yusuke1997/dblp-id-title huggingface dataset:
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis
VigSatDB: genome-wide microsatellite DNA marker database of three species of Vigna for germplasm characterization and improvement
Corrigendum to: the SNPcurator: literature mining of enriched SNP-disease associations
PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya
Autophagy and Tumor Database: ATdb, a novel database connecting autophagy and tumor
RHPCG: a database of the Regulation of the Hippo Pathway in Cancer Genome
ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings
TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species
Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases
Gold-standard ontology-based anatomical annotation in the CRAFT Corpus
How much does curation cost?
CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002
Chickspress: a resource for chicken gene expression
HFIP: an integrated multi-omics data and knowledge platform for the precision medicine of heart failure
The Ensembl gene annotation system
The Corvids Literature Database - 500 years of ornithological research from a crow's perspective
A combinatorial approach implementing new database structures to facilitate practical data curation management of QTL, association, correlation and heritability data on trait variants
The YeastGenome app: the Saccharomyces Genome Database at your fingertips
Data set of fraction unbound values in the in vitro incubations for metabolic studies for better prediction of human clearance
Peptipedia: a user-friendly web application and a comprehensive database for peptide research supported by Machine Learning approach
DAPredict: a database for drug action phenotype prediction
Pipeline to explore information on genome editing using large language models and genome editing meta-database
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer
HCSD: the human cancer secretome database
The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information
Authors' attitude toward adopting a new workflow to improve the computability of phenotype publications
StraPep: a structure database of bioactive peptides
A longitudinal analysis of function annotations of the human proteome reveals consistently high biases
A Simple Standard for Sharing Ontological Mappings (SSSOM)
PubTerm: a web tool for organizing, annotating and curating genes, diseases, molecules and other concepts from PubMed records
Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps
AllerBase: a comprehensive allergen knowledgebase
BrainTrap: a database of 3D protein expression patterns in the Drosophila brain
The Xenbase literature curation process
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data
EuroDia: a beta-cell gene expression resource
The systematic annotation of the three main GPCR families in Reactome
MMHub, a database for the mulberry metabolome
PlagueKD: a knowledge graph-based plague knowledge database
CGDSNPdb: a database resource for error-checked and imputed mouse SNPs
PhenoMiner: quantitative phenotype curation at the rat genome database
VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants
Semi-automatic translation of medicine usage data (in Dutch, free-text) from Lifelines COVID-19 questionnaires to ATC codes
CD-REST: a system for extracting chemical-induced disease relation in literature
Collaborative relation annotation and quality analysis in Markyt environment
Database of RNA binding protein expression and disease dynamics (READ DB)
MENSAdb: a thorough structural analysis of membrane protein dimers
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model
Integrated sequence and immunology filovirus database at Los Alamos
OliveNet™: a comprehensive library of compounds from Olea europaea
ODNA: a manually curated database of noncoding RNAs associated with orthopedics
The World Spider Trait database: a centralized global open repository for curated data on spider traits
Varietas: a functional variation database portal
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines
UPCLASS: a deep learning-based classifier for UniProtKB entry publications
HisgAtlas 1.0: a human immunosuppression gene database
tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis
H-SPAR DB: human spaceflight platform for analysis and research - an integrative omics database for space health
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity
Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population
BioSearch: a semantic search engine for Bio2RDF
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine
R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring
RegulatorDB: a resource for the analysis of yeast transcriptional regulation
HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect
Visualization and exploration of linked data using virtual reality
CiliaMiner: an integrated database for ciliopathy genes and ciliopathies
HRPDviewer: human ribosome profiling data viewer
A manual corpus of annotated main findings of clinical case reports
Using ODIN for a PharmGKB revalidation experiment
Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy
Correction to: RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome
Statistical principle-based approach for recognizing and normalizing microRNAs described in scientific literature
BelSmile: a biomedical semantic role labeling approach for extracting biological expression language from text
Is metadata of articles about COVID-19 enough for multilabel topic classification task?
