Back to 'III. Publishing Tools'

Topic outline

  • Session 2: ARPHA: Introducing a Semantic Publishing Platform

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    • Introducing the ARPHA Writing Tool


      This section presents the use of the ARPHA, an XML-based full-featured open-access publishing platform, covering all the stages of the editorial and publishing process. 

      ARPHA Publishing Platform provides an integrated solution for scholarly publishers to manage and disseminate academic content in a modern, user-friendly, and open-access manner. It is designed to support transparency, collaboration, and the efficient dissemination of scholarly knowledge.

      ARPHA provides tools and services to assist with the publishing of scientific journals, particularly those in the fields of biodiversity, ecology, and related disciplines. It is designed to streamline the publishing process and make it more efficient and accessible for researchers and publishers.

      ARPHA offers various features and functionalities to facilitate the publication of research articles, including manuscript submission, peer review management, article typesetting, and online publication. It also supports open-access publishing and complies with various standards in scholarly publishing.

      It can be used for Academic Journals, Open Access Books, Conference Proceedings, Conference Abstracts, and Preprints. The tool is used for abstract and paper submissions to numerous conferences in the field (see for example here).

      ARPHA provides the highest technological publishing and dissemination standards, including several innovations, for example:

      • The advanced semantics publishing module, which allows tagging and enhancement of content and the development of multiple interactive tools linked to the article’s content. This module is now fully operational for the domain of Biology but can be developed for any field on demand of the client.
      • The fully automated indexing and archiving module, which distributes content instantaneously on the day of its publication via web services, saving valuable time and effort in the editorial office.


      One of the most remarkable and well-known innovations of ARPHA was the 2013 launch of the first-ever entirely XML-based and fully integrated authoring, peer review, and publishing workflow, exemplified by Biodiversity Data Journal (BDJ). The ARPHA-XML workflow offered several globally unique features, for example, the import of data from data aggregators directly into the manuscripts via web services or the automated conversion and submission of metadata from data repositories into data paper manuscripts.

      In 2015, the ARPHA-XML workflow was used to establish the Research Ideas and Outcomes (RIO Journal) as the first open science journal aiming at publication of all outputs from the research cycle: from research ideas and grant proposals to methods, data, software, project reports, research articles and many more. Due to its unique features, RIO won the SPARC Innovator AWARD in 2016.

      The following graph presents the central role of the platform in the publishing process and demonstrates its links with other services of the BKH that were presented in Course I.


      The following sections are presenting the key functonalities of the ARPHA Writing Tool. We have also prepare an exercise to test your familiarization with the Tool at the end of the presentation. You can also follow this short video that highlights the top 10 distinctive features of the platform:



      Here is a general step-by-step guide for using ARPHA for various roles, such as an author, reviewer, or editor (keep in mind that the specific steps may vary slightly depending on the journal using ARPHA and its customization):

      As an Author:

      1. Select a Journal: First, choose the academic journal you want to submit your manuscript to. Ensure that it is hosted on the ARPHA platform.

      2. Register or Log In: If you're a new user, you'll need to register for an account on the journal's submission system. If you're an existing user, log in using your credentials.

      3. Prepare Your Manuscript: Follow the journal's specific guidelines for manuscript preparation, including formatting, referencing style, and any specific requirements. Prepare your manuscript and any supplementary materials.

      4. Submission: Once you're logged in, you'll find an option to submit your manuscript. Follow the submission process, which typically involves providing details about your manuscript, uploading files, and filling out submission forms.

      5. Peer Review: If your manuscript passes an initial check, it will be sent for peer review. You may need to respond to reviewer comments and make revisions as required.

      6. Publication: Once your manuscript is accepted, it will go through the final editing and proofreading process. After this, it will be published and made available to the public.


      As a Reviewer:

      1. Invitation: You'll receive an email invitation from the journal's editorial office to review a manuscript. This email will contain a link to the submission system.

      2. Log In: If you're not already registered with the journal's submission system, you may need to create an account. If you have an account, log in.

      3. Review: Access the manuscript and review materials provided by the journal. Write your review, addressing various aspects of the manuscript such as its quality, methodology, clarity, and originality.

      4. Submit Review: Submit your review through the online system, typically by answering a set of questions and providing comments. This feedback will be sent to the editorial office.


      As an Editor:

      1. Access Editorial Dashboard: Editors typically have access to a dashboard where they can manage the journal's submissions, reviewers, and published content.

      2. Manuscript Handling: Review submitted manuscripts and assign them to appropriate reviewers. Editors can communicate with authors and reviewers through the system.

      3. Decision Making: Based on reviewer feedback, you'll make decisions regarding manuscript acceptance, revision, or rejection. You can communicate these decisions to authors through the system.

      4. Publication: Once a manuscript is accepted, oversee the final editing and proofreading process. Then, approve the publication of the manuscript.


