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George M. Garrity, Catherine Lyons and James R. Cole NamesforLife, LLC

George M. Garrity, Catherine Lyons and James R. Cole NamesforLife, LLC Okemos, MI and Edinburgh, UK

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George M. Garrity, Catherine Lyons and James R. Cole NamesforLife, LLC

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  1. George M. Garrity, Catherine Lyons and James R. Cole NamesforLife, LLC Okemos, MI and Edinburgh, UK Funding for this portions of this research has been provide by the US Department of Energy, Grants No. DE-FG02-04ER63933, DE-FG02-99ER62848, DE –FG02-7ER86321and the Michigan University Commercialization Initiative (MUCI) program. Portions of this work are covered under US and foreign patents (pending) and are the intellectual property of the Michigan State University Board of Trustees. For further information contact garrity@names4life.com

  2. Names • Indicate a new discovery or invention • Constant source of frustration • End users of literature and scientific databases • Publishers and data providers • Names are not permanent • Queries can be incomplete or wrong • Difficult and costly to maintain • Render content inaccessible and obsolete • Poor identifiers

  3. Ogden Richards semiotic triangle THOUGHT OR REFERENCE Symbolizes (a causal relationship) Refers to (other causal relations) SYMBOL REFERENT Stands for (an imputed relation) Adapted from Ogden,CK and Richards, IA The Meaning of Meaning, Magdale, 1923

  4. Does the OGT apply to biological names? TAXONOMIC CONCEPT Symbolizes (a causal relationship) Refers to (other causal relations) NAME EXEMPLAR Stands for (an imputed relation)

  5. Biological naming conventions

  6. Fundamentals of bacterial nomenclature • Governed by Codes of Nomenclature • Scientific names are all latinized words • Purpose is to serve as a unique label • Each name is “anchored” by a nomenclatural type • Correct names are based upon • Valid publication • Legitimacy • Priority of publication • Names have standing only if validly published • Each taxon can bear only one correct name, based on • Circumscription • Position • Rank • Names should not be changed without sufficient reason Adapted from International Code of Nomenclature of Bacteria, 1990 Revision

  7. Anatomy of a bacterial name Alteromonas communis Bauman et al. 1972 Authority and priority date Latinized species name Species epithet Marinomonas commune (Bauman et al. 1972) van Landshoot and Delay 1984 Oceanomonas commune (Bauman et al. 1972) Bowditch et al. 1984 Alteromonas Baumann et al. 1972 (Approved Lists 1980) emend. Novick and Tyler 1985 Alteromonadaceae Ivanova and Mikhailov 2001 emend. Ivanova et al. 2004

  8. Nomenclatural assertions New name • Any rank from subspecies to order • Must assert novelty, declare type, circumscribe taxon, provide definition of name. • Effective vs. valid publication New combination • Subspecies or species split • Must assert novelty, declare type, circumscribe taxon, provide definition of new genus name. Species epithet retained. Synonymies Heterotypic Homotypic Orthographic corrections Rejected/conserved names

  9. An example of the problem…

  10. 1972 Alteromonas macleodii(T) communis vaga

  11. 1972 1973 Alteromonas macleodii(T) communis vaga haloplanktis

  12. 1972 19731976 Alteromonas macleodii(T) communis vaga haloplanktis rubra

  13. 1972 1973 19761977 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea

  14. 1972 1973 1976 19771978 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina

  15. 1972 1973 1976 1977 19781979 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia

  16. 1972 1973 1976 1977 1978 19791981 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai

  17. 1972 1973 1976 1977 1978 1979 19811982 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae

  18. Oceanosprillum Marinomonas linum(T) communis(T) japonicum minutium biejerinckii maris maris maris williamsae hiroshimense multiglobiferum pelagicum pusillum jannaschii kreigii 1972 1973 1976 1977 1978 1979 1981 19821984 Alteromonas macleodii(T) vaga communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae commune vagum

