Biological Science Collections Tagging and Tracking presented at SPNHC
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Biological Science Collections Tagging and Tracking presented at SPNHC
- 1. BiSciCol: Biological Science Collections Tracker Tracking Biodiversity Objects to Brokering Standards Brian Stucky, University of Colorado, Boulder John Deck, University of California, Berkeley Lukasz Ziemba, University of Florida, Gaineseville Nico Cellinese, University of Florida, Gainesville Rob Guralnick, University of Colorado, Boulder BiSciCol Team: Reed Beaman, Nico Cellinese, Jonathan Coddington, Neil Davies, John Deck, Rob Guralnick, Bryan P. Heidorn, Chris Meyer, Tom Orrell, Rich Pyle, Kate Rachwal, Brian Stucky, Rob Whitton, Lukasz Ziemba Univ. Hawai’i Univ. Arizona Smithsonian
- 2. • National Science Foundation funded 2010 – 2014 • Infrastructure to tag & track specimens & derivates in cyberspace • Relies on globally unique identifiers (GUIDs) to track objects • Implements a Linked Data approach
- 4. QUANTITY OF DATA IS FIRST LINK IN A LARGER CHAIN OF ISSUES
- 5. Here is the problem: Lots of Data …. Generates …
- 6. Data stores: Taxonomic concepts: Catalog of Life, WORMS, ITIS, EOL, GNA Geography: GBIF, IUCN ranges, Map of Life, WDPA Standards Genes/genomes: Genbank, TreeBase, ToL Web, AVATOL, BOLD Phenotypes and traits: MorphBank, TRY, Phenoscape
- 7. EOL GBIF NCBI A Growing Constellation of Biodiversity Data and Knowledge
- 8. How do we link all these data together?
- 9. Borrowing from Facebook and social media… Can we track relationships for Biological Objects as well?
- 10. A Biological Relationship Graph … Taxonomic Type Filter Class Filter X Specimens Tissues X Sequences Functions X Infer Relationships Across providers
- 11. Moorea Biocode Example: From field collection through analysis, across multiple systems Taxon (Taxon) Taxon*n Taxon Key (Key) Blast*n Blast (Biocode Event) (metagenomic Sequencing) (CAMERA Gut Sample Event) (Essig Museum Specimen) (Genbank Sequence) (Smithsonian Tissue)
- 13. Examples: Global Unique identifiers: • Globally unique (mandatory) • Persistent (not mandatory, but very helpful) http://example.org/urn:lsid:example.org:specimen/7217D220-836A-11DF-8395-0800200C9A66 • Resolvable (not mandatory, but very helpful) http://mycollection.org/specimen/JDeckSpecimen1 http://mycollection.org/specimen/uuid=7217D220-836A-11DF-8395-0800200C9A66 http://dx.doi.org/10.5072/FK2JW8GKM
- 14. Simple relationship terms: Graph relationships:
- 15. ONE FINAL PIECE OF THE PUZZLE: GIVING BIRTH TO DATA IN THE RIGHT FORMAT FOR LINKING
- 16. “Triplifier” - creating the format for linking biological objects Darwin Core Archive Darwin Core Archive Triplifier Create links from Native data formats Mysql KEMU Mysql
- 17. QUERY AND RESULTS ACROSS LINKED DATA Response Query
- 18. BISCICOL – EXAMPLE SEARCH Client Interface: Search Scientific Name: Aedes increpitus Run Results: OccurrenceID1 (Aedes increpitus Dyar, 1916 ) OccurrenceID3 (Aedes vittata Theobald, 1903) Taxon SERVICE (ITIS / GNUB) http://lsid.itis.gov/urn:lsid:itis.gov:itis_tsn:126314 http://lsid.itis.gov/urn:lsid:itis.gov:itis_tsn:126317 http://gnub.org/8E19F1DC-74BA-47D4-A505-6498414B4CCE BISCICOL SERVICE LOOKUP: dwc:IdentificationID1 :relatedTo http://lsid.itis.gov/urn:lsid:itis.gov:itis_tsn:126314 dwc:IdentificationID1 :relatedTo dwc:OccurrenceID1 dwc:IdentificationID2 :relatedTo http://lsid.itis.gov/urn:lsid:itis.gov:itis_tsn:126317 dwc:IdentificationID2 :relatedTo dwc:OccurrenceID3
- 19. IndividualID1 EventID1 GeoreferenceID1 EventID2 GeoreferenceID2 EventID3 GeoreferenceID3 Working with Locations: Tracking location in space of a moving individual (whales)
- 20. Data Impact Factor – Graph Metrics Collectors Graphs Gustav Paulay [ ] GBIF Relations Graph (102,000 direct children) [X] Moorea Biocode [X] SI MSNGR System [+] Add New Graph Christopher Meyer (83,000 direct children) Occurrences MBIO99999 Craig Moritz (1024 total descendents) (523 direct children) IMBL8888888 (723 total descendents) Events Cited occurrences over time Biocode10234 (4234 direct children) Expedition21234 (1023 direct children)
- 21. Why BiSciCol and Why SPNHC and Why Collaborations? • New era of collections digitization • new & derived data objects created, replicated, annotated • BiSciCol tackles preservation of nat. hist. collections challenge: • How to follow these digital objects • How to link together objects and derivatives back to specimens • BiSciCol is about community, collaborative practice • Commitment to standards, ontologies • Agreement on permanent, resolvable identifiers • Triplification of data sources to enhance linked data