Biodiversity data federation The Atlas of Living Australia

1. Biodiversity data federationThe Atlas of Living Australia Donald Hobern, Donald.Hobern@csiro.au Canberra, March 2010

2. The Atlas of Living Australia (ALA) • Government-funded (NCRIS/Super Science) to June 2012 • Mission: • To develop an authoritative, freely accessible, distributed and federated biodiversity data management system that links Australia’s biological knowledge with its scientific reference collections and other custodians of biological information • To share biodiversity knowledge to shape our future • Key data types: • Specimens and Observations • Names and Classifications • Descriptions and diagnostic keys • Images and other multimedia • Molecular sequences

3. Biodiversity information New Holland Honeyeater (Phylidonyris novaehollandiae) Root rot Phytophthora cinnamomi Banksia jewel beetle Cyrioides imperialis Feeds upon nectar Pathogen of Larvae mine stems Pollinates Banksia serrata L.f. = Isostylis serrata (L.f.) Britten Biology and ecology Identified as = Sirmuellera serrata (L.f.) Kuntze Old Man Banksia Saw Banksia Kingdom: Plantae Division: Magnoliophyta Family: Proteaceae Subfamily: Grevilleoideae Tribe: Banksieae Subtribe: Banksiinae Genus: Banksia L.f. Molecular biology Literature Distribution

4. Uses: Biosecurity • Questions • What is this organism? • Is it a pest? • Does it carry or cause disease? • Could it spread in Australia? • How can it be controlled? • Information needed • Names and classification • Identification keys • Images • Distribution data • Food webs • Literature (biology and control)

5. Uses: Land-use planning • Questions • What species are found here? • Are they threatened? • What are their needs? • How can impacts be minimised? • How can habitats be restored? • Information needed • Names and classification • Distribution data • Food webs • Literature (biology and control)

6. Repurposing data Uses (biosecurity, land-use, climate change, crop development, resource management, materials, forensics, taxonomy, etc.) Species Pages Regional Atlas Biosecurity Portal Annotation Tools Names and Classification Distribution Metadata repository Links to international projects Metadata (source, methods, ownership, access, etc.) Data (collections, field observations, literature, molecular, images, expert knowledge, etc.)

7. Data integration

8. Data integration

9. Harvest data Ontology Register Data Provider Sp Refers to Found in Geospatial cache Data resources Resource Species Region Discover Sp AFD Sp Sp Sp Harvest Harvest APNI/APC Harvest reports Sp Sp Sp Sp Sp Sp Sp Sp Sp Harvest reports Sp Sp Sp Sp Sp Sp Protected area DB Harvest reports Metadata repository Metadata Repository Taxonomy Services Metadata Annotation Server

10. Implementation • Version 1 • Fedora Commons • Ingestion of metadata as streams on Fedora objects • Version 2 • Ingest properties into BigTable • Generate RDF documents from BigTable • Original and derived properties • Preserve properties and values from original source • Where beneficial, derive standard interpreted properties and values

11. Vocabularies

12. Metamodel

13. Property mapping

14. Key challenges • Suitable meta-model – adopt or develop • Suitable vocabularies – adopt or develop • Appropriate mapping of original properties • Size of data – millions of attributable data elements