YMDB 2.0: a significantly expanded version of the yeast metabolome database
YMDB or the Yeast Metabolome Database (http://www.ymdb.ca/) is a comprehensive database containing extensive information on the genome and metabolome of Saccharomyces cerevisiae. Initially released in 2012, the YMDB has gone through a significant expansion and a number of improvements over the past 4 years. This manuscript describes the most recent version of YMDB (YMDB 2.0). More specifically, it provides an updated description of the database that was previously described in the 2012 NAR Database Issue and it details many of the additions and improvements made to the YMDB over that time. Some of the most important change...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Ramirez-Gaona, M., Marcu, A., Pon, A., Guo, A. C., Sajed, T., Wishart, N. A., Karu, N., Djoumbou Feunang, Y., Arndt, D., Wishart, D. S. Tags: Database Issue Source Type: research
XTALKDB: a database of signaling pathway crosstalk
Analysis of signaling pathways and their crosstalk is a cornerstone of systems biology. Thousands of papers have been published on these topics. Surprisingly, there is no database that carefully and explicitly documents crosstalk between specific pairs of signaling pathways. We have developed XTalkDB (http://www.xtalkdb.org) to fill this very important gap. XTalkDB contains curated information for 650 pairs of pathways from over 1600 publications. In addition, the database reports the molecular components (e.g. proteins, hormones, microRNAs) that mediate crosstalk between a pair of pathways and the species and tissue in wh...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Sam, S. A., Teel, J., Tegge, A. N., Bharadwaj, A., Murali, T. M. Tags: Database Issue Source Type: research
The TissueNet v.2 database: A quantitative view of protein-protein interactions across human tissues
Knowledge of the molecular interactions of human proteins within tissues is important for identifying their tissue-specific roles and for shedding light on tissue phenotypes. However, many protein–protein interactions (PPIs) have no tissue-contexts. The TissueNet database bridges this gap by associating experimentally-identified PPIs with human tissues that were shown to express both pair-mates. Users can select a protein and a tissue, and obtain a network view of the query protein and its tissue-associated PPIs. TissueNet v.2 is an updated version of the TissueNet database previously featured in NAR. It includes ove...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Basha, O., Barshir, R., Sharon, M., Lerman, E., Kirson, B. F., Hekselman, I., Yeger-Lotem, E. Tags: Database Issue Source Type: research
pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis
Molecular pathway data are essential in current computational and systems biology research. While there are many primary and integrated pathway databases, several challenges remain, including low proteome coverage (57%), low overlap across different databases, unavailability of direct information about underlying physical connectivity of pathway members, and high fraction of protein-coding genes without any pathway annotations, i.e. ‘pathway orphans’. In order to address all these challenges, we developed pathDIP, which integrates data from 20 source pathway databases, ‘core pathways’, with physical...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Rahmati, S., Abovsky, M., Pastrello, C., Jurisica, I. Tags: Database Issue Source Type: research
Updates in Rhea - an expert curated resource of biochemical reactions
Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation of enzymes and the description of metabolic networks. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions, using entities from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Here we describe developments in Rhea since our last report in the database issue of Nucleic Acids Research. These include the first implementation of a si...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Morgat, A., Lombardot, T., Axelsen, K. B., Aimo, L., Niknejad, A., Hyka-Nouspikel, N., Coudert, E., Pozzato, M., Pagni, M., Moretti, S., Rosanoff, S., Onwubiko, J., Bougueleret, L., Xenarios, I., Redaschi, N., Bridge, A. Tags: Database Issue Source Type: research
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks
The increasing number of experimentally detected interactions between proteins makes it difficult for researchers to extract the interactions relevant for specific biological processes or diseases. This makes it necessary to accompany the large-scale detection of protein–protein interactions (PPIs) with strategies and tools to generate meaningful PPI subnetworks. To this end, we generated the Human Integrated Protein–Protein Interaction rEference or HIPPIE (http://cbdm.uni-mainz.de/hippie/). HIPPIE is a one-stop resource for the generation and interpretation of PPI networks relevant to a specific research quest...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Alanis-Lobato, G., Andrade-Navarro, M. A., Schaefer, M. H. Tags: Database Issue Source Type: research
CGDB: a database of circadian genes in eukaryotes
