GO Sensu Terms and Taxonomy -- Apr 2007


Published on

New recommendations on linking terms to taxons in GO and OBO

Published in: Economy & Finance, Education
1 Comment
  • This presentation was an informal internal GO presentation which may be of some use to the OBO community. The slides do not credit Waclaw Kusnierczyk, who proposed the formalism for the term-taxon linkage (Waclaw was present during the presentation)
    Are you sure you want to  Yes  No
    Your message goes here
  • Be the first to like this

No Downloads
Total Views
On Slideshare
From Embeds
Number of Embeds
Embeds 0
No embeds

No notes for slide
  • 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 Terms 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>
    1. A particular slide catching your eye?

      Clipping is a handy way to collect important slides you want to go back to later.