Platform

Who uses us

Company
DrugCombDB / Drug Combination DataBase
Provides integrated drug combinations from various data sources. DrugCombDB is a comprehensive database that offers 1) high-throughput screening assays of drug combinations, 2) external databases, and 3) manual curations from PubMed literature. In total, this resource includes almost 1,128,000 experimental data points with quantitative dose response and concentrations of drug combinations covering more of 560 unique drugs and a hundred of human cancer cell lines.
AmyCo / Amyloidoses Collection
Provides a collection of amyloidoses and clinical disorders data related to amyloid deposition. AmyCo is an online resource that classifies more than 70 diseases associated with amyloid deposition into two distinct categories: 1) amyloidosis and 2) clinical conditions associated with amyloidosis. Each database entry is annotated with the major protein component (causative protein), other components of amyloid deposits and affected tissues or organs.
ENPD / Eukaryotic Nucleic acid binding Protein Database
Provides a library of nucleic acid binding proteins (NBPs) and their functional information. ENPD is based on manual curation and a pipeline that utilizes both sequenced transcriptomes and genomes. It records 2.8 million of NBPs and their binding motifs from more than 660 NBP families and almost 2420 species. It also focuses on the involvements of DNA binding proteins (DBPs), RNA binding proteins (RBPs), and DNA and RNA binding proteins (DRBPs) in non-coding RNA (ncRNA) mediated gene regulation.
ONCO.IO
Consists of an integrative resource for microRNA and transcription factors analysis in cancer. ONCO.IO enables users to explore complex gene regulatory networks involved in cancer. This database contains data based on the manually curated annotation of experimentally verified molecular interactions described in the literature. It includes microRNAs, lncRNAs, mRNAs, signaling proteins and transcription factors interactions. Network analysis tools are also available.
DVD / Deafness Variation Database
Provides a guide to genetic variation in genes known to be associated with deafness. DVD is a database that classifies and interprets variants in more of 150 genes and microRNAs implicated in genetic hearing loss. This resource is collated from major public databases. It provides a single classification for each variant based on collected evidence and is curated by experts in genetic hearing loss to provide a single-source guide to variant interpretation.
ResMarkerDB
Assists users with monoclonal antibody therapy in breast and colorectal cancer. ResMarkerDB is a database of biomarkers that enables the prediction of patients’ clinical outcome after treatment. This resource focuses on food and drug administration (FDA) approved antibodies: anti- epidermal growth factor receptor (EGFR) and anti- vascular endothelial growth factor (VEGF) antibodies, two wild-type mutations in the Kirsten-RAS (KRAS) and neuroblastoma-RAS (NRAS) colorectal cancer, and anti-HER2 antibodies for HER2-positive breast cancer.
Proçodic / Protein Concepts Dictionary
Aims to understand the fundamental principles of protein structure. Proçodic is a comprehensive online resource that correlates concepts with ligand binding sites to suggest function. It also applies sequence conservation observed within concepts to protein structure prediction. It allows the exploration of any structure or specific concepts provided by the user including the usages of concepts in other structures, both homologous and non-homologous or the inspection of frequently occurring keywords.
NRPPUR / Non-Ribosomal Peptide and Polyketide Urmite
Detects polyketides (PKS) and non-ribosomal peptide gene clusters (NRPS) in bacterial genomes. NRPPUR is a database that permits to make functional annotation using reverse position-specific BLAST (RPS-BLAST), in order to decipher NRPS-PKS biosynthetic gene clusters (BGCs). This application can be useful for the primary in silico selection of species with potential antimicrobial activity.
VIETHERB
Provides a database for herbs documented in Vietnamese traditional medicines. VIETHERB is a resource built to provide users with information about herbs and other side information including metabolites, diseases, morphologies, and geographical locations for each individual species. It consists of more than 2800 species, 10800 metabolites, 450 geographical locations, and 8000 therapeutic effects.
exRNA atlas
Provides a data repository of the extracellular RNA communication consortium (ERCC). exRNA Atlas is an online resource that includes exRNA profiles derived from various biofluids and conditions. This database stores data profiled from small RNA sequencing assays. The provided information can be analyzed in the context of source genomes (human and non-human), subtypes of RNA species within these genomes, and specific biological pathways and networks within cell types of origin and target cells.
