yusuke1997/dblp-id-title huggingface dataset:
MGDB: a comprehensive database of genes involved in melanoma
New extension software modules to enhance searching and display of transcriptome data in Tripal databases
Overview of the interactive task in BioCreative V
dbHiMo: a web-based epigenomics platform for histone-modifying enzymes
Deep Question Answering for protein annotation
FGCD: a database of fungal gene clusters related to secondary metabolism
ENcyclopedia of TRAnscription Factors in Bacteria and Archaea genomes (ENTRAF) version 2.0
Correction to: DDPD 1.0: a manually curated and standardized database of digital properties of approved drugs for drug-likeness evaluation and drug development
Cloud-based relational database for multimodal animal data
The extraction of complex relationships and their conversion to biological expression language (BEL) overview of the BioCreative VI (2017) BEL track
MetaHCR: a web-enabled metagenome data management system for hydrocarbon resources
Closing the loop: from paper to protein annotation using supervised Gene Ontology classification
Data mining using the Catalogue of Somatic Mutations in Cancer BioMart
Biological Database of Images and Genomes: tools for community annotations linking image and genomic information
Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data
https: //www.fungiofpakistan.com: a continuously updated online database of fungi in Pakistan
The 'straight mouse': defining anatomical axes in 3D embryo models
'Isotopo' a database application for facile analysis and management of mass isotopomer data
FishTEDB: a collective database of transposable elements identified in the complete genomes of fish
PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe
The Biomolecular Interaction Network Database in PSI-MI 2.5
CycADS: an annotation database system to ease the development and update of BioCyc databases
Extracting chemical-protein relations with ensembles of SVM and deep learning models
KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling
Text mining and expert curation to develop a database on psychiatric diseases and their genes
Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes
A change language for ontologies and knowledge graphs
Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata
LitSumm: large language models for literature summarization of noncoding RNAs
Opportunities for text mining in the FlyBase genetic literature curation workflow
Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data
OPTIK: a database for understanding catchment areas to guide mobilization of cancer center assets
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer
UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions
MantaID: a machine learning-based tool to automate the identification of biological database IDs
In-Cardiome: integrated knowledgebase for coronary artery disease enabling translational research
Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes
The MetaboLights repository: curation challenges in metabolomics
A semi-automated methodology for finding lipid-related GO terms
ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection
SilkPathDB: a comprehensive resource for the study of silkworm pathogens
MSGP: the first database of the protein components of the mammalian stress granules
Gene-oriented ortholog database: a functional comparison platform for orthologous loci
NaviCom: a web application to create interactive molecular network portraits using multi-level omics data
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse
PTS: a pharmaceutical target seeker
Halophytes.tn: an innovative database for Tunisian halophyte plant identification, distribution and characterization
The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud
Semalytics: a semantic analytics platform for the exploration of distributed and heterogeneous cancer data in translational research
PTGBase: an integrated database to study tandem duplicated genes in plants
HPVMD-C: a disease-based mutation database of human papillomavirus in China
Artificial intelligence with multi-functional machine learning platform development for better healthcare and precision medicine
ICEPO: the ion channel electrophysiology ontology
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria
PSL-LCCL: a resource for subcellular protein localization in liver cancer cell line SK_HEP1
The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation
eFG : an electronic resource for Fusarium graminearum
GrainGenes: a data-rich repository for small grains genetics and genomics
Wikidata as a semantic framework for the Gene Wiki initiative
Probabilistic and machine learning-based retrieval approaches for biomedical dataset retrieval
A comprehensive experimental comparison between federated and centralized learning
Localizatome: a database for stress-dependent subcellular localization changes in proteins
Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information
realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta)
High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis
Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning
Update notifications for the BioCyc collection of databases
TISSUES 2.0: an integrative web resource on mammalian tissue expression
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold
MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database
Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis
Integrating image caption information into biomedical document classification in support of biocuration
KOFFI and Anabel 2.0 - a new binding kinetics database and its integration in an open-source binding analysis software
ncStem: a comprehensive resource of curated and predicted ncRNAs in cancer stemness
The Immunopeptidomics Ontology (ImPO)
Classifying domain-specific text documents containing ambiguous keywords
Correction to: The importance of graph databases and graph learning for clinical applications
A controlled vocabulary for pathway entities and events
CBMAR: a comprehensive β-lactamase molecular annotation resource
At-C-RNA database, a one-stop source for information on circRNAs in Arabidopsis thaliana in a unified format
An exploratory study combining Virtual Reality and Semantic Web for life science research using Graph2VR
Circad: a comprehensive manually curated resource of circular RNA associated with diseases
Chemical-induced disease relation extraction via convolutional neural network
An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP)
The quail anatomy portal
CuPCA: a web server for pan-cancer association analysis of large-scale cuproptosis-related genes
An online analytical processing multi-dimensional data warehouse for malaria data
MANUDB: database and application to retrieve and visualize mammalian NUMTs
TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria
Coronavirus Immunotherapeutic Consortium Database
PolyQ Database - an integrated database on polyglutamine diseases
miRnalyze: an interactive database linking tool to unlock intuitive microRNA regulation of cell signaling pathways
GoSynthetic database tool to analyse natural and engineered molecular processes
The NIDDK Central Repository at 8 years - Ambition, Revision, Use and Impact
miRror-Suite: decoding coordinated regulation by microRNAs
3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families
TIARA genome database: update 2013
SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications
The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database
Correction to: LeishMANIAdb: a comparative resource for Leishmania proteins
ScaleNet: a literature-based model of scale insect biology and systematics
Text mining for the biocuration workflow
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes
CCSI: a database providing chromatin-chromatin spatial interaction information
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models
novPTMenzy: a database for enzymes involved in novel post-translational modifications
Identification and prioritization of novel uncharacterized peptidases for biochemical characterization
ImmuMethy, a database of DNA methylation plasticity at a single cytosine resolution in human blood and immune cells
HumanMine: advanced data searching, analysis and cross-species comparison
Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria
Improved ontology-based similarity calculations using a study-wise annotation model
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis
BC4GO: a full-text corpus for the BioCreative IV GO task
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles
MicroRNA childhood cancer catalog (M3Cs): a resource for translational bioinformatics toward health informatics in pediatric cancer
CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state
YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules
Exploiting syntactic and semantics information for chemical-disease relation extraction
InCliniGene enables high-throughput and comprehensive in vivo clonal tracking toward clinical genomics data integration
Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes
SmartWoodID - an image collection of large end-grain surfaces to support wood identification systems
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations
VarGuideAtlas: a repository of variant interpretation guidelines
Regulators of Androgen Action Resource: a one-stop shop for the comprehensive study of androgen receptor action
Comparison of sequence variants in transcriptomic control regions across 17 mouse genomes
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides
Full-text chemical identification with improved generalizability and tagging consistency
Atlas of Schistosoma mansoni long non-coding RNAs and their expression correlation to protein-coding genes
Rule-based deduplication of article records from bibliographic databases
CANCROX: a cross-species cancer therapy database
CRCDA - Comprehensive resources for cancer NGS data analysis
FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research
A dimensional warehouse for integrating operational data from clinical trials
Leveraging word embeddings and medical entity extraction for biomedical dataset retrieval using unstructured texts
PearMODB: a multiomics database for pear ( Pyrus ) genomics, genetics and breeding study
Capturing cooperative interactions with the PSI-MI format
AbDb: antibody structure database - a database of PDB-derived antibody structures
ONRLDB - manually curated database of experimentally validated ligands for orphan nuclear receptors: insights into new drug discovery
Dr. PIAS 2.0: an update of a database of predicted druggable protein-protein interactions
The annotation and the usage of scientific databases could be improved with public issue tracker software
collectNET: a web server for integrated inference of cell-cell communication network
Plant rDNA database: update and new features
Edaphostat: interactive ecological analysis of soil organism occurrences and preferences from the Edaphobase data warehouse
Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report
FixPred: a resource for correction of erroneous protein sequences
NutriGenomeDB: a nutrigenomics exploratory and analytical platform
MPD: a pathogen genome and metagenome database
ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank
The first comprehensive database of germline pathogenic variants in East Asian cancer patients
RiceMetaSys: Drought-miR, a one-stop solution for drought responsive miRNAs-mRNA module in rice
CHOmine: an integrated data warehouse for CHO systems biology and modeling
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins
Building resource-efficient community databases using open-source software
PhenoMiner: from text to a database of phenotypes associated with OMIM diseases
StopKB: a comprehensive knowledgebase for nonsense suppression therapies
MiCK: a database of gut microbial genes linked with chemoresistance in cancer patients
HEDD: the human epigenetic drug database
CancerPPD2: an updated repository of anticancer peptides and proteins
TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling
WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata
ANItools web: a web tool for fast genome comparison within multiple bacterial strains
CBD: a biomarker database for colorectal cancer
ePerturbDB: enhancer's experimental perturbation database
TparvaDB: a database to support Theileria parva vaccine development
PamulDB: a comprehensive genomic resource for the study of human- and animal-pathogenic Pasteurella multocida
The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies
SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets
NutriChem 2.0: exploring the effect of plant-based foods on human health and drug efficacy
The Halophile Protein Database
covid19census: U.S. and Italy COVID-19 metrics and other epidemiological data
Baseline and extensions approach to information retrieval of complex medical data: Poznan's approach to the bioCADDIE 2016
The radish genome database (RadishGD): an integrated information resource for radish genomics
PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks
OMICtools: an informative directory for multi-omic data analysis
tmBioC : improving interoperability of text-mining tools with BioC
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations
A roadmap for the functional annotation of protein families: a community perspective
' In silico expression analysis', a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis -regulatory sequences
UCbase 2.0: ultraconserved sequences database (2014 update)
RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information
A novel taxonomic database for eukaryotic mitochondrial cytochrome oxidase subunit I gene (eKOI), with a focus on protists diversity
OCCAM: prediction of small ORFs in bacterial genomes by means of a target-decoy database approach and machine learning techniques
CMBD: a manually curated cancer metabolic biomarker knowledge database
Automated extraction of genes associated with antibiotic resistance from the biomedical literature
Phenol-Explorer: an online comprehensive database on polyphenol contents in foods
UMD-MLH1/MSH2/MSH6 databases: description and analysis of genetic variations in French Lynch syndrome families
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges
The importance of digitized biocollections as a source of trait data and a new VertNet resource
Elsevier's approach to the bioCADDIE 2016 Dataset Retrieval Challenge
DENdb: database of integrated human enhancers
DrugCombo: an informatics bridge for anticancer drug combination Phase I trial design
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data
Exploring functionally annotated transcriptional consensus regulatory elements with CONREL
FoodBase corpus: a new resource of annotated food entities
Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes
AI4FoodDB: a database for personalized e-Health nutrition and lifestyle through wearable devices and artificial intelligence
GESDB: a platform of simulation resources for genetic epidemiology studies
PLIC: protein-ligand interaction clusters
MaizeCUBIC: a comprehensive variation database for a maize synthetic population
SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data
CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish
PLoV: a comprehensive database of genetic variants leading to pregnancy loss
BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics
Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy
miRwayDB: a database for experimentally validated microRNA-pathway associations in pathophysiological conditions
An online database for einkorn wheat to aid in gene discovery and functional genomics studies
MaizeGDB: curation and outreach go hand-in-hand
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat
QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice
FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability
ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome
PlaNC-TE: a comprehensive knowledgebase of non-coding RNAs and transposable elements in plants
Review of autism spectrum disorder databases for the identification of candidate genes
A terpenoids database with the chemical content as a novel agronomic trait
Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins
Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions
Automatic identification of relevant chemical compounds from patents
CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis
ncRNA orthologies in the vertebrate lineage
The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases
Erratum to: Large expert-curated database for benchmarking document similarity detection in biomedical literature search
IFIM: a database of integrated fitness information for microbial genes
BioMart: a data federation framework for large collaborative projects
YESdb: integrative analysis of environmental stress in yeast
The PRINTS database: a fine-grained protein sequence annotation and analysis resource - its status in 2012
The landscape of health disparities in the UK Biobank
SELER: a database of super-enhancer-associated lncRNA- directed transcriptional regulation in human cancers
FoPGDB: a pangenome database of Fusarium oxysporum , a cross-kingdom fungal pathogen
Carbohydrate Structure Database: tools for statistical analysis of bacterial, plant and fungal glycomes
New approaches in developing medicinal herbs databases
The Listeria monocytogenes strain 10403S BioCyc database
FlyVar: a database for genetic variation in Drosophila melanogaster
Identifying main finding sentences in clinical case reports
iCAZyGFADB: an insect CAZyme and gene function annotation database
CREDO: a structural interactomics database for drug discovery
The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups
Peptipedia v2.0: a peptide sequence database and user-friendly web platform. A major update
IBDTransDB: a manually curated transcriptomic database for inflammatory bowel disease
Crowdsourcing and curation: perspectives from biology and natural language processing
A negative storage model for precise but compact storage of genetic variation data
Transformer-based approach for symptom recognition and multilingual linking
OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture
Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database
MIPPIE: the mouse integrated protein-protein interaction reference
GMMID: genetically modified mice information database
TIDB: a comprehensive database of trained immunity
RAEdb: a database of enhancers identified by high-throughput reporter assays
Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy
PANGEN: an online platform for the comparison and creation of diagnostic gene panels
ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them
ParkDB: a Parkinson's disease gene expression database
PCorral - interactive mining of protein interactions from MEDLINE
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data
PEIMAN 1.0: Post-translational modification Enrichment, Integration and Matching ANalysis
Multi-source and ontology-based retrieval engine for maize mutant phenotypes
PigVar: a database of pig variations and positive selection signatures
HBFP: a new repository for human body fluid proteome
An approach to making life sciences FAIR - FAIR-DS as a tool for Aspergillus fumigatus
Post-translational modifications in proteins: resources, tools and prediction methods
ProbResist: a database for drug-resistant probiotic bacteria
SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation
Empirical substitution models of protein evolution: database, relationships, and modeling considerations
Towards the Collaborative Curation of the Registry underlying identifiers.org
Benchmarking database systems for Genomic Selection implementation
Using deep learning to identify translational research in genomic medicine beyond bench to bedside
Automated annotation of scientific texts for ML-based keyphrase extraction and validation
CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator
HITSZ_CDR: an end-to-end chemical and disease relation extraction system for BioCreative V
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank
BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies
UPObase: an online database of unspecific peroxygenases
MechanoBase: a comprehensive database for the mechanics of tissues and cells
LSD600: the first corpus of biomedical abstracts annotated with lifestyle-disease relations
Development of a biomarker database toward performing disease classification and finding disease interrelations
EfGD: the Erianthus fulvus genome database