[InterMine Dev] phenotype annotations are on either GO terms or Anatomy terms

Sierra Moxon staylor at cs.uoregon.edu
Tue Aug 25 17:01:31 BST 2009


Hi Julie-

I hope I have an easy modeling question for you: at ZFIN, phenotype 
annotations are associated either with an anatomical structure or a GO 
term (its a little more complicated than than, phenotypes are 
actually associated with compound terms so we can say things like "cell 
elongation of the neuron" where 'cell elongation' is a GO term and 
'neuron' is a cell/AO term).

For better or worse, the table that holds these annotations has one 
column that can contain either a GO termid or an AO termid.  It makes 
sense for us to treat all ontologies in the db the same (ie: storing all 
ontology terms in one table, for example, and then storing relationships 
between ontologies in another table that hangs off the term table).  Since 
there eventually should be links between ontologies (see: 
http://www.bioontology.org/wiki/index.php/RO:Main_Page), it makes sense 
for us to do it this way.  Could be that it changes in 
the future though, as the relation ontology grows.

On a more practical level, at ZFIN, we use interface code to provide 
the appropriate links/names to each of the respective ontologies.  Is 
there interface code that can do that for intermine?

How would you model it?

Thanks,
Sierra



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