tai lieu1
TRANSCRIPT
GUID-1 WorkshopNational 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. GarrityMicrobiology and Molecular Genetics
Michigan State University
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
During the next 25 minutes
An overview Digital Object IdentifiersWhat is an identifier?Comparison of DOI features to a native Handle implementationAddress Ricardo’s general questions
ExtensibilityHandling of metadataStrengthsWeaknessesOther relevant issues
Introduce the NamesforLife prototypeDevelopment of the modelA complete prokaryotic taxonomy implemented with DOIs
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
“Dual” interestsTrustee and Editor-in-Chief
Founded in 1936501 c3 Non-profit educational trustHeadquartered at Michigan State University
Produce reference works in prokaryotic biologyBergey’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
GUID-1 WorkshopNational 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 NSFhttp://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 InitiativeUS and WIPO patents pendingProperty of the Board of Trustees of Michigan State
University
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
I represent the following parties
An IUMS COMCOF
Body that oversees the nomenclature of prokaryotesPublication 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 ObjectIdentifier System
International Committee on Systematics of Prokaryotes
The International DOI FoundationEstablished in 1998Develop and manage the DOI SystemSupport 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 consortiumNamesforLife, LLC is a general member of the IDF
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Comparing identifiersA label that identifies an entity
ISBN 0-387-98771-1
ATCC 27126L-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 conventionAn arbitrary internal system
Collection accession numbers and sample tracking numbers are typically institution specific Establishes a 1:1 correspondence between labels and membersEnumeration
The number or label is simply a string
A numbering scheme
GUID-1 WorkshopNational 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 labelsDoes not create a managed environment
An infrastructure specification
Includes Unique identifiersA formalized infrastructureManagement policies for registration, structured
interoperable metadata, policy, and governance mechanisms.
ExamplesUPC/EAN barcodes and RFID tagsDigital object identifiers (digital identifiers of
objects)
A fully implementedidentifier system
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
The Digital ObjectIdentifier System
The DOI - Handle relationship
Handle System is one component of the DOI SystemGlobal name serviceSecure name resolution over the Internet and Grid
DOI System uses the Handle System as part of a value-added applicationDOIs provide persistent, semantically interoperable identification of IP resourcesThe DOI system provides a ready to use
Numbering syntaxResolution serviceData modelPolicies and procedures for implementationExpanded technical infrastructure and features specific to DOI applications
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Persistence
The Digital ObjectIdentifier System
The IDF extends the technical infrastructure of the Handle System by provides a social infrastructure guaranteeing persistenceFunction of organizations, not technologyFederation of Registration Agencies
IDF policies ensure DOIs “live” even if RAs failRAs provide the process of DOI transfer
IDF is persistent as it is self-fundingDOI System is backed by several major public companies, multiple RAs, and a large customer base
Persistence is not requiredNo appropriate social structure is
provided
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Consistency
The Digital ObjectIdentifier System
Adds consistent rules for multiple applicationsIDF set rules for DOI assignment
What DOIs can be applied toRestrictions on arbitrary/temporary assignmentRestrictions on removal
Management by a Directory Manager to enforce QCDOI API defines consistent way of accessing and managing DOI applications and servicesConsistent use of DOI prefix and numbering syntax provides numbering interoperability in the IP sector, brand recognition,
understanding of what a DOI conceptOptimal 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
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Ease of use
The Digital ObjectIdentifier System
Turn-key applicationIDF 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 supportHandle server must be installed and managed by
local technical staffFree, but not without real costs
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Expressing relationships
The Digital ObjectIdentifier System
Provides framework to achieve practical application of multiple resolutionApplication of Handle System that adds the necessary constraintsConstraints provided by metadata, which defines the entities
(data dictionary approach) and expresses the relationships.
