1 / 24

Imagine..

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

rashad-morin
Download Presentation

Imagine..

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Biological nomenclature in the postgenomic era: Biological and computational issues.George Garrity and Catherine LyonsBergey’s Manual Trust and Explicatrix, LLC

  2. 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…

  3. 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?

  4. 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

  5. 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

  6. Problems in nomenclature (cont.) • 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. Name+ Taxon Species+ Exemplar+ Sequence+

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

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

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

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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

More Related