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/

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

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

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

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

Toward a service-based workflow for automated information extraction from herbarium specimens

Over the past years, herbarium collections worldwide have started to digitize millions of specimens on an industrial scale. Although the imaging costs are steadily falling, capturing the accompanying label information is still predominantly done manually and develops into the principal cost factor. In order to streamline the process of capturing herbarium specimen metadata, we specified a formal extensible workflow integrating a wide range of automated specimen image analysis services. We implemented the workflow on the basis of OpenRefine together with a plugin for handling service calls and responses. The evolving system presently covers the generation of optical character recognition (OCR) from specimen images, the identification of regions of interest in images and the extraction of meaningful information items from OCR. These implementations were developed as part of the Deutsche Forschungsgemeinschaft-funded a standardised and optimised process for data acquisition from digital images of herbarium specimens (StanDAP-Herb) Project

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

Placing taxonomists at the heart of a definitive and comprehensive global resource on the world's plants

It is time to synthesize the knowledge that has been generated through more than 260 years of botanical exploration, taxonomic and, more recently, phylogenetic research throughout the world. The adoption of an updated Global Strategy for Plant Conservation (GSPC) in 2011 provided the essential impetus for the development of the World Flora Online (WFO) project. The project represents an international, coordinated effort by the botanical community to achieve GSPC Target 1, an electronic Flora of all plants. It will be a first‐ever unique and authoritative global source of information on the world's plant diversity, compiled, curated, moderated and updated by an expert and specialist‐based community (Taxonomic Expert Networks – “TENs” – covering a taxonomic group such as family or order) and actively managed by those who have compiled and contributed the data it includes. Full credit and acknowledgement will be given to the original sources, allowing users to refer back to the primary data. A strength of the project is that it is led and endorsed by a global consortium of more than 40 leading botanical institutions worldwide. A first milestone for producing the World Flora Online is to be accomplished by the end of 2020, but the WFO Consortium is committed to continuing the WFO programme beyond 2020 when it will develop its full impact as the authoritative source of information on the world's plant biodiversity