John Graybeal

All Publications

• NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation. Journal of biomedical semantics Martínez-Romero, M., Jonquet, C., O'Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. 2017; 8 (1): 21-?

  Abstract

  Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability across disparate datasets. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms.We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a novel recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four different criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data.Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies to use together. It also can be customized to fit the needs of different ontology recommendation scenarios.Ontology Recommender 2.0 suggests relevant ontologies for annotating biomedical text data. It combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability and usefulness. Ontology Recommender 2.0 recommends over 500 biomedical ontologies from the NCBO BioPortal platform, where it is openly available (both via the user interface at http://bioportal.bioontology.org/recommender , and via a Web service API).

  View details for DOI 10.1186/s13326-017-0128-y

  View details for PubMedID 28592275

• CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata BMC BIOINFORMATICS Bukhari, S., Martinez-Romero, M., Connor, M., Egyedi, A. L., Willrett, D., Graybeal, J., Musen, M. A., Cheung, K., Kleinstein, S. H. 2018; 19: 268

  Abstract

  Public biomedical data repositories often provide web-based interfaces to collect experimental metadata. However, these interfaces typically reflect the ad hoc metadata specification practices of the associated repositories, leading to a lack of standardization in the collected metadata. This lack of standardization limits the ability of the source datasets to be broadly discovered, reused, and integrated with other datasets. To increase reuse, discoverability, and reproducibility of the described experiments, datasets should be appropriately annotated by using agreed-upon terms, ideally from ontologies or other controlled term sources.This work presents "CEDAR OnDemand", a browser extension powered by the NCBO (National Center for Biomedical Ontology) BioPortal that enables users to seamlessly enter ontology-based metadata through existing web forms native to individual repositories. CEDAR OnDemand analyzes the web page contents to identify the text input fields and associate them with relevant ontologies which are recommended automatically based upon input fields' labels (using the NCBO ontology recommender) and a pre-defined list of ontologies. These field-specific ontologies are used for controlling metadata entry. CEDAR OnDemand works for any web form designed in the HTML format. We demonstrate how CEDAR OnDemand works through the NCBI (National Center for Biotechnology Information) BioSample web-based metadata entry.CEDAR OnDemand helps lower the barrier of incorporating ontologies into standardized metadata entry for public data repositories. CEDAR OnDemand is available freely on the Google Chrome store https://chrome.google.com/webstore/search/CEDAROnDemand.

  View details for DOI 10.1186/s12859-018-2247-6

  View details for Web of Science ID 000438972700004

  View details for PubMedID 30012108

  View details for PubMedCentralID PMC6048706

• AgroPortal: A vocabulary and ontology repository for agronomy COMPUTERS AND ELECTRONICS IN AGRICULTURE Jonquet, C., Toulet, A., Arnaud, E., Aubin, S., Yeumo, E., Emonet, V., Graybeal, J., Laporte, M., Musen, M. A., Pesce, V., Larmande, P. 2018; 144: 126–43

  View details for DOI 10.1016/j.compag.2017.10.012

  View details for Web of Science ID 000425072400014

• Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. AMIA ... Annual Symposium proceedings. AMIA Symposium Martinez-Romero, M., O'Connor, M. J., Shankar, R. D., Panahiazar, M., Willrett, D., Egyedi, A. L., Gevaert, O., Graybeal, J., Musen, M. A. 2017; 2017: 1272–81

  Abstract

  In biomedicine, high-quality metadata are crucial for finding experimental datasets, for understanding how experiments were performed, and for reproducing those experiments. Despite the recent focus on metadata, the quality of metadata available in public repositories continues to be extremely poor. A key difficulty is that the typical metadata acquisition process is time-consuming and error prone, with weak or nonexistent support for linking metadata to ontologies. There is a pressing need for methods and tools to speed up the metadata acquisition process and to increase the quality of metadata that are entered. In this paper, we describe a methodology and set of associated tools that we developed to address this challenge. A core component of this approach is a value recommendation framework that uses analysis of previously entered metadata and ontology-based metadata specifications to help users rapidly and accurately enter their metadata. We performed an initial evaluation of this approach using metadata from a public metadata repository.

  View details for PubMedID 29854196

• Issues in data management in observing systems and lessons learned OCEANS 2006, VOLS 1-4 Gornes, K. J., Graybeal, J., O'Reilly, T. C. 2006: 1187-1192

  View details for Web of Science ID 000246002100217

• Toward an ocean observing system of systems OCEANS 2006, VOLS 1-4 Bermudez, L., Bogden, P., Bridger, E., Creager, G., Forrest, D., Graybeal, J. 2006: 904-?

  View details for Web of Science ID 000246002100163

• MBARI's SSDS: Operational, extensible data management for ocean observatories 3rd International Workshop on Scientific Use Submarine Cables and Related Technologies Graybeal, J., Gomes, K., McCann, M., Schlining, B., Schramm, R., Wilkin, D. IEEE. 2003: 288–292

  View details for Web of Science ID 000186634900063