fems2006 madrid, spain symposium 20. biodiversity july 8, 2006 knowledge bleed, phenbank, and...

FEMS2006 Madrid, SpainSymposium 20. Biodiversity

July 8, 2006

Knowledge bleed,Phenbank, and NamesforLife

George M. Garrity, Catherine Lyons & James R. Cole

Michigan State University andNamesforLife, LLC

Funding for this research has been provide by the US Department of Energy, Grants No. DE-FG02-04ER63933 and DE-FG02-99ER62848, the

National Science Foundation Award No. DBI-0328255 and the Michigan University Commercialization Initiative (MUCI) program. Portions of this work are covered under US and foreign patents (pending) and are the intellectual property of the Michigan State University Board of

Trustees. For further information contact [email protected]


July 8, 2006

“…because as we know, there are known knowns; there are things we know we know. We also know there are known unknowns; that is to say we know there are some things we do not know. But there are also unknown unknowns -- the ones we don't know we don't know.”

Rumsfeld’s axiom and knowledge bleed


July 8, 2006

The knowledge gradient

Unkno

wnun

know

ns

Know

n kn

owns

Basic and applied research advances

knowledge

Knowledge bleed results is a loss of

knowledge that has already been gained

Semantic resolution provides a mechanism to combat knowledge

bleed

Unkno

wnkn

owns

Know

n un

know

ns


July 8, 2006

We do quagmires


July 8, 2006

macleodii(T)

communis

Alteromonas

1972

vaga


July 8, 2006

communisvaga

haloplanktis

Alteromonasmacleodii(T)

1972 1973


July 8, 2006

communisvaga

haloplanktisrubra

Alteromonas

1972 1973 1976

macleodii(T)


July 8, 2006

communisvaga

haloplanktisrubracitrea

Alteromonas

1972 1973 1976 1977

macleodii(T)


July 8, 2006

communisvaga

haloplanktisrubracitreaesperjianaundina

Alteromonas

1972 1973 1976 1977 1978

macleodii(T)


July 8, 2006

communisvaga

haloplanktisrubracitreaesperjianaundinaaurantia

Alteromonas

1972 1973 1976 1977 1978 1979

macleodii(T)


July 8, 2006

communisvaga

haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedai

Alteromonas

1972 1973 1976 1977 1978 1979 1981

macleodii(T)


July 8, 2006

communisvaga

haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceae

Alteromonas

1972 1973 1976 1977 1978 1979 1981 1982

macleodii(T)


July 8, 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?


July 8, 2006

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)


July 8, 2006

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)


July 8, 2006

communisvaga

haloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceaedenitrificans


Marinomonas Alteromonas Shewanella

japonicumminutium




Oceanosprillum

mariswilliamsae

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

colwelliana



July 8, 2006


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



July 8, 2006

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


July 8, 2006



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?


July 8, 2006



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



July 8, 2006



communisvaga



Alteromonas

colwelliana

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

japonicumminutium





Oceanosprillum

mariswilliamsae

distinctafuliginea


Pseudoalteromonas

undinaantartica

elyakoviii





July 8, 2006



communisvaga



Alteromonas

colwelliana

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

japonicumminutium





Oceanosprillum

mariswilliamsae

distinctafuliginea


Pseudoalteromonas

undinaantartica

elyakoviii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolacea

bacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolytica


mediterannea




July 8, 2006



communisvaga



Alteromonas

colwelliana

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

japonicumminutium





Oceanosprillum

mariswilliamsae

distinctafuliginea


Pseudoalteromonas

undinaantartica

elyakoviii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolacea

bacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolyticatetrodonis

japonica


mediterannea




July 8, 2006



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




July 8, 2006



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

distinctafuliginea

Pseudoalteromonas

elyakoviii




12 others

mariniintestinasaireschlegelianagaetbuli

mediteranneaprimoryensis



stellipolarislitorea 5 others


July 8, 2006



communisvaga



Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 2005

japonicumminutium





Oceanosprillum

mariswilliamsae

distinctafuliginea

Pseudoalteromonas

elyakoviii




14 others





stellipolarislitorea 8 others2 others


July 8, 2006



communisvaga



Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 2005 2006

japonicumminutium





Oceanosprillum

mariswilliamsae

distinctafuliginea

Pseudoalteromonas

elyakoviii




14 others





stellipolarislitorea 13 others2 others


July 8, 2006

The genus Alteromonas has undergone 18 “emendations” 21 species were added to the genus19 species were reassigned to four genera

3 of which are formed as new combinations of Alteromonas spp.

6 synonyms 2 species reduced to subspecies, then re-elevated to species

50 names, five genera, five families, and two classes but….only five validly published named species of Alteromonas

remain.

Since first being defined

This is not a very complicated example

But wait, there is still more


July 8, 2006

Alteromonas

Alteromonadacea

Alteromonadales

Gammaproteobacteria

Alishewanella

Aestuariibacter

Ferrimonas

Colwellia

Idiomarina

Glaciecola

Marinobacterium

Marinobacter

Pseudoalteromonas

Microbulbifer

Incertae sedis

Psychromonas

Teredinibacter

ShewanellaThalassomonas

Ferrimonadacea

Idiomarinaceae

Moritella

Moritellaceae

Pseudoalteromonadaceae

Ferrimonas

Idiomarina

Pseudoalteromonas

Psychromonadaceae

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?


July 8, 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

How could this be accomplished?


July 8, 2006

Modeling names and taxa…


July 8, 2006

Sequence+

Name+

Tax

on

Species+

Authority+

Strain+


July 8, 2006

Name+

Tax

on

Literature Governing bodies

GenBankDDBJEMBLothers

CollectionsBRC

Species+

Authority+

Strain+ Sequence+


July 8, 2006

Tax

on

Name+

Species+

Literature Governing bodies

GenBankDDBJEMBLothers

CollectionsBRC

Source+

Source+ProposalsSTM

Legal

Databases

PriorityValidity

SynonymyType

direct

indirect

BRC

Public Private

General

Authority+

Strain+ Feature+

GSC Core PhenotypeFAME

Biolog PA


July 8, 2006

However, rules are made to be broken…


July 8, 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*


July 8, 2006

Name+

Tax

on

Strain+ Feature+

Species+

Name+ Name+

Strain+Strain+

Feature+Feature+T

axon T

axon

Homotypic synonymy Heterotypic synonymy

Differing opinions…


July 8, 2006

The impact of “uncontrolled” labeling of environmental sequence and strain data …


July 8, 2006

Non-types, clones, environmental sequences

Feature+

Environmental sequence

Feature+

“Name”+

Misidentified taxon

Strain*

ID+


July 8, 2006

Top 25 labels on 16S rRNA sequences for type strains

0

200

400

600

800

1000

1200

1 3 4 5 A 6 7 B 8 10

Tanza

nia D C 9RB 11 14 12

I16 17 B2

n = 15232 unique sequences2.74X over defined


July 8, 2006


July 8, 2006

The case of the Verrucomicrobia


July 8, 2006

“Identifiers” on Verrucomicrobia 16S rRNA sequences, n=911

0

100

200

300

400

500

600

uncultured Verrucomicrobia bacterium

uncultured Verrucomicrobium sp.

uncultured Xiphinematobacteriaceae bacterium

uncultured Verrucomicrobiales bacteriumuncultured Verrucomicrobiaceae bacterium

uncultured Spartobacteria bacterium

Prosthecobacter dejongeii

uncultured Verrucomicrobia subdivision 3 bacterium

Verrucomicrobium spinosumProsthecobacter fusiformis

Prosthecobacter vanneervenii

Opitutus terrae

Prosthecobacter debontiiuncultured Opitutus sp.

Chthoniobacter flavus


July 8, 2006

Publication field from Genbank record, n=627

0

10

20

30

40

50

60

70

80

90

UnpublishedAppl. Environ.

Int. J. Syst. Evol.FEMS Microbiol.Appl. Environ.

Science 308 (5721),

Appl. Environ.Appl. Environ.Appl. Environ.Unpublished

Appl. Environ.Int. J. Syst. Evol.

Environ. Microbiol. 4Soil Biol. Biochem.

Proc. Natl. Acad.Int. J. Syst. Evol.FEMS Microbiol.Appl. Environ.Appl. Environ.

Microbiology 141,J. Ind. Microbiol. 17,

Int. J. Syst. Evol.FEMS Microbiol.Environ. Microbiol.

Biotechnol. Alia 8, 1-

Appl. Environ.Appl. Environ.Appl. Environ.Appl. Environ.


July 8, 2006

Verrucomicrobia, based on annotation (n=444)

Proteobacteria

Verrucomicrobia

Victivalalles &Lentisphaeralles

Optitutus

Xiphinematobact

Unclassified

Unclassified


July 8, 2006

Taxonomic structure of the Verrucomicrobia revealed

Lentisphaera

Akkermansia

Verrucomicrobium

Prosthecobacter

Rubritalea

Verrucomicrobium

Xiphenematobact

Chthoniobacter

Verrucomicrobium

Optitutus

Unclassified


July 8, 2006

Accessing the NamesforLife information objects


July 8, 2006

How NamesforLife disambiguates biological nomenclature


July 8, 2006

The underlying concepts

Persistent identifiers

A name or an identifier for a resource that uniquely identifies that resource and will be forever associated with that resource. It will never be reassigned to any other resource and will not change regardless of where the resource is located or whatever protocol is used to access it.

Use of a well managed persistent identifier rather than a location will ensure that when a document is moved, or its ownership changes, the links to it will remain actionable.

From: Diana Dack. 2001. Persistence is a Virtue Information Online Conference, Sydney.


July 8, 2006

The underlying concepts (cont.)

Semantic resolution

The process of identifying the precise meaning of terms or concepts and mapping them into different classifications.

Static conceptsUnaffected by new knowledge

Dynamic conceptsAffected by new knowledge

What’s so important about precise meaning in scientific, technical, or medical fields?

…in commerce?


July 8, 2006


Name resolution The process of mapping a persistent identifier to a URL that retrieves a resource. The URL locates the named resource identified by the persistent identifier (the name).

PID URLPID1

PID2

PID3

URL1

URL2

URL3

Resource

Identifies LocatesName resolution

Adapted from: Name Resolution Service: Introduction and Use, Harvard University Library


July 8, 2006


Handle The Handle system is a comprehensive system for assigning, managing, and resolving persistent identifiers, known as ‘handles’ for digital objects and other sources on the Internet. Handles can be used as Uniform Resource Names (URNs).

Digital object identifiers (DOIs)

It is implicit in the Handle design that a digital object has associated metadata (data about data; here: data about the digital object). The core piece of metadata is the Handle itself.


July 8, 2006

DOIdirectory

URLURL

URL

URL

URL

URL

URL

URL

URL

URL

URL

URL

URL

URL

Content

Content

Assigner

DOIdirectory

DOIdirectory

DOIDOI

DOI

DOI

DOI

DOI

DOIDOI

DOI

DOI

DOI

DOI

DOI

DOI

doi>doi>doi>

Courtesy of Norman Paskin,International DOI Foundation


July 8, 2006

NamesforLife

A novel technologyAn ontology, metadata model, and a mappingA transparent information layer on the InternetAn application of persistent identifiers

A semantic resolution service for the life sciences

What is it?

What is the purpose? Solve a well known problem

Ambiguity in terminology

Common problem

Pervasive in life sciences

The special case of biological nomenclature

Queries and literature searches

Assertions, assumptions, hypotheses

A content providerWhat isn’t it?


July 8, 2006

Why DOIs are the preferred GUID

Digital object identifiersStrengths - opaque, actionable, require metadata, identify an object, strong governance, widespread usage, not based on DNS, guarantee of persistence, proposed ISO standard.Weakness - Not free

DOIs

Proven technologyDOIs are layered on top of CNRI’s Handle serverScalable

Widespread use in publishing industry (CrossRef)> 1500 publishers and >1000 libraries subscribing> 22M DOIs assigned> 11M click-throughs (2/15/2006 - 3/15/2006)

Well understood technologyStrong social/legal framework to ensure persistence

Technically robust


July 8, 2006

Two componentsA transparent information layer to provide DOI services to the life science communityAn ontology with a schema that produces metadata consistent with requirements of the

International DOI FoundationSeven first class object types

Name, Taxon, Exemplar, Nomos, Practitioner, Feature, Nomenclatural Code

N4L architecture

Name objectTaxon object

HigherTaxon object

Exemplar object

Name DOINameName statusAuthoritySynonymsTaxon DOI

Taxon DOINameRankParent nameParent taxon DOIMethodologyType exemplar DOI

Taxon DOINameRankParent nameParent taxon DOIMethodologyMembers Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name Taxon DOI Name

Exemplar DOIBiodeposit FeatureBiodeposit FeatureTaxon DOISpecies name


July 8, 2006

Two components (continued)

The prototype

DOI:10.1601/tx.0

A proof-of-principle application

24,176 first-class objects

Track changes in concepts over time

Based on a nomenclatural taxonomy, but capable of supporting multiple taxonomic views and “time travel”

Initial DOI services conform to AP 0

Released January 17, 2006

Japanese prototype released June 21, 2006

Chinese version under development

Arabic version under consideration


July 8, 2006

Easy support of foreign languages


July 8, 2006

The mini-monograph

Name DOINameName statusAuthoritySynonymsTaxon DOI

Taxon DOINameRankParent nameParent taxon DOIMethodologyType exemplar DOINontype exemplar DOI

Exemplar DOIBiodeposit FeatureBiodeposit FeatureTaxon DOISpecies name

Preamble Name/Name DOI Name status, Authority Synonyms/Name DOI Member of: Parent Taxon DOI MethodologyType Exemplar DOI Biodeposit+ Feature+ Paired Sequences Genomic Paired phenotypic data Minimal description GSC Core description ImagesNontype exemplar Biodeposit+ Feature+ Paired Sequences Genomic Paired phenotypic data Minimal description GSC Core description ImagesReference DOIs

IJSEM/ICSPTaxonomic authorities

BRCs & CollectionsGenbank/EMBL/DDBJTaxonomic communityGenomics community

Instrument vendorsDatabase providers

Publishers


July 8, 2006

“Test ideas in the marketplace. You learn from hearing a range of perspectives. Consultation helps engender the support decisions need to be successfully implemented.”


July 8, 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”


July 8, 2006

Synergistic activities

Goals of NamesforLife

Collaborators/PartnersATCC - nomenclature support, conduit to new customers for existing goods and services, opportunity for new services (pay-for-view data)

Forsyth Research Institute - further testing and refinement of the N4L model, creation of mini-monographs, extension to nyc and uncultivated species

Midi Inc. - Integration of N4L services with instrument output, pay-for-view data

SGM/ICSP/JC - optimize N4L DOI imbedding, custom web tag libraries for on-the-fly updating of content

Synchronize usage of nomenclature in databases and elsewhere

Establish links between vertically integrated business

Help build new relationshipsStimulate new business opportunitiesBuild useful new tools and servicesBecome a self-supporting service for the community


July 8, 2006


July 8, 2006

Embedding N4L links into web content


July 8, 2006

PhenBank…

The federated database

Associate phenotypic data with emerging 16S sequence data

Potential value to the communityProblems

TechnicalInteroperability and data comparabilityVariable granularityLack of controlled vocabulary

Social issues of the centralized modelWho controls access?Who curates?Who pays?Incentives for participants?


July 8, 2006

A decade later Maturation of the 16S data Impact of emerging technologies

Large-scale sequencing effortsWealth of new tools

Predictive modelsOntology developmentPhenotypic arrays

Rapid emergence of web technologiesImpact on traditional publishingXML, DOIs Semantic technology

Impact of emerging social trendsCommunity annotation, social taggingOpen access and supplementary dataIncentives for data sharing

Distributed model, data discovery“Pay-for-view” vs. regeneration

PhenBank…


July 8, 2006

Sequencing the type strains

1231480435195329720311188625250

Cumulative genomes sequenced

4271284818981266844563376250Genomes/$5M

1171175626343951592688891333320000Cost/Genome*

3417227815191013675450300200BP per dollar

20142013201220112010200920082007Year

Selection of Targets

TypeCulture Material

JGISequencing

RapidAnnotation(24 Hours)

MetabolicReconstruction

ModelGeneration

PhenotypePrediction

DatabaseRepository

Source – Rick Stevens, Argonne National Laboratory and University of Chicago


July 8, 2006

Thanks toMSUJulia BellScott HarrisonJudy Leventhal

Donna McGarrellSiddique MohideenQiong Wang

Univ. MichiganPaul Saxman

Forsyth Inst.Floyd Dewhirst

Midi Inc.Myron SasserGary Jackoway

ATCCTim Lilburn

DSMZBrian Tindall

University of ToulouseJean Euzéby

IDFNorman Paskin

NexusTechVenturesTodd Zahn

NIES JapanJunko ShimuraKaduo Hiraki

Soc. General MicrobiologyRobin DunfordRon Fraser

Int. Com. System. Prok.Aharon OrenHans Juergen Busse

IJSEMPeter Kaempfer

Argonne National LabRick Stevens

FundingUS DOE BER NSFMich Univ. Comm. Init.

Questions?


July 8, 2006


July 8, 2006

AcknowledgementsMSUJim ColeDonna McGarrellAKS MohideenQiong WangScott HarrisonConnie WilliamsJudy LeventhalJulia BellDenise Searles

VPGR and OIPPaul M. HuntLorraine Hudson

ATCCTim Lilburn

DSMZBrian Tindall

University of ToulouseJean Euzaby

IDFNorman Paskin

FundingUS Department of Energy

Office of ScienceNational Science FoundationMichigan University

Commercialization Initiative


July 8, 2006

“I would not say that the future is necessarily less predictable than the past. I think the past was not predictable when it started."


July 8, 2006

Insert statement of problem here


July 8, 2006

"I believe what I said yesterday. I don't know what I said, but I know what I think, and, well, I assume it's what I said."


July 8, 2006

“Simply because you do not have evidence that something does exist does not mean that you have evidence that it doesn't exist."


July 8, 2006

"Learn to say 'I don't know.' If used when appropriate, it will be often."


July 8, 2006

"If I know the answer I'll tell you the answer, and if I don't, I'll just respond, cleverly."


July 8, 2006

“I don't do quagmires.”


July 8, 2006

Stan Falkow’s observation

“Given a choice, most taxonomists would rather wear each other’s underwear than use each other’s names”

Why is this so?


July 8, 2006

Consider the followingA simple exchange between a customer and

vendor of “technical” productsDiscussions among physicians, healthcare

providers, and insurers


July 8, 2006

The name/taxon disjunction

ImpactAccumulation of dubious names in literature/databases

Effects assertions of:Identity, commonality of pathways, common ancestry, homology, parology, xenology

Legal consequences


July 8, 2006

Problems in print publishing

Key requirementProposals and emendations must appear in print

Code specificProkaryotic Code

Effective, legitimate, and valid

Registration

Taxonomies are retrospectiveCan only cite earlier publicationsCannot cite future emendationsIncreasingly based on molecular sequence data

Deposit of sequence data in public databases

Not conveniently referenced in print


July 8, 2006

Problems with electronic publishingNo formal publishing mechanisms

Does not fulfill fundamental requirement of the Code(s)

Lack bibliographic informationNot citableNot persistent

Subject to uncontrolled changeMay disappear

Link rot404 Link not found


July 8, 2006

Problems in nomenclature

Marking territoryPersonal achievement

Systematic biologists

Everyone else(aka end-users)

Unfamiliar with literatureUnique aspects

Unaware of Codes of NomenclatureLegalistic framework

Formation and assignment of namesCircumscription and emendation of taxaPriority and citationSynonymy and homonymyCorrection of orthographic errorsAdjudication of nomenclatural disputes

ButDo not govern classification or identification


July 8, 2006

Primary entry point into STM literature and databases

Prominent role in laws/regulations

Poor identifiersFixed in time and scopeMay not be revisedSynonymies generally not addressPersist, but

obsolesce in relation to taxonAn archival record of a taxonomic definition for a single point in time

Problems in nomenclature (cont.)

Systematic biologists

But…

What are the alternatives?


July 8, 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 + + + + + + + + + + +


July 8, 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 implementation

Expanded technical infrastructure and features specific to DOI applications


July 8, 2006

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


July 8, 2006

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


July 8, 2006

Ease of use


Turn-key applicationIDF and RAs maintain technical support staff Interacts with users, standards community and othersResolve problems of RAs and broader user communityUnderwrites cost of directory manager

Support to RAsGuidance, troubleshooting, etc

DOI HandbookPolicies and procedures for various actorsGuidelines for RAs, developersDeveloped 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


July 8, 2006

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 resolution

Parent-child relationships

Other relationships

No preexisting constraints to make useful relationships


July 8, 2006

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


July 8, 2006

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


July 8, 2006

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


July 8, 2006

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


July 8, 2006

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


July 8, 2006

Relevance of names in content

Current web is designed for human-human communication

Future web will rely on machines for information gathering, filtering, and knowledge discovery

Need for semantic metadata for machine discovery and reasoning

Information retrieval

Keeping pace with the field

Volume of content produced annually*Books - 8 TbyteJournals - 2 Tbyte

Semantic technologiesN4L provides persistent semantic disambiguationRobust and economical

There is a pressing need for automation

*Scherf, et al., (2005) Brief Bioinform. 6: 287

July 8, 2006

VIRTUALLY all microorganisms . . .

. . . We report here the first structure determination, to our knowledge, of

the siderophores from an open-ocean bacterium, alterobactin A and B from

Alteromonas luteoviolacea.

A. luteoviolacea is found in oligotrophic10 and

coastal11 waters. Alterobactin A has an exceptionally high

affinity constant for ferric ion. We suggest that at least some marine

microorganisms may have developed higher-affinity iron chelators as part of

an efficient iron uptake mechanism which is more effective than that of their

terrestrial counterparts.



Find Organism Name in Code

July 8, 2006

VIRTUALLY all microorganisms . . .

. . . We report here the first structure determination, to our knowledge, of the

siderophores from an open-ocean bacterium, alterobactin A and B from

<n4l:checkupdate doi=“10.1601/nm.2821”>

Alteromonas luteoviolacea</n4l:checkupdate>.

A. luteoviolacea is found in oligotrophic10 and

coastal11 waters. Alterobactin A has an exceptionally high affinity

constant for ferric ion. We suggest that at least some marine microorganisms may

have developed higher-affinity iron chelators as part of an efficient iron uptake

mechanism which is more effective than that of their terrestrial counterparts.



Add N4L Tag Around Each Name to be Tracked


July 8, 2006

Comparing identifiersA label that identifies an entity

ISBN 0-387-98771-1ATCC 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


July 8, 2006

Comparing identifiers (cont.)

A syntax by which an identifier can be expressed in a form suitable for use within a specific infrastructure.

Actionable identifiersURI (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 identifiers

A 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


July 8, 2006

Globally unique identifiers (GUIDs)

Archival resource keysStrengths - opaque, require metadata, identify an objectWeakness - weak governance, not in widespread use, based on DNS, no guarantee of persistence, not a standard

ARKs

Life science identifiersStrengths - opaque, identify an object, actionableWeakness - no governance, not in widespread use, based on DNS, no metadata requirement, no guarantee of persistence, not a standard

LSID

Persistent URL/Persistent Object IdentifierStrengths - opaque, identify an object, actionable, require metatdataWeakness - no governance, not in widespread use, based on DNS, no guarantee of persistence, not a standard

PURL/POI


July 8, 2006

Timeline for next phase of N4L development

Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4

1.11.21.31.41.51.62.12.22.32.4

3.4

2.53.13.23.3

Database migration

Incorporate partner data

Tag libraries

Upgrade web hub

Automate name captureOntology & schema development

Deploy fault tolerant systemDeploy to broader publications

Determine FRSChange message system

Client-side automated message processing

PDF tools

Partner content linksLong-tail storefront

New targets for N4L implementation


July 8, 2006

Ramifications of misunderstanding a name or label

Wrong assumptions, assertions, or hypotheses Misdiagnosis of infectious diseasesMisapplication of public policies

Highly significant

Significant Lost opportunities

Failure to reach potential customers potentially interested in marketed content, goods, and services at point of need.

The long-tail phenomenon*

Names trigger specificresponses

But, the concepts to which names apply are not static

May not always map 1:1

May require expertise for accurate interpretation


July 8, 2006

NamesforLife

Leverages recent development in persistent identifier technology

Unique mechanismOccurrence of a name triggers contextually appropriate retrieval services Uses embedded N4L-DOIs for content discovery

Provides semantic enablement of existing content at minimal cost to data and content providers

The solution

Through A unique combination ofIdentifiersPersistenceResolution

July 8, 2006

Competing activities

Technologies

Initiatives TDWG/GBIFFocus on museums and herbariaNot supported by nomenclatural bodiesAdvocating use of LSIDAttempting to duplicate the IDF/RA infrastructure to avoid cost of DOI

LSID - lack governance, persistence, limited usage

Use covered in PCT/US 2005/001688Can use N4L to resolve DOI <-> LSID

CrossRef - bibliographic service, complementary to N4L

TIB - DOIs on earth science data setsNot directly citable, only on supplementary dataNo semantic metadata (Dublin Core)

Semantic web - bio-ontology initiativesNCBO, OBO, HCLS, GO, MGEDFocus on gene and genome annotationNot designed for automated reasoning


July 8, 2006

Interactivity and navigation, heatmaps as a GUI


July 8, 2006

Accessing the NamesforLife information objects

fems2006 madrid, spain symposium 20. biodiversity july 8, 2006 knowledge bleed, phenbank, and...

Documents