George M. Garrity, Catherine Lyons and James R. Cole NamesforLife, LLC

George M. Garrity, Catherine Lyons and James R. ColeNamesforLife, LLC

Okemos, MI and Edinburgh, UK

Funding for this portions of this research has been provide by the US Department of Energy, Grants No. DE-FG02-04ER63933, DE-FG02-99ER62848, DE –FG02-7ER86321 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]

Names

Indicate a new discovery or inventionConstant source of frustration

End users of literature and scientific databases

Publishers and data providers

Names are not permanentQueries can be incomplete or wrongDifficult and costly to maintainRender content inaccessible and obsoletePoor identifiers

Ogden Richards semiotic triangle

THOUGHT OR REFERENCE

SYMBOL REFERENT

Symbo

lizes

(a ca

usal

relat

ionsh

ip)

Refers to

(other causal relations)

Stands for(an imputed relation)

Adapted from Ogden,CK and Richards, IAThe Meaning of Meaning, Magdale, 1923

Does the OGT apply to biological names?

TAXONOMIC CONCEPT

NAME EXEMPLAR

Symbo

lizes

(a ca

usal

relat

ionsh

ip)

Refers to

(other causal relations)

Stands for(an imputed relation)

Biological naming conventions

Fundamentals of bacterial nomenclature• Governed by Codes of Nomenclature• Scientific names are all latinized words• Purpose is to serve as a unique label• Each name is “anchored” by a nomenclatural type• Correct names are based upon

– Valid publication– Legitimacy– Priority of publication

• Names have standing only if validly published• Each taxon can bear only one correct name, based on

– Circumscription– Position– Rank

• Names should not be changed without sufficient reason

Adapted from International Code of Nomenclature of Bacteria, 1990 Revision

Anatomy of a bacterial name

Alteromonas communis Bauman et al. 1972

Marinomonas commune (Bauman et al. 1972) van Landshoot and Delay 1984

Oceanomonas commune (Bauman et al. 1972) Bowditch et al. 1984

Alteromonas Baumann et al. 1972 (Approved Lists 1980) emend. Novick and Tyler 1985

Alteromonadaceae Ivanova and Mikhailov 2001 emend. Ivanova et al. 2004

Latinized species name Authority and priority date

Species epithet

Nomenclatural assertions

New name Any rank from subspecies to orderMust assert novelty, declare type, circumscribe taxon, provide definition of name.Effective vs. valid publication

New combination Subspecies or species splitMust assert novelty, declare type, circumscribe taxon, provide definition of new genus name. Species epithet retained.

Synonymies HeterotypicHomotypicOrthographic correctionsRejected/conserved names

An example of the problem…

macleodii(T)

communis

Alteromonas

1972

vaga

communisvagahaloplanktis

Alteromonasmacleodii(T)

1972 1973

communisvagahaloplanktisrubra

Alteromonas

1972 1973 1976

macleodii(T)

communisvagahaloplanktisrubracitrea

Alteromonas

1972 1973 1976 1977

macleodii(T)

communisvagahaloplanktisrubracitreaesperjianaundina

Alteromonas

1972 1973 1976 1977 1978

macleodii(T)

communisvagahaloplanktisrubracitreaesperjianaundinaaurantia

Alteromonas

1972 1973 1976 1977 1978 1979

macleodii(T)

communisvagahaloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedai

Alteromonas

1972 1973 1976 1977 1978 1979 1981

macleodii(T)

communisvagahaloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceae

Alteromonas

1972 1973 1976 1977 1978 1979 1981 1982

macleodii(T)

communisvagahaloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceae

vagacommunis(T)

Marinomonas Alteromonas

commune

vagum

1972 1973 1976 1977 1978 1979 1981 1982 1984

multiglobiferum

japonicumminutiumbiejerinckiimaris

maris

hiroshimense

pelagicumpusillum

jannaschiikreigii

Oceanosprillum

mariswilliamsae

linum(T) macleodii(T)

communisvagahaloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedai

vaga benthicahanedai

Marinomonas Alteromonasputrifaciens(T)

Shewanella


maris

hiroshimensemultiglobiferumpelagicumpusillumcommunejannaschiikreigiivagum

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

communisvagahaloplanktisrubracitreaesperjianaundinaaurantia

hanedailuteoviolaceaedenitrificans


Marinomonas Alteromonas Shewanella


maris


Oceanosprillum

mariswilliamsae

putrifaciens

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

communisvagahaloplanktisrubracitreaesperjianaundinaaurantiaputrifacienshanedailuteoviolaceaedenitrificans


Marinomonas Alteromonas Shewanella


maris


Oceanosprillum

mariswilliamsae

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

colwelliana



Marinomonas Shewanella


maris

hiroshimensemultiglobiferumpelagicumpusillumcommunejannaschiikreigiivagumbiejerinckii

pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae


tetradonis

Alteromonas

colwelliana

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

colwelliana


vaga benthicahanedaicolwellianaalgae



tetradonisatlanticacarageenovora

Alteromonas

colwelliana

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


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae





putrifacienshanedai

denitrificans

rubracitreaesperjianaundinaaurantia

luteoviolaceae


Alteromonas

colwelliana

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


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafuliginea





putrifacienshanedai

denitrificans

rubracitreaesperjianaundinaaurantia

luteoviolaceae


Alteromonas

colwelliana

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


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distincta

atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubra

haloplanktishaloplanktis(T)