  19. Shewanella putrifaciens(T) 1972 1973 1976 1977 1978 1979 1981 1982 19841986 Oceanosprillum Marinomonas Alteromonas linum(T) communis(T) macleodii(T) japonicum vaga communis benthica minutium hanedai vaga biejerinckii haloplanktis maris maris rubra citrea maris williamsae esperjiana undina hiroshimense aurantia multiglobiferum putrifaciens pelagicum hanedai pusillum luteoviolaceae commune jannaschii kreigii vagum

  20. 1972 1973 1976 1977 1978 1979 1981 1982 1984 19861987 Oceanosprillum Marinomonas Alteromonas Shewanella linum(T) communis(T) putrifaciens(T) macleodii(T) japonicum vaga communis benthica minutium hanedai vaga biejerinckii haloplanktis maris maris rubra citrea maris williamsae esperjiana undina hiroshimense aurantia multiglobiferum putrifaciens pelagicum hanedai pusillum luteoviolaceae commune denitrificans jannaschii kreigii vagum

  21. 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 19871988 Oceanosprillum Marinomonas Alteromonas Shewanella linum(T) communis(T) putrifaciens(T) macleodii(T) japonicum vaga communis benthica minutium hanedai vaga biejerinckii haloplanktis maris maris rubra citrea maris williamsae esperjiana undina hiroshimense aurantia multiglobiferum putrifaciens pelagicum hanedai pusillum luteoviolaceae commune denitrificans jannaschii colwelliana kreigii vagum

  22. 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 19881990 Oceanosprillum Marinomonas Alteromonas Shewanella linum(T) communis(T) putrifaciens(T) macleodii(T) japonicum vaga communis benthica minutium hanedai vaga biejerinckii colwelliana haloplanktis maris maris rubra citrea maris williamsae esperjiana undina hiroshimense aurantia multiglobiferum putrifaciens pelagicum hanedai pusillum luteoviolaceae commune denitrificans jannaschii colwelliana kreigii tetradonis vagum biejerinckii pelagicum maris hiroshimense

  23. 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 19901992 Oceanosprillum Marinomonas Alteromonas Shewanella linum(T) communis(T) putrifaciens(T) macleodii(T) japonicum vaga communis benthica minutium hanedai vaga biejerinckii colwelliana haloplanktis maris maris algae rubra citrea maris williamsae esperjiana undina hiroshimense aurantia multiglobiferum putrifaciens pelagicum hanedai pusillum luteoviolaceae commune denitrificans jannaschii colwelliana kreigii tetradonis vagum atlantica biejerinckii pelagicum carageenovora maris hiroshimense

  24. 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 19921995 Oceanosprillum Marinomonas Alteromonas Shewanella linum(T) communis(T) putrifaciens(T) macleodii(T) japonicum vaga communis benthica minutium hanedai vaga biejerinckii colwelliana haloplanktis maris maris algae rubra citrea maris williamsae esperjiana undina hiroshimense aurantia multiglobiferum putrifaciens pelagicum hanedai pusillum luteoviolaceae commune denitrificans jannaschii colwelliana kreigii tetradonis vagum atlantica biejerinckii pelagicum carageenovora distincta maris hiroshimense fuliginea

  25. Pseudoalteromonas haloplanktis haloplanktis(T) nigrifaciens pisicida 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 19921995 Oceanosprillum Marinomonas Alteromonas Shewanella linum(T) communis(T) putrifaciens(T) macleodii(T) japonicum vaga communis benthica haloplanktis tetradonis minutium hanedai vaga biejerinckii colwelliana haloplanktis atlantica maris maris algae rubra aurantia citrea maris williamsae carrageenovora esperjiana citrea undina hiroshimense esperjiana aurantia multiglobiferum luteoviolacea putrifaciens pelagicum hanedai pusillum luteoviolaceae commune rubra denitrificans jannaschii undina colwelliana kreigii tetradonis vagum atlantica biejerinckii pelagicum carageenovora distincta maris hiroshimense fuliginea

