Define scope of wetlab schema

[Zethson]

The wetlab schema is not clearly defined and has different types of models. We should agree on what wetlab is and what it isn't. I personally think that the current (bloated?) scope is okay because I'm not a fan of creating even more schema modules that we have to maintain and users have to find and use. Despite migrations.

Anyways, Claude thinks (https://claude.ai/share/007f775c-fb22-4bfb-82ba-a6d7480c2993), we could additionally have:

class Equipment(models.Model):
    name = models.CharField(max_length=100)
    model_number = models.CharField(max_length=50)
    location = models.CharField(max_length=100)
    maintenance_due = models.DateField()
    is_available = models.BooleanField(default=True)
    notes = models.TextField(blank=True)

class Reagent(models.Model):
    name = models.CharField(max_length=100)
    catalog_number = models.CharField(max_length=50)
    manufacturer = models.CharField(max_length=100)
    lot_number = models.CharField(max_length=50)
    expiration_date = models.DateField()
    storage_location = models.CharField(max_length=100)
    current_quantity = models.FloatField()
    unit = models.CharField(max_length=20)
    minimum_quantity = models.FloatField()

class Protocol(models.Model):
    name = models.CharField(max_length=200)
    version = models.CharField(max_length=20)
    created_by = models.ForeignKey(User, on_delete=models.CASCADE)
    created_at = models.DateTimeField(auto_now_add=True)
    updated_at = models.DateTimeField(auto_now=True)
    steps = models.TextField()
    reagents = models.ManyToManyField(Reagent)
    equipment = models.ManyToManyField(Equipment)

class Experiment(models.Model):
    STATUS_CHOICES = [
        ('planned', 'Planned'),
        ('in_progress', 'In Progress'),
        ('completed', 'Completed'),
        ('failed', 'Failed')
    ]
    
    title = models.CharField(max_length=200)
    protocol = models.ForeignKey(Protocol, on_delete=models.PROTECT)
    researcher = models.ForeignKey(User, on_delete=models.CASCADE)
    start_date = models.DateTimeField()
    end_date = models.DateTimeField(null=True, blank=True)
    status = models.CharField(max_length=20, choices=STATUS_CHOICES)
    results = models.TextField(blank=True)
    notes = models.TextField(blank=True)

class Measurement(models.Model):
    sample = models.ForeignKey(Sample, on_delete=models.CASCADE)
    equipment = models.ForeignKey(Equipment, on_delete=models.CASCADE)
    measured_by = models.ForeignKey(User, on_delete=models.CASCADE)
    measurement_date = models.DateTimeField()
    value = models.FloatField()
    unit = models.CharField(max_length=20)
    notes = models.TextField(blank=True)

where BioSample is similar to Sample`.

Claude thinks that:

Compound (chemical/drug database)
TreatmentTarget (molecular targets)
GeneticTreatment (genetic modifications)
CombinationTreatment (treatment protocols)

go beyond the scope of what the name wetlab implies.

The schema appears to be a broader "biological research management system" rather than just wetlab management. It encompasses:

Lab operations
Molecular biology
Treatment protocols
Sample tracking
Biological annotations

I asked Claude for names that would encompass everything:

• biolab
• bioresearch
• biolims
• bioprocess

[sunnyosun]

I think a lot of the suggested tables are already in EFO.

I agree Compound shouldn't be here, which we discussed many times before that it should belong to a chemistry schema. It's here just for simplicity right now.

I'm not sure biolab is better than wetlab, and why GeneticTreatment goes beyond wetlab. biolab can certainly include dry lab. 🤔