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A Chado case study: an ontology-based modular schema for representing genome-associated biological information
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1007/978-1-4615-2451-9openalex-snapshot
Computational Methods in Genome Research
inferredcites →https://doi.org/10.1038/75556openalex-snapshot
Gene Ontology: tool for the unification of biology
inferredcites →https://doi.org/10.1073/pnas.27.11.499openalex-snapshot
Genetic Control of Biochemical Reactions in Neurospora
inferredcites →https://doi.org/10.1086/278863openalex-snapshot
The Cause of Gynandromorphism in Insects
inferredcites →https://doi.org/10.1093/bib/5.1.59openalex-snapshot
Globally distributed object identification for biological knowledgebases
inferredcites →https://doi.org/10.1093/bib/bbl026openalex-snapshot
Open source tools and toolkits for bioinformatics: significance, and where are we?
inferredcites →https://doi.org/10.1093/nar/22.22.4673openalex-snapshot
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
inferredcites →https://doi.org/10.1093/nar/29.1.106openalex-snapshot
The ARKdb: genome databases for farmed and other animals
inferredcites →https://doi.org/10.1093/nar/gkh036openalex-snapshot
The Gene Ontology (GO) database and informatics resource
inferredcites →https://doi.org/10.1093/nar/gkl776openalex-snapshot
BeetleBase: the model organism database for Tribolium castaneum
inferredcites →https://doi.org/10.1093/nar/gkl777openalex-snapshot
ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data
inferredcites →https://doi.org/10.1101/gr.361602openalex-snapshot
The Bioperl Toolkit: Perl Modules for the Life Sciences
inferredcites →https://doi.org/10.1101/gr.403602openalex-snapshot
The Generic Genome Browser: A Building Block for a Model Organism System Database
inferredcites →https://doi.org/10.1186/gb-2002-3-12-research0081openalex-snapshot
An integrated computational pipeline and database to support whole-genome sequence annotation
inferredcites →https://doi.org/10.1186/gb-2002-3-12-research0082openalex-snapshot
Apollo: a sequence annotation editor
inferredcites →https://doi.org/10.1186/gb-2002-3-12-research0085openalex-snapshot
Heterochromatic sequences in a Drosophila whole-genome shotgun assembly
inferredcites →https://doi.org/10.1186/gb-2005-6-5-r44openalex-snapshot
The Sequence Ontology: a tool for the unification of genome annotations
inferredcites →https://doi.org/10.1186/gb-2005-6-5-r46openalex-snapshot
Relations in biomedical ontologies
inferredcites →https://doi.org/10.1371/journal.pcbi.0020015openalex-snapshot
Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase
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ASDB: A comprehensive omics database for Anopheles sinensis
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A set of ontologies to drive tools for the control of vector-borne diseases
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A set of ontologies to drive tools for the control of vector-borne diseases
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Evolution of the Sequence Ontology terms and relationships
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Evolution of the Sequence Ontology terms and relationships
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Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges
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Positive-unlabeled learning identifies vaccine candidate antigens in the malaria parasite Plasmodium falciparum
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Homo Sapiens Chromosomal Location Ontology: A Framework for Genomic Data in Biomedical Knowledge Graphs
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RNAStructuromeDB: A genome-wide database for RNA structural inference
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Genomewide SNP variation reveals relationships among landraces and modern varieties of rice
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Philosophy in Science: Can Philosophers of Science Permeate through Science and Produce Scientific Knowledge?
