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.