Tag: natural language processing

DisGeNET is a discovery platform containing one of the largest collections available of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models, and the scientific liter ...

TISSUES is a weekly updated web resource that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. All evidence to common protein identifiers and Brenda Tissue O ...

DISEASES is a weekly updated web resource that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. We further unify the evidence by assig ...

COMPARTMENTS is a weekly updated web resource that integrates evidence on protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods. We map all evidence to ...

An Open Access Knowledge Base for Microbial Natural Products Discovery. The Natural Products Atlas Network views of chemical space. The Natural Products Atlas provides a unique tools for exploring natural products chemical space, offering perspecti ...

Cancer-relevant proteins and compound interactions

Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including au ...

The COVID-19 Research Collaborations database stores information on researchers and institutions for the purposes of identifying potential research experts or collaborators in areas related to the coronavirus epidemic across basic science, translatio ...

ORGANISMS is a weekly updated web resource that facilitates taxonomy-aware search and retrieval of articles. To this end, the the resource performs named entity recognition of terms from the NCBI Taxonomy on PubMed abstracts. The resource further pro ...

Literature-mined resource for drivers, oncogenes and tumor suppressors in cancer.

Metagenomic BioMining Engine: homologs of commercially useful enzymes in metagenomic datasets

The Clinical Trials Ontology (CTO) is also known as the Clinical Trial Ontology-Neurodegenerative Diseases (CTO-NDD), and describes clinical trials in the field of neurodegeneration. This resource has been created for use in the IMI-funded AETIONOMY ...

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 ...

Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach | The exposome represents the sum of all exposures during the life-span of an organism (from chemicals to microbes, viruses, radiation and other sou ...

CIViCmine is a literature-mined database of clinically relevant cancer biomarkers from data from PubMed and Pubmed Central Open Access subset.

The COVID-19 ontology covers the role of molecular and cellular entities in virus-host-interactions, in the virus life cycle, as well as a wide spectrum of medical and epidemiological concepts linked to COVID-19.

Restructured version of Gene Expression Omnibus (GEO) that provides a user friendly interface for curating GEO database

DES-TOMATO is a topic-specific literature exploration system developed to allow the exploration of information related to tomato. The information provided in DES-TOMATO is obtained through the text-mining of available scientific literature, namely fu ...

COVID-19-CT-CXR is a public database of COVID-19 CXR and CT images, which are automatically extracted from COVID-19-relevant articles from the PubMed Central Open Access (PMC-OA) Subset.

Knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal (GI) cancer.

An End-to-End Deep Learning-Based Workflow for Biomedical Knowledge Graph Extraction, Optimization and Applications.

The Colorado Richly Annotated Full Text Corpus (CRAFT) is a manually annotated corpus consisting of 67 full-text biomedical journal articles from the PubMed Central Open Access Subset.

A knowledgebase for genome-wide R-loop formation and regulation.

Heart Failure Integrated Platform (HFIP) is an integrated multi-omics data and knowledge platform for the precision medicine of heart failure.

COVID-19 preVIEW is a tool for semantic search to explore COVID-19 research preprints.

A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. The main web resource to explore human mitochondrial variability data and their pathological correlation. HmtVar is a manually-curate ...

Berlin-Tübingen-Oncology corpus (BRONCO) is a large and freely available corpus of shuffled sentences from German oncological discharge summaries annotated with diagnosis, treatments, medications, and further attributes including negation and specula ...

Gene expression regulation database curated by mining abstracts from literature. Gene Expression Regulation Database. Gene Expression Regulation Database (GREDB) has been developed to facilitate systems-level analyses that will provide insights int ...

Language terms used in the domain of autism. The language terms were obtained via text mining and automatic retrieval of terms from the corpus of PubMed abstracts.

Application ontology for Ocular Immune-mediated Inflammatory Diseases, built from domain experts in ophthalmology, clinical guidelines, and enhanced with patient-preferred terms.

Web-Based Database and Predictor of Anti-Inflammatory Natural Products.

Model Zoo curates and provides a platform for deep learning researchers to easily find pre-trained models for a variety of platforms and uses.

Knowledgebase of Microbes’ Battling Agents for Therapeutics.

A large and continuously updated drug combination database.

A high-throughput database of macromolecular host-pathogen interactions on the Web.

Brain Research Hotspot Database (BRHD) a A comprehensive platform for the latest advances in brain research

It is an effective resource for improving named entity recognition, grounding, and relationship resolution in automated reading of biomedical text.

emiRIT is a text-mining based database for microRNA information.

FRCD (Food Risk Component Database) is a comprehensive food risk component database with molecular scaffold, chemical diversity, toxicity, and biodegradability analysis.

MicroRNA childhood Cancer Catalog (M3Cs) is a high-quality curated collection of published miRNA research studies on 16 pediatric cancer diseases.

COVID-19 Knowledge Extractor (COKE) is a tool and a web portal to extract drug - target protein associations from the CORD-19 corpus of scientific publications on COVID-19.

MEDI (MEDication Indication) is an ensemble medication indication resource for primary and secondary uses of electronic medical record (EMR) data.

a biomedical relation extraction dataset (BioRED) with multiple entity types (e.g. gene/protein, disease, chemical) and relation pairs (e.g. gene-disease; chemical-chemical) at the document level, on a set of 600 PubMed abstracts.

A comprehensive database for the linking of Traditional Chinese Medicine with modern medicine at molecular and phenotypic levels.

A scalable artificial intelligence platform that automatically finds copy number variations (CNVs) in journal articles and transforms them into a database.

EpiGraphDB is an analytical platform and database to support data mining in epidemiology. The platform incorporates a graph of causal estimates generated by systematically applying Mendelian randomization to a wide array of phenotypes, and augments t ...

CONSORT-TM is a corpus annotated with CONSORT checklist items, and studied baseline sentence classification methods as well as their combinations to recognize a subset of these items.