COPaKB RESTfulAPI

BD2K Center of Excellence for Big Data Computing at UCLA

Alan Kha            akhahaha@gmail.com
Hannah Chou         hannahjchou@gmail.com
Vincent Kyi         vincekyi@gmail.com
Kevin Sheu          kevinsheu@ucla.edu

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Overview

COPaKB database access functions for the RESTful API.

Calls

Disease

• addDisease
• searchDisease
• getInitializedDisease
• addDiseaseGene
• searchDiseaseGene
• limitedGeneList

Peptide

• addPeptide
• list
• limitedList
• getLocation
• searchById
• getInitializedPeptide
• searchBySequence
• searchPeptidesByProtein
• searchBySpecId
• searchByPartialSequence
• addSpectrum
• getSpectrum
• getInitializedSpectrum
• updateSpectrumSpecies
• updateSpectrumFeature
• searchSpectrum
• searchSpectrumBySequence
• searchSpectrumBySequenceAndCharge
• searchSpectrumByAll
• addSpecies
• searchSpecies
• searchSpecies
• addLibraryModule
• searchLibraryModuleWithId
• searchLibraryModuleWithModule
• getLibraryModules
• addPtmType
• searchPtmType

ProteinDAO

• addProteinCurrent
• updateProteinCurrent
• deleteProteinCurrent
• compareProteinCurrent
• addProteinHistory
• searchProteinHistory
• addSpectrumProteinHistory
• deleteSpectrumProtein
• searchSpectrumProteinHistory
• addVersion
• searchVersion
• searchLatestVersion
• searchByID
• getInitializedProtein
• searchByLikeID
• searchByPartialID
• searchByName
• searchByLikeName
• searchBySpecies
• searchBySpeciesName
• searchByPartialSequence
• list
• limitedList
• searchDbRefByID
• searchByPDB
• searchGene
• searchByGeneSymbol
• searchByGeneID
• searchByEnsg
• getProteinWithGenes
• addGoTerms
• searchByGOAccession
• getProteinWithGoTerms
• addSpecies
• searchSpecies
• addSpectrumProtein
• getProteinWithSpectra
• searchSpectrumProtein
• searchSpectrumProteins
• searchSpectrumProteins
• searchProteinsByPeptide
• addHPAProtein
• searchHPAByID
• getInitializedHPAProtein
• addAntibody
• searchAntibodyByID
• getProteinWithPTMs
• smartSearch

ServiceDAO

• getReferenceProteinBundle
• getReferencePeptideBundle
• getLibModNames

SpectrumDAO

• searchBySpecID
• searchByID
• retrieveSpectraList
• addSpectraInfo

StatisticsDAO

• getModuleStatistics
• list