The SYNTHESYS Specimen and Observation Portal
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The SYNTHESYS Specimen and Observation Portal Kelbert, P., Holetschek, J., Güntsch, A., Kusber, W.-H., Zippel, E. & Berendsohn, W.G. Freie Universität Berlin, Botanic Garden and Botanical Museum Berlin-Dahlem

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The SYNTHESYS Specimen and Observation Portal

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The synthesys specimen and observation portal

The SYNTHESYS Specimen and Observation Portal

Kelbert, P., Holetschek, J., Güntsch, A., Kusber, W.-H., Zippel, E. & Berendsohn, W.G.

Freie Universität Berlin, Botanic Garden and Botanical Museum Berlin-Dahlem

Dept. of Biodiversity Informatics and Laboratories Königin-Luise Str. 6-8, D-14195 Berlin, Germany

Email: [email protected]

Introduction

International networks and initiatives such as SYNTHESYS (www.synthesys.info), BioCASE (www.biocase.org) and GBIF (www.gbif.org) share the vision of free and open access to the world's primary biodiversity data. Observation and specimen data are drawn from a large number of databases worldwide and linked together, forming a huge number of records. Each object documents the occurrence of a given species at a specific time and location.

Currently (May 2009), the GBIF index lists 174 million occurrence records and the SYNTHESYS cache for European data holds 72 million records.

SYNTHESYS has developed a framework for setting up special interest networks; it consists of a mechanism to derive thematic subsets of the GBIF index and a highly configurable portal application.

Searching for Calendula aegyptiaca with query expansion – an example

The portal features both a simple taxon search function and an advanced query form. The queries can be expanded using taxonomic thesauri to synonyms, related concepts and misapplied names.

Comparing annotated units with original version

All BioCASE portals also feature an annotation service, which makes it possible to send data providers feedback about their data and to propose corrections or improvements for their biodiversity data.

  • 4. Results

  • overview of all units returned by your query

  • preview multimedia items

  • download the result as XML or CSV/XLS files.

1. Simple and advanced search

- select either a simple search on taxon name or advanced search with extended search functionality.

configure thesauri to use

incorrect

coordinates

click on the glasses

to activate the

query expansion

corrected

coordinates

pop up of taxon names

  • 5. Details

  • display details page for each unit with all original data from the provider

  • download the raw data from the provider

  • annotate unit data.

  • 2. Proposed query expansion

  • select the synonyms, misapplied names and related concepts you are interested in

  • click on the “Search!” button to expand the query with the selected names.

Linked maps from the Generic Point Mapper, a service provided by the Canadian Biological Information Facility. [http://www.cbif.gc.ca/mc/index_e.php]

Example from the EDIT/BioCASE portal (worldwide biodiversity data).

References

Kelbert, P., Hoffmann, N., Holetschek, J., Güntsch, A., Berendsohn, W. G. 2008: The new EDIT Specimen and Observation Explorer for Taxonomists. In: Weitzman, A. L. & Belbin, L. (ed.). Proceedings of TDWG (2008), Fremantle, Australia. [http://www.tdwg.org/proceedings/article/view/325]

Güntsch, A., Berendsohn, W. G., Ciardelli, P., Hahn, A., Kusber, W.-H. & Li, J. 2009: Adding content to content - a generic annotation system for biodiversity data. In: Studi Trent. Sci. Nat. 84: 123-128.

Kelbert, P., Güntsch, A., Hoffmann, N., Berendsohn, W. G. 2008: Checklist-driven access to European collection and observation data. Pp. 373 in: Gradstein, S. R. et al. (ed.): Systematics 2008 Programme and Abstracts, Göttingen. ISBN: 978-3-940344-23-6.

Güntsch, A., Kusber, W.-H., Döring, M., Ciardelli, P. & Berendsohn, W. G. 2007: Common access to distributed biodiversity information. Pp. 45-48 in: Kusber, W.-H. & Jahn, R. (ed.): Proceedings of the 1st Central European Diatom Meeting 2007, Berlin.[doi:10.3372/cediatom.109]

Hoffmann, N., Kelbert, P., Ciardelli, P. & Güntsch, A. 2007: TOQE - A Thesaurus Optimized Query Expander. Proceedings of the TDWG, 2007. [http://www.tdwg.org/proceedings/article/view/247]

Holetschek, J., Güntsch, A., Oancea, C., Döring, M., Berendsohn, W. G. 2006: Prototyping a Generic Slice Generation System for the GBIF Index. Pp. 51-52 in Belbin, L., Rissone, A. and Weitzman, A. (eds.). Proceedings of TDWG (2006), St Louis, MI. [http://www.tdwg.org/proceedings/article/view/63]

  • 3. Preview

  • refine the result data using the filters.

  • *the query returned 3347 units instead of 3 in the simple search*

filters

units found in the

GBIF/SYNTHESYS index

BioCASE/SYNTHESYS portal for Europe on the web

The portal can be used at http://search.biocase.org/europe

Documentation of the portal software, installation guide and the source code are available at http://www.biocase.org/products/portals/biocase_2


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