Compiles information related to the inter-individual gene expression variability through a diurnal cycle for individual genes in Arabidopsis thaliana. AraNoisy consists of a repository providing results of an analysis of 14 seedlings at each of the 12 time-points that have generate more than 160 transcriptomes. It allows users to investigate any inter-individual gene expression variability in genes of interest.
AtFusionDB / Arabidopsis Thaliana fusion Transcript DataBase
Consists of a knowledge base for fusion transcripts predicted in the model plant Arabidopsis thaliana. AtFusionDB contains more than 82,000 fusion transcript entries generated from about 17,180 different genes of A. thaliana. It also includes some additional data such as UniProt, gene coordinates, the function of parental genes, or junction sequence. The database also provides three modules for mapping and alignment of the query sequences: BLASTN, SW Align and Mapping.
Compiles information related to biological relationships. iBioGuide provides a repository of networks gathered by the Advaita company. This platform supplies a free-text search engine allowing queries by gene, pathway, miRNAs, gene ontology or diseases, where data can be filtered by organisms. Result page displays advanced information about a gene and its corresponding literature as well as panels allowing users to see which biological processes, molecular functions, cellular components, miRNAs, pathways, drugs or diseases can be linked to a given gene.
Provides a relational database for peripheral membrane proteins in eukaryotes. PerMemDB is a repository of data for eukaryotic peripheral membrane proteins deposited in UniProt or predicted with the use of MBPpred, a computational method specialized in the detection of proteins that interact non-covalently with membrane lipids, via membrane binding domains.
SDRED / Short‐chain Dehydrogenases/Reductases Engineering Database
Compiles information about short-chain dehydrogenases/reductases. SDRED consists of a repository of more than 168000 records, providing data on sequence, structure and function as well as taxonomic information. Users can download or visualize sequence, alignment or tree related to a target protein organized in 4 browsable super-families: classical, extended, intermediate and divergent.
Assists users in supporting rational drug development projects. eModel-BDB is an online database of comparative models of drug-bound proteins based on interaction data. These data can directly aid structure-based drug discovery pipelines and protein function analysis by providing atomic-level models of a large set of drug-protein interactions with known affinities.
Aims to provide a functional circRNA resource including experimentally validated and computationally predicted functions. CircFunBase is based on 7000 manually curated functional circRNA entries, mainly including Homo sapiens, Mus musculus etc. providing the visualization of circRNA-miRNA interaction networks. This tool serves as a more specific functional circRNA resource to efficiently investigate, browse a particular circRNA and provide insights into its function
Gathers information about zinc binding sites. ZincBind assists users in detecting instance of zinc binding to a protein and its binding site as well as clusters sites based on 90% sequence identity. This database hosts over 24 000 binding sites, clustered into about 7400 unique sites. Additionally, all the data contained in the database can be browsed and downloaded.
RadishGD / Radish Genome Database
Provides a radish genome database. RadishGD comprises several units: 1) a search unit providing gene structures and sequences, 2) a genome browser displaying graphic representations of gene models, mRNAs, repetitive sequences, genome-wide methylation and variomes, 3) an annotation unit that offers gene ontology, plant ontology, pathway and gene family information, 4) a genetic map unit providing information about markers and their genetic locations, and 5) expression units presenting transcriptional characteristics and methylation levels for each gene in tissues.
Offers a database of prokaryotic riboswitches. RiboD allows users to query a list of riboswitches based on a variety of search criteria and generates a table listing all riboswitches matching the query along with information about their genomic location and regulated gene/operon. This resource was developed to assist users in understanding riboswitch-based gene regulation in bacteria and archaea.
PFDB / Protein Folding kinetics Database
Stores single-domain globular proteins. PFDB is a large database of protein folding kinetics using as a standard for the developemnt of future predictive and theoretical studies of protein folding. This database consists of more than 140 (about 80 two-state and 50 non-two-state) single-domain globular proteins.
MIGREW / Molecular Identification of Genes for Resistance in Wheat
Catalogues information serving the interests of Russian wheat pathologists and breeders. MIGREW provides information assisting users in improving the potentials of national wheat breeding for immunity to rusts and powdery mildew. This resources focuses on effectiveness of wheat resistance genes in different regions of Russia.
