Open Plant Pathology: How Much Do We (Plant Pathologists) Value Openness and Transparency?

“We (Emerson Del Ponte and Adam Sparks) started this initiative (Open Plant Pathology) in early January 2018 with the idea that we would create a community in which plant pathologists could come together and share resources and ideas and encourage a freer exchange of information, code and data. One of the reasons for this was that a few years before that, we’d started working on analysis of randomly selected plant pathology papers, initially we looked at 300 published from 2012 until 2018, but it later grew to encompass 450 papers published from 2012 until 2021, with Kaique Alves, Zachary Foster and Nik Grünwald, which was published in Phytopathology® in January (Sparks et al. 2023b). What we were finding as we looked at papers across 21 journals that were dedicated to plant pathology research or published specialised sections or articles in the field of plant pathology was not surprising, but still disappointing. As a discipline, we simply do not make much, if any, effort to help ensure that others can easily reproduce our work after it is published (Sparks et al. 2023b).

We found that most articles were not reproducible according to our scoring system and failed to take advantage of open science and reproduciblity methods that would benefit both the authors and the readers. To wit, the vast majority of articles we looked at made no attempt to share code or data, scoring “0” in our system (Figure 1)….”

Open and reusable annotated mass spectrometry dataset of a chemodiverse collection of 1,600 plant extracts | GigaScience | Oxford Academic

Abstract:  As privileged structures, natural products often display potent biological activities. However, the discovery of novel bioactive scaffolds is often hampered by the chemical complexity of the biological matrices they are found in. Large natural extract collections are thus extremely valuable for their chemical novelty potential but also complicated to exploit in the frame of drug-discovery projects. In the end, it is the pure chemical substances that are desired for structural determination purposes and bioactivity evaluation. Researchers interested in the exploration of large and chemodiverse extract collections should thus establish strategies aiming to efficiently tackle such chemical complexity and access these structures. Establishing carefully crafted digital layers documenting the spectral and chemical complexity as well as bioactivity results of natural extracts collections can help prioritize time-consuming but mandatory isolation efforts. In this note, we report the results of our initial exploration of a collection of 1,600 plant extracts in the frame of a drug-discovery effort. After describing the taxonomic coverage of this collection, we present the results of its liquid chromatography high-resolution mass spectrometric profiling and the exploitation of these profiles using computational solutions. The resulting annotated mass spectral dataset and associated chemical and taxonomic metadata are made available to the community, and data reuse cases are proposed. We are currently continuing our exploration of this plant extract collection for drug-discovery purposes (notably looking for novel antitrypanosomatids, anti-infective and prometabolic compounds) and ecometabolomics insights. We believe that such a dataset can be exploited and reused by researchers interested in computational natural products exploration.

 

Kenyon | The Journal Article as a Means to Share Data: a Content Analysis of Supplementary Materials from Two Disciplines | Journal of Librarianship and Scholarly Communication

Abstract:  INTRODUCTION The practice of publishing supplementary materials with journal articles is becoming increasingly prevalent across the sciences. We sought to understand better the content of these materials by investigating the differences between the supplementary materials published by authors in the geosciences and plant sciences. METHODS We conducted a random stratified sampling of four articles from each of 30 journals published in 2013. In total, we examined 297 supplementary data files for a range of different factors. RESULTS We identified many similarities between the practices of authors in the two fields, including the formats used (Word documents, Excel spreadsheets, PDFs) and the small size of the files. There were differences identified in the content of the supplementary materials: the geology materials contained more maps and machine-readable data; the plant science materials included much more tabular data and multimedia content. DISCUSSION Our results suggest that the data shared through supplementary files in these fields may not lend itself to reuse. Code and related scripts are not often shared, nor is much ‘raw’ data. Instead, the files often contain summary data, modified for human reading and use. CONCLUSION Given these and other differences, our results suggest implications for publishers, librarians, and authors, and may require shifts in behavior if effective data sharing is to be realized.

 

A quest to digitize 1 million plant specimens

“The Australian National Herbarium in Canberra is imaging nearly a million plant specimens using an automated system developed by Netherlands company Picturae….

The full digital collection of the Australian National Herbarium will be made available through the Atlas of Living Australia, including for the general public.”

