TUOMS PRESS Office
12/8/25
TUOMS PRESS AI Guideline- Nov 25
Guidelines for the Utilization of Artificial Intelligence Tools in TUOMS Press Journals
Policy on using artificial intelligence (AI) tools at TUOMS PRESS for authors, editors, and reviewers
The use of artificial intelligence (AI) tools in research and publishing has become inevitable. Accordingly, Tabriz University of Medical Sciences (TUOMS PRESS), as an academic publisher, in alignment with the emergence of this technology, has since 2023 established and articulated policies regarding the use of AI tools and the requirements for transparency and disclosure in scholarly articles.
In the update scheduled for November 2025, TUOMS PRESS, drawing upon the STM Recommendations for a Classification of AI Use in Academic Manuscript Preparation, has categorized the activities that may be undertaken with AI in the preparation of manuscripts. Within this framework, TUOMS PRESS specifies permissible and non-permissible activities for authors, editors, and reviewers.
In table 1, AI-related activities are classified into 9 groups. For each group, the table provides:
- A description of the use of AI tools in manuscript preparation,
- A definition of the activity,
- Examples of the activity,
- Exclusions (activities not encompassed), and
- An indication of whether the activity is acceptable/permissible under TUOMS PRESS policies.
Table 1. Nine Recommended Classifications of AI Activities from STM Recommendations for a Classification of AI Use in Academic Manuscript Preparation
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1
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Refinement, correction, editing or formatting the manuscript to improve clarity of language (**)
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Machine tools were used to suggest language improvements within the manuscript
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Using spell checkers, grammar checkers, and similar tools (such as Microsoft 365’s inbuilt editing tools) to refine text written primarily by humans
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Using AI tools to generate text from prompts or generate summaries of text; using AI tools to analyze or summarize textual documents as part of the research process
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Permissible ✔
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2
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Writing or drafting manuscript content
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AI tools were used to generate part or all of the manuscript text
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Using AI tools to generate text from prompts; using AI tools to significantly expand on or rewrite text; using AI tools to generate machine summaries of text (e.g. to summarize arguments made in another publication)
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Use of simple spelling and grammar checkers; analyzing or summarizing textual documents as part of the research process
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Permissible ✔
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3
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Translation of manuscript text for the purpose of publishing
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AI tools were used to assist translation of an author’s original work into a secondary language for inclusion in the manuscript
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Using AI tools such as Google Translate or ChatGPT to assist with translating a manuscript draft
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Translation of materials (such as source documents) as part of the research process, unrelated to manuscript preparation
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Permissible ✔
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4
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Refining or formatting of data reported in the manuscript
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AI tools were used to assist with refinement of the presentation of data reported in the manuscript
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Using AI tools to improve clarity or readability (e.g. on the level of language) or format research data submitted as part of the manuscript or its associated materials (e.g. in supplementary materials or appropriate repositories)
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Using AI tools to visualize data sets (activity 6) or data manipulation; any generation, correcting, or editing of data used as part of the research process
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Permissible ✔
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5
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Generation, refinement, correction, editing or formatting of images, diagrams or other figures for illustrative purposes only
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AI tools were used to generate images, diagrams, or other figures in the manuscript for illustrative or aesthetic purposes only
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Using AI tools to create an image of e.g. people farming in an ancient society – the sort of image that might otherwise be created by a human artist
as an illustration
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Visualization of actual data or research outputs, editing of visualizations of actual data or results, presentation of generated images as research outputs in themselves or as representing research outputs
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Permissible ✔
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6
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Generation, refinement, correction, editing or formatting of visualizations of research data or results
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AI tools were used to visualize or refine visualizations of research data/results in the manuscript
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Using AI tools to generate graphs, tables, or other visualizations of research datasets
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Use of traditional statistical software (such as STATA, SAS, and R) to visualize data; generation of images or other content without any basis in real research data/outputs
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Not Permissible
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7
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Refinement or formatting of code reported in the submitted manuscript
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AI tools were used to assist with refinement of the presentation of code used in the research process and reported in the manuscript
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Using AI tools to improve the readability and clarity of code submitted as part of the manuscript or any associated materials (e.g. in supplementary materials or appropriate repositories), without altering its functionality
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Using AI tools to generate new code for use in research processes, or alter the functionality of code used in research processes before manuscript submission
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Conditional upon:
- Preservation of logic and results
- Final review and approval by the researcher
- Disclosure in the Methods section or Appendix
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8
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Assisting with gathering references
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AI tools were used to suggest references to include in the manuscript’s reference list
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Using AI tools to find and identify articles that are likely to be related to the research reported in the manuscript
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Using automated tools (such as BibTeX) to generate formatted citations for references identified by human authors; using AI tools to generate plausible-sounding references that do not exist; using AI tools to identify publications that may be useful to the research process
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Not Permissible
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9
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Presentation of any kind of content generated by AI tools as though it were original research data/results from non- machine sources (***)
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AI tools were used to create data, text, images, graphs, spectra, or other content that is presented as though it were original research data/results collected or analyzed from other, non-machine sources
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Any content generated wholesale by AI tools without any basis in original research data/outputs, presented as though it is based on original data/results
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Using AI tools to visualize original research data/results (activity 6); carrying out research on the outputs of generative AI (in which case outputs generated by the AI being studied can be considered research data)
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Not Permissible
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(*) We reiterate that use of AI in other stages of research processes is outside the scope of this classification. This classification considers only activities that use AI tools to assist with the preparation of manuscripts.
