Tag: literature and language

The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as Atrial septal defect. The HPO is currently being develope ...

MetaCyc is the largest curated collection of metabolic pathways currently available. It provides a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecu ...

This database provides a list of insertion sequences (IS) isolated from bacteria and archae. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequence ...

Europe PubMed Central (Europe PMC) is an on-line database that offers free access to a large and growing collection of biomedical research literature.

The Evidence and Conclusion Ontology (ECO) contains terms that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has fun ...

The Aspergillus Genome Database is a resource for genomic sequence data as well as gene and protein information for Aspergilli. This publicly available repository is a central point of access to genome, transcriptome and polymorphism data for the fun ...

Phospho.ELM is a manually curated database of eukaryotic phosphorylation sites. The resource includes data collected from published literature as well as high-throughput data sets.

PubMed® comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

The international glycan structure repository for glycans published in the literature. Any glycan structure, ranging in resolution from monosaccharide composition to fully defined structures can be registered and have an accession number assigned as ...

The COVID-19 Data Portal enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research ...

CellPhoneDB is a publicly available repository of curated receptors, ligands and their interactions. Subunit architecture is included for both ligands and receptors, representing heteromeric complexes accurately. This is crucial, as cell-cell communi ...

The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biol ...

This resource is a collection of all proteins identified to be localized on kinetochore, centrosome, midbody, telomere and spindle from two fungi (S. cerevisiae and S. pombe) and five animals, including C. elegans, D. melanogaster, X. laevis, M. musc ...

ChannelsDB is a comprehensive and regularly updated resource of channels, pores and tunnels found in biomacromolecules deposited in the Protein Data Bank.

NCBI information retrieval system, including GenBank, MMDB (structures), genomes, population sets, OMIM, taxonomy and PubMed.

a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions. gutMDisorder (http: bio-annotation.cn gutMDisorder), a manually curated database, aims at providing a comprehensive resource of dysbiosis of the gut microbi ...

Mammal ncRNA-disease repository with increased coverage and annotation. Mammalian ncRNA-Disease Repository. MNDR v3.1: Mammal NcRNA-Disease Repository. MNDR (Mammalian ncRNA-Disease Repository) is a database that curated associations between ncRNA ...

PhaSepDB is a novel database that provides a collection of phase separation related proteins manually curated from publications and public database. In addition to curated proteins, PhaSepDB also provides the researchers with molecular signatures th ...

A comprehensive database of genomic variations that disturb ceRNA network regulation. Genomic VA,T,C,G RIATION disturbing ceRNA regulations. LnCeVar is a comprehensive database that aims to infer genomic variations that disturb lncRNA-associated ce ...

Hydrogen/deuterium exchange data on protein folding and stability

Experimentally characterized CAZyme gene clusters

Experimentally characterized Prokaryotic GlycoProteins

UK PubMed Central is a full-text article database that extends the functionality of the original PubMed Central (PMC) repository. Now includes both a UKPMC and PubMed search, as well as access to other records such as Agricola, Patents and recent bio ...

A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand-alone tool.

BioConceptVec is a collection of concept embeddings on primary biological concepts mentioned in the biomedical literature.

A database of experimentally supported non-coding RNAs and drug targets in cancer. NoncoRNA (http: www.ncdtcdb.cn:8080 NoncoRNA ) is a manually curated database of experimentally supported non-coding RNAs (ncRNAs) and drug target associations that a ...

Protein stability data

Mother of All Databases (MOAD) - Polypharmacology Tools and Their Utility in Drug Repurposing.

A Comprehensive Database of Harmonized Genomic Variants Found in Autism Spectrum Disorder Sequencing Studies. VariCarta is a curated, web-based database housing ASD-linked genes created from the meta-analysis of -omic sequencing literature. VariCar ...

Curated Protein Aggregation Database (CPAD) is an integrated database which contains information related to amyloidogenic proteins, Aggregation prone regions, aggregation kinetics and structure of proteins relevant to aggregation. Authors are encoura ...

