Devising the EDIT Platform for Cybertaxonomy

This contribution describes the original ideas and preparatory work that led to the implementation of the EDIT Platform for Cybertaxonomy, a computing environment supporting the entire taxonomic workflow. It also briefly describes the current state of development of the project, which will end its EU-funded period in February, 2011

Using geographical and taxonomic metadata to set priorities in specimen digitization

Digitizing the information carried by specimens in natural history collections is a key endeavor providing falsifiable information about past and present biodiversity on a global scale, for application in a variety of research fields far beyond the current application in biosystematics. Existing digitization efforts are driven by individual institutional necessities and are not coordinated on a global scale. This led to an over-all information resource that is patchy in taxonomic and geographic coverage as well as in quality. Digitizing all specimens is not an achievable aim at present, so that priorities need to be set. Most biodiversity studies are both taxonomically and geographically restricted, but access to non-digitized collection information is almost exclusively by taxon name. Creating a “Geotaxonomic Index” providing metadata on the number of specimens from a specific geographic region belonging to a specific higher taxonomic category may provide a means to attract the attention of researchers and governments towards relevant non-digitized holdings of the collections and set priorities for their digitization according to the needs of information users outside the taxonomic community

EFFECTIVELY SEARCHING SPECIMEN AND OBSERVATION DATA WITH TOQE, THE THESAURUS OPTIMIZED QUERY EXPANDER

Today’s specimen and observation data portals lack a flexible mechanism, able to link up thesaurus-enabled data sources such as taxonomic checklist databases and expand user queries to related terms, significantly enhancing result sets. The TOQE system (Thesaurus Optimized Query Expander) is a REST-like XML web-service implemented in Python and designed for this purpose. Acting as an interface between portals and thesauri, TOQE allows the implementation of specialized portal systems with a set of thesauri supporting its specific focus. It is both easy to use for portal programmers and easy to configure for thesaurus database holders who want to expose their system as a service for query expansions. Currently, TOQE is used in four specimen and observation data portals. The documentation is available from http://search.biocase.org/toqe/

Freier Zugang zu den Informationen der Artenvielfalt - Wie werde ich Teil der Global Biodiversity Information Facility (GBIF)?

Die Global Biodiversity Information Facility ist ein internationaler Zusammenschluss von Staaten und Organisationen mit dem Ziel, die weltweit vorhandenen Primärdaten zur Artenvielfalt über das Internet frei verfügbar zu machen. Dieser Artikel gibt einen kurzen Überblick über die Ziele und den Aufbau von GBIF sowie die zugrunde liegenden Prinzipien, erläutert Architektur und Datenströme im Netzwerk und geht auf die verwendeten Standards, Protokolle, Datenschemata und deren Implementierung ein. Im Abschluss werden die notwendigen Schritte zur Anbindung einer bestehenden Sammlungsdatenbank an das GBIF-Netzwerk aufgezeigt sowie die Möglichkeiten einer Hilfestellung durch GBIF-Deutschland.StichwörterBiodiversity, GBIF, GBIF-D, database, network, collection, specimens, observations, XML, ABCD schema, provider software, Python wrapper, BioCASe protocol, mapping, search portal.The Global Biodiversity Information Facility is an international initiative of countries and organizations that aims at providing free access over the internet to the world's existing primary data on biodiversity. This article gives a short review of the goals and the organization of GBIF and its basic principles, illustrates the architecture and data flows within the network and illuminates the standards, protocols and schemas used for these purposes and their implementation. It describes the required steps for connecting an existing collection database to the GBIF network and the potential support by the GBIF helpdesk.KeywordsBiodiversity, GBIF, GBIF-D, database, network, collection, specimens, observations, XML, ABCD schema, provider software, Python wrapper, BioCASe protocol, mapping, search portal

Caryophyllales 2015 in Berlin and the Global Caryophyllales Initiative

Fil: Arias, Salvador. Universidad Nacional Autónoma de México; MéxicoFil: Berendsohn, Walter G.. Freie Universität Berlin; AlemaniaFil: Borsch, Thomas. Freie Universität Berlin; AlemaniaFil: Flores Olvera, Hilda. Universidad Nacional Autónoma de México; MéxicoFil: Ochoterena, Helga. Universidad Nacional Autónoma de México; MéxicoFil: von Mering, Sabine. Freie Universität Berlin; AlemaniaFil: Zuloaga, Fernando Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; Argentin

Descriptive Data in the EDIT Platform for Cybertaxonomy

This paper describes the integration of structured descriptive data in the EDIT platform for Cybertaxonomy. The platform is composed of several software modules supporting the taxonomic workflow from data capture and storage to publication. Descriptive data play an important role within the taxonomic work process. The integration of these data via import/export modules to and from the platform and the publication as natural language output or as keys are explained