Provides support for multiple resolutionParent-child relationshipsOther relationships
No preexisting constraints to make useful relationships
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Technical infrastructure
The Digital ObjectIdentifier System
Adds dedicated and improved technical infrastructureReplication servers for RAs, secondary sites, mirror servers, proxy servers all housed in a secure commercial hosting facility
More robust and scalable databaseDOI Directory Manager to provide technical oversight and evolutionary
growth
Provides a shared resolution service Global root servers, local Handle servers, clients, proxy serversScalable and interoperableLicense provides a reference implementation but the database does
not scale above a few million handles
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Semantic interoperability
The Digital ObjectIdentifier System
Adds semantic interoperability across application space
Feature of advanced DOI applicationsProvides 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 frameworkEnsures 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
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Development activities
The Digital ObjectIdentifier System
Adds to this resource for active development of DOI applications and advanced features
Working groups and technical support staffUse 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
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Costs to replicate a comparable system
The Digital ObjectIdentifier 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 assignmentVary 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 licenseOther licenses to enabling technologies
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Governance
The Digital ObjectIdentifier System
Independent not-for-profit organizationCNRI provides services under commercial agreement Elected board and nominated working groupsOpen membership
NamesforLife, LLC is a general member
Independent of IDFHandle System Advisory Committee
Major users and interested partiesIDF is a member
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Summary of identifier properties
OpaqueGovernancePersistentRegistrationMetadataAccepted standardGlobalWidespread useObjectActionableUniqueInteroperableAccession numbers - - V - V - - + + - -XRI - - - ? - - + - - + +LSID - - ? - V ? V ? - + +Gene names V - - - - + - + + - -PURL/POI - - - - + ? - - + + +Taxid + - - - + - - ? + V +DNS - + - + - + + + - + +Taxonomic names - + + v - + + + + - -OpenURL - + + + + + - + - + +Handle + - + + + - + ? + + +DOI + + + + + + + + + + +
GUID-1 WorkshopNational 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 SystemOne 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 dataRights of owners and assignees
Other actors
Business issues Underwriting of infrastructure and operational costs
Capital investment, systems administration, user support
Market demandsComposition of the user community
Leveraging investmentsCollaborations
Incentives in a changing funding environment
GUID-1 WorkshopNational 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 usefulWould link to…
Relevant literatureSequencesOther phenotypic dataSources of strains in Biological Resource CentersAncillary materials
PatentsLaws and regulations
Regardless of where the data residesWithout having to know anything about
SynonymiesOrthographic variantsMisapplications of the name
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Modeling names and taxa…
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Sequence+
Name+
Tax
on
Species+
Authority+
Strain+
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Name+
Tax
on
Literature Governing bodies
GenBankDDBJEMBLothers
CollectionsBRC
Species+
Authority+
Strain+ Sequence+
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Tax
on
Name+
Species+
Literature Governing bodies
GenBankDDBJEMBLothers
CollectionsBRC
Source+
Source+ProposalSTM
Legal
Databases
PriorityValidity
SynonymyExemplar req.
direct
indirect
BRC
Public Private
General
Authority+
Strain+ Feature+
PhenotypicFAME
Biolog PAothers
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
However, rules are made to be broken…
GUID-1 WorkshopNational 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 ondrawing or description
Feature+
“Name”+
Misidentified taxon
Strain*
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Name+
Tax
on
Strain+ Feature+
Species+
Name+ Name+
Strain+Strain+
Feature+Feature+T
axon
Taxon
Homotypic synonymy Heterotypic synonymy
Differing opinions…
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Proof of concept
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Alteromonas communis
Alte
rom
ona
s
107ATCC 27126DSM 6062
Y18228
Bauman et al. 1972emend. Yi et al. 2004
Marinomonas communisAlteromonas communis
Oceanospirillum commune
Mar
inom
onas
Van Landschoot and De Ley 1984
Oce
anos
piri
llum
Bowditch et al. 1984
Oceanospirillum communeAlteromonas communisMarinomonas communis
107ATCC 27126DSM 6062
Y18228
107ATCC 27126DSM 6062
Y18228
Basonym
Synonym
Paired 16Ssequence,other dataType strain
Species+
Species+
Species+
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Shewanella putrifaciensAlteromonas putrifaciens
Sh
ew
an
ella
Hammer 95ATCC 8071 X82133DSM 6067ICPB 352LMG 2268NCIB 1047OK-1ACAM 541ATCC 51192 AF005249IAM 14159 U91546ICP1 U85903ACAM 591 U85903DSM 12253
MacDonell and Colwell 1986 Shewanella algaeShewanella alga (corrig.)
