A botanical demonstration of the potential of linking data using unique identifiers for people

Natural history collection data available digitally on the web have so far only made limited use of the potential of semantic links among themselves and with cross-disciplinary resources. In a pilot study, botanical collections of the Consortium of European Taxonomic Facilities (CETAF) have therefore begun to semantically annotate their collection data, starting with data on people, and to link them via a central index system. As a result, it is now possible to query data on collectors across different collections and automatically link them to a variety of external resources. The system is being continuously developed and is already in production use in an international collection portal

History and development of ABCDEFG: a data standard for geosciences

Museums and their collections have specially customized databases in order to optimally gather and record their contents and associated metadata associated with their specimens. To share, exchange, and publish data, an appropriate data standard is essential. ABCD (Access to Biological Collection Data) is a standard for biological collection units, including living and preserved specimen, together with field observation data. Its extension, EFG (Extension for Geoscience), enables sharing and publishing data related to paleontological, mineralogical, and petrological objects. The standard is very granular and allows detailed descriptions, including information about the collection event itself, the holding institution, stratigraphy, chemical analysis, and host rock. The standard extension was developed in 2006 and has been used since then by different initiatives and applied for the publication of collection-related data in\ud domain-specific and interdisciplinary portals

The EDIT Platform for Cybertaxonomy - an integrated software environment for biodiversity research data management

The Platform for Cybertaxonomy [1], developed as part of the EU Network of Excellence EDIT (European Distributed Institute of Taxonomy), is an open-source software framework covering the full breadth of the taxonomic workflow, from fieldwork to publication [2]. It provides a number of tools for full, customized access to taxonomic data, editing and management, and collaborative team work. At the core of the platform is the Common Data Model [3], offering a comprehensive information model covering all relevant data domains: names and classifications, descriptive data (morphological and molecular), media, geographic information, literature, specimens, persons, and external resources [4]. The model adheres to community standards developed by the Biodiversity Information Standards organization TDWG [5]. Apart from its role as a software suite supporting the taxonomic workflow, the platform is a powerful information broker for a broad range of taxonomic data providing solid and open interfaces including a Java programmer’s library and a CDM Rest Service Layer. In the context of the DFG-funded "Additivity" project ("Achieving additivity of structured taxonomic character data by persistently linking them to preserved individual specimens", DFG project number 310530378), we are developing components for capturing and processing formal descriptions of specimens as well as algorithms for aggregating data from individual specimens in order to compute species-level descriptions [6]. Well-defined and agreed descriptive vocabularies referring to structures, characters and character states are instrumental in ensuring the consistency and comparability of measurements. This will be addressed with a new EDIT Platform module for specifying vocabularies based on existing ontologies for descriptive data. To ensure that these vocabularies can be re-used in different contexts, we are planning an interface to the Terminology Service developed by the German Federation for Biological Data (GFBio) [7]. The Terminology Service provides a semantic standards aware and harmonised access point for distributed or locally stored ontologies required for biodiversity research data management, archiving and publication processes [8]. The interface will work with a new OWL export function of the CDM library, which provides EDIT Platform vocabularies in a format that can be read by the import module of the Terminology Service. In addition, the EDIT Platform will be equipped with the ability to import semantic concepts from the Terminology Service using its API and keeping a persistent link to the original concept. With an active pipeline between the EDIT Platform and the GFBio Terminology Service, terminologies originating from the taxonomic research process can be re-used in different research contexts as well as for the semantic annotation and integration of existing research data processed by the GFBio archiving and data publication infrastructure. KEYWORDS: taxonomic computing, descriptive data, terminology, inference REFERENCES: 1. EDIT Platform for Cybertaxonomy. http://www.cybertaxonomy.org (accessed 17 May 2018). 2. Ciardelli, P., Kelbert, P., Kohlbecker, A., Hoffmann, N., Güntsch, A. & Berendsohn, W. G., 2009. The EDIT Platform for Cybertaxonomy and the Taxonomic Workflow: Selected Components, in: Fischer, S., Maehle, E., Reischuk, R. (Eds.): INFORMATIK 2009 – Im Focus das Leben. GI-Edition: Lecture Notes in Informatics (LNI) – Proceedings 154. Köllen Verlag, Bonn, pp. 28;625-638. 3. Müller, A., Berendsohn, W. G., Kohlbecker, A., Güntsch, A., Plitzner, P. & Luther, K., 2017. A Comprehensive and Standards-Aware Common Data Model (CDM) for Taxonomic Research. Proceedings of TDWG 1: e20367. https://doi.org/10.3897/tdwgproceedings.1.20367. 4. EDIT Common Data Model. https://dev.e-taxonomy.eu/redmine/projects/edit/wiki/CommonDataModel (accessed 17 May 2018). 5. Biodiversity Information Standards TDWG. http://www.tdwg.org/ (accessed 17 May 2018). 6. Henning T., Plitzner P., Güntsch A., Berendsohn W. G., Müller A. & Kilian N., 2018. Building compatible and dynamic character matrices – Current and future use of specimen-based character data. Bot. Lett. https://doi.org/10.1080/23818107.2018.1452791. 7. Diepenbroek, M., Glöckner, F., Grobe, P., Güntsch, A., Huber, R., König-Ries, B., Kostadinov, I., Nieschulze, J., Seeger, B.; Tolksdorf, R. & Triebel, D., 2014. Towards an Integrated Biodiversity and Ecological Research Data Management and Archiving Platform: The German Federation for the Curation of Biological Data (GFBio), in: Plödereder, E., Grunske, L., Schneider, E., Ull, D. (Eds.): Informatik 2014 – Big Data Komplexität meistern. GI-Edition: Lecture Notes in Informatics (LNI) – Proceedings 232. Köllen Verlag, Bonn, pp. 1711-1724. 8. Karam, N., Müller-Birn, C., Gleisberg, M., Fichtmüller, D., Tolksdorf, R., & Güntsch, A., 2016. A Terminology Service Supporting Semantic Annotation, Integration, Discovery and Analysis of Interdisciplinary Research Data. Datenbank-Spektrum, 16(3), 195–205. https://doi.org/10.1007/s13222-016-0231-8

