SBOLInventory

SBOLInventory is a Python package for SBOL 2 inventory modeling that separates:

• external storage hierarchy (Collection): fridges and shelves
• physical containers/items (Implementation): boxes, plates, and contained materials

Object graph

Fridge4C (Collection)
└── Shelf (Collection)
      └── SolidMediaPlate (Implementation from MD)
            └── PlatedStrain (Implementation from MD)

FridgeMinus80C (Collection)
└── Shelf (Collection)
      └── Box (Implementation from MD)
            └── BacterialStock (Implementation from MD)
            └── ProcuredMaterial (Implementation from MD)

FridgeMinus20C (Collection)
└── Shelf (Collection)
      └── Box (Implementation from MD)
            └── DilutedPlasmid (Implementation from MD)
            └── ProcuredMaterial (Implementation from MD)

Key concepts

• ModuleDefinition is a design.
• Physical items are always InventoryImplementation with built pointing to the design.
• SolidMediaPlate and Box are container implementations with explicit allowed row/column layout.
• Placed items record:
  • contained_in_container
  • container_row
  • container_column
• Every implementation has is_active and can be discarded (set inactive).

Example

from sbol_inventory import (
    make_document,
    add_all,
    make_fridge_4c,
    make_shelf,
    make_solid_media_plate,
    make_plated_strain,
    add_child,
    place_in_container,
)

# Storage hierarchy (Collections)
doc = make_document()
fridge4 = make_fridge_4c("https://example.org/storage/4C")
shelf = make_shelf("https://example.org/storage/4C/shelf1")

# Physical containers/items (Implementations)
plate = make_solid_media_plate(
    uri="https://example.org/implementation/plate1",
    plate_md_uri="https://example.org/designs/plate_md",
    rows=["A", "B", "C"],
    columns=range(1, 5),
)
plated_strain = make_plated_strain(
    uri="https://example.org/implementation/plated1",
    strain_md_uri="https://example.org/designs/strain_md",
)

add_all(doc, [fridge4, shelf, plate, plated_strain])
add_child(fridge4, shelf)
add_child(shelf, plate)

# Place by row/column, validated against allowed and occupancy
place_in_container(plate, plated_strain, row="A", column=1)

Main API additions

• make_box(...)
• make_diluted_plasmid(...)
• make_procured_material(...)
• make_plated_strain(...)
• place_in_container(...)
• move_item(...)
• remove_from_container(...)
• discard_implementation(...)