Collections¶

More than 50 entities are modeled (from chemicals, to datasets, through living stocks and engineered constructs) to establish a thorough lab inventory. Each item of the inventory is described by a set of properties associated to one or multiple values. Different model list different and/or unique properties but all of them track basic information: they all have a Unique Universal ID (UUID), a description, lifecycle information (owner, creation date, last modified date, etc.) and permissions.

A part of the information is automatically captured (e.g. creation date, owner, etc.), the rest is manually handled by users. When possible, controlled vocabulary is used to narrow value option to adequat terms.

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 main categories, each category below lists their collections.

Consumables

Items consumed when performing experiments

Antibody
Chemical
Plasmid
Oligo
Enzyme
Protein
Slide

Equipment

Centrifuges
Microscopes
IT Supplies
Software
Sequencer

Storage Equipment

Tower
Cabinet
Cryogenic
Freezers
Fridges
Hoods
Incubators

Specimen

Cell Line
Strain
Fly Line
Virus
Fish
Cnidaria
Planaria

Biomaterials

Sample
Sequencing sample

Protocols

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

Assays

Illumina Sequencing
Nanopore Sequencing
Light Microscopy Screen
Light Microscopy

Dataset Management

Study
Dataset Collections
Dataset
Datafile
Archive

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

Features available on all 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 feature

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