Taxonomic 'data' exchange as expression and synthesis of phylogenetic claimsRees claims-ievobio2014
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Taxonomic 'data' exchange as expression and synthesis of phylogenetic claimsRees claims-ievobio2014

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'Slides' from a 5-minute presentation at iEvoBio 2014.

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Taxonomic 'data' exchange as expression and synthesis of phylogenetic claimsRees claims-ievobio2014 Taxonomic 'data' exchange as expression and synthesis of phylogenetic claimsRees claims-ievobio2014 Presentation Transcript

  • Taxonomic 'data' exchange as expression and synthesis of phylogenetic claims Jonathan A. Rees National Evolutionary Synthesis Center IevoBio, 25 June 2014
  • Synergy CoL IRMNG NCBI GBIF EOL Union4 Treebase OpenTree... Finding inconsistencies = good but hard Collecting information is useful
  • 'Data' – BAH! 'data' 'information' 'representation' 'format' 'nomenclature' - how bland. Distracting. Claims, not data. Consequential.
  • Terminology Taxon: a set determined by a membership rule. ['taxon concept'] Character based Descent based Conspecifcity based Taxonomy: a collection of taxa that form a hierarchy. Some taxonomies are phylogenetic (all clades).
  • Taxonomies are collections of claims X A B C X includes A, B, and C A, B, C are mutually disjoint X, A, B, and C are clades - if phylogenetic.
  • The important claims are about biology X includes Y X1, X2, X3, … are mutually disjoint X is a clade X is a species
  • We have to designate taxa somehow, when we express a claim Many taxon names are polysemous To be clear, always say 'in the sense of' some static document (article or database snapshot) X = Mammalia sensu http://dx.doi.org/10.1126/science.1211028 If used multiple ways in some document, give further qualifcation Claims about taxa
  • Reasoning with claims X includes Y and Y includes Z → X includes Z X includes Y → X and Y are not disjoint X and Y are clades → one includes the other, or they are disjoint
  • Two ways to be wrong Wrong about designation Wrong about science
  • 'Alignment' = estimating coreference Alignment claims: X = Y (X and Y are the same taxon) Mammaliasensu http://dx.doi.org/10.1126/science.1211028} = MammaliasensuNCBI.20140515 Heuristics based on properties and relations (including names...) Manual 'curation' if necessary
  • Incertae sedis Confusing. X is incertae sedisin A means (1) A includes X (2) it's not known which of A's non-incertae- sedis'children' X belongs to, if any (2) is not a claim about biology. Logical content = (1).
  • 'Data exchange' Taxonomies - NP
  • Exchanging 'corrections' 'Rozellabelongs in Fungi.' 'Rhodophyceae is the same as Rhodophyta.' 'SILVA'sMorganellaisn't the same as Index Fungorum'sMorganella.' 'Anolisisn't a clade unless it isNoropsis merged into it.'
  • Interpreting advice “Rozellais in Fungi.” Rozella sensuSILVA115 and Fungisensu SILVA115 belong to a clade disjoint from the other SILVA115 children of Nucletmycea. How about let's apply the label 'Fungi' to such a clade and not to Fungisensu SILVA115.
  • Notation not so important, but for example - includes(X, Y) disjoint(A, B, C, …) clade(X) node(X, A, B, C, …) - abbreviation species(X) same(X, Y) notSame(X, Y) sensu('Name', source) + nomenclatural claims
  • On and on Synthesis Identifer stability Alignment details Compare 'macrotaxonomy' and 'microtaxonomy' Defense of scrufy Compare Rod's github proposal Philosophy of language
  • Separate science from nomenclature. Use logic to do science. Always use names withsensu. Use heuristics to prevent paralysis. Don't 'represent data' – express claims! https://github.com/OpenTreeOfLife/reference-taxonomy/wiki/Expressing-phylogenetic-claims Bottom line
  • Ack Nico Franz, David Thau, Rod Page Open Tree: Karen Cranston, Stephen Smith, Mark Holder, and legions of others Gerald Jay Sussman Jonathan A. Rees 2014 Copyright waived CC0 1.0