History and development of ABCDEFG: a data standard for geosciences

Museums and their collections have specially customized databases in orderto optimally gather and record their contents and associated metadataassociated with their specimens. To share, exchange, and publish data, anappropriate data standard is essential. ABCD (Access to BiologicalCollection Data) is a standard for biological collection units, includingliving and preserved specimen, together with field observation data. Itsextension, EFG (Extension for Geoscience), enables sharing and publishing datarelated to paleontological, mineralogical, and petrological objects. Thestandard is very granular and allows detailed descriptions, includinginformation about the collection event itself, the holding institution,stratigraphy, chemical analysis, and host rock. The standard extension was developed in 2006 and has been used since then by differentinitiatives and applied for the publication of collection-related data indomain-specific and interdisciplinary portals

Quality issues in georeferencing: from physical collections to digital data repositories for ecological research

Natural history collections constitute an enormous wealth of information of Life on Earth. It is estimated that over 2 billion specimens are preserved at institutions worldwide, of which less than 10% are accessible via biodiversity data aggregators such as GBIF. Moreover, they are a very important resource for eco¿evolutionary research, which greatly depends on knowing the precise location where the specimens were collected in order to characterize the environment in which they lived. Yet, only about 55% of the accessible records are georeferenced and only 31% have coordinate uncertainty information, which is critical for conducting rigorous studies. The awareness of this gap of knowledge which hinders the enormous potential of such data in research led to the organization of a workshop which brought together key players in georeferencing of natural history collections. The discussion and outcomes of this workshop are here presented

Quality issues in georeferencing: from physical collections to digital data repositories for ecological research

Natural history collections constitute an enormous wealth of information of Life on Earth. It is estimated that over 2 billion specimens are preserved at institutions worldwide, of which less than 10% are accessible via biodiversity data aggregators such as GBIF. Moreover, they are a very important resource for eco¿evolutionary research, which greatly depends on knowing the precise location where the specimens were collected in order to characterize the environment in which they lived. Yet, only about 55% of the accessible records are georeferenced and only 31% have coordinate uncertainty information, which is critical for conducting rigorous studies. The awareness of this gap of knowledge which hinders the enormous potential of such data in research led to the organization of a workshop which brought together key players in georeferencing of natural history collections. The discussion and outcomes of this workshop are here presented