Supporting the Allotrope Foundation with Scientific Publications

Close-up of a microscope with a digital network overlay and DNA strand, representing advanced genetic research and analysis.

In the October 5th webinar titled, “Supporting the Allotrope Foundation with Scientific Publications – An open invite” presented by the Della Corte Lab at BYU highlighted the history of publications from members of the Allotrope Foundation and invited collaborators to join in their initiative to gather additional user stories and insights. The presentation gave insights into the past and present publications which make use of the Allotrope Data Format (ADF) and a look ahead into their future goals of increasing the scientific footprint through academic partnerships.

The first thing the presentation shows is a comparison between the history of the PDF and the ADF. As the PDF was first announced in 1992, it didn’t make much of a splash because people simply weren’t thinking about how ubiquitous sending electronic documents would be in the future. However, once the IRS adopted PDFs for filing tax returns, the format became the norm in electronic documentation, and in 2008 became an ISO standard. Compare that to the ADF, which wasn’t much of a sensation when it was announced in 2015 because it wasn’t readily apparent how important sharing semantic data would be. However, the ADF’s ability to ameliorate the nightmares of pharma data sharing has showcased its usefulness.

Even with the usefulness of the ADF though, there is still limited visibility within academia. There were zero publications from the Allotrope Foundation and its members during 2018 and 2019 and two publications in 2020, both from the Della Corte Lab. The most recent publications focused on using the Allotrope Data Format and ZONTAL Space in library eArchiving and using ZONTAL and Allotrope to create a data-centric lab, highlighting how Allotrope enables data centricity which in turn enables the full utility of the digital age in modern science.

Currently, the Della Corte Lab is digging deeper into the concept of FAIR data and asking what interpretations are possible, particularly in the realms of interoperability and reuse (the I and R of FAIR). In order to be truly interoperable and reusable, the self-reporting data assets should be fully understandable, effective in usage, stable long term, and extensible. The current project explores how well these self-reporting data assets fulfill the goal of FAIR data through a comparison of ADF, JSON, and AnIML formats. The project is currently working with a biotech and Novartis and is extending an invitation for further contributions of datasets, filled data cubes, tabular, and graph models.

Download our whitepaper on FAIR data.

Looking ahead, the lab hopes to increase the scientific visibility of the ADF through reviewing the progress of the consortium. In order to achieve this, they will highlight the original business drivers, review case studies and proofs of value, hone the description of the consortium and the ability of its members to cooperate, summarize current Allotrope Connect talks, and look into options to expand beyond the pharma industry. Just as the ADF provides a method for real interoperability and data sharing, the Della Corte Lab is inviting additional collaborators to join their project, so that the consortium can benefit from the synergies and cooperation.