P. Stavropoulos 
Uptake in medical practice
History
| Version | Revision date | Revision | Author |
|---|---|---|---|
| 1.2 | 2024-04-24 | Review | Thomas Klebel |
| 1.1 | 2024-03-29 | Review | Tommaso Venturini |
| 1.0 | 2024-03-22 | First draft | Petros Stavropoulos |
Description
This indicator aims to capture the extent to which Open Science (OS) inputs such as code, data, and OA publications are integrated into medical practice, as evidenced by their mentions or references in medical guidelines and clinical trials.
A clinical trial is a research study that tests the safety and effectiveness of new medical interventions through structured phases involving participants who receive either the treatment or a placebo. In contrast, medical guidelines are comprehensive recommendations for healthcare providers, developed from a thorough review of existing evidence, including clinical trials, to standardize and improve patient care. While clinical trials generate new data about specific interventions, medical guidelines synthesize this data to offer evidence-based advice on best practices in clinical settings.
This indicator assesses the impact of OS inputs on medical guidelines, reflecting how scientific advancements and tools are translated into practical applications in healthcare. It serves as a measure of the practical adoption of open science contributions in the medical field, offering insights into how research outputs influence clinical guidelines and patient care.
Metrics
Number / Percentage of Medical Guidelines / Clinical Trials Referencing OS Inputs
This metric represents the proportion of medical guidelines or clinical trials that include references to OA publications, datasets, or software. It operationalizes the indicator by providing a quantifiable measure of how often they incorporate or acknowledge OS inputs. This metric is beneficial as it directly relates to the practical application of scientific research in clinical settings, demonstrating the real-world impact of open science.
However, a limitation is that it may not capture the quality or significance of the referenced OS inputs, which could be assessed by a more qualitative close reading of medical guidelines to examine the specific use they make of OS inputs. It also differs from other potential metrics that might focus on the impact of specific types of OS inputs (e.g., datasets vs. publications).
Measurement.
Measuring this metric involves a systematic approach to searching and analysing medical guidelines and clinical trials for mentions of OA publications, datasets, or software. This process, while straightforward in theory, is subject to several potential challenges and limitations.
Firstly, the variation in referencing styles across different guidelines can make it difficult to accurately identify all relevant references. Additionally, the coverage of medical guidelines and clinical trials in available databases may not be comprehensive, leading to potential gaps in the data collected.
Methodology:
Step 1: Database Selection. Choose databases that extensively indexes medical guidelines, with PubMed being the primary source due to its wide coverage of biomedical literature.
Step 2: Search Strategy Development. Develop a search strategy with terms (or filters in the case of PubMed) related to medical guidelines and optionally combine them with keywords identifying datasets, or software. This strategy should be tailored to capture the broadest possible range of relevant references while minimizing irrelevant results.
Step 3: Automated Searching. Utilize automated tools or scripts, where available, to search the selected databases according to the developed strategy. This may involve using APIs provided by the databases to efficiently process large volumes of data.
Step 4: Data Extraction. Extract data on the references identified in the search results, paying particular attention to mentions of OS inputs (OA publications, datasets, software). The publications can be searched in OpenAIRE Graph to find their best access rights and determine whether they are OA. The datasets and software in the medical guidelines can be extracted using the SciNoBo Research Artifact Analysis (RAA) Tool. This step may require manual review to ensure accuracy and relevance of the data extracted.
Step 5: Analysis. Analyze the extracted data to determine the percentage of medical guidelines referencing OS inputs. This analysis will likely involve categorizing guidelines according to the type of OS inputs referenced and calculating the proportion of guidelines in each category.
Step 6: Close reading. If the size of the corpus and the available research resources allow it, closely read all the mentions to OS input and assess the importance that OS resources play in each medical treatment or practice to which they contribute.
Existing datasources:
PubMed
PubMed is a free search engine primarily accessing the MEDLINE database, which contains references and abstracts on life sciences and biomedical topics provided by the United States National Library of Medicine. It is one of the most comprehensive resources for accessing biomedical literature, including research articles, reviews, and importantly for this metric, medical and clinical guidelines.
