the end of sensu&

what to do about taxonomy

Ontology content meetingGO

Apr 2007

GOApril 26, 2007 2

Two distinct but related projects

Part 1Elimination of taxon as a differentium

DesirabilityFeasibilityTimeline

Part 2Linking OBO terms to taxons

FrameworkShould GO do thisWhat to do about subsets?

GOApril 26, 2007 3

Taxon is not a good means of discriminating

Before:Taxon used in name and definition

cell wall (sensu Magnoliophyta)cell wall (sensu Bacteria)

After (ie now):Taxon eliminated from name and definition

cellulose and pectin-containing cell wallpeptidoglycan-based cell wall

(vestigial trace of taxonomic info in definitional gloss)

(old names retained as synonyms)Let’s call these “post-sensu terms” for the

purpose of this discussion

A more or less rigid stucture enclosing the protoplast of a cell and composed of

cellulose and pectin and other organic and inorganic substances. As in, but not

restricted to, the flowering plants (Magnoliophyta, ncbi_taxonomy_id:3398)

GOApril 26, 2007 4

Consensus check

Check: we all agree this is a good thing to do in principle?

Check: do we think this is possible to do for all current sensu terms?153 remaining to de-sensu-itizePut up difficult cases on sensu wiki page

E.g. gametogenesis in moss and fernDo we have any need for sensu as purely lexical

disambiguatorEg sensu-community; neurogenesis

Question: what (if anything) do we do about the taxonomic information?Currently being relegated to definition gloss.

GOApril 26, 2007 5

GO currently has some kind of association to taxons

In the OntologySubsets

Goslim_yeast Goslim_plant Gosubset_prok

Imprecisely defined associationSensu (now definitional gloss)

Semi-precisely defined (“as in, but not limited to…”)

In the AnnotationsVia gene products

Precisely defined (more or less)

GOApril 26, 2007 6

If GO terms are to have any kind of association to taxons then the meaning of that association should be clear

Meaning should be clear for annotationsMeaning is less clear for subsets and post-sensu

termsE.g. 417 unpropagated subsets

Intentional??

People are already using this information - and possibly in the wrong way

GOApril 26, 2007 7

position #1: No to taxa

If GO terms are to have any kind of association to taxons then the meaning of that association should be clearTherefore we should eliminate all

possible GO to taxon linksPhase out taxon slims/subsetsEliminate taxonomic info from definitional

gloss of post-sensu termsAnnotations are the only true sourceProblem solved!

GOApril 26, 2007 8

position #2 : Yes to some taxon links

If GO terms are to have any kind of association to taxons then the meaning of that association should be clearSome kind of taxonomic association is useful to

some peopleWith caveats

Therefore we should make this association clearWe need to define what it means to link a taxon to a term

Relevant_for Valid_for Specific_to Canonically_found_in ….

We should export our methods to other OBO ontologies

GOApril 26, 2007 9

Relevance (applicability)

Term relevant_for Taxon: Instances of Term found in some species of that

TaxonCurrent semantics for taxon-subsets?Current semantics of post-sensu taxon info?

Examples:peptidoglycan-based cell wall relevant_for BacteriaSuckling behaviour relevant_for Mammalia

This is a weak associationHatching relevant_for Mammalia

Because at least one Mammalian species has members that hatch

We can understatecell wall relevant_for Bacteria

(this is true but under-specified)

GOApril 26, 2007 10

Perhaps this is all we need for GO

But let’s look at some more

GOApril 26, 2007 11

specificity

Term specific_to Taxon: Instances of Term found only in Taxon

Examples:Apoplast specific_to ViridiplantaeSuckling behaviour specific_to Mammalia

We can err on the conservative side:Sucking behaviour specific_to Metazoa

Counter-examplesMaternal behaviour NOT specific_to Mammalia

GOApril 26, 2007 12

validity

Term valid_for Taxon:Instances of Term are found in some

organism of all sub-taxons of TaxonExamples

Suckling behaviour valid_for Mammalia(all Mammalian species suckle)

Trivially true:Biological process valid_for Viridiplantae

GOApril 26, 2007 13

As found in, but not restricted to

We are currently retaining this info in the gloss of the post-sensu termsE.g.

As in, but not restricted to, the flowering plants (Magnoliophyta, ncbi_taxonomy_id:3398)

Semantics same as relevant_forPerhaps stronger - we can say the Term

is exemplified in the TaxonIntended primarily for humans?

GOApril 26, 2007 14

Difficulties

Taxonomies are subject to revisionBiology keeps turning up surprises

But this is the same as any other part of GO?

GOApril 26, 2007 15

What should GO do?

Continue with eliminating taxa from names and definitions

What is our policy for taxon-subsets?Eliminate?At least formalize in terms of relevant_for?

What should we do about the taxonomic info consigned to definitional gloss?Get rid of it?Formalize it in terms of relevant_for, allowing it to be

used for dynamic slim-generation? Should we annotate other kinds of GO-taxon links?

Validity, specificity?

GOApril 26, 2007 16

Open questions

What are subsets/slims for anyway?

Are they dangerous?Eg annotations to “leaf sensescence”

would be mapped to biological_process if we use goslim_plant

Are there better ways of making them?Combination of annotations, specificity and

curated GO term <-> taxon associations

GOApril 26, 2007 17

Other OBO ontologies

Many OBO ontologies are using sensu in the old, bad wayMammalian PhenotypePlant anatomy

Other OBO ontologies are more entwined with phylogeny and homologyE.g. ZFIN CToL fish anatomy ontology

We want consistent usage across OBO

GOApril 26, 2007 18

Summary

Elimination of taxons from names and definitionAre we agreed?

What, if anything, do we do with the taxon information in the definitional gloss?

What is our policy on subsets/slims?GO should lead the way for (or at

least be consistent with) OBO