Adding content to content -a generic annotation system for biodiversity data

suMMArY -Adding content to content -a generic annotation system for biodiversity data -Biodiversity information networks such as GBiF and BiocAse provide access to a rapidly growing number of collection records, ranging from simple occurrence information to high resolution images. today, about 150 million observation and collection records are available at a global level. Although the technology for providing and retrieving primary biodiversity data is reasonably mature, the development of advanced techniques for feedback using annotations has been neglected. We have developed and implemented a web-based annotation system which fills this gap. rather than sending the annotation as a message to the collection holder, the system allows for adding, changing and removing information in a copy of the collection record. the modified record is then stored on a public annotation server together with all previous versions. this allows collection holders to compare the different versions and decide whether a given annotation will be fed back into the collection database. the system works with any GBiF-compliant information network. riAssunto -Aggiungere contenuti ai contenuti -un sistema per la gestione delle annotazioni per dati relativi alla biodiversità -le reti informatiche per i dati sulla biodiversità, come GBiF e BiocAse, consentono l'accesso a un numero, in rapido incremento, di schede sugli esemplari catalogati appartenenti a varie collezioni: le informazioni in esse contenute spaziano da semplici occorrenze in un'area geografica fino a immagini ad alta risoluzione. oggigiorno, a livello globale, sono disponibili circa 150 milioni di osservazioni e schede riferite a esemplari collezionati. sebbene la tecnologia in grado di fornire e recuperare dati primari relativi alla biodiversità si sia evoluta raggiungendo livelli di funzionalità ragionevoli, è stato tuttavia trascurato lo sviluppo di tecniche avanzate di feedback che fanno uso di annotazioni. Abbiamo allora elaborato e implementato un sistema di annotazioni basato sul web che colma questa lacuna. invece di inviare l'annotazione al curatore della collezione sotto forma di messaggio, tale sistema consente di aggiungere, cambiare e rimuovere informazioni in una copia della scheda catalogata della collezione. la scheda modificata viene quindi salvata su un server pubblico per le annotazioni insieme a tutte le versioni precedenti. Questo consente ai curatori delle collezioni di paragonare le differenti versioni e di decidere se accettare una certa annotazione nel database della collezione. il sistema può operare con qualsiasi rete informatica compatibile con GBiF

Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens

We present the model and implementation of a workflow that blazes a trail in systematic biology for the re-usability of character data (data on any kind of characters of pheno- and genotypes of organisms) and their additivity from specimen to taxon level. We take into account that any taxon characterization is based on a limited set of sampled individuals and characters, and that consequently any new individual and any new character may affect the recognition of biological entities and/or the subsequent delimitation and characterization of a taxon. Taxon concepts thus frequently change during the knowledge generation process in systematic biology. Structured character data are therefore not only needed for the knowledge generation process but also for easily adapting characterizations of taxa. We aim to facilitate the construction and reproducibility of taxon characterizations from structured character data of changing sample sets by establishing a stable and unambiguous association between each sampled individual and the data processed from it. Our workflow implementation uses the European Distributed Institute of Taxonomy Platform, a comprehensive taxonomic data management and publication environment to: (i) establish a reproducible connection between sampled individuals and all samples derived from them; (ii) stably link sample-based character data with the metadata of the respective samples; (iii) record and store structured specimen-based character data in formats allowing data exchange; (iv) reversibly assign sample metadata and character datasets to taxa in an editable classification and display them and (v) organize data exchange via standard exchange formats and enable the link between the character datasets and samples in research collections, ensuring high visibility and instant re-usability of the data. The workflow implemented will contribute to organizing the interface between phylogenetic analysis and revisionary taxonomic or monographic work

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

Cactaceae at Caryophyllales.org- A dynamic online species-level taxonomic backbone for the family

This data paper presents a largely phylogeny-based online taxonomic backbone for the Cactaceae compiled from literature and online sources using the tools of the EDIT Platform for Cybertaxonomy. The data will form a contribution of the Caryophyllales Network for the World Flora Online and serve as the base for further integration of research results from the systematic research community. The final aim is to treat all effectively published scientific names in the family. The checklist includes 150 accepted genera, 1851 accepted species, 91 hybrids, 746 infraspecific taxa (458 heterotypic, 288 with autonyms), 17,932 synonyms of accepted taxa, 16 definitely excluded names, 389 names of uncertain application, 672 unresolved names and 454 names belonging to (probably artificial) named hybrids, totalling 22,275 names. The process of compiling this database is described and further editorial rules for the compilation of the taxonomic backbone for the Caryophyllales Network are proposed. A checklist depicting the current state of the taxonomic backbone is provided as supplemental material. All results are also available online on the website of the Caryophyllales Network and will be constantly updated and expanded in the future. Citation: Korotkova N., Aquino D., Arias S., Eggli U., Franck A., Gómez-Hinostrosa C., Guerrero P. C., Hernández H. M., Kohlbecker A., Köhler M., Luther K., Majure L. C., Müller A., Metzing D., Nyffeler R., Sánchez D., Schlumpberger B. & Berendsohn W. G. 2021: Cactaceae at Caryophyllales.org- A dynamic online species-level taxonomic backbone for the family.-Willdenowia 51: 251-270. Version of record first published online on 31 August 2021 ahead of inclusion in August 2021 issue. Data published through: Http://caryophyllales.org/cactaceae/Checklis