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BioCASe, ABCD and its extensions

BioCASe is a protocol, schema, and software that allows communication between biodiversity data providers and networks. It translates queries, retrieves data, and sends them back in the form of ABCD documents. It is widely used and supports various data types.

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BioCASe, ABCD and its extensions

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  1. BioCASe, ABCD and its extensions Jörg Holetschek Botanic 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

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

  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) BioCASe, ABCD and its extensions. TDWG Annual Meeting, Jönköping, October 29th, 2014

  5. ABCD: General Parts • Metadata (dataset-wide) • Dataset title & description • IPR statements • Contactpersons • Links to additional resources • Record-level data • Gathering/observation Event • Localitydetails • 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 forObservationsCulture CollectionsMycological UnitsZoological UnitsPaleontological UnitsPlant Genetic Resources BioCASe, ABCD and its extensions. TDWG Annual Meeting, Jönköping, October 29th, 2014

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

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

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

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