methods. As a result,
two databases may store different data about the same interaction.
To integrate data from various databases, namely BioGRID, STRING, HIPPIE, IntAct, and
Reactome, into a single PPI database, the following process is undertaken. Initially, data
is downloaded from these databases in the MITAB format, encompassing all pertinent
interaction information such as protein identifiers, publication sources and other. In order
to obtain unique protein identifier...s in all PPIs in the database, the UniProt ID mapping tool
was used to determine UniProt IDs. Next, since scoring systems differ among databases,
for every interaction a new score is calculated using MISCORE tool as an additional metrics
unique for all the PPIs in the database. The resulting database contains tens of millions of
human PPIs from five different sources.
Кључне речи:
bioinformatics / protein-protein interaction / database / computer scienceИзвор:
4th Belgrade Bioinformatics Conference, 2023, 4, 92-92Издавач:
- Belgrade : Institute of molecular genetics and genetic engineering
Напомена:
- Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 2023
Колекције
Институција/група
Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Jošić, Bojana AU - Kovačević, Jovana AU - Perović, Vladimir AU - Veljković, Nevena PY - 2023 UR - https://belbi.bg.ac.rs/ UR - https://imagine.imgge.bg.ac.rs/handle/123456789/2037 AB - Protein-protein interactions’ data are stored in various publicly available databases of different types and formats. In this work, a new database for protein-protein interactions is created by integrating data from multiple existing databases. This task is not trivial since different databases use distinct gene or protein identifiers for protein annotation. Additionally, they use different methods to determine interaction scores, and the interactions are obtained through diverse experimental or predictive methods. As a result, two databases may store different data about the same interaction. To integrate data from various databases, namely BioGRID, STRING, HIPPIE, IntAct, and Reactome, into a single PPI database, the following process is undertaken. Initially, data is downloaded from these databases in the MITAB format, encompassing all pertinent interaction information such as protein identifiers, publication sources and other. In order to obtain unique protein identifiers in all PPIs in the database, the UniProt ID mapping tool was used to determine UniProt IDs. Next, since scoring systems differ among databases, for every interaction a new score is calculated using MISCORE tool as an additional metrics unique for all the PPIs in the database. The resulting database contains tens of millions of human PPIs from five different sources. PB - Belgrade : Institute of molecular genetics and genetic engineering C3 - 4th Belgrade Bioinformatics Conference T1 - Integrated relational database of human protein-protein interactions EP - 92 SP - 92 VL - 4 UR - https://hdl.handle.net/21.15107/rcub_imagine_2037 ER -
@conference{ author = "Jošić, Bojana and Kovačević, Jovana and Perović, Vladimir and Veljković, Nevena", year = "2023", abstract = "Protein-protein interactions’ data are stored in various publicly available databases of different types and formats. In this work, a new database for protein-protein interactions is created by integrating data from multiple existing databases. This task is not trivial since different databases use distinct gene or protein identifiers for protein annotation. Additionally, they use different methods to determine interaction scores, and the interactions are obtained through diverse experimental or predictive methods. As a result, two databases may store different data about the same interaction. To integrate data from various databases, namely BioGRID, STRING, HIPPIE, IntAct, and Reactome, into a single PPI database, the following process is undertaken. Initially, data is downloaded from these databases in the MITAB format, encompassing all pertinent interaction information such as protein identifiers, publication sources and other. In order to obtain unique protein identifiers in all PPIs in the database, the UniProt ID mapping tool was used to determine UniProt IDs. Next, since scoring systems differ among databases, for every interaction a new score is calculated using MISCORE tool as an additional metrics unique for all the PPIs in the database. The resulting database contains tens of millions of human PPIs from five different sources.", publisher = "Belgrade : Institute of molecular genetics and genetic engineering", journal = "4th Belgrade Bioinformatics Conference", title = "Integrated relational database of human protein-protein interactions", pages = "92-92", volume = "4", url = "https://hdl.handle.net/21.15107/rcub_imagine_2037" }
Jošić, B., Kovačević, J., Perović, V.,& Veljković, N.. (2023). Integrated relational database of human protein-protein interactions. in 4th Belgrade Bioinformatics Conference Belgrade : Institute of molecular genetics and genetic engineering., 4, 92-92. https://hdl.handle.net/21.15107/rcub_imagine_2037
Jošić B, Kovačević J, Perović V, Veljković N. Integrated relational database of human protein-protein interactions. in 4th Belgrade Bioinformatics Conference. 2023;4:92-92. https://hdl.handle.net/21.15107/rcub_imagine_2037 .
Jošić, Bojana, Kovačević, Jovana, Perović, Vladimir, Veljković, Nevena, "Integrated relational database of human protein-protein interactions" in 4th Belgrade Bioinformatics Conference, 4 (2023):92-92, https://hdl.handle.net/21.15107/rcub_imagine_2037 .