the end of sensu & what to do about taxonomy Ontology content meeting GO Apr 2007
Two distinct but related projects <ul><li>Part 1 </li></ul><ul><ul><li>Elimination of taxon as a  differentium </li></ul><...
Taxon is not a good means of discriminating <ul><li>Before: </li></ul><ul><ul><li>Taxon used in name and definition </li><...
Consensus check <ul><li>Check: we all agree this is a good thing to do in principle? </li></ul><ul><li>Check: do we think ...
GO currently has  some kind of association  to taxons <ul><li>In the  Ontology </li></ul><ul><ul><li>Subsets </li></ul></u...
<ul><li>If  GO terms are to have any kind of association to taxons  then  the meaning of that association should be clear ...
position #1: No to taxa <ul><li>If  GO terms are to have any kind of association to taxons  then  the meaning of that asso...
position #2 : Yes to some taxon links <ul><li>If  GO terms are to have any kind of association to taxons  then  the meanin...
Relevance (applicability) <ul><li>Term  relevant_for  Taxon: </li></ul><ul><ul><li>Instances of Term found in  some  speci...
<ul><li>Perhaps this is all we need for GO </li></ul><ul><li>But let’s look at some more </li></ul>
specificity <ul><li>Term  specific_to  Taxon: </li></ul><ul><ul><li>Instances of Term found  only  in Taxon </li></ul></ul...
validity <ul><li>Term  valid_for  Taxon: </li></ul><ul><ul><li>Instances of Term are found in some organism of all sub-tax...
As found in, but not restricted to <ul><li>We are currently retaining this info in the  gloss  of the post-sensu terms </l...
Difficulties <ul><li>Taxonomies are subject to revision </li></ul><ul><li>Biology keeps turning up surprises </li></ul><ul...
What should GO do? <ul><li>Continue with eliminating taxa from names and definitions </li></ul><ul><li>What is our policy ...
Open questions <ul><li>What are subsets/slims for anyway? </li></ul><ul><li>Are they dangerous? </li></ul><ul><ul><li>Eg a...
Other OBO ontologies <ul><li>Many OBO ontologies are using sensu in the old, bad way </li></ul><ul><ul><li>Mammalian Pheno...
Summary <ul><li>Elimination of taxons from names and definition </li></ul><ul><ul><li>Are we agreed? </li></ul></ul><ul><l...
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GO Sensu Term and Taxonomy (Apr 2007)

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recommendations for linking terms to taxons in GO and OBO

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  • And I’m going to be as dry and impersonal as possible. This is a purely technical talk. Mark gave his personal views and admitted to being confused I’m not sleeping either. We want very much to work together. Ontology development is about collaboration.
  • GO Sensu Term and Taxonomy (Apr 2007)

    1. 1. the end of sensu & what to do about taxonomy Ontology content meeting GO Apr 2007
    2. 2. Two distinct but related projects <ul><li>Part 1 </li></ul><ul><ul><li>Elimination of taxon as a differentium </li></ul></ul><ul><ul><ul><li>Desirability </li></ul></ul></ul><ul><ul><ul><li>Feasibility </li></ul></ul></ul><ul><ul><ul><li>Timeline </li></ul></ul></ul><ul><li>Part 2 </li></ul><ul><ul><li>Linking OBO terms to taxons </li></ul></ul><ul><ul><ul><li>Framework </li></ul></ul></ul><ul><ul><ul><li>Should GO do this </li></ul></ul></ul><ul><ul><ul><li>What to do about subsets? </li></ul></ul></ul>
    3. 3. Taxon is not a good means of discriminating <ul><li>Before: </li></ul><ul><ul><li>Taxon used in name and definition </li></ul></ul><ul><ul><ul><li>cell wall (sensu Magnoliophyta) </li></ul></ul></ul><ul><ul><ul><li>cell wall (sensu Bacteria) </li></ul></ul></ul><ul><li>After (ie now): </li></ul><ul><ul><li>Taxon eliminated from name and definition </li></ul></ul><ul><ul><ul><li>cellulose and pectin-containing cell wall </li></ul></ul></ul><ul><ul><ul><li>peptidoglycan-based cell wall </li></ul></ul></ul><ul><ul><li>(vestigial trace of taxonomic info in definitional gloss ) </li></ul></ul><ul><ul><li>(old names retained as synonyms) </li></ul></ul><ul><ul><li>Let’s call these “ post-sensu terms ” for the purpose of this discussion </li></ul></ul>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 )
