yusuke1997/dblp-id-title huggingface dataset:
A generic workflow for effective sampling of environmental vouchers with UUID assignment and image processing
Differential direct coding: a compression algorithm for nucleotide sequence data
KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins
A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing
Automatic query generation using word embeddings for retrieving passages describing experimental methods
Improved biomedical term selection in pseudo relevance feedback
ChlamBase: a curated model organism database for the Chlamydia research community
SPTEdb: a database for transposable elements in salicaceous plants
The impact of curation errors in the PDBBind Database on machine learning predictions of protein-protein binding affinity
HSDatabase - a database of highly similar duplicate genes from plants, animals, and algae
Towards BioDBcore: a community-defined information specification for biological databases
Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation
GeniePool 2.0: advancing variant analysis through CHM13-T2T, AlphaMissense, gnomAD V4 integration, and variant co-occurrence queries
Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical-protein relations
A new database of chestnut DNA fingerprints for genetic diversity assessment, precise varietal identification, and traceability
A Field Sensor: computing the composition and intent of PubMed queries
Improving the consistency of domain annotation within the Conserved Domain Database
Multi-field query expansion is effective for biomedical dataset retrieval
TuberQ: a Mycobacterium tuberculosis protein druggability database
RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals
GenoSurf: metadata driven semantic search system for integrated genomic datasets
Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource
MineProt: a stand-alone server for structural proteome curation
SCNBase: a genomics portal for the soybean cyst nematode (Heterodera glycines)
BioC: a minimalist approach to interoperability for biomedical text processing
Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes
NetREx: Network-based Rice Expression Analysis Server for abiotic stress conditions
BioMart: driving a paradigm change in biological data management
Addition of a breeding database in the Genome Database for Rosaceae
RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins
MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data
The importance of identifying alternative splicing in vertebrate genome annotation
New reasons for biologists to write with a formal language
Effect of database drift on network topology and enrichment analyses: a case study for RegulonDB
Database of resistance related metabolites in Wheat Fusarium head blight Disease (MWFD)
HNdb: an integrated database of gene and protein information on head and neck squamous cell carcinoma
AntiFam: a tool to help identify spurious ORFs in protein annotation
SPDB: a specialized database and web-based analysis platform for swine pathogens
AgingReG: a curated database of aging regulatory relationships in humans
MiDAS: the field guide to the microbes of activated sludge
MGFD: the maize gene families database
Community gene annotation in practice
Unified and pluralistic ideals for data sharing and reuse in biodiversity
GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii)
Improved ontology for eukaryotic single-exon coding sequences in biological databases
COTTONOMICS: a comprehensive cotton multi-omics database
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task
GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR
Phenol-Explorer 2.0: a major update of the Phenol-Explorer database integrating data on polyphenol metabolism and pharmacokinetics in humans and experimental animals
Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community
PIPEMicroDB: microsatellite database and primer generation tool for pigeonpea genome
The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data
Drug Target Commons 2.0: a community platform for systematic analysis of drug-target interaction profiles
The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge
SOCCOMAS: a FAIR web content management system that uses knowledge graphs and that is based on semantic programming
Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study
Fungal Stress Database (FSD)--a repository of fungal stress physiological data
LanceletDB: an integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues
BEAN 2.0: an integrated web resource for the identification and functional analysis of type III secreted effectors
ChemBioPort: an online portal to navigate the structure, function and chemical inhibition of the human proteome
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF
LiqBioer: a manually curated database of cancer biomarkers in body fluid
An overview of graph databases and their applications in the biomedical domain
VarStack: a web tool for data retrieval to interpret somatic variants in cancer
GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle
RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome
PvTFDB: a Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes
Integrating diverse databases into an unified analysis framework: a Galaxy approach
RAIN: RNA-protein Association and Interaction Networks
Developing the eHistology Atlas
MACSNVdb: a high-quality SNV database for interspecies genetic divergence investigation among macaques
Value, but high costs in post-deposition data curation
YQFC: a web tool to compare quantitative biological features between two yeast gene lists
'RetinoGenetics': a comprehensive mutation database for genes related to inherited retinal degeneration
Automated semantic annotation of rare disease cases: a case study
The BioMart interface to the eMouseAtlas gene expression database EMAGE
NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes
Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes
Chemical annotation of small and peptide-like molecules at the Protein Data Bank
An analysis of FRE @ BC8 SympTEMIST track: named entity recognition
The importance of graph databases and graph learning for clinical applications
Fishing for data and sorting the catch: assessing the data quality, completeness and fitness for use of data in marine biogeographic databases
AthRiboNC: an Arabidopsis database for ncRNAs with coding potential revealed from ribosome profiling
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics
MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase
A guide to best practices for Gene Ontology (GO) manual annotation
