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Knowledge bleed, NamesforLife, and Rumsfeld’s axiom

Knowledge bleed, NamesforLife, and Rumsfeld’s axiom. George M. Garrity, Catherine Lyons & James R. Cole Michigan State University and NamesforLife, LLC

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Knowledge bleed, NamesforLife, and Rumsfeld’s axiom

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  1. Knowledge bleed, NamesforLife, andRumsfeld’s axiom 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. Service related science Bioinformatics STM publishing End-users External forces Products and services Systematic and systems microbiology

  5. We do quagmires

  6. 1972 Alteromonas macleodii(T) communis vaga

  7. 1972 1973 Alteromonas macleodii(T) communis vaga haloplanktis

  8. 1972 19731976 Alteromonas macleodii(T) communis vaga haloplanktis rubra

  9. 1972 1973 19761977 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea

  10. 1972 1973 1976 19771978 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina

  11. 1972 1973 1976 1977 19781979 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia

  12. 1972 1973 1976 1977 1978 19791981 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai

  13. 1972 1973 1976 1977 1978 1979 19811982 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae

  14. 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?

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. November 2004 May 2004 Gammaproteobacteria Alteromonadales Colwelliaceae Idiomarinaceae Alteromonadacea Colwelliaceae Alteromonas Idiomarina Aestuariibacter Thalassomonas Alishewanella Ferrimonadacea Colwellia Psychromonadaceae • At the species level • 18 “emendations” • 21 new species • 19 species reassigned to 4 genera • 3 new combinations • 6 synonyms • 2 species to subspecies • 2 subspecies to species • 50 names, five genera, five families, and two classes but…. • only 5 validly published species. • At the higher level • 1 Family 16 genera -> 8 families 12 genera • 1 unclassified genus -> 7 unclassified genera • Which is correct? • Which is supported by the data? • What is the impact on MIGS? Ferrimonas Ferrimonas Psychromonas Glaciecola Idiomarina Pseudoalteromonadaceae Marinobacter 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. Authority+ Name+ Taxon Species+ Strain+ Sequence+

  31. 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 MLST Images etc. Collections BRC indirect BRC

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

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

  34. 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

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

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

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

  38. How NamesforLife disambiguates biological nomenclature

  39. NamesforLife • A novel combination of “unrelated” technologies • An ontology, metadata model, and a mapping • An application of persistent identifiers • A transparent information layer on the Internet • A semantic resolution service for the life sciences What is it? What isn’t it? A content provider (at least beyond the pilot stage) • Solve a well known problem • Ambiguity in terminology • Common problem • Pervasive in life sciences • The special case of biological nomenclature • Queries and literature searches • Assertions, assumptions, hypotheses What is the purpose?

  40. URL DOI URL DOI URL DOI DOI DOI URL URL URL URL URL DOI DOI DOI URL DOI URL DOI URL DOI URL DOI URL DOI URL DOI doi> doi> doi> Assigner Content DOI directory DOI directory DOI directory Content Courtesy of Norman Paskin, International DOI Foundation

  41. Why DOIs are the preferred GUID • Digital object identifiers • Strengths - opaque, actionable, require metadata, identify an object, strong governance, widespread usage, not based on DNS, guarantee of persistence, proposed ISO standard. • Weakness - Not free DOIs Technically robust • Proven technology • DOIs are layered on top of CNRI’s Handle server • Scalable • Widespread use in publishing industry (CrossRef) • 1674 publishers and 1098 libraries subscribing • 15,148 journals covered • 22,376,071 DOIs assigned • > 11M end-user clicks in previous month (8/9/06) • Well understood technology • Strong social/legal framework to ensure persistence

  42. Taxon DOI Name Rank Parent name Parent taxon DOI Methodology Members Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name Exemplar DOI Biodeposit Feature Biodeposit Feature Taxon DOI Species name Name DOI Name Name status Authority Synonyms Taxon DOI Taxon DOI Name Rank Parent name Parent taxon DOI Methodology Type exemplar DOI Higher Taxon object Exemplar object Name object Taxon object • Seven first class object types • Name, Taxon, Exemplar, • Nomos, Practitioner, Feature, Nomenclatural Code N4L architecture

  43. The prototype DOI:10.1601/tx.0 • A proof-of-principle application • 24,176 first-class objects • Track changes in concepts over time • Based on a nomenclatural taxonomy, but capable of supporting multiple taxonomic views and “time travel” • Initial DOI services conform to AP 0 • Released January 17, 2006 • Japanese prototype released June 21, 2006 • Chinese version under development • Arabic version under consideration

  44. The mini-monograph Preamble Name/Name DOI Name status, Authority Synonyms/Name DOI Member of: Parent Taxon DOI Methodology Type Exemplar DOI Biodeposit+ Feature+ Paired Sequences Genomic Paired phenotypic data Minimal description GSC Core description Images Nontype exemplar Biodeposit+ Feature+ Paired Sequences Genomic Paired phenotypic data Minimal description GSC Core description Images Reference DOIs Taxon DOI Name Rank Parent name Parent taxon DOI Methodology Type exemplar DOI Nontype exemplar DOI IJSEM/ICSP Taxonomic authorities Name DOI Name Name status Authority Synonyms Taxon DOI Exemplar DOI Biodeposit Feature Biodeposit Feature Taxon DOI Species name BRCs & Collections Genbank/EMBL/DDBJ Taxonomic community Genomics community Instrument vendors Database providers Publishers

  45. Easy support of foreign languages

  46. Accessing the NamesforLife information objects

  47. Embedding N4L links into web content

  48. PhenBank… • Associate phenotypic data with emerging 16S sequence data • Potential value to the community • Problems • Technical • Interoperability and data comparability • Variable granularity • Lack of controlled vocabulary • Social issues of the centralized model • Who controls access? • Who curates? • Who pays? • Incentives for participants? The federated database

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