Items tagged by lmichan in 🔓BioDATABASES https://tagteam.harvard.edu/hubs/biodbs/user/lmichan TagTeam social RSS aggregrator Sun, 30 Jan 2022 11:55:00 -0500 http://www.bigzju.com/ATdb/ database Sun, 30 Jan 2022 11:50:00 -0500 http://bis.zju.edu.cn/mppi/ database Inflammatory bowel disease (IBD) represents a group of inflammatory conditions that cause inflammation of the digestive tract.  Inflammatory Bowel Disease Inflammatory bowel disease (IBD) is a term mainly used to describe two conditions: Ulcerative colitis and Crohn's disease are long-term conditions that involve inflammation of the gut. Ulcerative colitis only affects the colon (large intestine). Crohn's disease can affect any part of the digestive system, from the mouth to the anus. People of any age can get IBD, but it's usually diagnosed between the ages of 15 and 40. Sun, 30 Jan 2022 11:50:00 -0500 https://www.cbrc.kaust.edu.sa/ibd/ database botryosphaeriales.org is a website dedicated to Botryosphaeriales. The website focuses on providing an up-to-date account of Botryosphaeriales with notes on orders, families and genera and species, keeping abreast of the current literature.  Sun, 30 Jan 2022 11:49:00 -0500 https://botryosphaeriales.org/ database Sun, 30 Jan 2022 04:54:00 -0500 https://spidertraits.sci.muni.cz/ database spider Sun, 30 Jan 2022 04:54:00 -0500 https://kaikobase.dna.affrc.go.jp/ database Sun, 30 Jan 2022 04:53:00 -0500 https://mahshaaban.shinyapps.io/LINPSAPP/ database Sun, 30 Jan 2022 04:53:00 -0500 https://v2.sinex.cl/ database eukaryotes Sun, 30 Jan 2022 04:51:00 -0500 http://heartfailure.medical-bigdata.com/Home database heart Prototheca-ID is an open-source, online toolbox for the identification of Prototheca species, based on molecular markers. Prototheca-ID allows for a fast and reliable identification using the cytochrome b (CYTB) gene partial sequences and the D1/D2 region of the large subunit (LSU) of the rRNA gene sequences. The accuracy of identification is supported by a carefully curated and regularly updated database with 172 validated, high-quality sequences of 87 Prototheca strains, representing all currently known species, including their type (T) strains. The database also contains some basic information on Prototheca strains, including the isolation source, country of isolation, and collection date. In addition, links to original papers, in which the strains were described or used, are provided. All sequences, and supplementary information, are easily filtered and extracted from the database, and can be freely used for scientific research and educational purposes. Sun, 30 Jan 2022 04:51:00 -0500 https://prototheca-id.org/ database Sun, 30 Jan 2022 04:50:00 -0500 https://qsdb.uni-konstanz.de/ database COGVIC is short for "Catalogue Of Germline Variants In Cancer". The COGVIC for germline variants in East Asian population provides variant description, analyzed results and associated disease information from large-scale exon sequencing data sets. We report germline variants from 2112 East Asian cancer studies across 19 cancer types. Sun, 30 Jan 2022 04:50:00 -0500 http://www.cogvic.vip/ database Acute Lymphoblastic Leukemia (ALL) is one of the most common heterogeneous diseases observed in paediatric age group and it differs in both, immunophenotypic and molecular characters. ALL is a complex blood disorder characterized by various underlying genetic abnormalities that block B or T cell differentiation and support abnormal cell proliferation. The incidence of ALL is about 60% of all acute leukemias in children. MicroRNAs (miRNAs), a class of small non-coding RNAs, regulate gene expression at transcriptional and post-transcriptional level and are found to be deregulated in various cancers including leukemias. Increasing evidences suggest the involvement of microRNAs in the development of different types of leukemias by the deregulation of various signaling pathways such as Jak-Stat, Notch, NF-kB etc. To provide an overall idea regarding the complex interaction among miRNAs, their plausible targets and the associated pathways, extensive mining of miRNAs implicated in ALL was carried out from different databases. The data has been compiled in order to provide collective information in a single platform, LeukmiR. This database with an easy user-interface, query based enquiry could provide the required information in a snapshot to the users in a retrievable form. Herein, we also report 51 novel miRNAs and their targets that are experimentally validated in human Acute Lymphoblastic Leukemia samples. Sun, 30 Jan 2022 04:49:00 -0500 http://tdb.ccmb.res.in/LeukmiR/ database a database for genetic divergence investigation among macaques Sun, 30 Jan 2022 04:48:00 -0500 http://big.cdu.edu.cn/macsnvdb/ database macaque Roots are of critical importance for plant biology because they link below and above ground systems and extract water and nutrients from soil. Identification of root-associated genes, their functions, and their interactions can reveal the physiological and molecular mechanisms that regulate the root growth and development and have the potential to improve crop production. Moreover, in plant biotechnology, synthetic promoters can provide precise spatial and temporal control of transgene expression to improve crop productivity. The information of promoters in root-associated genes help the synthetic biology tool development to generate plants with novel root traits to enhance plant performance. Therefore, we analyzed multiple types of omics data to identify root-associated genes in maize, soybean, and sorghum and their promoter sequences. For these root-associate genes and their promoter sequences, we constructed this database to provide a pivotal platform capable of stimulating and facilitating further studies on manipulating root growth and development.The current version of the database contains more than 1200 candidates of root-associated genes and their corresponding promoter sequences for maize (592), sorghum (363), and soybean (400). usage: Please click the following images to enter databases for different species. User can browse all genes and search specific genes with gene IDs and DNA sequences. Sun, 30 Jan 2022 04:47:00 -0500 http://sysbio.unl.edu/RGPDB/ database CNGBdb is recognized by international journals and alliances. CNGBdb is designated as a data repository by Elsevier and the Earth BioGenome Project (EBP), and recognized by Wiley & Oxford Publishing Group and Science journals; CNGBdb is certificated by FAIRsharing and is included in re3data, and the data submitted to CNGBdb is uniformly identified by DOI (Digital Object Identifier) ​​to promote sharing and utilization. The CNSA is a system for archiving global omics data, dedicated to the storage, management and sharing of omics data, promotes the reuse of omics data and the development of life sciences. Sun, 30 Jan 2022 04:46:00 -0500 https://db.cngb.org/cnsa/ database a comprehensive web-based tool to access and analyze glia secretome data Sun, 30 Jan 2022 04:46:00 -0500 https://www.gliome.org/ database PLANT METABOLIC PATHWAY DATABASES The PMN currently houses one multi-species reference database called PlantCyc and 126 species/taxon-specific databases. PMN Content Statistics - stats about pathways, enzymes, reactions, compounds, and more PMN Database Overview - description of data, algorithms, and software used to generate the databases PMN Release Notes - highlights of the most recent PMN release **Please make sure that your favorite database is selected in the Quick Search bar as you explore the PMN resources PlantCyc [ More Information ] [ Content Statistics ] PlantCyc provides access to manually curated or reviewed information about shared and unique metabolic pathways present in over 500 plant species. PMN Single-species/taxon Databases The PMN also provides access to manually curated and/or computationally predicted information about enzymes, pathways, and more for individual species. Sun, 30 Jan 2022 04:44:00 -0500 https://plantcyc.org/ database plant Sun, 30 Jan 2022 04:42:00 -0500 https://www.biosino.org/elmsg/index database  GTDB is an integrated repository of glycosyltransferases, which collects comprehensive information, including amino acid sequences, coding region sequences, available tertiary structures, protein classification families, catalytic reactions and metabolic pathways involved, from distinct well-known databases or predictions.  