Xconnector: Retrieving and visualizing metabolites and pathways information from various database resources.

Journal of Proteomics
Ali Mostafa AnwarSameh Magdeldin

Abstract

Metabolomics databases contain crucial information collected from various biological systems and experiments. Developers and scientists performed massive efforts to make the database public and accessible. The diversity of the metabolomics databases arises from the different data types included within the database originating from various sources and experiments can be confusing for biologists and researchers who need further manual investigation for the retrieved data. Xconnector is a software package designed to easily retrieve and visualize metabolomics data from different databases. Xconnector can parse information from Human Metabolome Database (HMDB), Livestock Metabolome Database (LMDB), Yeast Metabolome Database (YMDB), Toxin and Toxin Target Database (T3DB), ReSpect Phytochemicals Database (ReSpectDB), The Blood Exposome Database, Phenol-Explorer Database, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Small Molecule Pathway Database (SMPDB). Using Python language, Xconnector connects the targeted databases, recover requested metabolites from single or different database sources, reformat and repack the data to generate a single Excel CSV file containing all information from the databases, in an application progra...Continue Reading

References

Oct 10, 2013·Database : the Journal of Biological Databases and Curation·Joseph A RothwellAugustin Scalbert
Nov 10, 2013·Nucleic Acids Research·Timothy JewisonDavid S Wishart
Nov 8, 2014·Nucleic Acids Research·David WishartStephen M Rappaport
Oct 27, 2015·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Roberta Censi, Piera Di Martino
Dec 3, 2016·Nucleic Acids Research·Miguel Ramirez-GaonaDavid S Wishart
Dec 3, 2016·Nucleic Acids Research·Minoru KanehisaKanae Morishima
May 23, 2017·PloS One·Seyed Ali GoldansazDavid S Wishart
Nov 16, 2017·Nucleic Acids Research·David S WishartAugustin Scalbert
Sep 3, 2018·Cell Systems·Mingxun WangNuno Bandeira
Sep 27, 2019·Environmental Health Perspectives·Dinesh Kumar Barupal, Oliver Fiehn
Jan 8, 2020·Nature Methods·Arunima Singh
Mar 9, 2020·Metabolomics : Official Journal of the Metabolomic Society·Keiron O'Shea, Biswapriya B Misra

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.