Beispielbild BioCASe, ABCD and its extensions Jörg Holetschek Botanic Garden & Botanical Museum Berlin-Dahlem Dept. of Biodiversity Informatics and Laboratories.

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Presentation transcript:

Beispielbild BioCASe, ABCD and its extensions Jörg Holetschek Botanic Garden & Botanical Museum Berlin-Dahlem Dept. of Biodiversity Informatics and Laboratories Königin-Luise-Straße Berlin ABCD 3 – Which Way To Go? TDWG Annual Meeting, Jönköping, October 29 th, 2014

2 Protocol + schema + software enabling communication between - primary biodiversity data providers and - biodiversity networks (consumers/aggregators) 1.Accepts requests from the network BioCASe, ABCD and its extensions. TDWG Annual Meeting, Jönköping, October 29th, 2014 Biological Collection Access Service Marmota marmota? 2.Translates query to the source database SELECT * FROM specimen WHERE ScientificName LIKE “Marmota marmota%“ 3.Transforms results into ABCD documents and sends them back

3 Usage of ABCD/BioCASe Currently ~ 100 installations worldwide, serving ~ 40m records to GBIF and 5 Special Interest Networks BioCASe, ABCD and its extensions. TDWG Annual Meeting, Jönköping, October 29th, 2014

4 ABCD Data Schema Access to Biological Collection Data: Data schema for all types of primary biodiversity data (living/preserved/observational, botanical/zoological/bacterial/viral, marine/terrestrial) XML (eXtensible Markup Language) based  can be consumed by humans and machines Highly complex, hierarchical Version 2.06b: 840 leaf elements (+ 260 attributes) Extendable (plug-in slot for additional information) standard (currently version 2.06)

5 ABCD: General Parts Metadata (dataset-wide) -Dataset title & description -IPR statements -Contact persons -Links to additional resources Record-level data -Gathering/observation Event -Locality details -Determination(s) -Multimedia documents -References -Notes, additional facts BioCASe, ABCD and its extensions. TDWG Annual Meeting, Jönköping, October 29th, 2014

6 ABCD: Specialised Portions Specimen Unit: Acquisition, Accession, Peparation, Duplicate Distribution, Type Status Herbarium Unit: Loan Information Botanical Garden Unit: Location in Garden, Hardiness, Lineage, Cultivation, Planting Date Other Specialised Subtrees for Observations Culture Collections Mycological Units Zoological Units Paleontological Units Plant Genetic Resources

7BioCASe, ABCD and its extensions. TDWG Annual Meeting, Jönköping, October 29th, 2014 ABCD: Extensions

8 Current ABCD Extensions Extension for Geosciences (ABCD-EFG) DNA Bank Network/GGBN (ABCD-DNA) Herbarium Information Standards and Protocols for Interchange of Data (HISPID) BioCASe, ABCD and its extensions. TDWG Annual Meeting, Jönköping, October 29th, 2014

9 BioCASe Provider Software (PyWrapper) Implementation of the BioCASe protocol Can be used with any XML data schema (ABCD, DarwinCore, ABCD-EFG, ABCD-DNA) Works with most SQL-compliant databases (Access, MySQL, Postgres, SQL Server, Firebird, Oracle, FoxPro, Sybase) Platform independent

10 Thanks for your attention! BioCASe, ABCD and its extensions. TDWG Annual Meeting, Jönköping, October 29th, 2014