yusuke1997/dblp-id-title huggingface dataset:
Argo: enabling the development of bespoke workflows and services for disease annotation
RSIADB, a collective resource for genome and transcriptome analyses in Rhizoctonia solani AG1 IA
SAGER: a database of Symbiodiniaceae and Algal Genomic Resource
ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions
SesamumGDB: a comprehensive platform for Sesamum genetics and genomics analysis
MODEM: multi-omics data envelopment and mining in maize
Benchmarking distributed data warehouse solutions for storing genomic variant information
AutismKB 2.0: a knowledgebase for the genetic evidence of autism spectrum disorder
A review of the International Seabed Authority database DeepData from a biological perspective: challenges and opportunities in the UN Ocean Decade
MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution
piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation
GExplore 1.5: a comprehensive Caenorhabditis elegans database for the analysis of gene function with a new user-friendly web interface
PCOSBase: a manually curated database of polycystic ovarian syndrome
Progress in the study of genome size evolution in Asteraceae: analysis of the last update
TIMBAL v2: update of a database holding small molecules modulating protein-protein interactions
CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea
Identifying frequent patterns in biochemical reaction networks: a workflow
GeMI: interactive interface for transformer-based Genomic Metadata Integration
FishTrace: a genetic catalogue of European fishes
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research
PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes
miRBase Tracker: keeping track of microRNA annotation changes
Navigating open-source waters: the pharmaceutical industry's role in bioontology development
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation
MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses
Structured reviews for data and knowledge-driven research
Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text
Analysis and review of techniques and tools based on machine learning and deep learning for prediction of lysine malonylation sites in protein sequences
VineColD: an integrative database for global historical tracing and real-time monitoring of grapevine cold hardiness
iMITEdb: the genome-wide landscape of miniature inverted-repeat transposable elements in insects
Scaling drug indication curation through crowdsourcing
Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR
A BERT-based ensemble learning approach for the BioCreative VII challenges: full-text chemical identification and multi-label classification in PubMed articles
Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach
Directly e-mailing authors of newly published papers encourages community curation
The Homeodomain Resource: a comprehensive collection of sequence, structure, interaction, genomic and functional information on the homeodomain protein family
Small molecule annotation for the Protein Data Bank
Where differences resemble: sequence-feature analysis in curated databases of intrinsically disordered proteins
CellExpress: a comprehensive microarray-based cancer cell line and clinical sample gene expression analysis online system
Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado
Why data citation isn't working, and what to do about it
Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans
Portal of medical data models: information infrastructure for medical research and healthcare
Strengthening of banana breeding through data digitalization
DIRMC: a database of immunotherapy-related molecular characteristics
BLAB2CancerKD: a knowledge graph database focusing on the association between lactic acid bacteria and cancer, but beyond
AagingBase: a comprehensive database of anti-aging peptides
Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME
PLBD: protein-ligand binding database of thermodynamic and kinetic intrinsic parameters
Quantitative phenotype analysis to identify, validate and compare rat disease models
Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content
Genome-wide identification of SSR markers from coding regions for endangered Argania spinosa L. skeels and construction of SSR database: AsSSRdb
NipahVR: a resource of multi-targeted putative therapeutics and epitopes for the Nipah virus
ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls
FDRdb: a manually curated database of fibrotic disease-associated RNAome and high-throughput datasets
LocSigDB: a database of protein localization signals
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
HPIDB 2.0: a curated database for host-pathogen interactions
EnhancerDB: a resource of transcriptional regulation in the context of enhancers
LAMP2: a major update of the database linking antimicrobial peptides
dbPEC: a comprehensive literature-based database for preeclampsia related genes and phenotypes
Predicting structured metadata from unstructured metadata
The relational modeling of hierarchical data in biodiversity databases
TcEVdb: a database for T-cell-derived small extracellular vesicles from single-cell transcriptomes
CarrotDB: a genomic and transcriptomic database for carrot
Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms
An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar
COMPARTMENTS: unification and visualization of protein subcellular localization evidence
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort
PSINDB: the postsynaptic protein-protein interaction database
miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs
WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans
Autoinhibited Protein Database: a curated database of autoinhibitory domains and their autoinhibition mechanisms
TMC-SNPdb: an Indian germline variant database derived from whole exome sequences
CardioHotspots: a database of mutational hotspots for cardiac disorders
WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions
Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID
MESSI: metabolic engineering target selection and best strain identification tool
CCIDB: a manually curated cell-cell interaction database with cell context information
BRONCO: Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations
SoDCoD: a comprehensive database of Cu/Zn superoxide dismutase conformational diversity caused by ALS-linked gene mutations and other perturbations
GdbMTB: a manually curated genomic database of magnetotactic bacteria
Ontology application and use at the ENCODE DCC
FirebrowseR: an R client to the Broad Institute's Firehose Pipeline
miRIAD - integrating microRNA inter- and intragenic data
VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases
Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus
Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase
Multi-omics molecular biomarkers and database of osteoarthritis
Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems
Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases
Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications
toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research
Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies
DevMouse, the mouse developmental methylome database and analysis tools
Spfy: an integrated graph database for real-time prediction of bacterial phenotypes and downstream comparative analyses
CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization
InTxDB: interaction data between gram-negative bacteria secreted effectors and host proteins
BioSCOOP - Biobank Sample Communication Protocol. New approach for the transfer of information between biobanks
Mining clinical attributes of genomic variants through assisted literature curation in Egas
sc BrainMap: a landscape for cell types and associated genetic markers in the brain
BioCreative-2012 Virtual Issue
The African Human Microbiome Portal: a public web portal of curated metagenomic metadata
Ontology based text mining of gene-phenotype associations: application to candidate gene prediction
dbCRSR: a manually curated database for regulation of cancer radiosensitivity
MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups
SinEx DB: a database for single exon coding sequences in mammalian genomes
Extracting chemical-protein relations using attention-based neural networks
Review of databases for experimentally validated human microRNA-mRNA interactions
TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants
viruSITE - integrated database for viral genomics
RAC: Repository of Antibiotic resistance Cassettes
piRDisease v1.0: a manually curated database for piRNA associated diseases
Ensembl regulation resources
GreenCircRNA: a database for plant circRNAs that act as miRNA decoys
metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research
AneRBC dataset: a benchmark dataset for computer-aided anemia diagnosis using RBC images
MetaTropismDB: a database of organ-specific metastasis induced by human cancer cell lines in mouse models
LettuceDB: an integrated multi-omics database for cultivated lettuce
RabGTD: a comprehensive database of rabbit genome and transcriptome
Liposomal Cancer Drug Database (LCDD): a comprehensive resource for liposome research in cancer therapy and diagnosis
LMPID: A manually curated database of linear motifs mediating protein-protein interactions
Improving biomedical entity linking for complex entity mentions with LLM-based text simplification
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence
YY1TargetDB: an integral information resource for Yin Yang 1 target loci
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics
Curation of characterized glycoside hydrolases of Fungal origin
PRIDE: Quality control in a proteomics data repository
Integrated curation and data mining for disease and phenotype models at the Rat Genome Database
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII
PGP repository: a plant phenomics and genomics data publication infrastructure
CyanoClust: comparative genome resources of cyanobacteria and plastids
OntoMate: a text-mining tool aiding curation at the Rat Genome Database
NBDC RDF portal: a comprehensive repository for semantic data in life sciences
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity
ConTEdb: a comprehensive database of transposable elements in conifers
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium
Assessing the use of supplementary materials to improve genomic variant discovery