The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four- and five-codon combinations present in Saccharomyces cerevisiae genes
StaphyloBase: a specialized genomic resource for the staphylococcal research community
RegenBase: a knowledge base of spinal cord injury biology for translational research
Involving community in genes and pathway curation
Maser: one-stop platform for NGS big data from analysis to visualization
A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities
FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki
The text2term tool to map free-text descriptions of biomedical terms to ontologies
iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature
Siberian sturgeon multi-tissue reference transcriptome database
CerealsDB - new tools for the analysis of the wheat genome: update 2020
YeasTSS: an integrative web database of yeast transcription start sites
Automated annotation and validation of human respiratory virus sequences using VADR
Task reformulation and data-centric approach for Twitter medication name extraction
Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study
Tetrahymena genome database Wiki: a community-maintained model organism database
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs
CancerLivER: a database of liver cancer gene expression resources and biomarkers
Correction to: The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study
The Units Ontology: a tool for integrating units of measurement in science
Annotation of functional sites with the Conserved Domain Database
NCBI Taxonomy: a comprehensive update on curation, resources and tools
BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes
The Reactome BioMart
CHD@ZJU: a knowledgebase providing network-based research platform on coronary heart disease
The Australian Biosecurity Genomic Database: a new resource for high-throughput sequencing analysis based on the National Notifiable Disease List of Terrestrial Animals
LeishMicrosatDB: open source database of repeat sequences detected in six fully sequenced Leishmania genomes
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis
MIRKB: a myocardial infarction risk knowledge base
Colorectal cancer drug target prediction using ontology-based inference and network analysis
Methods and strategies for gene structure curation in WormBase
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins
A database for curating the associations between killer cell immunoglobulin-like receptors and diseases in worldwide populations
iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system
A general concept for consistent documentation of computational analyses
ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants
HypoxiaDB: a database of hypoxia-regulated proteins
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics
Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties
PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins
Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis
Recognition and normalization of multilingual symptom entities using in-domain-adapted BERT models and classification layers
GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development
The SNPcurator: literature mining of enriched SNP-disease associations
CreZOO - the European virtual repository of Cre and other targeted conditional driver strains
Shared resources, shared costs - leveraging biocuration resources
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV
dbLGL: an online leukemia gene and literature database for the retrospective comparison of adult and childhood leukemia genetics with literature evidence
THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes
HistoneDB 2.0: a histone database with variants - an integrated resource to explore histones and their variants
DDPD 1.0: a manually curated and standardized database of digital properties of approved drugs for drug-likeness evaluation and drug development
Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategy
RNABP COGEST: a resource for investigating functional RNAs
ProtoBug: functional families from the complete proteomes of insects
Echinobase: an expanding resource for echinoderm genomic information
PubMed Labs: an experimental system for improving biomedical literature search
Conference report: Biocuration 2021 Virtual Conference
FunSecKB: the Fungal Secretome KnowledgeBase
phytochemdb: a platform for virtual screening and computer-aided drug designing
Dataset of miRNA-disease relations extracted from textual data using transformer-based neural networks
MGH: a genome hub for the medicinal plant maca (Lepidium meyenii)
CasPDB: an integrated and annotated database for Cas proteins from bacteria and archaea
Literature mining of genetic variants for curation: quantifying the importance of supplementary material
GXD's RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest
RumimiR: a detailed microRNA database focused on ruminant species
PlantMP: a database for moonlighting plant proteins
'What's in the NIDDK CDR?' - public query tools for the NIDDK central data repository
Growing and cultivating the forest genomics database, TreeGenes
Tracking and coordinating an international curation effort for the CCDS Project
3DSwap: curated knowledgebase of proteins involved in 3D domain swapping
XePhIR: the zebrafish xenograft phenotype interactive repository
From library to landscape: integrative annotation workflows for compound libraries in drug repurposing
Automated generation of gene summaries at the Alliance of Genome Resources
ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species
Gene Loss DB: a curated database for gene loss in mammals - the cetacean collection
Correction to: Acinetobase: the comprehensive database and repository of Acinetobacter strains
AIMedGraph: a comprehensive multi-relational knowledge graph for precision medicine
Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE
The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification
A RESTful application programming interface for the PubMLST molecular typing and genome databases
curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome
A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning
FGDB: a comprehensive graph database of ligand fragments from the Protein Data Bank
Building deep learning models for evidence classification from the open access biomedical literature
One tool to find them all: a case of data integration and querying in a distributed LIMS platform
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis
PmiRExAt: plant miRNA expression atlas database and web applications
ReMeDy: a platform for integrating and sharing published stem cell research data with a focus on iPSC trials
WaspAtlas: a Nasonia vitripennis gene database and analysis platform
MuscleAtlasExplorer: a web service for studying gene expression in human skeletal muscle
The Annotation-enriched non-redundant patent sequence databases
Southern African Treatment Resistance Network (SATuRN) RegaDB HIV drug resistance and clinical management database: supporting patient management, surveillance and research in southern Africa
GREG - studying transcriptional regulation using integrative graph databases
Standardized naming of microbiome samples in Genomes OnLine Database
Tear fluid database: a reference website for tear fluid proteomics
