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DESM: portal for microbial knowledge exploration systems

Microorganisms produce an enormous variety of chemical compounds. It is of general interest for microbiology and biotechnology researchers to have means to explore information about molecular and genetic basis of functioning of different microorganisms and their ability for bioproduction. To enable...

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Autores principales: Salhi, Adil, Essack, Magbubah, Radovanovic, Aleksandar, Marchand, Benoit, Bougouffa, Salim, Antunes, Andre, Simoes, Marta Filipa, Lafi, Feras F., Motwalli, Olaa A., Bokhari, Ameerah, Malas, Tariq, Amoudi, Soha Al, Othum, Ghofran, Allam, Intikhab, Mineta, Katsuhiko, Gao, Xin, Hoehndorf, Robert, C. Archer, John A., Gojobori, Takashi, Bajic, Vladimir B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702830/
https://www.ncbi.nlm.nih.gov/pubmed/26546514
http://dx.doi.org/10.1093/nar/gkv1147
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author Salhi, Adil
Essack, Magbubah
Radovanovic, Aleksandar
Marchand, Benoit
Bougouffa, Salim
Antunes, Andre
Simoes, Marta Filipa
Lafi, Feras F.
Motwalli, Olaa A.
Bokhari, Ameerah
Malas, Tariq
Amoudi, Soha Al
Othum, Ghofran
Allam, Intikhab
Mineta, Katsuhiko
Gao, Xin
Hoehndorf, Robert
C. Archer, John A.
Gojobori, Takashi
Bajic, Vladimir B.
author_facet Salhi, Adil
Essack, Magbubah
Radovanovic, Aleksandar
Marchand, Benoit
Bougouffa, Salim
Antunes, Andre
Simoes, Marta Filipa
Lafi, Feras F.
Motwalli, Olaa A.
Bokhari, Ameerah
Malas, Tariq
Amoudi, Soha Al
Othum, Ghofran
Allam, Intikhab
Mineta, Katsuhiko
Gao, Xin
Hoehndorf, Robert
C. Archer, John A.
Gojobori, Takashi
Bajic, Vladimir B.
author_sort Salhi, Adil
collection PubMed
description Microorganisms produce an enormous variety of chemical compounds. It is of general interest for microbiology and biotechnology researchers to have means to explore information about molecular and genetic basis of functioning of different microorganisms and their ability for bioproduction. To enable such exploration, we compiled 45 topic-specific knowledgebases (KBs) accessible through DESM portal (www.cbrc.kaust.edu.sa/desm). The KBs contain information derived through text-mining of PubMed information and complemented by information data-mined from various other resources (e.g. ChEBI, Entrez Gene, GO, KOBAS, KEGG, UniPathways, BioGrid). All PubMed records were indexed using 4 538 278 concepts from 29 dictionaries, with 1 638 986 records utilized in KBs. Concepts used are normalized whenever possible. Most of the KBs focus on a particular type of microbial activity, such as production of biocatalysts or nutraceuticals. Others are focused on specific categories of microorganisms, e.g. streptomyces or cyanobacteria. KBs are all structured in a uniform manner and have a standardized user interface. Information exploration is enabled through various searches. Users can explore statistically most significant concepts or pairs of concepts, generate hypotheses, create interactive networks of associated concepts and export results. We believe DESM will be a useful complement to the existing resources to benefit microbiology and biotechnology research.
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spelling pubmed-47028302016-01-07 DESM: portal for microbial knowledge exploration systems Salhi, Adil Essack, Magbubah Radovanovic, Aleksandar Marchand, Benoit Bougouffa, Salim Antunes, Andre Simoes, Marta Filipa Lafi, Feras F. Motwalli, Olaa A. Bokhari, Ameerah Malas, Tariq Amoudi, Soha Al Othum, Ghofran Allam, Intikhab Mineta, Katsuhiko Gao, Xin Hoehndorf, Robert C. Archer, John A. Gojobori, Takashi Bajic, Vladimir B. Nucleic Acids Res Database Issue Microorganisms produce an enormous variety of chemical compounds. It is of general interest for microbiology and biotechnology researchers to have means to explore information about molecular and genetic basis of functioning of different microorganisms and their ability for bioproduction. To enable such exploration, we compiled 45 topic-specific knowledgebases (KBs) accessible through DESM portal (www.cbrc.kaust.edu.sa/desm). The KBs contain information derived through text-mining of PubMed information and complemented by information data-mined from various other resources (e.g. ChEBI, Entrez Gene, GO, KOBAS, KEGG, UniPathways, BioGrid). All PubMed records were indexed using 4 538 278 concepts from 29 dictionaries, with 1 638 986 records utilized in KBs. Concepts used are normalized whenever possible. Most of the KBs focus on a particular type of microbial activity, such as production of biocatalysts or nutraceuticals. Others are focused on specific categories of microorganisms, e.g. streptomyces or cyanobacteria. KBs are all structured in a uniform manner and have a standardized user interface. Information exploration is enabled through various searches. Users can explore statistically most significant concepts or pairs of concepts, generate hypotheses, create interactive networks of associated concepts and export results. We believe DESM will be a useful complement to the existing resources to benefit microbiology and biotechnology research. Oxford University Press 2016-01-04 2015-11-05 /pmc/articles/PMC4702830/ /pubmed/26546514 http://dx.doi.org/10.1093/nar/gkv1147 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
Salhi, Adil
Essack, Magbubah
Radovanovic, Aleksandar
Marchand, Benoit
Bougouffa, Salim
Antunes, Andre
Simoes, Marta Filipa
Lafi, Feras F.
Motwalli, Olaa A.
Bokhari, Ameerah
Malas, Tariq
Amoudi, Soha Al
Othum, Ghofran
Allam, Intikhab
Mineta, Katsuhiko
Gao, Xin
Hoehndorf, Robert
C. Archer, John A.
Gojobori, Takashi
Bajic, Vladimir B.
DESM: portal for microbial knowledge exploration systems
title DESM: portal for microbial knowledge exploration systems
title_full DESM: portal for microbial knowledge exploration systems
title_fullStr DESM: portal for microbial knowledge exploration systems
title_full_unstemmed DESM: portal for microbial knowledge exploration systems
title_short DESM: portal for microbial knowledge exploration systems
title_sort desm: portal for microbial knowledge exploration systems
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702830/
https://www.ncbi.nlm.nih.gov/pubmed/26546514
http://dx.doi.org/10.1093/nar/gkv1147
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