The center for expanded data annotation and retrieval

Abstract

The Center for Expanded Data Annotation and Retrieval is studying the creation of comprehensive and expressive metadata for biomedical datasets to facilitate data discovery, data interpretation, and data reuse. We take advantage of emerging community-based standard templates for describing different kinds of biomedical datasets, and we investigate the use of computational techniques to help investigators to assemble templates and to fill in their values. We are creating a repository of metadata from which we plan to identify metadata patterns that will drive predictive data entry when filling in metadata templates. The metadata repository not only will capture annotations specified when experimental datasets are initially created, but also will incorporate links to the published literature, including secondary analyses and possible refinements or retractions of experimental interpretations. By working initially with the Human Immunology Project Consortium and the developers of the ImmPort data repository, we are developing and evaluating an end-to-end solution to the problems of metadata authoring and management that will generalize to other data-management environments.

Keywords: biological ontologies; data collection; data curation; datasets as topic; standards.

Figure 1:

The CEDAR ecosystem for metadata management. Communities of biomedical scientists author metadata templates (and template components), which are stored in an online template repository (left panel). Investigators annotate their experimental data by assembling composite templates and by filling in the templates using metadata-acquisition forms to create collections of experimental metadata (center panel). The metadata are both stored in a CEDAR metadata repository (right panel) and exported along with the primary data to archives such as ImmPort, GEO, and the Stanford Digital Repository. Analysis of the CEDAR metadata repository (right panel) will reveal patterns in the metadata that will enable the tools for metadata acquisition (center panel) to use predictive data entry to ease the task of filling out the templates.

Figure 2:

HIPC metadata template. The Human Immunology Project Consortium creates templates such as this one (for annotating the results of multiplex bead array assays) to standardize all its experimental metadata. HIPC templates are providing the initial test of the CEDAR template-management technology.

Figure 3:

Prototype user interface for template selection and instantiation. Here, the end user has selected the “ImmPort Basic Study Design” template, and she has filled in values for the template’s slots for brief title, description, study type, and condition studied. The enumerated value sets for slots such as “study type” are taken from ontologies stored in the NCBO BioPortal repository.