We report a database of circadian genes in eukaryotes (CGDB, http://cgdb.biocuckoo.org), containing ~73 000 circadian-related genes in 68 animals, 39 plants and 41 fungi. Circadian rhythm is ~24 h rhythm in behavioral and physiological processes that exists in almost all organisms on the earth. Defects in the circadian system are highly associated with a number of diseases such as cancers. Although several databases have been established for rhythmically expressed genes, a comprehensive database of cycling genes across phyla is still lacking. From the literature, we collected 1382 genes of which transcript level oscillatio...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Li, S., Shui, K., Zhang, Y., Lv, Y., Deng, W., Ullah, S., Zhang, L., Xue, Y. Tags: Database Issue Source Type: research
COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)
We describe how these MeSH-associated co-expressions enable the identification of diseases and drugs previously unknown to be related to a gene or a gene group of interest. (Source: Nucleic Acids Research)
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Yang, S., Kim, C. Y., Hwang, S., Kim, E., Kim, H., Shim, H., Lee, I. Tags: Database Issue Source Type: research
BRENDA in 2017: new perspectives and new tools in BRENDA
The BRENDA enzyme database (www.brenda-enzymes.org) has developed into the main enzyme and enzyme-ligand information system in its 30 years of existence. The information is manually extracted from primary literature and extended by text mining procedures, integration of external data and prediction algorithms. Approximately 3 million data from 83 000 enzymes and 137 000 literature references constitute the manually annotated core. Text mining procedures extend these data with information on occurrence, enzyme-disease relationships and kinetic data. Prediction algorithms contribute locations and genome annotations. External...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Placzek, S., Schomburg, I., Chang, A., Jeske, L., Ulbrich, M., Tillack, J., Schomburg, D. Tags: Database Issue Source Type: research
The BioGRID interaction database: 2017 update
The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions for all major model organism species and humans. As of September 2016 (build 3.4.140), the BioGRID contains 1 072 173 genetic and protein interactions, and 38 559 post-translational modifications, as manually annotated from 48 114 publications. This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update. BioGRID curates the biomedical lite...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Chatr-aryamontri, A., Oughtred, R., Boucher, L., Rust, J., Chang, C., Kolas, N. K., O'Donnell, L., Oster, S., Theesfeld, C., Sellam, A., Stark, C., Breitkreutz, B.-J., Dolinski, K., Tyers, M. Tags: Database Issue Source Type: research
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible
A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein–protein association data for a large number of organisms. The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. Apart from collecting and reassessing available experimental data on protein–protein interactions, and importing known pathways and protein comp...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos, A., Doncheva, N. T., Roth, A., Bork, P., Jensen, L. J., von Mering, C. Tags: Database Issue Source Type: research
KEGG: new perspectives on genomes, pathways, diseases and drugs
KEGG (http://www.kegg.jp/ or http://www.genome.jp/kegg/) is an encyclopedia of genes and genomes. Assigning functional meanings to genes and genomes both at the molecular and higher levels is the primary objective of the KEGG database project. Molecular-level functions are stored in the KO (KEGG Orthology) database, where each KO is defined as a functional ortholog of genes and proteins. Higher-level functions are represented by networks of molecular interactions, reactions and relations in the forms of KEGG pathway maps, BRITE hierarchies and KEGG modules. In the past the KO database was developed for the purpose of defin...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., Morishima, K. Tags: Database Issue Source Type: research
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration
Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Ong, E., Xiang, Z., Zhao, B., Liu, Y., Lin, Y., Zheng, J., Mungall, C., Courtot, M., Ruttenberg, A., He, Y. Tags: Database Issue Source Type: research
Expansion of the Gene Ontology knowledgebase and resources
The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools. Among the highlights are 1) developmen...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: The Gene Ontology Consortium Tags: Database Issue Source Type: research
TSTMP: target selection for structural genomics of human transmembrane proteins
The TSTMP database is designed to help the target selection of human transmembrane proteins for structural genomics projects and structure modeling studies. Currently, there are only 60 known 3D structures among the polytopic human transmembrane proteins and about a further 600 could be modeled using existing structures. Although there are a great number of human transmembrane protein structures left to be determined, surprisingly only a small fraction of these proteins have ‘selected’ (or above) status according to the current version the TargetDB/TargetTrack database. This figure is even worse regarding those...
Source: Nucleic Acids Research - January 2, 2017 Category: Research Authors: Varga, J., Dobson, L., Remenyi, I., Tusnady, G. E. Tags: Database Issue Source Type: research