A limitation of using PubMed for this metric is its potential incomplete coverage of all medical guidelines, especially those not indexed in MEDLINE. Additionally, the specificity of search queries might not always capture all relevant documents, particularly if the terminology used in guidelines varies.
This metric can be calculated by using PubMed’s search functionality to identify guidelines that reference OA publications, datasets, or software. Results can be further refined by manual screening or automated filtering based on keywords related to OS inputs.
In steps:
- Search PubMed for medical guidelines and clinical trials mentioning OA resources using specific keywords and filters (e.g., “medical guidelines”, “clinical trials”, “practice guidelines”, “recommendations”).
- Extract the data from the search results, focusing on references to OA publications, datasets, or software. For the publications, the unique identifiers (PMIDs, DOIs) should be collected so that they can be searched in the OpenAIRE Research Graph.
ClinicalTrials.gov
ClinicalTrials.gov is a database of privately and publicly funded clinical studies conducted around the world. It offers information on the objectives, design, methodology, and status of clinical trials. For the metric at hand, it can provide data on new medical treatments and drugs being developed with Open Science resources by detailing the studies’ aims, methodologies, and use of open data or collaborative frameworks.
To utilize ClinicalTrials.gov for the calculation of the metric:
- Identify clinical trials mentioning OA resources using relevant keywords.
- Collect details on the use of OA publications, datasets, or software.
- Calculate the proportion of trials referencing OS inputs.
- Verify OA status using the OpenAIRE Research Graph.
- Manually validate data for accuracy.
OpenAIRE Research Graph
The OpenAIRE Research Graph is a comprehensive open access database that aggregates metadata on publications, research data, and project information across various disciplines. It includes details on open access publications and datasets, making it a valuable resource for tracking the output of academic-industry collaborations and their adherence to open science principles.
Use the OpenAIRE Research Graph to identify which of the publications cited by medical guidelines are open access. This involves:
- Extracting publication references from identified medical guidelines in PubMed.
- Querying the OpenAIRE Research Graph to determine which cited publications are open access.
Existing methodologies
SciNoBo Research Artifact Analysis (RAA) Tool
This is an automated tool (Stavropoulos et al., 2023), leveraging Deep Learning and Natural Language Processing techniques to identify research artifacts (datasets, software) mentioned in the scientific text and extract metadata associated with them, such as name, version, license, etc. This tool can also classify whether the dataset has been reused or created by the authors of the scientific text.
To measure the proposed metric, the tool can be used to identify the reused and created OS inputs in the patents text or the OA publication texts that the patents cite.
One limitation of this methodology is that it may not capture all instances of research artifacts if they are not explicitly mentioned in the scientific text. Additionally, the machine learning algorithms used by the tool may not always accurately classify whether a research artifact has been reused or created, and may require manual validation.
References
Stavropoulos, P., Lyris, I., Manola, N., Grypari, I., & Papageorgiou, H. (2023). Empowering Knowledge Discovery from Scientific Literature: A novel approach to Research Artifact Analysis. In L. Tan, D. Milajevs, G. Chauhan, J. Gwinnup, & E. Rippeth (Eds.), Proceedings of the 3rd Workshop for Natural Language Processing Open Source Software (NLP-OSS 2023) (pp. 37–53). Association for Computational Linguistics. https://doi.org/10.18653/v1/2023.nlposs-1.5
Reuse
Citation
@online{apartis2023,
author = {Apartis, S. and Catalano, G. and Consiglio, G. and Costas,
R. and Delugas, E. and Dulong de Rosnay, M. and Grypari, I. and
Karasz, I. and Klebel, Thomas and Kormann, E. and Manola, N. and
Papageorgiou, H. and Seminaroti, E. and Stavropoulos, P. and Stoy,
L. and Traag, V.A. and van Leeuwen, T. and Venturini, T. and
Vignetti, S. and Waltman, L. and Willemse, T.},
title = {PathOS - {D2.1} - {D2.2} - {Open} {Science} {Indicator}
{Handbook}},
date = {2023},
url = {https://handbook.pathos-project.eu/indicator_templates/quarto/3_societal_impact/uptake_in_medical_practice.html},
doi = {10.5281/zenodo.8305626},
langid = {en}
}