From the journal Digital Discovery Peer review history

26-Jan-2024

Dear Dr Lee:

Manuscript ID: DD-ART-12-2023-000243
TITLE: 2DMat.ChemDX.org: Experimental data platform for 2D materials from synthesis to physical properties

Thank you for your submission to Digital Discovery, published by the Royal Society of Chemistry. I sent your manuscript to reviewers and I have now received their reports which are copied below.

After careful evaluation of your manuscript and the reviewers’ reports, I will be pleased to accept your manuscript for publication after revisions.

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Linda Hung
Associate Editor
Digital Discovery
Royal Society of Chemistry

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Reviewer 1

Yang et al. present a well-structured article introducing the 2DMat.ChemDX.org platform, a modern and user-friendly resource for experimental data and analysis of 2D materials. While the platform appears to have undergone extensive internal testing, there are several areas that could benefit from improvements to enhance its utility for public access:
1) The dataset names, such as UOS and POSTECH, might not be immediately clear to users without prior knowledge of the related experiments.
2) Certain fields in the Web User Interface, such as notes and upload sections, still contain Korean characters.
3) It is not clear how the integration and accessibility of specific toolkits, such as those for RHEED fitting and Raman super-resolution are achieved within the webUI

Some additional notes:
1) The methodology for screening and uploading raw data should be detailed. For example, the authors should state how the fields with NaN values in some entries (e.g. 2D-POSTECH00264) are handled through the data cleaning pipelines
2) There appears to be inconsistency in how materials are categorized in the two datasets. For example, '1 layer 2D materials' are named differently in the POS and POSTECH datasets (e.g., MoS2-1L vs. WS2 single layer).
3) A detailed description of the web application's infrastructure, including backend and frontend components, and the integration of Machine Learning models, would strength the current manuscript.
4) While not mandatory, it would be helpful for the authors to disclose the availability and licensing terms of the web dataset's source code.

Reviewer 2

The manuscript entitled "2DMat.ChemDX.org: Experimental data platform for 2D materials from synthesis to physical properties" presents their recent development and launching of an online database and data analysis tools on 2D material synthesis and physical property characterization. In the manuscript, the authors summarized the components of the platform, the types of data, the data structure, as well as a set of data analysis tools available to the users. As the authors stated (which I agree), a database is missing for the experimental data on 2D materials. If the platform is successful, it will benefit researchers working in this field significantly. My only minor concern is that at the current stage, the data amount and the types of data included in the database is still limited. The authors may need to think about how to encourage more researchers throughout the world to contribute to this database and to use this platform. Other than that the manuscript is well written and the key message is well delivered.

Reviewer 3

The paper presents an online data platform for storing and presenting experimental data on 2D materials. I warmly welcome such an initiative as it not only supports research in 2D materials in general, but also underpins the standardisation, reproducibility, comparison and sharing of experimental data sets. A number of computational databases already exist, but there are no experimental databases (to the best of my knowledge) available. Unfortunately, I am not really able to judge whether the specific implementation of the database is the right one, i.e. is the data presented in the most useful way?, is the meta data and description of the samples/measurements sufficient and relevant?, etc. This should be judged by someone more into the details of the experimental data types presented. In the end the success of a data source like the present depends on the implementation, that is selection and presentation of data, quality assurance, curation of data, etc. I did play a bit around on the website and I did not find it too convincing (some data fields were missing and generation of images was slow). However, I suppose this should be seen as a first step. I could suggest that the developers insert links to the relevant materials in computational databases to make it easier to compare experimental and theoretical data. In particular, the C2DB database has many of the same/similar properties available for the same set materials, e.g. Raman spectra and optical absorption spectra for all the TMDs.

We thank the reviewers for their constructive comments (paraphrased in italics below) and separately address each of them below.

