Are you Matthew Brush?

Claim your profile

Publications (4)4.2 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Background / Purpose: We've developed an ontology to organize information about stem cells in a way that allows logical organization and sharing of iPS cell and related data. The developed platform was used to present information about ~600 iPSC lines along with linked primary cells, biospecimens, and human subjects making the eagle-i platform the largest repository of iPSC information in the world. Finally we developed a draft of an "advanced search" (accessed at nyscf.org/repository) allowing researchers to find stem cells of interest by filtering on desired parameters such as cell type, disease, age of onset, ethnicity, method of induction, and QC performed. Main conclusion: This ongoing project has hit a milestone where we can transform existing information from relation databases into a format that can be published as semantically rich linked open data. This has resulted in an open repository for iPSC information which is accessed through the eagle-i.net front-end.
    12th International Society for Stem Cell Research Annual Meeting 2014; 06/2014
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Scientific reproducibility has been at the forefront of many news stories and there exist numerous initiatives to help address this problem. We posit that a contributor is simply a lack of specificity that is required to enable adequate research reproducibility. In particular, the inability to uniquely identify research resources, such as antibodies and model organisms, makes it difficult or impossible to reproduce experiments even where the science is otherwise sound. In order to better understand the magnitude of this problem, we designed an experiment to ascertain the "identifiability" of research resources in the biomedical literature. We evaluated recent journal articles in the fields of Neuroscience, Developmental Biology, Immunology, Cell and Molecular Biology and General Biology, selected randomly based on a diversity of impact factors for the journals, publishers, and experimental method reporting guidelines. We attempted to uniquely identify model organisms (mouse, rat, zebrafish, worm, fly and yeast), antibodies, knockdown reagents (morpholinos or RNAi), constructs, and cell lines. Specific criteria were developed to determine if a resource was uniquely identifiable, and included examining relevant repositories (such as model organism databases, and the Antibody Registry), as well as vendor sites. The results of this experiment show that 54% of resources are not uniquely identifiable in publications, regardless of domain, journal impact factor, or reporting requirements. For example, in many cases the organism strain in which the experiment was performed or antibody that was used could not be identified. Our results show that identifiability is a serious problem for reproducibility. Based on these results, we provide recommendations to authors, reviewers, journal editors, vendors, and publishers. Scientific efficiency and reproducibility depend upon a research-wide improvement of this substantial problem in science today.
    PeerJ. 01/2013; 1:e148.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Development of biocuration processes and guidelines for new data types or projects is a challenging task. Each project finds its way toward defining annotation standards and ensuring data consistency with varying degrees of planning and different tools to support and/or report on consistency. Further, this process may be data type specific even within the context of a single project. This article describes our experiences with eagle-i, a 2-year pilot project to develop a federated network of data repositories in which unpublished, unshared or otherwise 'invisible' scientific resources could be inventoried and made accessible to the scientific community. During the course of eagle-i development, the main challenges we experienced related to the difficulty of collecting and curating data while the system and the data model were simultaneously built, and a deficiency and diversity of data management strategies in the laboratories from which the source data was obtained. We discuss our approach to biocuration and the importance of improving information management strategies to the research process, specifically with regard to the inventorying and usage of research resources. Finally, we highlight the commonalities and differences between eagle-i and similar efforts with the hope that our lessons learned will assist other biocuration endeavors. DATABASE URL: www.eagle-i.net.
    Database The Journal of Biological Databases and Curation 01/2012; 2012:bar067. · 4.20 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The eagle-­i project has been developing a semantic search portal for biomedical research resources. A unique feature of eagle-­i is that the data collection and search tools are completely driven by ontologies. This has been a source of challenges and opportunities regarding use of biomedical ontologies in real-­world applications. In this paper, we address our approach and lessons learned for balancing practical project requirements for design and implementation of an ontology driven application, with a desire to conform to best practices for biomedical ontology development.