OxyDB / Oxytricha Genome Database
Provides information on the genome, genes, and proteins of Oxytricha. OxyDB is an online database of information about the Oxytricha trifallax genome sequence. This resource is based on analyses performed at Princeton University, scientific literature published by the Oxytricha research community, and other sources.
StyloDB / Stylonychia Genome Database
Gathers genomic information about Stylonychia lemnae. StyloDB consists of a repository displaying data related to genes and proteins. The platform proposes set of genes with specifications about their gene ontology annotation, domains, gene expression profiles, homologs or the associated publications. This database is part of the Ciliate.org project.
IchDB / Ichthyophthirius Genome Database
Provides information about the Ichthyophthirius genome sequence. IchDB is an online resource that includes information on the genome, genes, and proteins of the ciliated protozoan Ichthyophthirius multifiliis collected from scientific literature, the research community, and other sources.
BIOLITMAP
Assists researchers, grant agencies and general public in evaluating the progress in bioinformatics. BIOLITMAP is an online geolocation system that allows exploration of the publications by institution, year and topic. This resource provides users with a visual and interactive way to navigate over the information to find scientific publications based on a period of time, journal, topic and institution, order them, as well as visualize the articles, print the search results and see the related statistics.
BaiHui
Provides a brain-specific functional gene network. BaiHui is an online resource that allows users to query networks of their genes of interest, visualize the resulting local networks, gain functional insight from enrichment analysis and download network data. It can be used to generate hypotheses about disease candidate genes of brain disorders including Parkinson’s disease (PD) and Alzheimer’s disease (AD).
HeartBioPortal
Gathers information on human cardiovascular diseases. HeartBioPortal provides community support for issuing gene/disease/variant-specific requests and visualizing the search results in a multiomics context. This database features gene expression, genetic association and ancestry allele frequency information for over 6000 variants in 22800 human genes, across 12 broadly defined cardiovascular diseases spanning at least 240 research studies.
PPICurator
Mines protein-protein interactions (PPIs) and their information from literature. PPICurator automates the extraction of PPI information, including PPI relations, as well as their confidential scores, interaction directions, effects and functional annotations. This resource is composed of four functional modules: (1) the "abstract localization & update" module, (2) the "retrieval & filter" module, (3) the "PPI information extraction & enrichment" module and (4) the "output & visualization" module.
EXtrACtor
Allows multiple queries in ExAC and gnomAD databases and processing of the results. EXtrACtor is an application that enables users either to upload a list of gene-names, locations or transcripts, or to enter them manually when querying a single or a limited number of terms. It then queries the ExAC or gnomAD website for the data which would normally be returned in the browser, such as variation data or coverage information.
ReLiance
Gathers information related to putative protein partner, or score serving for a prediction (hugo names, swissprot ids, PDB entries). ReLiance accepts as input annotated and enriched on-the-fly using the reflect API. Additionally, a mouse-click function is applied to the highlighted proteins and genes to generate informative pop-up windows hosting information where the specific bio-entities from public databases are summarized.
DEAP / Database for Emotion Analysis using Physiological Signals
Assists users in performing emotion analysis using physiological signals. DEAP is an online repository that explores the possibility of classifying emotion dimensions induced by showing music videos to different users. The data hosted in this database is intended to show the impact of images, music or non-musical video segments on people. Different types of data can be download by researchers such as: metadata, physiological recordings, or video recordings.
RICD / Rice Indica cDNA Database
Deals with information related to indica complementary DNA (cDNA) clones and their sequences in rice. RICD intends to furnish data to facilitate research about rice functional or comparative genomics research. The repository provides multiple searching features including by BLAST, keywords or chromosomes position. The database displays a three-parts page about each clone that gathers general information, sequence and related open reading frame (ORF) information, single nucleotide polymorphisms (SNPs) and InDels information, and the results of similarity search.
CORD / CO-Regulation Database
Offers a platform allowing users to query and identify in which gene expression datasets a given gene is differentially expressed. CORD is a repository gathering characteristics of gene expression data, curated from about 9000 microarrays datasets derived from ArrayExpress and GEO. This repository can also be used for the determination of genes that are coordinately expressed with a gene of interest. For each query, the application generates an Excel file directly sent to the user's mailbox.
CytokineDB
Provides an access to cytokines and chemokines for researchers working in immunological laboratories and for other users of scientific discipline. CytokineDB is as annotated dabatase that collects biological information from cytokines family in human.
