EXACT2: the semantics of biomedical protocols

© 2014 Soldatova et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.This article has been made available through the Brunel Open Access Publishing Fund.Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously ‘unseen’ (not used for the construction of EXACT2) protocols. Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.This work has been partially funded by the Brunel University BRIEF award and a grant from Occams Resources

D6.6: Report on Short Term Missions (STMs) : year 2 (2019)

Short Term Missions (STMs) provide small travel grants with the aim of sharing scientific expertise, methodologies, equipment and facilities to harmonise the existing approaches and methodologies within the large OHEJP network, and to drive the research forward in a collaborative and non-duplicative fashion to strengthen both the scientific capacity within the OHEJP and also future prevention, preparedness, detection and response of the EU to foodborne and other emerging threats across human-animal-environmental sectors. Read the report full report here of the first round of missions that were co-funded and took place in 2019

D6.9 - Report of the second CPD module in One Health : education and training

The one-week module centred around the use of innovative open-source software solutions supporting risk assessment, zoonotic outbreak investigations and data interoperability. The objective of this training module was to introduce new tools and technologies for One Health researchers and professionals. Specifically, solutions that support foodborne disease outbreak investigations, efficient surveillance data integration as well as the re-use of risk assessment models were introduced. The solutions presented have the potential to support the whole One Health community including national and international risk assessment agencies, risk managers and academic institutions.The virtual training was delivered by senior research scientists from BfR and partners from our consortium, including SVA, DTU Food, ANSES, RKI and NVI and stakeholders, EFSA with an extensive track record in providing training for research scientists from different research domains.Over 50 participants – from early-career researchers and PhD students, up to senior scientists – from 15 European countries attended the workshop. The event encouraged knowledge sharing and even allowed participants to present their digital innovation tools, which can be applied to scenarios of food safety, public health and animal health.Scientists of the One Health EJP Joint Research and Joint Integrative Projects, ORION, COHESIVE and RaDAR also shared their knowledge and lessons learned from their projects.The CPD module provided joint plenary presentation sessions, moderated interactive workshops with practical exercises, as well as an e-learning platform, that can still be used by participants to further improve their knowledge. For this, dedicated e-learning courses on the software FoodChain-Lab, the RAKIP and RADAR model repositories and on resources promoting the adoption of the Linked Open Data concept in One Health were developed. The e-learning platform was also used to measure knowledge gains and collect feedback from the workshop participants.The online workshop received approved accreditation by the Academy of Veterinary Continuing Education (ATF), therefore participants from across Europe who attended and participated in the entire module, received 22 ATF hours, and could convert these to CE credits in their respective country

D6.4 Report n°1 on the ’One Health’ Summer School (Y2) : WP6: education and training

The One Health concept recognises that human health is tightly connected to animals and the environment. Multiple reports have highlighted the need for ‘One Health’ interventions towards the delivery of better health outcomes across each of the health domains. In other words, One Health actions must contribute value over and above the status-quo traditionally characterised by isolated or domain-specific approaches. However, One Health operationalisation, or the identification of concrete actions to implement the One Health concept, remains a challenge. The mechanisms to support a value-driven and efficient One Health operationalisation was at the centre of our summer school in 2019. This event was hosted and organised by the University of Surrey from 19th-30th August 2019 hosting 20 delegates from across the globe