(**) 2023 STM Guidelines recommend that disclosure is not necessary for this use of automated tools.
(***) 2023 STM Guidelines recommend prohibiting this use of AI tools.
Reference: STM Recommendations for a Classification of AI Use in Academic Manuscript Preparation. SEPTEMBER 2025
Disclosure and declaration of AI use
In developing its policies for authors, editors, and reviewers, TUOMS PRESS has drawn upon Wiley’s comprehensive guidelines. We express our gratitude to Wiley for its efforts in clarifying these policies and providing guidance on their implementation.
Authors
TUOMS PRESS expects authors to provide transparency regarding the use of artificial intelligence (AI) tools in their manuscripts, in accordance with the classification outlined in the Table 1. Authors are required to provide sufficient information about the use of AI tools at the time of manuscript submission to the journal. Should editors or reviewers require additional clarification, they may contact the authors to request further details. Authors should disclose AI use in:
Acknowledgments: when AI assists with manuscript drafting, editing, translation, or formatting.
Methods: when AI is used to assist with your research methodology, data collection or analysis, or literature review processes.
How should author disclose the use of AI for drafting and editing assistance in Acknowledgments?
TUOMS PRESS considers the disclosure of information regarding the use of artificial intelligence (AI) tools to be mandatory. Such disclosure ensures transparency in the evaluation of manuscripts and guarantees the accountability of authors for the content.
Authors are required to provide sufficient information for evaluation at the time of manuscript submission. The information that must be included in the Acknowledgment section is as follows:
- AI Technology name and version
- Date/year of use
- The AI Technology's role in your work (language translation, substantial editing or text generation, organization of document or argument flow, etc.)
- Specific sections where the AI was used in the document
- The author’s role in directing or reviewing the work of the AI Technology
Authors may refer to the sample paragraphs provided below to disclose and clarify the use of artificial intelligence (AI) tools in their manuscripts. It must be emphasized that the type of activity performed, and the role of the author should be stated explicitly and comprehensively.
Sample Examples:
Example 1:
“The authors acknowledge the use of AI Technology name and version (accessed Date/year of use) to assist with grammar correction, sentence structure adjustments, and translation of selected phrases. All AI-assisted text was reviewed and revised by the authors to ensure accuracy and clarity of meaning.”
Example 2:
“The authors acknowledge the use of Claude 3.5 Sonnet (accessed July 2025) to support creation of the abstract and to suggest reorganization of Discussion section for clarity and flow. All AI-generated suggestions were reviewed, revised, and approved by the authors, who take full responsibility for the accuracy and integrity of the work.”
How should author disclose the use of AI in the research methodology?
TUOMS PRESS requires disclosure whenever artificial intelligence (AI) is utilized in research methodology, including study design, data collection, literature review, code development, and data analysis. The details provided by authors must correspond to the significance of the role played by AI technology in the research. The following common scenarios illustrate instances in which the use of AI must be disclosed. These examples are illustrative rather than exhaustive.