ZwolinskiEtAl2010
Contains record of 23 patients with severe epilepsy caused by different organic lesions. This database can be used for both: 1) evaluation of the currently available electroencephalography (EEG) Inverse Solutions performance as an auxiliary tool and, 2) comparing stability and accuracy of the plethora of difference EEG Inverse Solutions.
KimEtAl2012
Gathers genome information about agricultural plants. This database consists of multiple layer architecture which can be accessed using a web-based graphical interface. It has six major categories: genome research, gene expression, rice mutant, analysis tools, genome annotation, and other sub-databases. It aims to assist biologists in studying biological function based on sequences of genomes of rice (Oryza sativa), Chinese cabbage (Brassica rapa), microbes, and viral genome.
CBS / Conserved regulatory Binding Sites
Contains predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes. CBS is an online database that supplies tools for the data mining of individual sequences and groups of co-expressed genes with epigenomics information. Additionally, this resource can be useful for depicting functional sequences and conducting in silico regulatory screenings of target genes reported in high-throughput expression experiments.
[email protected]
Consists of an electronic reporting system for surveillance of notifiable infectious diseases. [email protected] is designed as a dynamic, relational database composed of about 70 reporting categories with more than 600 fields and about 7000 predefined entry values in look-up fields. Its integrated version management system documents deletion, undeletion, completion and correction of cases at any time and entry level and allows reproduction of previously conducted queries. This system can be useful for reporting cases and outbreaks of notifiable infectious diseases.
DarwishEtAl2016
Consists of a database for Phomopsis longicolla isolate MSPL 10-6. This repository contains the genome sequence of P. longicolla MSPL 10-6 and the 16,597 genes that were annotated. It provides information about the genome assemblies (contigs), gene models, gene descriptions and GO functional ontologies. This database can serve for research and agricultural communities and can assist in the development of control strategies for this pathogen.
EVEE Gene Browser / EVolutionary Estimates of Expression Gene Browser
Furnishes information assisting users in analyzing expression evolution across species. EVEE Gene Browser works co-jointly with a toolkit that permits researchers to identify expression pathways under neutral, stabilizing, and directional selection, and quantify the extent of selective pressure on a gene’s expression.
SigPath
Aims to support quantitative studies on the signaling pathways and networks of the cell. SigPath is an information system that includes (i) the use of background information such as names of molecules, aliases, and accession codes, (ii) a strategy to allow refinement of information over time by multiple users, (iii) the development of a data representation that stores both qualitative and quantitative information, and (iv) features to assist contributors and users in assembling custom quantitative models.
Ozymandias
Provides data for the Australian fauna. Ozymandias is an online biodiversity knowledge graph that offers a classification of animals from the atlas of living Australia (ALA) combined with data on taxonomic names and publications from the Australian faunal directory (AFD). It includes several entities such as taxa, publications, people, places, specimens, sequences, and institutions.
CARGO / Cancer And Related Genes Online
Aims to facilitate, integrate and visualize results from Internet resources, independently of their native format or access method. CARGO is a configurable biological web portal that uses a gene-based querying procedure that activates a number of small software agents to retrieve, relate and display relevant information. This application provides information obtained from several data sources such as Ensembl, CPATH, dbSNP, OMIM or iHOP.
AgBioData
Gathers multiple databases dealing with agricultural resources. AgBioData intends to propose standardized information for more than 30 repositories, such as Planteome, Soybase, Araport or CassavaBase. It aims to provide a facilitated access to curated and integrated data as well as to analysis and visualization tools to aid scientific discovery, translation and application. The platform also includes multiple forums and working groups.
KKB / Kinase KnowledgeBase
Gathers kinase structure-activity and chemical synthesis data. KKB is an online database that represents a gene-family wide implementation of the Eidogen-Sertanty's web-based technology for the capture, curation, and the visualization of biological activity and chemical synthesis data from scientific literature and patents. It is designed to support medicinal chemists during all project stages of drug discovery.
OGOB / Oomycete Gene Order Browser
Facilitates comparative genomic and syntenic analyses of Oomycete species. OGOB allows users to visualize orthology and synteny between a wide range of oomycetes. This resource hosts curated orthologs and syntenologs and provides bioinformatics tools to perform for instance homology searches, gene finding, multiple sequence alignments, evolutionary rates analysis, or phylogeny construction. Several plant and animal pathogenic oomycete species are available, including Phytophthora, Pythium, Plasmopara, Phytopythium, Albugo, Aphanomyces, Saprolegnia and downy mildews.
