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Names for Life

Names for Life. Catherine Lyons 1 and George M. Garrity 2,3 1 Explicatrix LLC, 2 Michigan State University and 3 Bergey’s Manual Trust.

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Names for Life

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  1. Names for Life Catherine Lyons1 and George M. Garrity2,3 1Explicatrix LLC, 2Michigan State University and 3Bergey’s Manual Trust Names for Life and the underlying systems and methods for resolving ambiguity between names and entities is proprietary technology of Michigan State University. Use of this technology requires a license from the University.

  2. ... nomenclators no longer spoke in terms of God or the divine name. Instead, current thinking held that there was a lexical universe as well as a physical one, and bringing an object together with a compatible name caused the latent potentialities of both to be realized. Nor was there a single 'true name' for a given object: depending on its precise shape, a body might be compatible with several names, known as its 'euonyms,' and conversely a simple name might tolerate significant variations in body shape ... Ted Chiang ‘72 Letters’ in Stories of your life and others A Boy’s Guide to Nomenclature

  3. Catherine Lyons Reference publishing Lexicography Information analysis disambiguation dissemination extension Background George Garrity • Systematic bacteriology • Pharmaceutical research • Editor in Chief, Bergey’s Manual of Systematic Bacteriology Project Nomenclature and taxonomy Disambiguation the information model Dissemination the information objects Extension of the model nomenclature

  4. nomenclature Nomenclature and taxonomy: a case studyAlteromonas over 32 years

  5. nomenclature 1972 Alteromonas macleodii(T) communis vaga

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

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

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

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

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

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

  12. nomenclature 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 nomenclature 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

  14. Shewanella putrifaciens(T) nomenclature 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. nomenclature 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. nomenclature 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. nomenclature 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. nomenclature 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

  19. Pseudoalteromonas haloplanktis haloplanktis(T) nigrifaciens pisicida nomenclature 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 fulginea

  20. nomenclature 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 fulginea elyakoviii

  21. woodyii amazonensis oneidensis pealeana violacea nomenclature 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 fulginea elyakovii elyakoviii peptidolytica

  22. nomenclature 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 fulginea elyakovii elyakoviii peptidolytica tetrodonis

  23. nomenclature 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 fulginea elyakovii elyakoviii peptidolytica tetrodonis

  24. nomenclature 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 fulginea saire elyakovii elyakoviii schlegeliana peptidolytica gaetbuli tetrodonis 11 others

  25. 17 new species 3 species reassigned as the type species (founding species) of new genera 16 species reassigned to those 3 genera and to a fourth, preexisting genus 6 synonyms 1 species split into subspecies which later became separate species in all, 46 names, 5 genera, 3 families, 2 classes only 1 Alteromonas species remains In procaryotic microbiology, this is a common pattern of change. nomenclature Alteromonas over 32 years

  26. controlled by Codes of Nomenclature (botanical, zoological, bacteriological), initiated over 200 years ago. A name is required by Code to be published in print Codes prescribe name formation and curation of organic material; version management of print publications is difficult provide the primary entry point into STM literature and scientific databases play a prominent role in laws and regulations governing commerce, public safety, and public health may or may not be revised; may or may not have synonyms obsolesce in relation to changing taxonomic definition A name functions as an archival record of a taxonomic definition for a single point in time nomenclature Biological names

  27. disambiguation Disambiguation: the information model an event in which the state of a taxon is named in a publication name taxon a set oftaxa or exemplars defined by a nomos and maintained over time

  28. disambiguation Disambiguation: the information model a representation of an organism by reference to curated material and data exemplar a rule governing taxonomy; a methodology or heuristic for differentiating taxa by referenceto curated data describing attributes of their exemplars; a means of separating competing views; a namespace to differentiate one taxonomy from another nomos

  29. two versions of the same taxonomic view; separated by time a single version of a competing taxonomic view emendedname’ name’ name’ taxon’ taxon’ nomos’ nomos’ exemplarattribute attribute attribute classify exemplars according to the value of attribute classify exemplars according to the value of attribute disambiguation Disambiguation: the information model

  30. name taxon exemplar nomos dissemination Dissemination: the information objects Information objects are persistent, online, public documents. They instantiate name events and the taxon, exemplar, and nomos entities. Information objects provide metadata; they link to other information objects and to online information outside Names for Life. Information objects are easy to link to from online journals, databases, and similar resources.

  31. dissemination Dissemination: the information objects name • publication date • link to publication (DOI of journal article) • status with regard to a code of nomenclature • link to the information object representing any synonymousname • link to the information object representing the taxon

  32. dissemination Dissemination: the information objects taxon • date of most recent revision • link to the information object(s) representing name(s) that label this taxon • link to the supporting nomos • link to the taxon information object that contains this taxon • links to the information object(s) representing the contents of this taxon (taxa or exemplars) • for a taxon of exemplars: reference to exemplar-derived data required by the nomos

  33. dissemination Dissemination: the information objects exemplar • specimen identifier(s); link(s) to online collection records • identifier(s) of associated gene sequence(s); link(s) to database deposits • in the future: phenotypic data • link to the information object for the taxon containing the specimen; where competing views (nomoi) associate an exemplar with different taxa; there are links to each (overlapping) taxon information object

  34. dissemination Dissemination: the information objects nomos • label (e.g. ‘The Bergey’s Taxonomy’) • citation(s) • type(s) of the exemplar-derived data used to group exemplars into a taxon (gene locus, phenotypic feature) • link to the information object representing the taxon at the root of the taxonomy • count of the number of taxa supported by the nomos

  35. links from the web links to the web journalarticle journalarticle name combinedname DOI DOI strainrecord taxon journalarticle DOI DOI geneannotation journalarticle exemplar DOI nomos geneannotation strainrecord anyonline information dissemination Dissemination: the information objects

  36. name combinedname Look up this name and all its synonyms in PubMed taxon Compare this name to the current state (contents) of the taxon exemplar nomos Determine whether thisexemplar is part of a taxon in another nomos dissemination Dissemination: services By reasoning over information objects, we construct services that can be offered through multiple resolution.

  37. dissemination disambiguation Names for Life a model of nomenclatureand taxonomy • disambiguation of • synonyms • competing taxonomies a metadataresolutionservice dissemination of archived and updated information objects through persistent links Named for Life

  38. taxon’ exemplarattribute attribute attribute classify exemplars according to the value of attribute extension Extending the model: ontology patchwork name’ nomos’

  39. depositedsequence gene ontology taxonomy oforganisms annotation locus taxon’ sequence exemplar organismexemplargene locus: sequence IDmetabolism:ID of pathway definition classify exemplars according tosome orthologousgene extension Extending the model: ontology patchwork name’ nomos’

  40. label name name organizingprinciple a namedtaxonomy taxon set of conforming taxa exemplarattribute attribute attribute dynamic entities nomos extension Extending the model: names as labels for versioning

  41. Lots and lots of clean data Standards consensus among overlapping communities Funding and revenue Next steps Exploratory work with potential partners (genomics researchers; curators of biological material; publishers) Implementation of Bergamot: Bergey’s AccuMulative Online Taxonomy, based on phylogenetic analysis at MSU Comments and questions? catherine@explicatrix.com nomenclature disambiguation dissemination extension What we need now

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