AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPsychiatry and PsychologyPhenomena and ProcessesDisciplines and OccupationsAnthropology, Education, Sociology and Social PhenomenaTechnology, Industry, AgricultureHumanitiesInformation ScienceHealth Care
Genome, HelminthDatabases, GeneticCaenorhabditisUser-Computer InterfaceCaenorhabditis elegansMolecular Sequence AnnotationInternetDatabases, FactualData MiningGenomicsInformation Storage and RetrievalGenes, HelminthComputational BiologySoftwareDatabases, Nucleic AcidDatabases, ProteinDatabase Management SystemsNematodaDatabases as TopicWorkflowToxicogeneticsDatabases, BibliographicProtein Interaction MappingVocabulary, ControlledSystems IntegrationTerminology as TopicDocumentationAbstracting and Indexing as TopicGenomeAlgorithmsMolecular Sequence DataCatalogs as TopicPhenotypePubMedPublicationsPhylogenyNatural Language ProcessingKnowledge BasesProteinsMetabolic Networks and PathwaysSequence AlignmentComputer GraphicsAmino Acid SequenceMEDLINEModels, BiologicalSequence Analysis, DNAPeriodicals as TopicEvolution, MolecularExpressed Sequence TagsSequence Analysis, ProteinZebrafishSearch EnginePharmacological PhenomenaGenome, BacterialEscherichia coli K12Databases, PharmaceuticalMutationModels, MolecularDiseaseProgramming LanguagesAutomationDatabases, ChemicalModels, AnimalGene Expression ProfilingArtificial IntelligenceGenome, FungalProtein Structure, TertiaryGene Regulatory NetworksDrosophila melanogasterDictionaries as TopicBrain-Computer InterfacesModels, GeneticProteomicsProteomeSaccharomyces cerevisiaeGenesBase SequenceSpecies SpecificitySemanticsSystems BiologyExpert TestimonyReproducibility of ResultsSequence Homology, Amino AcidComputer SimulationGenetic VariationChromosome MappingGene OntologyGenome, PlantBacterial ProteinsLongevityProtein BindingBacteriaMetric SystemSignal TransductionBinding SitesGenome, HumanAnimals, Genetically ModifiedBiological EvolutionOligonucleotide Array Sequence AnalysisProtein Conformation
DrosophilaElegansGenome-wideFlyBaseAnnotateOntologyGeneticsAnnotationsBiologicalExperimentalEnablesProcessesDataSingleToolsSequenceMolecularDiseaseExpressionHumanPreviouslyAnnotationCaenorhabditisPomBaseSpeciesEnsemblGenomicInteractionInteractionsGenomesTranscription factorTargetsResourceMainPublicProvideCellsProjectsFunctionJournal
Drosophila2
  • However, writing such summaries is a daunting task, given the number of genes in each organism (e.g. 13,929 protein coding genes in Drosophila melanogaster). (stanford.edu)
  • In FlyBase (the Drosophila genetics database) we have therefore developed a pipeline to obtain such summaries from researchers who have worked extensively on each gene. (stanford.edu)
Elegans1
  • TPC builds on the strengths of the original system by expanding the full text corpus to include the PubMed Central Open Access Subset (PMC OA), as well as the WormBase C. elegans bibliography. (biomedcentral.com)
Genome-wide2
  • In order to identify genes that may modify disease onset and progression, genome-wide association and gene expression studies have been performed 12 , 13 . (nature.com)
  • Brief summaries describing the function of each gene's product are of great value to the research community, especially when interpreting genome-wide studies that reveal changes to hundreds of genes. (stanford.edu)
FlyBase1
  • An in-house algorithm predicts and ranks expert authors for each gene based on the data within FlyBase and extracts their email addresses from papers that we have curated. (stanford.edu)
Annotate2
  • Other databases Nucleosome positioning region database These databases collect genome sequences, annotate and analyze them, and provide public access. (wikipedia.org)
  • To facilitate biocuration efforts, TPC also allows users to select text spans from the full text and annotate them, create customized curation forms for any data type, and send resulting annotations to external curation databases. (biomedcentral.com)
Ontology1
  • As an example of such a curation form, we describe integration of TPC with the Noctua curation tool developed by the Gene Ontology (GO) Consortium. (biomedcentral.com)
Genetics1
  • The include: DNA Data Bank of Japan (National Institute of Genetics) EMBL (European Bioinformatics Institute) GenBank (National Center for Biotechnology Information) DDBJ (Japan), GenBank (USA) and European Nucleotide Archive (Europe) are repositories for nucleotide sequence data from all organisms. (wikipedia.org)
Annotations3
  • Some add curation of experimental literature to improve computed annotations. (wikipedia.org)
  • It provides unique identifiers, names and synonyms, list of complex members with their unique identifiers (UniProt, ChEBI, RNAcentral), function, binding and stoichiometry annotations, descriptions of their topology, assembly structure, ligands and associated diseases as well as cross-references to the same complex in other databases (e.g. (stanford.edu)
  • It also allows users to create customized curation interfaces, use those interfaces to make annotations linked to supporting evidence statements, and then send those annotations to any database in the world. (biomedcentral.com)
Biological5
  • Biological databases are stores of biological information. (wikipedia.org)
  • The journal Nucleic Acids Research regularly publishes special issues on biological databases and has a list of such databases. (wikipedia.org)
