Using the Biological Collections Ontology to Advance Biodiversity Science
- 1. Using the Biological Collections Ontology to Advance Biodiversity Science TDWG 2014, Jönköping, Sweden Ramona Walls John Wieczorek Robert Guralnick John Deck
- 2. Overview 1. How we model biodiversity information in the Biological Collections Ontology 2. Integrating ontologies into biodiversity information workflows
- 3. Properties in an example Darwin Core record • occurrenceID • modified • rights • institutionCode • collectionCode • datasetName • basisOfRecord • dynamicProperty • catalogNumber • recordedBy • sex • preparations • otherCatalogNumbers • associatedMedia • associatedReferences • associatedSequences • eventDate • year • month • day • fieldNumber • eventRemarks • higherGeography • continent • waterBody • islandGroup • island • country • stateProvince • county • locality • minimumDepthInMeters • maximumDepthInMeters • locationRemarks • decimalLatitude • decimalLongitude • geodeticDatum • coordinateUncertaintyIn Meters • georeferencedBy • georeferencedDate • georeferenceSources • georeferenceRemarks • identifiedBy • dateIdentified • typeStatus • scientificName • kingdom • phylum • class • order • family • genus • specificEpithet • infraspecificEpithet • scientificNameAuthorship
- 4. Properties in an example Darwin Core record • occurrenceID • modified • rights • institutionCode • collectionCode • datasetName • basisOfRecord • dynamicProperty • catalogNumber • recordedBy • sex • preparations • otherCatalogNumbers • associatedMedia • associatedReferences • associatedSequences • eventDate • year • month • day • fieldNumber • eventRemarks • higherGeography • continent • waterBody • islandGroup • island • country • stateProvince • county • locality • minimumDepthInMeters • maximumDepthInMeters • locationRemarks • decimalLatitude • decimalLongitude • geodeticDatum • coordinateUncertaintyIn Meters • georeferencedBy • georeferencedDate • georeferenceSources • georeferenceRemarks • identifiedBy • dateIdentified • typeStatus • scientificName • kingdom • phylum • class • order • family • genus • specificEpithet • infraspecificEpithet • scientificNameAuthorship RECORD
- 5. Properties in an example Darwin Core record • occurrenceID • modified • rights • institutionCode • collectionCode • datasetName • basisOfRecord • dynamicProperty • catalogNumber • recordedBy • sex • preparations • otherCatalogNumbers • associatedMedia • associatedReferences • associatedSequences • eventDate • year • month • day • fieldNumber • eventRemarks • higherGeography • continent • waterBody • islandGroup • island • country • stateProvince • county • locality • minimumDepthInMeters • maximumDepthInMeters • locationRemarks • decimalLatitude • decimalLongitude • geodeticDatum • coordinateUncertaintyIn Meters • georeferencedBy • georeferencedDate • georeferenceSources • georeferenceRemarks • identifiedBy • dateIdentified • typeStatus • scientificName • kingdom • phylum • class • order • family • genus • specificEpithet • infraspecificEpithet • scientificNameAuthorship MATERIAL SAMPLE & ORGANISM
- 6. Properties in an example Darwin Core record • occurrenceID • modified • rights • institutionCode • collectionCode • datasetName • basisOfRecord • dynamicProperty • catalogNumber • recordedBy • sex • preparations • otherCatalogNumbers • associatedMedia • associatedReferences • associatedSequences • eventDate • year • month • day • fieldNumber • eventRemarks • higherGeography • continent • waterBody • islandGroup • island • country • stateProvince • county • locality • minimumDepthInMeters • maximumDepthInMeters • locationRemarks • decimalLatitude • decimalLongitude • geodeticDatum • coordinateUncertaintyIn Meters • georeferencedBy • georeferencedDate • georeferenceSources • georeferenceRemarks • identifiedBy • dateIdentified • typeStatus • scientificName • kingdom • phylum • class • order • family • genus • specificEpithet • infraspecificEpithet • scientificNameAuthorship EVENT & OCCURRENCE
- 7. Properties in an example Darwin Core record • occurrenceID • modified • rights • institutionCode • collectionCode • datasetName • basisOfRecord • dynamicProperty • catalogNumber • recordedBy • sex • preparations • otherCatalogNumbers • associatedMedia • associatedReferences • associatedSequences • eventDate • year • month • day • fieldNumber • eventRemarks • higherGeography • continent • waterBody • islandGroup • island • country • stateProvince • county • locality • minimumDepthInMeters • maximumDepthInMeters • locationRemarks • decimalLatitude • decimalLongitude • geodeticDatum • coordinateUncertaintyIn Meters • georeferencedBy • georeferencedDate • georeferenceSources • georeferenceRemarks • identifiedBy • dateIdentified • typeStatus • scientificName • kingdom • phylum • class • order • family • genus • specificEpithet • infraspecificEpithet • scientificNameAuthorship LOCATION
