Curation Core

NIH RePORTER · NIH · P41 · $997,688 · view on reporter.nih.gov ↗

Abstract

Abstract - CURATION COMPONENT The utility of the Gene Expression Database for Mouse Development (GXD) is proportional to its data content, the quality of data annotations, and the level of data integration that we provide. To foster GXD’s mission to facilitate insights into molecular mechanisms of development, differentiation and disease, the Curation Component will continue and expand GXD’s curation of expression data and anatomical ontologies and ensure high-quality data annotation and integration. We will (1) continue the curation of classical types of expression data. We will collect and integrate expression data from RNA in situ hybridization, in situ reporter knock-in, immunohistochemistry, RT-PCR, Northern blot and Western blot experiments. Data will be acquired from the literature, via electronic data submissions from laboratories, and by collaborations with projects that generate these data at a large scale. We will continue to ensure high-quality data annotation and integration through our editorial processes and quality controls. We will (2) continue and expand the curation of whole genome expression assays. Using the detailed controlled vocabularies and ontologies employed in GXD/MGI, we will annotate GXD-relevant bulk and single-cell RNA-seq and microarray expression data sets from GEO and ArrayExpress by attributes of the samples used, thus maintaining and expanding GXD’s up-to-date, searchable index to allow researchers to effectively find data sets of interest. We will continue to select consistently-processed, high-quality RNA-seq expression data sets from EBI’s Expression Atlas for inclusion in GXD. We will (3) continue the curation of anatomical ontologies and incorporate new anatomical concepts and relationships. We will enhance and refine the Mouse Developmental Anatomy Ontology and add “develops-from” relationships between anatomical structures of successive developmental stages to enable the analysis of differentiation pathways. We will maintain and refine the integration of expression and phenotypic data by referencing common anatomical objects, thus enhancing our tools for the direct anatomy-based comparison of expression, phenotype, and disease data. We will begin to annotate expression data at the cell type level by combining anatomy and cell ontology terms. We will extend the cell type (CL) ontology as needed by our annotation of expression data, in collaboration with the CL developers.

Key facts

NIH application ID
10827418
Project number
5P41HD062499-14
Recipient
JACKSON LABORATORY
Principal Investigator
MARTIN RINGWALD
Activity code
P41
Funding institute
NIH
Fiscal year
2024
Award amount
$997,688
Award type
5
Project period
2010-12-02 → 2026-04-30