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture
RegEl corpus: identifying DNA regulatory elements in the scientific literature
dbBIP: a comprehensive bipolar disorder database for genetic research
SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss
Bioinformatics tools developed to support BioCompute Objects
A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway
Curating gene sets: challenges and opportunities for integrative analysis
CPDMS: a database system for crop physiological disorder management
Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification
Identification of errors in the IEDB using ontologies
A probabilistic automated tagger to identify human-related publications
CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation
An update of miRNASNP database for better SNP selection by GWAS data, miRNA expression and online tools
Hybrid curation of gene-mutation relations combining automated extraction and crowdsourcing
CrossTope: a curate repository of 3D structures of immunogenic peptide: MHC complexes
TeaMiD: a comprehensive database of simple sequence repeat markers of tea
Using BioMart as a framework to manage and query pancreatic cancer data
miR-TV: an interactive microRNA Target Viewer for microRNA and target gene expression interrogation for human cancer studies
p53motifDB: integration of genomic information and tumour suppressor p53 binding motifs
CIGAF - a database and interactive platform for insect-associated trichomycete fungi
BGDB: a database of bivalent genes
A genotypic and phenotypic information source for marker-assisted selection of cereals: the CEREALAB database
TFLink: an integrated gateway to access transcription factor-target gene interactions for multiple species
In silico characterization of tandem repeats in Trichophyton rubrum and related dermatophytes provides new insights into their role in pathogenesis
Linking tissues to phenotypes using gene expression profiles
yStreX: yeast stress expression database
The Rat Genome Database Pathway Portal
DEXTER: Disease-Expression Relation Extraction from Text
The HIV oligonucleotide database (HIVoligoDB)
PIPE: a protein-protein interaction passage extraction module for BioCreative challenge
Choosing a genome browser for a Model Organism Database: surveying the Maize community
ThermoPCD: a database of molecular dynamics trajectories of antibody-antigen complexes at physiologic and fever-range temperatures
IGVBrowser-a genomic variation resource from diverse Indian populations
A curated database reveals trends in single-cell transcriptomics
Creating a Metabolic Syndrome Research Resource using the National Health and Nutrition Examination Survey
Ensembl comparative genomics resources
CropCircDB: a comprehensive circular RNA resource for crops in response to abiotic stress
STRIDE-DB: a comprehensive database for exploration of instability and phenotypic relevance of short tandem repeats in the human genome
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies
NetSlim: high-confidence curated signaling maps
HerDing: herb recommendation system to treat diseases using genes and chemicals
Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research
Annotating the biomedical literature for the human variome
An online system for metabolic network analysis
IPAD-DB: a manually curated database for experimentally verified inhibitors of proteins associated with Alzheimer's disease
GFDP: the gene family database in poplar
Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database
SpinachBase: a central portal for spinach genomics
CEG 2.0: an updated database of clusters of essential genes including eukaryotic organisms
Developing TeroENZ and TeroMAP modules for the terpenome research platform TeroKit
AGODB: a comprehensive domain annotation database of argonaute proteins
NERChem: adapting NERBio to chemical patents via full-token features and named entity feature with chemical sub-class composition
HTT-DB: new features and updates
GnpIS: an information system to integrate genetic and genomic data from plants and fungi
MaizeGDB becomes 'sequence-centric'
microPIR2: a comprehensive database for human-mouse comparative study of microRNA-promoter interactions
PCIR: a database of Plant Chloroplast Inverted Repeats
The eFIP system for text mining of protein interaction networks of phosphorylated proteins
DLREFD: a database providing associations of long non-coding RNAs, environmental factors and phenotypes
Extraction of chemical-protein interactions from the literature using neural networks and narrow instance representation
Tripal: a construction toolkit for online genome databases
Probe my Pathway (PmP): a portal to explore the chemical coverage of the human Reactome
Efficient chemical-disease identification and relationship extraction using Wikipedia to improve recall
Improving taxonomic accuracy for fungi in public sequence databases: applying 'one name one species' in well-defined genera with Trichoderma/Hypocrea as a test case
Uncovering hidden duplicated content in public transcriptomics data
SysPTM 2.0: an updated systematic resource for post-translational modification
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources
CobVar - a comprehensive resource of vitamin B12-associated genomic variants