- 8. Properties in an example Darwin Core record • occurrenceID • modified • rights • institutionCode • collectionCode • datasetName • basisOfRecord • dynamicProperty • catalogNumber • recordedBy • sex • preparations • otherCatalogNumbers • associatedMedia • associatedReferences • associatedSequences • eventDate • year • month • day • fieldNumber • eventRemarks • higherGeography • continent • waterBody • islandGroup • island • country • stateProvince • county • locality • minimumDepthInMeters • maximumDepthInMeters • locationRemarks • decimalLatitude • decimalLongitude • geodeticDatum • coordinateUncertaintyIn Meters • georeferencedBy • georeferencedDate • georeferenceSources • georeferenceRemarks • identifiedBy • dateIdentified • typeStatus • scientificName • kingdom • phylum • class • order • family • genus • specificEpithet • infraspecificEpithet • scientificNameAuthorship IDENTIFICATION/TAXON
- 9. Using DwC properties in BCO: Event as an example
- 10. Material entities, information entities, and processes in the Basic Formal Ontology
- 11. Mapping DwC classes to BCO: basisOfRecord terms as an example
- 12. How to create RDF triples (using Ontology terms) for biodiversity data Check for an easy way first! See if you can use the BiSciCol triplifier (http://biscicol.org/triplifier/) or similar tool that automates file conversion for specific formats. If not, proceed. Create Mapping File • Create groups of columns and assign to relevant classes • Define columns containing a URI identifier for each class within each distinct record. • If you’re not importing an existing ontology, create relationships between classes Assemble into Mapping File, the format depending on the tool used in the next step. Use Conversion Tool Check out WebKarma (http://www.isi.edu/integration/karma/) or D2RQ (http://d2rq.org/). Send to Triple-Store Upload data to a Triple-Store or SPARQL Endpoint (e.g Virtuoso http://www.openlinksw.com/) http://www.wikihow.com/Create-RDF-Triples-%28Using-Ontology-Terms%29-for-Biodiversity-Data
- 13. Specimen data from a Darwin Core Archive: VertNet
- 14. iMicrobe data links specimens to metagenomic sequences and environmental parameters Collecting event: location depth weather cruise biome site description temperature … * * * Metagenomic sequence: library accession # sequencing method molecule type number of reads … Parameters: salinity pH fluorescence turbidity sample volume silicate oxygen dissolved organic carbon ….
- 15. iMicrobe data mapped to BCO
- 16. Linking prospective data to ontologies is much easier! quer y
- 17. Conclusions • BCO can work across different data types, not just for DwC. • The work of producing BCO has forced us to look at DwC definitions more rigorously. • BCO provides an opportunity to manage parts of the DwC vocabulary as controlled vocabularies that are rigorously, logically defined. – example: basisOfRecord • Road map for this work includes the intention to propose BCO as a TDWG standard.
- 18. Acknowledgments • Dozens of participants at BCO workshops and hackathons over the past two years • NSF-EAGER: An Interoperable Information Infrastructure for Biodiversity Research (I3BR) • NSF: Research Coordination Network for GSC (RCN4GSC) • Gordon and Betty Moore Foundation (iMicrobe) • VertNet • University of Kansas Biodiversity Institute
Editor's Notes
- #2: Ramona and introductions
- #3: Ramona
- #4: JOhn Show typical metadata and how it confounds material entities and process and why this is a problem.
- #5: JOhn Show typical metadata and how it confounds material entities and process and why this is a problem.
- #6: John Show typical metadata and how it confounds material entities and process and why this is a problem.
- #7: John
- #8: John
- #9: John
- #10: Ramona
- #11: Ramona separation of processes, material entities, information content entities and how they link to one another
- #12: John Show structure of specimens and observations
- #13: Ramona
- #14: John
- #15: Ramona
- #17: Ramona data collection spreadsheet with an ontology behind it to a triple store you can query to new discoveries!
- #18: John
- #21: Keep this at the end as an example