Tony Rees: Towards a Hierarchical Classification of All Life

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Presentation at Marine Biological Laboratory (MBL), Woods Hole, October 2011

Presentation at Marine Biological Laboratory (MBL), Woods Hole, October 2011

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  • 1. Towards a Hierarchical Classification of All Life – the IRMNG data assembly project Tony Rees – CSIRO Marine and Atmospheric Research, Australia October 2011
  • 2. Why a hierarchical classification? Tony Rees: Hierarchical Classification of All Life
  • 3.
      • Hierarchical classifications assist us to organize knowledge
    Why a hierarchical classification? Tony Rees: Hierarchical Classification of All Life “ borrowed” from R. Page presentation, 2011
      • Hierarchical classifications allow us to infer information about lower levels from higher ones (don’t have to explicitly re-specify / verify / know everything)
      • Hierarchical classifications allow us to make / test predictions based on degree of “relatedness”
  • 4.
      • Hierarchical classifications assist us to construct +/- automated “expert systems”
    Why a hierarchical classification? Tony Rees: Hierarchical Classification of All Life Functional view The system Structural view genus / species name “X” useful information on taxon “X”
  • 5. What should “the system” ideally hold? – something like… Tony Rees: Hierarchical Classification of All Life (etc.)
  • 6.
      • Expanded to information on “all life”:
        • Animals, plants, fungi, protists, bacteria + archaea (prokaryotes), viruses
        • Both extant and fossil organisms
        • Aim for comprehensive coverage – no gaps – to desired level of the hierarchy
      • Information held in consistent terminology, machine-readable content
      • Either human user, or machine user access point (or both)
      • Hyperlinked cross-refs for web users
      • Continuously updated & upgraded
      • Provenance for all content
      • (probably plus more…)
    What should “the system” ideally hold? Tony Rees: Hierarchical Classification of All Life x 50+…
  • 7.
      • Taxon Scientific names are preferred units of currency & identity in the world of biology:
        • More stable / authoritative than common (vernacular) names
        • Indicate the genus to which a species belongs
        • Higher classification allows nesting into progressively larger taxa, each with definable characteristics
        • “ Linnaean” ranks: kingdom through species (NB some intermediate ranks also important, should handle in due course)
        • (* taxon = named “taxonomic unit”, a defined unit at any rank, i.e. species, genus, family, etc.)
    System is based on scientific names of taxa Tony Rees: Hierarchical Classification of All Life 2+ million ~250k ~10k ~2k Kingdoms (5/6/7/8) ~400 ~140 Phyla Classes Orders Families Genera Species
  • 8.
      • All life to family level:
        • Parker (ed.), 1982, Synopsis and Classification of Living Organisms , print, 2 vols, ~2,300 pp.: ~7k family descriptions in a common hierarchy (extant taxa only)
        • Benton (ed.), 1993, The Fossil Record 2 , print, ~850 pp.: ~5k family brief treatments, mainly fossil
      • Code-specific to genus level:
        • Zoology: Nomenclator Zoologicus (to 2004), (print + online) then Zoo. Record / ION , online (NB, Nomen. Zool. has no detailed higher taxonomy)
        • Botany: Index Nominum Genericorum (ongoing), online, also IPNI, TROPICOS, etc.
        • Bacteriology: List of Prokaryotic names with Standing in Nomenclature ( LPSN ) (online)
        • Viruses: International Committee on Taxonomy of Viruses (ICTV) database , online
    Availability of comprehensive treatments Tony Rees: Hierarchical Classification of All Life
  • 9.
      • Taxon specific to species level: Global Species Databases (“GSDs”) exist for specific groups e.g.
        • Mammals: Mammal Species of the World (2005, print + online)
        • Fishes: Eschmeyer’s Catalog of Fishes (ongoing, online)
        • Higher Plants: The Plant List (2010, online) + contributing DB’s
        • Fungi: Index Fungorum and Species Fungorum (ongoing, online)
        • Algae: AlgaeBase (ongoing, online)
        • Others: AntBase , Systema Dipterorum , LepIndex + many more
        • (also viruses and prokaryote lists as per previous slide)
        • … >100 GSDs aggregated into a single Catalogue of Life compilation (annual editions 2000-current) produced by Sp2000 + ITIS (USA)
    Availability of comprehensive treatments – cont’d Tony Rees: Hierarchical Classification of All Life
  • 10.
