Database snapshots

Below you can download the full database as a MySQL script, automatically created at monthly intervals. The script can be imported into any local MySQL database and will automatically create all relevant tables and their data.

FilenameCreation dateFilesize
131111.traitsdb.zipNovember 11 2013 13:07:141398821
131201.traitsdb.zipDecember 01 2013 00:00:011398839
140103.traitsdb.zipJanuary 03 2014 15:50:021403057
140201.traitsdb.zipFebruary 01 2014 00:00:011403511
140301.traitsdb.zipMarch 01 2014 00:00:021418893
140401.traitsdb.zipApril 01 2014 00:00:011458883
140501.traitsdb.zipMay 01 2014 00:00:021458884
140601.traitsdb.zipJune 01 2014 00:00:021470225
140701.traitsdb.zipJuly 01 2014 00:00:011478831
140801.traitsdb.zipAugust 01 2014 00:00:161481816
140901.traitsdb.zipSeptember 01 2014 00:00:021481688
141001.traitsdb.zipOctober 01 2014 00:00:021483440
141101.traitsdb.zipNovember 01 2014 00:00:021486029
141201.traitsdb.zipDecember 01 2014 00:00:021492757
150101.traitsdb.zipJanuary 01 2015 00:00:021492759
150201.traitsdb.zipFebruary 01 2015 00:00:021492759
150301.traitsdb.zipMarch 01 2015 00:00:021492759
150401.traitsdb.zipApril 01 2015 00:00:021492760
150501.traitsdb.zipMay 01 2015 00:00:021492761
150601.traitsdb.zipJune 01 2015 00:00:021492731
150701.traitsdb.zipJuly 01 2015 00:00:021492732
150801.traitsdb.zipAugust 01 2015 00:00:021493550
150901.traitsdb.zipSeptember 01 2015 00:00:021493549
151001.traitsdb.zipOctober 01 2015 00:00:011493551
151101.traitsdb.zipNovember 01 2015 00:00:021493549
151201.traitsdb.zipDecember 01 2015 00:00:011493553
160101.traitsdb.zipJanuary 01 2016 00:00:021493516
160201.traitsdb.zipFebruary 01 2016 00:00:021493516
160301.traitsdb.zipMarch 01 2016 00:00:031493516
160401.traitsdb.zipApril 01 2016 00:00:021493517
160501.traitsdb.zipMay 01 2016 00:00:031493518
160601.traitsdb.zipJune 01 2016 00:00:021493516
160701.traitsdb.zipJuly 01 2016 00:00:021493517
160801.traitsdb.zipAugust 01 2016 00:00:031493516
160901.traitsdb.zipSeptember 01 2016 00:00:021493516
161001.traitsdb.zipOctober 01 2016 00:00:021493517
161101.traitsdb.zipNovember 01 2016 00:00:021493516
161201.traitsdb.zipDecember 01 2016 00:00:021493517
170101.traitsdb.zipJanuary 01 2017 00:00:021493516
170201.traitsdb.zipFebruary 01 2017 00:00:021493516
170301.traitsdb.zipMarch 01 2017 00:00:021493516
170401.traitsdb.zipApril 01 2017 00:00:031493517
170501.traitsdb.zipMay 01 2017 00:00:021493518
170601.traitsdb.zipJune 01 2017 00:00:021493516
170701.traitsdb.zipJuly 01 2017 00:00:021493517

Database documentation

Author: Sarah Faulwetter
Date: 2013-10-09

Below you find a description of the database tables contained in the regular database snapshots which can be downloaded above. The snapshots only contain tables that contain relevant biological traits data - “helper” tables are not included. Likewise, some fields in the download are only used for certain functions of the web interface, these are described below as “internally used only” and greyed out.
This documentation can also be downloaded in pdf format.

Click to enlarge

Click on the image to enlarge it.

