Knowledge bleed, Phenbank, and NamesforLife

1. Knowledge bleed,Phenbank, and NamesforLife George M. Garrity, Catherine Lyons & James R. Cole Michigan State University and NamesforLife, LLC Funding for this research has been provide by the US Department of Energy, Grants No. DE-FG02-04ER63933 and DE-FG02-99ER62848, the National Science Foundation Award No. DBI-0328255 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@msu.edu

2. Rumsfeld’s axiom and knowledge bleed “…because as we know, there are known knowns; there are things we know we know. We also know there are known unknowns; that is to say we know there are some things we do not know. But there are also unknown unknowns -- the ones we don't know we don't know.”

3. The knowledge gradient Unknown unknowns Unknown knowns Known unknowns Known knowns Semantic resolution provides a mechanism to combat knowledge bleed Knowledge bleed results is a loss of knowledge that has already been gained Basic and applied research advances knowledge

4. We do quagmires

5. 1972 Alteromonas macleodii(T) communis vaga

6. 1972 1973 Alteromonas macleodii(T) communis vaga haloplanktis

7. 1972 19731976 Alteromonas macleodii(T) communis vaga haloplanktis rubra

8. 1972 1973 19761977 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea

9. 1972 1973 1976 19771978 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina

10. 1972 1973 1976 1977 19781979 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia

11. 1972 1973 1976 1977 1978 19791981 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai

12. 1972 1973 1976 1977 1978 1979 19811982 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae

13. 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 • Nomenclatural issues • Homotypic synonymy • Priority • Rule 37(a) 1 • Data issues • One to many relationship • Taxonomic issue • Which one is right?

14. 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

15. 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

16. 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

17. 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

18. 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 • Nomenclatural issue • Non-type strains hiroshimense aurantia multiglobiferum putrifaciens pelagicum hanedai pusillum luteoviolaceae commune denitrificans jannaschii colwelliana kreigii tetradonis vagum atlantica biejerinckii pelagicum carageenovora maris hiroshimense

19. 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 • Nomenclatural issues • Heterotypic synonymy • Data issue • Many to many relationship • Taxonomic issue • Which one is right? distincta maris hiroshimense fuliginea

20. 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

21. 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 elyakoviii

22. 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 elyakoviii peptidolytica

23. 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 elyakoviii peptidolytica tetrodonis

24. 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 elyakoviii peptidolytica tetrodonis

25. 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 elyakoviii schlegeliana peptidolytica gaetbuli stellipolaris tetrodonis 5 others litorea 12 others

26. 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 elyakoviii schlegeliana peptidolytica gaetbuli stellipolaris tetrodonis 8 others litorea 14 others 2 others

27. 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 elyakoviii schlegeliana peptidolytica gaetbuli stellipolaris tetrodonis 13 others litorea 14 others 2 others

28. Since first being defined • The genus Alteromonas has undergone 18 “emendations” • 21 species were added to the genus • 19 species were reassigned to four genera • 3 of which are formed as new combinations of Alteromonas spp. • 6 synonyms • 2 species reduced to subspecies, then re-elevated to species • 50 names, five genera, five families, and two classes but…. • only five validly published named species of Alteromonas remain. This is not a very complicated example But wait, there is still more

29. 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

30. Nomenclature (the end-user’s perspective) Wouldn’t it be nice if… • Biological names were really useful • Would link to… • Relevant literature • Sequences • Other phenotypic data • Sources of strains in Biological Resource Centers • Ancillary materials • Patents • Laws and regulations • Regardless of where the data resides • Without having to know anything about • Synonymies • Orthographic variants • Misapplications of the name How could this be accomplished?

31. Modeling names and taxa…

32. Authority+ Name+ Taxon Species+ Strain+ Sequence+

33. GenBank DDBJ EMBL others Collections BRC Literature Governing bodies Authority+ Name+ Taxon Species+ Strain+ Sequence+

34. Taxon Priority Proposals Source+ Validity Literature Governing bodies STM Synonymy Legal Type General Authority+ Databases Name+ Public Private Species+ Strain+ Feature+ direct GenBank DDBJ EMBL others Source+ GSC Core Phenotype FAME Biolog PA Collections BRC indirect BRC

35. However, rules are made to be broken…

36. Name+ Name+ Species+ Species+ Strain+ Feature+ Feature+ Feature+ A properly formed species Candidatus or exemplar lost Environmental sequence Name+ “Name”+ Species+ Strain+ Strain* Feature+ Old type strain, not yet sequenced Misidentified taxon Name+ Species+ Old type, exemplar based on drawing or description

37. Differing opinions… Name+ Name+ Name+ Strain+ Strain+ Taxon Taxon Taxon Species+ Feature+ Feature+ Strain+ Feature+ Homotypic synonymy Heterotypic synonymy

38. The impact of “uncontrolled” labeling of environmental sequence and strain data …

39. Feature+ Environmental sequence Non-types, clones, environmental sequences ID+ “Name”+ Strain* Feature+ Misidentified taxon

40. 1200 1000 800 600 400 200 0 I 1 3 4 5 6 7 8 9 A B D C 10 11 14 12 16 17 B2 RB Tanzania Top 25 labels on 16S rRNA sequences for type strains n = 15232 unique sequences 2.74X over defined

42. The case of the Verrucomicrobia

43. “Identifiers” on Verrucomicrobia 16S rRNA sequences, n=911

44. Publication field from Genbank record, n=627

45. Verrucomicrobia, based on annotation (n=444) Unclassified Victivalalles & Lentisphaeralles Unclassified Xiphinematobact Optitutus Verrucomicrobia Proteobacteria

46. Taxonomic structure of the Verrucomicrobia revealed Unclassified Optitutus Verrucomicrobium Chthoniobacter Xiphenematobact Verrucomicrobium Rubritalea Prosthecobacter Verrucomicrobium Akkermansia Lentisphaera

47. Accessing the NamesforLife information objects

48. How NamesforLife disambiguates biological nomenclature

49. The underlying concepts A name or an identifier for a resource that uniquely identifies that resource and will be forever associated with that resource. It will never be reassigned to any other resource and will not change regardless of where the resource is located or whatever protocol is used to access it. Use of a well managed persistent identifier rather than a location will ensure that when a document is moved, or its ownership changes, the links to it will remain actionable. Persistent identifiers From: Diana Dack. 2001. Persistence is a Virtue Information Online Conference, Sydney.

50. The underlying concepts (cont.) • Semantic resolution The process of identifying the precise meaning of terms or concepts and mapping them into different classifications. • Static concepts • Unaffected by new knowledge • Dynamic concepts • Affected by new knowledge • What’s so important about precise meaning in scientific, technical, or medical fields? • …in commerce?