Biological nomenclature in the postgenomic era:

Biological and computational issues.George Garrity and Catherine Lyons

Bergey’s Manual Trust and Explicatrix, LLC

Imagine..

• A clinical microbiologist’s predicament• The microbial ecologist’s dilemma• The case of Francisella novicida• The history of the Altermonadaceae

– Genus described in 1972• 15 emendations, 20 species

– 19 moved to four genera– 5 synonyms, two subspecies– 64 names, five genera, three families, two classes

• The common thread in all these stories…

Stan Falkow’s Underwear

“Given a choice, most taxonomists would rather wear each other’s

underwear than use each other’s names”

Why is this so?

My objective• Share some insights on problems in three areas

– Nomenclature and taxonomy– Publishing taxonomic information– A generalized taxonomic model

• Finite state machine• Simple grammar

– Global issues• Data equivalence• Data provenance• Data curation

Problems in nomenclature• Systematic biologists

– Marking territory– Personal achievement

• Other biologists– End-users

• Unfamiliar with literature– Unique aspects

• Unaware of Codes of Nomenclature– Legalistic framework

» Formation and assignment of names» Circumscription and emendation of taxa» Priority and citation» Synonymy and homonymy» Correction of orthographic errors» Adjudication of nomenclatural disputes

– But» Do not govern classification or identification

– Biological names• Primary entry point into STM literature• Prominent role in laws/regulations

– Commerce, public safety, public health• Primary entry point into scientific databases• Poor identifiers

– Fixed in time and scope– May not be revised– Synonymies generally not address– Persist, but

» obsolesce in relation to taxon» An archival record of a taxonomic

definition for a single point in time

Problems in nomenclature (cont.)

The name/taxon disjunction• Impact

– Accumulation of dubious names in literature/databases

– Effects assertions of:• Identity, commonality of pathways, common

ancestry, homology, parology, xenology• Legal consequences

Problems in print publishing• Key requirement

– Proposals and emendations must appear in print• Code specific

– Prokaryotic Code» Effective, legitimate, and valid» Registration

• Taxonomies are retrospective– Can only cite earlier publications– Cannot cite future emendations– Increasingly based on molecular sequence data

• Deposit of sequence data in public databases– Not conveniently referenced in print

Problems with electronic publishing• No formal publishing mechanisms

– Does not fulfill fundamental requirement of the Code(s)

– Lack bibliographic information• Not citable• Not persistent

– Subject to uncontrolled change– May disappear

• Link rot– 404 Link not found

A brief glimpse at where we’re headed

• The Bergamot/N4L model– Separates names from taxa

• Taxa nameless– Uniquely, persistently identified

– Supports multiple, overlapping taxonomies• Accumulation of new data vs. new methodologies• Rank agnostic

– Unique from all other approaches• An identifier resolution service, not an information space in

which to practice taxonomy.– Names provide an entry point into the literature

• Reliably• Persistently

• A lightweight information layer

A simple grammarspecies -> current.name.pointer, exemplar.deposit.pointer+,

sequence.deposit.pointer+taxon -> current.name.pointer, nomos.defined.data, (taxon+|

species+)nomos.defined.data -> (sequence|phenotypic.feature|text)+name -> (citation, bibliographic.record, name.status)exemplar -> exemplar.id, sourcesequence -> gene, sequence.depositsource -> exemplar|exemplar.deposit|textexemplar.deposit -> brc.id.pointer, deposit.id.pointer, sourcesequence.deposit -> brc.id.pointer, deposit.id.pointer, sourcephenotypic.feature -> feature.name, feature.value, deposit.id.pointer

Exemplar+ Sequence+

Name+

Taxo

n

Species+

Exemplar+ Sequence+

Name+

Taxo

n

Literature Governing bodies

GenBankDDBJEMBLothers

CollectionsBRC

Species+

Taxo

n

Exemplar+ Sequence+

Name+

Species+

Literature Governing bodies

GenBankDDBJEMBLothers

CollectionsBRC

Practitioner + Practitioner+

Practitioner+

genotypic“omics”

ProposalSTMLegal

Databases

PriorityValiditySynonymyExemplar req.

phenotypic

directindirect

BRC

Public Private

General

Exemplar+ Sequence+

Name+

Species+

A properly formed species

Sequence+

Name+

Species+

Candidatus or exemplarlost

Sequence+

Environmental sequence

Exemplar+

Name+

Species+

Old type strain, not yet sequenced

Name+

Species+

Old type, exemplar based ondrawing or description

Sequence+

“Name”+

Misidentifed taxon

Exemplar*

Exemplar+ Sequence+

Name+

Taxo

n

N4L/Bergamot

Literature Governing bodies

GenBankDDBJEMBLothers

CollectionsBRC

Species+

A bit of background information• Bergey’s Manual Trust

– Principal information source• Bergey’s Manual of Determinative Bacteriology• Bergey’s Manual of Systematic Bacteriology• Taxonomic Outline of the Procaryotes

A bit of background information• Bergey’s Manual Trust

– Principal information source• Bergey’s Manual of Determinative Bacteriology• Bergey’s Manual of Systematic Bacteriology• Taxonomic Outline of the Procaryotes

A bit of background information• Bergey’s Manual Trust

– Principal information source• Bergey’s Manual of Determinative Bacteriology• Bergey’s Manual of Systematic Bacteriology• Taxonomic Outline of the Procaryotes

– Expertise in content packaging/delivery• SGML/XML publishing

– The Systematics» XML compliant SGML instance

A bit of background information• Bergey’s Manual Trust

– Principal information source• Bergey’s Manual of Determinative Bacteriology• Bergey’s Manual of Systematic Bacteriology• Taxonomic Outline of the Procaryotes

– Expertise in content packaging/delivery• SGML/XML publishing

– The Systematics» XML compliant SGML instance

– The Outline» An experiment in SGML/XML publishing

A bit of background information• Bergey’s Manual Trust

– Principal information source• Bergey’s Manual of Determinative Bacteriology• Bergey’s Manual of Systematic Bacteriology• Taxonomic Outline of the Procaryotes

– Expertise in content packaging/delivery• SGML/XML publishing

– The Systematics» XML compliant SGML instance

– The Outline» An experiment in SGML/XML publishing

A bit of background information• Bergey’s Manual Trust

– Principal information source• Bergey’s Manual of Determinative Bacteriology• Bergey’s Manual of Systematic Bacteriology• Taxonomic Outline of the Procaryotes

– Expertise in content packaging/delivery• SGML/XML publishing

– The Systematics» XML compliant SGML instance

– The Outline» An experiment in SGML/XML publishing

– Derivative projects» Bergamot/N4L» The Determinative