yusuke1997/dblp-id-title huggingface dataset:
PCaLiStDB: a lifestyle database for precision prevention of prostate cancer
AnnoSys - implementation of a generic annotation system for schema-based data using the example of biodiversity collection data
Building an efficient curation workflow for the Arabidopsis literature corpus
Gene ontology concept recognition using named concept: understanding the various presentations of the gene functions in biomedical literature
Assisting manual literature curation for protein-protein interactions using BioQRator
CoopTFD: a repository for predicted yeast cooperative transcription factor pairs
ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides
SwissBioPics - an interactive library of cell images for the visualization of subcellular location data
Signalling maps in cancer research: construction and data analysis
Correction to: FEDA (Food Enzyme Database): a web application gathering information about food enzyme preparations available on the European market
BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences
Egas: a collaborative and interactive document curation platform
Micropublication: incentivizing community curation and placing unpublished data into the public domain
hUbiquitome: a database of experimentally verified ubiquitination cascades in humans
Assessing resource use: a case study with the Human Disease Ontology
Panorama: a database for the oncogenic evaluation of somatic mutations in pan-cancer
TransAtlasDB: an integrated database connecting expression data, metadata and variants
A database resource and online analysis tools for coronaviruses on a historical and global scale
Mining biomedical images towards valuable information retrieval in biomedical and life sciences
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII
Combining computational models, semantic annotations and simulation experiments in a graph database
Standard development at the Human Variome Project
International Cancer Genome Consortium Data Portal - a one-stop shop for cancer genomics data
GIDB: a knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal cancer
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language
Correction to: Standardized naming of microbiome samples in Genomes OnLine Database
TRSRD: a database for research on risky substances in tea using natural language processing and knowledge graph-based techniques
Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature
PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae
CircFunBase: a database for functional circular RNAs
CPMKG: a condition-based knowledge graph for precision medicine
An entropy-reducing data representation approach for bioinformatic data
PtRFdb: a database for plant transfer RNA-derived fragments
IsoPlot: a database for comparison of mRNA isoforms in fruit fly and mosquitoes
H3ABioNet genomic medicine and microbiome data portals hackathon proceedings
EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species
EpiFactors: a comprehensive database of human epigenetic factors and complexes
A teaching and training framework to promote findable, accessible, interoperable, and reusable data generation in agriculture
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards
bc-GenExMiner 4.5: new mining module computes breast cancer differential gene expression analyses
dbPepNeo: a manually curated database for human tumor neoantigen peptides
IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease
SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences
Tripal Developer Toolkit
Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects
AtFusionDB: a database of fusion transcripts in Arabidopsis thaliana
Prototheca-ID: a web-based application for molecular identification of Prototheca species
Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders
CyExpDB: a web-based multi-species tissue-specific gene expression platform for functional genomics in Cyprinidae fish
The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database
RGPDB: database of root-associated genes and promoters in maize, soybean, and sorghum
dbGENVOC: database of GENomic Variants of Oral Cancer, with special reference to India
StrainInfo - the central database for linked microbial strain identifiers
Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt
Biocurators and Biocuration: surveying the 21st century challenges
TRedD - A database for tandem repeats over the edit distance
DeepScreening: a deep learning-based screening web server for accelerating drug discovery
JAMIR-eQTL: Japanese genome-wide identification of microRNA expression quantitative trait loci across dementia types
Strategies for annotation and curation of translational databases: the eTUMOUR project
CancerEST: a web-based tool for automatic meta-analysis of public EST data
Integrated data-driven biotechnology research environments
SorghumFDB: sorghum functional genomics database with multidimensional network analysis
CancerMA: a web-based tool for automatic meta-analysis of public cancer microarray data
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII
Web services-based text-mining demonstrates broad impacts for interoperability and process simplification
