immune slim revision

[dosumis]

The first round of generating the blood_and_immune_upper_slim slim was done without the help of reporting tools. Now those tools are in place, I think we can see some room for improvement, and some ways we could write a better SOP.

The main use case for an upper slim is to summarise data. Things that potentially get in the way of this use case:

1. Classes in the slim with very small numbers of subclasses: Having 0-1 subclass => no capacity to summarise.
2. Classes with disproportionately large numbers of subclasses.
3. Overlapping classes - these clash with some types of summary - e.g. pie charts.

Potential clashing concern: It seems reasonable to want to make sure that very important cell types are not obscured in generating summaries, but this desire can clash with the considerations above. Some judgement may be needed.

Report for current slim

#####Coverage percentage#####
97.76%
#####Number of terms covered by each term in the slim#####
platelet,1
multinucleated giant cell,1
nucleated thrombocyte,1
natural helper lymphocyte,1
B-lymphoblast,1
lymphoblast,2
blood lymphocyte,2
mast cell,3
proerythroblast,3
immature B cell,3
myeloid suppressor cell,3
erythroid progenitor cell,4
megakaryocyte,4
nongranular leukocyte,4
reticulocyte,5
hematopoietic multipotent progenitor cell,5
basophil,6
erythrocyte,7
eosinophil,7
neutrophil,7
erythroblast,10
hematopoietic stem cell,12
plasmacytoid dendritic cell,12
plasma cell,13
monocyte,20
hematopoietic oligopotent progenitor cell,22
gamma-delta T cell,23
innate lymphoid cell,46
immature T cell,51
macrophage,55
conventional dendritic cell,61
hematopoietic lineage restricted progenitor cell,64
B cell,94
alpha-beta T cell,94
professional antigen presenting cell,199
mononuclear cell,422
#####Terms that are not covered by src/templates/blood_and_immune_upper_slim.csv under CL:0000988#####
http://purl.obolibrary.org/obo/CL_0002318,peripheral blood mesothelial cell
http://purl.obolibrary.org/obo/CL_0002355,primitive red blood cell
http://purl.obolibrary.org/obo/CL_0002356,primitive reticulocyte
http://purl.obolibrary.org/obo/CL_0002358,pyrenocyte
http://purl.obolibrary.org/obo/CL_0002361,primitive erythroid progenitor
http://purl.obolibrary.org/obo/CL_0000092,osteoclast
http://purl.obolibrary.org/obo/CL_0000385,prohemocyte (sensu Nematoda and Protostomia)
http://purl.obolibrary.org/obo/CL_0000390,blood cell (sensu Nematoda and Protostomia)
http://purl.obolibrary.org/obo/CL_0000588,odontoclast
http://purl.obolibrary.org/obo/CL_0000779,multinuclear osteoclast
http://purl.obolibrary.org/obo/CL_0000780,multinuclear odontoclast
http://purl.obolibrary.org/obo/CL_1001610,bone marrow hematopoietic cell
http://purl.obolibrary.org/obo/CL_2000074,splenocyte
http://purl.obolibrary.org/obo/CL_0002417,primitive erythroid lineage cell