  • Omics Discovery Index can be used to browse and search several biological databases. (wikipedia.org)
  • many are listed below Model organism databases provide in-depth biological data for intensively studied organisms. (wikipedia.org)
  • Biocuration is the process of "extracting and organizing" published biomedical research results, often using controlled vocabularies and ontologies to "enable powerful queries and biological database interoperability" [ 6 ]. (biomedcentral.com)
Experimental1
  • Moreover, database models cannot always capture the richness of scientific information, and in some cases, experimental details crucial for reproducibility can only be found in the references used as evidence for the structured data. (biomedcentral.com)
Enables2
  • Furthermore, the NIAID Data Ecosystem Discovery Portal developed by the National Institute of Allergy and Infectious Diseases (NIAID) enables searching across databases. (wikipedia.org)
  • Textpresso Central is an online literature search and curation platform that enables biocurators and biomedical researchers to search and mine the full text of literature by integrating keyword and category searches with viewing search results in the context of the full text. (biomedcentral.com)
Processes1
  • The large number of genes and the diversity of processes involved in the progression of neurological diseases in general, and HD in specific, emphasizes the need for comprehensive approaches in additional to studies of individual genes 14 . (nature.com)
Data8
  • Meta databases are databases of databases that collect data about data to generate new data. (wikipedia.org)
  • metadatabase is a database model for metadata management, global query of independent database, and distributed data processing. (wikipedia.org)
  • These three databases are primary databases, as they house original sequence data. (wikipedia.org)
  • It allows users to obtain, visualize and prioritize molecular interaction networks using HD-relevant gene expression, phenotypic and other types of data obtained from human samples or model organisms. (nature.com)
  • We discuss the general utility of this approach for other databases that capture data from the research literature. (stanford.edu)
  • Web Application Programming Interfaces (APIs) are interfaces that data providers build to empower the outside world to interact with their business logic. (stanford.edu)
  • 2022). Harmonizing model organism data in the Alliance of Genome Resources. (caltech.edu)
  • user interface extensions are straightforward to implement, as are alternative data back-ends. (biomedcentral.com)
Single2
Tools2
Sequence1
  • PomBase: the knowledgebase for the fission yeast Schizosaccharomyces pombe SubtiWiki: integrated database for the model bacterium Bacillus subtilis The primary databases make up the International Nucleotide Sequence Database (INSD). (wikipedia.org)
Molecular1
  • To facilitate research on HD in a network-oriented manner, we have developed HDNetDB, a database that integrates molecular interactions with many HD-relevant datasets. (nature.com)
Disease1
  • Huntington's disease (HD) is a progressive and fatal neurodegenerative disorder caused by an expanded CAG repeat in the huntingtin gene. (nature.com)
Expression1
  • Human Protein Atlas (HPA): a public database with expression profiles of human protein coding genes both on mRNA and protein level in tissues, cells, subcellular compartments, and cancer tumors. (wikipedia.org)
Human1
Previously1
  • The 2018 issue has a list of about 180 such databases and updates to previously described databases. (wikipedia.org)
Annotation4
  • The K-12 Resource will organize and increase the utility of sequence, sequence annotation, high throughput data, data mining algorithms, mathematical models, structural and functional data, and legacy information related to the biology of the K-12 Group, while identifying and filling any gaps in informatics activities needed by the research community. (nih.gov)
  • Dr. Arighi has extensive experience in the areas of database curation, community annotation, text mining for biocuration and ontologies. (nih.gov)
  • While C. elegans gene predictions have undergone continuous refinement, this is not true for the annotation of functional transcription factors. (biomedcentral.com)
  • Genomic annotations presented here were performed using the 'Ensembl gene annotation system', to ensure that comparative analyses and conclusions reflect biological differences, as opposed to arising from different methodologies underpinning transcript model identification. (bvsalud.org)
Caenorhabditis1
  • Caenorhabditis elegans provides a powerful model to study such metazoan networks because its genome is completely sequenced and many functional genomic tools are available. (biomedcentral.com)
PomBase2
  • PomBase: the knowledgebase for the fission yeast Schizosaccharomyces pombe SubtiWiki: integrated database for the model bacterium Bacillus subtilis The primary databases make up the International Nucleotide Sequence Database (INSD). (wikipedia.org)
  • BioGRID provides interaction data to the main model organism databases within the Alliance of Genome Resources, including SGD, PomBase, TAIR, Wormbase and FlyBase, as well as to meta-databases such as NCBI, UniProt, and PubChem. (nih.gov)
Species4
  • These databases may hold many species genomes, or a single model organism genome. (wikipedia.org)