A semantic-based workflow for biomedical literature annotation
LncCeRBase: a database of experimentally validated human competing endogenous long non-coding RNAs
MRdb: a comprehensive database of univariate and multivariate Mendelian randomization with large-scale GWAS summary data
Skeleton Genetics: a comprehensive database for genes and mutations related to genetic skeletal disorders
CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects
CircR2Disease: a manually curated database for experimentally supported circular RNAs associated with various diseases
siAbasic: a comprehensive database for potent siRNA-6Ø sequences without off-target effects
Applying graph database technology for analyzing perturbed co-expression networks in cancer
Novel methods included in SpolLineages tool for fast and precise prediction of Mycobacterium tuberculosis complex spoligotype families
CITGeneDB: a comprehensive database of human and mouse genes enhancing or suppressing cold-induced thermogenesis validated by perturbation experiments in mice
The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes
FerrDb: a manually curated resource for regulators and markers of ferroptosis and ferroptosis-disease associations
uORFlight: a vehicle toward uORF-mediated translational regulation mechanisms in eukaryotes
Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation
BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis
ZincBind - the database of zinc binding sites
Establishment of Kawasaki disease database based on metadata standard
TeloPIN: a database of telomeric proteins interaction network in mammalian cells
SITVITBovis - a publicly available database and mapping tool to get an improved overview of animal and human cases caused by Mycobacterium bovis
SGID: a comprehensive and interactive database of the silkworm
A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework
A Web-based database of genetic association studies in cutaneous melanoma enhanced with network-driven data exploration tools
EUKARYOME: the rRNA gene reference database for identification of all eukaryotes
ISTransbase: an online database for inhibitor and substrate of drug transporters
The eGenVar data management system - cataloguing and sharing sensitive data and metadata for the life sciences
Working in biocuration: contemporary experiences and perspectives
neXtA 5 : accelerating annotation of articles via automated approaches in neXtProt
RetrogeneDB-a database of plant and animal retrocopies
OGDA: a comprehensive organelle genome database for algae
Outreach and online training services at the Saccharomyces Genome Database
MACSFeD - a database of mosquito acoustic communication and swarming features
Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature
AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments
PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan
Updated regulation curation model at the Saccharomyces Genome Database
TogoGenome/TogoStanza: modularized Semantic Web genome database
Using binary classification to prioritize and curate articles for the Comparative Toxicogenomics Database
Extraction of causal relations based on SBEL and BERT model
MBS: a genome browser annotation track for high-confident microRNA binding sites in whole human transcriptome
Correction to: H3ABioNet genomic medicine and microbiome data portals hackathon proceedings
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery
AGD: Aneurysm Gene Database
Tripal MegaSearch: a tool for interactive and customizable query and download of big data
HAHmiR.DB: a server platform for high-altitude human miRNA-gene coregulatory networks and associated regulatory circuits
AmyloWiki: an integrated database for Bacillus velezensis FZB42, the model strain for plant growth-promoting Bacilli
Determining similarity of scientific entities in annotation datasets
Building a large gene expression-cancer knowledge base with limited human annotations
CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR
Integration of new alternative reference strain genome sequences into the Saccharomyces genome database
IRAM: virus capsid database and analysis resource
A curated online resource for SOX10 and pigment cell molecular genetic pathways
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function
DCMP: database of cancer mutant protein domains
ToxReporter: viewing the genome through the eyes of a toxicologist
CropGF: a comprehensive visual platform for crop gene family mining and analysis
GeneStoryTeller: a mobile app for quick and comprehensive information retrieval of human genes
A database of thermodynamic properties of the reactions of glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway
Comparison of human cell signaling pathway databases - evolution, drawbacks and challenges
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors
mPPI: a database extension to visualize structural interactome in a one-to-many manner
Differential ligand-signaling network of CCL19/CCL21-CCR7 system
SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data
VerSeDa: vertebrate secretome database
Bio-AnswerFinder: a system to find answers to questions from biomedical texts
Integrative Cancer Genomics (IntOGen) in Biomart