ABCD

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ABCD BioCASe

• A Quick Introduction

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Motivation Rationale ABCD I

• Access to Biological Collection Data
• v2.06 ratified by TDWG, v1.20 still in use
• Comprehensive data exchange format
• to share detailed primary collection data of all
  organisms (living preserved specimens and
  observations)
• lately Extended For Geoscience ABCDEFG
• Fossils, rocks, minerals, meteorites
• Covers 925 concepts (EFG adds 825)

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Motivation Rationale ABCD II

• Monolithic xml schema with single root including
  15 subschemas defining reusable types (-gtUBIF)
• To ease processing publishing ABCD refrains
  from
• keys no normalisation, no external standards
• recursive xml structures
• Contains xsdany extension slots for ad-hoc
  additions through external schemas
• Variable atomisation (polymorphism) allows
  provision of data in different degrees of detail
  standardisation
• simplifies publishing, but pushes work to
  consumers
• priority towards mobilisation of rich data sources

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Motivation Rationale BioCASe

• XML based protocol for discovery retrieval in
  distributed, heterogenous systems
• Derived from DiGIR to share ABCD records
• supports hierarchical, nested structures
• Shared ontology defined in xml schema(s)
• concept namespace simple xpath to element in
  potential instance document

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Publishing Software Implementations

• PyWrapper
• implements BioCASe protocol
• Security layer
• for BioCASe services
• roles, signatures, access restriction,
  encryption, SSL

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Publishing Software Deployments

• PyWrapper
• ABCD
• 65 installations, 85 databases, mainly in Europe
• GCP Passport
• 15 installations, 22 DBs, worldwide
• BioCASE Collection Metadata Profile
• 25 installations DBs, Europe
• SPICE / Species2000
• 4 installations DBs, Europe
• 35 installation p.a. (ABCD,MCPDH)

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Consuming Software Implementations

• Simple UI, a simple but truly distributed portal
• Quertool for a single BioCASE service
• uses XSLTs (ABCD EFG, DarwinCore)
• Synthesys portal, in prep.
• uses multilingual XSLTs central cache
• Germplasm clearing house mechanism
• for GCP Passport ABCD services cache
• GBIF indexer/portal

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Consuming Software Deployments

• Simple UI
• BioCASE
• GBIF germany botany
• Quertool for a single BioCASE service
• part of PyWrapper, customized layout 5 times
• Synthesys portal, in prep.
• Synthesys
• GBIF-DE
• GBIF-FR
• Germplasm clearing house mechanism portal

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Potential Publishers

• All biological geoscience collections
• thousands, probably gt 20.000 collections
• billions of records, 1.5-3 billions vouchered
• digitisation currently very low (5 ?)

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Potential Customers

• Researchers
• biologists (taxonomy, genetics, ecology)
• historians
• Policy Makers
• e.g. land planning
• Public, Education, ...
• more customers the more
• detailed the data (e.g. images)
• exhaustive covering of collection

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Success Factors

• Comprehensiveness
• Ease of use (software installation)
• Personal free technical support (for Europe)
• Allows for custom extensions

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Hurdles to Adoption

• Complexity, both for consumers and publishers
• lack of good documentation with examples

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Big Picture

• ABCD feeds into ontology
• modularisation (taxa, publications, ...)
• as UML, XML schema, OWL