MySQL database schema changelog

Below is a history of schema changes. For maps of each schema version: schema maps.

Schema version 10

Single column datatype changed.

Column modified

  • gene.Translation datatype = blob

Schema version 9

Substantial restructuring of trna and tmrna tables.

Column moved

  • trna_structures.Structure to trna.Structure

Column removed

  • trna.Sequence

  • trna.Product

  • trna.InfernalScore

Column renamed

  • trna.TrnaID TO trna.GeneID

  • tmrna.TmrnaID TO tmrna.GeneID

Column modified

  • trna.Structure datatype

  • trna.AminoAcid datatype

  • trna.PhageID position in table and foreign key constraint

  • trna.LocusTag position in table

  • tmrna.PhageID position in table and foreign key constraint

  • tmrna.LocusTag position in table

Column added

  • trna.Source

  • trna.Name

  • tmrna.Length

  • tmrna.Name

Table removed

  • trna_structures

Schema version 8

Modified foreign key constraint.

Column modified

  • gene.PhamID foreign key constraint

Schema version 7

Renamed several columns. Dropped the pham table and renamed the pham_color table.

Column removed

  • phage.Cluster

  • pham_color.ID (primary key)

  • gene.ID

Column renamed

  • phage.HostStrain TO phage.HostGenus

  • phage.Cluster2 TO phage.Cluster

  • phage.Subcluster2 TO phage.Subcluster

  • phage.SequenceLength TO phage.Length

  • pham_color.Name TO pham_color.PhamID

Column modified

  • pham_color.PhamID now primary key

Column added

  • gene.Parts

  • gene.PhamID

Table removed

  • pham

Table renamed

  • pham_color TO pham

Schema version 6

Standardized column nomenclature.

Column renamed

  • domain.id TO domain.ID

  • domain.description TO domain.Description

  • gene_domain.id TO gene_domain.ID

  • gene_domain.expect TO gene_domain.Expect

  • phage.status TO phage.Status

  • pham.name TO pham.Name

  • pham_color.id TO pham_color.ID

  • pham_color.name TO pham_color.Name

  • pham_color.color TO pham_color.Color

  • version.version TO version.Version

  • gene.translation TO gene.Translation

  • gene.id TO gene.ID

  • gene.cdd_status TO gene.DomainStatus

  • version.schema_version TO version.SchemaVersion

  • domain.hit_id TO domain.HitID

  • gene_domain.hit_id TO gene_domain.HitID

  • gene_domain.query_start TO gene_domain.QueryStart

  • gene_domain.query_end TO gene_domain.QueryEnd

Schema version 5

Removed several tables and columns.

Table removed

  • node

  • host_range

  • host

  • pham_history

  • pham_old

  • scores_summary

Column removed

  • phage.Prophage

  • phage.Isolated

  • phage.ProphageOffset

  • phage.DateLastSearched

  • phage.AnnotationQC

  • gene.StartCodon

  • gene.StopCodon

  • gene.GC1

  • gene.GC2

  • gene.GC3

  • gene.GC

  • gene.LeftNeighbor

  • gene.RightNeighbor

  • gene.clustalw_status

  • gene.blast_status

  • gene.TypeID

  • pham.orderAdded

Column modified

  • phage.status datatype = enum(‘unknown’,’draft’,’final’)

Schema version 4

Added several tables.

Table created

  • tmrna

  • trna

  • trna_structures

Column modified

  • gene.translation datatype = VARCHAR(5000)

Schema version 3

Added/removed several columns.

Column created

  • gene.LocusTag

  • version.schema_version

  • phage.Subcluster2

  • phage.Cluster2

Column removed

  • phage.Program

Schema version 2

Added several columns.

Column created

  • phage.AnnotationAuthor

  • phage.Program

  • phage.AnnotationQC

  • phage.RetrieveRecord

Schema version 1

Misc changes to maintain referential integrity.

Table created

  • version

Column created

  • gene.cdd_status

CASCADE setting updated

  • gene.PhageID

  • gene_domain.GeneID

  • pham.GeneID

  • scores_summary.query

  • scores_summary.subject

Schema version 0

The base schema.