Taxallnomy

Introduction

Taxallnomy is a taxonomic database based on NCBI Taxonomy that provides taxonomic lineages according to the ranks used on Linnean classification system (e.g. Kingdom, Phylum, Class etc.).

In this package you will find the following files/folder.

* generate_taxallnomy.pl- a script that generates files for Taxallnomy 
                          database;
* get_lineage.pl        - a script that accesses the Taxallnomy database 
                          to retrieve the taxonomic lineage of TaxIDs of interest;
* lib/                  - lib folder containing a PERL module required by the 
                          script 'get_lineage.pl'.

All scripts were developed with Perl and tested in a UNIX environment.

Installing database

The script generate_taxallnomy.pl generates all necessary file to load the Taxallnomy database in a local MySQL. The execution of this script requires internet connection. To run the script, just type in a UNIX terminal the following command:

> perl generate_taxallnomy.pl

The script will basically download the latest NCBI Taxonomy database and construct the Taxallnomy hierarchical structure from it. After the running, it will generate these files:

* taxallnomy_XXX.sql  - Dump file containing SQL commands to create Taxallnomy 
                        database and the table XXX;
* taxallnomy_XXX.tab  - Tab-delimited file containing contents of Taxallnomy  
                        database of table XXX;

XXX conrresponds to the table name of Taxallnomy database. They are lin, lin_name, tree_balanced, tree_original, tree_all, tax_data or rank. Detailed description of each table is presented below;

To load one of those tables in your local MySQL, go to the path where these files are located and type the following command line:

> mysql -u <username> -p < taxallnomy_XXX.sql

or go to MySQL environment and type:

mysql> source taxallnomy_XXX.sql

Loading Taxallnomy database to MySQL may take several minutes depending on which table is being loaded, so be patient.

After loading a single table, your MySQL should have a database called "taxallnomy" and, in that database, a table named XXX. There is no need to load all tables. Load only those that meet your needs.

Table descriptions

1) lin table

This table contains all taxonomic lineages of Taxallnomy database. From this table, you can query for the taxonomic lineage of an organism by its taxonomy ID (primary key). Each taxonomic ranks are represented in a column of this table. Keep in mind that the content of the taxonomic rank columns is not a taxon name, but a taxon code used by Taxallnomy (See the section "Taxallnomy taxon code"). The taxon names can be programmatically generated from the taxon code or by querying on table lin_name. You can also use the script "get_lineage.pl" to retrieve lineages with taxon name from this table.

• lin table content:

Column | Description ----------------|--------------------------------------------------- txid | NCBI taxonomy ID of a organism (primary key) superkingdom | Taxon code for Superkingdom rank
kingdom | Taxon code for Kingdom rank
subkingdom | Taxon code for Subkingdom rank
superphylum | Taxon code for Superphylum rank
phylum | Taxon code for Phylum rank
subphylum | Taxon code for Subphylum rank
superclass | Taxon code for Superclass rank
class | Taxon code for Class rank
subclass | Taxon code for Subclass rank
infraclass | Taxon code for Infraclass rank
cohort | Taxon code for Cohort rank
superorder | Taxon code for Superorder rank
order | Taxon code for Order rank
suborder | Taxon code for Suborder rank
infraorder | Taxon code for Infraorder rank
parvorder | Taxon code for Parvorder rank
superfamily | Taxon code for Superfamily rank
family | Taxon code for Family rank
subfamily | Taxon code for Subfamily rank
tribe | Taxon code for Tribe rank
subtribe | Taxon code for Subtribe rank
genus | Taxon code for Genus rank
subgenus | Taxon code for Subgenus rank
species_group | Taxon code for Species Group rank
species_subgroup| Taxon code for Species Subgroup rank
species | Taxon code for Species rank
subspecies | Taxon code for Subspecies rank
varietas | Taxon code for Varietas rank
forma | Taxon code for Forma rank

2) lin_name table

This table has the same structure as lin table, but instead of having taxon codes on each taxonomic rank column, it contains the taxon name. This table occupies more space than the lin table. Contents of this table could be retrieved using script get_lineage.pl (see below).

3) tree_balanced table

This table provides the balanced hierarchical structure of Taxallnomy database.

• tree_balanced table content:

Column | Description ---------------|--------------------------------------------------------- txid | Taxon code used by Taxallnomy (primary key)
parent | Taxon code of its parent taxon (indexed)

4) tree_all table

It has the same structure as the tree_balanced table. In this tree, no rank taxa that were deleted during the generation of the taxallnomy database (because no rank could be assigned to it), are preserved. Thus, the hierarchical strucuture of this table is not balanced.

5) tree_original table

It has the same structure as the tree_balanced table and the same hierarchical structure as the original database from NCBI Taxonomy.

6) tax_data table

This table provides information about each txid comprising the NCBI Taxonomy.

Column | Description ----------------|--------------------------------------------------------------------- txid | NCBI taxonomy ID of a organism (primary key) rank | Taxonomic rank of txid rankType | Specify if the rank of a txid was assigned by taxallnomy (1) or not (0) name | Scientific name of txid
comname | Common name of txid
unclassified | 1 if txid is part of unclassified group*, 0 otherwise
merged | Indicates the txid in which this txid was merged leaf | 1 if txid is a leaf taxon, 0 otherwise

* includes txid which has "unpublished", "unidentified", "unclassified", "environmental", "unassigned", "incertae sedis" or "other sequences" in its name.

7) rank table

A table containing some information about the taxonomic ranks comprising the database.

• rank table contents:

Column | Description -------------|--------------------------------------------------------------------- rank | taxonomic rank (TR) name
order | level of the TR
priority | priority order of TR according its frequency in the lineages
code | TR code
abbrev | TR abbreviation
dcount_ncbi | number of distinct ranked taxa among all lineages of leaf taxa
dcount_type1 | number of distinct taxa of type 1 among all lineages of leaf taxa dcount_type2 | number of distinct taxa of type 2 among all lineages of leaf taxa dcount_type3 | number of distinct taxa of type 3 among all lineages of leaf taxa count_ncbi | number of ranked taxa among all lineages of leaf taxa
count_type1 | number of taxa of type 1 among all lineages of leaf taxa
count_type2 | number of taxa of type 2 among all lineages of leaf taxa
count_type3 | number of taxa of type 3 among all lineages of leaf taxa

Taxallnomy taxon code and name

Taxallnomy primarily uses the Taxonomy ID provided by NCBI Taxonomy database to identify all nodes comprising its hierarchical structure. However, since Taxallnomy algorithm creates new nodes or assign ranks to existent nodes, we included in the identifier a code to identify them properly.

The Taxallnomy "code" is added to the NCBI taxonomy ID as decimal number of three digits. For example, in the taxon code 8287.071, 8287 is the NCBI Taxonomy ID (Sarcopterygii) and 071 is the code added by Taxallnomy algorithm. In the code, the first two digits indicates the taxonomic rank in which it belongs. It goes through the code "01" to "33", in which the first rank is Superkingdom ("01") and the last one is Forma ("33"). The third digit indicates the type of node and corresponds to the action performed by the algorithm on the node. This can be:

• 1 (type 1) - This taxon was originally unranked on NCBI Taxonomy tree and it was ranked by Taxallnomy algorithm.
• 2 (type 2) - This taxon was created by Taxallnomy algorithm and the name of one of its ranked descendant taxon was used to name it.
• 3 (type 3) - This taxon was created by Taxallnomy algorithm and the name of one of its ranked ascendant taxon was used to name it.

We use the following rules to name the nodes of each type:

• For type 1, we use the abbreviation of the rank name followed by the scientific name of the NC