Search—advanced search provides various queries to specify users’ concerns accurately.  Browse—browse data by diverse classifications and download those data in batches.  BLAST— sequence search of GTDB to annotate query glycosyltransferases’ functions.  GTdock—performs several glycosyltransferases docking with the same one acceptor easily by AutoDock Vina. Sun, 30 Jan 2022 04:41:00 -0500 https://www.biosino.org/gtdb/ database MaizeGDB is a community-oriented, long-term, federally funded informatics service to researchers focused on the crop plant and model organism Zea mays. Sun, 30 Jan 2022 04:38:00 -0500 https://www.maizegdb.org/ database Sun, 30 Jan 2022 04:38:00 -0500 https://www.brenda-enzymes.org/ database enzyme CHD-RF-KB (A knowledgebase for non-syndromic congenital heart disease associated risk factors) is a manually curated database of genetic variations and other risk factors associated with non-syndromic congenital heart disease (NS-CHD). CHD-RF-KB contains a comprehensive information of genetic variations and non-genetic factors for 609 subtypes (including 231 isolated and 378 non-isolated subtypes) of human NS-CHD reported in PubMed from 1998, which would provide an exhaustive and summary of current status of non-syndromic CHD genetic and risk-related research. CHD-RF-KB can not only help researchers better to interpret the human variants for illustrating NS-CHD causing variants, but also be an improvement tool to further provide assessment of recurrence risk and prognosis, guidance of diagnostic and outcomes, as well as disease precaution. The database will be updated about one year regularly. CHD-RF-KB has several distinct characters as follows: 1) CHD-RF-KB represents the comprehensive research synopsis in the field of genetics and other risk factors associated with NS-CHD; 2) All the entries in CHD-RF-KB are comprehensively annotated, including CHD type (ID, type, description), information of risk factors (genetic and non-genetic), sample information (Population, Region, Source, Method, Treatment and control group data), reference information (PubMed, Year, ID title); 3) CHD-RF-KB provides an interactive platform for the public to share the research results related to genetic and other risk factors associated with non-syndromic congenital heart disease and screen information of these two parts separately; 4) Based on the full-scale of CHD-RF-KB, public researchers can obtain homogeneous results from the statistical analysis of data, which help to further systemic analyses of mechanisms about NS-CHD at molecular level. In addition, CHD-RF-KB can also provide exhibition of the association graph between genotypes and phenotypes, along with graphs between phenotypes and risk factors associated with NS-CHD, which can contribute to elucidate the complex relationships between them. Should you have any questions, please do not hesitate to contact us (lilylan5930@sina.com). Citation: Yang L, Yang Y, Liu X, Chen Y, Chen Y, Lin Y, Sun Y, Shen B. CHDGKB: a knowledgebase for systematic understanding of genetic variations associated with non-syndromic congenital heart disease. Database (Oxford). 2020 Jan 1;2020:baaa048. doi: 10.1093/database/baaa048. PMID: 32608479. Sun, 30 Jan 2022 04:37:00 -0500 http://www.sysbio.org.cn/CHDRFKB/ database heart Meadow fescue (Festuca pratensis Huds.) is a diploid (2n =14) outbreeding species that belongs to the genus Festuca, together with Lolium the most important genera of forage grasses in temperate regions. Meadow fescue is a forage grass species with high quality dry matter yields, good winter survival and persistency, and is suitable for both frequent-cutting conservation regimes and grazing. The Lolium-Festuca species complex is unique since it is possible to combine genomes in interspecific hybrids (Festulolium). Fescues in general have evolved superior adaptations to abiotic stresses, e.g., winter survival in meadow fescue. Lolium species are known for superior nutritive quality, rapid establishment and growth, but lack persistency under harsh environmental conditions. Complementation of traits in Festulolium hybrids is thus a very interesting strategy for developing novel germplasm and cultivars with improved quality and persistency, which can contribute to a sustainable forage production. Relatively modest genomic resources have been developed for meadow fescue compared with other grass species like perennial ryegrass (L. perenne). In order to develop better festulolium hybrids, we have initiated sequencing of F.pratensis, combined with an efficient utilization of the close relationship with lolium and barley through comparative genomics approaches. Sun, 30 Jan 2022 04:36:00 -0500 https://foragegrass.org/ database GXD collects and integrates the gene expression information in MGI. Its primary emphasis is on endogenous gene expression during mouse development. Sun, 30 Jan 2022 04:36:00 -0500 http://www.informatics.jax.org/expression.shtml database Sun, 30 Jan 2022 04:35:00 -0500 http://conomode.qnlm.ac/conomode/conomode/index database The circR2Cancer is a manually curated database that provides reliable associations between circRNAs and cancers. The current version of the database contains 1439 experimentally verified circRNA-cancer relationships, including 1135 circRNAs and 82 cancers. At the same time, we offer users a simple friendly interface, making it convenient to browse, search and download the interactions mentioned above. Sun, 30 Jan 2022 04:34:00 -0500 http://www.biobdlab.cn:8000/ database cancer Peptide ligands play a very important role in life processes, whether in the field of antibacterial, antiviral, antifungal, organismal modulation or anticancer. Compared with small molecule drugs, there is still a huge gap in the research and application of peptides. The current screening technology of active peptides has become an obstacle to the widespread use of peptides, although techniques such as phage display have shown good advantages. Because of the flexible existence of peptides, the virtual screening technique has not been better applied, although this technique has been widely used in the field of small molecule drug screening. In order to study the peptide ligand-receptor interactions more deeply, our team collected and organized a database of peptide ligands (DPL). Our database focuses on the collection and organization of peptide ligands. All peptide ligands have clear receptor information, and this criterion is a prerequisite for data collection. In order to facilitate the research, this database not only collects the basic information of peptides, but also collates the related research literature and structural information. All peptide structure data will be available for everyone. Some of the most recent research hot articles are collected in the Research Papers section. Both the peptide database and the research articles are continuously updated by our team. We hope that everything we do can facilitate your peptide research. Sun, 30 Jan 2022 04:33:00 -0500 http://www.peptide-ligand.cn/ database Bread wheat (Triticum aetivum) consists of three closely related subgenomes (AABBDD), which provides the major of the calories and protein global populations consumed. Its origin is attributed to two evolutionary events: (1) the initial domestication of tetraploid wild emmer (Triticum dicoccoides, AABB) and the subsequent evolution of tetraploid domesticated emmer (Triticum dicoccum, AABB), and (2) hybridization between tetraploid domesticated emmer and diploid Ae. tauschii (Aegilops tauschii, DD). Here, we developed a comprehensive Wheat Genome Variation