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Advancing the International Plant Names Index (IPNI)

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The "names and taxa" information space is often thought of as being composed of three layers:
Taxonomic concepts
Code governed nomenclatural acts
Name occurrences
In many circumstances the distinction of these layers is blurred, leading to confusion and inefficiencies in information management. To date, IPNI has been mainly concerned with the middle layer comprising ICBN governed nomenclatural acts, and is formed of three key components: curated data, information services to expose this data, and dedicated editorial staff to provide nomenclatural expertise.
IPNI will be advanced from its current state to better connect to the layers above (taxonomic concepts) and below (name occurrences). This will require the expansion of data holdings, improved linkages, and the development of information services and associated workflows. These will be offered to key actors including name authors, publishers, taxonomists and managers of biodiversity information.

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Advancing the International Plant Names Index (IPNI)

  1. 1. Advancing the International Plant Names Index (IPNI) Nicky Nicolson, Alan Paton, Jim Croft, James Macklin, Paul Morris, Greg Whitbread, Kanchi Gandhi
  2. 2. Advancing IPNI <ul><li>Current - where IPNI is now </li></ul><ul><li>Issues </li></ul><ul><li>Future - where we’d like to go and how to get there </li></ul>
  3. 3. What data? <ul><li>What data types: </li></ul><ul><ul><li>ICBN governed nomenclatural acts </li></ul></ul><ul><ul><li>Standardised author list </li></ul></ul><ul><ul><li>Publications </li></ul></ul><ul><li>Which groups: </li></ul><ul><ul><li>Vascular plants </li></ul></ul><ul><li>Which ranks: </li></ul><ul><ul><li>Family and below </li></ul></ul>
  4. 13. How is data entered? <ul><li>Data entry: </li></ul><ul><ul><li>From literature scanning, journals received by library at Kew, Harvard, Canberra (2 years - 95%) </li></ul></ul><ul><ul><li>User reports of missing nomenclatural acts, usually accompanied by a link to digitised literature page (BHL) </li></ul></ul><ul><li>How many? </li></ul><ul><ul><li>About 7400 names entered in average year </li></ul></ul><ul><ul><li>About 6100 nomenclatural acts published / year </li></ul></ul><ul><ul><li>… of these about 2800 are tax. novs. </li></ul></ul>
  5. 14. How is data managed? <ul><li>Full audit history on core objects – names / authors / publications . </li></ul><ul><li>Average 300,000 edits on name records / year </li></ul><ul><li>Standardisation effort ongoing      : </li></ul><ul><ul><li>Epithet </li></ul></ul><ul><ul><li>Author citation </li></ul></ul><ul><ul><li>Publication title </li></ul></ul><ul><ul><li>Collation </li></ul></ul><ul><ul><li>Year </li></ul></ul>
  6. 15. Standardisation – author and title
  7. 16. Standardisation – epithet updates
  8. 17. Standardisation of epithets <ul><li>Why important </li></ul><ul><ul><li>Main search criterion </li></ul></ul><ul><ul><li>Improving epithets enables other improvements in dataset e.g.: </li></ul></ul><ul><ul><ul><li>basionym linkage </li></ul></ul></ul><ul><ul><ul><li>de-duplication </li></ul></ul></ul><ul><ul><li>Errors propagate </li></ul></ul>
  9. 18. Rhus kea mc yi was an OCR error for Rhus kea rne yi but the incorrect value persists in datasets derived from IPNI
  10. 19. Statistics <ul><li>Dataset can be used for trends analysis: </li></ul><ul><ul><li>Publication rates </li></ul></ul><ul><ul><li>Combination rates </li></ul></ul><ul><ul><li>Author collaborations </li></ul></ul><ul><li>Audit history used to determine changes in data-set over time </li></ul><ul><li>http://www.ipni.org/stats.html </li></ul>
  11. 20. http://www.ipni.org/stats.html
  12. 21. As well as the data… <ul><li>IPNI editors respond to user queries about the data, dealing with c. 50 cases / month </li></ul><ul><li>Includes an expert service re interpretation of ICBN </li></ul><ul><li>Can provide worked examples illustrating particular articles of the code </li></ul>
  13. 22. Why should anyone care? <ul><li>c55,000 searches / day </li></ul><ul><li>BUT </li></ul><ul><li>dataset is not being used to full advantage </li></ul><ul><li>inputs not being handled efficiently: </li></ul><ul><ul><li>limited to partnership </li></ul></ul><ul><ul><li>missing out on community input </li></ul></ul><ul><li>expertise is hidden </li></ul>
