FDM-Werkstatt: Metadata Magic - A Deep Dive into eLabFTW Customization
Abstract
This publication contains the presentation slides and handout from the workshop session "Metadata Magic - A Deep Dive into eLabFTW Cutomization" which took place on 2025-04-01 during the FDM-Werkstatt 2025 in Münster (Westf.), Germany. The session covered the following topics: Usage of built-in predefined (tags, categories, status) and user-defined metadata fields (extra fields) within eLabFTW Best practices for the definition of extra fields Example use cases Import and export of extra fields using JSON files Usage of API to retrieve and edit metadata
Full text
Metadata Magic Magic A Deep Dive into eLabFTW Customization Alexander Minges | FDM-Werkstatt 2025 | 2025-04-01 This work is licensed under a “CC BY 4.0” license. cb All logos are explicitly excluded from this license.
TrophyWorkshop Goals Enhancing metadata management using structured extra fields and built-in tools. Bulk metadata input via JSON import. Integrating metadata workflows using the elabFTW API. 2025-04-01 Metadata Magic 2
TasksWhat do you need? Alaptop with internet access. Access to an elabFTW instance. Atext editor with syntax highlighting for JSON files (e.g. Notepad++, VS Code). Workshop Handout CLIPBOARD https:///pad.athemis.de/s/nCZ6ZAc8w 2025-04-01 Metadata Magic 3
Question-CircleYour Experiences with Metadata in elabFTW Poll-H Or open https://claper.athemis.de and enter the code 8IQ7I 2025-04-01 Metadata Magic 4
Question-CircleYour Experiences with Metadata in elabFTW Further questions: How do you currently manage metadata in elabFTW? What challenges have you faced when structuring metadata? 2025-04-01 Metadata Magic 5
Metadata in elabFTW: Built-in Features elabFTW provides both predefined and user-defined metadata fields. Predefined: Tags Category Status Compound Database and Inventory (to be included in v.5.2) User-Defined: Custom metadata fields Extra Fields 2025-04-01 Metadata Magic 6
Metadata in elabFTW: Built-in Features elabFTW provides both predefined and user-defined metadata fields. Predefined: Tags Category Status Compound Database and Inventory (to be included in v.5.2) User-Defined: Custom metadata fields Extra Fields 2025-04-01 Metadata Magic 6
Metadata in elabFTW: Built-in Features elabFTW provides both predefined and user-defined metadata fields. Predefined: Tags Category Status Compound Database and Inventory (to be included in v.5.2) User-Defined: Custom metadata fields Extra Fields 2025-04-01 Metadata Magic 6
How to Define Extra Fields 2025-04-01 Metadata Magic 7
Example Use Cases Samples/Inventory plasmids bacterial strains Routine/Standardized experiments PCR Protein Expression Guided input Ensures crucial information is recorded Provide hints to inexperienced users (e.g. students) 2025-04-01 Metadata Magic 9
Populating Extra Fields with JSON Structured representation of “extra fields” as JSON. 1{ 2"elabftw" { 3"display_main_text":false, 4"extra_fields_groups": [ 5{"id":1,"name":"Some group" }, 6] 7}, 8"extra_fields": { 9"Some extra field name": { 10 "type":"date", 11 "value":"2023-06-23", 12 "group_id":1 13 } 14 } 15 } 2025-04-01 Metadata Magic 10
Populating Extra Fields with JSON Structured representation of “extra fields” as JSON. DownloadExport UPLOADimport of extra fields data. Advanced editing of extra fields 2025-04-01 Metadata Magic 11
Populating Extra Fields with JSON Structured representation of “extra fields” as JSON. DownloadExport UPLOADimport of extra fields data. Advanced editing of extra fields 2025-04-01 Metadata Magic 11
Using the API for Metadata Management The elabFTW API allows automation of metadata retrieval and updates. API Use Cases Bulk updates: Modify multiple entries at once. Integration with external databases: Fetch metadata from other systems. Automated metadata extraction: Use scripts to pull metadata for analysis. 2025-04-01 Metadata Magic 12
Using the API for Metadata Management The elabFTW API allows automation of metadata retrieval and updates. API Use Cases Bulk updates: Modify multiple entries at once. Integration with external databases: Fetch metadata from other systems. Automated metadata extraction: Use scripts to pull metadata for analysis. 2025-04-01 Metadata Magic 12
Using the API for Metadata Management How to access the API Direct access of API endpoints (e.g. by using curl or python-requests) Abstraction layer elabapi-python. 2025-04-01 Metadata Magic 13
Using the API for Metadata Management Example API request to retrieve metadata 1export KEY=3-cb2314b00d2845a… 2curl -H "Authorization: $KEY"-X GET "https://eln.example.org/api/v2/experiments/149" | jq 1 2… 3"metadata_decoded": { 4… 5"extra_fields": { 6"Name": { 7"type":"text", 8"value":" pET His6 Mocr TEV LIC cloning vector (1O)", 9"description":"Name of the plasmid. Usually also used as label on tubes.", 10 }, 11 … 12 }, 13 … 14 }, 15 … 2025-04-01 Metadata Magic 14
Using the API for Metadata Management Example API request to retrieve metadata 1export KEY=3-cb2314b00d2845a… 2curl -H "Authorization: $KEY"-X GET "https://eln.example.org/api/v2/experiments/149" | jq 1 2… 3"metadata_decoded": { 4… 5"extra_fields": { 6"Name": { 7"type":"text", 8"value":" pET His6 Mocr TEV LIC cloning vector (1O)", 9"description":"Name of the plasmid. Usually also used as label on tubes.", 10 }, 11 … 12 }, 13 … 14 }, 15 … 2025-04-01 Metadata Magic 14
ToolsHands-on Create a template (experiment or resource) and add extra fields Test your template with sample data Use extra fields in search queries Export and import metadata using JSON files CLIPBOARDHandout: https://pad.athemis.de/s/nCZ6ZAc8w CLIPBOARD 2025-04-01 Metadata Magic