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Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases
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Towards pharmacogenomics knowledge discovery with the semantic web
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Visualizing next-generation sequencing data with JBrowse
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Using GBrowse 2.0 to visualize and share next-generation sequence data
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The Protein Feature Ontology: a tool for the unification of protein feature annotations
inferred← citeshttps://doi.org/10.1093/bioinformatics/btp314openalex-snapshot
Apollo: a community resource for genome annotation editing
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq167openalex-snapshot
Ergatis: a web interface and scalable software system for bioinformatics workflows
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq173openalex-snapshot
Using semantic web rules to reason on an ontology of pseudogenes
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The GMOD Drupal Bioinformatic Server Framework
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Using Sybil for interactive comparative genomics of microbes on the web
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The Virtual Fly Brain browser and query interface
inferred← citeshttps://doi.org/10.1093/bioinformatics/bts046openalex-snapshot
Chado Controller: advanced annotation management with a community annotation system
inferred← citeshttps://doi.org/10.1093/bioinformatics/bts273openalex-snapshot
MicrobeDB: a locally maintainable database of microbial genomic sequences
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Badger—an accessible genome exploration environment
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Canto: an online tool for community literature curation
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ISDB: a database toolkit for storing and analyzing viral integration site data
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COMBAT-TB-NeoDB: fostering tuberculosis research through integrative analysis using graph database technologies
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Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases
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Tripal MegaSearch: a tool for interactive and customizable query and download of big data
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The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine
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CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota)
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Building resource-efficient community databases using open-source software
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Post-composing ontology terms for efficient phenotyping in plant breeding
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New mutant phenotype data curation system in the Saccharomyces Genome Database
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Meeting report: a workshop on Best Practices in Genome Annotation
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CycADS: an annotation database system to ease the development and update of BioCyc databases
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TparvaDB: a database to support Theileria parva vaccine development
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The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details
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Tripal: a construction toolkit for online genome databases
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The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data
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The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes
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The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species
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The Eimeria Transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria
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GnpIS: an information system to integrate genetic and genomic data from plants and fungi
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Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases
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Addition of a breeding database in the Genome Database for Rosaceae
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Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado
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TBro: visualization and management ofde novotranscriptomes
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SilkPathDB: a comprehensive resource for the study of silkworm pathogens
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MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data
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New extension software modules to enhance searching and display of transcriptome data in Tripal databases
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Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases
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AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture
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PamulDB: a comprehensive genomic resource for the study of human- and animal-pathogenic Pasteurella multocida
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Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases
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SCNBase: a genomics portal for the soybean cyst nematode (Heterodera glycines)
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Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata
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Building a pipeline to solicit expert knowledge from the community to aid gene summary curation
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The Rhodoexplorer Platform for Red Algal Genomics and Whole-Genome Assemblies for Several Gracilaria Species
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JaponicusDB: rapid deployment of a model organism database for an emerging model species