    4. 4. Consensus check <ul><li>Check: we all agree this is a good thing to do in principle? </li></ul><ul><li>Check: do we think this is possible to do for all current sensu terms? </li></ul><ul><ul><li>153 remaining to de-sensu-itize </li></ul></ul><ul><ul><li>Put up difficult cases on sensu wiki page </li></ul></ul><ul><ul><ul><li>E.g. gametogenesis in moss and fern </li></ul></ul></ul><ul><ul><li>Do we have any need for sensu as purely lexical disambiguator </li></ul></ul><ul><ul><ul><li>Eg sensu-community; neurogenesis </li></ul></ul></ul><ul><li>Question: what (if anything) do we do about the taxonomic information? </li></ul><ul><ul><li>Currently being relegated to definition gloss . </li></ul></ul>
    5. 5. GO currently has some kind of association to taxons <ul><li>In the Ontology </li></ul><ul><ul><li>Subsets </li></ul></ul><ul><ul><ul><ul><li>Goslim_yeast </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Goslim_plant </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Gosubset_prok </li></ul></ul></ul></ul><ul><ul><ul><li>Imprecisely defined association </li></ul></ul></ul><ul><ul><li>Sensu (now definitional gloss) </li></ul></ul><ul><ul><ul><li>Semi-precisely defined </li></ul></ul></ul><ul><ul><ul><ul><li>(“as in, but not limited to…”) </li></ul></ul></ul></ul><ul><li>In the Annotations </li></ul><ul><ul><li>Via gene products </li></ul></ul><ul><ul><ul><li>Precisely defined (more or less) </li></ul></ul></ul>
    6. 6. <ul><li>If GO terms are to have any kind of association to taxons then the meaning of that association should be clear </li></ul><ul><ul><li>Meaning should be clear for annotations </li></ul></ul><ul><ul><li>Meaning is less clear for subsets and post-sensu terms </li></ul></ul><ul><ul><ul><li>E.g. 417 unpropagated subsets </li></ul></ul></ul><ul><ul><ul><ul><li>Intentional?? </li></ul></ul></ul></ul><ul><ul><li>People are already using this information - and possibly in the wrong way </li></ul></ul>
    7. 7. position #1: No to taxa <ul><li>If GO terms are to have any kind of association to taxons then the meaning of that association should be clear </li></ul><ul><ul><li>Therefore we should eliminate all possible GO to taxon links </li></ul></ul><ul><ul><ul><li>Phase out taxon slims/subsets </li></ul></ul></ul><ul><ul><ul><li>Eliminate taxonomic info from definitional gloss of post-sensu terms </li></ul></ul></ul><ul><ul><ul><li>Annotations are the only true source </li></ul></ul></ul><ul><ul><ul><li>Problem solved! </li></ul></ul></ul>
    8. 8. position #2 : Yes to some taxon links <ul><li>If GO terms are to have any kind of association to taxons then the meaning of that association should be clear </li></ul><ul><ul><li>Some kind of taxonomic association is useful to some people </li></ul></ul><ul><ul><ul><li>With caveats </li></ul></ul></ul><ul><ul><li>Therefore we should make this association clear </li></ul></ul><ul><ul><ul><li>We need to define what it means to link a taxon to a term </li></ul></ul></ul><ul><ul><ul><ul><li>Relevant_for </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Valid_for </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Specific_to </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Canonically_found_in </li></ul></ul></ul></ul><ul><ul><ul><ul><li>… . </li></ul></ul></ul></ul><ul><ul><li>We should export our methods to other OBO ontologies </li></ul></ul>
    9. 9. Relevance (applicability) <ul><li>Term relevant_for Taxon: </li></ul><ul><ul><li>Instances of Term found in some species of that Taxon </li></ul></ul><ul><ul><li>Current semantics for taxon-subsets? </li></ul></ul><ul><ul><li>Current semantics of post-sensu taxon info? </li></ul></ul><ul><li>Examples: </li></ul><ul><ul><ul><li>peptidoglycan-based cell wall relevant_for Bacteria </li></ul></ul></ul><ul><ul><ul><li>Suckling behaviour relevant_for Mammalia </li></ul></ul></ul><ul><li>This is a weak association </li></ul><ul><ul><li>Hatching relevant_for Mammalia </li></ul></ul><ul><ul><ul><li>Because at least one Mammalian species has members that hatch </li></ul></ul></ul><ul><ul><li>We can understate </li></ul></ul><ul><ul><ul><li>cell wall relevant_for Bacteria </li></ul></ul></ul><ul><ul><ul><ul><li>(this is true but under-specified) </li></ul></ul></ul></ul>
