Taxonomic 'data' exchangeas

expression and synthesisof

phylogenetic claims

Jonathan A. ReesNational Evolutionary Synthesis Center

IevoBio, 25 June 2014

Synergy

CoL IRMNG NCBI GBIF EOL Union4 Treebase OpenTree...

Finding inconsistencies = goodbut 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 basedDescent basedConspecifcity 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 CA, B, C are mutually disjointX, 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)Mammalia sensu http://dx.doi.org/10.1126/science.1211028} = Mammalia sensu NCBI.20140515

Heuristics based on properties and relations (including names...)

Manual 'curation' if necessary

Incertae sedis

Confusing.

X is incertae sedis in 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'

'Rozella belongs in Fungi.'

'Rhodophyceae is the same as Rhodophyta.'

'SILVA's Morganella isn't the same as Index Fungorum's Morganella.''Anolis isn't a clade unless it is Norops is merged into it.'

Interpreting advice

“Rozella is in Fungi.”

Rozella sensu SILVA115 and Fungi sensu 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 Fungi sensu SILVA115.

Notation not so important, but for example -

includes(X, Y)

disjoint(A, B, C, …)

clade(X)

node(X, A, B, C, …) - abbreviationspecies(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 with sensu.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