# Computational tools for uniform processing and integration of human reference atlas data [2 of 5]

> **NIH NIH OT2** · CARNEGIE-MELLON UNIVERSITY · 2022 · $1,092,096

## Abstract

The HuBMAP Computational Tools Component is responsible for development of standardized 
processing pipeline for all HuBMAP data, which is the foundation that enables joint storage, indexing, 
display, querying and mapping of HuBMAP datasets. A key innovative aspect that we have championed 
and, which as far as we know is unique for large consortia with several groups, platforms and data 
modalities is the fact that all HuBMAP pipelines we implemented provide uniform processing of all data 
from the same modality. Specifically, for each of these modalities we use the same computational 
algorithm for initial and downstream processing. For example, all scRNA-Seq datasets, regardless of 
which of the 7 platforms they were generated by, are processed by our Salmon quantification pipeline. 
This makes integration and comparison much easier across all HuBMAP data. In addition, all 
downstream analysis including dimensionality reduction, clustering, differential expression etc. are also 
performed using the same methods for all platforms making it easy to organize the display of the data 
on the portal and to index the data for quantitative queries. Similar pipelines have been developed for 
other modalities.
In the production phase of the HuBMAP Consortium, we will extend these computational pipelines to 
support additional data types from new tissue mapping centers and other data providers. We will 
additionally extend our focus beyond single-cell image segmentation to support the mapping efforts of 
the Human Reference Atlas (HRA) collaboration, producing hierarchical links from cells to functional 
tissue units to higher-level anatomical structures.

## Key facts

- **NIH application ID:** 10534347
- **Project number:** 1OT2OD033761-01
- **Recipient organization:** CARNEGIE-MELLON UNIVERSITY
- **Principal Investigator:** Benedict Paten
- **Activity code:** OT2 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $1,092,096
- **Award type:** 1
- **Project period:** 2022-08-01 → 2026-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10534347

## Citation

> US National Institutes of Health, RePORTER application 10534347, Computational tools for uniform processing and integration of human reference atlas data [2 of 5] (1OT2OD033761-01). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10534347. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*