=Paper=
{{Paper
|id=Vol-2180/paper-19
|storemode=property
|title=Using Ontologies to Drive the Creation of High-Quality Metadata in CEDAR
|pdfUrl=https://ceur-ws.org/Vol-2180/paper-19.pdf
|volume=Vol-2180
|authors=Rafael S Gonçalves,Csongor I Nyulas,Marcos Martínez-Romero,Martin J. O'Connor,John Graybeal,Mark A Musen
|dblpUrl=https://dblp.org/rec/conf/semweb/GoncalvesNROGM18
}}
==Using Ontologies to Drive the Creation of High-Quality Metadata in CEDAR==
https://ceur-ws.org/Vol-2180/paper-19.pdf
Using Ontologies to Drive the Creation of High-Quality
Metadata in CEDAR
Rafael S. Gonçalves[0000-0003-1255-0125], Csongor I. Nyulas, Marcos Martínez-Romero,
Martin J. O’Connor, John Graybeal, and Mark A. Musen
Stanford Center for Biomedical Informatics Research
Stanford University, Stanford, CA, USA
rafael.goncalves@stanford.edu
Abstract. The Center for Expanded Data Annotation and Retrieval (CEDAR)
developed a suite of tools¾the CEDAR Workbench¾that allows users to build
metadata templates using ontologies to annotate template fields and to constrain
the options available to metadata authors for specific fields; to fill in those
templates with metadata; to upload data and their metadata to online repositories;
and to perform searches over the metadata stored in CEDAR’s metadata
repository. The CEDAR Workbench is released under a BSD 2-Clause open-
source license, and it is freely available at https://metadatacenter.org.
Keywords: Metadata, metadata authoring, metadata repository.
1 Introduction
We present the CEDAR [1] software to produce high-quality, structured, standards-
based metadata. The software we have developed¾the CEDAR Workbench [2]¾is a
suite of Web-based tools and APIs that offers users the ability to build highly-modular
metadata acquisition forms (templates) that can be annotated with ontology terms, and
whose fields can be constrained using terms or branches of terms from ontologies.
Rather than having a single monolithic template, CEDAR allows users to recursively
construct templates from existing, more granular templates. CEDAR template
designers can share templates with individuals or groups—the metadata authors, who
fill in the metadata templates, validate field entries, and submit the metadata to online
repositories. The metadata produced using CEDAR templates are, by design, adherent
to the FAIR data principles [3]. Our goal is ultimately to provide scientists with a
robust, end-to-end software solution to author and to manage high-quality FAIR
metadata about scientific experiments.
2 The CEDAR Workbench
The CEDAR Workbench is an open-source Web-based platform for the acquisition,
storage, search, and reuse of metadata templates and metadata instances. At the core
of the CEDAR technology lies a lightweight, standards-based model [4] designed to
provide a common format for describing templates and metadata. All CEDAR
resources are represented as JSON-LD documents that conform to our model, which is
specified by a JSON Schema. These resources can be viewed and retrieved as RDF
documents. Fig. 1 shows an overview of CEDAR.
EXPLORE METADATA DESIGN TEMPLATE CREATE METADATA VALIDATE METADATA
Metadata
Validator
Template authors use use
Template authors / Scientists Scientists
(e.g., standards committees)
validate
External Schema
Validator Validator
UPLOAD METADATA
Resource Manager Template Designer Metadata Editor
upload Metadata
use use use Uploader
create create
Intelligent
explore and manage
metadata
Authoring
> 500
biomedical
ontologies
Template Metadata
CEDAR METADATA REPOSITORY
Figure 1. Overview of CEDAR. Users can manage and search for resources; design metadata
templates using ontologies from BioPortal; create metadata with support from intelligent
authoring features; validate metadata; and upload metadata to external repositories.
The following are the main components of the CEDAR Workbench software.
Resource Manager. Template authors and scientists who use the CEDAR
Workbench are initially presented with the Resource Manager tool. The Resource
Manager allows users to create and store resources in the CEDAR Metadata Repository;
to organize templates and metadata into folders; and to search for these resources. From
the Resource Manager, users can define groups composed of their team members for
purposes of collaboration. CEDAR users can share resources (with read or write
permissions) among users, among groups, or with the general community.
Template Designer. Template authors can build metadata templates using the
Template Designer. In the Template Designer, users piece together fields of various
types (e.g., text, checkbox, and multiple choice) to form templates. Possible field
values can be constrained to terms from ontologies using an interactive look-up service
linked to NCBO’s BioPortal [5]. With the BioPortal lookup service (Fig. 2), users can
interactively create new ontology terms (which can be mapped to terms in other
ontologies) and value sets at template design-time for their annotation purposes. The
metadata templates and their fields can be annotated using properties from ontologies.
Metadata Editor. Scientists generate metadata instances by filling in metadata
templates using the Metadata Editor. This tool builds a metadata-acquisition form
interface from template specifications built in the Template Designer. We implemented
a computer-assisted value recommender [6] in the Metadata Editor that provides
context-sensitive suggestions for field values during metadata submission. The value
recommender learns associations between field values in previous metadata entries
using rule mining, and ranks their applicability to specific fields. The goal of the value
recommender is to ease the burden of authoring high-quality metadata. Metadata
generated through CEDAR templates can be submitted to external repositories, such as
the NCBI BioSample [7] and SRA [8] repositories, or the ImmPort repository for
immunology-related datasets [9].
Figure 2. The BioPortal lookup service allows users to search for ontology terms in BioPortal,
browse ontologies, and select terms or branches of terms to constrain the possible options
available when filling-in specific fields in CEDAR metadata templates. It also allows users to
create new terms, and to create value sets made up of existing terms in BioPortal.
The CEDAR Workbench can be used through the Web-based components described
above, or using the CEDAR API¾a collection of REST-based services that provide
comprehensive access to the CEDAR ecosystem. The API allows creating, reading,
updating, and deleting CEDAR resources programmatically. With this API, users can
also export templates or metadata to other repositories or applications. All our software
is distributed and versioned on GitHub, at https://github.com/metadatacenter.
3 Summary
The CEDAR Workbench provides a comprehensive solution for authoring, validating,
searching, and (re)using metadata. The goal behind CEDAR is to significantly improve
the way scientists work with metadata, and the quality and interoperability of the
metadata that they create. We meet this goal by equipping the community with a col-
laborative platform to build standards-based metadata templates that use ontologies as
sources for standard terms, and to author and submit high-quality metadata to online
repositories. CEDAR’s metadata repository gives scientists a means to search for and
to use metadata templates developed by the community, and to build new ones from
scratch or based on existing templates. CEDAR allows its users to submit their
metadata to external repositories, such as NCBI databases. We are working to allow
our users to submit metadata to an increasing number of external repositories.
Acknowledgements
CEDAR is supported by NIAID grant U54 AI117925 through funds provided by the
trans-NIH Big Data to Knowledge (BD2K) initiative. The NCBO BioPortal has been
supported by the NIH Common Fund under grant U54HG004028.
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