Database structure

Database structure (tables and fields)

Table Fields Comment
pr2_main pr2_accession, genbank_accession, species, editing hitory
pr2_sequence pr2_accession, , sequence linked to pr2_main by pr2_accession
pr2_metadata metadata from GenBank and from published references linked to pr2_main by genbank_accession
pr2_taxonomy kingdom -> species, editing history linked to pr2_main by species
pr2_countries geo-information linked to pr2_metadata by pr2_country
pr2_assign_silva assignment of pr2 sequences according to Silva linked to pr2_main by pr2_accession

pr2 database structure

Taxonomy structure

  • 8 levels : Kingdom / Supergroup / Division / Class / Order / Family / Genus / Species
  • All taxonomy paths are unique. For example for a given Class, all higher levels are similar (Division -> Supergroup -> Domain)
  • No taxon can appear at different levels. For example “Stramenopiles” cannot appear at both the Supergroup and Division levels.

Rules for naming taxonomic levels

  • No space (use underscore). For example Home_sapiens
  • If species is not known use “Genus_sp.” (note the . after sp). The Genus level can be a level with Xs (see next rule): e.g. “Stramenopiles_XXXX_sp.“,
  • If level i is unknown
    • if level i-1 is known, use level i-1 followed by “_X” , e.g. “Stramenopiles_X” at Division level
    • if level i-1 is unknown, use level i-1 followed by “X” , e.g. “Stramenopiles_XX” at Class level

Rules for sequences

  • Minimum length = 500 bp
  • Maximum number of ambiguities (N) = 20
  • No more than 2 consecutives N (so sequences such as ..ATGNNNAT.. are removed)

Construction of PR2 id (pr2_accession)


For example AF530536.1.1695_U

  • AF530536 : GenBank accession number
  • 1 : Start of the 18S rRNA in the GenBank sequence
  • 1695 : Start of the 18S rRNA in the GenBank sequence
  • X can take any of the following values:
    • G: genomic sequence containing a described intron (rDNA)
    • R: the previous genomic rRNA sequence, without the intron(s)
    • U: no intron described, but intron(s) may be present
    • UC: introns were detected in silico and removed from the sequence (putative rRNA)

History of database structure changes

PR2 version Table Field Action Comment
4.14.0 pr2_main quarantined_version A quarantined sequences do not appear in the released version but will be re-assigned latter
pr2_metadata gb_references R
gb_locus R
gb_division A
4.13.0 pr2_metadata pr2_depth A depth of sample in meter
gb_id A Genbank ID number (big integer)
gb_project_id A Genbank project ID for metagenomes
gb_sequence A original gb_sequence (longtext)
pr2_countries New table for country information
pr2_assign_silva New table for Silva assignation of sequences
4.12.0 pr2_main gene A 18S_RNA, 16S_RNA
organelle A nucleus, plastid, mitochondria, nucleomorph, apicoplast (left empty for cyanobacteria)
pr2_metadata gb_organelle A import the corresponding gb field
pr2_sequence_origin M add other possibilities such as genome and metagenome
pr2_continent, pr2_country, pr2_country_lat, pr2_country_lon A geographical origin extracted from gb_country field, gb_isolation_source, eukref_geo_loc_name
pr2_location, pr2_location_lat, pr2_location_lon A geographical origin extracted from gb_country field, gb_isolation_source, eukref_geo_loc_name
pr2_sea, pr2_sea_lat, pr2_sea_lon A geographical origin extracted from gb_country field, gb_isolation_source, eukref_geo_loc_name
pr2_sequence sequence_hash A hash value of the sequence (using R function digest::sha1
pr2_taxonomy taxon_trophic_mode A detailed trophic mode (e.g. “C-fixation constitutive; Mixotroph”) - for future use
4.11.1 pr2_metadata gb_reference A Contains the whole REFERENCE field from GenBank
eukref_publication eukref_authors eukref_journal M Merged into gb_publication, gb_authors, gb_journal
4.11.0 pr2_metadata eukref_publication eukref_authors eukref_journal eukref_notes A Added
4.11.0 pr2_metadata pr2_xxx M fields annotated by Eukref renamed back to eukref_xxx
4.11.0 pr2_main taxo_id R not used anymore since linked is done by species (this will be probably reinstated later on a different form using a different format for the taxonomy table).
4.9 pr2_metadata eukref_xxx M renamed to pr2_xxx to reflect the fact that these fields will also be updated independantly of EukRef
4.9 pr2_main reference_sequence A designate sequences that can be used as reference e.g. for alignment
4.8 pr2_main, taxo xx_date (e.g. edited_date) R redundant with xx_version (e.g. edited_version) fields
4.8 pr2_sequence sequence_length M Minimum length is now 500 bp.

Action : A=Added/R=Removed/M=Modified

Daniel Vaulot
NTU, Singapore

Focusing on marine (pico)phytoplankton .