Database and Selective Signatures for providing four main functionalities: Variation Search, Genomic Signature Search, Genome Browser and Alignment Search Tools (BLAST). In current version, WGVD contains 7,346,814 SNPs and 1,044,400 indels focusing on genic regions and upstream or downstream regions by combining the whole-genome resequencing and exome sequencing data of 968 individuals. Selective signatures Ae. tauschii, wild emmer, domesticated emmer, bread wheat landrace and bread wheat variety are evaluated with two statistical test (Pi, and FST) based on SNPs from 93 whole-genome resequencing data. WGVD will be a useful archive for in-depth analysis in wheat breeding. Sun, 30 Jan 2022 04:33:00 -0500 http://animal.nwsuaf.edu.cn/code/index.php/Wheat database The database contains more than 3000 confirmed GPCR (CG) and 3500 non-GPCR (CN) from more than 1200 different organisms including bacteria and viruses. About half of the non-GPCR sequences are transmembrane proteins (CNT). It also incorporates predicted GPCRs (PG) from three organisms. Each protein, with a unique identification number, is linked to its source organism, gene name, protein name, sequence length, and other features such as amino acid and dipeptide compositions. For the GPCRs, the lengths of characteristic structural regions (i.e., N-terminal, C-terminal, seven transmembrane helices, and the extracellular and intracellular loops) are provided. If available, GPCR family classification information is also included. Sun, 30 Jan 2022 04:31:00 -0500 https://gpcr.utep.edu/database database Storefish 2.0: a database on the reproductive strategies of teleost fishes   Teleost fishes show the most outstanding reproductive diversity of all vertebrates. Yet to date, no one has been able to decisively explain this striking variability, nor to perform large-scale phylogenetic analyses of reproductive modes. Here, we describe STOREFISH 2.0, an online database easing the sharing of an original dataset on reproduction published in 2007, enriched with automated data extraction and presentation to display the knowledge acquired on temperate freshwater fish species. Sun, 30 Jan 2022 04:31:00 -0500 https://www.storefish.org/ database The Predicted Rat Interactome Database (PRID) is prepared through the integration of six types of evidence for functional gene associations from 10 public databases. It includes 305,939 gene associations, including predicted 302,693 functional associations and 3,246 experimentally reported interactions. These 302,693 functional associations are expected to cover 13.02% of the protein-protein interactions of rat. Approximately 52.59% of these functional associations are expected to represent protein-protein interactions. Based on this high-quality functional association network of PRID, the Gene Set Linkage Analysis (GSLA) tool is provided to interpret the potential functional impacts of the multiple simultaneously changed genes. Sun, 30 Jan 2022 04:29:00 -0500 http://rat.biomedtzc.cn/ database rat gene The PR2 database was initiated in 2010 in the frame of the BioMarks project from work that had developed in the previous ten years in the Plankton Group of the Station Biologique of Roscoff. Its aim is to provide a reference database of carefully annotated 18S rRNA sequences using eight unique taxonomic fields (from kingdom to species). At present it contains about 205,000 sequences. A number of metadata fields are available for many sequences, including geo-localisation, whether it originates from a culture or a natural sample, host type etc... The annotation of PR2 is performed by experts from each taxonomic groups. One very important project in this respect is EukRef which has recently decided to merge its effort with PR2. EukRef has built bioinformatics pipelines that have been used during three workshops dedicated to specific taxonomic groups. Sun, 30 Jan 2022 04:28:00 -0500 https://github.com/pr2database/pr2database database protist gene The general objective of this database is to improve knowledge of wild coffee species in order to better protect and enhance them. More specifically, we: Gather for each species, the available information from referenced or non-referenced literature and personal observations on their natural distributions, habitats, morphological, phenological, biochemical, genetic/genomic characteristics, etc.) in order to make the published data accessible. Present specifically the wild species in living collection on the sites of Bassin-Martin, Reunion Island and Kianjavato, Madagascar (photo gallery) Present the wild species from the BaraCoffea group from Madagascar Sun, 30 Jan 2022 04:27:00 -0500 http://publish.plantnet-project.org/project/wildcofdb_en database cofeea About MetaTropismDB Despite the recent discoveries, the biological and molecular understanding of the formation and localization of metastases is not fully known yet. In order to study the tumor evolution, the research mostly uses murine models. A common type of experiment involves the inoculation, by various techniques, of human tumor cell lines in immunosuppressed mouse models to avoid rejection reactions. In particular, this experimental model allows the evaluation of the effectiveness of potential anticancer therapies in vivo. By hand-curated literature screening we collected, in MetaTropismDB database, experimentally assessed data about the organotropism of several human cancer cell lines. In the reviewed studies, human cell lines have been injected in murine models in order to assess the patterns of metastasis. In particular, we collected all the experimental conditions and the obtained results, including the organs NOT affected by metastases. Currently, it stores the results of 513 experiments in which cell line injection in mouse models have been carried out. The database allows to easily highlight cell lines or particular clones with metastatic activity with similar organotropism, or alternatively, cell lines and clones which, although deriving from the same type of primary tumor, have tropism for different organs. This allows researchers to choose, with greater awareness and accuracy, the cell lines to be analyzed at the molecular level in order to investigate the biological bases of metastasis organotropism. Sun, 30 Jan 2022 04:26:00 -0500 http://www.introni.it/Metastasis/metastasis.html database BarleyVarDB is a comprehensive genomic variation database for Barley. In summary, BarleyVar database mainly includes three types of data.     Data Processing and Validation The detailed methodology and relevant analysis scripts for genomic variation detection for the collected sequencing data can refer to our Github site. Briefly, all clean reads were mapped to the barley pseudo-molecular reference using BWA-MEN with default parameters, and SNPs/InDels were detected by running two rounds of variants calling analysis using SAMTools/BCFTools pipline and GATK. The accuracy of SNP and INDEL calling was up to 98.95% and evaluated using one of the largest de novel assemblied contigs (Bowman_contig_843756:34,593 bp). Please cite us: Tan,C., Chapman,B., Wang,P. et al. BarleyVarDB: a database of barley genomic variation. Database (2020). doi:10.1093/database/baaa091. IBGSC.A chromosome conformation capture ordered sequence of the barley genome. Nature (2017). doi:10.1038/nature22043 Sun, 30 Jan 2022 04:25:00 -0500 http://146.118.64.11/BarleyVar/ database genome Allostery is pertinent to regulate a protein’s functional activity induced by the action of an effector at a site distinct from the active site of biomolecules through alteration of conformation and/or dynamics. Allosteric Database (ASD) provides a versatile resource for structure, function, disease and related annotation for the well-established allosteric macromolecules and allosteric modulators since 1901, data in ASD is annually updated and freely served for biologists and medicinal chemists interested in allosteric regulation mechanism and allosteric drug discovery. Sun, 30 Jan 2022 04:23:00 -0500 