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diff --git a/issues/gn-uploader/handling-tissues-in-uploader.gmi b/issues/gn-uploader/handling-tissues-in-uploader.gmi new file mode 100644 index 0000000..669df06 --- /dev/null +++ b/issues/gn-uploader/handling-tissues-in-uploader.gmi @@ -0,0 +1,114 @@ +# Handling Tissue in Uploader + +## Tags + +* status: open +* priority: high +* assigned: fredm +* type: feature-request +* keywords: gn-uploader, tissues + +## Description + +"ProbeSet" studies in GeneNetwork seem to be linked to a specific tissue: + +```sql +MariaDB [db_webqtl]> DESC ProbeFreeze; ++---------------+----------------------+------+-----+------------+----------------+ +| Field | Type | Null | Key | Default | Extra | ++---------------+----------------------+------+-----+------------+----------------+ +| Id | smallint(5) unsigned | NO | PRI | NULL | auto_increment | +| ProbeFreezeId | int(5) | YES | | NULL | | +| ChipId | smallint(5) unsigned | NO | | 0 | | +| TissueId | smallint(5) unsigned | NO | | 0 | | +| Name | varchar(100) | NO | UNI | | | +| FullName | varchar(100) | NO | | | | +| ShortName | varchar(100) | NO | | | | +| CreateTime | date | NO | | 0000-00-00 | | +| InbredSetId | smallint(5) unsigned | YES | | 1 | | ++---------------+----------------------+------+-----+------------+----------------+ +9 rows in set (0.00 sec) +``` + +According to the [`ProbeFreeze` table schema][1], `TissueId` links to the +[`Tissue` table][2]. + +From that, we need the following data to add a non-existing tissue to the system: + +* *TissueName* +* *Name*: Name of the biological material used in the experiment +* *Short_Name* + +There does not seem to be any difference between *TissueName* and *Name* from +what I can tell so far, therefore, the UI can simply have a single element to +get the name. + +There are other fields in the `Tissue` table that do not seem to have much (if +any) utility - these are *BIRN_lex_ID* and *BIRN_lex_Name*: From what I have +figured out so far, they are probably linked to the Biomedical Informatics +Research Network (BIRN), but beyond that, I have no idea. Thankfully, these are +not required information, so we can ignore them for now. + +If I have the go-ahead, I can begin working on this, but I needed to start the +discussion, especially regarding the possible issues mentioned next. + + +## Possible Gotchas + +According to the [`ProbeFreeze` table schema][1], the `TissueId` is a mandatory +field and + +> Links to the information about the biological material analysed . ID1206 + +The [`Tissue` table][2] on the other hand, does not link the material to the +species. This makes it virtually impossible to filter out the tissues for UI +presentantion, and thus, the user will always be presented with all tissues from +all species in the system (and possibly some species the system is unaware of - +there's nothing to prevent that). + +The closest we come to linking tissues with the species is via the `ProbeFreeze` +table that refers to the `InbredSet` table that then refers to the `Species` +table. Even with that, on the **Tux02** database, we have 48 tissues that are +not connected to any species. + +```sql +MariaDB [db_webqtl]> SELECT COUNT(*) FROM Tissue WHERE Id NOT IN (SELECT TissueId FROM ProbeFreeze); ++----------+ +| COUNT(*) | ++----------+ +| 48 | ++----------+ +1 row in set (0.01 sec) +``` + +The other major gotcha is regarding datatypes, i.e. + +```sql +MariaDB [db_webqtl]> DESC Tissue; ++---------------+----------------------+------+-----+---------+----------------+ +| Field | Type | Null | Key | Default | Extra | ++---------------+----------------------+------+-----+---------+----------------+ +| Id | smallint(5) unsigned | NO | PRI | NULL | auto_increment | +| TissueId | int(5) | YES | | NULL | | +| TissueName | varchar(50) | YES | | NULL | | +| Name | char(50) | YES | UNI | NULL | | +| Short_Name | char(30) | NO | UNI | | | +| BIRN_lex_ID | char(30) | YES | | NULL | | +| BIRN_lex_Name | char(30) | YES | | NULL | | ++---------------+----------------------+------+-----+---------+----------------+ +``` + +The `Id` and `TissueId` field have different types, despite seemingly serving +the same purpose, "Uniquely identifying each record". + +We should probably fix that, maybe with something like: + +```sql +ALTER TABLE Tissue MODIFY Id INT(5) UNIQUE NOT NULL; +``` + + +## References + +[1] https://gn1.genenetwork.org/webqtl/main.py?FormID=schemaShowPage#ProbeFreeze +[2] https://gn1.genenetwork.org/webqtl/main.py?FormID=schemaShowPage#Tissue |