1. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Digital Object Identifiers as a technology Implementation of a full working prototype The NamesforLife model George M. Garrity Microbiology and Molecular Genetics Michigan State University

2. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 During the next 25 minutes An overview Digital Object Identifiers What is an identifier? Comparison of DOI features to a native Handle implementation Address Ricardo’s general questions Extensibility Handling of metadata Strengths Weaknesses Other relevant issues Introduce the NamesforLife prototype Development of the model A complete prokaryotic taxonomy implemented with DOIs

3. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 “Dual” interests Trustee and Editor-in-Chief Founded in 1936 501 c3 Non-profit educational trust Headquartered at Michigan State University Produce reference works in prokaryotic biology Bergey’s Manual of Systematic Bacteriology Principal monographic work in the field Validly published, named taxa > 650 international expert authors Published by Springer, NY Bergey’s Manual of Determinative Bacteriology Diagnostic Traditional “ink on paper” products Taxonomic Outline of the Prokaryotes Derived from MSU/DOE sponsored research Backbone of the Systematics Distributes as a locked PDF file http: //www.bergeysoutline.com

4. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 “Dual” interests (cont.) The major source of curated 16S rRNA sequences and on-line tools used in building prokaryotic phylogenies and identifying cultivated and yet to be cultivated prokaryotes. Funding by DOE Office of Science (BER) and NSF http://rdp.cme.msu.edu Visualization tools for exploratory data analysis of large sequence data set, a taxonomic atlas of the prokaryotes, and a repository of vetted 16S sequences. Funding by DOE Office of Science (BER) http://taxoweb.mmg.msu.edu Semantic resolution services for life sciences using digital object identifiers Funding by the Michigan University Commercialization Initiative US and WIPO patents pending Property of the Board of Trustees of Michigan State University

5. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 I represent the following parties An IUMS COMCOF Body that oversees the nomenclature of prokaryotes Publication of the “ Code ” and the International Journal of Systematic and Evolutionary Microbiology Judicial Commission Oversees application and modification of the code Taxonomic subcommittees The Digital Object Identifier System  International Committee on Systematics of Prokaryotes The International DOI Foundation Established in 1998 Develop and manage the DOI System Support the needs of the IP community in the digital environment by development and promotion of DOI system as a common infrastructure for content management An open member consortium NamesforLife, LLC is a general member of the IDF

6. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Comparing identifiers A label that identifies an entity ISBN 0-387-98771-1 ATCC 27126 L-681,572 A single unambiguous string A method of providing consistent syntax to denote a class membership of an entity. A formal standard or industry convention ISBN numbers follow an international industry convention An arbitrary internal system Collection accession numbers and sample tracking numbers are typically institution specific Establishes a 1:1 correspondence between labels and members Enumeration The number or label is simply a string A numbering scheme

7. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Comparing identifiers (cont.) A syntax by which an identifier can be expressed in a form suitable for use within a specific infrastructure. Actionable identifiers URI (URN and URL) ISBN numbers as UPC/EAN identifiers Does not mandate a method of creating labels Does not create a managed environment An infrastructure specification Includes Unique identifiers A formalized infrastructure Management policies for registration, structured interoperable metadata, policy, and governance mechanisms. Examples UPC/EAN barcodes and RFID tags Digital object identifiers (digital identifiers of objects) A fully implemented identifier system

8. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 The Digital Object Identifier System  The DOI - Handle relationship Handle System is one component of the DOI System Global name service Secure name resolution over the Internet and Grid DOI System uses the Handle System as part of a value- added application DOIs provide persistent, semantically interoperable identification of IP resources The DOI system provides a ready to use Numbering syntax Resolution service Data model Policies and procedures for implementation Expanded technical infrastructure and features specific to DOI applications

9. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Persistence The Digital Object Identifier System  The IDF extends the technical infrastructure of the Handle System by provides a social infrastructure guaranteeing persistence Function of organizations, not technology Federation of Registration Agencies IDF policies ensure DOIs “live” even if RAs fail RAs provide the process of DOI transfer IDF is persistent as it is self-funding DOI System is backed by several major public companies, multiple RAs, and a large customer base Persistence is not required No appropriate social structure is provided

10. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Consistency The Digital Object Identifier System  Adds consistent rules for multiple applications IDF set rules for DOI assignment What DOIs can be applied to Restrictions on arbitrary/temporary assignment Restrictions on removal Management by a Directory Manager to enforce QC DOI API defines consistent way of accessing and managing DOI applications and services Consistent use of DOI prefix and numbering syntax provides numbering interoperability in the IP sector, brand recognition, understanding of what a DOI concept Optimal data model provides semantic consistency for true interoperability Ensures interoperability for resolution purposes across Handle System implementations No requirements for interoperability at the application level

11. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Ease of use The Digital Object Identifier System  Turn-key application IDF and RAs maintain technical support staff Interacts with users, standards community and others Resolve problems of RAs and broader user community Underwrites cost of directory manager Support to RAs Guidance, troubleshooting, etc DOI Handbook Policies and procedures for various actors Guidelines for RAs, developers Developed by federation of DOI agencies, guaranteed by detailed legal agreements. No ongoing technical support Handle server must be installed and managed by local technical staff Free, but not without real costs

12. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Expressing relationships The Digital Object Identifier System  Provides framework to achieve practical application of multiple resolution Application of Handle System that adds the necessary constraints Constraints provided by metadata, which defines the entities (data dictionary approach) and expresses the relationships. Provides support for multiple resolution Parent-child relationships Other relationships No preexisting constraints to make useful relationships

13. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Technical infrastructure The Digital Object Identifier System  Adds dedicated and improved technical infrastructure Replication servers for RAs, secondary sites, mirror servers, proxy servers all housed in a secure commercial hosting facility More robust and scalable database DOI Directory Manager to provide technical oversight and evolutionary growth Provides a shared resolution service Global root servers, local Handle servers, clients, proxy servers Scalable and interoperable License provides a reference implementation but the database does not scale above a few million handles

14. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Semantic interoperability The Digital Object Identifier System  Adds semantic interoperability across application space Feature of advanced DOI applications Provides metadata kernel to specify entity identified by DOI Optional tool to map existing schema through a structured ontology Ensures DOI can be the key in building multi component media objects or managing multiple assets Data dictionary and application framework Ensures that DOIs act predictably in applications with defined series IDF maintains indecs data dictionary and will likely maintain MPEG-21 data dictionary No requirements as to what is being identified No assurance of semantic interoperability across resources

15. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Development activities The Digital Object Identifier System  Adds to this resource for active development of DOI applications and advanced features Working groups and technical support staff Use of DOIs in commercial settings RAs have an incentive to allocate their own resources to develop new features, collaborate with other RAs and share with the wider DOI community Provides upgrades of the global general-purpose naming system

16. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Costs to replicate a comparable system The Digital Object Identifier System  Preceding features are part of a turn-key system RAs provide value added services to their clients IDF holds production Handle license with right to sublicense Cost of DOI assignment Vary across RAs and depend on their business model Can be free as part of a service offering Need to add all preceding features not included in the general purpose software Cost of a production Handle license Other licenses to enabling technologies

17. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Governance The Digital Object Identifier System  Independent not-for-profit organization CNRI provides services under commercial agreement Elected board and nominated working groups Open membership NamesforLife, LLC is a general member Independent of IDF Handle System Advisory Committee Major users and interested parties IDF is a member

18. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Summary of identifier properties

19. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Other points to consider Intellectual property Handle System - Two key patents on underlying system to CNRI DOI System One pending patent on data dictionary to Context Consortium Seven pending applications on multiple resolution to Content Directions One pending application on use of GUIDs for resolving ambiguity between names and objects to MSU Board of Trustees Content and data Rights of owners and assignees Other actors Business issues Underwriting of infrastructure and operational costs Capital investment, systems administration, user support Market demands Composition of the user community Leveraging investments Collaborations Incentives in a changing funding environment

20. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 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

21. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Modeling names and taxa…

22. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Sequence+ Name+ Taxon Species+ Authority+ Strain+

23. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Name+ Taxon Literature Governing bodies GenBank DDBJ EMBL others Collections BRC Species+ Authority+ Strain+ Sequence+

24. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Taxon Name+ Species+ Literature Governing bodies GenBank DDBJ EMBL others Collections BRC Source+ Proposal STM Legal Databases Priority Validity Synonymy Exemplar req. direct indirect BRC PublicPrivate General Authority+ Strain+ Feature+ Phenotypic FAME Biolog PA others

25. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 However, rules are made to be broken…

26. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Strain+ Feature+ Name+ Species+ A properly formed species Feature+ Name+ Species+ Candidatus or exemplar lost Feature+ Environmental sequence Strain+ Name+ Species+ Old type strain, not yet sequenced Name+ Species+ Old type, exemplar based on drawing or description Feature+ “Name”+ Misidentified taxon Strain*

27. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Name+ Taxon Strain+ Feature+ Species+ Name+ Strain+ Feature+ Taxon Homotypic synonymyHeterotypic synonymy Differing opinions…

28. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Proof of concept

29. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Alteromonas communis Alteromonas 107 ATCC 27126 DSM 6062 Y18228 Bauman et al. 1972 emend. Yi et al. 2004 Marinomonas communis Alteromonas communis Oceanospirillum commune Marinomonas Van Landschoot and De Ley 1984 Oceanospirillum Bowditch et al. 1984 Oceanospirillum commune Alteromonas communis Marinomonas communis 107 ATCC 27126 DSM 6062 Y18228 107 ATCC 27126 DSM 6062 Y18228 Basonym Synonym Paired 16S sequence, other data Type strain Species+

30. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Shewanella putrifaciens Alteromonas putrifaciens Shewanella Hammer 95 ATCC 8071X82133 DSM 6067 ICPB 352 LMG 2268 NCIB 1047 OK-1 ACAM 541 ATCC 51192AF005249 IAM 14159U91546 ICP1U85903 ACAM 591U85903 DSM 12253 MacDonell and Colwell 1986 Shewanella algae Shewanella alga (corrig.) Shewanella Simidu et al., 1990 emend. Nozue et al. 1992 Shewanella Bowman et al. 1997 Shewanella frigidmarina Species+ OK-1 ACAM 541 ATCC 51192AF005249 IAM 14159U91546 ICP1U85903 ACAM 591U85903 DSM 12253Z

31. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Alteromonas citrea Alteromonas fulginea Alteromonas Gauthier et al. 1977 Pseudoalteromonas (Gauthier 1977) Gauthier et al. 1995 emend. Ivanova et al. 1998 Pseudoalteromonas citrea Alteromonas citrea Species+ Alteromonas Species+ Alteromonas fulginea Alteromonas citrea Romanenko et al. 1995 CIP 105339 AF529062 KMM 216 AF082563 ATCC 29719 DSM 6058 NCIMB 188 X82137 CIP 105339 AF529062 KMM 216 AF082563 ATCC 29719 DSM 6058 NCIMB 188 X82137 CIP 105339 AF529062 KMM 216 AF082563

32. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 The evolution of a taxon…

33. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 macleodii (T) communis Alteromonas 1972 vaga

34. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 communis vaga haloplanktis Alteromonas macleodii (T) 1972 1973

35. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 communis vaga haloplanktis rubra Alteromonas 1972 1973 1976 macleodii (T)

36. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 communis vaga haloplanktis rubra citrea Alteromonas 1972 1973 1976 1977 macleodii (T)

37. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 communis vaga haloplanktis rubra citrea esperjiana undina Alteromonas 1972 1973 1976 1977 1978 macleodii (T)

38. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 communis vaga haloplanktis rubra citrea esperjiana undina aurantia Alteromonas 1972 1973 1976 1977 1978 1979 macleodii (T)

39. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai Alteromonas 1972 1973 1976 1977 1978 1979 1981 macleodii (T)

40. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae Alteromonas 1972 1973 1976 1977 1978 1979 1981 1982 macleodii (T)

41. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 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?

42. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 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)

43. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 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)

44. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 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)

45. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 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)

46. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 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

47. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 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?

48. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 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)

49. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 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 fulginea atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra Pseudoalteromonas undina antartica elyakoviii haloplanktis tetradonis haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T)

50. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 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 fulginea atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra Pseudoalteromonas undina antartica elyakoviii 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)

51. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 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 fulginea atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra Pseudoalteromonas undina antartica elyakoviii fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetrodonis japonica haloplanktis tetradonis mediterannea haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T)

52. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 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 elyakoviii 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 tetrodonis haloplanktis tetradonis mediterannea haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T)

53. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 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 fulginea Pseudoalteromonas elyakoviii 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 tetrodonis 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

54. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Alteromonas Alteromonadacea Alteromonadales Gammaproteobacteria Alishewanella Aestuariibacter Ferrimonas Colwellia Idiomarina Glaciecola Marinobacterium Marinobacter Pseudoalteromonas Microbulbifer Incertae sedis Psychromonas Teredinibacter Shewanella Thalassomonas Ferrimonadacea Idiomarinacea Moritella Moritellaceae Pseudoalteromonadaceae Ferrimonas Idiomarina Pseudoalteromonas Psychromonadacea 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?

55. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 The genus Alteromonas has undergone 18 “emendations” 19 species were added to the genus 19 species were reassigned to four genera 3 of which are formed on new combinations of Alteromonas spp. 6 synonyms 2 species reduced to subspecies, then re-elevated to species 48 names, five genera, five families, and two classes but…. only three validly published named species of Alteromonas remain. Since first being defined This is not a very complicated example

56. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 What is NamesforLife?

57. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Two components A transparent information layer to provide DOI services to the life science community An ontology with a schema that produces metadata consistent with requirements of the International DOI Foundation N4L architecture The test case A proof-of-principle application 24,176 first-class objects Name, Taxon, Exemplar, Nomos, Practitioner, Feature, and Nomenclatural Code Track changes in concepts over time Based on a nomenclatural taxonomy, but capable of supporting multiple taxonomic views and “ time travel ” Initial DOI services will conform to AP 0 Released January 2006 Root taxon DOI: 10.1601/tx.010.1601/tx.0

58. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Two components (continued) Member of the International DOI Foundation Self-supporting model Four target groups End-users - access to N4L objects as a DOI service at no- charge Publishers - hosting N4L enabled content in which each name becomes actionable. Literature could be traversed based on named entities (organisms, genes, etc). Database providers, instrument vendors, BRCs rely on curated information for their own businesses Registrants who wish to provide data or services that are not readily available to the broader community Service for registration of “not-yet-cultivated” taxa and environmental clones N4L “ business ” We are soliciting input from the community as well as potential collaborators and “clients”

59. GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Acknowledgements MSU Jim Cole Donna McGarrell AKS Mohideen Qiong Wang Scott Harrison VPGR and OIP Paul M. Hunt Lorraine Hudson Bergey’s Editorial Office Connie Williams Judy Leventhal Julia Bell Denise Searles ATCC Tim Lilburn DSMZ Brian Tindall University of Toulouse Jean Euzaby IDF Norman Paskin Funding US Department of Energy Office of Science National Science Foundation Michigan University Commercialization Initiative