ABCD & BioCASe A Quick Introduction

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)

Motivation & Rationale – ABCD II Monolithic xml schema with single root including ~15 subschemas defining reusable types (->UBIF) To ease processing & publishing ABCD refrains from:  keys; no normalisation, no external standards  recursive xml structures Contains xsd:any 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

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

Publishing Software Implementations PyWrapper  implements BioCASe protocol Security layer  for BioCASe services  roles, signatures, access restriction, encryption, SSL

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 / Species installations & DBs, Europe  +35 installation p.a. (ABCD,MCPDH)

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

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

Potential Publishers All biological & geoscience collections  thousands, probably > collections  billions of records, billions vouchered  digitisation currently very low (5% ?)

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

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

Hurdles to Adoption Complexity, both for consumers and publishers lack of good documentation with examples

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