Pseudoalteromonas

undina

haloplanktistetradonis


fuliginea





Alteromonas

colwelliana

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


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafuliginea


Pseudoalteromonas

undinaantartica

elyakovii








Alteromonas

colwelliana

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


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafuliginea


Pseudoalteromonas

undinaantartica

elyakovii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolacea

bacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolytica


mediterannea







Alteromonas

colwelliana

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


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafuliginea


Pseudoalteromonas

undinaantartica

elyakovii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolacea

bacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolyticatetradonis

japonica


mediterannea







Alteromonas

colwelliana

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


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafuliginea

Pseudoalteromonas

elyakovii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolaceajaponicadenitrificanslivingstonensisalleyanna

atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubraundinaantarticabacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolyticatetradonis


mediterannea







Alteromonas

colwelliana

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


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafuliginea

Pseudoalteromonas

elyakovii




12 others

mariniintestinasaireschlegelianagaetbuli

mediteranneaprimoryensis



stellipolarislitorea 5 others





Alteromonas

colwelliana

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


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafuliginea

Pseudoalteromonas

elyakovii




14 others





stellipolarislitorea 8 others4 others





Alteromonas

colwelliana

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


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafuliginea

Pseudoalteromonas

elyakovii




15 others










Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 2005 2007


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafuliginea

Pseudoalteromonas

elyakovii




16 others






hanedailuteoviolaceae



communisvagahaloplanktisrubracitreaesperjianaundinaaurantiaputrifaciens

denitrificans


Alteromonas

colwelliana

1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 2005 2008


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafuliginea

Pseudoalteromonas

elyakovii




16 others






Eight additional species but over 50 name changes that affect more than

1400 published articles

Eight additional species but over 50 name changes that affect more than

1400 published articles

Alteromonas

Alteromonadacea

Alteromonadales

Gammaproteobacteria

Alishewanella

Aestuariibacter

FerrimonasColwellia

Idiomarina

Glaciecola

Marinobacterium

Marinobacter

Pseudoalteromonas

Microbulbifer

Incertae sedis

Psychromonas

Teredinibacter

Shewanella

Thalassomonas

Ferrimonadacea

Idiomarinaceae

Moritella

Moritellaceae

Pseudoalteromonadaceae

Ferrimonas

Idiomarina

Pseudoalteromonas

Psychromonadaceae

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 genera1 unclassified -> 7 unclassfied

Which is correct?Which is supported by the data?

In 36 years this genus of bacteria underwent 24 published changes 26 new species were added23 species moved to other genera50 names were created and today the genus contains 8 species.

This fairly simple example impacts 1443 other publications

>9500 nucleotide sequences

How does a publisher, library or archive keep legacy content relevant?

At what cost?

Bringing meaning to life…

1980 – 2257 classified and validly named2008 – 25628 classified and named

108847 taxonomic nodes

0.7 namesper day

4.2 namesper day

83 nodesper day

Prokaryotic names 1980 - 2008


Nomenclatural assertions

Nomenclatural assertions (cont.)

Nomenclatural assertions (cont.)

Object type Count Attribute Count

Name 11661 Assertion 17841

Reference 6672

Taxon 11169

Exemplar 7724 Strains 13410

16S rRNA 8518

A NamesforLife taxonomic hierarchy

NamesforLife information objects


IJSEM workflow

IJSEM workflow

The NamesforLife autotagger

What is it? Custom java server-side application or client side plug-in for <oXygen/>

Parses NLM-DTD* compliant manuscriptsIdentifies validly published bacterial names, wraps names in named-entity tags, inserts N4L DOIs into output XML, output name-data

XSLT/CSS to highlight name strings in content

Unintended benefit Auto-proofing tool to detectTagging errorsNomenclatural errors

Autotagger performance

191 Articles, XML, Aug - Dec 2007

17,188 Name-like strings

15,022 Correctly identified as VP names

3282 unique names and abbreviated names

2634 species/higher taxa

2167 Candidate names

208 newly proposed 3-letter abbreviations

184 autotagger errors (Latin strings)

183 fungal names

67 invalid bacterial names

61 plant names

30 animal names

7 misspelled names

1476 tagging errors

Autotagger performance (cont.)

Human Computer Total

Tags missed 18 24 42

Non-name tags 14 26 40

Partial/incorrect names 1 6 7

Total 33 56 89

Autotagger performance (cont.)

Lessons learned

N4L proof of principleInformation object modelTime travelDOI service

Instrument vendorDatabase provider

Pre-phase I

N4L enablement of publishers’ contentRefining time-travelMigration to RDBMSOn-the-fly output of nomenclatural taxonomy (TOBA)

Phase I

Next steps

Production-level N4L application (DOI service)

N4L enablement of IJS/SGM contentOther microbiological literatureOther STM literatureOther microbiological applicationsNon-microbiological applications

Pipeline approach to capture nomenclatural acts and auto-generation of prokaryotic taxonomiesBrowser plug-in for on-the-fly enablement

Phase II

Interested partiesTest tools and conceptsLeverage existing [email protected]

We’re looking for

Documents

George M. Garrity, Catherine Lyons and James R. Cole NamesforLife, LLC