TY - JOUR
T1 - DESM: portal for microbial knowledge exploration systems
AU - Salhi, Adil
AU - Essack, Magbubah
AU - Radovanovic, Aleksandar
AU - Marchand, Benoit
AU - Bougouffa, Salim
AU - Antunes, Andre
AU - Simoes, Marta
AU - Lafi, Feras Fawzi
AU - Motwalli, Olaa Amin
AU - Bokhari, Ameerah
AU - Malas, Tareq Majed Yasin
AU - Al Amoudi, Soha
AU - Othum, Ghofran
AU - Alam, Intikhab
AU - Mineta, Katsuhiko
AU - Gao, Xin
AU - Hoehndorf, Robert
AU - Archer, John A.C.
AU - Gojobori, Takashi
AU - Bajic, Vladimir B.
N1 - KAUST Repository Item: Exported on 2020-10-01
PY - 2015/11/5
Y1 - 2015/11/5
N2 - 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.
AB - 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.
UR - http://hdl.handle.net/10754/592836
UR - http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv1147
UR - http://www.scopus.com/inward/record.url?scp=84976874966&partnerID=8YFLogxK
U2 - 10.1093/nar/gkv1147
DO - 10.1093/nar/gkv1147
M3 - Article
C2 - 26546514
SN - 0305-1048
VL - 44
SP - D624-D633
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -