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GO Sensu Terms and Taxonomy -- Apr 2007
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Transcript of GO Sensu Terms and Taxonomy -- Apr 2007
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