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 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 grammar species -> 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, source sequence -> gene, sequence.deposit source -> exemplar|exemplar.deposit|text exemplar.deposit -> brc.id.pointer, deposit.id.pointer, source sequence.deposit -> brc.id.pointer, deposit.id.pointer, source phenotypic.feature -> feature.name, feature.value, deposit.id.pointer

Exemplar+ Sequence+ Name+ Taxon Species+

Exemplar+ Sequence+ Name+ Taxon Literature Governing bodies GenBank DDBJ EMBL others Collections BRC Species+

Taxon Exemplar+ Sequence+ Name+ Species+ Literature Governing bodies GenBank DDBJ EMBL others Collections BRC Practitioner + genotypic “omics” Proposal STM Legal Databases Priority Validity Synonymy Exemplar req. phenotypic direct indirect BRC PublicPrivate General

Exemplar+ Sequence+ Name+ Species+ A properly formed species Sequence+ Name+ Species+ Candidatus or exemplar lost Sequence+ Environmental sequence Exemplar+ Name+ Species+ Old type strain, not yet sequenced Name+ Species+ Old type, exemplar based on drawing or description Sequence+ “Name”+ Misidentifed taxon Exemplar*

Exemplar+ Sequence+ Name+ Taxon N4L/Bergamot Literature Governing bodies GenBank DDBJ EMBL others Collections BRC 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