TableCategories

From GUS Wiki
Jump to: navigation, search

GUS 3.5 Table categories

This page organizes the gus schema by Super Categories and Categories. Each table is in one Category. Each Category is in one Super Category.

Please send comments on this to the gusdev list.

There are three sections below

#Super Categories


#Categories

Sequence and Features

  1. NA Sequence
  2. AA Sequence
  3. NA Sequence Features
  4. AA Sequence Features
  5. Feature Relations
  6. GenBank Sequence Record
  7. Similarity
  8. Assembly
  9. Motifs

Function

  1. Central Dogma
  2. Paralog and Family
  3. Sequence Ortholog, Paralog, Family
  4. AA Ortholog
  5. Mapping
  6. Clones
  7. Interaction
  8. GO Association
  9. Variation
  10. Raw Mass Spectrometry Results
  11. Protein Identification (From Mass Spec Analysis)

Transcription Regulation

  1. Regulatory Moieties
  2. Regulatory Activities
  3. Regulatory Sequences
  4. Comments

Sequence and Feature Modeling

  1. Models
  2. Multinomial Models
  3. Bounded Collection Grammars
  4. Families of Similar Models
  5. Occam's Razor
  6. High Volume Genome Annotation
  7. Training Sets

Experimental Set-up and Analyses

  1. Experimental Design
  2. Biomaterials
  3. Protocols
  4. Data Transformations and Analyses
  5. Learning Models
  6. Model-based Regulatory Feature Prediction
  7. Evaluating Models.

High-throughput Experiment

  1. Platform
  2. Assay
  3. Quantified Data
  4. Integrity

Provenance

  1. Algorithm
  2. External Database
  3. Bibliographic
  4. Evidence

Vocabularies and Ontologies

  1. Anatomy Vocabulary
  2. Gene Ontology
  3. Enzymes Vocabulary
  4. Taxon Vocabulary
  5. Developmental Stage Vocabulary
  6. Disease Vocabulary
  7. General Ontology
  8. Genetic Code Vocabulary
  9. MGED Ontology
  10. Mutagens Vocabulary
  11. Phenotype Vocabulary
  12. Sequence Ontology
  13. Repeat Types Vocabulary
  14. Sequence Types Vocabulary

