egenomics: cataloguing our complete genome collection cambridge, uk septermber 7-9, 2005 phenbank...

eGenomics: Cataloguing our complete genome collection

Cambridge, UK Septermber 7-9, 2005

Phenbank

George M. Garrity

Microbiology and Molecular Genetics &

Bergey’s Manual Trust

Michigan State University



Limited data typesUniversally applicable across all taxaCumulative

Controlled vocabularyLinks to primary literatureSuite of robust toolsStrong public support

Large user baseFunding

Data curation weak

GenBankDDBJ/EMBL

Taxonomicdata sources

Unlimited data typesSome broadly applicable across all taxa, most are notSome are cumulative, many are comparative

Numerous taxon specific vocabulariesFew links to primary literature or original data setsTools of variable quality, most are “one-off”Limited public support

User bases vary with economic importanceFunding poor to non-existant

Data curation variable



Doesn’t exist (yet)What it might provide to the community?Share some thoughts on what it might take to create such a resourceWill borrow heavily on Field and Hughes commentary in Microbiology

Technical issuesWhat data and information currently existsWhat’s on the horizon

Sociological issuesImportance of the primary literatureData provenance and other hurdlesData curation

Self-supporting vs public funding

Goals of presentation



Four synergistic projects at MSUCompilation and publication of the principle

monographic work in prokaryotic biology

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

Visualization tools for exploratory data analysis of large sequence data set, a taxonomic atlas of the prokaryotes, and a repository of vetted 16S sequences

Semantic resolution services for life sciences using digital object identifiers

Phenbank ?



Bergey’s Manual of Systematic Bacteriology

Print publicationFive volumes (approximately 6000 pg when completed)Compilation with contributions by over 800 authors to date

Focus Predominantly types of validly published named taxa

OrganizationNomenclatural taxonomy following 16S rRNA gene treeGenus treatments

Etymology, defining publication(s), fourteen major categories (variable) plus sections on enrichment and isolation, maintenance, procedures for special testing, differential features, taxonomic comments, and lists of validly published species, effectively published (invalid), and other organisms, and species incertae sedis

Species listsEtymology, defining publication(s), key

characteristics including culture collection accession numbers, GenBank accessions, and key differential characteristics

Higher taxon treatments Etymology, defining publication(s), common

characteristics and membership



A peak inside the ManualThe Manual is produced electronically

Custom SGML DTD (Lyons, Garrity and Usdin)600 elements in contextFormatting done using FOSIContent in unconstrained English

Manuscript -> tagged instance -> printManuscript -> HTMLKey features reported at genus level

Constant contentEnrichment/isolation, maintenance,

special methods, taxonomic comments, species lists (valid, invalid, species incertae sedis)

Variable contentAntimicrobial sensitivity, cell

morphology, cell wall composition, cultural characteristics, ecology, fine structure, genetics, growth, metabolism, mutants, pathogenesis, physiology, serological reactivity

Extensive linked bibliography, figures, tables



Seeing the gene can fake you out…Ken Nealson, Microbial Environmental Genomics Workshop I



However, The Manual is not a substitute to the primary literature

Contains information and summarized interpretations of the literature by experts

Does not currently cover Yet-to-be cultivated taxa (with the

exception of Candidatus species)Environmental sequencesCommunities or mixed culturesInvalidly named and unnamed taxa

With the exception of sequence identifiers, does not provide direct access to raw data

Is static, so changes in taxonomic view cannot be readily conveyed*

So, the Manual provides a good foundation for Phenbank, but much is still missing.



Genus

Number of species/genus

0 200 400 600 800 1000 1200

0

100

200

300

400

500

Orphan taxa

Streptomyces 544

Clostridium 179

Bacillus 167

Pseudomonas 161

Lactobacillus 136

Mycoplasmafs 120

Mycobacterium 119

Corynebacterium 96

Streptococcus 95

Vibrio 74

10 – 73 species 136 genera

5 – 9 species 163

2 – 4 species 368

Orphans 651



Species frequency by phylumProteobacteria 2542 2Actinobacteria 1890 4Firmicutes 1653 3Bacteroidetes 362 5Euryarchaeota 247 1Spirochaetes 102 5Cyanobacteria 82 1Crenarchaeota 51 1Fusobacteria 42 5Deinococcus-Thermus 29 1Thermotogae 26 1Chlorobi 21 1Aquificae 20 1Chlamydiae 17 5Chloroflexi 14 1Verrucomicrobia 12 5Planctomycetes 12 5Deferribacteres 9 5Nitrospira 8 1Thermodesulfobacteria 6 1Fibrobacteres 3 5Acidobacteria 3 5Thermomicrobia 2 1Dictyoglomi 2 5Gemmatimonadetes 1 5Chrysiogenetes 1 1

Species

Number of species/phylum

5 10 15 20 25

0

500

1000

1500

2000

2500



Wouldn’t it be nice if…

End-user’s perspective

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



Categories and properties of identifiers

A label that identifies an entityA single unambiguous string

Adapted from: Paskin, N., (2005) The DOI Handbook Edition 4.2.0

A formal standard or industry convention

Arbitrary

Consistent syntax

Denotes and distinguishes separate members of a class of entities

Establishes a 1:1 correspondece between labels and members

Enumeration

The number or label is simply a string

A numbering scheme




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

identifiersDoes not mandate a method of creating labelsDoes not create a managed environment

An infrastructure specification




Includes Unique identifiers,A formalized infrastructureManagement policies

ExamplesUPC/EAN barcodes and RFID tagsDigital object identifiers

A system for implementing labels



What’s at DOI ?

