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Diffstat (limited to 'topics/gn-uploader')
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diff --git a/topics/gn-uploader/adding-species.gmi b/topics/gn-uploader/adding-species.gmi new file mode 100644 index 0000000..8a57fa8 --- /dev/null +++ b/topics/gn-uploader/adding-species.gmi @@ -0,0 +1,79 @@ +## Tags + +* status: open +* priority: medium +* type: documentation +* assigned: fredm, flisso, acenteno +* keywords: doc, documentation, platform, gn-uploader, uploader, adding data + +## 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 +=> https://gn1.genenetwork.org/webqtl/main.py?FormID=schemaShowPage#Species 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: + +=> https://www.ncbi.nlm.nih.gov/ 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"; +``` |