Model discovery
Browses models of interest and displays the annotated information through a web platform. Model discovery allows users to explore models through the Physiome Model Repository (PMR), encoded in CellML. Searches can be made by multiple options such as CellML model entity, by name of the model, the component, the variable or the protein as well as by species and genes used during experiments associated to these models.
TCGA Premier
Provides copy number information from The Cancer Genome Atlas (TCGA). TCGA Premier offers access to curated copy number variations (CNVs) and sequence variants by re-analyzing TCGA data and manually curating the results of each sample by trained scientists. It enables users to query the database, retrieve samples of interest along with annotations, and perform further analysis. The data can be useful for studies such as survival analysis or tumor sub-type profiling.
CentoMD
Compiles information related to mutations in rare diseases. CentoMD consists of a repository leaning on the curation of clinical diagnosis recorded about individuals from heterogenous geographical distribution. This database can be used for molecular biology applications and proposes variants that have been assessed according to the American college of medical genetics and genomics (ACMG) guidelines.
Nexus DB
Consists of a searchable reference data built for nexus integration. Nexus DB is a database that permits users to host their data thanks to the Amazon’s AWS platform. This platform is configured in such a way that users can perform query by gene or region of interest to find samples and clinical annotations. Additionally, this repository includes an option to share data with selected people.
CanDiD / Cancer Diagnostic Database
Compiles more than 11000 variants and their corresponding annotations. CanDiD consists of a repository aiming at assisting users in diagnosis, with a focus on cancer diagnosis. It includes functions allowing personalized queries to filter variant by preferred transcripts, targeted zones or according its frequency in a database or interest. This database can also be queried from a Django API.
SWISS-2DPAGE
Collects data on proteins identified on various 1-DE and 2-DE maps. SWISS-2DPAGE is an online resource available for nonprofit organizations. Users can search by description, by accession number, by clicking on a spot, by author, by spot serial number, by experimental pI/Mw range, by experimental identification methods, by full text search, or by reference map. In addition, entries can be reached through 2-D gel analysis software such as ImageMaster 2D Platinum.
PLDB / Protein-Ligand Database
Detects trends and patterns in structural data. PLDB aims to simplify statistical analysis of protein-ligand structures on a protein data bank (PDB)-wide scale. This database contains the full PDB dataset that has been processed using a validated scientific workflow employing multiple Schrödinger’s technologies. Additionally, users can search for standard protein-ligand interactions, hydrogen bonds, pi-pi interactions, and salt bridges.
SpliProt3D
Consists of a database of proteins structures of the human spliceosome. SpliProt3D allows users to browse, select and download representative models determined by experimental methods, and theoretical models built with computational methods. In this platform, proteins are associated with sequence alignments annotated with predictions of intrinsic order versus disorder, predictions of secondary structure, protein-binding disorder, solvent accessibility and coiled-coils.
ChemDBS
Enables users to search chemical compounds for structure recognition and similarity. ChemDBS is a database search tool that provides a chemoinformatics based approach to drug discovery and also completes the ligand-based approach to discovery. It permits users to derive information from databases that leads to knowledge about chemically matching structures that can serve for replacement or modification of existing known chemical form. This resource can be queried in the form of descriptors, 2D template, 3D template, pharmacophore or molecular fingerprints.
Accelrys ACD / Accelrys Available Chemicals Directory
Provides a resource for chemical sourcing in pharmaceutical, biotechnology, chemical, and agrochemical companies. Accelrys ACD permits users to (i) identify and locate commercial sources, (ii) make side-by-side comparisons of purity, quantity and price, (iii) save valuable time by accessing information from a single source, and (iv) identify the optimal set of compounds for a synthesis or library.
MolCart
Allows researchers to host large chemical compound libraries for searching and analysis. MolCart enables research using smiles and smarts patterns, fingerprint similarity, similarity/substructure comb and exact match. It also permits to search by set of text fields or numerical data.
BuruList
Focuses on the analysis of the genome of Mycobacterium ulcerans, the Buruli ulcer bacillus. BuruList is a database that provides access to DNA and protein sequences derived from the epidemic strain Agy99, linked to the relevant annotations and functional assignments. It is composed of three frames containing: (1) the controls to carry out usual queries, (2) different types of information such as the chromosome figure of M. ulcerans or the list of genes; and (3) detailed information about a given gene.
