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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.

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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 –FG02-7ER86321 and 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.comgarrity@

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 SYMBOLREFERENT Symbolizes (a causal relationship) Refers to (other causal relations) 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 NAMEEXEMPLAR Symbolizes (a causal relationship) Refers to (other causal relations) 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 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 Latinized species name Authority and priority date Species epithet

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 macleodii (T) communis Alteromonas 1972 vaga

11 communis vaga haloplanktis Alteromonas macleodii (T) 1972 1973

12 communis vaga haloplanktis rubra Alteromonas 1972 1973 1976 macleodii (T)

13 communis vaga haloplanktis rubra citrea Alteromonas 1972 1973 1976 1977 macleodii (T)

14 communis vaga haloplanktis rubra citrea esperjiana undina Alteromonas 1972 1973 1976 1977 1978 macleodii (T)

15 communis vaga haloplanktis rubra citrea esperjiana undina aurantia Alteromonas 1972 1973 1976 1977 1978 1979 macleodii (T)

16 communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai Alteromonas 1972 1973 1976 1977 1978 1979 1981 macleodii (T)

17 communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae Alteromonas 1972 1973 1976 1977 1978 1979 1981 1982 macleodii (T)

18 communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae vaga communis (T) MarinomonasAlteromonas commune vagum 1972 1973 1976 1977 1978 1979 1981 1982 1984 multiglobiferum japonicum minutium biejerinckii maris hiroshimense pelagicum pusillum jannaschii kreigii Oceanosprillum maris williamsae linum (T) macleodii (T) Nomenclatural issues Homotypic synonymy Priority Rule 37(a) 1 Data issues One to many relationship Taxonomic issue Which one is right?

19 communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai vagabenthica hanedai MarinomonasAlteromonas putrifaciens (T) Shewanella japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum Oceanosprillum maris williamsae 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 luteoviolaceae communis (T) linum (T) macleodii (T)

20 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 communis vaga haloplanktis rubra citrea esperjiana undina aurantia hanedai luteoviolaceae denitrificans vagabenthica hanedai MarinomonasAlteromonasShewanella japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum Oceanosprillum maris williamsae putrifaciens putrifaciens (T) communis (T) linum (T) macleodii (T)

21 communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans vagabenthica hanedai MarinomonasAlteromonasShewanella japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum Oceanosprillum maris williamsae 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 colwelliana putrifaciens (T) communis (T) linum (T) macleodii (T)

22 vagabenthica hanedai MarinomonasShewanella japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 colwelliana putrifaciens (T) communis (T) linum (T) macleodii (T)

23 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae putrifaciens (T) communis (T) linum (T) macleodii (T) Nomenclatural issue Non-type strains

24 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis putrifaciens hanedai denitrificans rubra citrea esperjiana undina aurantia luteoviolaceae tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea putrifaciens (T) communis (T) linum (T) macleodii (T) Nomenclatural issues Heterotypic synonymy Data issue Many to many relationship Taxonomic issue Which one is right?

25 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis putrifaciens hanedai denitrificans rubra citrea esperjiana undina aurantia luteoviolaceae tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra haloplanktis haloplanktis (T) Pseudoalteromonas undina haloplanktis tetradonis putrifaciens (T) communis (T) linum (T) macleodii (T)

26 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra Pseudoalteromonas undina antartica elyakovii haloplanktis tetradonis haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T)

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

28 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra Pseudoalteromonas undina antartica elyakovii fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetradonis japonica haloplanktis tetradonis mediterannea haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T)

29 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea Pseudoalteromonas elyakovii fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetradonis haloplanktis tetradonis mediterannea haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T)

30 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea Pseudoalteromonas elyakovii fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetradonis haloplanktis tetradonis 12 others mariniintestina saire schlegeliana gaetbuli mediterannea primoryensis haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T) stellipolaris litorea 5 others

31 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 2005 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea Pseudoalteromonas elyakovii fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetradonis haloplanktis tetradonis 14 others mariniintestina saire schlegeliana gaetbuli mediterannea primoryensis haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T) stellipolaris litorea 8 others 4 others

32 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 2005 2006 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea Pseudoalteromonas elyakovii fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetradonis haloplanktis tetradonis 15 others mariniintestina saire schlegeliana gaetbuli mediterannea primoryensis haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T) stellipolaris litorea 19 others 4 others

33 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 2005 2007 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea Pseudoalteromonas elyakovii fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetradonis haloplanktis tetradonis 16 others mariniintestina saire schlegeliana gaetbuli mediterannea primoryensis haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T) stellipolaris litorea 27 others 6 others

34 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 2005 2008 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea Pseudoalteromonas elyakovii fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetradonis haloplanktis tetradonis 16 others mariniintestina saire schlegeliana gaetbuli mediterannea primoryensis haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T) stellipolaris litorea 27 others 6 others

35 macleodii (T) communis Alteromonas 1972 vaga

36 communis vaga haloplanktis Alteromonas macleodii (T) 1972 1973

37 communis vaga haloplanktis rubra Alteromonas 1972 1973 1976 macleodii (T)

38 communis vaga haloplanktis rubra citrea Alteromonas 1972 1973 1976 1977 macleodii (T)

39 communis vaga haloplanktis rubra citrea esperjiana undina Alteromonas 1972 1973 1976 1977 1978 macleodii (T)

40 communis vaga haloplanktis rubra citrea esperjiana undina aurantia Alteromonas 1972 1973 1976 1977 1978 1979 macleodii (T)

41 communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai Alteromonas 1972 1973 1976 1977 1978 1979 1981 macleodii (T)

42 communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae Alteromonas 1972 1973 1976 1977 1978 1979 1981 1982 macleodii (T)

