IBEX Imaging KB directory structure and contents.

Infrastructure related files are found in the data, docs_in, and root directories. Content of interest for the general user is found in the data and docs directories. Using text-based files and a data lake approach enables easy navigation, viewing, and editing of the raw KB content without requiring dedicated software.

Schematic overview of IBEX KB design and contents.

The IBEX KB enables open exploration of reagents, protocols, datasets, and advice related to multiplexed imaging from members of the global scientific community. The overall design consists of three facets: a GitHub source repository (purple mountain), a static website (green mountain), and a Zenodo data repository hosting citable archival versions of the data (blue mountain). Every addition to the KB initiates an update to the IBEX Imaging Community Website outlined in steps 1-4. In contrast, updates to the authoritative version on Zenodo are initiated by community members when a significant update to the state of knowledge justifes a new release.

Computational worklow for static website generation.

Data displayed on the static website is generated from human and machine readable comma-separated value (csv), bibliography database (bib), jpg images, and markdown template (M down arrow) files. Following a new submission, custom Python scripts expand the template markdown files to include the new data. Existing data (unprocessed markdown files) remain unchanged. Website is automatically generated via Python scripts utilizing the GitHub continuous integration compute infrastructure and static website creation services (Jekyll).

The IBEX KB provides several ways to contribute and use data.

Summary of supported data types and ways to contribute or use the KB. Crown icon indicates contributions that result in authorship on the Zenodo archival versions.

Guidelines for contributing data and low chart detailing how to add a reagent contribution.

(A) Details for contributing data to the IBEX KB. Files that need to be modified are highlighted in blue with data file name bolded. (B) Flow chart demonstrating how to add a reagent contribution. Files that need to be modified are highlighted in green with data file name bolded.