    • A great project BUT…
      • ~30% of extant species (plus relevant higher taxa) still missing
      • only a subset of species synonyms included, and no genus synonyms stated
      • no fossil taxa (although Paleobiology Database has some / many of these)
    Can we use Catalogue of Life as a comprehensive resource? Tony Rees: Hierarchical Classification of All Life
      • a few higher tax. conflicts
      • no intermediate ranks (e.g. subphylum, infraorder)
      • no genus authors or publication info
      • latency for new names (esp. in some groups)
      • no target completion date
      • … GBIF experience: only ~30% of incoming species names are in the Catalogue of Life (not much good for data aggregators).
  • 11. What about “names aggregator” activities Tony Rees: Hierarchical Classification of All Life
      • Collect names as used in primary + secondary sources, mix of “clean” (verified) and “dirty” (unverified) names
      • Authority portion of the names not standardized (same name may appear on the list multiple times)
      • Frequently lacking coherent / any higher taxonomy
      • … Potentially a useful “superset” of (most) “good” names, but requires work to filter these out.
    (etc.)
  • 12.
    • Answer “yes” BUT…
      • Need to knit them all together across Codes, also no single source is complete, even within a Code
      • Need to add family allocations where missing, e.g. from Nomenclator Zoologicus, also taxonomic synonyms, consistent hierarchy information, etc. etc.
      • Need to deal with inconsistencies / overlaps between data sources (editorial decisions), also “house style” issues
      • Need to back-fill residual data gaps
      • As desired, also would like to add non-taxonomic “attributes” e.g. extant / fossil status / geologic range, habitat information, geographic distribution, more ???
    • Bonus short cut
      • Leverage the hierarchy to avoid having to add attributes at every lower level – e.g. inherit genus / species attributes from higher up where these are unambiguous
        • Examples: all dinosaurs are extinct, all cephalopods are marine, etc. etc.
        • Similarly, all species of a marine-only genus will also be marine, etc.
    Genus level compilations are much more complete, can we use those? Tony Rees: Hierarchical Classification of All Life
  • 13.
    • IRMNG – the Interim Register of Marine and Nonmarine Genera
      • Aims to fill the gaps and produce an “interim” hierarchical classification of all life (HCAL), extant + fossil, to at least genus level (species lists to be added as readily accessible)
      • Utilizes Parker, 1982 and Benton, 1993 family compilations as starting point for higher classification
      • Specific sectors then upgraded through time, also incorporating relevant marine/nonmarine and extant/fossil flags
      • Genera added from the most comprehensive available sources (over time)
      • “ Interim” status used to indicate lesser degree of scrutiny / authoritativeness than e.g. Cat. of Life, however hopefully still useable
      • home page: www.obis.org.au/irmng , data access page: www.cmar.csiro.au/datacentre/irmng/
      • Will hold more names than valid taxa, due to synonymy:
        • Nomenclatural synonyms – add maybe 5% to genera, 300% to species
        • Taxonomic synonyms – add maybe 100%-200% to genera and species
    The IRMNG concept Tony Rees: Hierarchical Classification of All Life
  • 14.
      • 1 record per every name / publication instance (valid or invalid) including:
        • the name itself
        • the author and year for the name (1 version only)
        • publication details as available
        • source/s used, with or without editorial adjustment
        • for botanical names, include full (not abbreviated) author name, also year of publication (normally omitted)
        • nomenclatural and taxonomic status, as known (plus any relevant comments)
        • placement in the tax. hierarchy (every record knows its parent, child records reference this one), plus cross-links as required
        • selected attributes, initially:
          • Extant/fossil status: Extant / Fossil / both / unknown
          • Habitat flag: Marine / Nonmarine / both / unknown
        • provenance, degree of verification for all content
    IRMNG desired content Tony Rees: Hierarchical Classification of All Life
  • 15. Family placement – editorial decisions may be needed Tony Rees: Hierarchical Classification of All Life
      • e.g. for (botanical) genus “Pachydiscus”:
  • 16. Data aggregation complicated by genus level homonyms e.g.: Tony Rees: Hierarchical Classification of All Life
      • also by variant authority citations e.g.:
      • (etc.)
  • 17. Perseverance produces the following (subset of genus table, 453k names as at Oct 2011): Tony Rees: Hierarchical Classification of All Life
  • 18. A glimpse of the IRMNG “master genus” table (currently 452,827 records) Tony Rees: Hierarchical Classification of All Life
  • 19. A glimpse of the IRMNG “master genus” table (currently 452,827 records) Tony Rees: Hierarchical Classification of All Life (Mabberley plant names list)
  • 20. Detail showing example source/s used Tony Rees: Hierarchical Classification of All Life
  • 21.