PathCase-SB / PathCase Systems Biology
Provides a resource to facilitate the development of kinetic models for biological systems. PathCase-SB aims to integrate systems biology models data and metabolic network data of selected biological data sources. It includes multiple interfaces to visualize networks of models and/or pathways, to browse models and pathways, to query models and pathways, to comparatively simulate models, and to compose models from existing samples.
Collects information about cancer from public internet. Web Plus is a web-based application offering three functions: follow-back efforts, file upload and download, and online abstracting. This database allows uploading of abstracts generated from death certificate and pathology lab files partially filled abstracts generated from death certificate and pathology lab files.
Provides access to evidence-based information about vaccines and vaccination. ReadyVax is a mobile smartphone app for healthcare providers, pharmacists, and patients. This resource contains data about vaccines and the diseases they prevent, vaccine recommendations, and vaccine safety. Users can be notified of important vaccine information. It can also be used in the event of an emergency to empower public health authorities to convey messages to target populations. ReadyVax is available for download in the Apple iTunes app store.
Consists in a central registry database program. CRS Plus provides features such as comparison of incoming and stored data, management reports, automated preparation of files for national calls for data or exporting records in North American Association of Central Cancer Registries (NAACCR) format.
SPARCS data interactive visualization
Allows visualization of patient level data from hospitals in the United States of America. SPARCS data interactive visualization presents inpatient deidentified dataset of discharge level detail on patient characteristics, diagnoses, treatments, services and charges. The data can be filtered by county and several types of information are provided, such as gender, type of admission, diagnosis group, length of stay, payment sources, age group, severity of illness or diagnosis.
Offers access to users working with cancer data to standard coding instructions from multiple sources. Online Help is a resource containing a collection of cross-referenced, indexed, and context-linked standard coding manuals, with the aims to reduce the need for reference to printed manuals during abstracting. It is annually updated with the latest published version of the included manuals, plus published errata or additions.
Allows users to download genome and assembly reports from NCBI. genomes can extract the genus name and the species name from a scientific name, removal of single quotes, brackets and candidate qualifiers.
Enables users to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. GA4GHshiny also integrates with Beacon Network.
Compiles information related to gene flow, breeding systems, genetic diversity and population structure for a range of tropical trees important to rural communities. tropiTree gathers expressed transcripts, their related microsatellites and primer pairs, coupled with a model for presenting tree next generation sequencing (NGS) data. This repository can be used for presenting large data sets or single-nucleotide polymorphism (SNP) discovery in the sequenced species.
Contains presumably all compounds for which the antiviral activity or viral protein binding was measured at least once. ViralDB stores antiviral activity data from ChEMBL obtained via a semi-automatic procedure extraction. These data were annotated by virus taxa according to International Committee for Taxonomy of Viruses (ICTV) taxonomy, and compound structures and activity values were standardized to obtain antiviral activity profile for each compound.
Provides a manually curated database of around experimentally verified immunosuppressive peptides compiled from research article and patents. ImmunoSPdb is an online resource that contains peptides having natural, protein derived or synthetic origin. Users can browse on major significant fields such as (i) category of peptides, (ii) modification of peptides, (iii) peptide length, (iv) assay type, and (v) target.
Compiles data about more than 8000 small molecules that interact with Leishmania sp. LeishInDB is a manually curated database aiming at assisting users in choosing and repurposing compounds, to investigate new therapeutics. It includes information about activity details and protein target. Searches can be made by IC50 range, enzyme, organism, experiment type, predicted oral toxicity or predicted carcinogenicity.
Gathers information about rice blast and bacterial blight (BB) responsive genes (RGs). RiceMetaSysB consists of a repository that exploits meta-analysis of publicly available microarray experiments with the aim of determining the most robust genes for rice blast and BB diseases. It includes features for physical position and simple sequence repeats (SSRs) search. It can be used by breeders, pathologists and molecular biologists.
3D Genome Browser
Stores and queries genomic data in a 3D space. 3D Genome Browser is an online resource that includes two components: (i) a database to store and query the 3D genomic data, and (ii) a web-based genome browser to visualize and navigate 3D genome structures. Users can access and visualize data via a GUI, allowing to navigate through the structure in real-time, fetching genomic data as well as high-resolution 3D meshes representing the DNA backbone from the server.