  26. 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 19951997 Oceanosprillum Marinomonas Alteromonas Shewanella Pseudoalteromonas linum(T) communis(T) putrifaciens(T) haloplanktis haloplanktis(T) macleodii(T) japonicum vaga communis benthica haloplanktis tetradonis minutium hanedai vaga biejerinckii colwelliana haloplanktis atlantica maris maris algae rubra aurantia citrea maris williamsae carrageenovora esperjiana citrea undina hiroshimense esperjiana aurantia multiglobiferum luteoviolacea putrifaciens pelagicum nigrifaciens hanedai pusillum pisicida luteoviolaceae commune rubra denitrificans jannaschii undina colwelliana kreigii antartica tetradonis vagum atlantica biejerinckii pelagicum carageenovora distincta maris hiroshimense fuliginea elyakovii

  27. woodyii amazonensis oneidensis pealeana violacea 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 19972000 Oceanosprillum Marinomonas Alteromonas Shewanella Pseudoalteromonas linum(T) communis(T) putrifaciens(T) haloplanktis haloplanktis(T) macleodii(T) japonicum vaga communis benthica haloplanktis tetradonis minutium mediterannea hanedai vaga biejerinckii colwelliana haloplanktis atlantica maris maris algae rubra aurantia citrea fridgidimarina maris williamsae carrageenovora esperjiana geldimarina citrea undina hiroshimense esperjiana aurantia multiglobiferum luteoviolacea putrifaciens baltica pelagicum nigrifaciens hanedai pusillum pisicida luteoviolaceae commune rubra denitrificans jannaschii undina colwelliana kreigii antartica tetradonis vagum bacteriolytica atlantica biejerinckii pelagicum prydzensis carageenovora tunicata distincta maris hiroshimense distincta fuliginea elyakovii elyakovii peptidolytica

  28. 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 20002001 Oceanosprillum Marinomonas Alteromonas Shewanella Pseudoalteromonas linum(T) communis(T) putrifaciens(T) haloplanktis haloplanktis(T) macleodii(T) japonicum vaga communis benthica haloplanktis tetradonis minutium mediterannea hanedai vaga biejerinckii colwelliana haloplanktis atlantica maris maris algae rubra aurantia citrea fridgidimarina maris williamsae carrageenovora esperjiana geldimarina citrea undina woodyii hiroshimense esperjiana aurantia amazonensis multiglobiferum luteoviolacea putrifaciens baltica pelagicum nigrifaciens hanedai oneidensis pusillum pisicida luteoviolaceae pealeana commune rubra denitrificans violacea jannaschii undina colwelliana japonica kreigii antartica tetradonis vagum bacteriolytica atlantica biejerinckii pelagicum prydzensis carageenovora tunicata distincta maris hiroshimense distincta fuliginea elyakovii elyakovii peptidolytica tetradonis

  29. 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 20012002 Oceanosprillum Marinomonas Alteromonas Shewanella Pseudoalteromonas linum(T) communis(T) putrifaciens(T) haloplanktis haloplanktis(T) macleodii(T) japonicum vaga communis benthica haloplanktis tetradonis minutium mediterannea hanedai vaga biejerinckii colwelliana haloplanktis atlantica maris maris algae rubra aurantia citrea fridgidimarina maris williamsae carrageenovora esperjiana geldimarina citrea undina woodyii hiroshimense esperjiana aurantia amazonensis multiglobiferum luteoviolacea putrifaciens baltica pelagicum nigrifaciens hanedai oneidensis pusillum pisicida luteoviolaceae pealeana commune rubra denitrificans violacea jannaschii undina colwelliana japonica kreigii antartica tetradonis denitrificans vagum bacteriolytica atlantica livingstonensis biejerinckii pelagicum prydzensis carageenovora alleyanna tunicata distincta maris hiroshimense distincta fuliginea elyakovii elyakovii peptidolytica tetradonis

