Lab Integrated Data ¶

Web Platform for Research Data Management ¶

Lab Integrated Data (LabID) is a web platform for fundamental research data-management, featuring an inventory system coupled to a powerful Electronic Lab Notebook (ELN). It is designed to help scientists and research groups better managing their lab inventory, research notes, and datasets. It facilitates documenting and referencing research progress throughout the experimental and analysis chains, effectively preserving data integrity and enhancing traceability.

At a glance

At a glance: An Electronic Lab Notebook (ELN) to record your daily notes (digitally timestamped to guarantee intellectual property),; A Lab Inventory Module to manage and share lab collections (plasmids, chemicals, etc.), instruments (microscopes, freezers, etc.) or animal collections (fly lines, mouse strains, etc.),; A Protocol Module to version and share protocols,; A Sample Module to samples, their lineage (parent-child relationships), and their connections to your experiments (lab notes) and assays; A Dataset Module to manage datasets i.e. track assays and instruments ran to acquire the data, track datasets lineage up to the samples initially used,; A Controlled Vocabulary Module to ensure the consistent use of appropriate semantics, important when e.g. submitting data to public repositories (like ENA); An Advanced Permission System on all modules to fine-tune access to the data (read, write, delete permissions at the user or group level); An Order Module to track orders information,

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Users can efficiently browse through their lab inventory and access detailed information such as the exact location of a consumable. The description of each item can be modified and items can be enriched with attachments and notes. Inventory listings are presented in interactive data tables, which users can customize and filter to their preferences. Each item has a set of defined properties, and it can be enriched with annotations. Additionally, our powerful permission system ensures protection against unwanted modifications.

New items can be added either individually or in batch (using excel-based templates).
Items can be modified either individually or in batch - from list pages.

Integration with other tools

The integration with Galaxy allows for synchronizing data both ways between Galaxy and LabID,
The Integrated Online Editor (powerted by LibreOffice) allows for collaborative edition of documents,
The Application Programming Interface (API) enables programmers to interact with LabID programmatically, providing e.g. automated registration and transfe rof datasets, ensuring full traceability and minimizing user input.
The Data export allows for exporting the data (inventory, lab notes, etc.) as spreadsheets or PDFs (no vendor lock-in!),

LabID is developed by the Genome Biology Computational Support at the European Molecular Biology Laboratory in Heidelberg. This documentation is updated often to follow our release cycle.

LabID is under active development, often releasing new feature with continuous integration. Parts of this documentation may show screenshots and videos recorded using previous versions. There may therefore be discrepancies between the visual examples, or the text, and the latest version available at https://labid-demo.embl.de.

Lab inventory¶

A great variety of entities can be registered, linked, and organized. Everywhere applicable, controlled vocabulary is used to describe those entities. Covering most of a lab inventory, it out-of-the-box supports: Lab consumables, scientific equipment, lab specimen (living stocks), biomaterials (samples), storage locations, assays (sequencing and light microscopy), datasets, and more.

These categories are organised into multiple collections. For instance, the consumables category includes among others: antibodies, chemicals, plasmids, oligos, enzymes, etc. Each item is described following property: value scheme, some of which are available on all models (e.g. Universal Unique ID, creation date, ownership information, etc.). Certain collections have specific describing properties (e.g. a CAS Number on chemicals).

FAIR: Search, Browse, Unique Identifiers and Cross-Referencing¶

The platform is developed to assist scientist performing FAIR science.

Lists views

All collections have associated list views, exhaustively listing inventory content. List views heavily rely on interactive data table which are entirely customisable (adding or removing properties (columns) and search/filtering records (rows))
Global Search

To find the needle in the haystack several ways to search and filter inventory content are provided. This include filters on list pages as well as a global search to find items by name.
Unique Identifiers (UUID) and permalink

Every item is assigned a Unique Universal Identifier (UUID) upon registration. UUIDs ensure items can be uniquely identified within and across instances. The details of a given items is accessible at its permalink e.g. https://labid-demo.embl.de/<UUID> . Permalinks allow for cross-referencing, for example from within the lab notebook.

Electronic Lab Notebook¶

The Electronic Lab Notebook (ELN) is a powerful tool to let scientists extensively describe each and every link of the experimental chain. One can digitally record the whole experimental process, cross-referencing the used inventory items (consumables, samples, etc.) as well as all the relevant processes, protocols, scientific instruments, etc.

The ELN features a visual text editor where one can write and format text (with e.g. hyperlinks), and embed images and tables. Every lab note can be enriched with attachments containing related documents (spreadsheets, word documents, etc.), but also pictures, comments, and more. Attached office documents can be collaboratively editable online.

Each note is uniquely identifiable, dated, and digitally signed (time-stamped) by relevant third-party authorities to ensure intellectual property.

Dataset Management¶

The platform assists scientists in adhering to data management best practices. Scientists can access exhaustively described and annotated raw datasets, files, and file versions. Processed files created by the computational analysis of raw data, as well as any publicly available dataset, can be registered, and organised. Relationships are recorded from samples to raw data, and beyond. This for example includes parent-child relationships, when one entity derives from another. This strategy applies for all datafiles handled within the system.

When a project wraps up, the existing record of the analysis chain - from raw material, to raw data, to publication material - greatly simplifies the publication process.