Managing and publishing fungal community barcoding data by use of the process-oriented schema MOD-CO and a GFBio data publication pipeline

The need to fulfil FAIR guiding principles for data management and publication [1] directly affects researchers, i.e., data producers as well as data managers. Data management has to be set up well already at an early stage of the data life cycle. This is demonstrated by a best practice work- and dataflow 'Fungal community barcoding data', which has been established as side product in the context of the project 'GBOL 2 Mycology‘, German Barcode of Life initiative (https://www.bolgermany.de/). The work- and dataflow was set up by applying the newly published MOD-CO schema, Version 1.0 which has been implemented as an instance of the database application DiversityDescriptions for data management, and for making data compliant to GFBio infrastructure for data archiving and publication. The comprehensive conceptual schema MOD-CO for 'Meta-Omics Data of Collection Objects' Version 1.0 was published as Linked Open Data representation in spring 2018 [2]. The process-oriented schema describes operations and object properties along the work- and dataflow from gathering environmental samples, to the various transformation, transaction, and measurement steps in the laboratory up to sample and data publication and archiving. By supporting various kinds of relationships, the MOD-CO schema allows for the concatenation of individual records of the operational steps along a workflow. The MOD-CO descriptor structure in version 1.0 comprises 653 descriptors (concepts) and 1,810 predefined descriptor states, organised in 37 concept collections. The published version 1.0 is available as various schema representations of identical content (https://www.mod-co.net/wiki/Schema_Representations). This schema has been implemented as data structure in the relational database DiversityDescriptions (DWB-DD) (https://diversityworkbench.net/Portal/DiversityDescriptions), a generic component of the Diversity Workbench environment (https://diversityworkbench.net). DWB-DD is considered being appropriate to be applied as a LIMS (Laboratory Information Management System) and ELN (Electronic Laboratory Notebook) for organising Fungal community barcoding data' and similar data collections in molecular laboratories. Its data export interface provides guidance to generate data and metadata in the formats CSV and XML, the latter following the SDD metadata schema with involvement of extensions by metadata elements from EML and ABCD standards; for community standards see: https://gfbio.biowikifarm.net/wiki/Data_exchange_standards,_protocols_and_formats_relevant_for_the_collection_data_domain_within_the_GFBio_network. The research data themselves are organised according to the MOD-CO data schema. The data package of the work- and dataflow 'Fungal community barcoding data' is going to be submitted to GFBio after having been checked for GFBio compliance and to be published under a creative common license. Suggestions for standardized citation will be provided, a DOI assigned, and long-term data archiving ensured. KEYWORDS: DiversityDescriptions, German Barcode of Life (GBOL), German Federation for Biological Data (GFBio), MOD-CO conceptual schema, use case for community barcoding data REFERENCES: 1. Wilkinson, M.D. et al. 2016. The FAIR Guiding Principles for scientific data management and stewardship. – Sci. Data 3: 160018. DOI: 10.1038/sdata.2016.18. 2. Rambold, G., Yilmaz, P., Harjes, J., Link, A., Glöckner, F.O., Triebel, D. 2018. MOD-CO schema – a conceptual schema for processing sample data in meta’omics research (version 1.0). http://mod-co.net/wiki/MOD-CO_Schema_Reference

Software infrastructure and data pipelines established for technical interoperability within a cross-border cooperation for the flora of the Bohemian Forest

The timely and geographical resolutions, as well as the quantity and taxon concepts of records on the occurrence of plants near national borders is often ambiguous. This is due to the regional focus and different approaches of the contributing national and regional databases and networks of the neighbouring countries. Careful data transformation between national data providers is essential for understanding distribution patterns and its dynamics for organisms in areas along the national borders. Sharing occurrence data through the international data aggregator Global Biodiversity Information Facility (GBIF) is also complicated and has to consider that the underlying taxonomic concept and geographic information system of each single GBIF dataset might be different. In addition, some regional data providers have a restrictive (non-cc) licensing policy which does not allow data publication via the GBIF network. Therefore, it is necessary to investigate new ways to make data fit for use for a better and comprehensive understanding of the Flora of the Bohemian Forest.In this paper, we present a bilateral technical interoperability solution for vascular plant occurrence data for the area between the Czech Republic and Bavaria. We describe the initial state of data providers in both countries and the factual and technical challenges in finding a sustainable concept to establish mutual data sharing. The resulting solution for a functional infrastructure and an agreed data pipeline is described in a step-by-step approach. The new distributed infrastructure allows botanists and other stakeholders from both countries to work within the cross-border context of historical and current plants' distribution