LIVE / LncRNA Interaction Validated Encyclopaedia
Provides interactions of long noncoding RNAs (lncRNAs) with genes, proteins, ncRNAs, transcription factors and diseases in humans and mice. LIVE is an online resource that was developed by mining and manually curating publications to extract experimentally validated interactions. This database also includes search engines and interactive visualization tools.
Provides genotypic and phenotypic information from almost 50 000 individuals who were sequenced for 30 genes associated with hereditary cancer. Color Data is a cloud-based database that focuses on genotypic–phenotypic correlations in hereditary cancer in an aggregated population and includes information of genes, variants and classifications, as well as personal and family history of cancer.
Consists of a corpus of naturally-occurring non-handcrafted sentence pairs within the subject of regulation of gene expression in E. coli K-12 literature. Corpus-Transcriptional-Regulation was used as training and evaluation source of truth for Natural Language Processing (NLP) tools.
Consists of a genome-scale kinetic model of Escherichia coli metabolism that approaches genome-scale coverage. k-ecoli457 contains about 450 model reactions, 330 metabolites and 290 substrate-level regulatory interactions. It was parameterized by combining a machine-learning algorithm and the ensemble modelling (EM formalism). This model can be used to predict genetically perturbed E. coli phenotypes under different growth conditions.
BIRI / BioInformatics Resource Inventory
Enables automaticdiscovering and indexing of available public bioinformatics resources using information extracted from the scientific literature. BIRI is a public online searchable index of bioinformatics resources annotated with metadata regarding their functionality. The index is automatically updated by analyzing new papers describing resources such as databases, tools or services.
Aims to facilitate the storage and retrieval of phylogenetic data. CDAO-Store is an RDF-based store of phylogenetic data, including a complete import of TreeBASE. This repository is composed of three modules: (i) a data importer module for importing phylogenies and their related data into the repository, (ii) a repository module for storage and querying, and (iii) an exporter module allowing users to interact with the repository and providing a way to visualize the stored data.
Provides files for mapping between NCBI taxonomy ID and species.
Consists of an abbreviation dictionary automatically constructed from MEDLINE. Acromine is a dictionary of common acronyms and their expanded forms, which identifies abbreviation definitions by assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form. It extracted about 68,000 abbreviation candidates and recognized more around 467,400 expanded forms.
Serves to investigate and categorize field of academic access research repositories. OpenDOAR enables users to identify, browse and search for repositories on the basis of features such as location, software or type of material. It only collects and offers information about sites which provide open access to full text resources that are of use to academic researchers. Other types of data, like images or data-sets having metadata or documentation are also listed.
Predicts potential interaction between miRNA and disease for further biological experiments.MDPredict is a database using the following biological information: the miRNA family information, miRNA cluster information, experimentally valid miRNA-target association and disease-miRNA information.
Enables exploration of the patent domain. LifeQuest uses common life science ontologies such as MeSH, SNOMEDCT, and phenotype/trait ontologies for allowing users to search the entire global life science patent domain. The obtained set of documents can be saved as a “workfile”, where users can drill into document details and annotations.
AOE / All Of gene Expression
TISIDB / Tumor and Immune System Interaction Database
AICD / Anti-Inflammatory Compounds Database
DEE2 / Digital Expression Explorer 2
HuVarBase / HUmanVARiantdataBASE
MGD / Mouse Genome Database
EMIL / Example Mediated Innovation for Lead Evolution
Pre-clinical Safety Store
Essential Science Indicators
MAdb / Mammalian Annotation Database
CasPDB / Cas Protein Data Bank
PPTdb / Pathogenic Protist Transmembrane database
sAOP / stressor AOP
ASFVdb / African Swine Fever Database
CCRDB / Cancer circRNAs-related Database
lncRNAKB / long non-coding RNA KnowledgeBase
Protein Homeostatis Database
TACCO / Transcriptome Alterations in CanCer Omnibus
TCGD / Tetrahymena Comparative Genomics Database
TCR3d / T cell Receptors
The Terabase Search Engine
GSDB / Genome Structure DataBase
Permits users to improve the epitope analysis in the context of organ transplantation by providing the 3D structures of HLA molecules present in current solid phase assays for serum antibodies screening.
MepmiRDB / Medicinal plant microRNA DataBase
MolMeDB / Molecules on Membranes Database
PTSDDB / Post-Traumatic Stress Disorder DataBase
SAPdb / Self-Assembly of short Peptides DataBase