SCHEMA
MSDbase

Table of Contents

Primitive Value Classes
Controlled Value Classes
Object Classes
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Primitive Value Classes

aminoTorsion
cvLocalID
MSD_ID
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Controlled Value Classes

cvBondTypes
cvDatabaseDict
cvExperimentTypes
cvFlagDict
cvHelixClass
cvMacroMoleculeType
cvMtrixType
cvPDBResidueType
cvResourceType
exp_resolution
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Object Classes

oAnnotations
oAsu
oAtom
oAtomAnisoU
oAtomAnisoUSigma
oAtomSigma
oBond
oChain
oCrystal
oExtRefDict
oExternalReference
oHelixPDB
oHet
oHetDictionary
oMSDExportObj
oExperiment
oDiffractStudy
oNMRStudy
oMacroMolecule
oMatrix
oModel
oPerson
oPrimarySeq
oRefinement
oDiffractRefinement
oNMRRefinement
oResidueMolec
oAmino_acid
oSeqAdv
oSheetPDB
oSheetStrand
oSitePDB
oSolventMolecule
oSource
oTurnPDB
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PRIMITIVE VALUE CLASS aminoTorsion
Description:
Torsion angles for amino acids
Data Type:
FLOAT
Alternative Representations
OPM Class Definition
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PRIMITIVE VALUE CLASS cvLocalID
Description:
Internal ID for objects that do not have a natural ID like MATRIX
Data Type:
INTEGER
Alternative Representations
OPM Class Definition
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PRIMITIVE VALUE CLASS MSD_ID
Data Type:
VARCHAR(4)
Default:
"4"
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS cvBondTypes
Description:
Types of bonds found in molecules
Controlled Values or Ranges:
  • covalent-single (0)
  • covalent-double (1)
  • covalent-triple (2)
  • covalent-aromatic (3)
  • covalent-peptide (4)
  • SS-bond (5)
  • H-bond (6)
  • Salt Bridge (7)
  • covalent-coordinate (8)
Code Type:
INTEGER
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS cvDatabaseDict
Description:
Controlled vocabulary for valid databases
Synonyms:
  • Medline_si_type
  • Seq_annot_db
  • EMBL_dbname_code
Controlled Values or Ranges:
  • 0
    Description: PDB
  • 1
    Description: SwissProt
  • 2
    Description: GDB
  • 3
    Description: GenBank
  • 4
    Description: PIR
  • 5
    Description: Medline
  • 6
    Description: Enzyme
  • 7
    Description: PDB_HET_DICT
  • 8
    Description: CitDB
  • 9
    Description: Protein Mutant Database
Similar Classes:
  • Class Medline_si_type (in schema NCBI) (comment: Medline database names)
  • Class Seq_annot_db (in schema NCBI) (comment: annot database names)
  • Class EMBL_dbname_code (in schema NCBI) (comment: EMBL database names)
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS cvExperimentTypes
Description:
Contents of EXPDTA
Controlled Values or Ranges:
  • 0
    Description: X-Ray
  • 1
    Description: NMR
  • 2
    Description: Theoretical Model
  • 3
    Description: Neutron Diffraction
  • 4
    Description: Fiber Diffraction
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS cvFlagDict
Description:
Controlled vocabulary for boolean values YES and NO
Controlled Values or Ranges:
  • 1
    Description: Yes
  • 0
    Description: No
Default:
0
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS cvHelixClass
Description:
standard PDB helix class
Controlled Values or Ranges:
  • right-handed alpha (0)
  • right-handed pi (1)
  • right-handed 3/10 (2)
  • left-handed omega (3)
  • 2/7 ribbon/helix (4)
  • right-handed omega (5)
  • right-handed gamma (6)
  • left-handed alpha (7)
  • left-handed gamma (8)
  • polyproline (9)
Code Type:
INTEGER
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS cvMacroMoleculeType
Description:
contains what kind of macmromolecule this is
Controlled Values or Ranges:
  • 0
    Description: protein
  • 1
    Description: dna
  • 2
    Description: rna
  • 3
    Description: polysaccharide
  • 4
    Description: other - must annotate
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS cvMtrixType
Controlled Values or Ranges:
  • 1
    Description: Generative
  • 0
    Description: Descriptive
Default:
0
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS cvPDBResidueType
Description:
residues in PDB entries are atoms,hetatms, and solvents
Controlled Values or Ranges:
  • atom (0)
  • heterogen (1)
  • solvent (2)
Code Type:
INTEGER
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS cvResourceType
Controlled Values or Ranges:
  • image (0)
  • movie (1)
  • gelfile (2)
  • database (3)
  • lookup table (4)
  • archive (5)
  • directory (6)
Code Type:
INTEGER
Alternative Representations
OPM Class Definition
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CONTROLLED VALUE CLASS exp_resolution
Controlled Values or Ranges:
  • 0 - 10
Default:
1
Alternative Representations
OPM Class Definition
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OBJECT CLASS oAmino_acid
Superclasses:
oResidueMolec
Attributes:
aPhi
  • Constraints: single-valued, can be null
  • Domain: aminoTorsion
aPsi
  • Constraints: single-valued, can be null
  • Domain: aminoTorsion
aOmega
  • Constraints: single-valued, can be null
  • Domain: aminoTorsion
aChi1
  • Constraints: single-valued, can be null
  • Domain: aminoTorsion
aChi2
  • Constraints: single-valued, can be null
  • Domain: aminoTorsion
aChi3
  • Constraints: single-valued, can be null
  • Domain: aminoTorsion
aChi4
  • Constraints: single-valued, can be null
  • Domain: aminoTorsion
Alternative Representations
OPM Class Definition
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OBJECT CLASS oAnnotations
Description:
REMARK and FTNOTE records go here
Synonyms:
  • annotation
Identified by:
aLocalID
Represented by:
aRemarkNum
Attributes:
aAnnotations
  • Description: "long paragraphs get extra lines"
  • Constraints: single-valued, can be null
  • Domain: TEXT
aRemarkNum
  • Constraints: single-valued, not null
  • Domain: VARCHAR(10)
aLocalID
  • Constraints: single-valued, not null
  • Domain: cvLocalID
Similar Classes:
  • Class Annotdesc (in schema NCBI) (comment: NCBI annotation)
  • Class Annotation (in schema HGD) (comment: HGD annotation)
Alternative Representations
OPM Class Definition
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OBJECT CLASS oAsu
Description:
crystal asymmetric unit
Identified by:
aMSDID
Represented by:
aMSDID
Attributes:
aAsuChains
  • Constraints: set-valued, Min # of values: 0
  • Domain: oChain
aHetGroups
  • Constraints: set-valued, Min # of values: 0
  • Domain: oHet
aSolvent
aMSDID
  • Constraints: single-valued, not null
  • Domain: MSD_ID
Alternative Representations
OPM Class Definition
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OBJECT CLASS oAtom
Description:
each PDB atoms
Identified by:
aLocalID
Represented by:
aAtomName
Subclasses:
oAtomAnisoU oAtomAnisoUSigma oAtomSigma
Attributes:
aAlternate_site
  • Description: "atoms which are disordered must have alternate sites assigned"
  • Constraints: single-valued, can be null
  • Domain: CHAR(1)
aAtomName
  • Constraints: single-valued, not null
  • Domain: VARCHAR(4)
aElementSymbol
  • Description: "element name, in some cases include the ionic form"
  • Constraints: single-valued, not null
  • Domain: VARCHAR(4)
aOccupancy
  • Constraints: single-valued, can be null
  • Domain: FLOAT
aTempFact
  • Constraints: single-valued, can be null
  • Domain: FLOAT
aCoord (x, y, z)
  • Constraints: single-valued, not null
  • Component Attributes:
    x
    • Domain: FLOAT
    • Constraints: not null
    y
    • Domain: FLOAT
    • Constraints: not null
    z
    • Domain: FLOAT
    • Constraints: not null
aBondAtom (aBondType, aAtom)
  • Constraints: set-valued, Min # of values: 0
  • Component Attributes:
    aBondType
    aAtom
    • Domain: oAtom
    • Constraints: can be null
aLocalID
  • Constraints: single-valued, not null
  • Domain: cvLocalID
Alternative Representations
OPM Class Definition
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OBJECT CLASS oAtomAnisoU
Description:
Anisotropic Thermal Parameters
Superclasses:
oAtom
Attributes:
u11
  • Constraints: single-valued, not null
  • Domain: FLOAT
u13
  • Constraints: single-valued, not null
  • Domain: FLOAT
u22
  • Constraints: single-valued, not null
  • Domain: FLOAT
u23
  • Constraints: single-valued, not null
  • Domain: FLOAT
u33
  • Constraints: single-valued, not null
  • Domain: FLOAT
Alternative Representations
OPM Class Definition
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OBJECT CLASS oAtomAnisoUSigma
Description:
Anisotropic Thermal Parameters
Superclasses:
oAtom
Attributes:
sigmau11
  • Constraints: single-valued, not null
  • Domain: FLOAT
sigmau13
  • Constraints: single-valued, not null
  • Domain: FLOAT
sigmau22
  • Constraints: single-valued, not null
  • Domain: FLOAT
sigmau23
  • Constraints: single-valued, not null
  • Domain: FLOAT
sigmau33
  • Constraints: single-valued, not null
  • Domain: FLOAT
Alternative Representations
OPM Class Definition
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OBJECT CLASS oAtomSigma
Description:
each PDB atoms
Superclasses:
oAtom
Attributes:
sigmaX
  • Constraints: single-valued, not null
  • Domain: FLOAT
sigmaY
  • Constraints: single-valued, not null
  • Domain: FLOAT
sigmaZ
  • Constraints: single-valued, not null
  • Domain: FLOAT
Alternative Representations
OPM Class Definition
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OBJECT CLASS oBond
Description:
bonding between two atoms
Identified by:
aBondType aLocalID
Represented by:
aBondType
Attributes:
aBondType
  • Constraints: single-valued, not null
  • Domain: cvBondTypes
aAtom1
  • Description: "first atoms in a bonding pair"
  • Constraints: single-valued, not null
  • Domain: oAtom
aAtom2
  • Description: "second atom in a bonding pair"
  • Constraints: single-valued, not null
  • Domain: oAtom
aLocalID
  • Constraints: single-valued, not null
  • Domain: cvLocalID
Alternative Representations
OPM Class Definition
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OBJECT CLASS oChain
Description:
polypeptide chain
Identified by:
aLocalID
Represented by:
aChainID
Attributes:
aChainID
  • Constraints: single-valued, not null
  • Domain: CHAR(1)
aResRun
  • Constraints: list-valued, Min # of values: 1
  • Domain: oResidueMolec
aHetGroups
  • Constraints: set-valued, Min # of values: 0
  • Domain: oResidueMolec
aSolvents
  • Constraints: set-valued, Min # of values: 0
  • Domain: oResidueMolec
aMSDID
  • Constraints: single-valued, can be null
  • Domain: MSD_ID
aLocalID
  • Constraints: single-valued, not null
  • Domain: cvLocalID
Alternative Representations
OPM Class Definition
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OBJECT CLASS oCrystal
Identified by:
aMSDID
Represented by:
aMSDID
Attributes:
aCellDimensions (a, b, c, alpha, beta, gamma)
  • Constraints: single-valued, not null
  • Component Attributes:
    a
    • Domain: FLOAT
    • Constraints: not null
    b
    • Domain: FLOAT
    • Constraints: not null
    c
    • Domain: FLOAT
    • Constraints: not null
    alpha
    • Domain: FLOAT
    • Constraints: not null
    beta
    • Domain: FLOAT
    • Constraints: not null
    gamma
    • Domain: FLOAT
    • Constraints: not null
aSpaceGroups
  • Constraints: single-valued, not null
  • Domain: VARCHAR(12)
aZvalue
  • Constraints: single-valued, not null
  • Domain: INTEGER
aCellVolume
  • Constraints: single-valued, not null
  • Domain: FLOAT
aStdSettingFlag
  • Constraints: single-valued, not null
  • Domain: BOOLEAN
aVs
  • Description: "% solvent"
  • Constraints: single-valued, not null
  • Domain: FLOAT
aMatthewsCoeff
  • Constraints: single-valued, not null
  • Domain: FLOAT
oOperators
  • Constraints: set-valued, Min # of values: 0
  • Domain: VARCHAR(15)
aMSDID
  • Constraints: single-valued, not null
  • Domain: MSD_ID
Alternative Representations
OPM Class Definition
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OBJECT CLASS oDiffractRefinement
Represented by:
aRefineType
Superclasses:
oRefinement
Attributes:
aAnalysis
aRefineType
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(80)
aRvalue
  • Constraints: single-valued, can be null
  • Domain: FLOAT
aRmsdBondDist
  • Constraints: single-valued, can be null
  • Domain: FLOAT
Alternative Representations
OPM Class Definition
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OBJECT CLASS oDiffractStudy
Superclasses:
oExperiment
Attributes:
aResolution
  • Constraints: single-valued, can be null
  • Domain: FLOAT
aRefinement
aCrystalData
  • Constraints: single-valued, can be null
  • Domain: oCrystal
aORIGX
  • Constraints: single-valued, can be null
  • Domain: oMatrix
aSCALE
  • Constraints: single-valued, can be null
  • Domain: oMatrix
aMTRIX (aMtrixNum, aTransfrm, aRes1, aRes2, aTransfType)
  • Constraints: set-valued, Min # of values: 0
  • Component Attributes:
    aMtrixNum
    • Domain: INTEGER
    • Constraints: not null
    aTransfrm
    • Domain: oMatrix
    • Constraints: not null
    aRes1
    aRes2
    aTransfType
aCrystalContents
  • Constraints: single-valued, can be null
  • Domain: oAsu
Alternative Representations
OPM Class Definition
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OBJECT CLASS oExperiment
Subclasses:
oDiffractStudy oNMRStudy
Superclasses:
oMSDExportObj
Attributes:
aTitle
  • Constraints: list-valued, Min # of values: 1
  • Domain: VARCHAR(255)
aDepositor
  • Constraints: list-valued, Min # of values: 1
  • Domain: oPerson
aKeywords
  • Constraints: set-valued, Min # of values: 0
  • Domain: VARCHAR(80)
aExpdta
  • Description: "experiment type"
  • Constraints: single-valued, not null
  • Domain: cvExperimentTypes
aReference
aRemarks
  • Constraints: set-valued, Min # of values: 0
  • Domain: oAnnotations
Alternative Representations
OPM Class Definition
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OBJECT CLASS oExtRefDict
Identified by:
aURL
Represented by:
aURL
Attributes:
aDBname
aURL
  • Constraints: single-valued, not null
  • Domain: VARCHAR(255)
aSummLine
  • Description: "Store explanation or description here"
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
aAlternateAccess
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
Alternative Representations
OPM Class Definition
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OBJECT CLASS oExternalReference
Description:
pointer to external database
Identified by:
aLocalID
Represented by:
aExDBExportObj aSummLine
Attributes:
aExDBExportObj
  • Constraints: single-valued, not null
  • Domain: VARCHAR(20)
aSelectStart
  • Constraints: single-valued, can be null
  • Domain: INTEGER
aSelectEnd
  • Constraints: single-valued, can be null
  • Domain: INTEGER
aExtDBName
  • Constraints: single-valued, can be null
  • Domain: oExtRefDict
aExDBAlias
  • Constraints: set-valued, Min # of values: 0
  • Domain: VARCHAR(20)
aLocalID
  • Constraints: single-valued, not null
  • Domain: cvLocalID
aSummLine
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
Alternative Representations
OPM Class Definition
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OBJECT CLASS oHelixPDB
Identified by:
aLocalID
Attributes:
aHelixName
  • Constraints: single-valued, not null
  • Domain: CHAR(3)
aStartRes
aEndRes
aHelixClass
  • Constraints: single-valued, can be null
  • Domain: cvHelixClass
aHelixAnnotation
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
aHelixLen
  • Constraints: single-valued, can be null
  • Domain: INTEGER
aLocalID
  • Constraints: single-valued, not null
  • Domain: cvLocalID
aMSDID
  • Constraints: single-valued, can be null
  • Domain: MSD_ID
Alternative Representations
OPM Class Definition
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OBJECT CLASS oHet
Identified by:
aLocalID
Represented by:
aMolName
Attributes:
aFormula
  • Constraints: single-valued, not null
  • Domain: VARCHAR(80)
aMolName
  • Description: "Macromolecule or Het Name"
  • Constraints: single-valued, not null
  • Domain: VARCHAR(255)
aHetAnnotate
  • Constraints: single-valued, can be null
  • Domain: oAnnotations
aLocalID
  • Constraints: single-valued, not null
  • Domain: cvLocalID
aHetRes
  • Constraints: set-valued, Min # of values: 0
  • Domain: oResidueMolec
Alternative Representations
OPM Class Definition
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OBJECT CLASS oHetDictionary
Description:
Contents of Current Connect file
Identified by:
aHetID
Attributes:
aConectDat
  • Constraints: single-valued, not null
  • Domain: TEXT
aHetName
  • Constraints: set-valued, Min # of values: 1
  • Domain: VARCHAR(255)
aFormula
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(80)
aHetSample
  • Constraints: set-valued, Min # of values: 0
  • Domain: oResidueMolec
aBonds
  • Constraints: list-valued, Min # of values: 0
  • Domain: oBond
aHetID
  • Constraints: single-valued, not null
  • Domain: CHAR(3)
aHetPicture
  • Constraints: single-valued, can be null
  • Domain: TEXT
Alternative Representations
OPM Class Definition
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OBJECT CLASS oMSDExportObj
Description:
External ID for entry
Identified by:
aMSDID aMODID
Represented by:
aMSDID
Subclasses:
oExperiment
Attributes:
aMSDID
  • Constraints: single-valued, not null
  • Domain: MSD_ID
aMODID
  • Constraints: single-valued, not null
  • Domain: VARCHAR(10)
aAccessionDate
  • Constraints: single-valued, not null
  • Domain: DATETIME
aRevdat (revDate, revType, revComment, revID)
  • Constraints: list-valued, Min # of values: 0
  • Component Attributes:
    revDate
    • Domain: DATETIME
    • Constraints: not null
    revType
    • Domain: TINYINT
    • Constraints: not null
    revComment
    • Domain: VARCHAR(255)
    • Constraints: can be null
    revID
    • Domain: VARCHAR(10)
    • Constraints: not null
Alternative Representations
OPM Class Definition
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OBJECT CLASS oMacroMolecule
Identified by:
aLocalID
Attributes:
aMSDID
  • Description: "MSD-Ident Code"
  • Constraints: single-valued, can be null
  • Domain: CHAR(4)
aMolName
  • Constraints: set-valued, Min # of values: 0
  • Domain: VARCHAR(80)
aSrcDescr
  • Constraints: single-valued, can be null
  • Domain: oSource
aMolType
aBioMol
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
aCoordinates
  • Constraints: set-valued, Min # of values: 0
  • Domain: oChain
aMolSequence
  • Constraints: list-valued, Min # of values: 0
  • Domain: oPrimarySeq
aDomain
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(100)
aEngineered
  • Constraints: single-valued, can be null
  • Domain: cvFlagDict
aEnzyme
aMutation
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
aFormula
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(80)
aMolWeight
  • Constraints: single-valued, can be null
  • Domain: FLOAT
aLocalID
  • Description: "use identity"
  • Constraints: single-valued, not null
  • Domain: cvLocalID
aAnnotate (aSummLine, aExtDB)
  • Description: "Include other annotations on the molecule here"
  • Constraints: set-valued, Min # of values: 0
  • Component Attributes:
    aSummLine
    • Domain: VARCHAR(255)
    • Constraints: can be null
    aExtDB
Alternative Representations
OPM Class Definition
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OBJECT CLASS oMatrix
Identified by:
aLocalID
Represented by:
aSummLine
Attributes:
aSummLine
  • Constraints: single-valued, not null
  • Domain: VARCHAR(80)
a11
  • Constraints: single-valued, not null
  • Domain: FLOAT
a12
  • Constraints: single-valued, not null
  • Domain: FLOAT
a13
  • Constraints: single-valued, not null
  • Domain: FLOAT
a14
  • Constraints: single-valued, not null
  • Domain: FLOAT
a21
  • Constraints: single-valued, not null
  • Domain: FLOAT
a22
  • Constraints: single-valued, not null
  • Domain: FLOAT
a23
  • Constraints: single-valued, not null
  • Domain: FLOAT
a24
  • Constraints: single-valued, not null
  • Domain: FLOAT
a31
  • Constraints: single-valued, not null
  • Domain: FLOAT
a32
  • Constraints: single-valued, not null
  • Domain: FLOAT
a33
  • Constraints: single-valued, not null
  • Domain: FLOAT
a34
  • Constraints: single-valued, not null
  • Domain: FLOAT
aLocalID
  • Constraints: single-valued, not null
  • Domain: cvLocalID
Alternative Representations
OPM Class Definition
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OBJECT CLASS oModel
Identified by:
aLocalID
Represented by:
aMSDID
Attributes:
aModelNumber
  • Constraints: single-valued, not null
  • Domain: INTEGER
aModelContents
  • Constraints: set-valued, Min # of values: 0
  • Domain: oChain
aLocalID
  • Constraints: single-valued, not null
  • Domain: INTEGER
aMSDID
  • Constraints: single-valued, can be null
  • Domain: MSD_ID
Alternative Representations
OPM Class Definition
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OBJECT CLASS oNMRRefinement
Superclasses:
oRefinement
Attributes:
aNMRAnalysis
aRmsdBondDist
  • Constraints: single-valued, can be null
  • Domain: FLOAT
Alternative Representations
OPM Class Definition
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OBJECT CLASS oNMRStudy
Superclasses:
oExperiment
Attributes:
aModels
  • Constraints: set-valued, Min # of values: 1
  • Domain: oModel
aRefinement
Alternative Representations
OPM Class Definition
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OBJECT CLASS oPerson
Description:
person
Identified by:
person_id
Represented by:
surname
Attributes:
address
  • Constraints: single-valued, can be null
  • Domain: CHAR(80)
affiliation
  • Constraints: single-valued, can be null
  • Domain: CHAR(24)
department
  • Constraints: single-valued, can be null
  • Domain: CHAR(20)
email
  • Constraints: single-valued, can be null
  • Domain: CHAR(24)
employer
  • Constraints: single-valued, can be null
  • Domain: CHAR(16)
given_name
  • Constraints: single-valued, can be null
  • Domain: CHAR(16)
person_id
  • Constraints: single-valued, not null
  • Domain: VARCHAR(32)
phone
  • Constraints: single-valued, can be null
  • Domain: CHAR(16)
position
  • Constraints: single-valued, can be null
  • Domain: CHAR(40)
surname
  • Constraints: single-valued, can be null
  • Domain: CHAR(16)
Alternative Representations
OPM Class Definition
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OBJECT CLASS oPrimarySeq
Identified by:
aLocalID
Represented by:
aSummLine
Attributes:
aSeqRef
aMSDSeqStart
aMSDSeqEnd
aSeqAdv
  • Constraints: list-valued, Min # of values: 0
  • Domain: oSeqAdv
aSummLine
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(10)
aLocalID
  • Constraints: single-valued, not null
  • Domain: cvLocalID
Alternative Representations
OPM Class Definition
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OBJECT CLASS oRefinement
Identified by:
todefine
Represented by:
todefine
Subclasses:
oDiffractRefinement oNMRRefinement
Attributes:
todefine
  • Constraints: single-valued, not null
  • Domain: VARCHAR(10)
Alternative Representations
OPM Class Definition
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OBJECT CLASS oResidueMolec
Identified by:
aLocalID
Represented by:
aResName
Subclasses:
oAmino_acid
Attributes:
aOrdSeq
  • Description: "Ordinal Sequence Number from Origin Entry"
  • Constraints: single-valued, can be null
  • Domain: INTEGER
aSeqWithInsc
  • Constraints: single-valued, not null
  • Domain: VARCHAR(5)
aResName
  • Constraints: single-valued, can be null
  • Domain: CHAR(3)
aAtoms
  • Constraints: list-valued, Min # of values: 0
  • Domain: oAtom
aNumAtoms
  • Derivation: count of aAtoms
aModRes (aStdName, aModName, aModDscr)
  • Constraints: single-valued, can be null
  • Component Attributes:
    aStdName
    • Domain: CHAR(3)
    • Constraints: can be null
    aModName
    • Domain: CHAR(3)
    • Constraints: can be null
    aModDscr
    • Domain: VARCHAR(41)
    • Constraints: can be null
aResMolChain
  • Constraints: single-valued, not null
  • Domain: VARCHAR(4)
aLocalID
  • Constraints: single-valued, not null
  • Domain: cvLocalID
aMSDID
  • Constraints: single-valued, can be null
  • Domain: MSD_ID
Alternative Representations
OPM Class Definition
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OBJECT CLASS oSeqAdv
Identified by:
aLocalID
Represented by:
aConflictSum
Attributes:
aMSDSeq
aConflictSeq (aConflictName, aConflictNum)
  • Constraints: single-valued, can be null
  • Component Attributes:
    aConflictName
    • Domain: VARCHAR(3)
    • Constraints: can be null
    aConflictNum
    • Domain: INTEGER
    • Constraints: can be null
aConflictSum
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(20)
aLocalID
  • Description: "use an _id type here"
  • Constraints: single-valued, not null
  • Domain: cvLocalID
Alternative Representations
OPM Class Definition
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OBJECT CLASS oSheetPDB
Identified by:
aLocalID
Represented by:
aSheetID
Attributes:
aSheetID
  • Constraints: single-valued, not null
  • Domain: VARCHAR(3)
aNumStrands
  • Derivation: count of aStrands
aStrands
  • Constraints: list-valued, Min # of values: 0
  • Domain: oSheetStrand
aMSDID
  • Constraints: single-valued, can be null
  • Domain: MSD_ID
aLocalID
  • Constraints: single-valued, not null
  • Domain: cvLocalID
Alternative Representations
OPM Class Definition
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OBJECT CLASS oSheetStrand
Identified by:
aLocalID
Represented by:
aSumLine
Attributes:
aStartRes
aEndRes
aStrandLen
  • Constraints: single-valued, can be null
  • Domain: INTEGER
aStrandSense
  • Constraints: single-valued, can be null
  • Domain: INTEGER
aRgstrnInCurrent
  • Constraints: single-valued, can be null
  • Domain: oAtom
aSumLine
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(40)
aLocalID
  • Constraints: single-valued, not null
  • Domain: cvLocalID
Alternative Representations
OPM Class Definition
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OBJECT CLASS oSitePDB
Identified by:
aLocalID
Attributes:
aSiteID
  • Description: "Store SiteID + MSDID here"
  • Constraints: single-valued, not null
  • Domain: VARCHAR(3)
aSiteRes
  • Constraints: set-valued, Min # of values: 0
  • Domain: oResidueMolec
aResNumInSite
  • Derivation: count of aSiteRes
aSiteAnnotate
  • Constraints: single-valued, can be null
  • Domain: oAnnotations
aMSDID
  • Constraints: single-valued, can be null
  • Domain: MSD_ID
aLocalID
  • Constraints: single-valued, not null
  • Domain: cvLocalID
Alternative Representations
OPM Class Definition
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OBJECT CLASS oSolventMolecule
Identified by:
aSolventRes
Represented by:
aMolName
Attributes:
aFormula
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(80)
aMolName
  • Description: "Macromolecule or Het Name"
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
aHetAnnotate
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
aSolventRes
Alternative Representations
OPM Class Definition
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OBJECT CLASS oSource
Synonyms:
  • source
Identified by:
aSourceID
Represented by:
aSummLine
Attributes:
aATCC
aCellLine
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(60)
aCellType
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(60)
aExpressionSys (gene, name, plasmid)
  • Constraints: single-valued, can be null
  • Component Attributes:
    gene
    • Domain: VARCHAR(40)
    • Constraints: can be null
    name
    • Domain: VARCHAR(255)
    • Constraints: can be null
    plasmid
    • Domain: VARCHAR(60)
    • Constraints: can be null
aNonBiolSrc
  • Constraints: single-valued, can be null
  • Domain: cvFlagDict
aOrganName
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(20)
aOrganelle
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(20)
aOrganismName (common, scientific)
  • Constraints: single-valued, not null
  • Component Attributes:
    common
    • Domain: VARCHAR(80)
    • Constraints: not null
    scientific
    • Domain: VARCHAR(80)
    • Constraints: not null
aStrain
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(60)
aTissueName
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(20)
aVariant
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(60)
aSummLine
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
aSourceID
  • Constraints: single-valued, not null
  • Domain: INTEGER
Similar Classes:
  • Class BioSource (in schema NCBI) (comment: NCBI source)
  • Class Source (in schema GSDB) (comment: GSDB source)
Alternative Representations
OPM Class Definition
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OBJECT CLASS oTurnPDB
Identified by:
aTurnID aLocalID
Represented by:
aTurnID
Attributes:
aTurnID
  • Constraints: single-valued, not null
  • Domain: VARCHAR(3)
aStartRes
aEndRes
aTurnAnnotate
  • Constraints: single-valued, can be null
  • Domain: VARCHAR(255)
aTurnLen
  • Constraints: single-valued, can be null
  • Domain: INTEGER
aMSDID
  • Constraints: single-valued, can be null
  • Domain: MSD_ID
aLocalID
  • Constraints: single-valued, not null
  • Domain: cvLocalID
Alternative Representations
OPM Class Definition
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