obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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Close all stalled issues? #1234

Closed gouttegd closed 2 years ago

gouttegd commented 3 years ago

From the CL meeting on August 18th, 2021:

Shall we automatically close existing issues that have not been updated in the past 3 years, as we have recently done for Uberon?

If so:

For information, as of today there are 182 issues that have not seen any update in the last 3 years.

CL editors who were not present in the August 18th meeting are invited to weigh in.

shawntanzk commented 3 years ago

Think 3 years is a good amount of time :)

paolaroncaglia commented 3 years ago

Shall we automatically close existing issues that have not been updated in the past 3 years, as we have recently done for Uberon?

If so:

* [ ]  Shall an editor do a pass on those issues before we trigger the closing script, to protect some worthy issues from auto-closing (again similar to what we have done for Uberon)?

* [ ]  Should we use the same age threshold as for Uberon (3 years)?

For information, as of today there are 182 issues that have not seen any update in the last 3 years.

I had a quick glance at some of those 182 tickets. At least some of them look worthy of consideration before auto-closing en masse. E.g., several tickets look neuron-related, so may be in scope for specific funded projects. Other may be in scope for the Human Cell Atlas. Others still may have been addressed, or out of date, or ok to close anyway. If we're willing/able to put in a bit of our time, we could split say the 100 oldest tickets among as many of us as possible and take a quick look? Even 5-10 minutes per ticket would make a difference, even if we can't fully address all requests. Then apply Damien's workflow on what's left. And repeat once per quarter?

shawntanzk commented 3 years ago

Happy to do so :) I've seen some of the neuro ones and think they can probably be closed (or maybe some discussion continuing that imo is secondary) - havent done so just cause if we are going to implement the above, it might be better use the automated thing to ping the people assigned on them to see if they have anything else to add/change. Happy to split tickets and go through instead :)

paolaroncaglia commented 3 years ago

(...) it might be better use the automated thing to ping the people assigned on them to see if they have anything else to add/change.

Unfortunately, most old tickets are unassigned, and the "creator" is mostly GoogleCodeExporter (or Chris when he migrated issues from SourceForge). So the automated message will go, broadly, to anyone monitoring the CL tracker. But that's probably ok - we're cleaning up the tracker a little anyway. :-)

gouttegd commented 2 years ago

We are now at 117 issues that would be closed with a threshold set at 3 years.

I propose to give us one more month to check some more of those issues (and either fix them directly or at least tag them or comment on them — anything to mark them as "active"), and then by the end of October I unleash the auto-closing script.

Would everyone be happy with that?

gouttegd commented 2 years ago

For reference, here are the issues that would be closed as of today:

