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 manage 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 track 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 used to acquire the data, and track dataset 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 order information

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

LabID is under active development, often releasing new features 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¶

Exhaustively describe your inventory¶

A great variety of entities can be registered, linked, and organised. Your inventory is organised into multiple collections: Lab consumables, scientific equipment, lab specimen (living stocks), biomaterials (samples), storage locations, assays, datasets, and more. Each collection is further organised into different types, for example consumables includes among others: antibodies, chemicals, plasmids, oligos, enzymes, etc.

Access detailed information¶

Each item has its own set of attributes to be associated with describing values. Some attributes are available on all models (e.g. Universal Unique ID (UUID), Creation Date, Ownership, Group Ownership, etc.). Other attributes are specific to certain collections and/or item types (e.g. the CAS Number available on chemicals). The description of each item can be modified and items can be enriched with annotations, attachments, and notes. Everywhere applicable, controlled vocabulary is used.

Efficiently browse through your inventory and find the needle in the haystack¶

Inventory listings are presented in interactive data tables, which users can customise and filter to their preferences. With this, you are able to quickly find, for example, the exact location of a consumable.

Quickly create and modify multiple items¶

Every item can individually be created and edited via web forms; however, it is also possible to create or modify multiple items using spreadsheets.

Restrict access to your group or go public¶

Our powerful permission system ensures protection against unauthorised access and unwanted modifications. By default, most items are created and visible to your group, but their access can either be restricted to single individuals or shared publicly.

Data Management¶

Data isolated from its metadata becomes meaningless. LabID helps you adhere to data management best practices and ensures enough metadata is recorded about your data so that its value is preserved over time.

Register your data and all the important information about it¶

We have developed fine data models and registering mechanisms to ensure important metadata is captured during data registration. Some information is automatically collected and some is directly provided by you.

Simple data management entity relationship

Record domain specific information¶

We've developed multiple sample, data, and assay models so that domain-specific information is properly registered.

Maintain relationships¶

Relationships are recorded from samples to raw data, and beyond. This includes, for example, parent-child relationships, when one entity derives from another. This strategy applies for all data files handled within the system.

Automate well-defined registration processes¶

In cases where a large volume of data is generated following well-defined processes, the registration can be automated.

Access a FAIR data registry¶

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.

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.

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 edited online.

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

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

The platform is developed to assist scientists in performing FAIR science.

List views¶

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

Global Search¶

To find the needle in the haystack, several ways to search and filter the inventory content are provided. This includes 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 item are accessible at its permalink e.g. https://labid-demo.embl.de/<UUID>. Permalinks allow for cross-referencing, for example from within the lab notebook.

Integration with other tools

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