a. Study design and data collection
- Study design: AI generates survey questions based on research objectives
- Image processing: AI processes medical images or microscopy data for analysis
- Protocol development: AI develops or expands experimental protocols by analyzing existing methods
- Infrastructure support: AI creates databases, patient registries, or study recruitment platforms
- Organization: AI organizes experimental protocols in notebooks or databases
- Troubleshooting: AI helps troubleshoot software errors
- Learning support: AI explains research methodology concepts for learning purposes
- Formatting: AI helps format research materials or templates
b. Literature review
- Agentic search: AI independently generates or executes search strategies (designing full search strings, running database queries, or pre-filtering results) for a literature review or systematic review
- Screening and selection: AI applies inclusion/exclusion criteria to filter or select literature for systematic reviews or meta-analyses
- Synthesis (used in manuscript): AI clusters studies, identifies themes, or generates comparative insights across multiple papers when included in the manuscript
- Citation extraction: AI pulls references or metadata from papers or databases
- Search support: AI assists with keyword or phrase-based searching to suggest relevant resources; the author reviews and decides on final inclusion
- Reference management: AI organizes citations and references
- Reference formatting: AI assists with citation style formatting
- Literature summarization: AI generates summaries of papers to support author understanding of dense or lengthy content
c. Code development++
- Programming: AI writes analysis scripts or algorithms
- Software generation: AI develops custom research software or applications
- Data pipeline design: AI builds automated workflows to clean, process, and integrate datasets
- Modeling: AI develops or adapts computational or statistical models for research analysis
- Debugging: AI checks syntax errors or suggestions fixes
- Code style: AI formats code structure/style
- Documentation: AI generates comments or documentation
- Suggestions: AI recommends standard library functions or common approaches
d. Data and analysis
- Qualitative analysis: AI codes interview or textual data; identifies patterns or themes in large datasets
- Quantitative/statistical analysis: AI performs statistical analyses, flags outliers that alter conclusions, interprets results of tests
- Exploratory or advanced analyses: AI generates interpretations of results, highlights relationships or trends in data, or synthesizes findings across datasets
Authors must provide sufficient information for evaluation at the time of submission in the Methods section. The information that needs to be included is as follows:
- AI Technology name and version
- Date/year of use
- The AI Technology’s role in your work (image processing, code development, statistical analysis, etc.)
- The author’s role in directing or reviewing the work of the AI Technology
- For sensitive, proprietary, or human subject data describe how privacy and compliance requirements were maintained
Examples of how to provide explanatory statements for transparency are as follows:
Example 1:
"Literature screening was assisted by AI Technology name and version (accessed Date/year of use) to categorize 500+ abstracts by predefined relevance criteria. AI-assisted outputs were reviewed and validated by the authors, who confirmed the final inclusion and exclusion decisions.”
Example 2:
“Analysis scripts for regression models were generated using Claude 3.5 Sonnet (accessed June 2025). All AI-generated code was reviewed, tested, and revised by the authors, who confirmed accuracy and reproducibility of results.”
Example 3:
“AI-assisted analysis was conducted using LLaMA 3 (accessed May 2025) to extract themes from qualitative interview data. All AI-generated outputs were reviewed and validated by the authors, who confirmed the accuracy of the interpretations. Prompts and system settings are included in Supplementary File S2 for reproducibility. All data were de-identified in compliance with institutional privacy standards prior to analysis.”
Note: If artificial intelligence (AI) plays a significant role in the analysis or methodology of the manuscript, authors may be requested to provide supplementary documentation to the journal in order to support reproducibility and enhance transparency. Such supplementary documentation may include:
- Prompts or parameters used
- AI settings or configurations
- Code repository
- Data protection approach
- Compliance with institutional requirements
Reviewers
In order to safeguard the confidentiality of manuscripts submitted to its journals, TUOMS PRESS does not permit reviewers to use artificial intelligence (AI) tools in the peer review process. Reviewers and editors are therefore not allowed to upload or copy the text of manuscripts under review into generative AI systems.
The circumstances in which reviewers may employ generative AI in preparing their review reports include:
- Use AI to organize your thoughts and prioritize feedback
- Use AI to improve review clarity and tone or translate your review
- Ask AI general questions about research methods or statistical approaches without referencing manuscript specifics
If artificial intelligence (AI) tools are used to assist in drafting the review report, the following information must be provided to the editor:
- AI Technology's name and version
- Date/year of use
- AI Technology's role in drafting or editing assistance
- The author’s role in directing or reviewing the work of the AI Technology
Example:
"GPT-5 was used to prioritize and polish review feedback. All original review feedback was provided by the peer reviewer, and all AI-generated content was reviewed, revised, and approved by the peer reviewer prior to sending this review.”