GoSynthetic
Enables the analysis of biological processes applying a hierarchical database. GoSynthetic is a resource for understanding, designing and modifying molecular processes. This platform contains different organisms and different data sources including several model organisms as well as more than one million proteins, along with crosslinks to external databases. It offers several searching and visualization possibilities.
SBPkb
Enables querying and retrieval of standard biological parts for research and use in synthetic biology. SBPkb is a publically accessible Semantic Web resource for synthetic biology that was built on knowledge from the Registry of Standard Biological Parts adapted and transformed from the registry into SBOL-semantic. This resource can be queried using standard RDF technology (SPARQL queries) to retrieve parts that can be relevant to a synthetic biologist.
Gene ORGANizer
Links human genes to the body parts they affect. Gene ORGANizer is built upon a curated database that relives over 7,000 genes to about 150 anatomical parts using more than 150,000 gene-organ associations. This platform permits analysis of the anatomical effects of individual genes, and identification of trends within groups of genes. Additionally, it can be used to make new discoveries and to study the phenotypic effects of genes.
PDBeMotif
Facilitates the exploration of the Protein Data Bank (PDB). PDBeMotif is a search tools allowing users to combining protein sequence, chemical structure and 3D data in a single search. This resource can serve for studying characteristics of the binding sites of single proteins or classes of proteins, such as kinases and the conserved structural features of their immediate environments, either within the same specie or across different species. It can be used online or downloaded and installed locally.
D360
Proposes a data retrieval platform. D360 includes functions for data filtering, exploration and visualization. This program permits users to create project dashboards and to formulate complex queries without important specifications about data localization. It also incorporates tools and supports for virtual compounds as well as features for real and conceptual compound prioritization.
PhosPhAt
Provides information about Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments by different research groups. PhosPhAt is a resource allowing users to search for experimental and predicted phosphorylation sites of individual proteins, as well as for known substrates for a given kinase or kinase family. A motif search function is also available, and experimentally determined and predicted phosphorylation hotspots are hosted in the database and highlighted in the protein sequence view.
D360 Express
Proposes a data retrieval platform. D360Express gathers several external and internal sources to provides a unified access to researchers of a given organization. This software proposes features for (i) data filtering and exploration; (ii) structure visualization; (iii) a scientific literature search module; (iv) tools and support for virtual compounds, such as an ability for real and conceptual compound prioritization.
PCSS / Pre-clinical Safety Store
Allows users to upload, validate and match pre-clinical study data for desired terminology. PCSS is a program made for study managers, toxicologists, pathologists, and data scientists. It can capture and query file-based pre-clinical study data based upon the CDISC SEND standards. It can also serve for mapping alternate names for scientifically equivalent tests to preferred terms using a terminology tool.
Clinical Trial Outcomes Databases
Allows users to improve exploitation of external therapeutic data. Clinical Trial Outcomes Databases gathers, formates, and standardizes several types of medical data. It can provide information, for instance, on the topics of oncology and immunology.
Setaria
Stores compound data following the ICH M7 guidelines. Setaria consists of a data management repository, initially made for fitting GlaxoSmithKline (GSK) PLC company’s needs. This platform intends to host information related to track internal Ames data, consensus permitted daily exposure (PDE) and acceptable intake (AI) limits as well as external Ames and carcinogenicity data. It can be used in conjunction with tools such as Sarah Nexus or Derek Nexus.
ICH M7
Determines ICH M7 classification to detect impurities and avoid potential carcinogenic risks. ICH M7 consists of a method for computational toxicology assessment that can be used for the detection of mutagenic impurities at different steps including identification or qualification. This method leans on two complementary approaches which are rule- and statistical-based.
iKinase
Gives access to kinases data. iKinase is a mobile app that permits users to explore Eidogen-Sertanty's Kinase Knowledgebase (KKB), a small molecule activity database that is curated from patents and peer-reviewed publications by an experienced team of PhD chemists and biologists. The information in the app is organized alphabetically by the name of the kinase target. Upon selection of a kinase, users can browse the various molecules targeting that specific enzyme.
iKinasePro
Gives access to kinases data. iKinasePro is a mobile app that provides access to Eidogen-Sertanty's Kinase Knowledgebase (KKB) with substructure-, similarity-, and super-similarity searching capability. In addition, users can search the kinome by target name, by finger-drawn chemical structures, and/or tap through a vast array of ring structures to circumnavigate the Kinome from several different perspectives.
iOncology
Offers access into Eidogen-Sertanty's Oncology Knowledgebase (OKB). iOncology is a mobile app that permits users to search by disease, registry number, molecule name, and chemical abstracts service (CAS) numbers. With registration, user's can initiate substructure and similarity searches.