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PomBase: a Global Core Biodata Resource—growth, collaboration, and sustainability
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Machado: Open source genomics data integration framework
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Genome Annotation Generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission
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Genome Context Viewer (GCV) version 2: enhanced visual exploration of multiple annotated genomes
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GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database
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Pathema: a clade-specific bioinformatics resource center for pathogen research
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TriTrypDB: a functional genomic resource for the Trypanosomatidae
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DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila
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Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera
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SOBA: sequence ontology bioinformatics analysis
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The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl
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TADB: a web-based resource for Type 2 toxin–antitoxin loci in bacteria and archaea
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ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia
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PomBase: a comprehensive online resource for fission yeast
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modMine: flexible access to modENCODE data
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Xenbase: expansion and updates of the Xenopus model organism database
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The Genome Database for Rosaceae (GDR): year 10 update
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FlyBase 102—advanced approaches to interrogating FlyBase
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SNP-Seek database of SNPs derived from 3000 rice genomes
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PomBase 2015: updates to the fission yeast database
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FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations
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The coffee genome hub: a resource for coffee genomes
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GenoBase: comprehensive resource database of Escherichia coli K-12
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The i5k Workspace@NAL—enabling genomic data access, visualization and curation of arthropod genomes
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Bovine Genome Database: new tools for gleaning function from theBos taurusgenome
inferred← citeshttps://doi.org/10.1093/nar/gkv1137openalex-snapshot
GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes
inferred← citeshttps://doi.org/10.1093/nar/gkv1208openalex-snapshot
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine
inferred← citeshttps://doi.org/10.1093/nar/gkv966openalex-snapshot
ANISEED 2015: a digital framework for the comparative developmental biology of ascidians
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CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
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Rice SNP-seek database update: new SNPs, indels, and queries
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TADB 2.0: an updated database of bacterial type II toxin–antitoxin loci
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qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms
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PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information
inferred← citeshttps://doi.org/10.1093/nar/gkz944openalex-snapshot
Bovine Genome Database: new annotation tools for a new reference genome
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ParameciumDB 2019: integrating genomic data across the genus for functional and evolutionary biology
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MGOS: Development of a Community Annotation Database for Magnaporthe oryzae
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Genome and proteome annotation: organization, interpretation and integration
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Formalization of Genome Interval Relations
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Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research
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GiraFFe Browse: A lightweight web based tool for inspecting GFF and FASTA data
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GenIE-Sys: Genome Integrative Explorer System
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Citrusgreening.org: An open access and integrated systems biology portal for the Huanglongbing (HLB) disease complex
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JBrowse: A next-generation genome browser
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The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program
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A Community-Based Annotation Framework for Linking Solanaceae Genomes with Phenomes
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Managing data provenance in genome project workflows
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Development and implementation of CARAS algorithm for automatic annotation, visualization, and GenBank submission of chloroplast genome sequences
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rCAD: A Novel Database Schema for the Comparative Analysis of RNA
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Experiences with DERIVA: An Asset Management Platform for Accelerating eScience
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Survey: The Application of GMOD in Bioinformatics Research
inferred← citeshttps://doi.org/10.1109/ictai.2011.12openalex-snapshot
Flexible, Efficient and Interactive Retrieval for Supporting In-silico Studies of Endobacteria
