Co l+ clearinghouse
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This document outlines a proposed model for a clearinghouse to integrate taxonomic and nomenclatural data from various sources. The clearinghouse would: 1) Separate taxonomic information from nomenclatural names to allow integration of data from different sources and expert working groups. 2) Contain both reviewed, authoritative data as well as provisional data imported from external sources. 3) Provide APIs and workspaces for experts to review, edit, and publish changes to taxonomic data and classifications.
Co l+ clearinghouse
- 1. Champaign, 27th July 2017 A Clearinghouse for Taxonomy & Nomenclature Markus Döring, GBIF
- 2. CLEARINGHOUSE MODEL For reviewFor review For review For review IPNI Index Fungorum ZooBank Global Species Database 1 GSD 2 GSD 3 … Provisional Datasets Clearing House Catalogue of Life (Reviewed) “Index of Names” (Reviewed) ExtendedCatalogueSeparates names & taxa Different authorities: nomenclator & GSD Integrate sources on distinct name single consensus taxonomy Provisional & authoritative sources Offers a review queue to every source
- 3. NAMES A unique name is based on: Genus, species-, infraspecific epithet Rank Authorship regardless of spelling Name types Included: Linnean names, Named hybrids, Virus names Exclude: hybrid formulas, cultivars, OTUs NameID from nomenclator Otherwise preliminary clearinghouse nameID Major information (draft) Code (ICN, ICZN, …) Homotypic synonyms (basionym & replacement names ) Original publication isFossil Available Conserved, rejected Nomenclatural notes Acacia (Juliflorae) aneura F. Muell. ex Benth. var. latifolia J.M. Black Acacia (Juliflorae) aneura var. latifolia J.M. Black Acacia aneura Benth. var. latifolia J. Black Acacia aneura var. latifolia J. Black Acacia aneura var. latifolia J.M. Black
- 4. TAXA Single consensus view Track historic concepts Manage CoL classification in clearinghouse Heterotypic synonymy Assign taxon IDs Computable rules based on synonymy & siblings Reviewed and provisional taxon ids might differ Supplementary CoL information Distribution Vernacular names Lifezone & fossil flags
- 5. CLEARINGHOUSE API All services expose both Reviewed data only Extended data including provisional information Nomenclatural services Name matching List homotypic synonymy Correct spelling Name history (nomenclatural events around a basionym) Taxonomic services Search Browse children List entire synonymy
- 6. STAGING WORKSPACE Initial import of sources, cleaning & interpretation Reader for ACEF, DwC-A, TCS Clean whitespace, html entities, encoding issues Interpret values (e.g. dates, rank, country, language) Parse names (if not parsed yet, DwC only) Match to clearinghouse names (assign nameID) Integrity checks for review Check name structure, accepted name for synonyms, … Check for duplicate name within source or outer CoL More existing workbench checks, add over time Change metrics (# of new, updated & deleted names) Editorial decisions Map taxa to CoL classification Block name Change name status Publish to clearinghouse Staging API for review, preview & editorial decisions Staging Workspace Source editorial control
- 7. CLEARINGHOUSE WORKSPACE Represents current best knowledge Includes both reviewed & provisional placement Maintains the CoL classification Mints taxon identifier Community contributions Fully versioned Comments everywhere Edits in areas without authority Content bots adding provisional information Basionym relations BHL literature links Review queues for sources Editorial decisions Manage authorization for taxonomic groups Move taxa to other group (to change source authority) Release CoL Clearinghouse Workspace review queue Public Staging Workspace Source editorial control
- 8. COL RELEASE SPACE Contains latest interim (monthly) release Not archived Archive of all annual releases API & portal expose them GSD decides name fidelity Name exactly as provided Name spelling from nomenclator Homotypic synonymy added CoL Release Public Clearinghouse Workspace review queue Public Staging Workspace Source editorial control
- 9. OPTIONS FOR EVOLUTION Extended nomenclatural model Nomenclatural acts Type specimen Name Author entities Reference entities More name relations Concurrent taxon concepts Multiple classifications Multiple concepts per name Allows precise identifications, national lists, etc. Species images Reference image selected by community
Editor's Notes
- #2: T1-23-06 The Global Biodiversity Information Facility: A Review of Progress and Challenges in Plant Data Mobilization and Integration Siro Masinde1 Hobern Donald1 1. Global Biodiversity Information Facility (GBIF) GBIF - the Global Biodiversity Information Facility (http://www.gbif.org/) is the leading aggregator of species occurrence data, including botanical and fungal data. As of January 2017, GBIF had more than 700 million records harvested from over 32,000 data resources published by more than 800 data providers. Since its establishment in 2002, GBIF has provided leadership in delivering tools, standards and best practices for mobilizing biodiversity data for free and open use by the research community and to support policy applications. Established tools and processes now support the aggregation and integration of species distribution data from natural history collections, field research, environmental genomics, citizen science and literature into a single, unified resource. Modern approaches to linked-open data management point the way to this data resource becoming the focal point for connecting the full spectrum of recorded information about species and communities. GBIF strives to provide well integrated data of high quality and in large quantity to enable users to query and summarize data, with answers that are as complete and accurate as possible. This can only be achieved if data providers worldwide mobilize large, high quality data across a wide spatial, temporal and taxonomic spectrum and publish them openly using interoperable standard data formats. We review GBIF progress in plant data mobilization and integration, and provide insights on future directions. We also highlight the challenges encountered and invite a discussion on future expectations of the botanical community and the role the community can play in developing and curating the GBIF database to meet the needs and expectations of users. Keywords: data mobilization data integration data management GBIF linked-open data
- #4: No subgenus or infraspecific hierarchy for quadrinomials Also valid / correct name? Orthographic variants ???