Author guideline / formatting instructions - needs central location

[li-lcp]

Currently, the author submission instructions are a bit scattered. Can we pull all instructions into one location, e.g., at https://alpha.physionet.org/about/publish/

For example, the following instructions under the "File" button in the submission process can be added to the Author's guideline:

5. Project Files

PhysioNet resources should be reusable by the greater scientific community. To facilitate the reuse of your content, please adhere to the following reusability guidelines. General Guidelines

Files must contain no protected health information.
Files are provided in an open format such as text, csv, or WFDB, rather than a proprietary format.
Code must be provided in source format.
Data files must be machine readable.
Large regularly-sampled time-series data, especially waveforms, are provided in WFDB format.
Filenames must only contain letters, numbers, dashes, underscores, and dots.
If appropriate, provide a csv file named subject-info.csv containing information on all subjects, such as age and gender.

WFDB Files

Provide a list of all WFDB format records, named RECORDS. Example file. If you upload this file, you will see a link to view your project's waveforms in LightWAVE.
Provide a tab delimited list of all WFDB format annotation files, named ANNOTATORS. Example file.

[li-lcp]

A related issue on the Author Guideline -- we need clear guidelines on various sections of the project description. There seems to be confusion among contributors about what to put into the "Abstract", "Method","Background",... sections in a project description. Authors tend to include description of the overall study design, analysis and findings instead of the description of the data.

As a reference, here are the instructions we have given in the past: https://physionet.org/users/help/pnw-howto.shtml#publishing-requirements

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Publishing Requirements

These requirements must be satisfied in order for us to publish your project. Physiobank Databases

This is what an example database should look like/contain: https://physionet.org/physiobank/database/example/. Please provide the indicated descriptive fields.

The experimental procedure used to collect the data must be clearly described. Supporting information or diagrams must be provided for irregular data capturing devices.
The data itself must be clearly described regarding its content and how the files are organized.
High resolution data/waveforms such as all ECG and EEG recordings must be stored in a WFDB compatible format - either MIT or EDF format. We allow other open source formats such as text and csv for small contributions, low resolution data and time series, and tabular information/relational databases.

For guidance on creating MIT format signal files, see the tutorial. If you need assistance with converting files, feel free to contact the PhysioNet editor.
Annotations or event locations must be provided as WFDB annotation files.
Waveforms should be stored in digital format. There must also be information to obtain the physical values from these digital files, eg. the gain and baseline fields of MIT format header files.
(Optional) Information about the subjects contained either at the bottom of the signal header files or all together in a separate text file. Preferred information includes age, gender, height, weight, medications, and diagnoses. If relevant: gestational age.
Links to relevant supporting publications which describe the data's creation or usage should be provided.
The owner must agree to provide the data under the ODC Public Domain Dedication and License v1.0 standard for all PhysioBank databases.
All protected health information must be removed.

Physiotoolkit Software Packages

A brief description of the algorithms, including the signal processing/machine learning methods they are based on.
Reference publication(s) users of the software tool should cite
Basic instructions on how to run the software tool with usage examples. Include a demo/test script to validate that the tool is working correctly
If applicable, provide sample input input data for the test script, and clearly document the expected results/output for validation purposes.
Platform(s) tested and date of testing.
Names and contact information for authors.
(Optional) Any eye-catching visuals for the web page.
(Optional) A version number for current release of the code, if applicable.
(Optional) Other credits/acknowledgements.
(Optional) Description of and links to the accompanied data set for testing.
(Optional) Link to any tutorials or detailed instructions of the software tool.
(Optional) Any other information you think users should know, ie. known issues.
The owner must agree to provide the software under the GNU Public License (GPL). If so, they must provide at least one copy of the following notice in the package's source code, and at least the 'copyright' line with pointers to the full notice in the other files:

    [The program's name and a brief idea of what it does.]
    Copyright (C) [year]  [name of author]

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see http://www.gnu.org/licenses/.

In order to add or edit descriptive information about a project, go to your PhysioNetWorks home page, click for the specified project, click , and fill in the Project Abstract section.

[tompollard]

Updates to the instructions were added in https://github.com/MIT-LCP/physionet-build/pull/539. See: https://alpha.physionet.org/about/publish/#guidelines

[li-lcp]

We need to update our instructions about file format/organization so LightWAVE can view the contributed files properly. Here is what I suggest. Benjamin, please check and edit! Specifically, I don't know if relative paths should be specified for ANNOTATORS file as well.

• Provide a list of all WFDB format records, named RECORDS, where each row is the name of a WFDB file (without any .hea or .dat extensions) in your contribution. Example file (https://alpha.physionet.org/static/published-projects/mitdb/1.0.0/RECORDS). If you upload this file, you will see a link to view your project's waveforms in LightWAVE. Please make sure that you can view your project's waveforms in LightWAVE properly.
• Note that the RECORDS file must be at the top-level directory in your submission, and must be named exactly RECORDS for LightWAVE to locate the file. If your WFDB files are organized in a sub-directory in your project, the relative path of the file location must be specified in the RECORDS file. For example, if you have WFDB file named "subject1_ecg.dat" under a subdirectory "ECG", then a row in the RECORDS file should read:

ECG/subject1_ecg

• Provide a tab delimited list of all WFDB format annotation files, named ANNOTATORS. Example file. (https://alpha.physionet.org/static/published-projects/mitdb/1.0.0/ANNOTATORS)

[tompollard]

This is great, thanks @li-lcp. @bemoody once you're happy, we can add this to the "Preparing your project files" section at: https://alpha.physionet.org/about/publish/#guidelines (we should perhaps also add this section to the secondary nav bar).

[li-lcp]

The Author Guideline page on the alpha site (see https://alpha.physionet.org/about/publish/#guidelines) should mention WFDB as a file format, with links to instructions.

Again, I suggest we post content of the following link on the Guideline page on alpha site. https://physionet.org/users/help/pnw-howto.shtml#publishing-requirements