Application of beta and gamma carbonic anhydrase sequences as tools for identification of bacterial contamination in the whole genome sequence of inbred Wuzhishan minipig (Sus scrofa) annotated in databases
A survey of ontology learning techniques and applications
Prot2HG: a database of protein domains mapped to the human genome
piRBase: a web resource assisting piRNA functional study
A database of wild rice germplasm of Oryza rufipogon species complex from different agro-climatic zones of India
A scalable, aggregated genotypic-phenotypic database for human disease variation
The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species
Biocuration in the structure-function linkage database: the anatomy of a superfamily
Gramene QTL database: development, content and applications
The InterPro BioMart: federated query and web service access to the InterPro Resource
SymbioGenomesDB: a database for the integration and access to knowledge on host-symbiont relationships
ctcRbase: the gene expression database of circulating tumor cells and microemboli
The state of the human coding gene catalogues
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer
mutTCPdb: a comprehensive database for genomic variants of a tropical country neglected disease - tropical calcific pancreatitis
Drug-Path: a database for drug-induced pathways
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation
The challenge of increasing Pfam coverage of the human proteome
Chemical-gene relation extraction using recursive neural network
Reefgenomics.Org - a repository for marine genomics data
Meeting report: a workshop on Best Practices in Genome Annotation
DPTEdb, an integrative database of transposable elements in dioecious plants
The Breeding Information Management System (BIMS): an online resource for crop breeding
Research resources: curating the new eagle-i discovery system
dbCRY: a Web-based comparative and evolutionary genomics platform for blue-light receptors
Phenotype-genotype network construction and characterization: a case study of cardiovascular diseases and associated non-coding RNAs
TP53LNC-DB, the database of lncRNAs in the p53 signalling network
Quality assurance for the query and distribution systems of the RCSB Protein Data Bank
MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins
MET network in PubMed: a text-mined network visualization and curation system
Oomycete Gene Table: an online database for comparative genomic analyses of the oomycete microorganisms
YHMI: a web tool to identify histone modifications and histone/chromatin regulators from a gene list in yeast
A new unbiased and highly automated approach to find new prognostic markers in preclinical research
Biocuration with insufficient resources and fixed timelines
Nencki Genomics Database - Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs
URS DataBase: universe of RNA structures and their motifs
NALDB: nucleic acid ligand database for small molecules targeting nucleic acid
Autophagy3D: a comprehensive autophagy structure database
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database
BRACS: A Dataset for BReAst Carcinoma Subtyping in H&E Histology Images
ASAP: a machine learning framework for local protein properties
Document triage for identifying protein-protein interactions affected by mutations: a neural network ensemble approach
FARME DB: a functional antibiotic resistance element database
ResMarkerDB: a database of biomarkers of response to antibody therapy in breast and colorectal cancer
ORION-VIRCAT: a tool for mapping ICTV and NCBI taxonomies
ROSBASE1.0: a comprehensive database of reactive oxygen species (ROS): categorization of cell organelles, proteins, taxonomy, and diseases based on ROS-related activities
YAAM: Yeast Amino Acid Modifications Database
Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework
GTDB: an integrated resource for glycosyltransferase sequences and annotations
BioC viewer: a web-based tool for displaying and merging annotations in BioC
Building a biomedical semantic network in Wikipedia with Semantic Wiki Links
PlantCAZyme: a database for plant carbohydrate-active enzymes
Ensembl variation resources
GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques
Damming the genomic data flood using a comprehensive analysis and storage data structure
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods
GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics
WASP: the World Archives of Species Perception
kpath: integration of metabolic pathway linked data
FairBase: a comprehensive database of fungal A-to-I RNA editing
Leveraging prior knowledge for protein-protein interaction extraction with memory network
Neisseria Base: a comparative genomics database for Neisseria meningitidis
PolED: a manually curated database of functional studies of POLE and POLD1 variants reported in humans
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins
HPVdb: a data mining system for knowledge discovery in human papillomavirus with applications in T cell immunology and vaccinology
BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences
NONATObase: a database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules
Which methods are the most effective in enabling novice users to participate in ontology creation? A usability study
BbGSD: Black-boned Sheep Genome SNP Database
Enhancing statistical analysis of real world data