      • High-level overview + relevant statistics for “all life” (currently possible for names, in future for valid taxa)
      • Navigate the hierarchy in any direction
      • Generate hierarchical lists
      • Generate alphabetic lists
      • Sort / filter by any desired criteria
      • Generate lists of homonyms, within or across Codes
      • Indicate current tax. hierarchy, nomenclatural / taxonomic status, and attributes (to varying degrees) for any input name
      • Indicate near match targets to any input name (“did you mean…”) – using TAXAMATCH fuzzy matching (custom solution for tax. databases)
    Services / views this currently supports Tony Rees: Hierarchical Classification of All Life
  • 22. IRMNG-generated statistics for “all life” (web query 6 Oct 2011) Tony Rees: Hierarchical Classification of All Life
      • (Important note – can actually generate these lists as required, by navigating the hierarchy)
  • 23. Other services / products e.g. full hierarchical lists Tony Rees: Hierarchical Classification of All Life however with caveat: some / many genera may still be classified only at higher level (e.g. “Mammalia – unallocated”) at this time (more work to do).
  • 24. Check batches of entered names Tony Rees: Hierarchical Classification of All Life (1,406 genus names…)
  • 25. Check batches of entered names Tony Rees: Hierarchical Classification of All Life (start of IRMNG search result)
  • 26. Check batches of entered names Tony Rees: Hierarchical Classification of All Life
  • 27. Check batches of entered names Tony Rees: Hierarchical Classification of All Life ?
  • 28. Query by taxon name (correctly spelled or misspelled) Tony Rees: Hierarchical Classification of All Life
  • 29. Check batches of entered names Tony Rees: Hierarchical Classification of All Life
      • Basically this is then a Taxonomic Name Resolution Service (TNRS), similar to the one developed in 2011 by the (U.S.) iPlant team over TROPICOS, but across all groups:
  • 30. Linking names with literature Tony Rees: Hierarchical Classification of All Life
  • 31. Tony Rees: Hierarchical Classification of All Life The “microcitation” (Nomenclator’s favourite…)
      • Typically just author name, year, page no. in work, e.g.:
      • Would prefer full article-level titles / authors / pagination if possible – i.e. a bibliographic module
      • Could optionally offer onward links to page views in BHL, abstracts, full text as pdfs, etc. as available (small sample populated in IRMNG at this time)
    Name plus page in work List of all works as data objects
  • 32. Expanded citation info in IRMNG - example Tony Rees: Hierarchical Classification of All Life
  • 33. Expanded citation info in IRMNG - example Tony Rees: Hierarchical Classification of All Life
  • 34. Expanded citation info in IRMNG - example Tony Rees: Hierarchical Classification of All Life
  • 35. IP issues regarding bibliographies, etc. Tony Rees: Hierarchical Classification of All Life
      • Many sources assert copyright over bibliographies, potentially an issue
      • Does copyright exist in individual references extracted from a third party collection
      • What about subsets of the collection
      • What about new composite supersets
      • Law may be different in different countries
      • Licensing / terms of use may be different from law
      • … still very unclear (to this author) what is / is not permissible with respect to assembling new bibliographies which include content from elsewhere – including copy/paste vs. re-keying…
      • Will be a recurring issue for other bibliography-assembly projects e.g. CiteBank, Mendeley… but think of the value (a “bibliography of life”)
  • 36. IRMNG content – recent missing genera… Tony Rees: Hierarchical Classification of All Life
  • 37. IRMNG content – genus names published by year, 1995-current (as at Oct 2011), excluding virus names (which are undated) Tony Rees: Hierarchical Classification of All Life (NB could disaggregate further as desired, e.g. by detailed tax. group, or extant vs. fossil…) … also would expect a small number of residual names missed for ostensibly “complete” years presumed missing names
  • 38. IRMNG 2011 content cf. Cat. of Life 2011 Tony Rees: Hierarchical Classification of All Life Note, Chapman, 2009 estimates c.1.9m described extant species (see earlier slide) On that basis, CoL has 70% of valid extant species names, maybe 70% of valid extant genera (with subset of genus-level synonyms) IRMNG is missing est. 10k genera from 2004-2011 (from last slide), maybe further 2-3% overall (say 10k-15k), “complete” list would thus be ~475k at this time (increasing at ~2k/year). Cat. of Life - 2011 edition % with auth's IRMNG – Oct 2011 - extant + fossil % with auth's IRMNG – Oct 2011 - fossil only           Kingdoms 8   7   0 Phyla 111   153   12 Classes 288   509   64 Orders 1,233   2,645   715 Families 8,071 0% 19,639 22.1% 6,542 Subfamilies           Genera 178,515 0% 452,848 97.1% 90,278 Subgenera           Species (valid) 1,347,224 ~100% 1,020,519 ~100% 16,792 Species (synonyms) 895,441 ~100% 440,738 ~100% 100
  • 39. Many unfinished tasks Tony Rees: Hierarchical Classification of All Life
      • Update / standardize the higher classification across groups (start made, much still to do)
      • Fill gaps in nomenclatural / taxonomic status, synonym reconciliation, family allocations for significant subset of names
      • Legacy names acquisition, where currently missing (i.e., not in major nomenclators)
      • New names acquisition (~25k species, 2k+ genera / year…), plus taxonomic reallocations – ongoing task, requires resources or (preferably) automated feeds
      • Extension to “all species”… ???