Administration

  1. Meta Info
  2. Administration
  3. Misc Applications
  4. Text Search


#Tables

#Sequence and Features

  1. NA Sequence
    • DoTS::Assembly
    • DoTS::DbRefNASequence
    • DoTS::ExternalNASequence
    • DoTS::GenomicSequence
    • DoTS::NASequence
    • DoTS::SequencePiece
    • DoTS::SplicedNASequence
    • DoTS::VirtualSequence
  1. AA Sequence
    • DoTS::AASequence
    • DoTS::ExternalAASequence
    • DoTS::TranslatedAASequence
    • DoTS::TrivialTranslation
    • DoTS::MotifAASequence
    • DoTS::NRDBEntry
    • DoTS::PfamEntry
    • DoTS::DBRefPfamEntry
  1. NA Sequence Features
    • DoTS::AlleleFeature
    • DoTS::BindingSiteFeature
    • DoTS::ChromosomeElementFeature
    • DoTS::CollectionNAFeature
    • DoTS::DNARegulatory
    • DoTS::DNAStructure
    • DoTS::ExonFeature
    • DoTS::GeneFeature
    • DoTS::HexamerFeature
    • DoTS::Immunoglobulin
    • DoTS::InflectionPointFeature
    • DoTS::IntronFeature
    • DoTS::LowComplexityNAFeature
    • DoTS::Miscellaneous
    • DoTS::NAFeatureImp
    • DoTS::NAFeature
    • DoTS::PolyAFeature
    • DoTS::PromoterFeature
    • DoTS::ProteinFeature
    • DoTS::Repeats
    • DoTS::ReplicationOriginFeature
    • DoTS::RestrictionFragmentFeature
    • DoTS::RNAFeature
    • DoTS::RNARegulatoryFeature
    • DoTS::RNAStructure
    • DoTS::RNAType
    • DoTS::SAGETagFeature
    • DoTS::ScaffoldGapFeature
    • DoTS::SeqVariation
    • DoTS::Source
    • DoTS::SpliceSiteFeature
    • DoTS::STS
    • DoTS::TandemRepeatFeature
    • DoTS::Transcript
    • DoTS::UTRFeature
    • DoTS::TransposableElement
  1. AA Sequence Features
    • DoTS::AAFeature
    • DoTS::AAFeatureImp
    • DoTS::AASeqVariation
    • DoTS::DomainFeature
    • DoTS::EpitopeFeature
    • DoTS::LowComplexityAAFeature
    • DoTS::MassSpecFeature
    • DoTS::PlasmoAPFeature
    • DoTS::PostTranslationalModFeature
    • DoTS::PredictedAAFeature
    • DoTS::RepeatRegionAAFeature
    • DoTS::SecondaryStructureAAFeature
    • DoTS::SignalPeptideFeature
    • DoTS::TertiaryStructureAAFeature
    • DoTS::TranslatedAAFeature
    • DoTS::TranslatedAAFeatSeg
    • DoTS::PostTranslationalModFeature
    • DoTS::SecondaryStructureAAFeature
    • DoTS::RepeatRegionAAFeature
  1. Feature Relations
    • DoTS::AALocation
    • DoTS::DbRefNAFeature
    • DoTS::ExonLocation
    • DoTS::FeatureName
    • DoTS::GeneFeatureSAGETagLink
    • DoTS::NAFeatureComment
    • DoTS::NAFeatureRelationship
    • DoTS::NAFeatRelationshipType
    • DoTS::NALocation
    • DoTS::RNAFeatureExon
  1. GenBank Sequence Record
    • DoTS::AAComment
    • DoTS::AAEntry
    • DoTS::AAGene
    • DoTS::AAGeneSynonym
    • DoTS::AASequenceKeyword
    • DoTS::AASequenceOrganelle
    • DoTS::AASequenceTaxon
    • DoTS::AASequenceRef
    • DoTS::NAComment
    • DoTS::NAEntry
    • DoTS::NAGene
    • DoTS::NAPrimaryTranscript
    • DoTS::NAProtein
    • DoTS::NASeqCytoLocation
    • DoTS::Keyword
    • DoTS::NAFeatureNAGene
    • DoTS::NAFeatureNAProtein
    • DoTS::NAFeatureNAPT
    • DoTS::NASequenceKeyword
    • DoTS::NASequenceOrganelle
    • DoTS::NASequenceRef
    • DoTS::Organelle
    • DoTS::CommentName
    • DoTS::SecondaryAccs
  1. Similarity
    • DoTS::Similarity
    • DoTS::SimilaritySpan
    • DoTS::BlatAlignmentQuality
    • DoTS::BlatAlignment
    • DoTS::ConsistentAlignment
  1. Assembly
    • DoTS::AssemblyAnatomyPercent
    • DoTS::AssemblySequence
    • DoTS::AssemblySequenceSNP
    • DoTS::AssemblySNP
    • DoTS::MergeSplit
    • DoTS::GeneTrapAssembly
  1. Motifs
    • DoTS::MotifRejectionReason
    • DoTS::Motif
    • DoTS::RejectedMotif
  1. Secondary Structure
    • DoTS::RNASecondaryStructure
    • DoTS::SecondaryStructure
    • DoTS::SecondaryStructureCall

