# Mining the Scientific Literature and Building a Pan-Echinoderm Gene Expression Database

> **NIH NIH P41** · CARNEGIE-MELLON UNIVERSITY · 2021 · $120,456

## Abstract

CURATION COMPONENT- ABSTRACT
 Echinoderms (sea urchins and their allies) are a pre-eminent model for analysis of the genomic control
of embryonic development. For example, the most complete gene regulatory networks (GRNs) for
development that we have for any animal have recently been solved for sea urchin embryos. Data on genes,
genomes, and gene expression are fundamental to all aspects of modern developmental biology, including
GRN biology. Effective access to these data has become vital not only to members of the echinoderm research
community but to a broader audience studying developmental processes (including GRNs) in other model
systems. The activities of Echinobase are essential in order to ultimately apply this scientific information to
human development and disease.
 Model organism databases enhance the value of research by consolidating and storing data,
integrating different types of information and representing it in useful ways, and linking similar kinds of data
across organisms. Echinobase was created to enhance the value of scientific data related to the genes and
genomes of sea urchins and other echinoderms and to serve as a centralized, definitive resource for
information related to these important model organisms. The Curate Component (Curate) plays a central role
in the overall mission of Echinobase by identifying, extracting, and organizing scientific data.
 During this project period, Curate has two overarching goals: 1) the curation of scientific literature
related to echinoderm development, and 2) the development of a comprehensive gene expression database,
including the formulation of an anatomical ontology for echinoderm embryos that will serve as a framework for
the annotation of gene expression data. Literature curation will allow users to effectively mine information from
the large body of published studies on echinoderm development, and the bibliography of published papers will
serve as a backbone to which all curated biological data can be attributed. Among the most important classes
of biological data are those pertaining to spatial and temporal patterns of gene expression during development.
A wealth of gene expression data has been generated for sea urchins and other echinoderms in recent years,
and there is a pressing need to curate these data and to develop new tools that will allow scientists to take full
advantage of this information. Our curation efforts will be supported through a collaboration with Xenbase,
which will provide a suite of data entry, storage, and analysis tools that are well-suited to our needs. Through
its activities, Curate will extend the capabilities of Echinobase and thereby greatly enhance its utility to the
research community.

## Key facts

- **NIH application ID:** 10241292
- **Project number:** 5P41HD095831-04
- **Recipient organization:** CARNEGIE-MELLON UNIVERSITY
- **Principal Investigator:** CHARLES A. ETTENSOHN
- **Activity code:** P41 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $120,456
- **Award type:** 5
- **Project period:** 2018-09-20 → 2023-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10241292

## Citation

> US National Institutes of Health, RePORTER application 10241292, Mining the Scientific Literature and Building a Pan-Echinoderm Gene Expression Database (5P41HD095831-04). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10241292. Licensed CC0.

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