Adding Species

Description

We do not have a UI for adding new species. In this case, we need to add the data manually by running a query.

As an example, I document how I added the C. elegans species to the https://staging.genenetwork.org server:

We begin by looking at the schema for the Species table:

MariaDB [db_webqtl]> DESC Species;
+---------------+----------------------+------+-----+---------+----------------+
| Field         | Type                 | Null | Key | Default | Extra          |
+---------------+----------------------+------+-----+---------+----------------+
| Id            | smallint(5) unsigned | NO   | PRI | NULL    | auto_increment |
| SpeciesId     | int(5)               | YES  |     | NULL    |                |
| SpeciesName   | varchar(50)          | YES  |     | NULL    |                |
| Name          | char(30)             | NO   | MUL |         |                |
| MenuName      | char(50)             | YES  |     | NULL    |                |
| FullName      | char(100)            | NO   |     |         |                |
| Family        | varchar(50)          | YES  |     | NULL    |                |
| FamilyOrderId | smallint(6)          | YES  |     | NULL    |                |
| TaxonomyId    | int(11)              | YES  |     | NULL    |                |
| OrderId       | smallint(6)          | YES  |     | NULL    |                |
+---------------+----------------------+------+-----+---------+----------------+
10 rows in set (0.00 sec)

From

the schema docs

and looking at the data, we know the following about the fields:

Id: Internal GeneNetwork species identifier
SpeciesId: Same as 'Id'
SpeciesName: A layman's name for the species, e.g. Mouse, Roundworm, Barley, etc.
Name: Mostly the same as SpeciesName, but in all lowercase
MenuName: A display name to show on the UI - computed for 'SpeciesName' and 'FullName'
FullName: The species binomial name (scientific name) e.g. Mus musculus, Caenorhabditis elegans, etc.
Family: A loose, largish grouping for the species, e.g. Vertebrates, Plants, etc.
FamilyOrderId: ???
TaxonomyId: The Taxonomy ID for the species on https://www.ncbi.nlm.nih.gov/
OrderId: ???

Preparing the Data

With this in mind, we can now get any missing data for the species.

To find the Taxonomy ID value:

Go to NCBI

In the "All Databases" drop-down, select "Taxonomy"
In the search box, enter the species' FullName, e.g. Caenorhabditis elegans
Click "Search"
If the species exists, a link with the species' binomial name shows up. Click it.
Near the top of the page, you should see something like " Taxonomy ID: 6239 (for references in articles please use NCBI:txid6239)". The number after the "Taxonomy ID: " is what you want.

***TODO: Figure out what FamilyOrderId and OrderId are, and how to get the data. Update this page.***

Adding the Species to the Database

We can now run the query to insert the data:

INSERT INTO Species(SpeciesName,Name,MenuName,FullName,Family,FamilyOrderId,TaxonomyId,OrderId)
VALUES ("Roundworm", "roundworm", "Roundworm (C. elegans)", "Caenorhabditis elegans", "Nematodes", NULL, "6239", NULL);

now update the "SpeciesId":

UPDATE Species SET SpeciesId=Id WHERE SpeciesName="Roundworm";

Adding Species

Tags

Description

Preparing the Data

Adding the Species to the Database