Referee: 1
Comments to the Author
Yang et al. present a well-structured article introducing the 2DMat.ChemDX.org platform, a modern and user-friendly resource for experimental data and analysis of 2D materials. While the platform appears to have undergone extensive internal testing, there are several areas that could benefit from improvements to enhance its utility for public access:
1) The dataset names, such as UOS and POSTECH, might not be immediately clear to users without prior knowledge of the related experiments.

We appreciate the reviewer’s comment on the unclear dataset names. We have added brief introductions to the UOS and POSTECH groups on the platform's main page. Additionally, to enable more intuitive access to each database, we have consolidated access under a DATA tab and modified the UI to allow the selection of UOS and POSTECH as subgroups.

2) Certain fields in the Web User Interface, such as notes and upload sections, still contain Korean characters.

We have updated all Korean text in the UI, but notes within the data remain unchanged. These notes, written by users uploading the data to add additional information, cannot be modified to preserve the originality and integrity of the already uploaded data. However, we will provide sufficient guidance to ensure that notes in future data updates are written in English.

3) It is not clear how the integration and accessibility of specific toolkits, such as those for RHEED fitting and Raman super-resolution are achieved within the webUI

Our ML toolkits are designed for processing images and videos, thus requiring extensive computing resources and could strain the server. To mitigate this, we are sharing the source code and examples on GitHub, enabling users to conveniently use the model independently on their workstations. This update is detailed on the toolkit page and in the main text (line 227 of page 10, highlighted by yellow).

Some additional notes:
1) The methodology for screening and uploading raw data should be detailed. For example, the authors should state how the fields with NaN values in some entries (e.g. 2D-POSTECH00264) are handled through the data cleaning pipelines.

To ensure data integrity, we upload raw data without any post-processing, resulting in fields without records being marked as NaN. This approach maintains the originality and integrity of the data while minimizing human error during data extraction. Our parsing modules are designed to check only the validity of parameters necessary for visualization through the web UI, not to alter or assess the data's intrinsic validity. However, recognizing that the presence of NaN values can cause confusion for users, we have updated the platform to display empty fields instead of NaN. This modification enhances clarity without compromising data integrity. These updates and methodologies are detailed in the main text (line 141 of page 6, highlighted by yellow).

2) There appears to be inconsistency in how materials are categorized in the two datasets. For example, '1 layer 2D materials' are named differently in the POS and POSTECH datasets (e.g., MoS2-1L vs. WS2 single layer).

The observed inconsistency in material categorization between the UOS and POSTECH datasets arises because each database was developed independently, leading to variations in naming conventions. We have now standardized the naming of materials, such as '1 layer 2D materials,' to a unified format using "1ML" or "2ML" to address this issue. We plan to update the platform to ensure consistency across the entire database, reflecting these changes.

3) A detailed description of the web application's infrastructure, including backend and frontend components, and the integration of Machine Learning models, would strength the current manuscript.

A detailed description of our platform's infrastructure, including both backend and frontend components as well as the integration of Machine Learning models, has been provided in the manuscript. This includes information on our server operations on CentOS 7 hosted on the Naver Cloud Platform for public institutions, with Gabia providing hosting services. Our comprehensive backup policy, development environment using the Laravel library, data storage solutions with MariaDB 10.5 and MongoDB 3.6, and the use of Vue2 and Vuetify2 frameworks for the web UI, alongside Poltly.js for interactive graph visualization, are all outlined (line 99 of page 5, highlighted by yellow).

4) While not mandatory, it would be helpful for the authors to disclose the availability and licensing terms of the web dataset's source code.

We have specified the CC-BY 4.0 license for the availability and licensing terms of the web dataset's source code, both at the bottom of the platform page and in the Data Availability Statement of the manuscript.


Referee: 2
Comments to the Author
The manuscript entitled "2DMat.ChemDX.org: Experimental data platform for 2D materials from synthesis to physical properties" presents their recent development and launching of an online database and data analysis tools on 2D material synthesis and physical property characterization. In the manuscript, the authors summarized the components of the platform, the types of data, the data structure, as well as a set of data analysis tools available to the users. As the authors stated (which I agree), a database is missing for the experimental data on 2D materials. If the platform is successful, it will benefit researchers working in this field significantly. My only minor concern is that at the current stage, the data amount and the types of data included in the database is still limited. The authors may need to think about how to encourage more researchers throughout the world to contribute to this database and to use this platform. Other than that the manuscript is well written and the key message is well delivered.