  14. 23. Future <ul><li>Increase efficiency of input </li></ul><ul><ul><li>provision of core data </li></ul></ul><ul><ul><li>annotating and linking existing data </li></ul></ul><ul><ul><li>solving nomenclatural problems </li></ul></ul><ul><li>Increase output </li></ul><ul><ul><li>usage of IPNI data </li></ul></ul><ul><ul><li>benefit from on-going curation effort </li></ul></ul><ul><ul><li>benefit from nomenclatural expertise </li></ul></ul>
  15. 24. Data in - contributor services <ul><li>Pre-publication data entry </li></ul><ul><li>Batch submission of datasets </li></ul><ul><li>Annotation </li></ul><ul><li>Addition of links within dataset </li></ul><ul><li>Facilitate interpretation of nomenclatural issues </li></ul><ul><li>Accreditation – credit for helping improve the data </li></ul>
  16. 25. Pre-publication data entry <ul><li>Workflow currently being trialled </li></ul><ul><ul><li>Author or publisher submits data to IPNI once article has been accepted for publication </li></ul></ul><ul><ul><li>Generated record suppressed until publication effective under the code </li></ul></ul><ul><ul><li>But this not yet automated! </li></ul></ul>
  17. 26. Electronic Publication Example - Phytokeys <ul><li>A nomenclator of Pacific oceanic island Phyllanthus (Phyllanthaceae), including Glochidion </li></ul><ul><li>Warren L. Wagner, David H. Lorence </li></ul><ul><li>5. Phyllanthus atalotrichus ( A.C. Sm.) W.L. Wagner & Lorence, comb. nov. </li></ul><ul><li>urn:lsid:ipni.org:names:77112693-1 </li></ul>PhytoKeys 4: 67–94 (2011) doi: 10.3897/phytokeys.4.1581 www.phytokeys.com
  18. 27. Pre-publication issues <ul><li>Name squatting – mitigated by only entering names which are in papers accepted for publication </li></ul><ul><li>Curation of record throughout publication process </li></ul><ul><li>Electronic and effective publication – before this the record will not be visible </li></ul><ul><li>IPNI editors provide visible expert service re validity of name </li></ul>
  19. 28. Where IPNI data are placed Any name occurrence: e.g. specimens, reports, literature citation concepts Standard form of name
  20. 29. Data out - links <ul><li>To concept layer: </li></ul><ul><ul><li>embed IPNI identifiers </li></ul></ul><ul><ul><li>storage of factual concepts / links to concept layer </li></ul></ul><ul><li>To name occurrence layer: </li></ul><ul><ul><li>seed lexical reconciliation projects (e.g. GNI) </li></ul></ul><ul><li>To allied information: </li></ul><ul><ul><li>literature </li></ul></ul><ul><ul><li>types </li></ul></ul>
  21. 30. Links to concept layer <ul><li>Embed IPNI identifiers in externally held names lists </li></ul><ul><ul><li>IPNI holds curated name data, labelled with persistent identifiers. </li></ul></ul><ul><ul><li>Need a tool to seed IPNI identifiers into datasets (in prototype) </li></ul></ul><ul><ul><li>Can devolve curation of name elements in other systems to IPNI </li></ul></ul><ul><ul><li>Benefit from on-going curation: </li></ul></ul><ul><ul><ul><li>300,000 edits per year </li></ul></ul></ul><ul><ul><li>Report on changes in name list since date </li></ul></ul>
  22. 31. Links to the Concept Layer Example The Plant List
  23. 32. Link to name occurrence layer <ul><li>IPNI’s version history can be used to seed lexical reconciliation projects (GNI), e.g.: </li></ul><ul><ul><li>Plectranthus macrophylius -> Plectranthus macrophyllus </li></ul></ul><ul><li>These editorialised translations of higher value than programmatically derived operations of the same edit distance, e.g: </li></ul><ul><ul><li>Plectranthus microphyllus -> Plectranthus macrophyllus </li></ul></ul><ul><li>Standardisation tools and techniques opened up for use in allied projects </li></ul>
  24. 33. Conclusion <ul><li>Faciliate electronic publication - pilot registration </li></ul><ul><li>Foster larger community to support the data and automate workflows </li></ul><ul><li>Stronger links between: </li></ul><ul><ul><li>the people who produce names </li></ul></ul><ul><ul><li>the places where they are published </li></ul></ul><ul><ul><li>the downstream users </li></ul></ul><ul><li>Technical redevelopment </li></ul>

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