Overlap report (generated by Anita

sub	obj	sub_label	obj_label
http://purl.obolibrary.org/obo/CL_0000784	http://purl.obolibrary.org/obo/CL_0000145	plasmacytoid dendritic cell	professional antigen presenting cell
http://purl.obolibrary.org/obo/CL_0000786	http://purl.obolibrary.org/obo/CL_0000236	plasma cell	B cell
http://purl.obolibrary.org/obo/CL_0000784	http://purl.obolibrary.org/obo/CL_0000842	plasmacytoid dendritic cell	mononuclear cell
http://purl.obolibrary.org/obo/CL_0000786	http://purl.obolibrary.org/obo/CL_0000842	plasma cell	mononuclear cell
http://purl.obolibrary.org/obo/CL_0000038	http://purl.obolibrary.org/obo/CL_0002031	erythroid progenitor cell	hematopoietic lineage restricted progenitor cell
http://purl.obolibrary.org/obo/CL_0000235	http://purl.obolibrary.org/obo/CL_0000145	macrophage	professional antigen presenting cell
http://purl.obolibrary.org/obo/CL_0000236	http://purl.obolibrary.org/obo/CL_0000842	B cell	mononuclear cell
http://purl.obolibrary.org/obo/CL_0000990	http://purl.obolibrary.org/obo/CL_0000145	conventional dendritic cell	professional antigen presenting cell
http://purl.obolibrary.org/obo/CL_0000816	http://purl.obolibrary.org/obo/CL_0000236	immature B cell	B cell
http://purl.obolibrary.org/obo/CL_0000576	http://purl.obolibrary.org/obo/CL_0000842	monocyte	mononuclear cell
http://purl.obolibrary.org/obo/CL_0000789	http://purl.obolibrary.org/obo/CL_0000842	alpha-beta T cell	mononuclear cell
http://purl.obolibrary.org/obo/CL_0000798	http://purl.obolibrary.org/obo/CL_0000842	gamma-delta T cell	mononuclear cell
http://purl.obolibrary.org/obo/CL_0000816	http://purl.obolibrary.org/obo/CL_0000842	immature B cell	mononuclear cell
http://purl.obolibrary.org/obo/CL_0000990	http://purl.obolibrary.org/obo/CL_0000842	conventional dendritic cell	mononuclear cell
http://purl.obolibrary.org/obo/CL_0001065	http://purl.obolibrary.org/obo/CL_0000842	innate lymphoid cell	mononuclear cell
http://purl.obolibrary.org/obo/CL_0017006	http://purl.obolibrary.org/obo/CL_0000842	B-lymphoblast	mononuclear cell
http://purl.obolibrary.org/obo/CL_4030029	http://purl.obolibrary.org/obo/CL_0000842	blood lymphocyte	mononuclear cell
http://purl.obolibrary.org/obo/CL_0002420	http://purl.obolibrary.org/obo/CL_0000842	immature T cell	mononuclear cell
http://purl.obolibrary.org/obo/CL_0002679	http://purl.obolibrary.org/obo/CL_0000842	natural helper lymphocyte	mononuclear cell
http://purl.obolibrary.org/obo/CL_0017005	http://purl.obolibrary.org/obo/CL_0000842	lymphoblast	mononuclear cell
http://purl.obolibrary.org/obo/CL_0017006	http://purl.obolibrary.org/obo/CL_0017005	B-lymphoblast	lymphoblast

query: https://api.triplydb.com/s/_b0O6UP2A

SOme conclusions:

These do not group (a score of 1 = no subclasses)

platelet,1 multinucleated giant cell,1 nucleated thrombocyte,1 natural helper lymphocyte,1 B-lymphoblast,1 lymphoblast,2 blood lymphocyte,2

Mononuclear cell has >400 subclasses and is a source of much of the overlap. Using OLS with coverage (subclass) counts displayed shows some good possibilities for choosing more specific terms.

Judgement required. There are no perfect solutions - but some are better than others.

[ghost]

@dosumis, please describe an action item and acceptance criteria for this ticket. As it is, I'm unsure how to proceed.

[dosumis]

Use your judgement - given the specified use-case.

[dosumis]

Also see SOP ticket. https://github.com/obophenotype/cell-ontology/issues/1919

[ghost]

Use your judgement

Thanks for the link.

My pending question is: Use judgement to do what exactly? I would need some acceptance criteria to know what the revised intended goal is.

The originally submitted list of classes (before the removal of overlaps) was my determination of a balance between overlap and specificity. If you can specify metrics that would constitute an improvement on that list, I can re-review the original list against those clarified metrics.

Dropping all classes with score of 1 and replacing with the parent class seems like a large gap in granularity in some cases, e.g. platelet and 'myeloid cell'. Can you provide a metric on how to determine which of those two terms would be appropriate?

Happy to discuss offline and record the clarified action item and acceptance criteria in this ticket.

[dosumis]

before the removal of overlaps

I don't think overlaps have been removed.

[ghost]

before the removal of overlaps

I don't think overlaps have been removed.

@anitacaron, can you confirm the blood_and_immune_upper_slim overlap terms will be removed once #1939 is merged? Based on this comment, it seems like they will be, but can you confirm?

[anitacaron]

@bvarner-ebi, @ubyndr put them back on this commit and removed the QC for overlapping classes, requested by David offline.

[ghost]

All action items appear to be addressed. If anything else is required, kindly reopen with required action items.