taxa
Taxonomic backbone of the database, contains all taxonomic names their rank and their synonymy. The hierarchy is stored both as a parent-child model as well as a nested set model.
field name description
id_taxon primary key of the table
taxon the taxon name without authority
author the authority and year of the taxon's description
fk_valid foreign key, links to id_taxon in the same table and points to the name/taxon that is currently considered as the accepted one. In case of no synonymy, fk_valid and id_taxon have the same value
fk_unacc_reason foreign key, links to table taxa_unacc_reason, describes the reason for synonymy (e.g. objective synonym, subjective synonym, ...)
fk_parent foreign key, links to id_taxon in the same table and points to the direct parent of the current taxon in the taxonomic classification
lft left value of a nested set hierarchy model
rgt right value of a nested set hierarchy model
fk_rank foreign key, links to table ranks
fk_publication_synonym foreign key, links to table publications and points to the publication which contains information on the synonymy of the taxon
datemodify date of last modification of this entry
creator user who created this entry
ranks
Contains a list of the biological ranks (e.g. species, genus...) and their hierarchy
field name description
id_rank primary key of the table
rank name of the rank (e.g. species, genus)
ranklevel internally used only
fk_parentrank foreign key, links to id_rank in table rank,stores the next higher rank in the hierarchy
parent_rankgroup internally used only
rankpath internally used only
datemodify date of last modification of this entry
creator user who created this entry
taxa_unacc_reason
Stores a list of reasons why a taxonomic name is not accepted (e.g. synonymy, misspelling)
field name description
id_unacc_reason primary key of the table
unaccept_reason list of reasons for synonymy (e.g. objective synonym, subjective synonym, ...)
modalities
Stores all modalities (=trait categories) used in the database
field name description
id_modality primary key of the table
modality name of the modality
modality_shortname abbreviated name of the modality
fk_trait foreign key, links to table traits
rule_present internally used only
definition definition of the modality. Can contain literature references in the form "[123]" which correspond to id_publication in table publications.
term_identifier unique identifier of the term in form of a URL, pointing to the term's definition
related_terms related, similar or synonymous terms which are often found in the literature
description any additional explanations to clarify the scope of the term. Can contain literature references in the form "[123]" which correspond to id_publication in table publications.
sorting_weight internally used only
temp_trait internally used only
temp_reference internally used only
datemodify date of last modification of this entry
creator user who created this entry
traits
Stores all traits used in the database
field name description
id_trait primary key of the table
trait name of the trait
fk_mode foreign key, links to table modes
trait_shortname abbreviated name of the trait
definition definition of the trait. Can contain literature references in the form "[123]" which correspond to id_publication in table publications.
related_terms related, similar or synonymous terms which are often found in the literature
term_identifier unique identifier of the term in form of a URL, pointing to the term's definition
description any additional explanations to clarify the scope of the term. Can contain literature references in the form “[123]” which correspond to id_publication in table publications.
datemodify date of last modification of this entry
creator user who created this entry
modes
Stores a list that groups the traits into adult traits, reproductive traits and larval traits
field name description
id_mode primary key of the table
mode name of the mode
datemodify date of last modification of this entry
creator user who created this entry
publications
Stores all publications used in the database.
field name description
id_publication primary key of the table
pub_year the journal's title
title title of the publication
volume volume of the publication (where applicable, e.g. journals)
pages page range or number of pages of the publication
issue issue of the publication (where applicable, e.g. journals)
other any description of a publication not classifiable into a publication type such as journal article, book, etc.
label internally used only
DOI Digital Object identifier of the publication
fk_journal foreign key, links to table journals
booktitle title of the publication if it is a monograph-type of publication (e.g. book, report)
publisher publisher of the publication
city city of the publisher
institution name of the institution that published the publication (mainly applied to theses or reports)
seriestitle title of the book or report series
thesistype if publication is a thesis, this stores the type of thesis (e.g. BSc, MSc, PhD)
referencetype type of the publication (e.g. journal article, book, book chapter, thesis, report, URL...)
abstract abstract of the publication
url Unified Resource Locator - internet address linking to the publication
fullref automatically assembled full citation of the reference
shortref short version of the reference (e.g. Smith et al. 1999)
datemodify date of last modification of this entry
creator user who created this entry
keywords
Contains a list of keywords with which publications can be annotated.
id_keyword primary key of the table
keyword the term / keyword
datemodify date of last modification of this entry
creator user who created this entry
keyword_pub
Links table “publication” to table “keywords”
fk_keyword foreign key, linking to table keywords
fk_pub foreign key, linking to table publications
datemodify date of last modification of this entry
creator user who created this entry
persons
Stores a list of all authors and editors of the publications contained in the database.
id_person primary key of the table
last_name last name of the person
first_name first name of the person
datemodify date of last modification of this entry
creator user who created this entry
pers_pub
Links table “publications” to table “persons”.
fk_pers foreign key, linking to table persons
fk_pub foreign key, linking to table publications
order_appear stores the order of the authors in a given publication
flag_editor flags a person to be an editor of the given publication
datemodify date of last modification of this entry
creator user who created this entry
journals
Stores a list of all journal names of publications contained in the database.
id_journal primary key of the table
journal the journal's title
datemodify date of last modification of this entry
creator user who created this entry
sourcedata
Stores the exact text passage from a literature source that supports the assignment of a modality to a taxon.
id_sourcedata primary key of the table
sourcedata contains the exact text passage supporting the assignment of a modality to a taxon
date_modify date of last modification of this entry
creator user who created this entry
relations
Links tables “taxon” and “modalities” and assigns a present/absent value to this relationship, indicating whether a modality is present or absent in a taxon
id_relation primary key of the table
fk_taxon foreign key, links to table taxa
fk_modality foreign key, links to table modalities
traitvalue present/absent value, describes whether a modality is present in a taxon or not
datemodify date of last modification of this entry
creator user who created this entry
relation_pub
links table “relations” to table “publications” to support each taxon-modality-traitvalue entity by a publication
fk_relation foreign key, links to table relations; primary key in combination with fk_publication
fk_publication foreign key, links to table publications; primary key in combination with fk_relation
fk_original foreign key, links to table sourcedata
datemodify date of last modification of this entry
creator user who created this entry
users
lists all users of the database
user foreign key, links to field “creator” in all other tables
firstname first name of the user
lastname last name of the user