Comments (5)
See also: geneontology/noctua#788
from noctua-landing-page.
@tmushayahama I think adding the following fq
fixes this:
OR is_obsolete:true
I.e.:
http://noctua-golr.berkeleybop.org/select?defType=edismax&indent=on&qt=standard&wt=json&rows=50&start=0&packet=1&callback_type=search&qf=annotation_class^3&qf=annotation_class_label_searchable^5.5&qf=description_searchable^1&qf=comment_searchable^0.5&qf=synonym_searchable^1&qf=alternate_id^1&qf=isa_closure^1&qf=isa_closure_label_searchable^1&_=1682010874400&fq=document_category:%22ontology_class%22&fq=isa_closure:%22GO:0003674%22%20OR%20isa_closure:%22GO:0008150%22%20OR%20isa_closure:%22GO:0005575%22%20OR%20isa_closure:%22GO:0044848%22%20OR%20isa_closure:%22CARO:0000000%22%20OR%20isa_closure:%22CL:0000003%22%20OR%20isa_closure:%22UBERON:0000105%22%20OR%20is_obsolete:true&q=obsol*&json.wrf=ng_jsonp_callback_0
from noctua-landing-page.
@kltm Thank you, yes it works now
from noctua-landing-page.
Something weird is happening with the search results. I searched on 'obsolete regulation of cell death' from the landing page on Noctua-dev. The search returned models that look like they have nodes that USED TO BE children of this term. For example:
- The search returns gomodel:60418ffa00001019 which has 'regulation of programmed cell death' nodes.
- The search returns gomodel:5ce58dde00001215 which has a 'negative regulation of intrinsic apoptotic signaling pathway' node.
- The search returns gomodel:613aae0000000813 which has 'negative regulation of hepatocyte apoptotic process' nodes.
This is strange behavior because these terms should no longer be is_a children of an obsolete term. Is there a synchronization issue on Noctua-dev?
from noctua-landing-page.
Tested again on 2023-05-18 Noctua workbenches call.
Updating the ontology on noctua-dev fixed the issue @ukemi reported above.
Searching for an obsolete term now returns the expected results.
Okay to move into production.
from noctua-landing-page.
Related Issues (20)
- Getting all annotations to an obsolete term in a single search HOT 1
- Browse by Species field is wrong size HOT 1
- Standardize Organism filter
- Add option or default to search over 'regulates' for 'Filter by Term' for models
- Add reference input helper popup
- add ability to filter on model id from the landing page HOT 14
- add expand/collapse option to landing page to quickly scan annotations in models HOT 1
- Figure out a way to limit what groups are listed on the landing page HOT 2
- SARS-CoV2 is listed as a blank entry in the browse species list HOT 14
- Model state not displaying on landing page for a particular model HOT 5
- Add columns and icons for 'errors' and 'unsaved' model-level metadata HOT 1
- Consider adding an 'announcements' banner HOT 4
- Organisms on the autocomplete not displaying HOT 3
- Protein-containing complex (GO:0032991) and children no longer available in term search autocomplete HOT 2
- New bug in mousing over form and graph icons HOT 1
- Add Pathway Editor icon to the Open In menu on the Noctua landing page HOT 1
- Blank entries at the top of the list for Organism filter HOT 13
- Save functionality under the Model Info section is not working HOT 1
- "exact term" is no longer default
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