DOI syntaxCan include any existing identifier, formal or informal, of any entityopaque

Numbering

Resolve from DOI to dataInitially a location (URL; not persistent)May be to multiple data including multiple locations, metadata, service.ExtensibleBased on the Handle system

Implement the URI/URN conceptGranularity, scalability, administration, and security

Resolution



Modeling names and taxa…



Sequence+

Name+

Tax

on

Species+

Authority+

Strain+



Sequence+

Name+

Tax

on

Literature Governing bodies

GenBankDDBJEMBLothers

CollectionsBRC

Species+

Authority+

Strain+



Tax

on

Sequence+

Name+

Species+

Literature Governing bodies

GenBankDDBJEMBLothers

CollectionsBRC

Source+ Source+

Source+

phenotypic

“omics”

ProposalSTM

Legal

Databases

PriorityValidity

SynonymyExemplar req.

phenotypic

direct

indirect

BRC

Public Private

General

Authority+

Strain+



However, rules are made to be broken…



Strain+ Sequence+

Name+

Species+

A properly formed species

Sequence+

Name+

Species+

Candidatus or exemplar lost

Sequence+

Environmental sequence

Strain+

Name+

Species+

Old type strain, not yet sequenced

Name+

Species+

Old type, exemplar based ondrawing or description

Sequence+

“Name”+

Misidentifed taxon

Strain*



Name+

Tax

on

Strain+ Sequence+

Species+

Name+ Name+

Strain+Strain+

Sequence+Sequence+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



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)

Nomenclatural issuesHomotypic synonymyPriorityRule 37(a) 1

Data issuesOne to many relationship

Taxonomic issueWhich one is right?



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


Nomenclatural issueNon-type strains






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


Nomenclatural issuesHeterotypic synonymy

Data issueMany to many relationship

Taxonomic issueWhich one is right?






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

atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubra

haloplanktishaloplanktis(T)

Pseudoalteromonas

undina

haloplanktistetradonis








Alteromonas

colwelliana

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


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafulginea


Pseudoalteromonas

undinaantartica

elyakoviii










Alteromonas

colwelliana

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


maris


pelagicummaris

hiroshimense

Oceanosprillum

mariswilliamsae

distinctafulginea


Pseudoalteromonas

undinaantartica

elyakoviii

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

distinctafulginea


Pseudoalteromonas

undinaantartica

elyakoviii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolacea

bacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolyticatetrodonis

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

elyakoviii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolaceajaponicadenitrificanslivingstonensisalleyanna

atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubraundinaantarticabacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolyticatetrodonis


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

distinctafulginea

Pseudoalteromonas

elyakoviii

fridgidimarinageldimarinawoodyiiamazonensisbalticaoneidensispealeanaviolaceajaponicadenitrificanslivingstonensisalleyanna

atlanticaaurantiacarrageenovoracitreaesperjianaluteoviolaceanigrifacienspisicidarubraundinaantarticabacteriolyticaprydzensistunicatadistinctaelyakoviipeptidolyticatetrodonis


12 others

mariniintestinasaireschlegelianagaetbuli

mediteranneaprimoryensis



stellipolarislitorea 5 others



Alteromonas

Alteromonadacea

Alteromonadales

Gammaproteobacteria

Alishewanella

Aestuariibacter

FerrimonasColwellia

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 genera1 unclassified -> 7 unclassfied

Which is correct?Which is supported by the data?



Since first being defined the genus Alteromonas has undergone…

18 emendations,

19 species added

19 species in four genera

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

6 synonyms

2 reduced to subspecies, then re-elevated to species

48 names, five genera, five families, and two classes but….

only three validly named species remain.This is not an uncommon occurrence



Species

Genera

Basonyms

Heterotypic synonyms

Homotypic synonyms

Year

Cum

ulat

ive

num

ber

of n

ew p

roka

ryot

ic t

axa

1980 1985 1990 1995 2000

010

0020

0030

0040

0050

0060

00

Year

Cum

ulat

ive

num

ber

of s

ynon

yms

1980 1985 1990 1995 2000

020

040

060

080

010

00

Publication of prokaryotic taxa 1980-2004

egenomics: cataloguing our complete genome collection cambridge, uk septermber 7-9, 2005 phenbank...

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