  • Complete coverage of the primary literature is maintained for budding yeast ( S. cerevisiae ), fission yeast ( S. pombe ), and thale cress ( A. thaliana ), as well as partial coverage for other model species. (nih.gov)
  • There is built-in support for over 50 species, 60 identifier (ID) systems, 4 ontologies and 7 pathways/gene-sets, along with customization support for any species, gene associations, ontology or pathways. (genmapp.org)
  • Only the stand-alone version of GO-Elite and source-code allow the user to manually update or modify the GO-Elite gene systems, pathways/ontologies/gene-sets and species configurations. (genmapp.org)
Ensembl1
Genomic2
  • The Protein Information Resource (PIR) is an integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies. (nih.gov)
  • They also provide a rich foundation for post-genomic research, including the selection of candidate gene-targets for innovative whitefly and virus-control strategies. (bvsalud.org)
Interaction3
  • The Biological General Repository for Interaction Datasets (BioGRID) is an open-access public database that uses structured curation to capture protein, genetic, and chemical interaction data from model organisms and humans. (nih.gov)
  • The dashed line represents TF-TF protein-protein interaction (heterodimer). (biomedcentral.com)
  • the blunt 'arrow' represents protein-DNA interaction that results in repression of transcription. (biomedcentral.com)
Interactions5
  • Curation of interactions in human cells is focused on aspects of biology that are particularly relevant to human health, including disease-themed projects such as for COVID-19. (nih.gov)
  • phosphorylation-dependent protein-protein interactions, and miRNA-target). (nih.gov)
  • Transcription regulatory networks are composed of interactions between transcription factors and their target genes. (biomedcentral.com)
  • The comprehensive identification of transcription factors is essential for the systematic mapping of transcription regulatory networks because it enables the creation of physical transcription factor resources that can be used in assays to map interactions between transcription factors and their target genes. (biomedcentral.com)
  • Protein-protein interactions between TFs and protein-DNA interactions between TFs and their target genes can be visualized in transcription regulatory networks. (biomedcentral.com)
Genomes2
  • Secondary databases are:[clarification needed] 23andMe's database HapMap OMIM (Online Mendelian Inheritance in Man): inherited diseases RefSeq 1000 Genomes Project: launched in January 2008. (wikipedia.org)
  • Metazoan genomes contain thousands of predicted protein-coding genes. (biomedcentral.com)
Transcription factor4
  • By computational searches and extensive manual curation, we have identified a compendium of 934 transcription factor genes (referred to as wTF2.0). (biomedcentral.com)
  • We find that manual curation drastically reduces the number of both false positive and false negative transcription factor predictions. (biomedcentral.com)
  • In contrast to mouse transcription factor genes, we find that C. elegans transcription factor genes do not undergo significantly more splicing than other genes. (biomedcentral.com)
  • We identify candidate redundant worm transcription factor genes and orthologous worm and human transcription factor pairs. (biomedcentral.com)
Targets1
  • Such networks are composed of two types of components, or nodes: the gene targets that are subject to transcriptional control and the TF proteins that execute transcriptional control. (biomedcentral.com)
Resource3
  • EggNOG Database: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. (wikipedia.org)
  • In 2005, Dr. Arighi joined the Protein Information Resource (PIR) as a biocurator and was appointed Research Assistant Professor of Biochemistry and Molecular & Cellular Biology at Georgetown University Medical Center. (nih.gov)
  • She is the lead of curation and text mining efforts at the Protein Information Resource. (nih.gov)
Main1
  • Four main interfaces are available for GO-Elite: (1) graphical user interface (GUI), (2) command-line, (3) online web-service and (4) GenMAPP-CS. (genmapp.org)
Public2
  • Other databases Nucleosome positioning region database These databases collect genome sequences, annotate and analyze them, and provide public access. (wikipedia.org)
  • Human Protein Atlas (HPA): a public database with expression profiles of human protein coding genes both on mRNA and protein level in tissues, cells, subcellular compartments, and cancer tumors. (wikipedia.org)
Provide1
Cells1
  • During development, pathology, and in response to environmental changes, each of these genes is expressed in different cells, at different times and at different levels. (biomedcentral.com)
Projects1
  • current database projects may seek to expand their scope to encompass the objectives defined below. (nih.gov)
Function1
  • We include comparative analyses of gene families related to detoxification, sugar metabolism, vector competency and evaluate the presence and function of horizontally transferred genes, essential for understanding the evolution and unique biology of constituent B. tabaci. (bvsalud.org)
Journal1
  • She is currently a member of the editorial board for the journal Database and the Europe PubMed Central Advisory Board. (nih.gov)