Sh
ew
an
ella
Simidu et al., 1990emend. Nozue et al. 1992
Sh
ew
an
ella
Bowman et al. 1997
Shewanella frigidmarina
Species+
Species+
Species+OK-1ACAM 541ATCC 51192 AF005249IAM 14159 U91546
ICP1 U85903ACAM 591 U85903DSM 12253Z
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Alteromonas citreaAlteromonas fulginea
Alte
rom
ona
sGauthier et al. 1977
Pse
udo
alte
rom
onas
(Gauthier 1977) Gauthier et al. 1995 emend. Ivanova et al. 1998
Pseudoalteromonas citreaAlteromonas citrea
Species+
Species+
Alte
rom
ona
s
Species+
Alteromonas fulgineaAlteromonas citrea
Romanenko et al. 1995
CIP 105339 AF529062KMM 216 AF082563
ATCC 29719DSM 6058NCIMB 188 X82137CIP 105339 AF529062KMM 216 AF082563
ATCC 29719DSM 6058NCIMB 188 X82137CIP 105339 AF529062KMM 216 AF082563
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
The evolution of a taxon…
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
macleodii(T)
communis
Alteromonas
1972
vaga
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
communisvaga
haloplanktis
Alteromonasmacleodii(T)
1972 1973
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
communisvaga
haloplanktisrubra
Alteromonas
1972 1973 1976
macleodii(T)
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
communisvaga
haloplanktisrubracitrea
Alteromonas
1972 1973 1976 1977
macleodii(T)
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
communisvaga
haloplanktisrubracitreaesperjianaundina
Alteromonas
1972 1973 1976 1977 1978
macleodii(T)
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
communisvaga
haloplanktisrubracitreaesperjianaundinaaurantia
Alteromonas
1972 1973 1976 1977 1978 1979
macleodii(T)
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
communisvaga
haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedai
Alteromonas
1972 1973 1976 1977 1978 1979 1981
macleodii(T)
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
communisvaga
haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceae
Alteromonas
1972 1973 1976 1977 1978 1979 1981 1982
macleodii(T)
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
communisvaga
haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceae
vagacommunis(T)
Marinomonas Alteromonas
commune
vagum
1972 1973 1976 1977 1978 1979 1981 1982 1984
multiglobiferum
japonicumminutium
biejerinckiimarismaris
hiroshimense
pelagicumpusillum
jannaschiikreigii
Oceanosprillum
mariswilliamsae
linum(T) macleodii(T)
Nomenclatural issuesHomotypic synonymyPriorityRule 37(a) 1
Data issuesOne to many relationship
Taxonomic issueWhich one is right?
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
communisvaga
haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedai
vaga benthicahanedai
Marinomonas Alteromonasputrifaciens(T)
Shewanella
japonicumminutium
biejerinckiimarismaris
hiroshimensemultiglobiferumpelagicumpusillumcommune
jannaschiikreigiivagum
Oceanosprillum
mariswilliamsae
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986
luteoviolaceae
communis(T)linum(T) macleodii(T)
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987
communisvaga
haloplanktisrubracitreaesperjianaundinaaurantia
hanedailuteoviolaceaedenitrificans
vaga benthicahanedai
Marinomonas Alteromonas Shewanella
japonicumminutium
biejerinckiimarismaris
hiroshimensemultiglobiferumpelagicumpusillumcommune
jannaschiikreigiivagum
Oceanosprillum
mariswilliamsae
putrifaciens
putrifaciens(T)communis(T)linum(T) macleodii(T)
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
communisvaga
haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceaedenitrificans
vaga benthicahanedai
Marinomonas Alteromonas Shewanella
japonicumminutium
biejerinckiimarismaris
hiroshimensemultiglobiferumpelagicumpusillumcommune
jannaschiikreigiivagum
Oceanosprillum
mariswilliamsae
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988
colwelliana
putrifaciens(T)communis(T)linum(T) macleodii(T)
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
vaga benthicahanedai
Marinomonas Shewanella
japonicumminutium
biejerinckiimarismaris
hiroshimensemultiglobiferumpelagicumpusillumcommune
jannaschiikreigiivagumbiejerinckii
pelagicummarishiroshimense
Oceanosprillum
mariswilliamsae
communisvaga
haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceaedenitrificans
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)
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
vaga benthicahanedaicolwellianaalgae
Marinomonas Shewanella
communisvaga
haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceaedenitrificans
tetradonisatlanticacarageenovora
Alteromonas
colwelliana
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992
japonicumminutium
biejerinckiimarismaris
hiroshimensemultiglobiferumpelagicumpusillumcommune
jannaschiikreigiivagumbiejerinckii
pelagicummarishiroshimense
Oceanosprillum
mariswilliamsae
putrifaciens(T)communis(T)linum(T) macleodii(T)
Nomenclatural issueNon-type strains
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
vaga benthicahanedaicolwellianaalgae
Marinomonas Shewanella
communisvaga
haloplanktis
putrifacienshanedai
denitrificans
rubracitreaesperjianaundinaaurantia
luteoviolaceae
tetradonisatlanticacarageenovora
Alteromonas
colwelliana
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995
japonicumminutium
biejerinckiimarismaris
hiroshimensemultiglobiferumpelagicumpusillumcommune
jannaschiikreigiivagumbiejerinckii
pelagicummarishiroshimense
Oceanosprillum
mariswilliamsae
distinctafuliginea
putrifaciens(T)communis(T)linum(T) macleodii(T)
Nomenclatural issuesHeterotypic synonymy
Data issueMany to many relationship
Taxonomic issueWhich one is right?
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
vaga benthicahanedaicolwellianaalgae
Marinomonas Shewanella
communisvaga
haloplanktis
putrifacienshanedai
denitrificans
rubracitreaesperjianaundinaaurantia
luteoviolaceae
tetradonisatlanticacarageenovora
Alteromonas
colwelliana
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995
japonicumminutium
biejerinckiimarismaris
hiroshimensemultiglobiferumpelagicumpusillumcommune
jannaschiikreigiivagumbiejerinckii
pelagicummarishiroshimense
Oceanosprillum
mariswilliamsae
distinctafuliginea
atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubra
haloplanktishaloplanktis(T)
Pseudoalteromonas
undina
haloplanktistetradonis
putrifaciens(T)communis(T)linum(T) macleodii(T)
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
vaga benthicahanedaicolwellianaalgae
Marinomonas Shewanella
communisvaga
haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceaedenitrificans
tetradonisatlanticacarageenovora
Alteromonas
colwelliana
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997
japonicumminutium
biejerinckiimarismaris
hiroshimensemultiglobiferumpelagicumpusillumcommune
jannaschiikreigiivagumbiejerinckii
pelagicummarishiroshimense
Oceanosprillum
mariswilliamsae
distinctafulginea
atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubra
Pseudoalteromonas
undinaantartica
elyakoviii
haloplanktistetradonis
haloplanktishaloplanktis(T)
putrifaciens(T)communis(T)linum(T) macleodii(T)
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
vaga benthicahanedaicolwellianaalgae
Marinomonas Shewanella
communisvaga
haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceaedenitrificans
tetradonisatlanticacarageenovora
Alteromonas
colwelliana
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000
japonicumminutium
biejerinckiimarismaris
hiroshimensemultiglobiferumpelagicumpusillumcommune
jannaschiikreigiivagumbiejerinckii
pelagicummarishiroshimense
Oceanosprillum
mariswilliamsae
distinctafulginea
atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubra
Pseudoalteromonas
undinaantartica
elyakoviii
fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolacea
bacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolytica
haloplanktistetradonis
mediterannea
haloplanktishaloplanktis(T)
putrifaciens(T)communis(T)linum(T) macleodii(T)
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
vaga benthicahanedaicolwellianaalgae
Marinomonas Shewanella
communisvaga
haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceaedenitrificans
tetradonisatlanticacarageenovora
Alteromonas
colwelliana
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001
japonicumminutium
biejerinckiimarismaris
hiroshimensemultiglobiferumpelagicumpusillumcommune
jannaschiikreigiivagumbiejerinckii
pelagicummarishiroshimense
Oceanosprillum
mariswilliamsae
distinctafulginea
atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubra
Pseudoalteromonas
undinaantartica
elyakoviii
fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolacea
bacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolyticatetrodonis
japonica
haloplanktistetradonis
mediterannea
haloplanktishaloplanktis(T)
putrifaciens(T)communis(T)linum(T) macleodii(T)
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
vaga benthicahanedaicolwellianaalgae
Marinomonas Shewanella
communisvaga
haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceaedenitrificans
tetradonisatlanticacarageenovora
Alteromonas
colwelliana
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002
japonicumminutium
biejerinckiimarismaris
hiroshimensemultiglobiferumpelagicumpusillumcommune
jannaschiikreigiivagumbiejerinckii
pelagicummarishiroshimense
Oceanosprillum
mariswilliamsae
distinctafuliginea
Pseudoalteromonas
elyakoviii
fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolaceajaponicadenitrificanslivingstonensisalleyanna
atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubraundinaantarticabacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolyticatetrodonis
haloplanktistetradonis
mediterannea
haloplanktishaloplanktis(T)
putrifaciens(T)communis(T)linum(T) macleodii(T)
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
vaga benthicahanedaicolwellianaalgae
Marinomonas Shewanella
communisvaga
haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceaedenitrificans
tetradonisatlanticacarageenovora
Alteromonas
colwelliana
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004
japonicumminutium
biejerinckiimarismaris
hiroshimensemultiglobiferumpelagicumpusillumcommune
jannaschiikreigiivagumbiejerinckii
pelagicummarishiroshimense
Oceanosprillum
mariswilliamsae
distinctafulginea
Pseudoalteromonas
elyakoviii
fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolaceajaponicadenitrificanslivingstonensisalleyanna
atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubraundinaantarticabacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolyticatetrodonis
haloplanktistetradonis
12 others
mariniintestinasaireschlegelianagaetbuli
mediteranneaprimoryensis
haloplanktishaloplanktis(T)
putrifaciens(T)communis(T)linum(T) macleodii(T)
stellipolarislitorea 5 others
GUID-1 WorkshopNational 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
ShewanellaThalassomonas
Ferrimonadacea
Idiomarinacea
Moritella
Moritellaceae
Pseudoalteromonadaceae
Ferrimonas
Idiomarina
Pseudoalteromonas
Psychromonadacea
Algicola
Psychromonas
Moritella
ShewanellaceaeShewanella
Incertae sedis
Teredinibacter
Agarvorans
Alishewanella
Marinobacterium
Marinobacter
MicrobulbiferSalinomonas
Colwelliaceae ColwelliaceaeThalassomonas
May 2004 November 2004
1 Family 16 genera -> 8 families 12 genera1 unclassified -> 7 unclassfied
Which is correct?Which is supported by the data?
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
The genus Alteromonas has undergone 18 “emendations” 19 species were added to the genus19 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
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
What is NamesforLife?
GUID-1 WorkshopNational 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 timeBased on a nomenclatural taxonomy, but capable of
supporting multiple taxonomic views and “time travel”Initial DOI services will conform to AP 0Released January 2006
Root taxon DOI: 10.1601/tx.0
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Two components (continued)
Member of the International DOI FoundationSelf-supporting model
Four target groupsEnd-users - access to N4L objects as a DOI
service at no-chargePublishers - 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 communityas well as potential collaborators and “clients”
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
AcknowledgementsMSUJim ColeDonna McGarrellAKS MohideenQiong WangScott Harrison
VPGR and OIPPaul M. HuntLorraine Hudson
Bergey’s Editorial OfficeConnie WilliamsJudy LeventhalJulia BellDenise Searles
ATCCTim Lilburn
DSMZBrian Tindall
University of ToulouseJean Euzaby
IDFNorman Paskin
FundingUS Department of Energy Office of ScienceNational Science FoundationMichigan University Commercialization Initiative