http://mdl.shsmu.edu.cn/ASD/ database The Bovine Genome Database supports the efforts of bovine genomics researchers by providing data mining, genome navigation and annotation tools for the bovine reference genome based on the hereford cow, L1 Dominette 01449. Sun, 30 Jan 2022 04:22:00 -0500 https://bovinegenome.elsiklab.missouri.edu/home database genome bovine Sun, 30 Jan 2022 04:21:00 -0500 https://www.ebi.ac.uk/ena/browser/home database Long non-coding RNAs (lncRNAs) are emerging as key factors in the regulation of various cellular processes and diseases. LncRNASNP is a database providing comprehensive resources of single nucleotide polymorphisms (SNPs) in human/mouse lncRNAs. It contains SNPs in lncRNAs, SNP effects on lncRNA structure, mutation in lncRNAs and lncRNA:miRNA binding. Sun, 30 Jan 2022 04:21:00 -0500 http://bioinfo.life.hust.edu.cn/lncRNASNP database Sun, 30 Jan 2022 04:21:00 -0500 https://brp.kfshrc.edu.sa/ared database Sun, 30 Jan 2022 04:20:00 -0500 https://zinc.docking.org/catalogs/uefsnp/ database natural_product Natural Products Online is an open source project for Natural Products (NPs) storage, search and analysis. The present version hosts COCONUT, the COlleCtion of Open Natural ProdUcTs, one of the biggest and best annotated resources for NPs available free of charge and without any restriction. Sun, 30 Jan 2022 04:20:00 -0500 https://coconut.naturalproducts.net/ database natural_product Sun, 30 Jan 2022 04:17:00 -0500 https://zinc.docking.org/catalogs/hitnp/ database natural_product South African Natural Compounds Database (SANCDB) Sun, 30 Jan 2022 04:16:00 -0500 https://sancdb.rubi.ru.ac.za/ database natural_product AfroDb is a database of natural products from African sources. The paper was published in October 2013 in PLOS One. AfroDb: A Select Highly Potent and Diverse Natural Product Library from African Medicinal Plants by Fidele Ntie-Kang, Denis Zofou, Smith B. Babiaka, Rolande Meudom, Michael Scharfe, Lydia L. Lifongo, James A. Mbah, Luc Meva'a Mbaze, Wolfgang Sippl and Simon M. N. Efange PLOS One 8(10): e78085. doi: 10.1371/journal.pone.0078085 We are grateful to the authors for allowing us to incorporate the molecular structrues of this database in ZINC. Sun, 30 Jan 2022 04:16:00 -0500 https://zinc.docking.org/catalogs/afronp/ database natural_product  NPACT is a curated database of Plant derived natural compounds that exhibit anti-cancerous activity. It contains 1574 entries and each record provides information on their structure, properties (physical, elemental and topological), cancer type, cell lines, inhibitory values (IC50, ED50, EC50, GI50), molecular targets, commercial suppliers and drug likeness of compounds. NPACT concentrates on anti-cancer natural compounds found in plants only. NPACT is unique in providing bioactivities of these natural compounds against different cancer cell lines and their molecular target Sun, 30 Jan 2022 04:15:00 -0500 http://crdd.osdd.net/raghava/npact/ database natural_product cancer Sun, 30 Jan 2022 04:14:00 -0500 https://nubbe.iq.unesp.br/portal/nubbe-search.html database natural_product African Natural Products Database (ANPDB) Natural products (NPs) have oftentimes represented a source of drugs, drug leads or a "source of inspiration" for the discovery of novel drugs. In a recent survey of the African flora, it was shown that this continent could be a huge repository of bioactive NPs with diverse scaffolds and activities. Consequently, many NPs have been extracted from plants used in traditional African medicine and some of which have already been FDA-approved, such as the antimalarial artemimisin. Sun, 30 Jan 2022 04:13:00 -0500 http://african-compounds.org/anpdb/ database natural_product Streptomyces is the largest genus of Actinobacteria presenting a complex developmental life cycle. Bacteria of these genus play a major role in the production of drugs with natural origin. More than 40% of all known antibiotics are produced by streptomyces spec. though many of these secondary metabolites are also used as chemotherapy or immunosuppressant drugs. An enormous number of crucial data related to this genus have been collected up to the present but the exploiting of the chemical diversity of bioactive compounds produced by this genus is still essential for novel drug discovery. It comes from the University of Freiburg, Germany: http://StreptomeDB.pharmaceutical-bioinformatics.de We are grateful to the authors for creating and curating this database and thank them for allowing us to incorporate its structures in ZINC. Sun, 30 Jan 2022 04:13:00 -0500 https://zinc.docking.org/catalogs/streptome/ database streptomyces compounds Sun, 30 Jan 2022 04:12:00 -0500 https://www.ibscreen.com/ database compounds Sun, 30 Jan 2022 04:10:00 -0500 https://zinc15.docking.org/substances/subsets/natural-products/ database natural_product A database of In-Silico predicted MS/MS spectrum of Natural Products Sun, 30 Jan 2022 04:10:00 -0500 http://oolonek.github.io/ISDB/ database natural_product XMetDB is an open access database for drugs and other xenobiotics and their respective metabolites. The database contains chemical structures of xenobiotic biotransformations with substrate atoms annotated as reaction centra, the resulting product formed, and the catalyzing enzyme, type of experiment, and literature references. Associated with the database is a web interface for the submission and retrieval of experimental metabolite data for drugs and other xenobiotics in various formats, and a web API for programmatic access is also available. The database is open for data deposition, and a curation scheme is in place for quality control. An extensive guide on how to enter experimental data into is available from the XMetDB wiki. XMetDB formalizes how biotransformation data should be reported, and the openly available systematically labeled data is a big step forward towards better models for predictive metabolism. Read more in the XMetDB paper! Sun, 30 Jan 2022 04:08:00 -0500 https://pharmb.io/tool/xmetdb/ database Sun, 30 Jan 2022 04:07:00 -0500 https://www.selleckchem.com/screening/natural-product-library.html database natural_product Sun, 30 Jan 2022 04:07:00 -0500 http://www.researchdsf.unict.it/S2RSLDB/ database CUPAC (Cornell University Plant Anatomy Collection) is an historically important collection of anatomical slide preparations of a wide array of plant parts. These slides include materials prepared by renowned Cornell Plant Anatomists, both for teaching and publication. Included are slides from the collections of Arthur Eames, Mary Wilde, David W. Bierhorst, Hal Moore and Natalie Uhl; and from other famous plant anatomists such as K. Esau, Johri and Maheshwari. Slides are being imaged by volunteers and undergraduate student workers, and simultaneously barcoded and databased. Post-processing involves automated resizing and labeling as well as magnification calibration that allows online measurement tools to be used as overlays on the images. Sun, 30 Jan 2022 04:06:00 -0500 http://cupac.bh.cornell.edu/ database plant anatomy Sun, 30 Jan 2022 04:05:00 -0500 http://naturaldatabaseconsumer.therapeuticresearch.com/nd/Search.aspx?pt=7&referer=kaiserpermanenteconsumer&lang=0 database Sun, 30 Jan 2022 04:05:00 -0500 http://naturaldatabaseconsumer.therapeuticresearch.com/(X(1)S(gwzeyw55htt3ko55ztw02045))/nd/search.aspx?referer=kaiserpermanenteconsumer&lang=0&&AspxAutoDetectCookieSupport=1 database The Fungarium at the Royal Botanic Gardens, Kew contains the largest collection of dried fungi in the world. Together with the CABI collection [collection code IMI], it contains about 1.25 million specimens, including the British National Collections (ca. 300,000 specimens), approximately 50,000 types, and other specimens from over 240 countries on all seven continents. The collection was founded in 1879 with the donation of 20,000 specimens from the Rev. Miles J. Berkeley, and continues to grow by about 3-4,000 accessions each year. Many important historical specimens are maintained in