IRNdb: the database of immunologically relevant non-coding RNAs
HCoVDB: a comprehensive database encompassing viral genomes, drug targets, and therapeutics of human coronaviruses
A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements
The strategies WDK: a graphical search interface and web development kit for functional genomics databases
Correction to: Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium
Cryptosporidium hominis gene catalog: a resource for the selection of novel Cryptosporidium vaccine candidates
The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions
nhanesA: achieving transparency and reproducibility in NHANES research
OpenFluDB, a database for human and animal influenza virus
DMLS: an automated pipeline to extract the Drosophila modular transcription regulators and targets from massive literature articles
MtiBase: a database for decoding microRNA target sites located within CDS and 5′UTR regions from CLIP-Seq and expression profile datasets
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank
3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale
Zoonosis: a comprehensive database of zoonotic pathogens
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study
Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype
BioCreative V CDR task corpus: a resource for chemical disease relation extraction
Minimizing proteome redundancy in the UniProt Knowledgebase
Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora
The Progenetix oncogenomic resource in 2021
The human DEPhOsphorylation Database DEPOD: 2019 update
CCRDB: a cancer circRNAs-related database and its application in hepatocellular carcinoma-related circRNAs
Gene Ontology curation of the blood-brain barrier to improve the analysis of Alzheimer's and other neurological diseases
MisPred: a resource for identification of erroneous protein sequences in public databases
Modeling biochemical pathways in the gene ontology
yApoptosis: yeast apoptosis database
An effective biomedical document classification scheme in support of biocuration: addressing class imbalance
Nabe: an energetic database of amino acid mutations in protein-nucleic acid binding interfaces
FooDrugs: a comprehensive food-drug interactions database with text documents and transcriptional data
A CTD-Pfizer collaboration: manual curation of 88 000 scientific articles text mined for drug-disease and drug-phenotype interactions
ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases
CPPsite: a curated database of cell penetrating peptides
Curation of cancer hallmark-based genes and pathways for in silico characterization of chemical carcinogenesis
Comprehensive comparative homeobox gene annotation in human and mouse
SLOAD: a comprehensive database of cancer-specific synthetic lethal interactions for precision cancer therapy via multi-omics analysis
TopoDB: a novel multifunctional management system for laboratory animal colonies
QSDB - a graphical Quorum Sensing Database
GEMiCCL: mining genotype and expression data of cancer cell lines with elaborate visualization
IQdb: an intelligence quotient score-associated gene resource for human intelligence
miRGate: a curated database of human, mouse and rat miRNA-mRNA targets
Human metabolic atlas: an online resource for human metabolism
cancercelllines.org - a novel resource for genomic variants in cancer cell lines
Towards building a trustworthy pipeline integrating Neuroscience Gateway and Open Science Chain
LPS-annotate: complete annotation of compositionally biased regions in the protein knowledgebase
MolMeDB: Molecules on Membranes Database
Crowd-sourcing and author submission as alternatives to professional curation
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses
Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance
AuDis: an automatic CRF-enhanced disease normalization in biomedical text
Annotation and curation of the causality information in LncRNADisease
Overview of the gene ontology task at BioCreative IV
Human Breathomics Database
PurificationDB: database of purification conditions for proteins
A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)
Plant Regulomics Portal (PRP): a comprehensive integrated regulatory information and analysis portal for plant genomes
Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences
Biomedical relation extraction with knowledge base-refined weak supervision
Improving average ranking precision in user searches for biomedical research datasets
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences
PotatoBSLnc: a curated repository of potato long noncoding RNAs in response to biotic stress
ToxDB: pathway-level interpretation of drug-treatment data
BCEDB: a linear B-cell epitopes database for SARS-CoV-2
CitrusKB: a comprehensive knowledge base for transcriptome and interactome of Citrus spp. infected by Xanthomonas citri subsp. citri at different infection stages
SalivaDB - a comprehensive database for salivary biomarkers in humans
DUVEL: an active-learning annotated biomedical corpus for the recognition of oligogenic combinations
A comprehensive view of the web-resources related to sericulture
Mouse Resource Browser - a database of mouse databases
Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis
An open-access data set of pig skin anatomy and physiology for modelling purposes
The Odonata of China: a data-driven, open-access resource for biodiversity research and conservation
Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms
PMBD: a Comprehensive Plastics Microbial Biodegradation Database
Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments
RRMdb - an evolutionary-oriented database of RNA recognition motif sequences
Managing and monitoring a pandemic: showcasing a practical approach for the genomic surveillance of SARS-CoV-2
The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data
A nomenclature for echinoderm genes
PathCards: multi-source consolidation of human biological pathways
Automatic extraction of transcriptional regulatory interactions of bacteria from biomedical literature using a BERT-based approach
The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses
Automatic genetic phenotype normalization from dysmorphology physical examinations: an overview of the BioCreative VIII - Task 3 competition
Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs
Biopanning data bank 2018: hugging next generation phage display
Design of the formalized and integrated Alzheimer's Disease Ontology and its application in retrieving textual data via text mining
BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans
PCPPI: a comprehensive database for the prediction of Penicillium-crop protein-protein interactions
DisGeNet: a disease-centric interaction database among diseases and various associated genes
EssOilDB: a database of essential oils reflecting terpene composition and variability in the plant kingdom
dbPPT: a comprehensive database of protein phosphorylation in plants
myPhyloDB: a local web server for the storage and analysis of metagenomic data
athisomiRDB: A comprehensive database of Arabidopsis isomiRs
AntiTbPdb: a knowledgebase of anti-tubercular peptides
AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba
The UniProtKB guide to the human proteome
COVIDium: a COVID-19 resource compendium
Correction to: ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides
Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system
An immunologically friendly classification of non-peptidic ligands
CCProf: exploring conformational change profile of proteins
MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse
MicroScope: a platform for microbial genome annotation and comparative genomics
Exploring convolutional neural networks for drug-drug interaction extraction
Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens
T-HOD: a literature-based candidate gene database for hypertension, obesity and diabetes
AnthraxKP: a knowledge graph-based, Anthrax Knowledge Portal mined from biomedical literature
SigReannot-mart: a query environment for expression microarray probe re-annotations
PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus . Application in hypertension and renal disease
circExp database: an online transcriptome platform for human circRNA expressions in cancers
iCAV: an integrative database of cancer-associated viruses
KRGDB: the large-scale variant database of 1722 Koreans based on whole genome sequencing
PvaxDB: a comprehensive structural repository of Plasmodium vivax proteome
LymPHOS 2.0: an update of a phosphosite database of primary human T cells
BioC interoperability track overview
GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies
A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge
CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations
PubMed and beyond: a survey of web tools for searching biomedical literature
The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database
A late-binding, distributed, NoSQL warehouse for integrating patient data from clinical trials
pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes
Understanding PubMed ® user search behavior through log analysis
MODB: a comprehensive mitochondrial genome database for Mollusca
PDBWiki: added value through community annotation of the Protein Data Bank
MyxoPortal: a database of myxobacterial genomic features
PalmXplore: oil palm gene database
Curcumin Resource Database
GrameneMart: the BioMart data portal for the Gramene project
AllerGAtlas 1.0: a human allergy-related genes database
RiceSRTFDB: A database of rice transcription factors containing comprehensive expression, cis -regulatory element and mutant information to facilitate gene function analysis
An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries
EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape
A sequence labeling framework for extracting drug-protein relations from biomedical literature
The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development
eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality
The Chinchilla Research Resource Database: resource for an otolaryngology disease model
Standardization of assay representation in the Ontology for Biomedical Investigations
SPRENO: a BioC module for identifying organism terms in figure captions
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT
The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes
FR database 1.0: a resource focused on fruit development and ripening
SuCComBase: a manually curated repository of plant sulfur-containing compounds
Reviewing knowledgebase and database grant proposals in the life sciences: the role of innovation
JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms
A large and accurate collection of peptidase cleavages in the MEROPS database
The BEL information extraction workflow (BELIEF): evaluation in the BioCreative V BEL and IAT track
FusoBase: an online Fusobacterium comparative genomic analysis platform
hLGDB: a database of human lysosomal genes and their regulation
An optimized relational database for querying structural patterns in proteins
CaspNeuroD: a knowledgebase of predicted caspase cleavage sites in human proteins related to neurodegenerative diseases
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse
SyntenyViewer: a comparative genomics-driven translational research tool
RefPrimeCouch - a reference gene primer CouchApp
dbPSP: a curated database for protein phosphorylation sites in prokaryotes
An open-source multi-semantic annotation dataset and automated recognition tool for viral carcinogenesis factors
Integration of 1: 1 orthology maps and updated datasets into Echinobase
Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase
RBPTD: a database of cancer-related RNA-binding proteins in humans
PhytoTypeDB: a database of plant protein inter-cultivar variability and function
Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives
bc-GenExMiner 3.0: new mining module computes breast cancer gene expression correlation analyses
AnnCovDB: a manually curated annotation database for mutations in SARS-CoV-2 spike protein
Query expansion using MeSH terms for dataset retrieval: OHSU at the bioCADDIE 2016 dataset retrieval challenge
Fisheries data management systems in the NW Mediterranean: from data collection to web visualization
LOTUS-DB: an integrative and interactive database for Nelumbo nucifera study
PKAD: a database of experimentally measured pKa values of ionizable groups in proteins
Targeted journal curation as a method to improve data currency at the Comparative Toxicogenomics Database
A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki Subti Wiki
KMDATA: a curated database of reconstructed individual patient-level data from 153 oncology clinical trials
Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases
LncReg: a reference resource for lncRNA-associated regulatory networks
HAltORF: a database of predicted out-of-frame alternative open reading frames in human
HOFE: an interactive forensic entomological database
The NCBI BioCollections Database
BioM2MetDisease: a manually curated database for associations between microRNAs, metabolites, small molecules and metabolic diseases
PRRDB 2.0: a comprehensive database of pattern-recognition receptors and their ligands
SoyFN: a knowledge database of soybean functional networks