Tag: biology

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Streamlined import of omics metadata from the European Nucleotide Archive (ENA) into an OMICS Data Paper manuscript

By Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Lyubomir Penev

Data papers are scientific papers which describe a dataset rather than present and discuss research results. The concept was introduced to the biodiversity community by Chavan and Penev in 2011 as the result of a joint project of GBIF and Pensoft.

Since then, Pensoft has implemented the data paper in several of its journals (Fig. 1). The recognition gained through data papers is an important incentive for researchers and data managers to author better quality metadata and to make it Findable, Accessible, Interoperable and Re-usable (FAIR). High quality and FAIRness of (meta)data are promoted through providing peer review, data audit, permanent scientific record and citation credit as for any other scholarly publication. One can read more on the different types of data papers and how they help to achieve these goals in the Strategies and guidelines for scholarly publishing of biodiversity data  (https://doi.org/10.3897/rio.3.e12431). 

Fig. 1 Number of data papers published in Pensoft’s journals since 2011.

The data paper concept was initially based on the standard metadata descriptions, using the  Ecological Metadata Language (EML). Apart from distinguishing a specialised place for dataset descriptions by creating a data paper article type, Pensoft has developed multiple workflows for streamlined import of metadata from various repositories and their conversion into data paper a manuscripts in Pensoft’s ARPHA Writing Tool (AWT). You can read more about the EML workflow in this blogpost.

Similarly, we decided to create a specialised data paper article type for the omics community within Pensoft’s Biodiversity Data Journal to reflect the specific nature of omics data. We established a manuscript template to help standardise the description of such datasets and their most important features. This initiative was supported in part by the IGNITE project.

How can authors publish omics data papers?

There are two ways to do publish omics data papers – (1) to write a data paper manuscript following the respective template in the ARPHA Writing Tool (AWT) or (2) to convert metadata describing a project or study deposited in EMBL-EBI’s European Nucleotide Archive (ENA) into a manuscript within the AWT.

The first method is straightforward but the second one deserves more attention. We focused on metadata published in ENA, which is part of the International Nucleotide Sequence Database Collaboration (INSDC) and synchronises its records with these of the other two members (DDBJ and NCBI). ENA is linked to the ArrayExpress and BioSamples databases, which describe sequencing experiments and samples, and follow the community-accepted metadata standards MINSEQE and MIxS. To auto populate a manuscript with a click of a button, authors can provide the accession number of the relevant ENA Study of Project and our workflow will automatically retrieve all metadata from ENA, as well as any available ArrayExpress or BioSamples records linked to it (Fig. 2). After that, authors can edit any of the article sections in the manuscript by filling in the relevant template fields or creating new sections, adding text, figures, citations and so on.

An important component of the OMICS data paper manuscript is a supplementary table containing MIxS-compliant metadata imported from BioSamples. When available, BioSamples metadata is automatically converted to a long table format and attached to the manuscript. The authors are not permitted to edit or delete it inside the ARPHA Writing Tool. Instead, if desired, they should correct the associated records in the sourced BioSamples database. We have implemented a feature allowing the automatic re-import of corrected BioSamples records inside the supplementary table. In this way, we ensure data integrity and provide a reliable and trusted source for accessing these metadata. 

Fig. 2 Automated generation of omics data paper manuscripts through import and conversion of metadata associated with the Project ID or Study ID at ENA

Here is a step-by-step guide for conversion of ENA metadata into a data paper manuscript:

  1. The author has published a dataset to any of the INSDC databases. They copy its ENA Study or Project accession number.
  2. The author goes to the Biodiversity Data Journal (BDJ) webpage, clicks the “Start a manuscript” buttоn and selects OMICS Data Paper template in the ARPHA Writing Tool (AWT). Alternatively, the author can also start from the AWT website,  click “Create a manuscript”, and select “OMICS Data Paper” as the article type, the Biodiversity Data Journal will be automatically marked by the system. The author clicks the “Import a manuscript” button at the bottom of the webpage.
  3. The author pastes the ENA Study or Project accession number inside the relevant text box (“Import an European Nucleotide Archive (ENA) Study ID or Project ID”) and clicks “Import”.
  4. The Project or Study metadata is converted into an OMICS data paper manuscript along with the metadata from ArrayExpress and BioSamples if available. The author can start making changes to the manuscript,  invite co-authors and then submit it for technical evaluation, peer review and publication. 

For a detailed description of authoring an OMICS data paper, please refer to the Author Guidelines: https://bdj.pensoft.net/about#OmicsDataPapers

Our innovative workflow makes authoring omics data papers much easier and saves authors time and efforts when inserting metadata into the manuscript. It takes advantage of existing links between data repositories to unify biodiversity and omics knowledge into a single narrative. This workflow demonstrates the importance of standardisation and interoperability to integrate data and metadata from different scientific fields. 

We have established a special collection for OMICS data papers in the Biodiversity Data Journal. Authors are invited to describe their omics datasets by using the novel streamlined workflow for creating a manuscript at a click of a button from metadata deposited in ENA or by following the template to create their manuscript via the non-automated route.

To stimulate omics data paper publishing, the first 10 papers will be published free of charge. Upon submission of an omics data paper manuscript, do not forget to assign it to the collection Next-generation publishing of omics data.