Assessing Open Science Practices in Phytolith Research

Abstract:  Open science is an integral part of all scientific research, but the extent of open science practices in phytolith research is unknown. Phytolith analysis examines silica bodies that are initially formed within and between plant cells during the life of the plant but become deposited in sediments once the plant dies. The use of phytoliths in archaeobotanical and palaeoecological studies has been increasing in recent years resulting in an upsurge in publications. The aims of this article are to assess open science practices in phytolith research by reviewing data and metadata sharing, and open access, in a sample of journal articles containing primary phytolith data from 16 prominent archaeological and palaeoecological journals (341 articles). This study builds on similar studies conducted for zooarchaeology (Kansa et al. 2020) and macro-botanical remains (Lodwick 2019). This study shows that 53% of papers shared data in any format but only 4% of papers contained reusable data, 74% included some pictures of phytolith morphotypes for identification purposes, 69% had a fully described method, 47% used the International code for phytolith nomenclature (ICPN 1.0) and only 13% of articles were open access. Steps forward are then proposed, including planning for open projects, making more articles openly accessible and implementing the FAIR data principles, to use as a starting point for discussions in the wider phytolith and archaeological communities to develop guidelines for greater integration of open science practices.

 

Museum digitises five millionth specimen to unlock secrets of collection | Natural History Museum

“A naturally bright green stonefly has signalled full speed ahead for the Museum’s digitisation project, as it releases its five millionth specimen online.

As well as making the Museum’s specimens available online for anyone to access, the digitisation of these collections could contribute billions of pounds to the global economy….”

Dynamic visualisation of million?tip trees: The OneZoom project – Wong – – Methods in Ecology and Evolution – Wiley Online Library

Abstract:  

 

The complete tree of life is now available, but methods to visualise it are still needed to meet needs in research, teaching and science communication. Dynamic visualisation of million-tip trees requires many challenges in data synthesis, data handling and computer graphics to be overcome.
Our approach is to automate data processing, synthesise data from a wide range of available sources, then to feed these data to a client-side visualisation engine in parts. We develop a way to store the whole tree topology locally in a highly compressed form, then dynamically populate metadata such as text and images as the user explores.
The result is a seamless and smooth way to explore the complete tree of life, including images and metadata, even on relatively old mobile devices.
The underlying methods developed have applications that transcend tree of life visualisation. For the whole complete tree, we describe automated ID mappings between well known resources without resorting to taxonomic name resolution, automated methods to collate sets of public domain representative images for higher taxa, and an index to measure public interest of individual species.
The visualisation layout and the client user interface are both abstracted components of the codebase enabling other zoomable tree layouts to be swapped in, and supporting multiple applications including exhibition kiosks and digital art.
After 10 years of work, our tree of life explorer is now broadly complete, it has attracted nearly 1.5 million online users, and is backed by a novel long-term sustainability plan. We conclude our description of the OneZoom project by suggesting the next challenges that need to be solved in this field: extinct species and guided tours around the tree.”

“The Google Earth of Biology” – Visually Stunning Tree of All Known Life Unveiled Online

 

“The OneZoom explorer – available at onezoom.org – maps the connections between 2.2 million living species, the closest thing yet to a single view of all species known to science. The interactive tree of life allows users to zoom in to any species and explore its relationships with others, in a seamless visualisation on a single web page. The explorer also includes images of over 85,000 species, plus, where known, their vulnerability to extinction.

OneZoom was developed by Imperial College London biodiversity researcher Dr. James Rosindell and University of Oxford evolutionary biologist Dr. Yan Wong. In a paper published today in Methods in Ecology and Evolution, Drs Wong and Rosindell present the result of over ten years of work, gradually creating what they regard as “the Google Earth of biology.” …”

Dr. Wong added: “It’s extraordinary how much research there is still to be done. Building the OneZoom tree of life was only possible through sophisticated methods to gather and combine existing data – it would have been impossible to curate all this by hand.”

WUR gives away CRISPR intellectual property licenses for free in fight against hunger – Reader Mode

“The ultimate aim of plant breeding has always been to make plants resistant to drought and diseases. That could help eliminate hunger around the world. This is no longer a distant thought, thanks to a technology called CRISPR-Cas. Today Wageningen University & Research (WUR) announces it will provide potential partners with free licenses to work on its patented CRISPR technology. The license must be applied to gene-editing of plants for non-profit applications….”