43 communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae vaga communis (T) MarinomonasAlteromonas commune vagum 1972 1973 1976 1977 1978 1979 1981 1982 1984 multiglobiferum japonicum minutium biejerinckii maris hiroshimense pelagicum pusillum jannaschii kreigii Oceanosprillum maris williamsae linum (T) macleodii (T)

44 communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai vagabenthica hanedai MarinomonasAlteromonas putrifaciens (T) Shewanella japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum Oceanosprillum maris williamsae 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 luteoviolaceae communis (T) linum (T) macleodii (T)

45 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 communis vaga haloplanktis rubra citrea esperjiana undina aurantia hanedai luteoviolaceae denitrificans vagabenthica hanedai MarinomonasAlteromonasShewanella japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum Oceanosprillum maris williamsae putrifaciens putrifaciens (T) communis (T) linum (T) macleodii (T)

46 communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans vagabenthica hanedai MarinomonasAlteromonasShewanella japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum Oceanosprillum maris williamsae 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 colwelliana putrifaciens (T) communis (T) linum (T) macleodii (T)

47 vagabenthica hanedai MarinomonasShewanella japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 colwelliana putrifaciens (T) communis (T) linum (T) macleodii (T)

48 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae putrifaciens (T) communis (T) linum (T) macleodii (T)

49 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis putrifaciens hanedai denitrificans rubra citrea esperjiana undina aurantia luteoviolaceae tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea putrifaciens (T) communis (T) linum (T) macleodii (T)

50 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis putrifaciens hanedai denitrificans rubra citrea esperjiana undina aurantia luteoviolaceae tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra haloplanktis haloplanktis (T) Pseudoalteromonas undina haloplanktis tetradonis putrifaciens (T) communis (T) linum (T) macleodii (T) fuliginea

51 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra Pseudoalteromonas undina antartica elyakovii haloplanktis tetradonis haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T)

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

53 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra Pseudoalteromonas undina antartica elyakovii fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetradonis japonica haloplanktis tetradonis mediterannea haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T)

54 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea Pseudoalteromonas elyakovii fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetradonis haloplanktis tetradonis mediterannea haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T)

55 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea Pseudoalteromonas elyakovii fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetradonis haloplanktis tetradonis 12 others mariniintestina saire schlegeliana gaetbuli mediterannea primoryensis haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T) stellipolaris litorea 5 others

56 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 2005 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea Pseudoalteromonas elyakovii fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetradonis haloplanktis tetradonis 14 others mariniintestina saire schlegeliana gaetbuli mediterannea primoryensis haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T) stellipolaris litorea 8 others 4 others

57 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 2005 2006 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea Pseudoalteromonas elyakovii fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetradonis haloplanktis tetradonis 15 others mariniintestina saire schlegeliana gaetbuli mediterannea primoryensis haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T) stellipolaris litorea 19 others 4 others

58 vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 2005 2007 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea Pseudoalteromonas elyakovii fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetradonis haloplanktis tetradonis 16 others mariniintestina saire schlegeliana gaetbuli mediterannea primoryensis haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T) stellipolaris litorea 27 others 6 others

59 hanedai luteoviolaceae vagabenthica hanedai colwelliana algae MarinomonasShewanella communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens denitrificans tetradonis atlantica carageenovora Alteromonas colwelliana 1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 2005 2008 japonicum minutium biejerinckii maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea Pseudoalteromonas elyakovii fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetradonis haloplanktis tetradonis 16 others mariniintestina saire schlegeliana gaetbuli mediterannea primoryensis haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T) stellipolaris litorea 27 others 6 others Eight additional species but over 50 name changes that affect more than 1400 published articles

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

61 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…

62 1980 – 2257 classified and validly named 2008 – 25628 classified and named 108847 taxonomic nodes 0.7 names per day 4.2 names per day 83 nodes per day Prokaryotic names 1980 - 2008 Bringing meaning to life…

63 Nomenclatural assertions

64 Nomenclatural assertions (cont.)

65

66 Object typeCountAttributeCount Name11661Assertion17841 Reference6672 Taxon11169 Exemplar7724Strains13410 16S rRNA8518 A NamesforLife taxonomic hierarchy

67 NamesforLife information objects Bringing meaning to life…

68 IJSEM workflow

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76 The NamesforLife autotagger What is it? Custom java server-side application or client side plug-in for Parses NLM-DTD* compliant manuscripts Identifies validly published bacterial names, wraps names in named-entity tags, inserts N4L DOIs into output XML, output name-data XSLT/CSS to highlight name strings in content Unintended benefit Auto-proofing tool to detect Tagging errors Nomenclatural errors

77 Autotagger performance 191Articles, XML, Aug - Dec 2007 17,188Name-like strings 15,022Correctly identified as VP names 3282unique names and abbreviated names 2634species/higher taxa 2167Candidate names 208newly proposed 3-letter abbreviations 184autotagger errors (Latin strings) 183fungal names 67invalid bacterial names 61 plant names 30animal names 7misspelled names 1476tagging errors

78 Autotagger performance (cont.) HumanComputerTotal Tags missed182442 Non-name tags142640 Partial/incorrect names167 Total335689

79 Autotagger performance (cont.)

80 Lessons learned N4L proof of principle Information object model Time travel DOI service Instrument vendor Database provider Pre-phase I N4L enablement of publishers’ content Refining time-travel Migration to RDBMS On-the-fly output of nomenclatural taxonomy (TOBA) Phase I

81 Next steps Production-level N4L application (DOI service) N4L enablement of IJS/SGM content Other microbiological literature Other STM literature Other microbiological applications Non-microbiological applications Pipeline approach to capture nomenclatural acts and auto-generation of prokaryotic taxonomies Browser plug-in for on-the-fly enablement Phase II Interested parties Test tools and concepts Leverage existing opportunities garrity@names4life.com We’re looking for

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