#Function

  1. Central Dogma
    • DoTS::Gene
    • DoTS::
    • DoTS::GeneChromosomalLocation
    • DoTS::GeneInstance
    • DoTS::
    • DoTS::GeneSynonym
    • DoTS::Protein
    • DoTS::
    • DoTS::ProteinInstance
    • DoTS::
    • DoTS::ProteinProperty
    • DoTS::ProteinPropertyType
    • DoTS::
    • DoTS::ProteinSynonym
    • DoTS::RNA
    • DoTS::RNAAnatomy
    • DoTS::RNAAnatomyLOE
    • DoTS::
    • DoTS::RNAIConstruct
    • DoTS::RNAInstance
    • DoTS::
    • DoTS::RNAIPhenotype
    • DoTS::
    • DoTS::RNASecondaryStructure
  1. Paralog and Family
    • DoTS::AAFamilyExperiment
    • DoTS::AAParalogExperiment
    • DoTS::AAParalogGroup
    • DoTS::AASequenceFamily
    • DoTS::AASequenceGroupFamily
  1. Sequence Ortholog, Paralog, Family
    • DoTS::InParalogExperiment
    • DoTS::InParalogGroup
    • DoTS::OrthologExperiment
    • DoTS::OrthologGroup
    • DoTS::OutParalogExperiment
    • DoTS::OutParalogGroup
    • DoTS::SeqGroupExperiment
    • DoTS::SeqGroupExperimentImp
    • DoTS::SequenceFamilyExperiment
    • DoTS::SequenceFamily
    • DoTS::SequenceGroupFamily
    • DoTS::SequenceGroupImp
    • DoTS::SequenceGroup
    • DoTS::SequenceSequenceGroup
  1. AA Ortholog
    • DoTS::BestSimilarityPair
    • DoTS::AAOrthologExperiment
    • DoTS::AAOrthologGroup
    • DoTS::AASeqGroupExperimentImp
    • DoTS::AASeqGroupExperiment
    • DoTS::AASequenceGroupImp
    • DoTS::AASequenceGroup
    • DoTS::AASequenceSequenceGroup
  1. Phylogenetic Profile
    • DoTS::PhylogeneticProfile
    • DoTS::PhylogeneticProfileSet
    • DoTS::PhylogeneticProfileMember
    • DoTS::MutualInformationScore
  1. Mapping
    • DoTS::FingerprintClone
    • DoTS::FingerprintCloneContig
    • DoTS::FingerprintCloneMarker
    • DoTS::FingerprintContig
    • DoTS::FingerprintMap
    • DoTS::RHMap
    • DoTS::RHMarker
    • DoTS::RHMapMarker
    • DoTS::OpticalMapAlignment
    • DoTS::OpticalMapAlignmentSpan
    • DoTS::OpticalMapFragment
    • DoTS::EPCR
    • DoTS::EndSequencePairMap
    • DoTS::MicroSatelliteMap
  1. Clones
    • DoTS::EST
    • DoTS::AnatomyLibrary
    • DoTS::AnatomyLOE
    • DoTS::CloneInSet
    • DoTS::Clone
    • DoTS::CloneSet
    • DoTS::Library
    • DoTS::DevStageLibrary
  1. Interaction
    • DoTS::InteractionInteractionLOE
    • DoTS::InteractionLOE
    • DoTS::Interaction
    • DoTS::InteractionType
    • DoTS::PathwayInteraction
    • DoTS::Pathway
    • DoTS::EffectorActionType
    • DoTS::RowSetMember
    • DoTS::RowSet
    • DoTS::Complex
    • DoTS::ComplexAnatomy
    • DoTS::ComplexComponent
    • DoTS::ComplexType
  1. GO Association
    • DoTS::GOAssociationInstanceLOE
    • DoTS::GOAssociationInstance
    • DoTS::GOAssociation
    • DoTS::GOAssocInstEvidCode
  1. Variation
    • DoTS::Complementation
    • DoTS::AlleleComplementation
    • DoTS::AlleleInstance
    • DoTS::AllelePhenotype
    • DoTS::AllelePhenotypeClass
    • DoTS::Allele

#Transcription Regulation

  1. Regulatory Moieties
    • TESS::MoietyImp
    • TESS::Moiety
    • TESS::MoietyComplex
    • TESS::MoietyHeteroDimer
    • TESS::MoietyMember
    • TESS::MoietyMonomer
    • TESS::MoietyMultimer
    • TESS::MoietySynonym
    • TESS::MoietyInstance
  1. Regulatory Activities
    • TESS::ActivityImp
    • TESS::Activity
    • TESS::ActivityProteinDnaBinding
    • TESS::ActivityConditions
    • TESS::ActivityGeneRegulation
    • TESS::ActivityInferenceSource
    • TESS::ActivityModel
  1. Regulatory Sequences
    • TESS::Footprint
  1. Comments
    • TESS::Note
  1. Models
    • TESS::ModelImp
    • TESS::Model
    • TESS::ModelMarkovChain
    • TESS::ModelSbcgGrammar
    • TESS::MarkovChainObs
    • TESS::ParameterGroup
    • TESS::ParameterSubgroup
    • TESS::ParameterValue
  1. Multinomial Models
    • TESS::MultinomialLabel
    • TESS::MultinomialLabelSet
    • TESS::MultinomialObservation
    • TESS::MultinomialObservationSet
  1. Bounded Collection Grammars
    • TESS::SbcgAnnotationFilter
    • TESS::SbcgAnnotationFilterTerm
    • TESS::SbcgAnnotationGuide
    • TESS::SbcgComparisonType
    • TESS::SbcgNonterminal
    • TESS::SbcgPathTermRelationType
    • TESS::SbcgProduction
    • TESS::SbcgProductionType
    • TESS::SbcgRecogConsensusString
    • TESS::SbcgRecogGap
    • TESS::SbcgRecogMultiObs
    • TESS::SbcgRecogPathExpression
    • TESS::SbcgRecogPosition
    • TESS::SbcgRecogString
    • TESS::SbcgRecogWeightMatrix
    • TESS::SbcgRecognition
    • TESS::SbcgRecognitionImp
    • TESS::SbcgRhsTerm
    • TESS::SbcgStream
    • TESS::SbcgStreamParameter
  1. Families of Similar Models
    • TESS::ModelFamily
    • TESS::ModelFamilyAnalysis
    • TESS::ModelSimilarity
    • TESS::ModelFamilyMember
  1. Occam's Razor
    • TESS::PredecessorGraph
    • TESS::PredecessorGraphRelation
  1. High Volume Genome Annotation
    • TESS::ArchipelagoOfInterest
    • TESS::IslandOfInterest
    • TESS::RegionOfInterest
    • TESS::PredictedBindingSite
  1. Training Sets
    • TESS::TrainingSet
    • TESS::TrainingSetParameter
    • TESS::TrainingSetMember
  1. Evaluating Models
    • TESS::PerformanceSummary
    • TESS::ModelParameterValue
  1. Model-based Regulatory Feature Prediction
    • TESS::ParserItem
    • TESS::ParserItemEdgeType
    • TESS::ParserItemLink


#Experiment

  1. Protocols
    • RAD::LabelMethod
    • RAD::Protocol
    • RAD::ProtocolParam
    • RAD::ProtocolQCParam
    • RAD::ProtocolStep
    • TESS::Protocol
    • TESS::ProtocolStep
    • TESS::ProtocolParam
    • TESS::ProtocolQcParam
    • TESS::FootprintMethodProtocol
    • TESS::TrainingSetProcotolParam
    • TESS::TrainingSetQcParam
    • TESS::AnalysisProcotolParam
    • TESS::AnalysisQcParam
    • TESS::ModelFamilyAnalysisProcotolParam
    • TESS::ModelFamilyAnalysisQcParam
    • PROT::Parameterizable
    • PROT::ParameterizableLink
    • PROT::ParameterizableInstance
    • PROT::Parameter
    • PROT::ParameterInstance
    • PROT::Protocol
    • PROT::Action
    • PROT::Software
    • PROT::Hardware
    • PROT::ProtocolAction
    • PROT::ProtocolHardware
    • PROT::ProtocolSoftware
    • PROT::ProtocolInstance
    • PROT::ActionInstance
  1. Raw Mass Spectrometry Results
    • Prot::MZRun
    • Prot::MZScan
    • Prot::MZPeak
    • Prot::MZPeakResult
  1. Protein Identification (from Mass Spectrometry)
    • DoTS::MassSpecSummary
    • Prot::Quantification
    • Prot::ElementResult (subclasses not yet defined)
  1. Data Transformations and Analyses
    • RAD::Analysis
    • RAD::AnalysisInput
    • RAD::AnalysisParam
    • RAD::AnalysisQCParam
    • RAD::AnalysisResult
    • RAD::AnalysisResultImp
    • RAD::ArrayStatTwoConditions
    • RAD::AssayAnalysis
    • RAD::DataTransformationResult
    • RAD::HQSpecificity
    • RAD::LogicalGroup
    • RAD::LogicalGroupLink
    • RAD::SAM
    • RAD::SpliceArrayAnalysisResult
    • TESS::Analysis
    • TESS::AnalysisInput
    • TESS::LogicalGroup
    • TESS::LogicalGroupLink
    • TESS::ModelResult
    • TESS::PredictionResult
    • PROT::DataTransformation
  1. Platform
    • RAD::ArrayDesign
    • RAD::ArrayDesignAnnotation
    • RAD::ArrayDesignGroup
    • RAD::ArrayDesignGroupLink
    • RAD::CompositeElement
    • RAD::CompositeElementAnnotation
    • RAD::CompositeElementImp
    • RAD::Control
    • RAD::Element
    • RAD::ElementAnnotation
    • RAD::ElementImp
    • RAD::SAGETag
    • RAD::SAGETagMapping
    • RAD::ShortOligo
    • RAD::ShortOligoFamily
    • RAD::Spot
    • RAD::SpotFamily
    • PROT::Feature
    • PROT::FeatureInput
    • PROT::FeatureSet
    • PROT::FSGAnnotation
    • PROT::MALDIPlate
    • PROT::MALDISpot
  1. Assay
    • RAD::Assay
    • RAD::AssayControl
    • RAD::AssayParam
    • RAD::Acquisition
    • RAD::AcquisitionParam
    • RAD::RelatedAcquisition
    • RAD::Quantification
    • RAD::QuantificationParam
    • RAD::RelatedQuantification
    • PROT::Assay
    • PROT::AssayAnnotation
    • PROT::AssayChain
    • PROT::AssayParentFile
    • PROT::AssayInput
    • PROT::AssayProduct
    • PROT::Acquisition
    • PROT::AcquisitionChain
    • PROT::AcquisitionChannel
    • PROT::AcquisitionQuantification
    • PROT::Quantification
    • PROT::MZRun
    • PROT::MZScan
    • PROT::ParentFile
  1. Quantified Data
    • RAD::AffymetrixCEL
    • RAD::AffymetrixMAS4
    • RAD::AffymetrixMAS5
    • RAD::AgilentElementResult
    • RAD::ArrayVisionElementResult
    • RAD::CompositeElementResult
    • RAD::CompositeElementResultImp
    • RAD::ElementResult
    • RAD::ElementResultImp
    • RAD::GEMToolsElementResult
    • RAD::GenePixElementResult
    • RAD::MOIDResult
    • RAD::ProbeProfiler
    • RAD::QuantArrayElementResult
    • RAD::RMAExpress
    • RAD::SAGETagResult
    • RAD::ScanAlyzeElementResult
    • RAD::SpotElementResult
    • PROT::ElementResult
    • PROT::MZPeak
    • PROT::MZPeakResult
  1. Experimental Design
    • RAD::StudyAssay
    • RAD::StudyDesignAssay
    • RAD::StudyFactorValue
    • Study::StudyBioMaterial
    • Study::Study
    • Study::StudyDesign
    • Study::StudyDesignDescription
    • Study::StudyDesignType
    • Study::StudyFactor
    • PROT::StudyAssay
    • PROT::StudyBioMaterial
    • PROT::StudyDesignAssay
    • PROT::StudyFactorValue
  1. Biomaterials
    • RAD::AssayBioMaterial
    • RAD::AssayLabeledExtract
    • RAD::BioMaterialMeasurement
    • RAD::Treatment
    • RAD::TreatmentParam
    • Study::BMCRelationship
    • Study:BioMaterial
    • Study::BioMaterialCharacteristic
    • Study::BioMaterialImp
    • Study::BioSample
    • Study::BioSource
    • Study::LabeledExtract
    • PROT::BioMaterialMeasurement
  1. Integrity
    • RAD::IntegrityStatInput
    • RAD::IntegrityStatistic

#Provenance

  1. External Database
    • SRes::ExternalDatabaseEntry
    • SRes::ExternalDatabaseKeyword
    • SRes::ExternalDatabaseLink
    • SRes::ExternalDatabaseRelease
    • SRes::ExternalDatabase
    • SRes::DbRef
  1. Bibliographic
    • SRes::Abstract
    • SRes::Author
    • SRes::BibliographicReference
    • SRes::BibRefAuthor
    • SRes::BibRefType
    • SRes::Reference
    • SRes::Contact
    • SRes::SequenceReference
    • DoTS::Attribution
  1. Evidence
    • DoTS::Evidence
    • SRes::ReviewStatus
    • DoTS::Comments

#Vocabularies and Ontologies

  1. SAEL Vocabulary
    • Sres::SAEL
    • Sres::AnatomySAEL
  1. Anatomy Vocabulary
    • SRes::AnatomyLineage
    • SRes::Anatomy
    • SRes::Lineage
    • DoTS::IsExpressed
  1. Gene Ontology
    • SRes::GOEvidenceCode
    • SRes::GORelationship
    • SRes::GORelationshipType
    • SRes::GOSynonym
    • SRes::GOTerm
  1. Enzymes Vocabulary
    • SRes::ECPathwayEnzymeClass
    • SRes::ECPathway
    • SRes::EnzymeClassAttribute
    • SRes::EnzymeClass
    • DoTS::AASequenceEnzymeClass
  1. Taxon Vocabulary
    • SRes::TaxonName
    • SRes::Taxon
  1. Developmental Stage Vocabulary
    • SRes::DevelopmentalStage
  1. Disease Vocabulary
    • SRes::Disease
  1. Genetic Code Vocabulary
    • SRes::GeneticCode
  1. General Ontology
    • SRes::OntologyRelationshipType
    • SRes::OntologyTermType
    • Study::OntologyEntry
  1. Mutagens Vocabulary
    • SRes::Mutagen
  1. Phenotype Vocabulary
    • SRes::PATOAttribute
    • SRes::PhenotypeClass
    • SRes::Phenotype
  1. Sequence Ontology
    • SRes::SequenceOntology
  1. Repeat Types Vocabulary
    • DoTS::RepeatType
  1. Sequence Types Vocabulary
    • DoTS::SequenceType

#Administration

  1. Text Search
    • DoTS::IndexWordLink
    • DoTS::IndexWord
  1. Algorithm
    • Core::AlgorithmImplementation
    • Core::AlgorithmInvocation
    • Core::AlgorithmParamKey
    • Core::AlgorithmParamKeyType
    • Core::AlgorithmParam
    • Core::Algorithm
  1. Meta Info
    • Core::DatabaseDocumentation
    • Core::
    • Core::TableInfo
    • Core::DatabaseInfo
  1. Administration
    • Core::GroupInfo
    • Core::Machine
    • Core::ProjectInfo
    • Core::UserGroup
    • Core::UserInfo
    • Core::UserProject
    • DoTS::ProjectLink
    • RAD::ProjectLink
  1. Misc Applications
    • DoTS::GeneFeatureSeqOverlap
    • DoTS::AAMotifGoTermRule
    • DoTS::AAMotifGOTermRuleSet