  30. 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 20022004 Oceanosprillum Marinomonas Alteromonas Shewanella Pseudoalteromonas linum(T) communis(T) putrifaciens(T) haloplanktis haloplanktis(T) macleodii(T) japonicum vaga communis benthica haloplanktis tetradonis minutium mediterannea hanedai vaga biejerinckii primoryensis colwelliana haloplanktis atlantica maris maris algae rubra aurantia citrea fridgidimarina maris williamsae carrageenovora esperjiana geldimarina citrea undina woodyii hiroshimense esperjiana aurantia amazonensis multiglobiferum luteoviolacea putrifaciens baltica pelagicum nigrifaciens hanedai oneidensis pusillum pisicida luteoviolaceae pealeana commune rubra denitrificans violacea jannaschii undina colwelliana japonica kreigii antartica tetradonis denitrificans vagum bacteriolytica atlantica livingstonensis biejerinckii pelagicum prydzensis carageenovora alleyanna tunicata distincta mariniintestina maris hiroshimense distincta fuliginea saire elyakovii elyakovii schlegeliana peptidolytica gaetbuli stellipolaris tetradonis 5 others litorea 12 others

  31. 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 20022004 2005 Oceanosprillum Marinomonas Alteromonas Shewanella Pseudoalteromonas linum(T) communis(T) putrifaciens(T) haloplanktis haloplanktis(T) macleodii(T) japonicum vaga communis benthica haloplanktis tetradonis minutium mediterannea hanedai vaga biejerinckii primoryensis colwelliana haloplanktis atlantica maris maris algae rubra aurantia citrea fridgidimarina maris williamsae carrageenovora esperjiana geldimarina citrea undina woodyii hiroshimense esperjiana aurantia amazonensis multiglobiferum luteoviolacea putrifaciens baltica pelagicum nigrifaciens hanedai oneidensis pusillum pisicida luteoviolaceae pealeana commune rubra denitrificans violacea jannaschii undina colwelliana japonica kreigii antartica tetradonis denitrificans vagum bacteriolytica atlantica livingstonensis biejerinckii pelagicum prydzensis carageenovora alleyanna tunicata distincta mariniintestina maris hiroshimense distincta fuliginea saire elyakovii elyakovii schlegeliana peptidolytica gaetbuli stellipolaris tetradonis 8 others litorea 14 others 4 others

  32. 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 200220042005 2006 Oceanosprillum Marinomonas Alteromonas Shewanella Pseudoalteromonas linum(T) communis(T) putrifaciens(T) haloplanktis haloplanktis(T) macleodii(T) japonicum vaga communis benthica haloplanktis tetradonis minutium mediterannea hanedai vaga biejerinckii primoryensis colwelliana haloplanktis atlantica maris maris algae rubra aurantia citrea fridgidimarina maris williamsae carrageenovora esperjiana geldimarina citrea undina woodyii hiroshimense esperjiana aurantia amazonensis multiglobiferum luteoviolacea putrifaciens baltica pelagicum nigrifaciens hanedai oneidensis pusillum pisicida luteoviolaceae pealeana commune rubra denitrificans violacea jannaschii undina colwelliana japonica kreigii antartica tetradonis denitrificans vagum bacteriolytica atlantica livingstonensis biejerinckii pelagicum prydzensis carageenovora alleyanna tunicata distincta mariniintestina maris hiroshimense distincta fuliginea saire elyakovii elyakovii schlegeliana peptidolytica gaetbuli stellipolaris tetradonis 19 others litorea 15 others 4 others

