TableCategories

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
• #Tables

Super Categories

• #Sequence and Features
• #Function
• #Transcription Regulation
• #Sequence and Feature Modeling
• #Experimental Set-up and Analyses
• #High-throughput Experiment
• #Provenance
• #Vocabularies and Ontologies
• #Administration

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

2. AA Sequence

   • DoTS::AASequence
   • DoTS::ExternalAASequence
   • DoTS::TranslatedAASequence
   • DoTS::TrivialTranslation
   • DoTS::MotifAASequence
   • DoTS::NRDBEntry
   • DoTS::PfamEntry
   • DoTS::DBRefPfamEntry

3. 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

4. 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

5. Feature Relations

   • DoTS::AALocation
   • DoTS::DbRefNAFeature
   • DoTS::ExonLocation
   • DoTS::FeatureName
   • DoTS::GeneFeatureSAGETagLink
   • DoTS::NAFeatureComment
   • DoTS::NAFeatureRelationship
   • DoTS::NAFeatRelationshipType
   • DoTS::NALocation
   • DoTS::RNAFeatureExon

6. 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

7. Similarity

   • DoTS::Similarity
   • DoTS::SimilaritySpan
   • DoTS::BlatAlignmentQuality
   • DoTS::BlatAlignment
   • DoTS::ConsistentAlignment

8. Assembly

   • DoTS::AssemblyAnatomyPercent
   • DoTS::AssemblySequence
   • DoTS::AssemblySequenceSNP
   • DoTS::AssemblySNP
   • DoTS::MergeSplit
   • DoTS::GeneTrapAssembly

9. Motifs

   • DoTS::MotifRejectionReason
   • DoTS::Motif
   • DoTS::RejectedMotif

10. Secondary Structure

    • DoTS::RNASecondaryStructure
    • DoTS::SecondaryStructure
    • DoTS::SecondaryStructureCall

Function

1. Central Dogma

   • DoTS::Gene
   • DoTS::GeneCategory
   • DoTS::GeneChromosomalLocation
   • DoTS::GeneInstance
   • DoTS::GeneInstanceCategory
   • DoTS::GeneSynonym
   • DoTS::Protein
   • DoTS::ProteinCategory
   • DoTS::ProteinInstance
   • DoTS::ProteinInstanceCategory
   • DoTS::ProteinProperty
   • DoTS::ProteinPropertyType
   • DoTS::ProteinProteinCategory
   • DoTS::ProteinSynonym
   • DoTS::RNA
   • DoTS::RNAAnatomy
   • DoTS::RNAAnatomyLOE
   • DoTS::RNACategory
   • DoTS::RNAIConstruct
   • DoTS::RNAInstance
   • DoTS::RNAInstanceCategory
   • DoTS::RNAIPhenotype
   • DoTS::RNARNACategory
   • DoTS::RNASecondaryStructure

2. Paralog and Family

   • DoTS::AAFamilyExperiment
   • DoTS::AAParalogExperiment
   • DoTS::AAParalogGroup
   • DoTS::AASequenceFamily
   • DoTS::AASequenceGroupFamily

3. 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

4. AA Ortholog

   • DoTS::BestSimilarityPair
   • DoTS::AAOrthologExperiment
   • DoTS::AAOrthologGroup
   • DoTS::AASeqGroupExperimentImp
   • DoTS::AASeqGroupExperiment
   • DoTS::AASequenceGroupImp
   • DoTS::AASequenceGroup
   • DoTS::AASequenceSequenceGroup

5. Phylogenetic Profile

   • DoTS::PhylogeneticProfile
   • DoTS::PhylogeneticProfileSet
   • DoTS::PhylogeneticProfileMember
   • DoTS::MutualInformationScore

6. 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

7. Clones

   • DoTS::EST
   • DoTS::AnatomyLibrary
   • DoTS::AnatomyLOE
   • DoTS::CloneInSet
   • DoTS::Clone
   • DoTS::CloneSet
   • DoTS::Library
   • DoTS::DevStageLibrary

8. 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

9. GO Association

   • DoTS::GOAssociationInstanceLOE
   • DoTS::GOAssociationInstance
   • DoTS::GOAssociation
   • DoTS::GOAssocInstEvidCode

10. 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

2. Regulatory Activities

   • TESS::ActivityImp
   • TESS::Activity
   • TESS::ActivityProteinDnaBinding
   • TESS::ActivityConditions
   • TESS::ActivityGeneRegulation
   • TESS::ActivityInferenceSource
   • TESS::ActivityModel

3. Regulatory Sequences

   • TESS::Footprint

4. Comments

   • TESS::Note

5. Models

   • TESS::ModelImp
   • TESS::Model
   • TESS::ModelMarkovChain
   • TESS::ModelSbcgGrammar
   • TESS::MarkovChainObs
   • TESS::ParameterGroup
   • TESS::ParameterSubgroup
   • TESS::ParameterValue

6. Multinomial Models

   • TESS::MultinomialLabel
   • TESS::MultinomialLabelSet
   • TESS::MultinomialObservation
   • TESS::MultinomialObservationSet

7. 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

8. Families of Similar Models

   • TESS::ModelFamily
   • TESS::ModelFamilyAnalysis
   • TESS::ModelSimilarity
   • TESS::ModelFamilyMember

9. Occam's Razor

   • TESS::PredecessorGraph
   • TESS::PredecessorGraphRelation

10. High Volume Genome Annotation

    • TESS::ArchipelagoOfInterest
    • TESS::IslandOfInterest
    • TESS::RegionOfInterest
    • TESS::PredictedBindingSite

11. Training Sets

    • TESS::TrainingSet
    • TESS::TrainingSetParameter
    • TESS::TrainingSetMember

12. Evaluating Models

    • TESS::PerformanceSummary
    • TESS::ModelParameterValue

13. 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

2. Raw Mass Spectrometry Results

   • Prot::MZRun
   • Prot::MZScan
   • Prot::MZPeak
   • Prot::MZPeakResult

3. Protein Identification (from Mass Spectrometry)

   • DoTS::MassSpecSummary
   • Prot::Quantification
   • Prot::ElementResult (subclasses not yet defined)

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. Integrity

    • RAD::IntegrityStatInput
    • RAD::IntegrityStatistic

Provenance

1. External Database

   • SRes::ExternalDatabaseEntry
   • SRes::ExternalDatabaseKeyword
   • SRes::ExternalDatabaseLink
   • SRes::ExternalDatabaseRelease
   • SRes::ExternalDatabase
   • SRes::DbRef

2. Bibliographic

   • SRes::Abstract
   • SRes::Author
   • SRes::BibliographicReference
   • SRes::BibRefAuthor
   • SRes::BibRefType
   • SRes::Reference
   • SRes::Contact
   • SRes::SequenceReference
   • DoTS::Attribution

3. Evidence

   • DoTS::Evidence
   • SRes::ReviewStatus
   • DoTS::Comments

Vocabularies and Ontologies

1. SAEL Vocabulary

   • Sres::SAEL
   • Sres::AnatomySAEL

2. Anatomy Vocabulary

   • SRes::AnatomyLineage
   • SRes::Anatomy
   • SRes::Lineage
   • DoTS::IsExpressed

3. Gene Ontology

   • SRes::GOEvidenceCode
   • SRes::GORelationship
   • SRes::GORelationshipType
   • SRes::GOSynonym
   • SRes::GOTerm

4. Enzymes Vocabulary

   • SRes::ECPathwayEnzymeClass
   • SRes::ECPathway
   • SRes::EnzymeClassAttribute
   • SRes::EnzymeClass
   • DoTS::AASequenceEnzymeClass

5. Taxon Vocabulary

   • SRes::TaxonName
   • SRes::Taxon

6. Developmental Stage Vocabulary

   • SRes::DevelopmentalStage

7. Disease Vocabulary

   • SRes::Disease

8. Genetic Code Vocabulary

   • SRes::GeneticCode

9. General Ontology

   • SRes::OntologyRelationshipType
   • SRes::OntologyTermType
   • Study::OntologyEntry

10. Mutagens Vocabulary

    • SRes::Mutagen

11. Phenotype Vocabulary

    • SRes::PATOAttribute
    • SRes::PhenotypeClass
    • SRes::Phenotype

12. Sequence Ontology

    • SRes::SequenceOntology

13. Repeat Types Vocabulary

    • DoTS::RepeatType

14. Sequence Types Vocabulary

    • DoTS::SequenceType

Administration

1. Text Search

   • DoTS::IndexWordLink
   • DoTS::IndexWord

2. Algorithm

   • Core::AlgorithmImplementation
   • Core::AlgorithmInvocation
   • Core::AlgorithmParamKey
   • Core::AlgorithmParamKeyType
   • Core::AlgorithmParam
   • Core::Algorithm

3. Meta Info

   • Core::DatabaseDocumentation
   • Core::TableCategory
   • Core::TableInfo
   • Core::DatabaseInfo

4. Administration

   • Core::GroupInfo
   • Core::Machine
   • Core::ProjectInfo
   • Core::UserGroup
   • Core::UserInfo
   • Core::UserProject
   • DoTS::ProjectLink
   • RAD::ProjectLink

5. Misc Applications

   • DoTS::GeneFeatureSeqOverlap
   • DoTS::AAMotifGoTermRule
   • DoTS::AAMotifGOTermRuleSet