ANCO-GeneDB: annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine and opioid dependence
Corrigendum to: QSDB - a graphical Quorum Sensing Database
Advancing microbiome research through standardized data and metadata collection: introducing the Microbiome Research Data Toolkit
Variation benchmark datasets: update, criteria, quality and applications
A cross-source, system-agnostic solution for clinical data review
MnTEdb, a collective resource for mulberry transposable elements
Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase
Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases
BENviewer: a gene interaction network visualization server based on graph embedding model
RAvariome: a genetic risk variants database for rheumatoid arthritis based on assessment of reproducibility between or within human populations
MSV3d: database of human MisSense variants mapped to 3D protein structure
lncRNome: a comprehensive knowledgebase of human long noncoding RNAs
InSexBase: an annotated genomic resource of sex chromosomes and sex-biased genes in insects
BuffExDb: web-based tissue-specific gene expression resource for breeding and conservation programmes in Bubalus bubalis
aSynPEP-DB: a database of biogenic peptides for inhibiting α-synuclein aggregation
ppiTrim: constructing non-redundant and up-to-date interactomes
INOH: ontology-based highly structured database of signal transduction pathways
The Protein Model Portal - a comprehensive resource for protein structure and model information
PPInterFinder - a mining tool for extracting causal relations on human proteins from literature
Boechera microsatellite website: an online portal for species identification and determination of hybrid parentage
RiceRelativesGD: a genomic database of rice relatives for rice research
NTTMUNSW BioC modules for recognizing and normalizing species and gene/protein mentions
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations
Argo: an integrative, interactive, text mining-based workbench supporting curation
MetaProx: the database of metagenomic proximons
DBM-DB: the diamondback moth genome database
BCL2DB: database of BCL-2 family members and BH3-only proteins
DDRprot: a database of DNA damage response-related proteins
LitCovid ensemble learning for COVID-19 multi-label classification
GRONS: a comprehensive genetic resource of nicotine and smoking
<tt>met v1</tt>: expanding on old estimations of biodiversity from eDNA with a new database framework
BioMart as an integration solution for the International Knockout Mouse Consortium
Chemical-protein relation extraction with ensembles of carefully tuned pretrained language models
BioMart Central Portal: an open database network for the biological community
GEOMetaCuration: a web-based application for accurate manual curation of Gene Expression Omnibus metadata
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms
Large-scale automated machine reading discovers new cancer-driving mechanisms
ConoMode, a database for conopeptide binding modes
BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph
BioC implementations in Go, Perl, Python and Ruby
WellExplorer: an integrative resource linking hydraulic fracturing chemicals with hormonal pathways and geographic location
MEDFORD: A human- and machine-readable metadata markup language
The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update
Text mining resources for the life sciences
Building a pipeline to solicit expert knowledge from the community to aid gene summary curation
Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data
PPCRKB: a risk factor knowledge base of postoperative pulmonary complications
PlantGF: an analysis and annotation platform for plant gene families
ScLineageAtlas: a comprehensive single-cell genomics database for characterizing cellular clones in cancer
Tetrahymena Functional Genomics Database (TetraFGD): an integrated resource for Tetrahymena functional genomics
DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions
Revenant: a database of resurrected proteins
Mesophotic.org: a repository for scientific information on mesophotic ecosystems
CARD*Shark: automated prioritization of literature curation for the Comprehensive Antibiotic Resistance Database
SMMDB: a web-accessible database for small molecule modulators and their targets involved in neurological diseases
NeuroTransDB : highly curated and structured transcriptomic metadata for neurodegenerative diseases
CeleryDB: a genomic database for celery
The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions
GrainGenes: centralized small grain resources and digital platform for geneticists and breeders
ChagasDB: 80 years of publicly available data on the molecular host response to Trypanosoma cruzi infection in a single database
Characterization and automated classification of sentences in the biomedical literature: a case study for biocuration of gene expression and protein kinase activity
KinMod database: a tool for investigating metabolic regulation
ChemDIS 2: an update of chemical-disease inference system
A comprehensive database for biological data derived from sewage in five European cities
CorkOakDB - The Cork Oak Genome Database Portal
Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer
GNIFdb: a neoantigen intrinsic feature database for glioma