  33. 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 200220042005 2007 Oceanosprillum Marinomonas Alteromonas Shewanella Pseudoalteromonas linum(T) communis(T) putrifaciens(T) haloplanktis haloplanktis(T) macleodii(T) japonicum vaga communis benthica haloplanktis tetradonis minutium mediterannea hanedai vaga biejerinckii primoryensis colwelliana haloplanktis atlantica maris maris algae rubra aurantia citrea fridgidimarina maris williamsae carrageenovora esperjiana geldimarina citrea undina woodyii hiroshimense esperjiana aurantia amazonensis multiglobiferum luteoviolacea putrifaciens baltica pelagicum nigrifaciens hanedai oneidensis pusillum pisicida luteoviolaceae pealeana commune rubra denitrificans violacea jannaschii undina colwelliana japonica kreigii antartica tetradonis denitrificans vagum bacteriolytica atlantica livingstonensis biejerinckii pelagicum prydzensis carageenovora alleyanna tunicata distincta mariniintestina maris hiroshimense distincta fuliginea saire elyakovii elyakovii schlegeliana peptidolytica gaetbuli stellipolaris tetradonis 27 others litorea 16 others 6 others

  34. Eight additional species but over 50 name changes that affect more than 1400 published articles 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 200220042005 2008 Oceanosprillum Marinomonas Alteromonas Shewanella Pseudoalteromonas linum(T) communis(T) putrifaciens(T) haloplanktis haloplanktis(T) macleodii(T) japonicum vaga communis benthica haloplanktis tetradonis minutium mediterannea hanedai vaga biejerinckii primoryensis colwelliana haloplanktis atlantica maris maris algae rubra aurantia citrea fridgidimarina maris williamsae carrageenovora esperjiana geldimarina citrea undina woodyii hiroshimense esperjiana aurantia amazonensis multiglobiferum luteoviolacea putrifaciens baltica pelagicum nigrifaciens hanedai oneidensis pusillum pisicida luteoviolaceae pealeana commune rubra denitrificans violacea jannaschii undina colwelliana japonica kreigii antartica tetradonis denitrificans vagum bacteriolytica atlantica livingstonensis biejerinckii pelagicum prydzensis carageenovora alleyanna tunicata distincta mariniintestina maris hiroshimense distincta fuliginea saire elyakovii elyakovii schlegeliana peptidolytica gaetbuli stellipolaris tetradonis 27 others litorea 16 others 6 others

  35. November 2004 May 2004 Gammaproteobacteria Alteromonadales Colwelliaceae Idiomarinaceae Alteromonadacea Colwelliaceae Alteromonas Idiomarina Aestuariibacter Thalassomonas Alishewanella Ferrimonadacea Colwellia Psychromonadaceae Ferrimonas Ferrimonas Psychromonas Glaciecola Idiomarina Pseudoalteromonadaceae Marinobacter 1 Family 16 genera -> 8 families 12 genera 1 unclassified -> 7 unclassfied Which is correct? Which is supported by the data? Incertae sedis Pseudoalteromonas Marinobacterium Agarvorans Algicola Microbulbifer Alishewanella Moritella Marinobacter Shewanellaceae Pseudoalteromonas Marinobacterium Shewanella Psychromonas Microbulbifer Shewanella Salinomonas Moritellaceae Thalassomonas Teredinibacter Moritella Incertae sedis Teredinibacter

  36. In 36 years this genus of bacteria underwent • 24 published changes • 26 new species were added • 23 species moved to other genera • 50 names were created • and today the genus contains 8 species. This fairly simple example impacts 1443 other publications >9500 nucleotide sequences How does a publisher, library or archive keep legacy content relevant? At what cost? Bringing meaning to life…

  37. Prokaryotic names 1980 - 2008 1980 – 2257 classified and validly named 2008 – 25628 classified and named 108847 taxonomic nodes 83 nodes per day 4.2 names per day 0.7 names per day Bringing meaning to life…

  38. Nomenclatural assertions

  39. Nomenclatural assertions (cont.)

  40. Nomenclatural assertions (cont.)

  41. A NamesforLife taxonomic hierarchy

  42. NamesforLife information objects Bringing meaning to life…

  43. IJSEM workflow

  44. IJSEM workflow

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