the Fungarium, including specimens collected by Charles Darwin during his voyage on the H.M.S. Beagle. More information on the collections is available here. These collections remain the focus of much active collections-based research pursued by the Kew Mycology Team (further information is available on the Science Directory). This site is a portal to the internal database (Herbtrack) for the collections that have been accessioned to Kew [herbarium code K(M)]. Searching the CABI collection (HerbIMI) is available here. Integration of these two databases will occur in the near future. Simple searches can be initiated from this page. Please refer to the help pages for advice as to how to formulate database queries. Advanced search options are also available by clicking on the 'More Search Options' button. Quality of data with regard to the presence of a taxon in any particular country varies from 'high' where the record is based on material of known provenance to 'low' where a record is based on, for example, a quarantine intercept where the exact origin of the material is not available. Information in the database should not be regarded as definitive proof of the presence of a species in a particular country. Please contact us (mycology@kew.org) if you have enquiries about the records, to request a loan, or if you have any ideas as to how we can improve Sun, 30 Jan 2022 04:04:00 -0500 https://herbtrack.science.kew.org/search database fungus Sun, 30 Jan 2022 04:03:00 -0500 https://insidewood.lib.ncsu.edu/search?0 database wood Sun, 30 Jan 2022 04:03:00 -0500 https://medlineplus.gov/spanish/druginformation.html database drugs   wd:https://www.wikidata.org/wiki/Q110316068 Sun, 30 Jan 2022 04:01:00 -0500 https://marinlit.rsc.org/ database literature wikidata marine natural_product Sun, 30 Jan 2022 03:58:00 -0500 https://www.malariagen.net/data database gene genome malaria Sun, 30 Jan 2022 03:58:00 -0500 https://tritrypdb.org/tritrypdb/app database Sun, 30 Jan 2022 03:56:00 -0500 https://fungidb.org/fungidb/app fungus database https://twitter.com/WBParaSite Sun, 30 Jan 2022 03:55:00 -0500 https://parasite.wormbase.org/index.html database twitter Sun, 30 Jan 2022 03:55:00 -0500 https://plasmodb.org/plasmo/app database plasmodium Translation of circular RNAs (circRNAs) now has drawn increasing attention from researchers due to their emerging roles of the functional peptides encoded by circRNAs as new players involved in the regulation of gene expression. However, the scope of circRNA translation is not yet clear. To this end, we analyzed 3,168 publicly available Ribo-seq datasets and 1,970 matched RNA-seq datasets from the same samples involving 314 studies covering 21 species to determine the prevalence of circRNA translation, and developed a translatome data-oriented circRNA database named riboCIRC, which aims to provide: (1) a comprehensive repository of computationally predicted ribosome-associated circRNAs (Ribo-circRNAs), together with multiple lines of evidence further supporting their translation, including cORF, IRES, m6A and mass spectrometric proofs; (2) a manually curated collection of experimentally verified translated circRNAs; (3) an evaluation of cross-species conservation of translatable circRNAs; (4) a systematic de novo annotation of putative circRNA-encoded peptides, including sequence, structure, and function, and (5) a genome browser to visualize the context-specific occupant footprints of circRNAs. Sun, 30 Jan 2022 03:54:00 -0500 http://www.ribocirc.com/ database An automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species. Sun, 30 Jan 2022 03:53:00 -0500 https://www.ncbi.nlm.nih.gov/homologene database eukaryotes Sun, 30 Jan 2022 03:53:00 -0500 https://cryptodb.org/cryptodb/app database The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Please, check the reference page to find articles describing the DIP database in greater detail. This page serves also as an access point to other projects related to DIP, such as The Database of Ligand-Receptor Partners (DLRP) and JDIP. Sun, 30 Jan 2022 03:51:00 -0500 https://dip.doe-mbi.ucla.edu/dip/Main.cgi database protein Sun, 30 Jan 2022 03:51:00 -0500 https://www.biocyc.org/ database genome COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer. Sun, 30 Jan 2022 03:50:00 -0500 https://cancer.sanger.ac.uk/cosmic database cancer Sun, 30 Jan 2022 03:50:00 -0500 https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/drug-product-database.html database drug EchoBase is a database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. See the Introduction Page for more information on our data sources, annotation and credits. If you are interested in comparing E. coli K-12 genomes to those of pathogenic E. coli, we suggest that you use our sister site coliBase and for general information then see the E. coli index. As of today, Sunday, January 30, 2022, there are 304 curated references in the database relating to the 4506 genes in this bacterium. This is version 2.0 of Echobase which was released on the 4th May 2006 & was last updated in January 2015. If you use EchoBASE please cite the following paper: Misra et al. EchoBASE: an integrated post-genomic database for Escherichia coli. 2005, Nucleic Acids Research. Sun, 30 Jan 2022 03:49:00 -0500 https://www.york.ac.uk/res/thomas/ database ecoli gene The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery. Using Nucleotide Quick Start Guide FAQ Help GenBank FTP RefSeq FTP Nucleotide Tools Submit to GenBank LinkOut E-Utilities BLAST Batch Entrez Other Resources GenBank Home RefSeq Home Gene Home SRA Home INSDC You are here: NCBI > DNA & RNA > Nucleotide DatabaseSupport Center Sun, 30 Jan 2022 03:48:00 -0500 https://www.ncbi.nlm.nih.gov/nuccore database The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. Protein sequences are the fundamental determinants of biological structure and function. Sun, 30 Jan 2022 03:47:00 -0500 https://www.ncbi.nlm.nih.gov/protein database protein Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide. Sun, 30 Jan 2022 03:47:00 -0500 https://www.ncbi.nlm.nih.gov/gene?db=Gene database world Sun, 30 Jan 2022 03:46:00 -0500 http://urgi.versailles.inra.fr/Platform database plant fungus The resource for approved human gene nomenclature Sun, 30 Jan 2022 03:45:00 -0500 https://www.genenames.org/ database human gene H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing variants, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, and molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. H-InvDB was produced based upon the annotation technology established in the H-Invitational Project for annotation of human full-length cDNAs (2004), was updated by the "Genome Information Integration Project" (2005-2008) and "METI integrated database project" (2008-2011) as a key integrated database of human genes, and then updated by AIST and Tokai University School of Medicine with support from JSPS KAKENHI, Grant-in-Aid for Publication of Scientific Research Results. Sun, 30 Jan 2022 03:44:00 -0500 http://www.h-invitational.jp/ database human gene InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as signatures, provided by several different databases (referred to as member databases) that make up the InterPro consortium. We combine protein signatures from these member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool. Sun, 30 Jan 2022 03:40:00 -0500 http://www.ebi.ac.uk/interpro/ database protein Protein-Protein Interaction Networks Functional Enrichment Analysis Sun, 30 Jan 2022 03:39:00 -0500 https://string-db.org/ database protein The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains; therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains. The table below shows examples of the PIRSF classification levels. The primary level is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). At a lower level are the subfamilies which are clusters representing functional specialization and/or domain architecture variation within the family. Above the homeomorphic level there may be parent superfamilies that connect distantly related families and orphan proteins based on common domains. Because proteins can belong to more than one domain superfamily, the PIRSF structure is formally a network (Wu et al., 2004). Sun, 30 Jan 2022 03:37:00 -0500 https://proteininformationresource.org/pirsf/ database protein The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The Summary page describing a given peptidase can be reached by use of an index under its Name, MEROPS Identifier or source Organism. The Summary describes the classification and nomenclature of the peptidase and offers links to supplementary pages showing sequence identifiers, the structure if known, literature references and more. The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these again have indexes. Each of the Summary pages offers links to supplementary pages. Please use the Menu in the side-bar to navigate through the database, and consult the About pages to discover more. To reach the Inhibitors side of MEROPS click the button at the top of the sidebar. The MEROPS website and database are run by Neil D. Rawlings, alumnus at the EMBL-European Bioinformatics Institute, Cambridge CB10 1SD, UK (merops@ebi.ac.uk). Sat, 29 Jan 2022 17:11:00 -0500 https://www.ebi.ac.uk/merops/ database enzyme OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily. OMIM is authored and edited at the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, under the direction of Dr. Ada Hamosh. Its official home is omim.org. Sat, 29 Jan 2022 17:09:00 -0500 https://www.ncbi.nlm.nih.gov/omim?db=OMIM database human gene The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download. The miRBase Registry provides miRNA gene hunters with unique names for novel miRNA genes prior to publication of results. Visit the help pages for more information about the naming service. Sat, 29 Jan 2022 17:09:00 -0500 https://www.mirbase.org/ database The portal for rare diseases and orphan drugs "Rare diseases are rare, but rare disease patients are numerous" Sat, 29 Jan 2022 17:08:00 -0500 https://www.orpha.net/consor/cgi-bin/index.php?lng=EN database disease drug KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. See Release notes (January 1, 2022) for new and updated features. Sat, 29 Jan 2022 17:07:00 -0500 https://www.genome.jp/kegg/ database Sat, 29 Jan 2022 17:02:00 -0500 http://130.88.97.239/PRINTS/index.php database protein Sat, 29 Jan 2022 17:02:00 -0500 http://prodom.prabi.fr/prodom/current/html/home.php database protein Long noncoding RNAs (LncRNAs) are endogenous noncoding RNAs, arbitrarily longer than 200-nucleotide, that play critical roles in diverse biological processed via mechanisms that remain obscure. LncRNAs exist in different genomes range from animals to plants. Here our database PlncRNA is a searchable database of lncRNA sequences and annotation in plants. Sat, 29 Jan 2022 16:55:00 -0500 http://bis.zju.edu.cn/PlncRNADB/ database plant RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping. Sat, 29 Jan 2022 16:52:00 -0500 http://bis.zju.edu.cn/ricenetdb/ database rice The Dfam database is a open collection of Transposable Element DNA sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome annotations. Less... Transposable elements (or interspersed repeats) account for a substantial portion of eukaryotic genomes. Accurate annotation of TEs enables research into their biology and can shed light on the evolutionary processes that shape genomes. Dfam represents a collection of multiple sequence alignments, each containing a set of representative members of a specific transposable element family. These alignments (seed alignments) are used to generate HMMs and consensus sequences for each family. The Dfam website gives information about each family, and provides genome annotations for a collection of core genomes. The HMM models, and consensus sequences may also be downloaded from the ftp site, for example to mask repeats in new genomes. Sat, 29 Jan 2022 16:51:00 -0500 https://www.dfam.org/home database The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models Sat, 29 Jan 2022 16:51:00 -0500 http://rfam.xfam.org/ database Sat, 29 Jan 2022 16:50:00 -0500 http://www.treefam.org/ database animal Use this tool as a guide to the ever-changing landscape of restriction enzymes. REBASE is a dynamic, curated database of restriction enzymes and related proteins. Sat, 29 Jan 2022 16:49:00 -0500 http://rebase.neb.com/rebase/rebase.html database enzyme Sat, 29 Jan 2022 16:49:00 -0500 https://pubmed.ncbi.nlm.nih.gov/?db=PubMed database literature A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein. Sat, 29 Jan 2022 16:48:00 -0500 https://www.ncbi.nlm.nih.gov/refseq/ database Sat, 29 Jan 2022 16:47:00 -0500 https://www.jcvi.org/research/tigrfams database Sat, 29 Jan 2022 16:47:00 -0500 https://tcdb.org/ database Xenopus Sat, 29 Jan 2022 16:46:00 -0500 http://54.244.126.206:9080/entry/ database xenopus A repository for high-quality gene models produced by the manual annotation of vertebrate genomes. Sat, 29 Jan 2022 16:46:00 -0500 https://vega.archive.ensembl.org/index.html database vertebrate genome WheatQTLdb V2.0 is a manually curated QTL database for wheat that includes information about QTL identified through interval mapping and MTA identified using GWAS. The available information on metaQTL, epistatic QTL and candidate genes, wherever available, is also included in the database. Users could browse and download the database to find information regarding the genetic architecture of the traits of interest, which include the following: (i) tolerance to abiotic stresses including drought/water logging/heat/pre-harvest sprouting/salinity; (ii) resistance to biotic stresses including not only viral, bacterial and fungal diseases, but also to infestation by nematodes and insects; (iii) traits for biofortification (Fe/Se/Zn contents); (iv) developmental traits; (v) morphological traits; (vi) N/P/K use efficiency traits; (vii) physiological traits; (viii) quality traits; and (ix) yield and its related traits. WheatQTLdb is the largest web resource having collection of QTL (27,518), metaQTL (1,321), epistatic QTL (202) in Triticum aestivum and 07 other related wheat species to serve the international wheat research community including plant breeders and geneticists for further studies involving fine mapping, cloning and marker assisted selection (MAS) during wheat breeding. Sat, 29 Jan 2022 16:42:00 -0500 http://www.wheatqtldb.net/ database PlantCircNet is the first database that provides plant circRNA-miRNA-gene regulatory networks, as well as circRNA information and circRNA expression profiles. Sat, 29 Jan 2022 16:40:00 -0500 http://bis.zju.edu.cn/plantcircnet/ database plant Sat, 29 Jan 2022 16:39:00 -0500 http://bis.zju.edu.cn/pcernadb/index.jsp database Sat, 29 Jan 2022 16:39:00 -0500 http://bis.zju.edu.cn/MCA/ atlas cell mouse Sat, 29 Jan 2022 16:38:00 -0500 https://www.genecards.org/annotations:eNIKeoB7Eey6lde9IBRoiQ database hume gene dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations. Sat, 29 Jan 2022 16:37:00 -0500 https://www.ncbi.nlm.nih.gov/snp/ database human Essential genes Sat, 29 Jan 2022 16:37:00 -0500 http://origin.tubic.org/deg/public/index.php database gene Sat, 29 Jan 2022 16:35:00 -0500 http://eugenes.org/ database gene genome Microbial https://twitter.com/IMG_DATA Sat, 29 Jan 2022 16:33:00 -0500 https://img.jgi.doe.gov/cgi-bin/m/main.cgi database genome twitter transcription factor binding sites Sat, 29 Jan 2022 16:31:00 -0500 https://jaspar.genereg.net/ database eukaryotes Sat, 29 Jan 2022 16:30:00 -0500 https://www.mitomap.org/MITOMAP database genome human mitochondrial Sat, 29 Jan 2022 16:29:00 -0500 https://gnomad.broadinstitute.org/ database genome Sat, 29 Jan 2022 16:29:00 -0500 https://www.internationalgenome.org/ database genome human Sat, 29 Jan 2022 16:28:00 -0500 https://www.medicinalplantbd.com/ database plant Sat, 29 Jan 2022 16:27:00 -0500 http://www.candidagenome.org/ database candida genome Sat, 29 Jan 2022 16:27:00 -0500 https://agbase.arizona.edu/ database Sat, 29 Jan 2022 16:26:00 -0500 https://disprot.org/ database Sat, 29 Jan 2022 16:24:00 -0500 https://www.ebi.ac.uk/metabolights/ database metabolomic narid:https://www.oxfordjournals.org/nar/database/summary/601 Sat, 29 Jan 2022 16:23:00 -0500 https://www.ncbi.nlm.nih.gov/genome/organelle/ database genome narid:https://www.oxfordjournals.org/nar/database/summary/601 Sat, 29 Jan 2022 16:23:00 -0500 http://labs.mcdb.lsa.umich.edu/organelledb/ database organelle https://www.oxfordjournals.org/nar/database/summary/1115 Sat, 29 Jan 2022 16:22:00 -0500 http://podb.nibb.ac.jp/Organellome/ database plant organelle narid:https://www.oxfordjournals.org/nar/database/summary/722 Sat, 29 Jan 2022 16:21:00 -0500 http://www.plprot.ethz.ch/ database plastid proteome Macromolecul Sat, 29 Jan 2022 16:20:00 -0500 http://jenalib.leibniz-fli.de/ database macromolecul Sat, 29 Jan 2022 16:19:00 -0500 https://clingen.igib.res.in/almena/ database Sat, 29 Jan 2022 16:19:00 -0500 http://cgga.org.cn:9091/gliomasdb/ database Sat, 29 Jan 2022 16:18:00 -0500 http://ciliate.org/index.php/home/welcome database NOTES https://twitter.com/pseudocap https://twitter.com/i/lists/1475461947860688896 Sat, 29 Jan 2022 16:18:00 -0500 https://www.pseudomonas.com/ database pseudomona twitter genome Sat, 29 Jan 2022 16:17:00 -0500 http://plants.ensembl.org/info/website/index.html database plant Sat, 29 Jan 2022 16:15:00 -0500 http://fungi.ensembl.org/index.html database fungus Sat, 29 Jan 2022 16:15:00 -0500 https://www.gramene.org/ database plant Sat, 29 Jan 2022 16:11:00 -0500 https://ecoliwiki.org/colipedia/index.php/Welcome_to_EcoliWiki database ecology nar:https://doi.org/10.1093/nar/gkx1235 narid:https://www.oxfordjournals.org/nar/database/summary/12 Sat, 29 Jan 2022 16:11:00 -0500 http://dbcorc.cam-su.org/ database nar:https://doi.org/10.1093/nar/gkx1235 narid:https://www.oxfordjournals.org/nar/database/summary/20 Sat, 29 Jan 2022 16:10:00 -0500 http://itsonedb.cloud.ba.infn.it/ database narid:https://doi.org/10.1093/nar/gkx1235 Sat, 29 Jan 2022 16:10:00 -0500 https://research.bioinformatics.udel.edu/iptmnet/ database nar:https://doi.org/10.1093/nar/gkx1235 narid:https://www.oxfordjournals.org/nar/database/summary/19 Sat, 29 Jan 2022 16:09:00 -0500 http://icg.big.ac.cn/index.php/Main_Page database nar:https://doi.org/10.1093/nar/gkx1235 narid:https://www.oxfordjournals.org/nar/database/summary/17 Sat, 29 Jan 2022 16:09:00 -0500 http://www.exorbase.org/ database https://www.wikidata.org/wiki/Q8051009 narid:https://www.oxfordjournals.org/nar/database/summary/53 Sat, 29 Jan 2022 16:06:00 -0500 http://www.yeastract.com/ database yeast nar:https://doi.org/10.1093/nar/gkx1235 narid:https://www.oxfordjournals.org/nar/database/summary/54 Sat, 29 Jan 2022 16:06:00 -0500 http://mirandola.iit.cnr.it/ database nar:https://doi.org/10.1093/nar/gkx1235 narid:https://www.oxfordjournals.org/nar/database/summary/27 Sat, 29 Jan 2022 16:05:00 -0500 https://ccg.epfl.ch//mga/ database nar:https://doi.org/10.1093/nar/gkx1235 narid:https://www.oxfordjournals.org/nar/database/summary/26 Sat, 29 Jan 2022 16:05:00 -0500 https://mcube.nju.edu.cn/jwang/lab/soft/mirtrans/ database nar:https://doi.org/10.1093/nar/gkx1235 narid:https://www.oxfordjournals.org/nar/database/summary/24 Sat, 29 Jan 2022 16:04:00 -0500 https://cm.jefferson.edu/MINTbase/ database nar:https://doi.org/10.1093/nar/gkx1235 narid:https://www.oxfordjournals.org/nar/database/summary/23 Sat, 29 Jan 2022 16:04:00 -0500 http://medreader.org/home database nar:https://doi.org/10.1093/nar/gkx1235 narid:https://www.oxfordjournals.org/nar/database/summary/25 Sat, 29 Jan 2022 16:04:00 -0500 https://mircarta.cs.uni-saarland.de/ database nar:https://academic.oup.com/nar/article/49/D1/D1/6059975 nar:https://doi.org/10.1093/nar/gkx1235 narid:https://www.oxfordjournals.org/nar/database/summary/22 Sat, 29 Jan 2022 16:03:00 -0500 https://rmvar.renlab.org/ database Sat, 29 Jan 2022 16:02:00 -0500 https://brp.kfshrc.edu.sa/ared/ database Sat, 29 Jan 2022 16:01:00 -0500 https://www.inaturalist.org/ database citizenscience imagen Sat, 29 Jan 2022 16:01:00 -0500 http://www.reptile-database.org/ database reptil Sat, 29 Jan 2022 15:58:00 -0500 https://www.itis.gov/index.html database Sat, 29 Jan 2022 15:58:00 -0500 http://www.organismnames.com/query.htm database organism Sat, 29 Jan 2022 15:57:00 -0500 http://www.tolweb.org/tree/ database organism Sat, 29 Jan 2022 15:56:00 -0500 https://soil-modeling.org/resources-links/data-portal/fine-root-ecology-database-fred-version-2.0 database ecology NOTES https://twitter.com/iDigBio https://twitter.com/i/lists/1475461947860688896 Sat, 29 Jan 2022 14:37:00 -0500 https://www.idigbio.org/home database specimen imagen Sat, 29 Jan 2022 14:31:00 -0500 https://www.algaebase.org/ database alga world Sat, 29 Jan 2022 14:31:00 -0500 https://avibase.bsc-eoc.org/avibase.jsp?lang=EN database bird world Sat, 29 Jan 2022 14:30:00 -0500 https://bacdive.dsmz.de/ database bacteria   wd:(https://www.wikidata.org/wiki/Q110607004) nar:https://academic.oup.com/nar/article/50/D1/D1/6495890 Sat, 29 Jan 2022 14:27:00 -0500 http://www.biomedical-web.com/covid19db/home database covid-19 drugs Sat, 29 Jan 2022 14:23:00 -0500 https://celltypes.brain-map.org/ database cell Sat, 29 Jan 2022 14:22:00 -0500 https://www.med.harvard.edu/aanlib/ atlas brain NOTES https://twitter.com/WikiPathways https://twitter.com/i/lists/1475461947860688896 Sat, 29 Jan 2022 14:21:00 -0500 https://www.wikipathways.org/index.php/WikiPathways database twitter La Biblioteca de Sonidos de Aves del Museo de Zoología de la Facultad de Ciencias Sat, 29 Jan 2022 14:14:00 -0500 http://biologia.fciencias.unam.mx/BSAMZFC/BSAMZFC.htm database mexico bird sound mirDIP : microRNA Data Integration Portal Sat, 29 Jan 2022 14:11:00 -0500 http://ophid.utoronto.ca/mirDIP/ database Vir-Mir database Sat, 29 Jan 2022 14:08:00 -0500 http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/miRNA.cgi database nar:https://doi.org/10.1093/nar/gkx1235 Sat, 29 Jan 2022 14:01:00 -0500 http://tardis.cgu.edu.tw/msignaturedb/ database Sat, 29 Jan 2022 13:58:00 -0500 http://lncexplore.bmi.nycu.edu.tw/ database cancer Sat, 29 Jan 2022 13:58:00 -0500 http://cnvintegrate.cgm.ntu.edu.tw/ database medicine cancer Sat, 29 Jan 2022 13:57:00 -0500 http://tcm.cmu.edu.tw/ database medicine Sat, 29 Jan 2022 13:46:00 -0500 https://insectcolor.com/about/ database insect 🦋biocolores Sat, 29 Jan 2022 13:45:00 -0500 http://www.reflectance.co.uk/ database plant 🦋biocolores Sat, 29 Jan 2022 13:45:00 -0500 https://data.color.com/ database 🦋biocolores human Sat, 29 Jan 2022 13:43:00 -0500 http://www.hprd.org/ database human protein Sat, 29 Jan 2022 13:43:00 -0500 https://varsome.com/ database human Sat, 29 Jan 2022 13:43:00 -0500 http://bio-bigdata.hrbmu.edu.cn/diseasemeth/ database human Sat, 29 Jan 2022 13:43:00 -0500 http://srv00.recas.ba.infn.it/ASPicDB/ database human Sat, 29 Jan 2022 13:40:00 -0500 https://www.cibnor.gob.mx/investigacion/colecciones-biologicas/coleccion-de-microalgas/listas-de-cepas database mexico alga Sat, 29 Jan 2022 13:39:00 -0500 http://unibio.unam.mx/irekani/ database mexico imagen Sat, 29 Jan 2022 13:38:00 -0500 https://bdlacet.mx/ database mexico alga Sat, 29 Jan 2022 13:37:00 -0500 http://www.conabio.gob.mx/malezasdemexico/2inicio/home-malezas-mexico.htm database plant mexico Sat, 29 Jan 2022 13:29:00 -0500 https://www.gencodegenes.org/human/covid19.html database covid-19 nar:https://academic.oup.com/nar/article/50/D1/D1/6495890 wikidata:https://www.wikidata.org/wiki/Q110607118 Sat, 29 Jan 2022 13:28:00 -0500 https://covid-19.ensembl.org/index.html database covid-19 wikidata nar:https://academic.oup.com/nar/article/50/D1/D1/6495890 wikidata:https://www.wikidata.org/wiki/Q110607139 Sat, 29 Jan 2022 13:28:00 -0500 https://clingen.igib.res.in/esc/ database covid-19 wikidata Sat, 29 Jan 2022 13:27:00 -0500 http://bio-annotation.cn/scovid/ database covid-19 wikidata:https://www.wikidata.org/wiki/Q110607505 nar:https://academic.oup.com/nar/article/50/D1/D1/6495890 Sat, 29 Jan 2022 13:26:00 -0500 https://submission.gpcrmd.org/covid19/home/ database covid-19 wikidata nar:https://academic.oup.com/nar/article/50/D1/D1/6495890 wikidata:https://www.wikidata.org/wiki/Q110607626 Sat, 29 Jan 2022 13:25:00 -0500 https://nmdc.cn/ncovn/ database covid-19 wikidata Sat, 29 Jan 2022 13:25:00 -0500 https://antibodyregistry.org/covid19 database covid-19 nar:https://academic.oup.com/nar/article/49/D1/D1/6059975 wd:https://www.wikidata.org/wiki/Q110584892 nar:Aparece en el artículo pero no lo encuentro en la base de datos dc_subject: "COVID-19" dc_date: 2021 Sat, 29 Jan 2022 13:24:00 -0500 https://covirus.cc/drugs/ database covid-19 wikidata tw:https://twitter.com/covid19RDB Sat, 29 Jan 2022 13:24:00 -0500 https://covid19researchdatabase.org/ database covid-19 twitter Sat, 29 Jan 2022 13:24:00 -0500 https://www.wikipathways.org/index.php/Portal:COVID-19 database covid-19 nar:https://academic.oup.com/nar/article/49/D1/D1/6059975 wd:https://www.wikidata.org/wiki/Q110584966 dc:subject: "COVID-19" dc:date: 2021 Sat, 29 Jan 2022 13:23:00 -0500 https://wan-bioinfo.shinyapps.io/GESS/ database covid-19 https://github.com/lmichan/BioDBS wd:https://www.wikidata.org/wiki/Q110577226 narid:https://www.oxfordjournals.org/nar/database/summary/2224?action=Search§ion=all&term=CoV3D dc_subject:"COVID-19" dc_date:2021 Sat, 29 Jan 2022 13:22:00 -0500 https://cov3d.ibbr.umd.edu/about database covid-19 https://github.com/lmichan/BioDBS   nar:https://academic.oup.com/nar/article/50/D1/D1/6495890   wd:https://www.wikidata.org/wiki/Q110607528   NOTAS:     Falta agregar el artículo de la fuente a wikidata 10.1093/nar/gkab701 Sat, 29 Jan 2022 13:21:00 -0500 https://t-cov.hse.ru/ database covid-19 wikidata Sat, 29 Jan 2022 13:20:00 -0500 https://www.ebi.ac.uk/interpro/proteome/uniprot/UP000464024/ database covid-19 Sat, 29 Jan 2022 13:20:00 -0500 https://www.ncbi.nlm.nih.gov/datasets/coronavirus/genomes/ database covid-19 Sat, 29 Jan 2022 13:16:00 -0500 https://clinicaltrials.gov/ct2/results?cond=COVID-19 database covid-19 literature Sat, 29 Jan 2022 13:16:00 -0500 https://pubmed.ncbi.nlm.nih.gov/?term=covid-19 database covid-19 literature Sat, 29 Jan 2022 13:16:00 -0500 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database covid-19 literature Sat, 29 Jan 2022 13:15:00 -0500 https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism:noexp%5D%20NOT%200[Mbases database covid-19 Sat, 29 Jan 2022 13:14:00 -0500 https://www.britishecologicalsociety.org/publications/journals/journal-of-ecology/biological-flora-database/ database plant Sat, 29 Jan 2022 13:14:00 -0500 http://db.worldagroforestry.org/ database ecology data Sat, 29 Jan 2022 13:13:00 -0500 https://data.esa.org/esa/style/skins/esa/index.jsp database ecology plot Sat, 29 Jan 2022 13:13:00 -0500 http://vegbank.org/vegbank/index.jsp database plant wd:https://www.wikidata.org/wiki/Q901755 narid:https://www.oxfordjournals.org/nar/database/summary/7 Type: Nucleotide Sequence Databases Stats: https://www.ncbi.nlm.nih.gov/genbank/statistics/ Sat, 29 Jan 2022 13:12:00 -0500 https://www.ncbi.nlm.nih.gov/genbank/ database nucleotide meta.analysis Sat, 29 Jan 2022 13:11:00 -0500 https://sesmad.dartmouth.edu/ database ecology Sat, 29 Jan 2022 13:09:00 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covid-19 Sat, 29 Jan 2022 11:35:00 -0500 http://www.animalbase.org/ database Sat, 29 Jan 2022 11:35:00 -0500 http://greencirc.cn/ database Sat, 29 Jan 2022 11:35:00 -0500 http://genolist.pasteur.fr/LegioList/ database Sat, 29 Jan 2022 11:34:00 -0500 http://cpdb.molgen.mpg.de/ database Sat, 29 Jan 2022 11:34:00 -0500 http://genolist.pasteur.fr/TubercuList/ database Sat, 29 Jan 2022 11:34:00 -0500 http://genolist.pasteur.fr/Leproma/ database Sat, 29 Jan 2022 11:33:00 -0500 http://www.peroxisomedb.org/ database Sat, 29 Jan 2022 11:32:00 -0500 https://hsibraindatabase.iuma.ulpgc.es/ database Sat, 29 Jan 2022 11:32:00 -0500 https://www.proteinatlas.org/humanproteome/brain database Sat, 29 Jan 2022 11:32:00 -0500 https://www.brainsimagebank.ac.uk/ database Sat, 29 Jan 2022 11:31:00 -0500 https://brainweb.bic.mni.mcgill.ca/ database Sat, 29 Jan 2022 11:31:00 -0500 https://primatedatabase.com/ database Sat, 29 Jan 2022 11:31:00 -0500 https://db.humanconnectome.org/app/template/Login.vm database 🔐close Sat, 29 Jan 2022 11:31:00 -0500 https://neurodata.io/project/connectomes/ database Sat, 29 Jan 2022 11:28:00 -0500 https://nucleus.iaea.org/sites/naipc/ididas/Pages/Browse-IDIDAS.aspx database Sat, 29 Jan 2022 11:28:00 -0500 https://www.brc.ac.uk/dbif/ database Sat, 29 Jan 2022 11:28:00 -0500 https://www.entsoc.org/publications/common-names database Sat, 29 Jan 2022 11:27:00 -0500 https://insectbraindb.org/app/ database Sat, 29 Jan 2022 11:26:00 -0500 https://data.nal.usda.gov/dataset/us-national-insect-collection-database database Sat, 29 Jan 2022 11:21:00 -0500 https://gullstothehorizon.wordpress.com/tag/marked-bird-database/ database Sat, 29 Jan 2022 11:21:00 -0500 https://www.insectimages.org/ database Sat, 29 Jan 2022 11:20:00 -0500 https://birdsoftheworld.org/bow/home database Sat, 29 Jan 2022 11:18:00 -0500 http://www.restoration-ecology.eu/databases/ database Sat, 29 Jan 2022 04:35:00 -0500 http://covdb.popgenetics.net/v3/ database covid-19 Sat, 29 Jan 2022 03:44:00 -0500 https://www.ncbi.nlm.nih.gov/labs/virus/vssi/ database covid-19 virus wd:https://www.wikidata.org/wiki/Q172266 tw:https://twitter.com/BioDivLibrary Fri, 19 Feb 2021 04:47:00 -0500 https://www.biodiversitylibrary.org/ database literature "The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. An unprecedented number of scientific efforts are taking place worldwide in order to help combat the new coronavirus epidemic (COVID-19). One of the biggest challenges in this fast-moving situation is to share data and findings in a coordinated way, in order to understand the disease and to develop treatments and vaccines. To address this challenge, EMBL-EBI and partners have has set up the COVID-19 Data Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. The COVID-19 Data Portal will enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into the functions of a wider project, the European COVID-19 Data Platform....   Tue, 21 Apr 2020 14:29:00 -0400 https://www.covid19dataportal.org/ database covid-19 "LitCovid is a curated literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus. It is the most comprehensive resource on the subject, providing a central access to 1121 (and growing) research articles in PubMed. The articles are updated daily and are further categorized by different research topics and geographic locations for improved access...." nar:https://academic.oup.com/nar/article/49/D1/D1/6059975 wd:https://www.wikidata.org/wiki/Q107654190 narid:(https://www.oxfordjournals.org/nar/database/summary/2261?action=Search§ion=all&term=litcovid dc_subject: "COVID-19" dc_date: 2021 Mon, 16 Mar 2020 14:23:00 -0400 https://www.ncbi.nlm.nih.gov/research/coronavirus/ database covid-19 "bioRxiv (pronounced "bio-archive") is a free online archive and distribution service for unpublished preprints in the life sciences. It is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals...." Sat, 14 Apr 2018 14:11:00 -0400 https://www.biorxiv.org/ database literature "A preprint archive for Paleontology." Sat, 14 Apr 2018 14:08:00 -0400 https://paleorxiv.org/ database literature fossil "The Human Protein Atlas is a Swedish-based program initiated in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome....The Human Protein Atlas program has already contributed to several thousands of publications in the field of human biology and disease and it is selected by the organization ELIXIR (www.elixir-europe.org) as a European core resource due to its fundamental importance for a wider life science community. The Human Protein Atlas consortium is funded by the Knut and Alice Wallenberg Foundation...." Fri, 15 Dec 2017 03:42:00 -0500 https://www.proteinatlas.org/ atlas human protein