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diff --git a/topics/data-uploads/inserting-data.gmi b/topics/data-uploads/inserting-data.gmi new file mode 100644 index 0000000..33b500c --- /dev/null +++ b/topics/data-uploads/inserting-data.gmi @@ -0,0 +1,163 @@ +## Tags + +* assigned: bonfacem, zachs + +### Introduction + +The current uploader work documented in `editing-data.gmi` only caters +for the following operations by people with the right access: + +- Editing phenotype and probeset metadata + +- Editing sample data from a published phenotype + +- Deleting sample data from published phenotypes + +- Inserting data from strains that already exist in a ".geno" file + +However, one of our beta users ran into a problem when attempting to +insert new trait data for BDL_10001. ATM, we can't add new samples. +Also, adding case attributes for new samples is a manual process. New +samples cannot be added because new genotype files need to be +generated when new strains/ samples are added. Addition of these +genotype files has always been manual. We can add strain data +(inserting new strains into the Strain table(s) if it's not already +there) by hacking existing code. However, this will show up-- the +strains-- in a separate "sample group" on the trait page and won't be +used for mapping until the new .geno file containing the new strains +is generated. + +How is this genotype file generated? + +[From Rob] Genotypes should be added by code. For some species like +humans, this won't happen; but for experimental animals and plant, +many families may grow and spread e.g. BXDs grow to the BXD Dax, then +they expand tot he BXDx Collaborative Cross DAX. + +New strains are added by entering strains based on groups(InbredSetId) and SpeciesId. This is why we have the "StrainXRef" table. This is demonstrated below: + +``` +MariaDB [db_webqtl]> desc Strain; + ++-----------+----------------------+------+-----+---------+----------------+ + +| Field | Type | Null | Key | Default | Extra | + ++-----------+----------------------+------+-----+---------+----------------+ + +| Id | int(20) | NO | PRI | NULL | auto_increment | + +| Name | varchar(100) | YES | MUL | NULL | | + +| Name2 | varchar(100) | YES | | NULL | | + +| SpeciesId | smallint(5) unsigned | NO | | 0 | | + +| Symbol | varchar(20) | YES | MUL | NULL | | + +| Alias | varchar(255) | YES | | NULL | | + ++-----------+----------------------+------+-----+---------+----------------+ + +6 rows in set (0.001 sec) + +MariaDB [db_webqtl]> desc StrainXRef; + ++------------------+----------------------+------+-----+---------+-------+ + +| Field | Type | Null | Key | Default | Extra | + ++------------------+----------------------+------+-----+---------+-------+ + +| InbredSetId | smallint(5) unsigned | NO | PRI | 0 | | + +| StrainId | int(20) | NO | PRI | NULL | | + +| OrderId | int(20) | YES | | NULL | | + +| Used_for_mapping | char(1) | YES | | N | | + +| PedigreeStatus | varchar(255) | YES | | NULL | | + ++------------------+----------------------+------+-----+---------+-------+ + +5 rows in set (0.001 sec) + +MariaDB [db_webqtl]> select max(Id) from Strain; + ++---------+ + +| max(Id) | + ++---------+ + +| 66085 | + ++---------+ + +1 row in set (0.000 sec) + +MariaDB [db_webqtl]> insert into Strain (Name, +Name2,SpeciesId,Symbol,Alias) value ("Test1","Test1",30,"Test1","Test1"); + +Query OK, 1 row affected (0.000 sec) + +MariaDB [db_webqtl]> select max(Id) from Strain; + ++---------+ + +| max(Id) | + ++---------+ + +| 66086 | + ++---------+ + +1 row in set (0.000 sec) + +MariaDB [db_webqtl]> select * from Strain where Id=66086; + ++-------+-------+-------+-----------+--------+-------+ + +| Id | Name | Name2 | SpeciesId | Symbol | Alias | + ++-------+-------+-------+-----------+--------+-------+ + +| 66086 | Test1 | Test1 | 30 | Test1 | Test1 | + ++-------+-------+-------+-----------+--------+-------+ + +1 row in set (0.000 sec) + +``` + +### Problems + +- Integration with genotype files complicates things e.g. we can only + generate individual BXD genotypes from the "main" BXD genotype files + iff when we have the strains of each individual stored somewhere. + +- CaseAttributes need to be updated manually. One option is to enable + this using the UI. ATM we need to query the Case Attribute tables + to look the BXD strain for each individual when generating the + genotype files. + +- We should ideally be able to generate a set of genotype files or a + set of DB tables with all possible 20,000 BXD family genomes. As a + reference see David's smoothed WGS-based genotype files. + +- Genotype files will most likely not be static. Soon, we should be + able to support the need for them to change during runtime. + +- When the sample list for BDL_10001 is updated, will the sample list + for all other records be synchronized automatically. + + +### Goal + +- (Low hanging fruit) Ability to add insert new strains. + +- There are 1000s of mice with computable genomes that have never been + born yet. Can we compute their phenotype? This is as difficult as + getting to Mars.
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