An immunoinformatic database of T-cell-defined neoantigens. Interior-Design-Responsive-Website-Templates-Edge. NeoPeptide is a catalog of epitopes derived from neoantigens, arising from somatic mutations, captured from the literatures and immunolog ...

This tool is a PubMed article recommendation system based on content-based filtering, based on preferred articles.

The FoldamerDB is an open source database of foldamers. Foldamers are molecules which mimics the folding of biological molecules into well defined conformation

A manually curated database for experimentally supported lncRNAs during various cancer metastatic events. A database for experimentally supported lncRNAs during various cancer metastatic events.

Checkpoint Therapeutic Targets and Modulators Database (CKTTD) for Cancer Immunotherapy is a comprehensive database for checkpoint targets and their modulators in cancer immunotherapy. Immune checkpoints are regulators of the immune system which prev ...

CancerLivER (Liver Cancer Expression Resource) is a database of liver cancer that maintains gene expression datasets and biomarkers curated from public repositories and literature respectively. It contains the following three modules for extracting a ...

An international, open and dynamic library for up-to-date clinical information. Collect information about clinic management and research projects.

A database for eukaryotic peripheral membrane proteins. The majority of all proteins in cells interact with membranes either permanently or temporarily. Peripheral membrane proteins form transient complexes with membrane proteins and or lipids, via ...

A database for the study of genomic reassortments among influenza viruses.

Protein-Nucleic Acid Binding Energetic Database

FLHdb is database of variants of Familial Hemophagocytic Lymphohistiocytosis from the Clinical and Translational Bioinformatics Research Group at Vall Hebron Institute of Research (VHIR).

CMBD (Cancer Metabolic Biomarker knowledge Database) a manually curated cancer metabolic biomarker knowledge database.

a database of promiscuous proteins. Promiscuous behaviour in proteins and enzymes remains a challenging feature to understand the structure-function relationship. Here we present ProtMiscuity, a manually curated online database of proteins showing c ...

A software designed for the analysis of binding curves with which to evaluate the interactions of biomolecules.

A database of eukaryotic rRNA primers and primer sets for metabarcoding studies compiled from the literature.

A comprehensive database of trained immunity.

CANNUSE is a database containing the traditional uses of Cannabis.

Database for membrane protein thermodynamics for understanding folding and stability. MPTherm is a thermodynamic database of membrane proteins and their mutants, contains the thermodynamic data of membrane proteins collected from literature and ProT ...

An integrative database of quantitative post-translational modifications in plants.

Is an online platform 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.

DenvInD is a database containing dengue virus inhibitors for clinical and molecular research.

An Open-Access Platform for the Genomics of Brassica campestris (syn. Brassica rapa) ssp. chinensis.

Automatization and self-maintenance of the O-GlcNAcome catalog.

The Organonitrogen Degradation Database (ONDB) is used to catalog information about the cost, chemical properties, and biodegradation potential of commonly used organonitrogen compounds.

RNAPhaSep is a novel database that collects phase separation related RNAs manually curated from publication and public databases. Various properties of RNAs together with the corresponding phase separation conditions validated by experiments were col ...

new binding kinetics database and its integration in an open-source binding analysis software. Kinetics OF Featured Interactions. KOFFI-DB (???) is an article based database for kinetic constants of biomolecular interactions. We focused on interact ...

A database and toolkit for researchers working on environmental mercury geochemistry. AQUA-MER is useful for researchers who want to investigate mercury speciation in defined environments i.e., to which chemical elements and groups it will bind and i ...

NEPdb is a database of T-cell experimentally-validated neoantigens and pan-cancer predicted neoepitopes for cancer immunotherapy. It contains more than 17,000 validated human immunogenic and non-immunogenic neoepitope entries with human leukocyte ant ...

BioModels Parameters is a resource that facilitates easy search and retrieval of parameter values used in the SBML models stored in the BioModels repository.

Database for skin permeation of xenobiotics. Jupyter Notebook which leads through the code used to create huskinDB publication Figures. huskinDB is a human skin permeation database containing information on experimental protocols used. It provides ...

