# BioGPS, BioThings and BioReel: illuminating dark data for biomedical research

> **NIH NIH R01** · SCRIPPS RESEARCH INSTITUTE, THE · 2020 · $483,750

## Abstract

The overall goal of this project is to promote the accessibility and dissemination of biomedical information so that
the research community can better leverage existing knowledge. Science is most efficient when hypotheses are
based on the entirety of knowledge available to date. Unfortunately, up-to-date and comprehensive access to
relevant knowledge is rarely achieved. This proposals put a particular emphasis on illuminating biomedical “dark
data.” By analogy to the dark matter that is unaccounted for in the universe, dark data is defined by being unseen
or underutilized by the scientific community. In this project, we will continuously strengthen our currently widely-
used applications BioGPS and MyGene.info, and also develop two new applications: BioThings and BioReel.
These applications, collectively, are targeted to make dark data resources Findable, Accessible, Interoperable,
and Reusable (FAIR).
BioGPS and BioReel are designed for non-computational scientists. BioGPS (http://biogps.org) is a gene portal
for aggregating information on human genes and proteins. It illuminates dark data by creating a simple platform
to discover and access gene-centric websites. BioGPS users can benefit each other by sharing the specific
resources they discovered, and how they use or like them. BioReel will be developed as a tool to periodically
monitor the relevant resources for researchers, and keep them notified when the knowledge about their genes
of interest have been updated (e.g. new datasets available, annotated in a new pathway).
MyGene.info and BioThings are designed for bioinformatics developers, who often face fragmented source data
in terms of both the content and the heterogeneous formats. The significant amount of repetitive data-wrangling
efforts has to be done by almost every bioinformaticians. We developed MyGene.info to integrate gene and
protein annotation data into a simple and high performance web Application Programming Interface (API). It
illuminates dark data on gene and protein annotations by pre-integrating over 200 annotation types in a
standardized format. In this proposal, we will continue expand MyGene.info to include additional highly-
requested annotations, both from a major data repository and smaller domain-specific data sources. In addition,
we will generalize the infrastructure and the software pattern underlying the MyGene.info project, to make a
generic API framework called the “BioThings SDK”. Two new APIs will be built using this framework, focusing
on drugs/chemicals and diseases respectively, where the data fragmentation across resources are equally a
problem.

## Key facts

- **NIH application ID:** 9899250
- **Project number:** 5R01GM083924-12
- **Recipient organization:** SCRIPPS RESEARCH INSTITUTE, THE
- **Principal Investigator:** ANDREW I SU
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $483,750
- **Award type:** 5
- **Project period:** 2008-08-01 → 2022-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9899250

## Citation

> US National Institutes of Health, RePORTER application 9899250, BioGPS, BioThings and BioReel: illuminating dark data for biomedical research (5R01GM083924-12). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9899250. Licensed CC0.

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