  • 40. Potential integration / replacement with “GN” components… Tony Rees: Hierarchical Classification of All Life
      • MBL staff and collaborators are currently engaged in constructing components of a “Global Names Architecture” i.e.:
        • GNI – Global Names Index
        • GNUB – Global Names Usage Bank
        • GNITE – Global Names Index Taxonomic Editor
        • GNA CLR / GBIF ChecklistBank
        • CiteBank – publication citation repository
        • ZooBank – register for new / old animal names
        • more…
      • Some / much of this has potential overlap with IRMNG (present focus of my MBL visit).
  • 41. Potential integration / replacement with “GN” components… Tony Rees: Hierarchical Classification of All Life
      • D. Patterson et al., from 2010-11 NSF proposal
      • Proposed “Global Names” infrastructure components:
  • 42. Thank you Thanks to: - OBIS, GBIF and Atlas of Living Australia for financial support, numerous data providers for data - CSIRO for salary and in-kind support, 2006-present - D. Patterson / MBL / NSF (this trip funding + hosting) Tony Rees: Hierarchical Classification of All Life Contact details Phone: +61 3 6232 5318 Email: Tony.Rees@csiro.au Web: www.cmar.csiro.au/datacentre/
  • 43. Supplementary slides Tony Rees: Hierarchical Classification of All Life
  • 44. Tony Rees: Hierarchical Classification of All Life
      • Where to from here…
      • The names publishing / discovery landscape:
  • 45. New names: potential discovery paths Tony Rees: Hierarchical Classification of All Life new virus names new prokaryote names new botanical names – algae & fungi (except fossils) new botanical names – bryophytes through angiosperms (except fossils) new zoological names publication discovery official registers taxon-specific DB’s integrated DB’s “ all names” Botany Zoology Newly published names – primary literature (print, electronic) ICTV Viruses DB LPSN (Prokaryote names) ICBN Decisions ICZN Decisions Journal TOC’s, RSS feeds, text mining Abstracting services Subject bibliographies Reviews, secondary literature Zoological Record ION (Index of Organism Names) ChecklistBank GNI GNUB ZooBank? Catalogue of Life annual editions ITIS NCBI Taxonomy WoRMS etc. CyanoDB Index Fungorum MycoBank AlgaeBase Plant GSD’s PaleoDB Animal GSD’s other compilations e.g. regional lists, Wikispecies, Wikipedia, more… IRMNG
  • 46. New names: potential discovery paths Tony Rees: Hierarchical Classification of All Life new virus names new prokaryote names new botanical names – algae & fungi (except fossils) new botanical names – bryophytes through angiosperms (except fossils) new zoological names publication discovery official registers taxon-specific DB’s integrated DB’s “ all names” Botany Zoology Newly published names – primary literature (print, electronic) ICTV Viruses DB LPSN (Prokaryote names) ICBN Decisions ICZN Decisions Journal TOC’s, RSS feeds, text mining Abstracting services Subject bibliographies Reviews, secondary literature Zoological Record ION (Index of Organism Names) ChecklistBank GNI GNUB ZooBank? Catalogue of Life annual editions ITIS NCBI Taxonomy WoRMS etc. CyanoDB Index Fungorum MycoBank AlgaeBase Plant GSD’s PaleoDB Animal GSD’s other compilations e.g. regional lists, Wikispecies, Wikipedia, more… IRMNG Lots of manual effort