Issue Author Team? Assignee(s)
Define strategy for handling new proposed cell types derived from clustering transcriptomic and other data @cmungall Yes
Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes @cmungall Yes
suppressor macrophage @cmungall Yes @addiehl
fibrocyte @cmungall Yes
kidney interstitial cell subtypes @cmungall Yes
glomerular mesangial cell @cmungall Yes
renal interstitial pericyte @cmungall Yes
KCD renal intercalated cell @cmungall Yes
Proposal: obsolete meso/metanephros subtypes for many kidney cell types @cmungall Yes
"juxtaglomerular complex cell" is an unintuitive group @cmungall Yes @addiehl
Add is_a edge between CL:0000451 and CL:0000145 @mbernste No
Add icon images from Reactome @cmungall Yes
Add synonym 'Treg' for term CL:0000815 @mbernste No
Add edge CL:0008001 is_a CL:0011115 @mbernste No
Bad ZFA mappings @balhoff Yes
Fibro/adipogenic progenitors @Alessandro-Palma No
peripheral blood @tuli No
Faulty term ID in obo file for 'alobate nucleus' @cmpich No
Two term stanza do not have a name tag in the obo file @cmpich No
No default-namespace in obo file header @cmpich No
Distribute nif_import.owl in RDF/XML? @jonathanbona No
lacks part relation @lgcowell No
create mapping of CL to NCIt cell classes @nicolevasilevsky Yes @cmungall
adipocyte (white/brown/beige) classification, definitions and axioms @cmungall Yes
NTR: annulus fibrosus cell @jahilton Yes
NTR: HFF-Myc @jahilton Yes
Definition update for CL_0000178 @cerivs Yes
Fix import generation @cmungall Yes
Ensure correct annotation properties are always used @cmungall Yes @cmungall
'female germ cell' not capable of oogenesis relationship @dosumis Yes
Update CL xrefs to species-specific AOs @cmungall Yes
vestibular afferent neuron @dosumis Yes
Cede fungal cell types to FAO @cmungall Yes
Are APUD (amine precursor uptake and decarboxylation) cells always NC-derived? @cmungall Yes @cerivs, @ybradford
NTRs @jahilton Yes @addiehl
neutrophil CL:0000775 logical definition @cerivs Yes
linking CL terms to UBERON terms @jahilton Yes
NTR: keratinized cell of hair follicle @YasminAF No @dosumis
Use a consistent obo-namespace tag in obo format exports @cmungall Yes @cmungall
temporal relation used in CL @GoogleCodeExporter No
CL_0008023 is a replaced term @GoogleCodeExporter No
missing classifications under "animal cell" and "eukaryotic cell" @GoogleCodeExporter No
Classification under 'somatic cell' @GoogleCodeExporter No
Failed to parse cl.obo due to a loop in the term relationships: StackOverflowError @GoogleCodeExporter No
Fix def of granulosa cell @GoogleCodeExporter No
NTRs for 'adult Leydig cell' and for 'fetal Leydig cell', possibly split or relabel existing CL:0000178 @GoogleCodeExporter No
cholangiocte improvements @GoogleCodeExporter No
NTR: otic epithelial cell @GoogleCodeExporter No
NTR: anterior visceral endoderm cell @GoogleCodeExporter No
olfactory epithelium cells @GoogleCodeExporter No
Hepatic pit cell @GoogleCodeExporter No
intraepithelial cells @GoogleCodeExporter No
NTR: @GoogleCodeExporter No
'visual pigment cell' needs definition @GoogleCodeExporter No
melanocyte should not be a subclass of neurecto-epithelial cell @GoogleCodeExporter No
Add part_of axioms for horizontal cel @GoogleCodeExporter No
NTR: Segmented neutrophil in Bone marrow @GoogleCodeExporter No
Review precursor B-Cell and its subclasses, proposing parallel minimal commitment EC axioms @GoogleCodeExporter No
NTR: CD8/CD4 positive T cell @GoogleCodeExporter No
cl-plus-fbbt is incoherent @GoogleCodeExporter No
Add MESH xrefs @GoogleCodeExporter No
Project: Review all cases where cell types have multiple develops_from relatiionships @GoogleCodeExporter No
Project: separate out developmental precursor cells from stem cell heirarchy @GoogleCodeExporter No
Proposal for segregating marker axioms in CL @GoogleCodeExporter No
mesenchymal cell / mesenchymal stem cell (CL_0000134) @GoogleCodeExporter No
