tai lieu1

67 %
33 %
Information about tai lieu1

Published on November 20, 2007

Author: lebahiep

Source: slideshare.net

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

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

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

“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

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

“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

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

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

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 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 The Digital Object Identifier System 

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 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

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

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

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

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

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)

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 The Digital Object Identifier System 

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

Persistence 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 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

Consistency 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 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

Ease of use 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 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.

Expressing relationships 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 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

Technical infrastructure 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 The Digital Object Identifier System 

Semantic interoperability 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 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

Development activities 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 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

Costs to replicate a comparable 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 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

Governance 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 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

Summary of identifier properties

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

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

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

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

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

Modeling names and taxa…

Sequence+ Name+ Taxon Species+ Authority+ Strain+

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

Name+ Species+ Literature Governing bodies GenBank DDBJ EMBL others Collections BRC Source+ Source+ Proposal STM Legal Databases Priority Validity Synonymy Exemplar req. direct indirect BRC Public Private General Authority+ Strain+ Feature+ Phenotypic FAME Biolog PA others Taxon

However, rules are made to be broken…

Name+ Species+ Old type, exemplar based on drawing or description 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 Feature+ “ Name”+ Misidentified taxon Strain*

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

Proof of concept

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+ Species+ Species+

Shewanella putrifaciens Alteromonas putrifaciens Shewanella Hammer 95 ATCC 8071 X82133 DSM 6067 ICPB 352 LMG 2268 NCIB 1047 OK-1 ACAM 541 ATCC 51192 AF005249 IAM 14159 U91546 ICP1 U85903 ACAM 591 U85903 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 OK-1 ACAM 541 ATCC 51192 AF005249 IAM 14159 U91546 ICP1 U85903 ACAM 591 U85903 DSM 12253 Z Species+ Species+ Species+

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 Alteromonas 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 Species+ Species+ Species+

The evolution of a taxon…

macleodii (T) communis Alteromonas 1972 vaga

communis vaga haloplanktis Alteromonas macleodii (T) 1972 1973

communis vaga haloplanktis rubra Alteromonas 1972 1973 1976 macleodii (T)

communis vaga haloplanktis rubra citrea Alteromonas 1972 1973 1976 1977 macleodii (T)

communis vaga haloplanktis rubra citrea esperjiana undina Alteromonas 1972 1973 1976 1977 1978 macleodii (T)

communis vaga haloplanktis rubra citrea esperjiana undina aurantia Alteromonas 1972 1973 1976 1977 1978 1979 macleodii (T)

communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai Alteromonas 1972 1973 1976 1977 1978 1979 1981 macleodii (T)

communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae Alteromonas 1972 1973 1976 1977 1978 1979 1981 1982 macleodii (T)

communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae vaga Alteromonas commune vagum 1972 1973 1976 1977 1978 1979 1981 1982 1984 macleodii (T) Nomenclatural issues Homotypic synonymy Priority Rule 37(a) 1 Data issues One to many relationship Taxonomic issue Which one is right? communis (T) Marinomonas multiglobiferum japonicum minutium biejerinckii maris maris hiroshimense pelagicum pusillum jannaschii kreigii Oceanosprillum maris williamsae linum (T)

Nomenclatural issues

Homotypic synonymy

Priority

Rule 37(a) 1

Data issues

One to many relationship

Taxonomic issue

Which one is right?

communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai vaga benthica hanedai Marinomonas Alteromonas japonicum minutium biejerinckii maris 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) putrifaciens (T) Shewanella

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 communis vaga haloplanktis rubra citrea esperjiana undina aurantia hanedai luteoviolaceae denitrificans vaga benthica hanedai Marinomonas Alteromonas Shewanella japonicum minutium biejerinckii maris maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum Oceanosprillum maris williamsae putrifaciens putrifaciens (T) communis (T) linum (T) macleodii (T)

communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans vaga benthica hanedai Marinomonas Alteromonas Shewanella japonicum minutium biejerinckii maris 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)

vaga benthica hanedai Marinomonas Shewanella japonicum minutium biejerinckii maris 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)

vaga benthica hanedai colwelliana algae Marinomonas Shewanella 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 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

Nomenclatural issue

Non-type strains

vaga benthica hanedai colwelliana algae Marinomonas Shewanella 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 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?

Nomenclatural issues

Heterotypic synonymy

Data issue

Many to many relationship

Taxonomic issue

Which one is right?

vaga benthica hanedai colwelliana algae Marinomonas Shewanella 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 maris hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Oceanosprillum maris williamsae distincta fuliginea atlantica aurantia carrageenovora citrea esperjiana luteoviolacea rubra undina haloplanktis tetradonis putrifaciens (T) communis (T) linum (T) macleodii (T) nigrifaciens pisicida haloplanktis haloplanktis (T) Pseudoalteromonas

vaga benthica hanedai colwelliana algae Marinomonas Shewanella 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 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)

vaga benthica hanedai colwelliana algae Marinomonas Shewanella 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 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 baltica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica haloplanktis tetradonis mediterannea haloplanktis haloplanktis (T) putrifaciens (T) communis (T) linum (T) macleodii (T) woodyii amazonensis oneidensis pealeana violacea

vaga benthica hanedai colwelliana algae Marinomonas Shewanella 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 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)

vaga benthica hanedai colwelliana algae Marinomonas Shewanella 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 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)

vaga benthica hanedai colwelliana algae Marinomonas Shewanella 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 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

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 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?

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

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.

What is NamesforLife?

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.0

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

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.0

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”

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

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

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

Add a comment

Related presentations