A content-based dataset recommendation system for researchers - a case study on Gene Expression Omnibus (GEO) repository
Curation of over 10 000 transcriptomic studies to enable data reuse
Correction to: A Terpenoids Database with the Chemical Content as A Novel Agronomic Trait
gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes
NbThermo: a new thermostability database for nanobodies
Integrating deep learning architectures for enhanced biomedical relation extraction: a pipeline approach
Continuous development of the semantic search engine preVIEW : from COVID-19 to long COVID
DBatVir: the database of bat-associated viruses
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations
An effective biomedical data migration tool from resource description framework to JSON
Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies
TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat - Stem rust host-pathogen interactome
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language
GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics
Large-scale regulatory and signaling network assembly through linked open data
Enhancing biomedical relation extraction through data-centric and preprocessing-robust ensemble learning approach
RareLSD: a manually curated database of lysosomal enzymes associated with rare diseases
A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases
DBH2H: vertebrate head-to-head gene pairs annotated at genomic and post-genomic levels
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design
EpimiR: a database of curated mutual regulation between miRNAs and epigenetic modifications
Improving the dictionary lookup approach for disease normalization using enhanced dictionary and query expansion
Chemical-protein interaction extraction via contextualized word representations and multihead attention
Automatic Extraction of Medication Mentions from Tweets - Overview of the BioCreative VII Shared Task 3 Competition
AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini
PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples
Sieve-based coreference resolution enhances semi-supervised learning model for chemical-induced disease relation extraction
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture
LnChrom: a resource of experimentally validated lncRNA-chromatin interactions in human and mouse
BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language
A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae
Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12
Genic insights from integrated human proteomics in GeneCards
EnzyMine: a comprehensive database for enzyme function annotation with enzymatic reaction chemical feature
A comprehensive morphological database of hognose Porthidium pitvipers (Viperidae: Crotalinae)
A web resource for mining HLA associations with adverse drug reactions: HLA-ADR
Do syntactic trees enhance Bidirectional Encoder Representations from Transformers (BERT) models for chemical-drug relation extraction?
CoMentG: comprehensive retrieval of generic relationships between biomedical concepts from the scientific literature
COVIDOUTCOME - estimating COVID severity based on mutation signatures in the SARS-CoV-2 genome
IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2)
3CDB: a manually curated database of chromosome conformation capture data
rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots
A checklist recipe: making species data open and FAIR
Mining drug-target and drug-adverse drug reaction databases to identify target-adverse drug reaction relationships
ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles
Gliome database: a comprehensive web-based tool to access and analyze glia secretome data
SEPDB: a database of secreted proteins
OCDB: a database collecting genes, miRNAs and drugs for obsessive-compulsive disorder
APADB: a database for alternative polyadenylation and microRNA regulation events
dbAMEPNI: a database of alanine mutagenic effects for protein-nucleic acid interactions
Integrated querying and version control of context-specific biological networks
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters
AHP DB: a reference database of proteins in the human aqueous humor
Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus
SDADB: a functional annotation database of protein structural domains
Notes on the data quality of bibliographic records from the MEDLINE database
BrAPI v2: real-world applications for data integration and collaboration in the breeding and genetics community
The TOXIN knowledge graph: supporting animal-free risk assessment of cosmetics
PIRSitePredict for protein functional site prediction using position-specific rules
Integrating text mining into the MGI biocuration workflow
VianniaTopes: a database of predicted immunogenic peptides for Leishmania (Viannia) species
Using the OntoGene pipeline for the triage task of BioCreative 2012
The MetaGens algorithm for metagenomic database lossy compression and subject alignment
MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data
CANNUSE, a database of traditional Cannabis uses - an opportunity for new research
Disease named entity recognition by combining conditional random fields and bidirectional recurrent neural networks
UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation
UniProt Knowledgebase: a hub of integrated protein data
Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research
Enabling semantic queries across federated bioinformatics databases
Knowledge-rich temporal relation identification and classification in clinical notes
LPTK: a linguistic pattern-aware dependency tree kernel approach for the BioCreative VI CHEMPROT task
MiRIAD update: using alternative polyadenylation, protein interaction network analysis and additional species to enhance exploration of the role of intragenic miRNAs and their host genes
CBPDdb: a curated database of compounds derived from Coumarin-Benzothiazole-Pyrazole
CoIN: a network analysis for document triage
agl genes, a curated and searchable database of archaeal N-glycosylation pathway components
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students
AtmiRNET: a web-based resource for reconstructing regulatory networks of Arabidopsis microRNAs
DCDB 2.0: a major update of the drug combination database
The Microbe Directory: a centralized database for biological interpretation of microbiome data
Extraction of chemical-induced diseases using prior knowledge and textual information
dbDEPC 3.0: the database of differentially expressed proteins in human cancer with multi-level annotation and drug indication
MalaCards: an integrated compendium for diseases and their annotation
ImmunoSPdb: an archive of immunosuppressive peptides
YeastMine - an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit
On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase
PhenoDigm: analyzing curated annotations to associate animal models with human diseases
Ureidoglycolate hydrolase, amidohydrolase, lyase: how errors in biological databases are incorporated in scientific papers and vice versa
Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems
Bookshelf: a simple curation system for the storage of biomolecular simulation data
Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes