SCHEMA
MSDbase
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Primitive Value Classes
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Controlled Value Classes
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Object Classes
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aminoTorsion
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cvLocalID
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MSD_ID
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cvBondTypes
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cvDatabaseDict
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cvExperimentTypes
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cvFlagDict
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cvHelixClass
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cvMacroMoleculeType
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cvMtrixType
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cvPDBResidueType
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cvResourceType
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exp_resolution
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oAnnotations
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oAsu
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oAtom
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oAtomAnisoU
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oAtomAnisoUSigma
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oAtomSigma
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oBond
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oChain
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oCrystal
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oExtRefDict
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oExternalReference
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oHelixPDB
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oHet
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oHetDictionary
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oMSDExportObj
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oExperiment
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oDiffractStudy
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oNMRStudy
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oMacroMolecule
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oMatrix
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oModel
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oPerson
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oPrimarySeq
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oRefinement
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oDiffractRefinement
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oNMRRefinement
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oResidueMolec
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oAmino_acid
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oSeqAdv
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oSheetPDB
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oSheetStrand
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oSitePDB
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oSolventMolecule
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oSource
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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:
- 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:
- 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:
- 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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