Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt

Britan, Aurore; Cusin, Isabelle; Hinard, Valérie; Mottin, Luc; Pasche, Emilie; Gobeill, Julien; Laval, Valentine Rech de; Gleizes, Anne; Teixeira, Daniel; Michel, Pierre-André; Ruch, Patrick; Gaudet, Pascale

doi:10.1093/database/bay129

Cited by 8 publications

(6 citation statements)

References 46 publications

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“…For example, the annotation of IDP-mediated interactions directly into the IMEx consortium annotation portal would provide a pre-built environment for such an endeavour. Automatic triage and pre-compiling of data based on Europe PMC data would also greatly boost productivity, allowing the community to cope with the increasing amount and complexity of data being published ( Britan et al , 2018). The large number of articles describing the structure and function of IDPs has highlighted the need to exploit text-mining approaches in order to eventually leverage automatic annotation from the literature.…”

Section: Identification Of Community Challengesmentioning

confidence: 99%

An intrinsically disordered proteins community for ELIXIR

et al. 2019

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Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled “An intrinsically disordered protein user community proposal for ELIXIR” held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders.

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Section: Identification Of Community Challengesmentioning

confidence: 99%

An intrinsically disordered proteins community for ELIXIR

et al. 2019

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“… 96 106 Ongoing measurement and stakeholder engagement were noted across industries and types of workflows to identify changes to optimize automation. 56 107 108 …”

Section: Workflow Automation Approaches Across Industriesmentioning

confidence: 99%

Identifying Opportunities for Workflow Automation in Health Care: Lessons Learned from Other Industries

2021

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Background Workflow automation, which involves identifying sequences of tasks that can be streamlined by using technology and modern computing, offers opportunities to address the United States health care system's challenges with quality, safety, and efficiency. Other industries have successfully implemented workflow automation to address these concerns, and lessons learned from those experiences may inform its application in health care. Objective Our aim was to identify and synthesize (1) current approaches in workflow automation across industries, (2) opportunities for applying workflow automation in health care, and (3) considerations for designing and implementing workflow automation that may be relevant to health care. Methods We conducted a targeted review of peer-reviewed and gray literature on automation approaches. We identified relevant databases and terms to conduct the searches across sources and reviewed abstracts to identify 123 relevant articles across 11 disciplines. Results Workflow automation is used across industries such as finance, manufacturing, and travel to increase efficiency, productivity, and quality. We found automation ranged from low to full automation, and this variation was associated with task and technology characteristics. The level of automation is linked to how well a task is defined, whether a task is repetitive, the degree of human intervention and decision-making required, and the sophistication of available technology. We found that identifying automation goals and assessing whether those goals were reached was critical, and ongoing monitoring and improvement would help to ensure successful automation. Conclusion Use of workflow automation in other industries can inform automating health care workflows by considering the critical role of people, process, and technology in design, testing, implementation, use, and ongoing monitoring of automated workflows. Insights gained from other industries will inform an interdisciplinary effort by the Office of the National Coordinator for Health Information Technology to outline priorities for advancing health care workflow automation.

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“…Provenance and evidence types affect trust that a data user may have and influence the decision of incorporating a causal statement in a model. For instance, one may consider a manually curated statement more valuable and trustworthy than an automatically generated one because of the errors that may be associated with computational inference and text-mining extraction of causal interactions ( Britan et al , 2018 ).…”

Section: Rule 3: the Provenance And Evidence Types Of The Annotation Must Be Specifiedmentioning

confidence: 99%

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)

et al. 2020

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Abstract Motivation A large variety of molecular interactions occurs between biomolecular components in cells. When a molecular interaction results in a regulatory effect, exerted by one component onto a downstream component, a so-called ‘causal interaction’ takes place. Causal interactions constitute the building blocks in our understanding of larger regulatory networks in cells. These causal interactions and the biological processes they enable (e.g., gene regulation) need to be described with a careful appreciation of the underlying molecular reactions. A proper description of this information enables archiving, sharing, and reuse by humans and for automated computational processing. Various representations of causal relationships between biological components are currently used in a variety of resources. Results Here, we propose a checklist that accommodates current representations, called the Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). This checklist defines both the required core information, as well as a comprehensive set of other contextual details valuable to the end user and relevant for reusing and reproducing causal molecular interaction information. The MI2CAST checklist can be used as reporting guidelines when annotating and curating causal statements, while fostering uniformity and interoperability of the data across resources. Availability The checklist together with examples is accessible at https://github.com/MI2CAST/MI2CAST Supplementary information Supplementary data are available at Bioinformatics online.

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Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt

Cited by 8 publications

References 46 publications

An intrinsically disordered proteins community for ELIXIR

An intrinsically disordered proteins community for ELIXIR

Identifying Opportunities for Workflow Automation in Health Care: Lessons Learned from Other Industries

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)

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