A database of organ-specific metastasis induced by human cancer cell lines in mouse models. The organotropism is the propensity of metastatic cancer cells to colonize preferably certain distant organs, resulting in a non-random distribution of metas ...

CMTTdb (The Cancer Molecular-Targeted Therapy database) is an integrated database to store relevant information about molecular targeted agents as well as their combinatorial approaches in clinical trials and studies for cancer treatment. It contains ...

A constructing a bilingual website with validated database for Herb and Western medicine interactions using Ginseng, Ginkgo and Dong Quai as examples.

A repository for scientific information on mesophotic ecosystems. Repository for information on mesophotic coral ecosystems. Mesophotic.org: an information repository on mesophotic coral ecosystems. Mesophotic.org is a curated repository for infor ...

DatumKB is a freely accessible database of experimental results involving the function and regulation of human proteins in cultured cells. The results are manually curated from biological research literature using a shorthand language and stored as d ...

Orphadata provides the scientific community with comprehensive, quality datasets related to rare diseases and orphan drugs from the Orphanet knowledge base, in reusable formats.

MolMeDB is an open chemistry database concerning the interaction of molecules with membranes.

Anti-CRISPRdb is a comprehensive online resource that effectively organizes anti-CRISPR proteins determined by experimental and bioinformatics methods. Additionally, it also provides nucleotide sequences, interactors, three-dimensional structures, ...

Combine literature search with text mining tools for biology.

A repository for DNA and RNA nanostructures.

A database and semantic analysis engine for literature, clinical trials and patents related to probiotics.

open-access repository for surveys of antimicrobial resistance in animals.

A manually curated database of human and mouse essential lncRNA genes.

An Evidence-based Database of Genes and Phenotypes of Male Infertility.

A database of manually curated biomarkers for Prostate Cancer.

A positive miRNA-target regulations database.

Interactive encyclopedia of proteins, RNA, DNA and other molecules with 3D structures.

A PROkaryotic Chromatin ImmunoPrecipitation DataBase

Biologer is an open platform for collecting biodiversity data.

A database of biomarkers of cancer stem cells.

A database of the phylogeny and physiology of thermophilic and hyperthermophilic organisms.

A Manually Curated Database for Tracking and Predicting Genes Associated With Meiosis.

Scaling up oligogenic diseases research with OLIDA.

A new expert system for drug-excipient compatibility evaluation.

A microbial strain database of manually curated CRISPR/Cas genetic manipulation system information for biomanufacturing.

DiZyme open access resource for quantitative prediction of nanozyme catalytic activity

DRscDB is a single-cell RNA-seq resource for data mining and data comparison across species.

A knowledge database of dense granule proteins of the Apicomplexa.

ChemHub is a comprehensive database for selecting biosynthetic target molecules based on compound functions.

The Database of Pollinator Interactions (DoPI) documents British pollinator-plant associations.

A database of food-derived bioactive peptides (DFBP), containing a total of 6276 peptide entries in 31 types from different sources.

A systematic evidence map of health studies on 29 per- and polyfluoroalkyl substances.

B-AMP is an Antimicrobial Peptide (AMP) repository for biofilms, consisting of a vast library of 5544 structural AMP models, AMPs annotated to relevant biofilm literature, and protein-peptide interaction models with potential biofilm targets.

BCGene is a online database for brain cancer-implicated genes: exploring the subtype-specific mechanisms of brain cancer

Diatoms.org represents such a content curation community, providing open, online access to a vast amount of recent and historical information on North American diatom taxonomy and ecology.

ACovPepDB is a comprehensive peptides database of anti-coronavirus peptides, which contains 518 enrties with 214 unique ACovPs manually extracted from research articles and public databases.

circR2Cancer is a manually curated database of associations between circRNAs and cancers. circR2Cancer contains the information of cancer exacted from Disease Ontology and basic biological information of circRNAs from circBase.

ZebraShare is intended to help establish fruitful collaborations by sharing mutant fish lines, and information about these mutants, particularly when authors do not otherwise see a clear path to publication.