      IMPORTANT: these are general steps, and the specific procedures may differ between different journals hosted on the ARPHA platform. It is essential to refer to the guidelines and instructions provided by the journal you are submitting to or working with, as they may have their own customized workflows and requirements.



    • Authoring and submission of manuscripts 


      Authoring and submission of manuscripts in the ARPHA Writing Tool is possible online through the online submission module. To create a manuscript in ARPHA, authors are required to register or log in.

      Once logged in, click on the “Start a manuscript” tab on the right side of the screen.

      Before you proceed, you need to select a Journal and an Article type. To see an example for each article type click the corresponding box.

      Please note that once you choose your article type, you can not change it. You can format and structure your article by

      • Using templates and styles
      • Adding citations and references
      • Inserting figures, tables, and supplementary materials
      • Ensuring compliance with journal guidelines


      A set of Web-based services offered by the tool allows, e.g. for search and import of literature or data references, cross-referencing of in-text citations, import of tables, upload of images and multimedia, assembling images for display as reusable composite figures, and even adding videos to your article.


      All the user/author needs to do to add content to an article is to select the right type from the side menu and then navigate through the instructions in the pop-up window. If in doubt, the authors can also consult the ‘Tips and Tricks’ on the tool website (https://arpha.pensoft.net/).


    • Import a data paper from Ecological Metadata Language 

      You can also import a data paper from an Ecological Metadata Language (EML) file (e.g. generated from GBIF IPT, DataONE, and LTER), or any other manuscript via the service provider API. Then, you will be able to continue working on it in the ARPHA Writing Tool.

      The Review and Revision Process 
      After the finalization of the article's preparation, you can submit your manuscript for review. The Tool offers the opportunity to facilitate the interaction with the reviewers and to guide the process for responding to reviewers' comments, revising your manuscript within ARPHA, and finalizing your submission.

      Publication and Beyond 

      The ARPHA Tool supports the user in understanding the overall publication process while it offers a series of services to facilitate the tracking of your article’s status by using numerous analytics as well as services for sharing and promoting your article.

      Practical Exercise with ARPHA Writing Tool 

      Here's an example of a practical exercise on the use of the ARPHA Writing Tool. This exercise is designed to familiarize participants with the process of starting a new manuscript and collaborating with co-authors.

      Practical Exercise: Starting a New Manuscript and Collaborating Objective:

      To create a new manuscript draft in the ARPHA Writing Tool and invite collaborators to join the writing process.

      Tools Needed:

      Access to the ARPHA Writing Tool with a registered account.

      A research topic or a mock-up research title for the exercise.

      Instructions:

      1. Log in and Manuscript Setup:

      • Log into your ARPHA Writing Tool account,
      • Navigate to the 'My Manuscripts' section,
      • Click on 'Create a New Manuscript',
      • Select the appropriate journal template if prompted.

      2. Manuscript Information:

      • Enter a mock-up title for your manuscript.
      • Add an abstract (can be a summary or placeholder text for this exercise),
      • Fill in keywords relevant to your mock-up research topic.

      3. Inviting Collaborators:

      • Go to the 'Collaborators' section within your manuscript draft,
      • Click on 'Invite Collaborators’.
      • Enter the email addresses of your mock collaborators (these can be your alternative email addresses for this exercise),
      • Assign roles to your collaborators (e.g., co-author, reviewer).

      4. Collaborative Writing:

      • Begin writing the introduction section of your manuscript,
      • Use the commenting feature to leave a note for your collaborators on a specific paragraph, asking for their input on a particular point,
      • Save your changes and notify collaborators of the update.

      5. Version Control:

      • Make a significant change to a section of your manuscript, o Save the version with a clear label (e.g., ' Revised Introduction - [Your Name]”),
      • View the version history to see the changes made.

      6. Responding to Collaborator Input:

      • Check for updates or comments made by your collaborators,
      • Respond to their comments and make any agreed-upon changes to the manuscript.

      Outcomes:

      • A draft manuscript with the title, abstract, and introduction section.
      • Evidence of collaboration, such as comments left by and for collaborators.
      • A version history showing at least one major revision.

      Reflection:

      After completing the exercise, reflect on the following questions:

      • How intuitive did you find the process of starting a new manuscript and inviting collaborators?
      • What features of the ARPHA Writing Tool did you find most useful during this exercise?
      • Were there any challenges you faced while using the tool? How did you overcome them?

      This exercise not only helps users get hands-on experience with the ARPHA Writing Tool but also encourages them to think critically about the collaborative writing process and how the tool facilitates it.


      Going Mobile 

      A new integration with a mobile app Researcher allows readers to receive the latest articles from Pensoft journals straight to their smartphone. Researcher is an innovative mobile and web application, currently used by 1.8 million people globally, which allows you to set up your social media-style feed of research papers by following your favorite academic journals or research topics.