    10. 10. <ul><li>Perhaps this is all we need for GO </li></ul><ul><li>But let’s look at some more </li></ul>
    11. 11. specificity <ul><li>Term specific_to Taxon: </li></ul><ul><ul><li>Instances of Term found only in Taxon </li></ul></ul><ul><li>Examples: </li></ul><ul><ul><li>Apoplast specific_to Viridiplantae </li></ul></ul><ul><ul><li>Suckling behaviour specific_to Mammalia </li></ul></ul><ul><li>We can err on the conservative side: </li></ul><ul><ul><li>Sucking behaviour specific_to Metazoa </li></ul></ul><ul><li>Counter-examples </li></ul><ul><ul><li>Maternal behaviour NOT specific_to Mammalia </li></ul></ul>
    12. 12. validity <ul><li>Term valid_for Taxon: </li></ul><ul><ul><li>Instances of Term are found in some organism of all sub-taxons of Taxon </li></ul></ul><ul><li>Examples </li></ul><ul><ul><li>Suckling behaviour valid_for Mammalia </li></ul></ul><ul><ul><ul><li>(all Mammalian species suckle) </li></ul></ul></ul><ul><li>Trivially true: </li></ul><ul><ul><li>Biological process valid_for Viridiplantae </li></ul></ul>
    13. 13. As found in, but not restricted to <ul><li>We are currently retaining this info in the gloss of the post-sensu terms </li></ul><ul><ul><li>E.g. </li></ul></ul><ul><li>As in, but not restricted to, the flowering plants </li></ul><ul><li>(Magnoliophyta, ncbi_taxonomy_id:3398 ) </li></ul><ul><li>Semantics same as relevant_for </li></ul><ul><ul><li>Perhaps stronger - we can say the Term is exemplified in the Taxon </li></ul></ul><ul><li>Intended primarily for humans? </li></ul>
    14. 14. Difficulties <ul><li>Taxonomies are subject to revision </li></ul><ul><li>Biology keeps turning up surprises </li></ul><ul><li>But this is the same as any other part of GO? </li></ul>
    15. 15. What should GO do? <ul><li>Continue with eliminating taxa from names and definitions </li></ul><ul><li>What is our policy for taxon-subsets? </li></ul><ul><ul><li>Eliminate? </li></ul></ul><ul><ul><li>At least formalize in terms of relevant_for? </li></ul></ul><ul><li>What should we do about the taxonomic info consigned to definitional gloss? </li></ul><ul><ul><li>Get rid of it? </li></ul></ul><ul><ul><li>Formalize it in terms of relevant_for, allowing it to be used for dynamic slim-generation? </li></ul></ul><ul><li>Should we annotate other kinds of GO-taxon links? </li></ul><ul><ul><li>Validity, specificity? </li></ul></ul>
    16. 16. Open questions <ul><li>What are subsets/slims for anyway? </li></ul><ul><li>Are they dangerous? </li></ul><ul><ul><li>Eg annotations to “leaf sensescence” would be mapped to biological_process if we use goslim_plant </li></ul></ul><ul><li>Are there better ways of making them? </li></ul><ul><ul><li>Combination of annotations, specificity and curated GO term <-> taxon associations </li></ul></ul>
    17. 17. Other OBO ontologies <ul><li>Many OBO ontologies are using sensu in the old, bad way </li></ul><ul><ul><li>Mammalian Phenotype </li></ul></ul><ul><ul><li>Plant anatomy </li></ul></ul><ul><li>Other OBO ontologies are more entwined with phylogeny and homology </li></ul><ul><ul><li>E.g. ZFIN CToL fish anatomy ontology </li></ul></ul><ul><li>We want consistent usage across OBO </li></ul>
    18. 18. Summary <ul><li>Elimination of taxons from names and definition </li></ul><ul><ul><li>Are we agreed? </li></ul></ul><ul><li>What, if anything, do we do with the taxon information in the definitional gloss? </li></ul><ul><li>What is our policy on subsets/slims? </li></ul><ul><li>GO should lead the way for (or at least be consistent with) OBO </li></ul>

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