beispielbild biocase, abcd and its extensions jörg holetschek botanic garden & botanical museum...

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