cardioblast has no relationship to 'cardiac muscle myoblast' @GoogleCodeExporter No
Consider adding axiom: glandular epithelial cells are columnar/cuboidal @GoogleCodeExporter No
NTR: mature dendritic cell @GoogleCodeExporter No
add part_of relation in CL:0000066 and in CL:0000586 @GoogleCodeExporter No
Should a "naive regulatory T cell" be is_a "regulatory T cell"? @GoogleCodeExporter No
(flowCL project) CD11c in "myeloid dendritic cell, human" @GoogleCodeExporter No
(flowCL project) Lacks pmp “C-X-C chemokine receptor type 3” missing in "Tc17 cell" @GoogleCodeExporter No
(flowCL project) Lacks pmp “low affinity immunoglobulin gamma Fc region receptor III” missing in "myeloid dendritic cell, human" @GoogleCodeExporter No
(flowCL project) Lacks pmp “CD14 molecule” missing in "myeloid dendritic cell, human" @GoogleCodeExporter No
(flowCL project) Lacks pmp “low affinity immunoglobulin gamma Fc region receptor III” missing in "plasmacytoid dendritic cell, human" @GoogleCodeExporter No
(flowCL project) Lacks pmp “CD14 molecule” missing in "plasmacytoid dendritic cell, human" @GoogleCodeExporter No
(flowCL project) Lacks pmp “low affinity immunoglobulin gamma Fc region receptor III” missing in "dendritic cell, human" @GoogleCodeExporter No
(flowCL project) Lacks pmp “CD14 molecule” missing in "dendritic cell, human" @GoogleCodeExporter No
NTR: 3 new terms @GoogleCodeExporter No
Ensure FBbt xrefs are up to date @GoogleCodeExporter No
new term proposal catecholaminergic neuron @GoogleCodeExporter No
Create importer that brings plant and animal cells into same ontology @GoogleCodeExporter No
Create strategy for maintaining axioms connecting ssAOs to CL @GoogleCodeExporter No
merge egg (cell) and female gamete @GoogleCodeExporter No
New neuron grouping term/cell types. @GoogleCodeExporter No
rename 'skeletal muscle cell' to 'cell of skeletal muscle' ?? @GoogleCodeExporter No
NTR: intestinal stem cell @GoogleCodeExporter No
"lacks" relations as object properties (between individuals) are not meaningful: @GoogleCodeExporter No
relabel 'phenotype' classes @GoogleCodeExporter No
remove in appropriate Schwann cell syns @GoogleCodeExporter No
Review request: basic muscle cell hierarchy @GoogleCodeExporter No
NTR: undifferentiated osteoblast @GoogleCodeExporter No
Update label for CL:0002000 @GoogleCodeExporter No
NTR: antigen-presenting cell @GoogleCodeExporter No
use IAO replaced_by property for obsoletes @GoogleCodeExporter No
adding support for evidence codes to CL @GoogleCodeExporter No
peripheral ganglia should have neruon that they are part of @GoogleCodeExporter No
Align thymocyte / DN T Cell with MP @GoogleCodeExporter No
axioms of pancreas related cell types @GoogleCodeExporter No
NTR: electrocyte @GoogleCodeExporter No
CL:1000409 'myocyte of sinoatrial node' vs CL:1000477 'cardiac pacemaker cell of sinoatrial node' @GoogleCodeExporter No
CL:0002339 'prostate stem cell' vs CL:0002341 'basal cell of prostate epithelium' @GoogleCodeExporter No
merge CL:1000416 'myoepithelial cell of lactiferous gland' into CL:0002324 'myoepithelial cell of mammary gland' @GoogleCodeExporter No
Adopt common naming conventions for compositional terms @GoogleCodeExporter No
NTRs: subclasses of blastoderm cell @GoogleCodeExporter No
NTR: Koniocellular cell @GoogleCodeExporter No
mesenchymal cell @GoogleCodeExporter No
Cell type terms required by GO @GoogleCodeExporter No
PATO differentium for non-terminallly differentiated cell @GoogleCodeExporter No
displaced (inverted) amacrine cell @cmungall Yes @cmungall
lacks_part and lacks_plasma_membrane_part @cmungall Yes @cmungall
CL:0000432 ! reticular cell - definition @cmungall Yes @cmungall
CL:0002520 ! nephrocyte @cmungall Yes @cmungall
CL:0000746 ! A myocyte located in the heart. The contractile @cmungall Yes @cmungall
NTR: endothelial progenitor cell @cmungall Yes @cmungall
CL to AO part_of links @cmungall Yes @cmungall
sensu terms @cmungall Yes @cmungall
addiehl commented 2 years ago

