Dragon exploration system on marine sponge compounds interactions

Sagar, Sunil; Kaur, Mandeep; Radovanović, Aleksandar; Bajic, Vladimir B.

doi:10.1186/1758-2946-5-11

Cited by 17 publications

(10 citation statements)

References 37 publications

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“…The text-mining process, as demonstrated in the left panel of Figure 1 , is performed by a King Abdullah University of Science and Technology (KAUST)-customized implementation of the dragon exploration system (DES), similar to that in ( 33 ). The original DES is a proprietary text-mining and data-mining tool from OrionCell ( http://www.orioncell.org ).…”

Section: Text-mining Methodologymentioning

confidence: 99%

DEOP: a database on osmoprotectants and associated pathways

et al. 2014

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Microorganisms are known to counteract salt stress through salt influx or by the accumulation of osmoprotectants (also called compatible solutes). Understanding the pathways that synthesize and/or breakdown these osmoprotectants is of interest to studies of crops halotolerance and to biotechnology applications that use microbes as cell factories for production of biomass or commercial chemicals. To facilitate the exploration of osmoprotectants, we have developed the first online resource, ‘Dragon Explorer of Osmoprotection associated Pathways’ (DEOP) that gathers and presents curated information about osmoprotectants, complemented by information about reactions and pathways that use or affect them. A combined total of 141 compounds were confirmed osmoprotectants, which were matched to 1883 reactions and 834 pathways. DEOP can also be used to map genes or microbial genomes to potential osmoprotection-associated pathways, and thus link genes and genomes to other associated osmoprotection information. Moreover, DEOP provides a text-mining utility to search deeper into the scientific literature for supporting evidence or for new associations of osmoprotectants to pathways, reactions, enzymes, genes or organisms. Two case studies are provided to demonstrate the usefulness of DEOP. The system can be accessed at.Database URL: http://www.cbrc.kaust.edu.sa/deop/

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Section: Text-mining Methodologymentioning

confidence: 99%

DEOP: a database on osmoprotectants and associated pathways

et al. 2014

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“…Both contained only a few hundreds of entries according to their respective publications but these were comprising rich metadata which is now lost. The Dragon Exploration System on Marine Sponge Compounds Interactions (DESMCI) [159] is still accessible but seems not to be maintained as the actual data, such as molecular structures and the corresponding metadata is not visible when one tries to access it. The Seaweed Metabolite Database (SWMD) [160] is the only one really maintained and it contains 1110 entries, with only 423 unique structures.…”

Section: Natural Products By the Geographic Origin Of Producing Organmentioning

confidence: 99%

Review on natural products databases: where to find data in 2020

2020

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Natural products (NPs) have been the centre of attention of the scientific community in the last decencies and the interest around them continues to grow incessantly. As a consequence, in the last 20 years, there was a rapid multiplication of various databases and collections as generalistic or thematic resources for NP information. In this review, we establish a complete overview of these resources, and the numbers are overwhelming: over 120 different NP databases and collections were published and re-used since 2000. 98 of them are still somehow accessible and only 50 are open access. The latter include not only databases but also big collections of NPs published as supplementary material in scientific publications and collections that were backed up in the ZINC database for commercially-available compounds. Some databases, even published relatively recently are already not accessible anymore, which leads to a dramatic loss of data on NPs. The data sources are presented in this manuscript, together with the comparison of the content of open ones. With this review, we also compiled the open-access natural compounds in one single dataset a COlleCtion of Open NatUral producTs (COCONUT), which is available on Zenodo and contains structures and sparse annotations for over 400,000 non-redundant NPs, which makes it the biggest open collection of NPs available to this date.

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“…DES is a text mining and data mining system that allows the exploration of text through enriched concepts and enriched pairs of concepts in topic-specific literature. We used the DES framework to create several topic-specific KBs [32,33,54,67,[69][70][71][72][73][74][75][76][77][78][79][80][81][82]. The underlying systems, workflow, and concept enrichment process used in the current version of DES have been described in [69].…”

Section: The Des-rod Exploration Systemmentioning

confidence: 99%

DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases

Essack

Salhi

Neste

et al. 2020

Oxidative Medicine and Cellular Longevity

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Normal cellular physiology and biochemical processes require undamaged RNA molecules. However, RNAs are frequently subjected to oxidative damage. Overproduction of reactive oxygen species (ROS) leads to RNA oxidation and disturbs redox (oxidation-reduction reaction) homeostasis. When oxidation damage affects RNA carrying protein-coding information, this may result in the synthesis of aberrant proteins as well as a lower efficiency of translation. Both of these, as well as imbalanced redox homeostasis, may lead to numerous human diseases. The number of studies on the effects of RNA oxidative damage in mammals is increasing by year due to the understanding that this oxidation fundamentally leads to numerous human diseases. To enable researchers in this field to explore information relevant to RNA oxidation and effects on human diseases, we developed DES-ROD, an online knowledgebase that contains processed information from 298,603 relevant documents that consist of PubMed abstracts and PubMed Central full-text articles. The system utilizes concepts/terms from 38 curated thematic dictionaries mapped to the analyzed documents. Researchers can explore enriched concepts, as well as enriched pairs of putatively associated concepts. In this way, one can explore mutual relationships between any combinations of two concepts from used dictionaries. Dictionaries cover a wide range of biomedical topics, such as human genes and proteins, pathways, Gene Ontology categories, mutations, noncoding RNAs, enzymes, toxins, metabolites, and diseases. This makes insights into different facets of the effects of RNA oxidation and the control of this process possible. The usefulness of the DES-ROD system is demonstrated by case studies on some known information, as well as potentially novel information involving RNA oxidation and diseases. DES-ROD is the first knowledgebase based on text and data mining that focused on the exploration of RNA oxidation and human diseases.

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Dragon exploration system on marine sponge compounds interactions

Cited by 17 publications

References 37 publications

DEOP: a database on osmoprotectants and associated pathways

DEOP: a database on osmoprotectants and associated pathways

Review on natural products databases: where to find data in 2020

DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases

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