# Comprehensive, Flexible and FAIR Tools for the HuBMAP HIVE

> **NIH NIH OT2** · CARNEGIE-MELLON UNIVERSITY · 2021 · $1,304,599

## Abstract

Abstract
The Human BioMolecular Atlas Program (HuBMAP) will redefine our understanding of the human
body by recovering multi-scale tissue organization -- anatomical, histological, and molecular, at
unprecedented resolution, through computational integration of diverse experimental
measurements. We propose to develop computational methods and tools to enable the use of
HuBMAP collected data by consortium participants, the international research community and the
large software and method development community. Our proposal is focused on three key
directions for the Tools Component: (1) Community involvement: Development of repositories,
APIs, interfaces and schemas to enable the hosting, discovery and integration of tools and
libraries developed by us and others. We would put specific emphasis on making sure that this
process is efficient, reduces duplicated efforts and transparent enabling involvement of the
general developer community. All tools would be developed as open source software. (2)
Innovative tool development: While we intend to rely and use existing tools as much as
possible, we also propose to develop a comprehensive set of innovative tools for the specific
challenges presented by the HuBMAP long term vision and data. These include tools for querying
and retrieving data collected by the HUBMAP, expression and image analysis methods and
libraries, tools for the analysis of spatial and temporal data from the MAP and tools for modeling
and data integration which would enable the integration of HuBMAP data with the vast amounts
of other publicly available biological data. (3) Flexibility: We expect that improved technology
and variance in the specific plans of the Tissue Mapping Centers would lead to additional types
of data that we have not designed tools for in the past. We have thus assembled an experienced
and diverse group of investigators, all with significant experience in tool development that,
together, span the spectrum of potential types of data.
Our proposal includes detailed plans for ensuring that the tools we develop and implement are
findable, accessible, interoperable and reusable (FAIR) and addresses issues related to validation
of tool accuracy and usefulness, data privacy and reproducibly. The Tools component would work
very closely with other HIVE components to disseminate the tools and to connect with both the
developers and the international research communities.

## Key facts

- **NIH application ID:** 10397722
- **Project number:** 3OT2OD026682-01S4
- **Recipient organization:** CARNEGIE-MELLON UNIVERSITY
- **Principal Investigator:** Benedict Paten
- **Activity code:** OT2 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $1,304,599
- **Award type:** 3
- **Project period:** 2021-06-21 → 2022-06-20

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10397722

## Citation

> US National Institutes of Health, RePORTER application 10397722, Comprehensive, Flexible and FAIR Tools for the HuBMAP HIVE (3OT2OD026682-01S4). Retrieved via AI Analytics 2026-06-01 from https://api.ai-analytics.org/grant/nih/10397722. Licensed CC0.

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