Is adding a new label enough to spare from closing? There are multiple kidney related items that should be addressed as part of the KPMP and HuBMAP project work. I am adding the 'KPMP' label to these.

gouttegd commented 2 years ago

Yes, adding a label counts as an "activity" from the point of view of the auto-closing script, so it's enough to prevent auto-closing.

gouttegd commented 2 years ago

We are down to 53 old issues inactive for the past three years (well done !)

Issue Author Team? Assignee(s)
Add taxon contraints on cell types @pgaudet No
Define strategy for handling new proposed cell types derived from clustering transcriptomic and other data @cmungall Yes
Add icon images from Reactome @cmungall Yes
Bad ZFA mappings @balhoff Yes
Fibro/adipogenic progenitors @Alessandro-Palma No
Faulty term ID in obo file for 'alobate nucleus' @cmpich No
No default-namespace in obo file header @cmpich No
Distribute nif_import.owl in RDF/XML? @jonathanbona No
lacks part relation @lgcowell No
create mapping of CL to NCIt cell classes @nicolevasilevsky Yes @cmungall
adipocyte (white/brown/beige) classification, definitions and axioms @cmungall Yes
Definition update for CL_0000178 @cerivs Yes
Ensure correct annotation properties are always used @cmungall Yes @cmungall
'female germ cell' not capable of oogenesis relationship @dosumis Yes
Update CL xrefs to species-specific AOs @cmungall Yes
vestibular afferent neuron @dosumis Yes
Are APUD (amine precursor uptake and decarboxylation) cells always NC-derived? @cmungall Yes @cerivs, @ybradford
NTRs @jahilton Yes @addiehl
NTR: keratinized cell of hair follicle @YasminAF No @dosumis
Use a consistent obo-namespace tag in obo format exports @cmungall Yes @cmungall
missing classifications under "animal cell" and "eukaryotic cell" @GoogleCodeExporter No
Classification under 'somatic cell' @GoogleCodeExporter No
NTRs for 'adult Leydig cell' and for 'fetal Leydig cell', possibly split or relabel existing CL:0000178 @GoogleCodeExporter No
cholangiocte improvements @GoogleCodeExporter No
NTR: otic epithelial cell @GoogleCodeExporter No
NTR: anterior visceral endoderm cell @GoogleCodeExporter No
olfactory epithelium cells @GoogleCodeExporter No
intraepithelial cells @GoogleCodeExporter No
Add part_of axioms for horizontal cel @GoogleCodeExporter No
Review precursor B-Cell and its subclasses, proposing parallel minimal commitment EC axioms @GoogleCodeExporter No
cl-plus-fbbt is incoherent @GoogleCodeExporter No
Add MESH xrefs @GoogleCodeExporter No
Project: Review all cases where cell types have multiple develops_from relatiionships @GoogleCodeExporter No
Project: separate out developmental precursor cells from stem cell heirarchy @GoogleCodeExporter No
Proposal for segregating marker axioms in CL @GoogleCodeExporter No
mesenchymal cell / mesenchymal stem cell (CL_0000134) @GoogleCodeExporter No
Consider adding axiom: glandular epithelial cells are columnar/cuboidal @GoogleCodeExporter No
add part_of relation in CL:0000066 and in CL:0000586 @GoogleCodeExporter No
(flowCL project) CD11c in "myeloid dendritic cell, human" @GoogleCodeExporter No
Ensure FBbt xrefs are up to date @GoogleCodeExporter No
Create importer that brings plant and animal cells into same ontology @GoogleCodeExporter No
Create strategy for maintaining axioms connecting ssAOs to CL @GoogleCodeExporter No
"lacks" relations as object properties (between individuals) are not meaningful: @GoogleCodeExporter No
relabel 'phenotype' classes @GoogleCodeExporter No
remove in appropriate Schwann cell syns @GoogleCodeExporter No
peripheral ganglia should have neruon that they are part of @GoogleCodeExporter No
CL:0002339 'prostate stem cell' vs CL:0002341 'basal cell of prostate epithelium' @GoogleCodeExporter No
Adopt common naming conventions for compositional terms @GoogleCodeExporter No
NTRs: subclasses of blastoderm cell @GoogleCodeExporter No
Cell type terms required by GO @GoogleCodeExporter No
PATO differentium for non-terminallly differentiated cell @GoogleCodeExporter No
displaced (inverted) amacrine cell @cmungall Yes @cmungall
lacks_part and lacks_plasma_membrane_part @cmungall Yes @cmungall
NTR: endothelial progenitor cell @cmungall Yes @cmungall

Unless anybody objects I will forcefully close them on Monday, as agreed above.

gouttegd commented 2 years ago

44 old issues have now been closed. They are all tagged with the autoclosed-unfixed label.

Thanks to those who contributed to cut down the number of inactive issues by 75% (down from 182 issues when this ticket was opened) in the last two months!

Now that we have an automated procedure to regularly flag and close stale issues, there will be no more need for mass closures like this one.