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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| Veröffentlicht in: | Nucleic acids research 2016-01, Vol.44 (D1), p.D624-D633 |
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| creator | 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 |
| 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. |
| doi_str_mv | 10.1093/nar/gkv1147 |
| format | Article |
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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.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkv1147</identifier><identifier>PMID: 26546514</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Antitubercular Agents - pharmacology ; Archaea - genetics ; Archaea - metabolism ; Bacteria - genetics ; Bacteria - metabolism ; Data Mining ; Database Issue ; Databases, Factual ; Dictionaries as Topic ; Drug Repositioning ; Fungi - genetics ; Fungi - metabolism ; Humans ; Industrial Microbiology ; Internet ; Knowledge Bases ; Viruses - genetics ; Viruses - metabolism ; Vocabulary, Controlled</subject><ispartof>Nucleic acids research, 2016-01, Vol.44 (D1), p.D624-D633</ispartof><rights>The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><rights>The Author(s) 2015. 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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. 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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.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>26546514</pmid><doi>10.1093/nar/gkv1147</doi><orcidid>https://orcid.org/0000-0001-9218-6452</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Nucleic acids research, 2016-01, Vol.44 (D1), p.D624-D633 |
| issn | 0305-1048 1362-4962 |
| language | eng |
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| source | Oxford Journals Open Access Collection; MEDLINE; DOAJ Directory of Open Access Journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Antitubercular Agents - pharmacology Archaea - genetics Archaea - metabolism Bacteria - genetics Bacteria - metabolism Data Mining Database Issue Databases, Factual Dictionaries as Topic Drug Repositioning Fungi - genetics Fungi - metabolism Humans Industrial Microbiology Internet Knowledge Bases Viruses - genetics Viruses - metabolism Vocabulary, Controlled |
| title | DESM: portal for microbial knowledge exploration systems |
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