cmungall
commented
16 years ago Logged In: YES user_id=254723 Originator: NO
see also http://www.obofoundry.org/wiki/index.php/Species\_specificity
Original comment by: cmungall
Open cmungall opened 17 years ago
cmungall
commented
16 years ago Logged In: YES user_id=254723 Originator: NO
see also http://www.obofoundry.org/wiki/index.php/Species\_specificity
Original comment by: cmungall
cmungall
commented
16 years ago Logged In: YES user_id=254723 Originator: NO
see also http://www.obofoundry.org/wiki/index.php/Species\_specificity
Original comment by: cmungall
cmungall
commented
16 years ago Logged In: YES user_id=1509142 Originator: NO
Thanks for the advance notification! Is there any ETA / expected timeline for this change?
Original comment by: ohofmann
cmungall
commented
9 years ago Original comment by: nicolevasilevsky
cmungall
commented
9 years ago this ticket should be moved to the github tracker
Original comment by: nicolevasilevsky
paolaroncaglia
commented
2 years ago There are still plenty of 'sensu' terms in CL, so I presume we wouldn't wish to close this ticket.
ghost
commented
1 year ago @cmungall, @dosumis, currently this is the most ancient open ticket in CL. It looks like there are around 50 CL class labels that end in (sensu %).
Can either of you kindly advise if this ticket is something you would like to either prioritise and pursue, close, or keep in the backlog?
ghost
commented
10 months ago To facilitate discussion and determine action items, below are the 48 current classes in CL that contain "sensu" in the label and are not obsolete. At least these labels should be updated to follow the current label standard of '{cell label}, {taxon}'.
For example, 'hemocyte (sensu Arthropoda)' would become 'hemocyte, arthropod' and CNS neuron (sensu Nematoda and Protostomia)' would become 'CNS neuron, protostome'.
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT DISTINCT ?entity ?label WHERE
{
VALUES ?property {
rdfs:label
}
?entity rdfs:isDefinedBy <http://purl.obolibrary.org/obo/cl.owl> .
?entity ?property ?label .
FILTER NOT EXISTS {FILTER contains (?label, "obsolete") }
FILTER contains (?label, "sensu")
}
ORDER BY ?label
It is likely that the GO terms containing sensu will be obsoleted, merged, or renamed and that taxon specific information will be captured by some other mechanism. This should also be done for the cell ontology.
What this means is that for each cell type containing a sensu in the name, it should be determined if the term has a different definition than its parent. If true, then it may need a new name and perhaps a sibling. If not, then it may be appropriate to merge the parent and child.
This has become an issue for ZFIN due to our cell slurp. For example, we need to annotate to neuroblast (sensu vertebrata). Does this mean we should import the parent, neuroblast as well? we'd never use the term for annotation. It looks funny to have a term here called neuroblast (sensu vertebrata), so we'd have to rename it just neuroblast. This seems silly. Really the information regarding taxa is already there - its a zebrafish neuroblast.
Request forthcoming from Doug Howe with regard to this particular example.
I just wanted to put on our (long) list of to do items the general cleanup of the sensu terms.
Thanks, melissa
Original comment by: mellybelly