BICCN Data Dashboard - Brain Cell Data Center (BCDC)

The BICCN was a five year consortium effort to generate data to inform our understanding of cell tyeps in the brain. Although most data generation was completed by end of 2022, a few grants continue to generate data. This dashboard provides an exploratory tool to see what types of data and how much data were generated and made available to the community by BICCN scientists (2018Q3-2023Q1).

Three dashboard views are available. Click on the picture to access each view:

Dashboard Home:

This summary view showcases the cumulative count of unique specimens [1] reported to be profiled by diverse methodologies over the life of BICCN in chronological order. Different specimen types are being shown in different panels to ensure the readability of the plots. Descriptions of methodologies can be found in the "glossary".

Data Collection View:

This views allows a user to search and download specimen and donor counts by data collection.

Specimen Records Count: shows the total number of specimen records [2] submitted for each specimen type by individual data collections.
Data Collection Search: allows the user to search by individual data collection names and review the total number of specimen records submitted only for the selected data collections, including links to Data Collection entry in the Data Catalog.

Modality View:

This view allows a user to drill down and create a report or download a csv of data counts separated by data modalities. The user can parse by different variables including grant (participating grants list), species, project, data collection, archive, or technique.

Specimen Counts by Modality Groups: shows the count of unique specimens [1] in different modality groups in chronological order. The user has an option to view cumulative counts of unique specimens by selecting 'Cumulative' as the metric type, or select 'Per Term' to review the unique number of specimens deposited per each submission quarter. Please note that different modality group counts different specimen types.
Subject/Donor Counts by Modality Groups: shows the cumulative number of unique mice subject/human donors in each year and modalities, and the number of unique mice subject/human donors received per submission quarter. Also shows the number of subject/donors reported by each grant.

The Dashboard page is located at: BICCN Data Catalog Dashboard

Count Strategy

There are a total of 5 metric types being tracked by the dashboard: subject/donor counts, brain counts, cell counts, tissue sample counts, library counts. Users can use the dropdown filters on the left side of the dashboard to toggle between selections and view counts for different metrics. It is worth noting that the metric strategy listed below is a generic map of how each metric is being calculated - further business logic is applied to calculate the total number of unique specimens or specimen records. For example, on top of identifying which rows belong to cell counts..

For subspecimen counts, 4 subspecimen types are being calculated in the dashboard:

brain_counts: calculate the sum of the total processed specimen column for rows when the reported Subspecimen type falls under the ‘Brain Count’ category in the glossary map
cell_counts: calculate the sum of the total processed specimen column for rows when the reported Subspecimen Type falls under the ‘Cell Count’ category in the glossary map
tissue_sample_counts: calculate the sum of the total processed specimen column for rows when the reported Subspecimen Type falls under the ‘Tissue Sample Count’ category in the glossary map
library_counts: calculate the sum of the total processed specimen column for rows when either the reported Sample Type or Subspecimen Type falls under the ‘Library Count’ category in the glossary map

For human donor/mice subject counts, we count the unique number of unique Subject IDs in the metadata template, along with the backfilled counts with the below strategies in the event where the Subject ID is blank:

The number of whole brains can be counted towards the number of subject/donors
Specific interpretations can be done for certain data collection to identify the number of subjects/donors present in the experiments, including but not limited to reviewing parent sample ID patterns, referring to project descriptions or subject metadata the lab submitted to archives, etc.

Glossary of Terminologies used in BICCN Dashboard

A glossary of which techniques are included in each modality group, and what species are included in each species group are provided for reference.

[1] Count of unique specimens reflects how many unique numbers of brains/cells/specimens were reported in the submitted data. For example, some data collections may perform multimodal experiments on the same specimen and report different steps of the experiments separately; 'Count of unique specimens' counts only the unique number of specimens used in the reports.

[2] Total number of specimen records counts how many records were in the submitted data. In the event of a data collection performing multimodal experiments on the same specimen and reports different steps separately to different archives, 'Total number of specimen records' keeps track of all reports and which archive they each was submitted to.