Collections¶

LabID provides comprehensive laboratory inventory management with over 50 entity types - from chemicals and datasets to living specimens and engineered constructs.

Each item of the inventory is described by a set of properties to which you associate one or multiple values of your choice.

All modeled entities are sharing a set of common properties (e.g. each have their own Unique Universal ID (UUID), description, lifecycle information, permissions). Certain models come with additional specific properties (e.g. chemicals have a CAS number, etc.).

Some data is automatically captured (e.g. creation date, owner), while other information requires user input. Controlled vocabularies and field validation ensure consistent data entry where applicable.

Semantics

The word item is used to refer to an entry of a collection whether it be a chemical, a cell line or a fridge.
The words attribute, property, or field (of an item) is used interchangeably.

Inventory goods are organised into the following categories and subcategories:

Consumables

Items consumed when performing experiments (below are examples, always check your own installation to see what is available)

Antibody
Chemical
Plasmid
Oligo
Enzyme
Protein
Slide

Equipment

Items used when performing experiments (below are examples, always check your own installation to see what is available)

Centrifuges
Microscopes
IT Supplies
Software
Sequencer

Storage Equipment

Items used for bio-banking i.e. used to store consumables or samples (below are examples, always check your own installation to see what is available)

Tower
Cabinet
Cryogenic
Freezers
Fridges
Hoods
Incubators

Specimen

The bio-source of your samples (below are examples, always check your own installation to see what is available)

Cell Line
Strain
Fly Line
Virus
Fish
Cnidaria
Planaria

Biomaterials

The different sample types used in experiments & assays.

Sample, this is the most common sample type and should be used unless one the more specialized sample types below applies to your situation.
Sequencing sample, this is a sample that is intended to be sequenced and offer sequencing specific properties required when publishing data to public repositories.
EMSample, this is a sample that has been prepared for Electron Microscopy.

Protocols

The different protocol types used in the lab (below are examples, always check your own installation to see what is available)

Biochemistry
Media & Buffer
Data Analysis
Extraction
Culture & Growth
Fixation
Labeling
Library Preparation
Molecular Biology
Sequencing

The Protocol List is a special model representing a list of protocols (order matters). Template lists of protocols reprenting standard procedures can be assembled and shared with the lab.

Assays

The different assay types generating datasets.

Illumina Sequencing
Nanopore Sequencing
Light Microscopy Screen
Light Microscopy
Transmission Electron Microscopy (TEM)
Volume Electron Microscopy (VEM)

Dataset Management

Study
Dataset Collections
Dataset
Datafile
Datafile copies (a datafile can have multiple copies in different locations)
Archive

The list above is exhaustive, but our collections list can be extended

Features available on collections¶

Import

Registering new items within a collection is typically done by filling online forms up; In addition, entire lab collections can be imported in batch. This is especially useful when legacy collections need to be imported upon joining.: See how to import items...

Edit

Registering new items within a collection is typically done by filling online forms up; In addition, entire lab collections can be imported in batch. This is especially useful when legacy collections need to be imported upon joining.: See how to edit single items...; See how to edit single items...

Rich-text description

Describe the item with great details and pictures. Other items can be cross-referenced in text with hyperlinks.: See feature

File Attachment

Attach all sorts of documents to an item. Office documents become editable online.: See feature

Notes

Add authored and dated notes to items. Anyone with view access can view and add notes.: See feature

Sharing

Fine tune the list of user(s) and group(s) who can view, edit and/or delete items.: See feature

Annotations

Describe any aspect of the item not covered by the item properties. Item attributes are meant to be universally relevant - and therefore the items are described with what is strictly necessary - but annotations add a layer of flexibility. Annotate your item with attributes controlled vocabulary that are relevant to you and/or your group.: See feature

Customization

Instance administrators can both enrich existing collection and add new ones.: See feature

ID: Each item is uniquely identifiable with its Unique ID

Each registered item gets assigned a Universal Unique ID (UUID) and a detail page (available at https://labid-demo.embl.de/<uuid> ). Detail pages exhaustively list items properties and allow user to edit values. Detail pages is also where one is attaching documents, adding notes or adding annotations