  • 47. New names: potential discovery paths Tony Rees: Hierarchical Classification of All Life new virus names new prokaryote names new botanical names – algae & fungi (except fossils) new botanical names – bryophytes through angiosperms (except fossils) new zoological names publication discovery official registers taxon-specific DB’s integrated DB’s “ all names” Botany Zoology Newly published names – primary literature (print, electronic) ICTV Viruses DB LPSN (Prokaryote names) ICBN Decisions ICZN Decisions Journal TOC’s, RSS feeds, text mining Abstracting services Subject bibliographies Reviews, secondary literature Zoological Record ION (Index of Organism Names) ChecklistBank GNI GNUB ZooBank? Catalogue of Life annual editions ITIS NCBI Taxonomy WoRMS etc. CyanoDB Index Fungorum MycoBank AlgaeBase Plant GSD’s PaleoDB Animal GSD’s other compilations e.g. regional lists, Wikispecies, Wikipedia, more… IRMNG Lots of automated feeds + expert curation
  • 48. New names: potential discovery paths Tony Rees: Hierarchical Classification of All Life new virus names new prokaryote names new botanical names – algae & fungi (except fossils) new botanical names – bryophytes through angiosperms (except fossils) new zoological names publication discovery official registers taxon-specific DB’s integrated DB’s “ all names” Botany Zoology Newly published names – primary literature (print, electronic) ICTV Viruses DB LPSN (Prokaryote names) ICBN Decisions ICZN Decisions Journal TOC’s, RSS feeds, text mining Abstracting services Subject bibliographies Reviews, secondary literature Zoological Record ION (Index of Organism Names) ChecklistBank GNI GNUB ZooBank? Catalogue of Life annual editions ITIS NCBI Taxonomy WoRMS etc. CyanoDB Index Fungorum MycoBank AlgaeBase Plant GSD’s PaleoDB Animal GSD’s other compilations e.g. regional lists, Wikispecies, Wikipedia, more… IRMNG Lots of automated feeds + expert curation Lots of useful services
  • 49. How many taxa? Tony Rees: Hierarchical Classification of All Life valid extant + fossil taxa (est.) How many species? estimates according to Chapman, 2009 (valid, extant taxa only); “others” comprise c. 54k protists, 10k prokaryotes, 2k viruses NB inverts. includes “~1,000,000” for Insects – probably +/- 60k Fossil species – no published estimates – maybe 500k names, 300k valid 2+ million ~250k ~10k ~2k Kingdoms (5/6/7/8) ~400 ~140 Phyla Classes Orders Families Genera Species
  • 50. Relevant information domain: all life Tony Rees: Hierarchical Classification of All Life PROTISTS Fig. i-1 in Margulis & Schwartz, 1998
  • 51. How many kingdoms… Tony Rees: Hierarchical Classification of All Life PROTISTS Fig. i-1 in Margulis & Schwartz, 1998 7 kingdoms (5 in Margulis & Schwartz, 8 in Cat. of Life…): Animals, Fungi, Plants : 3 kingdoms Protists : 1 (or 2 if Stramenopiles [Heterokonts] recognized, = Cavalier-Smith’s Kingdom “Chromista”) Bacteria + Archaea : 2 (=1 in Margulis & Schwartz) Viruses : 1 (not in Margulis & Schwartz)
  • 52. Nomenclature governed by four separate Codes , i.e. Zoological, Botanical, Bacteriological, Viruses Tony Rees: Hierarchical Classification of All Life PROTISTS Zoo. Code Bact. Code Bot. Code Vir. Code: viruses (not shown) Fig. i-1 in Margulis & Schwartz, 1998
  • 53. CiteBank as a remote references repository? Tony Rees: Hierarchical Classification of All Life
      • Unexplored questions…
      • how well populated is CiteBank either now, or in near future
      • can third party bibliographies be uploaded into it (with / without infringing IP)
      • Zoo. Record and similar operators do this already on a commercial basis – how to reconcile these activities / avoid redundant effort
      • would CiteBank IDs / outward links be an adequate substitute to storing / inspecting / displaying this info locally
  • 54. Parker, 1982 content example Tony Rees: Hierarchical Classification of All Life
  • 55. Benton, 1993 content example Tony Rees: Hierarchical Classification of All Life
  • 56. Rees TAXAMATCH fuzzy matching poster (start) Tony Rees: Hierarchical Classification of All Life
  • 57. Schematic of TAXAMATCH operation Tony Rees: Hierarchical Classification of All Life