Exposome of Human Milk across India (ExHuMId) is a curated resource and analysis of exposome of human milk across India.

The Bibliome Variant Database is a collection of variants mined from open-access primary literature. All variants included in the database have been mapped to the human genome and are presented in a manner ordered by genomic location. The goal of thi ...

Esc (Immune escape variants in SARS-CoV-2) is a comprehensive and manually curated compendium of genetic variants in SARS-CoV-2 associated with immune escape. The data on variants and associations have been compiled from published literature as well ...

ProModb (Protein interaction-based functional Module database) is a repository that documents computationally generated whole-cell protein-protein interaction network-based functional modules of an organism.

CRITTERBASE, a publicly accessible data warehouse and interactive portal that currently hosts quality-controlled and taxonomically standardized presence/absence, abundance, and biomass data for 18,644 samples and 3,664 benthic taxa (2,824 of which at ...

A comprehensive manually curated database for transcription factors and related markers in specific cell and tissue types in human.

A machine learning-based phosphorylation sites prediction tool for Plasmodium proteins.

Top ‱ cited papers from PUBMED. Unicorn Papers are based on an equal contribution (EC) citation model in which the total number of citations had been divided by the number of the authors. Currently, the list contains 3405 papers with ECcit ≥ 847.0 ( ...

Ebolabase is a comprehensive source for ebola-human interactions has been developed. Ebolabase contains experimentally verified entries of ebola-human interactions. The interactions are visualized as network images. This study provides the informatio ...

A curated natural product database specific to secondary metabolites of medicinal fungi. Medicinal Fungi Secondary metabolites And Therapeutics. MeFSAT (Medicnal Fungi Secondary metabolites and Therapeutics). Medicinal Fungi Secondary Metabolite A ...

IND-enzymes is a repository for hydrolytic enzymes derived from thermophilic and psychrophilic bacterial species with potential industrial usage.

Molecular Prognostic Indicators in Cirrhosis Database for Clinical Context-Specific in Silico Prognostic Biomarker Validation. Molecular Prognostic Indicators in Cirrhosis. Database for clinical context-specific in silico prognostic biomarker valid ...

TFcancer is a manually curated database of transcription factors associated with human cancer. TFcancer features in comprehensive annotations of TFs in human cancers. TFcancer mainly focused on the influence of transcription factors on four dimension ...

A comprehensive genetic resource of nicotine and smoking. Genetic resources of nicotine and smoking. Genetic Resources Of Nicotine and Smoking (GRONS) is a database devoted to provide a comprehensive and systematic collection of cross-platform gene ...

Database Of Reconstructed MetAbolic Networks. We apologize for the inconvenience, but it appears that an internal error has occurred in the Dorman system. If this is the first time you have encountered this message, please use the Back button on you ...

FADB-China is a molecular-level food adulteration database in China based on molecular fingerprints and similarity algorithms prediction expansion.

A web-based chemical repository of flavonoid compounds. Flavonoids are richly diverse polyphenolic plant secondary metabolites that are known to be crucial component of human diet. These compounds are attributed with variety of nutritional as well a ...

CACHET-CADB is 259 days long contextualised single-channel ECG arrhythmia database from 24 patients recording under a free-living ambulatory setting

An online database for the dragonflies and damselflies of Bangladesh. Welcome to the Odonata of Bangladesh, database of the dragonflies and damselflies of Bangladesh. Situated in the South-east Asia, Bangladesh is gifted with the rich network of wat ...

A Web Resource of Structure-Function Annotations to Unravel the Allostery of Nicotinic Acetylcholine Receptors. Database of structural-functional annotations of nicotinic acetylcholine receptors. NAChRDB is a web-accessible database of residue-leve ...

DiversityExsiccatae (DWB-DE) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data doma ...

The BIONDA biomarker database provides structured information on all biomarker candidates published in PubMed articles. There is no limitation to any kind of diseases. To this end, PubMed article abstracts and renowned databases such as UniProt and H ...