WUR gives away CRISPR intellectual property licenses for free in fight against hunger – Reader Mode

“The ultimate aim of plant breeding has always been to make plants resistant to drought and diseases. That could help eliminate hunger around the world. This is no longer a distant thought, thanks to a technology called CRISPR-Cas. Today Wageningen University & Research (WUR) announces it will provide potential partners with free licenses to work on its patented CRISPR technology. The license must be applied to gene-editing of plants for non-profit applications….”

Vegetation of planet Earth: Researchers publish unique database as open access

It’s a treasure trove of data: The global geodatabase of vegetation plots “sPlotOpen” is now freely accessible. It contains data on vegetation from 114 countries and from all climate zones on Earth. The database was compiled by an international team of researchers led by Martin Luther University Halle-Wittenberg (MLU), the German Centre for Integrative Biodiversity Research (iDiv) and the French National Centre for Scientific Research (CNRS). Researchers around the world finally have a balanced, representative dataset of the Earth’s vegetation at their disposal, as the team reports in the journal Global Ecology & Biogeography.

Language extinction triggers the loss of unique medicinal knowledge | PNAS

Abstract:  The United Nations proclamation of 2022–2032 as the International Decade of Indigenous Languages aims to raise global awareness about their endangerment and importance for sustainable development. Indigenous languages contain the knowledge that communities have about their surrounding plants and the services they provide. The use of plants in medicine is a particularly relevant example of such ecosystem services. Here, we find that most medicinal knowledge is linguistically unique—i.e., known by a single language—and more strongly associated with threatened languages than with threatened plants. Each indigenous language is therefore a unique reservoir of medicinal knowledge—a Rosetta stone for unraveling and conserving nature’s contributions to people.

 

The Global Extinction of Languages Is Threatening a Vital Type of Human Knowledge

“As human languages are driven to extinction around the world, a verbal encyclopedia of medical knowledge is on the brink of being forgotten.

Among 12,495 medicinal uses for plants in indigenous communities, new research has found over 75 percent of those plants are each tied to just one local language. If these unique words trickle out of use, so too may the knowledge they contain….

Language extinction is a tragic phenomenon that’s been occurring worldwide, as languages spoken by precious few people are replaced by larger ones. Roughly one language ceases to be spoken every four months, and 3,054 languages are currently endangered around the world….

The vast majority of plant species in the study were found to have medical properties described in just one indigenous language, many of which are themselves endangered….

In North America, for instance, the authors found waning indigenous languages held 86 percent of all unique knowledge on plant medicine. In the northwest Amazon, on the other hand, 100 percent of medicinal plant knowledge is restricted to languages on the edge of extinction. …”

3 ways that preprints help researchers in agricultural and plant sciences – The CABI Blog

“The use of preprints (pre-peer reviewed versions of scholarly papers) has accelerated in the last few years with many researchers now sharing their latest work with the scientific community before or in parallel to publication with a journal. After a slower start compared to other research fields, adoption of preprints in the plant sciences and agriculture is growing well.

As part of this growing trend, CABI relaunched agriRxiv (pronounced agri-archive and previously known as AgriXiv) in 2020 as a platform for posting preprints. agriRxiv makes preprints across agriculture and allied sciences available to researchers and gives those who wish to share their papers online an opportunity to gain valuable feedback before submitting a final version to a journal and formal peer-review….”

Webinar ‘Preprints – Accelerating plant sciences and agriculture’

“The use of preprints has accelerated in the last few years with many researchers now sharing their latest work with the scientific community before or in parallel to publication with a journal. After a slower start compared to other research fields, adoption of preprints in the plant sciences and agriculture is growing well.

Why are researchers in plant and agricultural sciences posting preprints? What should you consider before you post a preprint? How does a preprint relate to a journal publication? In this webinar, we will discuss the outlook of preprints in plant sciences and agriculture, explore what can be learned from fields with a longer tradition of preprint use and hear from researchers who have successfully used preprints for the communication of their research.”