OKB / Oncology Knowledgebase
Provides a database of structure-activity data across numerous targets of oncological interest. Oncology Knowledgebase cover a broad spectrum of targets relevant to colon cancer, esophageal cancer, glioma, head and neck cancer, kidney cancer, leukemia, liver cancer, lung cancer, lymphoma, melanoma, ovarian cancer, prostate cancer, skin cancer, and stomach cancer. This resource was developed to complement the Kinase Knowledgebase (KKB).
iProtein
Gives access to the Eidogen-Sertanty's target informatics platform (TIP). iProtein is a mobile app that amplifies the body of experimental protein structural information found in the Protein Data Bank (PDB) by generating protein structural models across sequences found in Swiss-Prot, RefSeq, Ensembl, or IPI. Through this resource, the TIP database can be surveyed by sequence, structure/model, site, protein family, and by co-complexed ligand structures.
OncoPortal
Provides an interface for biologists and clinicians working on solid tumors and hematological malignancies. OncoPortal is a platform based on precision medicine intelligence with curated and reliable databases on gene biomarkers and clinical trials. It contains annotations of associations between human gene variants, disease causality, progression and drug efficacy and toxicity. It offers access to somatic classification, specific drug association with the disease and clinical evidence summaries.
PharmaTrek
Consists of an interactive semantic web explorer. PharmaTrek is designed for researchers in the field of multitarget pharmacology to address complex queries. This rresource enablesthe navigation of pharmacological space in a flexible and interactive way, by accessing the content of ChEMBL via the Open PHACTS Discovery Platform. Users can submit complex multitarget queries and visualize in a manner allowing to take informed decisions on the original objective multitarget queries.
Green Solvents
Offers access to information about the safety and environmental properties of commonly used lab solvents. Green Solvents is a reference-card application that provides data information about solvents’ structures, names, environmental hazard ratings, health, safety and environmental malignancy, as well as links to online resources. The source data is derived from the solvent selection guide provided by the ACS Green Chemical Institute Pharmaceutical Roundtable and the GlaxoSmithKline Solvent Selection Guide. This application is available on the App Store.
SPRESImobile
Offers access to a chemical resource. SPRESImobile permits users to explore ChemReact, a resource that contains over 400,000 chemical reactions and related references.
TIP / Target Informatics Platform's
Gathers information on over 190 000 high resolution protein structures. TIP gives access to annotated small molecule binding sites, including about 260 000 chains and comparative models of human proteins. This ressources covers every major drug target family: proteases, kinases, phosphatases, phosphodiesterases, nuclear receptors, and G protein-coupled receptors (GPCRs).
ARTADE2DB / ARabidopsis Tiling-Array-based Detection of Exons version 2 DataBase
Stores dynamic gene structures and their predicted functions. ARTADE2DB integrates informations predicted by ARTADE2-ORA, annotations and other functional informations, such as phenotypes and literature citations, and is expected to contribute to the study of the functional genomics of A. thaliana.
OmicsDB
Provides access to analysed transcriptomics data from multiple species, with a focus on plant pathogens. OmicsDB is a resource that gathers expression data and relationships between genes from a variety of species. It can be queried, for a species of interest, by identifier, a text string related to the function, Interpro domain or eggNog groups. The information available about a gene includes gene ontology, Interpro domain, eggNogg homology group, expression pattern, list of co-expressed genes and network of co-expressed genes.
Bruker FUSION-SV
Allows users to integrate high resolution accurate mass (HRAM) mass spectrometry (MS) and complementary nuclear magnetic resonance (NMR) data for unrivalled structure verification. Bruker FUSION-SV allows access to joint spectroscopic data allowing projects to be shared by collaborating scientists. In addition, individuals can work on multiple projects in parallel. The software also delivers to lab managers information ensuring visibility of workflow within the laboratory and providing an overview of on-going projects.
BBIOREFCODE
Gathers a set of more than 800 spectra of compounds. BBIOREFCODE consists of a library composed of compounds known as metabolites in body fluids, typical contaminants or components in samples from food, feed and beverage analysis. The repository consists in several packages that can be downloaded individually. It has to be used in conjunction with the AMIX software.
