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

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



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



“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



“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



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



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



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




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



Persistence


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



Consistency


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



Ease of use


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



Expressing relationships


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



Technical infrastructure


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



Semantic interoperability


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



Development activities


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



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 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



Governance


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



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 + + + + + + + + + + +



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



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



Modeling names and taxa…



Sequence+

Name+

Tax

on

Species+

Authority+

Strain+



Name+

Tax

on

Literature Governing bodies

GenBankDDBJEMBLothers

CollectionsBRC

Species+

Authority+

Strain+ Sequence+



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



However, rules are made to be broken…



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*



Name+

Tax

on

Strain+ Feature+

Species+

Name+ Name+

Strain+Strain+

Feature+Feature+T

axon

Taxon

Homotypic synonymy Heterotypic synonymy

Differing opinions…



Proof of concept



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+



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



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



The evolution of a taxon…



macleodii(T)

communis

Alteromonas

1972

vaga



communisvaga

haloplanktis

Alteromonasmacleodii(T)

1972 1973



communisvaga

haloplanktisrubra

Alteromonas

1972 1973 1976

macleodii(T)



communisvaga

haloplanktisrubracitrea

Alteromonas

1972 1973 1976 1977

macleodii(T)



communisvaga

haloplanktisrubracitreaesperjianaundina

Alteromonas

1972 1973 1976 1977 1978

macleodii(T)



communisvaga

haloplanktisrubracitreaesperjianaundinaaurantia

Alteromonas

1972 1973 1976 1977 1978 1979

macleodii(T)



communisvaga

haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedai

Alteromonas

1972 1973 1976 1977 1978 1979 1981

macleodii(T)



communisvaga

haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceae

Alteromonas

1972 1973 1976 1977 1978 1979 1981 1982

macleodii(T)



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?



communisvaga

haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedai

vaga benthicahanedai

Marinomonas Alteromonasputrifaciens(T)

Shewanella

japonicumminutium


hiroshimensemultiglobiferumpelagicumpusillumcommune

jannaschiikreigiivagum

Oceanosprillum

mariswilliamsae

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986

luteoviolaceae

communis(T)linum(T) macleodii(T)



1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987

communisvaga

haloplanktisrubracitreaesperjianaundinaaurantia

hanedailuteoviolaceaedenitrificans


Marinomonas Alteromonas Shewanella

japonicumminutium




Oceanosprillum

mariswilliamsae

putrifaciens

putrifaciens(T)communis(T)linum(T) macleodii(T)



communisvaga

haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceaedenitrificans


Marinomonas Alteromonas Shewanella

japonicumminutium




Oceanosprillum

mariswilliamsae

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988

colwelliana





Marinomonas Shewanella

japonicumminutium



jannaschiikreigiivagumbiejerinckii

pelagicummarishiroshimense

Oceanosprillum

mariswilliamsae

communisvaga


tetradonis

Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990

colwelliana




vaga benthicahanedaicolwellianaalgae


communisvaga


tetradonisatlanticacarageenovora

Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992

japonicumminutium





Oceanosprillum

mariswilliamsae


Nomenclatural issueNon-type strains





communisvaga

haloplanktis

putrifacienshanedai

denitrificans

rubracitreaesperjianaundinaaurantia

luteoviolaceae


Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995

japonicumminutium





Oceanosprillum

mariswilliamsae

distinctafuliginea


Nomenclatural issuesHeterotypic synonymy

Data issueMany to many relationship

Taxonomic issueWhich one is right?





communisvaga

haloplanktis

putrifacienshanedai

denitrificans

rubracitreaesperjianaundinaaurantia

luteoviolaceae


Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995

japonicumminutium





Oceanosprillum

mariswilliamsae

distinctafuliginea

atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubra

haloplanktishaloplanktis(T)

Pseudoalteromonas

undina

haloplanktistetradonis






communisvaga



Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997

japonicumminutium





Oceanosprillum

mariswilliamsae

distinctafulginea


Pseudoalteromonas

undinaantartica

elyakoviii








communisvaga



Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000

japonicumminutium





Oceanosprillum

mariswilliamsae

distinctafulginea


Pseudoalteromonas

undinaantartica

elyakoviii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolacea

bacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolytica


mediterannea







communisvaga



Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001

japonicumminutium





Oceanosprillum

mariswilliamsae

distinctafulginea


Pseudoalteromonas

undinaantartica

elyakoviii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolacea

bacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolyticatetrodonis

japonica


mediterannea







communisvaga



Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002

japonicumminutium





Oceanosprillum

mariswilliamsae

distinctafuliginea

Pseudoalteromonas

elyakoviii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolaceajaponicadenitrificanslivingstonensisalleyanna

atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubraundinaantarticabacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolyticatetrodonis


mediterannea







communisvaga



Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004

japonicumminutium





Oceanosprillum

mariswilliamsae

distinctafulginea

Pseudoalteromonas

elyakoviii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolaceajaponicadenitrificanslivingstonensisalleyanna

atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubraundinaantarticabacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolyticatetrodonis


12 others

mariniintestinasaireschlegelianagaetbuli

mediteranneaprimoryensis



stellipolarislitorea 5 others



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?



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



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 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



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”



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

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

Documents

Transcript of GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Digital Object...