inferred← citeshttps://doi.org/10.1109/tcbb.2013.68openalex-snapshot
GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations
inferred← citeshttps://doi.org/10.1111/1755-0998.12756openalex-snapshot
Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae)
inferred← citeshttps://doi.org/10.1111/age.12295openalex-snapshot
Software solutions for the livestock genomics SNP array revolution
inferred← citeshttps://doi.org/10.1111/j.1365-2583.2009.00930.xopenalex-snapshot
AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome
inferred← citeshttps://doi.org/10.1111/j.1744-7909.2012.01120.xopenalex-snapshot
InterStoreDB: A Generic Integration Resource for Genetic and Genomic DataF
inferred← citeshttps://doi.org/10.1111/nph.14321openalex-snapshot
Re‐annotation, improved large‐scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus
inferred← citeshttps://doi.org/10.1111/nyas.13289openalex-snapshot
Antimicrobial resistance surveillance in the genomic age
inferred← citeshttps://doi.org/10.1111/ppl.14600openalex-snapshot
High‐resolution gene expression atlases of two contrasting major Greek olive (Olea europaea L.) tree cultivars for oil and table olive production
inferred← citeshttps://doi.org/10.1128/aac.00419-13openalex-snapshot
The Comprehensive Antibiotic Resistance Database
inferred← citeshttps://doi.org/10.1159/000430427openalex-snapshot
Database and Informatic Challenges in Representing Both Diploid and Tetraploid Xenopus Species in Xenbase
inferred← citeshttps://doi.org/10.11606/d.45.2013.tde-04022014-074453openalex-snapshot
PATO: um ambiente integrado com interface gráfica para a curadoria de dados de sequências biológicas
inferred← citeshttps://doi.org/10.11606/d.95.2013.tde-18072013-100518openalex-snapshot
Genômica translacional: integrando dados clínicos e biomoleculares
inferred← citeshttps://doi.org/10.11606/d.95.2016.tde-05042016-093735openalex-snapshot
Ferramenta computacional para análise integrada de dados clínicos e biomoleculares
inferred← citeshttps://doi.org/10.11606/d.95.2018.tde-14032018-150144openalex-snapshot
Modelagem e implementação de banco de dados clínicos e moleculares de pacientes com câncer e seu uso para identificação de marcadores em câncer de pâncreas
inferred← citeshttps://doi.org/10.1186/1471-2105-10-447openalex-snapshot
Next generation transcriptomes for next generation genomes using est2assembly
inferred← citeshttps://doi.org/10.1186/1471-2105-10-67openalex-snapshot
Quantitative measures for the management and comparison of annotated genomes
inferred← citeshttps://doi.org/10.1186/1471-2105-11-s12-s2openalex-snapshot
SeqWare Query Engine: storing and searching sequence data in the cloud
inferred← citeshttps://doi.org/10.1186/1471-2105-11-s6-s15openalex-snapshot
Next generation models for storage and representation of microbial biological annotation
inferred← citeshttps://doi.org/10.1186/1471-2105-12-491openalex-snapshot
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
inferred← citeshttps://doi.org/10.1186/1471-2105-12-s10-s17openalex-snapshot
Scenario driven data modelling: a method for integrating diverse sources of data and data streams
inferred← citeshttps://doi.org/10.1186/1471-2105-13-s1-s7openalex-snapshot
Transparent mediation-based access to multiple yeast data sources using an ontology driven interface
inferred← citeshttps://doi.org/10.1186/1471-2105-13-s4-s4openalex-snapshot
GIDL: a rule based expert system for GenBank Intelligent Data Loading into the Molecular Biodiversity database
inferred← citeshttps://doi.org/10.1186/1471-2105-14-180openalex-snapshot
Computational framework to support integration of biomolecular and clinical data within a translational approach
inferred← citeshttps://doi.org/10.1186/1471-2105-14-s11-s6openalex-snapshot
Provenance in bioinformatics workflows
inferred← citeshttps://doi.org/10.1186/1471-2164-11-547openalex-snapshot
Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia
inferred← citeshttps://doi.org/10.1186/1471-2164-11-645openalex-snapshot
Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome
inferred← citeshttps://doi.org/10.1186/1471-2164-12-302openalex-snapshot
Single nucleotide polymorphism discovery in elite north american potato germplasm
inferred← citeshttps://doi.org/10.1186/1471-2164-13-715openalex-snapshot
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences
inferred← citeshttps://doi.org/10.1186/1475-2859-8-29openalex-snapshot
Genome, secretome and glucose transport highlight unique features of the protein production host Pichia pastoris
inferred← citeshttps://doi.org/10.1186/2041-1480-4-30openalex-snapshot
The Drosophila phenotype ontology
inferred← citeshttps://doi.org/10.1186/gb-2007-8-7-r129openalex-snapshot
FlyMine: an integrated database for Drosophila and Anopheles genomics
inferred← citeshttps://doi.org/10.1186/gb-2008-9-6-r102openalex-snapshot
GMODWeb: a web framework for the generic model organism database
inferred← citeshttps://doi.org/10.1186/gb-2010-11-3-r27openalex-snapshot
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
inferred← citeshttps://doi.org/10.1186/gb-2013-14-8-r93openalex-snapshot
Web Apollo: a web-based genomic annotation editing platform
inferred← citeshttps://doi.org/10.1186/s12859-017-1494-2openalex-snapshot
ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data
inferred← citeshttps://doi.org/10.1186/s12859-018-2459-9openalex-snapshot
GLUE: a flexible software system for virus sequence data
inferred← citeshttps://doi.org/10.1186/s12866-016-0680-0openalex-snapshot
SuperPhy: predictive genomics for the bacterial pathogen Escherichia coli
inferred← citeshttps://doi.org/10.1186/s12915-016-0276-zopenalex-snapshot
Model organism databases: essential resources that need the support of both funders and users
inferred← citeshttps://doi.org/10.1186/s12915-020-00820-5openalex-snapshot
The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest
inferred← citeshttps://doi.org/10.1186/s13007-015-0053-yopenalex-snapshot
An ontology approach to comparative phenomics in plants
inferred← citeshttps://doi.org/10.1186/s13059-016-0924-1openalex-snapshot
JBrowse: a dynamic web platform for genome visualization and analysis
inferred← citeshttps://doi.org/10.1186/s13326-016-0067-zopenalex-snapshot
FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation
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