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Beispielbild BioCASe, ABCD and its extensions
Jörg HoletschekBotanic Garden & Botanical Museum Berlin-DahlemDept. of Biodiversity Informatics and LaboratoriesKönigin-Luise-Straße 6-814195 Berlin
ABCD 3 – Which Way To Go?TDWG Annual Meeting, Jönköping, October 29th, 2014
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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
Marmotamarmota? 2. Translates query to the source
database
SELECT *FROM specimenWHERE ScientificName LIKE “Marmota marmota%“
3. Transforms results into ABCD documents and sends them back
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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
4BioCASe, ABCD and its extensions. TDWG Annual Meeting, Jönköping, October 29th, 2014
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)
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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
6BioCASe, ABCD and its extensions. TDWG Annual Meeting, Jönköping, October 29th, 2014
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 forObservationsCulture CollectionsMycological UnitsZoological UnitsPaleontological UnitsPlant Genetic Resources
7BioCASe, ABCD and its extensions. TDWG Annual Meeting, Jönköping, October 29th, 2014
ABCD: Extensions
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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
9BioCASe, ABCD and its extensions. TDWG Annual Meeting, Jönköping, October 29th, 2014
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
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Thanks for your attention!
BioCASe, ABCD and its extensions. TDWG Annual Meeting, Jönköping, October 29th, 2014