Hierarchical bi-directional attention-based RNNs for supporting document classification on protein-protein interactions affected by genetic mutations
mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support
KTCNlncDB - a first platform to investigate lncRNAs expressed in human keratoconus and non-keratoconus corneas
blend4php: a PHP API for galaxy
An update of KAIKObase, the silkworm genome database
The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine
Annotation of gene product function from high-throughput studies using the Gene Ontology
SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population
PepPSy: a web server to prioritize gene products in experimental and biocuration workflows
NRDTD: a database for clinically or experimentally supported non-coding RNAs and drug targets associations
BmTEdb: a collective database of transposable elements in the silkworm genome
Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL)
MycoResistance: a curated resource of drug resistance molecules in Mycobacteria
OakRootRNADB - a consolidated RNA-seq database for coding and noncoding RNA in roots of pedunculate oak ( Quercus robur )
Tissue-specific transcriptomes reveal potential mechanisms of microbiome heterogeneity in an ancient fish
RTeQTL: Real-Time Online Engine for Expression Quantitative Trait Loci Analyses
RiceATM: a platform for identifying the association between rice agronomic traits and miRNA expression
Ensembl BioMarts: a hub for data retrieval across taxonomic space
RNA CoSSMos 2.0: an improved searchable database of secondary structure motifs in RNA three-dimensional structures
A general approach for improving deep learning-based medical relation extraction using a pre-trained model and fine-tuning
To increase trust, change the social design behind aggregated biodiversity data
HeartBioPortal2.0: new developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations
SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes
PASS2: update of database of structure-based sequence alignments
GATMD: γ-Aminobutyric Acid Transporter Mutagenesis Database
The Prion Disease Database: a comprehensive transcriptome resource for systems biology research in prion diseases
The Global Genome Biodiversity Network (GGBN) Data Standard specification
SNPversity: a web-based tool for visualizing diversity
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation
Potent pairing: ensemble of long short-term memory networks and support vector machine for chemical-protein relation extraction
hCoronavirusesDB: an integrated bioinformatics resource for human coronaviruses
Tetrahymena Comparative Genomics Database (TCGD): a community resource for Tetrahymena
Correction to: SEPDB: a database of secreted proteins
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells
HyperCAT: an extension of the SuperCAT database for global multi-scheme and multi-datatype phylogenetic analysis of the Bacillus cereus group population
CAS: enhancing implicit constrained data augmentation with semantic enrichment for biomedical relation extraction and beyond
G4RNA: an RNA G-quadruplex database
GAN: a platform of genomics and genetics analysis and application in Nicotiana
DATABASE : A new forum for biological databases and curation
Allie: a database and a search service of abbreviations and long forms
NDDVD: an integrated and manually curated Neurodegenerative Diseases Variation Database
PHILM2Web: A high-throughput database of macromolecular host-pathogen interactions on the Web
Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications
DemaDb: an integrated dematiaceous fungal genomes database
MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes
CHDGKB: a knowledgebase for systematic understanding of genetic variations associated with non-syndromic congenital heart disease
Curated protein information in the Saccharomyces genome database
HTS-DB: an online resource to publish and query data from functional genomics high-throughput siRNA screening projects
First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes
Incorporation of a unified protein abundance dataset into the Saccharomyces genome database
Sequencing and comparative analysis of the gorilla MHC genomic sequence
Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain
TEx-MST: tissue expression profiles of MANE select transcripts
DFVF: database of fungal virulence factors
Diseases 2.0: a weekly updated database of disease-gene associations from text mining and data integration
MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens
Proficiency of data interpretation: identification of signaling SNPs/specific loci for coronary artery disease
Global Globin Network and adopting genomic variant database requirements for thalassemia
SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases
PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding
Curation accuracy of model organism databases
Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications
Acinetobase: the comprehensive database and repository of Acinetobacter strains
Mining chemical patents with an ensemble of open systems
RecipeDB: a resource for exploring recipes
Landscape of racial and ethnic health disparities in the All of Us Research Program
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling