yusuke1997/dblp-id-title huggingface dataset:
Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins
MoPSeq-DB: a user-friendly web application for genomic data management and analysis of marine mollusc pathogens
ImmRNA : a database of RNAs associated with tumor immunity
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details
Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task
LeptoDB: an integrated database of genomics and proteomics resource of Leptospira
Translational drug-interaction corpus
ImmuneData: an integrated data discovery system for immunology data repositories
Information retrieval for biomedical datasets: the 2016 bioCADDIE dataset retrieval challenge
DBATE: database of alternative transcripts expression
PolyprOnline: polyproline helix II and secondary structure assignment database
ABCMdb reloaded: updates on mutations in ATP binding cassette proteins
DISPEL: database for ascertaining the best medicinal plants to cure human diseases
FAIR digital objects in environmental and life sciences should comprise workflow operation design data and method information for repeatability of study setups and reproducibility of results
Endometriosis Knowledgebase: a gene-based resource on endometriosis
The Genomic SSR Millets Database (GSMDB): enhancing genetic resources for sustainable agriculture
ForageGrassBase: molecular resource for the forage grass meadow fescue (Festuca pratensis Huds.)
Automated detection of discourse segment and experimental types from the text of cancer pathway results sections
The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies
AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants
IsopiRBank: a research resource for tracking piRNA isoforms
HGV&TB: a comprehensive online resource on human genes and genetic variants associated with tuberculosis
tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles
The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research
Food Enzyme Database (FEDA): a web application gathering information about food enzyme preparations available on the European market
DoSA: Database of Structural Alignments
APICURON: a database to credit and acknowledge the work of biocurators
CaviDB: a database of cavities and their features in the structural and conformational space of proteins
WaspBase: a genomic resource for the interactions among parasitic wasps, insect hosts and plants
FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events
RegulomePA: a database of transcriptional regulatory interactions in Pseudomonas aeruginosa PAO1
HotSpotAnnotations - a database for hotspot mutations and annotations in cancer
Automated PDF highlighting to support faster curation of literature for Parkinson's and Alzheimer's disease
MIPD: Molecules, Imagings, and Clinical Phenotype Integrated Database
TMPL: a database of experimental and theoretical transmembrane protein models positioned in the lipid bilayer
PVCbase: an integrated web resource for the PVC bacterial proteomes
Erratum: Strategies towards digital and semi-automated curation in RegulonDB
New mutant phenotype data curation system in the Saccharomyces Genome Database
BBGRE: brain and body genetic resource exchange
The Histone Database: an integrated resource for histones and histone fold-containing proteins
Analysis of disease-associated objects at the Rat Genome Database
APDB: a database on air pollutant characterization and similarity prediction
Kalium: a database of potassium channel toxins from scorpion venom
A tutorial of diverse genome analysis tools found in the CoGe web-platform using Plasmodium spp. as a model
BgDB: a comprehensive genomic resource information system of bitter gourd for accelerated breeding programme
AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database
EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species
RADB: a database of rheumatoid arthritis-related polymorphisms
MDDOmics: multi-omics resource of major depressive disorder
RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature
From one to many: expanding the Saccharomyces cerevisiae reference genome panel
The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop
NPInter v3.0: an upgraded database of noncoding RNA-associated interactions
Construction of biological networks from unstructured information based on a semi-automated curation workflow
Assigning species information to corresponding genes by a sequence labeling framework
PDC: a highly compact file format to store protein 3D coordinates
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata
Community annotation and bioinformatics workforce development in concert - Little Skate Genome Annotation Workshops and Jamborees
PncStress: a manually curated database of experimentally validated stress-responsive non-coding RNAs in plants
Ewé: a web-based ethnobotanical database for storing and analysing data
https: //invertebratefungi.org/: an expert-curated web-based platform for the identification and classification of invertebrate-associated fungi and fungus-like organisms
NEMAR: an open access data, tools and compute resource operating on neuroelectromagnetic data
Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D
FLUTE: Fast and reliable knowledge retrieval from biomedical literature
Follicle Online: an integrated database of follicle assembly, development and ovulation
Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database
Unsupervised gene function extraction using semantic vectors
The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms
ASFVdb: an integrative resource for genomic and proteomic analyses of African swine fever virus
CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer
Collaborative biocuration - text-mining development task for document prioritization for curation
TBro: visualization and management of de novo transcriptomes
RiceMetaSysB: a database of blast and bacterial blight responsive genes in rice and its utilization in identifying key blast-resistant WRKY genes
Text-mining-assisted biocuration workflows in Argo
Expression of Concern: DisGeNet: a disease-centric interaction database among diseases and various associated genes
BELTracker: evidence sentence retrieval for BEL statements
FOBI: an ontology to represent food intake data and associate it with metabolomic data
Post-composing ontology terms for efficient phenotyping in plant breeding
NanoLAS: a comprehensive nanobody database with data integration, consolidation and application
Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources
DGPD: a knowledge database of dense granule proteins of the Apicomplexa
The CARLSBAD Database: A Confederated Database of Chemical Bioactivities
GCDB: a glaucomatous chemogenomics database for in silico drug discovery
BioKC: a collaborative platform for curation and annotation of molecular interactions
decodeRNA - predicting non-coding RNA functions using guilt-by-association
PGD: a pangolin genome hub for the research community
Finding and sharing: new approaches to registries of databases and services for the biomedical sciences
iPathCons and iPathDB: an improved insect pathway construction tool and the database
Interactive tools for functional annotation of bacterial genomes
Biocuration Virtual Issue 2012
lncSLdb: a resource for long non-coding RNA subcellular localization
BaMBa: towards the integrated management of Brazilian marine environmental data
hERGAPDbase: a database documenting hERG channel inhibitory potentials and APD-prolongation activities of chemical compounds
SCAN database: facilitating integrative analyses of cytosine modification and expression QTL
Extracting chemical-protein interactions from literature using sentence structure analysis and feature engineering
NPBS database: a chemical data resource with relational data between natural products and biological sources
RampDB: a web application and database for the exploration and prediction of receptor activity modifying protein interactions
AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana
LiverCancerMarkerRIF: a liver cancer biomarker interactive curation system combining text mining and expert annotations
GigaDB: promoting data dissemination and reproducibility
CNSA: a data repository for archiving omics data
Impact of translation on named-entity recognition in radiology texts
Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase
An update on the Symbiotic Genomes Database (SymGenDB): a collection of metadata, genomic, genetic and protein sequences, orthologs and metabolic networks of symbiotic organisms
The COMPARE Data Hubs
Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II
Color Data v2: a user-friendly, open-access database with hereditary cancer and hereditary cardiovascular conditions datasets
Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment
Radiation Genes: a database devoted to microarrays screenings revealing transcriptome alterations induced by ionizing radiation in mammalian cells
The mouse-human anatomy ontology mapping project
PlantIntronDB: a database for plant introns that host functional elements
Integrating information retrieval with distant supervision for Gene Ontology annotation
Surveying the Maize community for their diversity and pedigree visualization needs to prioritize tool development and curation
dbAQP-SNP: a database of missense single-nucleotide polymorphisms in human aquaporins
Analysis of CASP8 targets, predictions and assessment methods
Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology
DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning
Toward a service-based workflow for automated information extraction from herbarium specimens
Chemical-induced disease relation extraction with various linguistic features
emiRIT: a text-mining-based resource for microRNA information
Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa
CATA: a comprehensive chromatin accessibility database for cancer
TumorAgDB1.0: tumor neoantigen database platform
Strategies towards digital and semi-automated curation in RegulonDB
The Eimeria Transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria
Overview of the BioCreative VI text-mining services for Kinome Curation Track
Better living through ontologies at the Immune Epitope Database
Disease model curation improvements at Mouse Genome Informatics
2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein-protein interactions
BarleyVarDB: a database of barley genomic variation
Literature curation of protein interactions: measuring agreement across major public databases
A crowdsourcing workflow for extracting chemical-induced disease relations from free text
dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions
MIAMI-AD (Methylation in Aging and Methylation in AD): an integrative knowledgebase that facilitates explorations of DNA methylation across sex, aging, and Alzheimer's disease
CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands
An Ebola virus-centered knowledge base
The integrated National NeuroAIDS Tissue Consortium database: a rich platform for neuroHIV research
GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species
A robust data-driven approach for gene ontology annotation
Enhanced taxonomy annotation of antiviral activity data from ChEMBL
People are essential to linking biodiversity data
Models for financial sustainability of biological databases and resources
EcoliNet: a database of cofunctional gene network for Escherichia coli
Medicinal Materials DNA Barcode Database (MMDBD) version 1.5 - one-stop solution for storage, BLAST, alignment and primer design
LBD: a manually curated database of experimentally validated lymphoma biomarkers
The tragedy of the biodiversity data commons: a data impediment creeping nigher?
HDncRNA: a comprehensive database of non-coding RNAs associated with heart diseases
Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease
PvP01-DB: computational structural and functional characterization of soluble proteome of PvP01 strain of Plasmodium vivax
Carotenoids Database: structures, chemical fingerprints and distribution among organisms
RettDb: the Rett syndrome omics database to navigate the Rett syndrome genomic landscape
Human variation databases
Standardized description of scientific evidence using the Evidence Ontology (ECO)
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database
mAML: an automated machine learning pipeline with a microbiome repository for human disease classification
RPGeNet v2.0: expanding the universe of retinal disease gene interactions network
APID database: redefining protein-protein interaction experimental evidences and binary interactomes
The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation
Chemical entity recognition in patents by combining dictionary-based and statistical approaches
The Natural History Museum Data Portal
SEND: a suite of tools for the easy sharing of linked biological data
CrisprGE: a central hub of CRISPR/Cas-based genome editing
Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation
Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps
ATD: a comprehensive bioinformatics resource for deciphering the association of autophagy and diseases
The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization
Challenges and opportunities for mining adverse drug reactions: perspectives from pharma, regulatory agencies, healthcare providers and consumers
CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats
An end-to-end deep learning architecture for extracting protein-protein interactions affected by genetic mutations
MorusDB: a resource for mulberry genomics and genome biology
A review on Gene Ontology evaluations
ENCD: a manually curated database of experimentally supported endocrine system disease and lncRNA associations
PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database
BCSCdb: a database of biomarkers of cancer stem cells
CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses
Large expert-curated database for benchmarking document similarity detection in biomedical literature search
LINPS: a database for cancer-cell-specific perturbations of biological networks
Groups: knowledge spreadsheets for symbolic biocomputing
EnDisease: a manually curated database for enhancer-disease associations
Collecting and managing in situ banana genetic resources information ( Musa spp.) using online resources and citizen science
Preproject 'Swiss Virtual Natural History Collection'
GraP: platform for functional genomics analysis of Gossypium raimondii
PMBC: a manually curated database for prognostic markers of breast cancer
Creation and evaluation of full-text literature-derived, feature-weighted disease models of genetically determined developmental disorders
PeptiCKDdb - peptide- and protein-centric database for the investigation of genesis and progression of chronic kidney disease
PVsiRNAdb: a database for plant exclusive virus-derived small interfering RNAs
KM-express: an integrated online patient survival and gene expression analysis tool for the identification and functional characterization of prognostic markers in breast and prostate cancers
PheNormGPT: a framework for extraction and normalization of key medical findings
miRò: a miRNA knowledge base
DEOP: a database on osmoprotectants and associated pathways
ParaPep: a web resource for experimentally validated antiparasitic peptide sequences and their structures
Machine learning approach to literature mining for the genetics of complex diseases
MSGD: a manually curated database of genomic, transcriptomic, proteomic and drug information for multiple sclerosis
YummyData: providing high-quality open life science data
Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint
Cildb: a knowledgebase for centrosomes and cilia
LIVE: a manually curated encyclopedia of experimentally validated interactions of lncRNAs
dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts
FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants
SynVectorDB: embedding-based retrieval system for synthetic biology parts
RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou's five-step rule
RNAiAtlas: a database for RNAi (siRNA) libraries and their specificity
PharmaKoVariome database for supporting genetic testing
An advanced web query interface for biological databases
PROFESS: a PROtein Function, Evolution, Structure and Sequence database
ProtMiscuity: a database of promiscuous proteins
SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery
dbPTB: a database for preterm birth
Developing a disease-specific annotation protocol for VHL gene curation using Hypothes.is
Improving the learning of chemical-protein interactions from literature using transfer learning and specialized word embeddings
ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data
QuickGO: a user tutorial for the web-based Gene Ontology browser
AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences
MechanoProDB: a web-based database for exploring the mechanical properties of proteins
PeptiHub: a curated repository of precisely annotated cancer-related peptides with advanced utilities for peptide exploration and discovery
A set of domain rules and a deep network for protein coreference resolution
HSPMdb: a computational repository of heat shock protein modulators
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine
The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology
DATABASE, The Journal of Biological Databases and Curation , is now the official journal of the International Society for Biocuration
RNAWRE: a resource of writers, readers and erasers of RNA modifications
ProPepper: a curated database for identification and analysis of peptide and immune-responsive epitope composition of cereal grain protein families
HeteroGenome: database of genome periodicity
CoReCG: a comprehensive database of genes associated with colon-rectal cancer
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
Evaluation of an automatic article selection method for timelier updates of the Comet Core Outcome Set database
BC-TFdb: a database of transcription factor drivers in breast cancer
CSCdb: a cancer stem cells portal for markers, related genes and functional information
A web-based tool for the prediction of rice transcription factor function
CarrotOmics: a genetics and comparative genomics database for carrot ( Daucus carota )
MepmiRDB: a medicinal plant microRNA database
'RE: fine drugs': an interactive dashboard to access drug repurposing opportunities
Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases
Biomedical literature-based clinical phenotype definition discovery using large language models
Genomic Predicted cross performance: a tool for optimizing parental combinations in breeding programs
The Grass Carp Genome Database (GCGD): an online platform for genome features and annotations
Towards discovery: an end-to-end system for uncovering novel biomedical relations
PTSD Biomarker Database: deep dive metadatabase for PTSD biomarkers, visualizations and analysis tools
Improved insights into the SABIO-RK database via visualization
ChiloDB: a genomic and transcriptome database for an important rice insect pest Chilo suppressalis
'One DB to rule them all' - the RING: a Regulatory INteraction Graph combining TFs, genes/proteins, SNPs, diseases and drugs
SInCRe - structural interactome computational resource for Mycobacterium tuberculosis
The Banana Genome Hub
Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow
Update on cpnDB: a reference database of chaperonin sequences
Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence
Reactome and ORCID - fine-grained credit attribution for community curation
GeneCards Version 3: the human gene integrator
Prevention of data duplication for high throughput sequencing repositories
Cancer Odor Database (COD): a critical databank for cancer diagnosis research
A database on the historical and current occurrences of snakes in Eswatini
Assisting document triage for human kinome curation via machine learning
ILDgenDB: integrated genetic knowledge resource for interstitial lung diseases (ILDs)
NeuroPep: a comprehensive resource of neuropeptides
Increased interactivity and improvements to the GigaScience database, GigaDB
HopBase: a unified resource for Humulus genomics
From manual curation to visualization of gene families and networks across Solanaceae plant species
ZFLNC: a comprehensive and well-annotated database for zebrafish lncRNA
LeukmiR: a database for miRNAs and their targets in acute lymphoblastic leukemia
RTPDB: a database providing associations between genetic variation or expression and cancer prognosis with radiotherapy-based treatment
LeishMANIAdb: a comparative resource for Leishmania proteins
mirTarCLASH: a comprehensive miRNA target database based on chimeric read-based experiments
Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues
Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database