DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web

Maxat Kulmanov; Fernando Zhapa-Camacho; Robert Hoehndorf

doi:10.1093/nar/gkab373

DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web

Maxat Kulmanov, Fernando Zhapa-Camacho, Robert Hoehndorf

Research output: Contribution to journal › Article › peer-review

17 Scopus citations

Abstract

Abstract Understanding the functions of proteins is crucial to understand biological processes on a molecular level. Many more protein sequences are available than can be investigated experimentally. DeepGOPlus is a protein function prediction method based on deep learning and sequence similarity. DeepGOWeb makes the prediction model available through a website, an API, and through the SPARQL query language for interoperability with databases that rely on Semantic Web technologies. DeepGOWeb provides accurate and fast predictions and ensures that predicted functions are consistent with the Gene Ontology; it can provide predictions for any protein and any function in Gene Ontology. DeepGOWeb is freely available at https://deepgo.cbrc.kaust.edu.sa/.

Original language	English (US)
Journal	Nucleic Acids Research
DOIs	https://doi.org/10.1093/nar/gkab373
State	Published - May 21 2021

Bibliographical note

KAUST Repository Item: Exported on 2021-05-26
Acknowledged KAUST grant number(s): FCC/1/1976-08-01, URF/1/3790-01-01, URF/1/4355-01-01
Acknowledgements: King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) [URF/1/3790-01-01, URF/1/4355-01-01, FCC/1/1976-08-01, FCC/1/1976-08-08].
Funding for open access charge: King Abdullah University of Science and Technology.

ASJC Scopus subject areas

Genetics

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https://repository.kaust.edu.sa/bitstream/10754/669238/1/gkab373.pdf

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title = "DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web",

abstract = "Abstract Understanding the functions of proteins is crucial to understand biological processes on a molecular level. Many more protein sequences are available than can be investigated experimentally. DeepGOPlus is a protein function prediction method based on deep learning and sequence similarity. DeepGOWeb makes the prediction model available through a website, an API, and through the SPARQL query language for interoperability with databases that rely on Semantic Web technologies. DeepGOWeb provides accurate and fast predictions and ensures that predicted functions are consistent with the Gene Ontology; it can provide predictions for any protein and any function in Gene Ontology. DeepGOWeb is freely available at https://deepgo.cbrc.kaust.edu.sa/.",

author = "Maxat Kulmanov and Fernando Zhapa-Camacho and Robert Hoehndorf",

note = "KAUST Repository Item: Exported on 2021-05-26 Acknowledged KAUST grant number(s): FCC/1/1976-08-01, URF/1/3790-01-01, URF/1/4355-01-01 Acknowledgements: King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) [URF/1/3790-01-01, URF/1/4355-01-01, FCC/1/1976-08-01, FCC/1/1976-08-08]. Funding for open access charge: King Abdullah University of Science and Technology.",

year = "2021",

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doi = "10.1093/nar/gkab373",

language = "English (US)",

journal = "Nucleic Acids Research",

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AU - Kulmanov, Maxat

AU - Zhapa-Camacho, Fernando

AU - Hoehndorf, Robert

N1 - KAUST Repository Item: Exported on 2021-05-26 Acknowledged KAUST grant number(s): FCC/1/1976-08-01, URF/1/3790-01-01, URF/1/4355-01-01 Acknowledgements: King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) [URF/1/3790-01-01, URF/1/4355-01-01, FCC/1/1976-08-01, FCC/1/1976-08-08]. Funding for open access charge: King Abdullah University of Science and Technology.

PY - 2021/5/21

Y1 - 2021/5/21

N2 - Abstract Understanding the functions of proteins is crucial to understand biological processes on a molecular level. Many more protein sequences are available than can be investigated experimentally. DeepGOPlus is a protein function prediction method based on deep learning and sequence similarity. DeepGOWeb makes the prediction model available through a website, an API, and through the SPARQL query language for interoperability with databases that rely on Semantic Web technologies. DeepGOWeb provides accurate and fast predictions and ensures that predicted functions are consistent with the Gene Ontology; it can provide predictions for any protein and any function in Gene Ontology. DeepGOWeb is freely available at https://deepgo.cbrc.kaust.edu.sa/.

AB - Abstract Understanding the functions of proteins is crucial to understand biological processes on a molecular level. Many more protein sequences are available than can be investigated experimentally. DeepGOPlus is a protein function prediction method based on deep learning and sequence similarity. DeepGOWeb makes the prediction model available through a website, an API, and through the SPARQL query language for interoperability with databases that rely on Semantic Web technologies. DeepGOWeb provides accurate and fast predictions and ensures that predicted functions are consistent with the Gene Ontology; it can provide predictions for any protein and any function in Gene Ontology. DeepGOWeb is freely available at https://deepgo.cbrc.kaust.edu.sa/.

UR - http://hdl.handle.net/10754/669238

UR - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab373/6279831

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DO - 10.1093/nar/gkab373

M3 - Article

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SN - 0305-1048

JO - Nucleic Acids Research

JF - Nucleic Acids Research

ER -

DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web

Abstract

Bibliographical note

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