Introduction to Data Liberation and Publishing Tools in Biodiversity

Data Liberation and Publishing Tools 

Publication of biodiversity-linked data increasingly stands as a critical component of biodiversity knowledge. It reflects the research outcomes and allows access to updated information that might be instrumental for other strands of investigation. Similarly, it benefits interdisciplinary research and cross-cutting approaches.

To increase the impact of scientific results and facilitate their acknowledgment and further use, the publication of data becomes strategic. Along that line, accelerating publishing and quick and easy extraction of published data becomes essential. For decades, researchers have struggled to create tools, improve mechanisms and harmonize workflows and methodologies that foster and contribute to the linking of data that may remain hidden or lost in the nebulous and increasingly complex landscape of biodiversity-related publications. The proliferation of open-access journals, sharable repositories, and accessible publishing tools are good examples of responses to the data linkage demand from researchers in the biodiversity realm.

Direct access to citation of data and the interlinkage across instruments and platforms require a proper way of publishing research outcomes so as not to break the workflow and create bottlenecks for the seamless links between information. They are built to enrich biodiversity information by linking and integrating related data coming from diverse and not explicitly linked information, beyond expressed citations and references, despite where the data was originally stored or through which services are currently provided.

Course Theme 

The present course on Publication of biodiversity data aims to tackle both sides of the publication process:

• firstly, the facilitation of publishing in the format and with the tools that allow further share and use of the information contained in the publication., and
• secondly, the enhancement of data extraction by utilizing the right pipelines and mechanisms.

Therefore, the Course is divided into two main sections:

1. Publishing tools - providing best practices for improving writing and publishing formats to ensure effective linkage to scientific content.
2. Data liberation workflows - facilitating data import and export, ensuring correct and updated references, and boosting sharing and use of the published data.

These sections correspond to the two tools that are embedded in the Biodiversity Knowledge Hub (the BKH) built under the EU-funded project ‘’Biodiversity Community Integrated Knowledge Library’’ (BiCIKL). Together with their description, we present the rationale for the development of these tools and provide step-by-step guidance for their use.

Data liberation, often referred to as "data freedom" or "data portability," is a concept and practice that involves the ability of individuals and organizations to freely access, use, and move their data across different platforms, services, or systems without being locked into a particular vendor or provider. It is rooted in the idea that data should be portable and not controlled or owned by a single entity.

Key aspects of data liberation include:

1. Data Access: Users should have the ability to easily access and retrieve their data from the services and platforms they use.
2. Data Control: Users should have control over their data, including the ability to edit, delete, or modify it as they see fit.
3. Data Portability: Users should be able to transfer their data from one service or platform to another without significant barriers or restrictions.
4. Interoperability: Data should be structured and standardized in a way that makes it easy to integrate with other systems and services.

Data liberation is associated with open standards and formats, as well as initiatives to make data more open and accessible. It can have important implications for user privacy, competition, and innovation, as it reduces the risk of vendor lock-in and fosters a more open and competitive marketplace.

ARPHA Tool and PLAZI Workflow 

In this section of the course, we are presenting two tools (The ARPHA and the PLAZI Workflow) that are offered by and allocated in the Biodiversity Knowledge Hub (the BKH) built under the EU-funded project named Biodiversity Community Integrated Knowledge Library BiCIKL. 

The choice between Plazi and the ARPHA platform for publishing a paper on biodiversity research depends on your specific needs and goals. Each platform serves a distinct purpose, and your decision should be based on factors such as the type of research you're conducting, the scope of your paper, and your publication preferences. Here are some considerations for each platform:

1. Plazi:

   • Data Liberation and Taxonomic Data: Plazi is known for its focus on digitizing and liberating taxonomic and biodiversity data from the scientific literature. If your paper involves taxonomic descriptions, treatments, and the integration of data from historical taxonomic literature, Plazi's services can be highly relevant.

2. ARPHA:

   • Full Manuscript Publishing: The ARPHA platform is a comprehensive solution for publishing entire research manuscripts in open-access journals. If your paper covers a wide range of biodiversity topics beyond taxonomic descriptions, and you want to publish it as a complete scholarly article, ARPHA may be the more suitable choice.
   • Peer Review: ARPHA facilitates the peer review process, which is crucial for validating your research. If you want your paper to undergo a rigorous peer review before publication, ARPHA provides the necessary infrastructure.

Consider the following questions to guide your decision:

• Is your paper primarily focused on taxonomic descriptions and data liberation? If so, Plazi may be the better choice.
• Do you want to publish a full research manuscript on a broader biodiversity topic? If this is the case, ARPHA's platform may be more appropriate.
• Do you need peer review and the infrastructure for comprehensive journal publishing? If peer review and full journal publication are essential, ARPHA offers these services.

Ultimately, you may also want to explore specific journals and publishers on both platforms to determine if there is a journal that aligns well with your paper's subject matter and goals. Depending on the specifics of your research, you may find that one platform better suits your needs and preferences over the other. Together with their definition, we will present the rationale for the development of these tools and we will provide step-by-step guidance for their use.