Acknowledging the constructive feedback, we are deeply committed to enhancing the scope and utility of our platform to better serve the 2D materials science community. Currently focusing on RHEED and PL/Raman data, we acknowledge data variety and volume limitations. However, our platform is fundamentally designed for scalability and adaptability, enabling us to seamlessly integrate additional data types upon request from interested research groups. The development of straightforward parsers for analyzing raw data across different data types like RHEED, PL, and Raman demonstrates our system's capability for easy application to new datasets. We are dedicated to continuous expansion and support, aiming to inclusively cater to the evolving needs of this dynamic research field. This commitment is detailed in the manuscript (line 297 of page 13, highlighted by yellow).


Referee: 3
Comments to the Author
The paper presents an online data platform for storing and presenting experimental data on 2D materials. I warmly welcome such an initiative as it not only supports research in 2D materials in general, but also underpins the standardisation, reproducibility, comparison and sharing of experimental data sets. A number of computational databases already exist, but there are no experimental databases (to the best of my knowledge) available. Unfortunately, I am not really able to judge whether the specific implementation of the database is the right one, i.e. is the data presented in the most useful way?, is the meta data and description of the samples/measurements sufficient and relevant?, etc. This should be judged by someone more into the details of the experimental data types presented. In the end the success of a data source like the present depends on the implementation, that is selection and presentation of data, quality assurance, curation of data, etc. I did play a bit around on the website and I did not find it too convincing (some data fields were missing and generation of images was slow). However, I suppose this should be seen as a first step. I could suggest that the developers insert links to the relevant materials in computational databases to make it easier to compare experimental and theoretical data. In particular, the C2DB database has many of the same/similar properties available for the same set materials, e.g. Raman spectra and optical absorption spectra for all the TMDs.

We appreciate the reviewer’s feedback on the 2D materials database initiative and understand the reviewer’s concerns about our limitations, such as challenges in comprehensive metadata collection and occasional missing data. Despite these issues, we have endeavored to maximize data collection from process conditions to measurement results and to provide convenient environments for database analysis through automated analysis techniques. Importantly, based on user feedback, we are committed to progressively expanding our metadata collection to address these gaps and improve data comprehensiveness, as detailed in the manuscript (line 297 of page 13, highlighted by yellow).
Additionally, we recognize the technical challenges in reducing the loading time for large image and video data, often reaching hundreds of megabytes in size. To enhance overall performance, we will keep investing in improved infrastructure.
In response to the reviewer’s suggestion regarding a comparison with computational data, we have explored Raman spectra and optical absorption spectra from the C2DB database. However, the computational data primarily comprises idealized 2D samples, whereas our experimental samples contain various impurities such as defects, strain, and folding, depending on different processing conditions. Consequently, direct comparisons between the two databases remain limited, particularly in capturing detailed variations due to the absence of extensive results. We believe that incorporating computational results with diverse impurities would greatly enhance the interpretability of our results.
Finally, by incorporating detailed feedback from users, we are dedicated to expanding our metadata and refining the platform to accurately reflect the diverse nature of experimental data, thereby providing a more comprehensive resource for the 2D materials science community.

19-Feb-2024

Dear Dr Lee:

Manuscript ID: DD-ART-12-2023-000243.R1
TITLE: 2DMat.ChemDX.org: Experimental data platform for 2D materials from synthesis to physical properties

Thank you for submitting your revised manuscript to Digital Discovery. I am pleased to accept your manuscript for publication in its current form. I have copied any final comments from the reviewer(s) below.

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Associate Editor
Digital Discovery
Royal Society of Chemistry

Reviewer 3

The authors have provided reasonable replies to the concerns raised in my first report.