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Published byAugustus Perkins Modified over 8 years ago
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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 (->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
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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 > 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
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