# 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