LIAS light – Towards the ten thousand species milestone

Volume: 8Start Page: 11End Page: 1

An online authoring and publishing platform for field guides and identification tools

Various implementation approaches are available for digital field guides and identification tools that are created for the web and mobile devices. The architecture of the “biowikifarm” publishing platform and some technical and social advantages of a document- and author-centric approach based on the MediaWiki open source software over custom-developed, database driven software are presented

A flexible Diversity Workbench tool to publish biodiversity data from SQL database networks through platforms like GFBio

The Diversity Workbench (DWB, www.diversityworkbench.net) is a suite of MS SQL databases and data processing tools designed for the management of research data in biology, ecology and geosciences. The software apart from the underlying DBMS is open source. The complete software package is freely available. The DWB with ten data domain-specific databases, one generic database and some independent data processing tools is the result of 20 years software development. The DWB is suitable for single researchers, research groups of any size but also appropriate to set up networks for long-term data repositories and data centers. To operate automated transfer of bio- and geodiversity data for publication from those in-house networks, a new DWB tool was implemented. The core functions include the filtering and transformation of data and metadata from selected in-house data collections stored in productive master SQL databases. The tool is designed for use by database administrators and scientific data curators. It fulfils three major steps for each single data collection: • term, taxa and metadata assignment with parallel data export and creation of a not publicly accessible first-level cache MS SQL database independent from the DWB master database network; unifying data from data domain-specific DWB source databases inside of a (institutional) firewall • re-organisation of data, filtering according later data package assignment and creation of a second-level publicly accessible PostgreSQL database • creation of a publicly accessible data package properly formatted for data harvesting tools of web portals and for data mapping and provision software like the BIOCASe Provider Software. With this DWB tool for guiding data publication some major challenges in bio- and geodiversity research are addressed: a) The data filtering, transformation and publication can be done periodically and is realized without data change and information loss in the linked in-house master databases which might be curated in the long-run. b) A data expert and data scientist is able to handle this transformation tool and organize data publication with minor involvement of a database administrator. c) The data packages are configured for publication according to the individual requests of data producers who often ask for anonymization of certain persons, intend to withhold single data units, set embargos and have to blur geographic coordinates. d) With the automated data transfer for publication, the tool guarantees a reproducible path from the original source to the presentation on a platform. The data centers SMNS and SNSB are using the tool to guide their data publication through the GBIF global biodiversity data network (https://www.gbif.org/) and through the GFBio platform (https://www.gfbio.org/). Furthermore, it is used to create specifically formatted, publicly accessible cache databases with filtered and aggregated content for thematically focused information portals like the Botanischer Informationsknoten Bayern (http://daten.bayernflora.de/de/index.php). Summarizing, the new DWB tool is able to support a wide range of data transfer and transformation tasks for data publication from DWB networks. It is included in the published software versions of DiversityCollection and described in its manual. Future planning includes the extension of the tool to involve the data filtering and transformation from DiversityDescriptions as a generic DWB source database. KEYWORDS: automated data transfer, biodiversity data, data filtering, data publication, GFBio data center

Taxonomy based on science is necessary for global conservation

Peer reviewe

Notes on the Genus Sagediopsis (Verrucariales, Adelococcaceae)

Volume: 1Start Page: 273End Page: 28

Was ist Lecidea whakatipae Knight?

Volume: 23Start Page: 343End Page: 34