HybridMolDB / Hybrid Molecule Database
Collects, validates and annotates known hybrid molecules from publicly available resources. HybridMolDB is an online repository that gathers over 4900 experimentally validated hybrid molecules. These data assist researchers in performing drug discovery and chemical biology projects for such molecule. Additionally, this tool can be used for developing or optimizing related in-silico tools.
EK-DRD / Experimental Knowledge-based Drug Repositioning Database
Contains experimentally validated drug repositioning annotation for 1861 FDA-approved and 102 withdrawn small molecule drugs. EK-DRD is a database containing four different types of repositioning bioassay data: target, cell, organism and clinical trials. It's a publicly available comprehensive resource for hosting and analyzing experimental-knowledge-based drug-repositioning datatsets.
Lab Solvents
Provides a reference list of solvents, with structures, names, physical properties, and auxiliary information about their health, safety and environmental impact. Lab Solvents is a reference-card application inspired by the Green Solvents app. It includes functionalities for browsing, filtering and sorting content. Data about Health, safety and environment were collected from the American Chemical Society Green Chemical Institute pharmaceutical roundtable report on green solvents, and the GlaxoSmithKline Solvent Selection Guide. The application runs on Android-based devices.
MORE / MObile Reagents
Provides access to over 9.7 million molecules and 17.6 million product variations. MORE is a scientific app searchable by name, CAS#, formula or by structure within a hitlist or by drawing a structural query. It offers functionalities to limit the search to specific suppliers and bookmark search results. This application can also convert a picture of a chemical structure taken from the iPhone camera into a structurally searchable molecule using Optical Structure Recognition Application (OSRA).
WENDI / Web Engine for Non-obvious Drug Information
Searches for non-obvious relationships between a query compound and scholarly publications, biological properties, genes and diseases using multiple information sources. WENDI is a data mining tool for drug discovery that aims to build a full picture of potential biological activities of a chemical compound through the aggregation of data from web services that represent diverse multiple sources. The platform calls multiple web services for computation and database search and returns an XML file that aggregates this information.
DEECOII / Dragon Explorer of Enzymes and Compounds Of Industrial Importance
Highlights industrially important biological entities. DEECOII is an online ressource of enzymes, microorganisms or chemical compounds.
INDIGO / INtegrated Data warehouse of mIcrobial GenOmes
Consists of a data warehouse for microbial genomes. INDIGO allows integration of annotations for exploration and analysis of microbial genomes. It contains information from three species: two bacterial species (Salinisphaera shabanensis and Haloplasma contractile), and one archaeal species (Halorhabdus tiamatea), all isolated from deep-sea anoxic brine lakes of the Red Sea.
miRNAVISA
Allows customized interrogation and comparisons of miRNA families for hypotheses generation, and comparison of per-species chromosomal distribution of miRNA genes in different families. miRNAVISA allows inquiry of and comparison of the genomic distribution of family-annotated genes in a given species, as well as comparison between species. This tool can be used to query the existence of sub-classes of miRNA genes by generating data-dependent relationships that may define such miRNA sub-classes.
AberOWL
Allows users to browse biological data through an ontology-based mean. AberOWL is built around two main panels: the first one allows users to freely query the compiled ontologies though a semantic search engine. Additionally, ontology terms can be used for querying Pubmed and PubMed central articles. The second panel gives access to a submission interface, permitting researchers to integrate a novel ontology.
outbreaks
Consists of a set of public empirical or simulated disease outbreak data. outbreaks is a package providing information related to more than 10 diseases including dengue, Ebola, influenza, smallpox and zika in multiple geographic areas encompassing England, Colombia or Micronesia. The information hosted can be downloaded as R objects or as text files or functions generating a dataset.
DLAD4U / Disease List Automatically Derived For You
Offers a platform for disease retrieval and prioritization. DLAD4U is a search engine that uses the hypergeometric test to prioritize retrieved diseases for a query term. This program leans on the MEDLINE database and lists PubMed IDs that can be related to the user query. For each search, the repository delivers a ranked disease list, information associated with each disease, chronologically-ordered supporting publications, a summary of the run, and links for file export.
RRMdb / RNA Recognition Motif database
Compiles information related to RNA-recognition motif (RRM) domains. RRMdb is organized into more than 400 families with their corresponding literature, sequence and structural data. Users can submit a protein sequence of interest and obtain its RRM domains with a description. Additionally, information can be explored through a global network organized by pairwise sequence similarity.