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Field research in Turkmenistan’s highest mountain reveals high biological diversity

New open-access book presents a comprehensive report on the remarkable ecosystems of the Koytendag nature reserve

Location of Koytendag
Image by Atamyrat Veyisov

Situated in the extreme south-east of Turkmenistan: on the border with Uzbekistan and close to the border with Afghanistan, Koytendag presents one of the most distinct landscapes in Central Asia. Reaching elevations of up to 3,137 m, this is also the highest mountain in Turkmenistan.

Koytendag State Nature Reserve and its three Wildlife Sanctuaries: Hojapil, Garlyk and Hojaburjybelent, were established between 1986 and 1990 to protect and preserve the mountain ecosystem of the Koytendag region and maintain the ecological balance between the environment and increasing economic activities.

Since 2013, a series of scientific expeditions and assessments were coordinated and funded by the Royal Society for the Protection of Birds (RSPB) to pave the way for the protection and preservation of the unique landscape and rare wildlife the site is recognised for.

As a result, the efforts of the conducted field studies of multidisciplinary international research teams are brought together in a comprehensive report, which is now openly available as an Advanced Book from the scientific publisher and technology provider Pensoft, edited by Geoff Welch (RSPB) and Prof. Pavel Stoev (National National Museum of Natural History of Bulgaria and Pensoft). Soon, the book will also be available in Russian.

The book is split into eight sections focused on different areas within the study of biodiversity: Flora, Surface dwelling invertebrates, Cave fauna, Fish, Amphibians, Reptiles, Birds and Mammals. An additional chapter is dedicated to the hydrogeology of the site because of its key role in supporting both the cave fauna and the local communities.

Entrance to the newly discovered record-breaking underground lake at the Koytendag State Nature Reserve
Photo by Mikhail Pereladov

In the summary of the report, the authors make a list of the most significant findings made during the research. These include the discovery of a cave hosting the largest underground lake in the whole North Eurasia (4,400 m2) and a total of 48 species of higher plants that can only be found in Koytendag. In terms of Koytendag’s surface-dwelling fauna, the report lists a number of species new to science: a scorpion (most likely yet unnamed species currently recognised as a species complex) and a spider. Meanwhile, a total of seven previously unknown species were found underground, including the very first exclusively subterranean animal found in the country: the insect-like ‘marvellous’ dipluran named Turkmenocampa mirabilis, and a strongly adapted to the underground waters of a desert sinkhole Gammarus troglomorphus. Additionally, the annual monitoring, conducted since 1995 by the reserve staff, report an encouraging increase in the populations of the rare markhors and mouflons. An intact predator-prey community was also identified as a result of observations of numerous Eurasian lynxes and grey wolves, as well as prey species.

Entrance of the cave Kaptarhana, (Lebap Province, Eastern Turkmenistan), where scientists discovered the first ever exclusively subterranean dweller for the country in 2017 (find more here).
Photo by Aleksandr Degtyarev

Stephanie Ward, RSPB Central Asia Partner Development Officer, says:

“RSPB has been working in Turkmenistan under a Memorandum of Understanding with the Government since 2004. In that time we have had the privilege of working with a team of talented and dedicated national experts across the diverse and inspiring nature of this fascinating country. Our work in Koytendag has captured the attention and interest of many international scientists who hope that their contemporary biodiversity research will help to deepen the understanding and therefore ensure protection of the unique wonders of this mountain ecosystem. As a potential UNESCO World Heritage Site, we will continue to collaborate with the Turkmen people on the research and promotion of Koytendag State Nature Reserve.

Book editor and member of the research team Prof. Pavel Stoev adds:

“Koytendag Mountain is among the least explored and, simultaneously, one of the most biologically diverse regions in Central Asia. The rapid assessments of its flora and fauna revealed a high number of highly specialised species, all of which have undergone a long evolution to adapt to the harsh environments of the mountain. The establishment of Koytendag State Nature Reserve and the associated wildlife sanctuaries is a step in the right direction for the protection of this unique biota.”

The report, published in an openly accessible Advanced Book format, is available from
https://doi.org/10.3897/ab.e37858.

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Original source:

Welch G, Stoev P (2019) A report of RSPB-supported scientific research at Koytendag State Nature Reserve, East Turkmenistan. Advanced Books. https://doi.org/10.3897/ab.e37858

Additional information:

This work was carried out under the Memorandum of Understanding between the Ministry of Agriculture and Environment Protection of Turkmenistan and the RSPB, within the Project on “Improvement of the status of birds and other biodiversity in Turkmenistan”.

About Koytendag State Nature Reserve:

Koytendag State Nature Reserve was established in 1986 to protect and preserve the mountain ecosystem of the Koytendag region and maintain the ecological balance between the environment and the increasing anthropogenic activities. Of particular importance was the protection of rare species, such as the markhor; important habitats, including pistachio and juniper forests; and the impressive dinosaur trackways at Hojapil.

Advanced Books publishing by Pensoft:

Launched by Pensoft and powered by the scholarly publishing platform ARPHA, the Advanced Books approach aims to issue new books or re-issue books previously only available in print or PDF. In the Advanced Books format, the publications are semantically enhanced and available in HTML and XML as well, in order to accelerate open access, data publication, mining, sharing and reuse. The Advanced books builds on the novel approaches developed by the Pensoft’s journals.