BROWSING

The Molecular Biology Database Directory and Schema Library


Component Databases:

GDB's Human Genome Database (HGD)
Genome Sequence Database (GSDB)
NCBI's Databases
PDB's Molecular Structure Database (MSDbase)

Schema for GDB's Human Genome Database (HGD)

Database:
hgd
Description:
Human Genome Database part of the Genome Database (GDB), at Johns Hopkins School of Medicine, Baltimore.
Alternative Formats:
OPM Schema File (Ascii)
Schema Document (Postscript) ...
Schema Diagrams (Postscript) ...
Related to:
Genome Sequence Database (GSDB)
  • GDB class NucleicAcidSequenceLink references sequences stored in external databases, including GSDB, GenBank and EMBL. Attribute externalDB of NucleicAcidSequenceLink determines which database is being referenced, via attribute searchName of class a ExternalDB.
    • References to GSDB can be found using OPM condition:
      NucleicAcidSequenceLink.externalDB[ExternalDB]searchName = "gsdb"
    • An object in a foreign database is determined via attribute attributeID of NucleicAcidSequenceLink , which subsequently needs to be joined attribute ic_accession of class Sequence of GSDB:
      GSDB:Sequence.ic_accession = GDB:NucleicAcidSequenceLink.accessionID
NCBI's Databases
  • GDB class NucleicAcidSequenceLink (see above) is also used to reference sequences in NCBI's GenBank database.
    • References to Genbank can be found using OPM condition:
      NucleicAcidSequenceLink.externalDB[ExternalDB]searchName = "genbank"
    • Attribute accessionID should reference a Genbank Seq_entry object. It is not clear at present what attribute path of Seq_entry should be joined with accessionID. Seq_entry.seq.id.genbank.accession is a likely candidate.
PDB's Molecular Structure Database
(StructureLink subclass of ExternalLink references PDB, but target class is unknown)

Schema Browsing

Schema GSDB

Description:
retrofitted GSDB schema
Original Schema Representation:
relational
Alternative Formats:
OPM Schema File (Ascii)
Schema Document (Postscript) ...
Schema Diagrams (Postscript) ...
Related to:
NCBI
(Archival Sequence data shared with NCBI GenBank)
HGD
(References GDB Gene objects through DBLink class. Sequence class referenced by GDB NucleicAcidSequenceLink class)
MSDbase
(Links to PDB unknown)

Schema Browsing

Schema NCBI

Description:
retrofitted NCBI schema
Original Schema Representation:
ASN.1
Alternative Formats:
OPM Schema File (Ascii)
Schema Document (Postscript) ...
Schema Diagrams (Postscript) ...
Related to:
GSDB
(Shares archival sequence data with GSDB)
HGD
(somehow related to GDB)
MSDbase
(contains overlapping data from PDB)

Schema Browsing

Schema MSDbase

Database:
MSDbase
Description:
PDB MSDbase schema
Alternative Formats:
OPM Schema File (Ascii)
Schema Document (Postscript) ...
Schema Diagrams (Postscript) ...
Related to:
NCBI
(links unknown)
HGD
(links unknown)
GSDB
(links unknown)

Schema Browsing