UbiHub
Assists users with the exploration of ubiquitination pathways. UbiHub enables the visualization of diverse array of biological, structural, and chemical data on phylogenetic trees of human protein families involved in ubiquitination signaling, including E3 ligases and deubiquitinates. This interface can be used in target prioritization and drug design, and serves as a navigation tool for medicinal chemists, structural and cell biologists exploring ubiquitination pathways.
Flyexpress
Compiles more than 100,000 images dealing with Drosophila melanogaster embryogenesis. FlyExpress gathers a curated library of genes derived from in situ hybridization studies and from peer-reviewed publications. It enables users to investigate specific coordinates in a developing embryo and to reveal genes expressed at that location with its corresponding scientific literature. Searches can be made by gene symbol, PubMedID, ontology, or keywords.
PhosphoDB
Deals with information related to phosphorylation sites. PhosphoDB gathers data derived from multiple proteases mass spectrometry (MS)-based proteomics experiments and compiles more than 18000 sites encompassing about 37000 phosphopeptides sequences. This repository is organized for browsing by sites or by proteins and intends to assist researchers in easing analysis in signaling and proteomics fields.
PancanQTL
Allows users to search, browse and download expression quantitative trait loci (eQTLs). PancanQTL is a database that gathers cis-eQTLs, trans-eQTLs, survival-associated eQTLs and genome-wide association studies (GWAS)-related eQTLs. This resource can serve as resource for human cancer genetics and provide opportunities to bridge the knowledge gap from variants in sequence to phenotypes. It can also assist researchers with the understanding of the effects of inherited variants in tumorigenesis and development.
PRISM / PRoteIn Structure Modification
Provides a database for post-translational modifications (PTMs). PRISM is a publicly available 3D structure-based resource that offers an interactive knowledgebase focused on 3D structural information of PTM proteins. It includes a variety of customizable search options and data browsing functions. These capabilities allow users to access to data via keyword, ID, or advanced options combination search.
SMTB / Smooth Muscle Transcriptome Browser
Offers genetic references and expression profiles of all expressed transcripts. SMTB is an online resource that provides the number and expression level of transcriptional variant for mapped genes expressed in cells within the mucosa and muscularis layers of the jejunum and colon. This database allows researchers to analyze each transcriptional variant in terms of gene structure (promoter region, exons, and introns), expression levels within each cell type and tissue, and open reading frames (coding protein) within each variant.
Quiver Fusion Database
Allows users to search for published gene fusions. Quiver Fusion Database provides access to more than 9,300 published gene fusion partners and 10,800 unique breakpoints derived from about 3,000 peer-reviewed publications. This repository collates information from 6 publicly available information sources: COSMIC, Mitleman, ChimerDB, dbCRiD, TICdb and ChiTars. Synonymous gene names in the literature can be distinguished, and disease states associated with particular gene fusions in the literature can be showed.
ApicoTFdb
Consists of experimentally validated as well as computationally predicted transcription factors (TFs) and transcription associated factors (TAFs) in 14 apicomplexan species. ApicoTFdb can be use for the researchers interested in less-studied gene regulatory mechanisms mediating the complex life cycle of the apicomplexan parasites. This tool hosts the classified list of apicomplexans regulators and information related to their domain architecture, molecular function(s), biological pathway(s), interlogs and dynamically linked to related literature.
InsectiPAD / Insecticide Physicochemical-properties Analysis Database
Covers about 490 approved insecticides, over 22 200 related physicochemical properties, 2 900 qualitative analysis and 1 500 quantitative scores for insecticides and provides comprehensive insecticide-likeness analysis for any compounds. InsectiPAD is an available web-enabled platform including features for viewing, sorting, downloading, qualitative and quantitative evaluating insecticide-likeness.
ASmiR
Identifies all splice isoforms from linear and circRNAs originated from the same locus with or without miRNA target sites. ASmiR database provides comprehensive alternative splicing (AS) information for future comparative studies between gymno sperm and angiosperm species. In summary, this tool is a powerful platform for studying the inter-play between miRNA and AS for model plants, woody perennials and any plant species.
YeasTSS / Yeast Transcription Start Sites
Assists users with visualization and integration of the transcription start sites (TSSs) maps, core promoters and functional genomic data related to transcription initiation. YeasTSS is a public database for yeast that was developed to improve genome annotation, studies of promoter structure, regulated control of transcription initiation and to infer gene regulatory networks.
AraNoisy
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.
iBioGuide
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.
PerMemDB
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.