Review Thymus 1.1 log

[dosumis]

Errors from error_ind_Thymus.log WARNING - Unrecognised cell content '' WARNING - Unrecognised cell content 'Added new term'

Author added unexpected content to ID column in table

Thymus 1.1. sheet

Tables Relationships in ASCT+B tables but not in Uberon Most are generic terms: Report generated on 29 September 2021

n	s	slabel	user_slabel	o	olabel	user_olabel
1	UBERON:0002384	connective tissue	connective tissue	UBERON:0002370	thymus	thoracic thymus
2	UBERON:0001021	nerve	nerve	UBERON:0002370	thymus	thoracic thymus
3	UBERON:0001021	nerve	nerve	UBERON:0004791	thymus trabecula	thymus trabecula
4	UBERON:0018243	thymic artery	thymic artery	UBERON:0004791	thymus trabecula	thymus trabecula
5	UBERON:0001013	adipose tissue	adipose tissue	UBERON:0004791	thymus trabecula	thymus trabecula
6	UBERON:0003483	thymus epithelium	thymus epithelium	UBERON:0004791	thymus trabecula	thymus trabecula
7	UBERON:0002384	connective tissue	connective tissue	UBERON:0004791	thymus trabecula	thymus trabecula
8	UBERON:0002125	thymus lobule	thymus lobule	UBERON:0005483	thymus lobe	thymus lobe
9	UBERON:0006936	thymus subcapsular epithelium	thymus subcapsular epithelium	UBERON:0002125	thymus lobule	thymus lobule
10	UBERON:0003846	thymus lymphoid tissue	thymus lymphoid tissue	UBERON:0006936	thymus subcapsular epithelium	thymus subcapsular epithelium
11	UBERON:0003483	thymus epithelium	thymus epithelium	UBERON:0006936	thymus subcapsular epithelium	thymus subcapsular epithelium
12	UBERON:0001021	nerve	nerve	UBERON:0006936	thymus subcapsular epithelium	thymus subcapsular epithelium
13	UBERON:0018243	thymic artery	thymic artery	UBERON:0006936	thymus subcapsular epithelium	thymus subcapsular epithelium
14	UBERON:0002123	cortex of thymus	cortex of thymus	UBERON:0002125	thymus lobule	thymus lobule
15	UBERON:0003483	thymus epithelium	thymus epithelium	UBERON:0002123	cortex of thymus	cortex of thymus
16	UBERON:0001021	nerve	nerve	UBERON:0002123	cortex of thymus	cortex of thymus
17	UBERON:0018243	thymic artery	thymic artery	UBERON:0002123	cortex of thymus	cortex of thymus
18	UBERON:0003846	thymus lymphoid tissue	thymus lymphoid tissue	UBERON:0002123	cortex of thymus	cortex of thymus
19	UBERON:0003483	thymus epithelium	thymus epithelium	UBERON:0003988	thymus corticomedullary boundary	corticomedullary boundary of thymus
20	UBERON:0001013	adipose tissue	adipose tissue	UBERON:0003988	thymus corticomedullary boundary	corticomedullary boundary of thymus
21	UBERON:0001021	nerve	nerve	UBERON:0003988	thymus corticomedullary boundary	corticomedullary boundary of thymus
22	UBERON:0018243	thymic artery	thymic artery	UBERON:0003988	thymus corticomedullary boundary	corticomedullary boundary of thymus
23	UBERON:0001591	thymic vein	thymic vein	UBERON:0003988	thymus corticomedullary boundary	corticomedullary boundary of thymus
24	UBERON:0010397	efferent lymphatic vessel	efferent lymphatic	UBERON:0003988	thymus corticomedullary boundary	corticomedullary boundary of thymus
25	UBERON:0003846	thymus lymphoid tissue	thymus lymphoid tissue	UBERON:0003988	thymus corticomedullary boundary	corticomedullary boundary of thymus
26	UBERON:0002124	medulla of thymus	medulla of thymus	UBERON:0002125	thymus lobule	thymus lobule
27	UBERON:0003483	thymus epithelium	thymus epithelium	UBERON:0002124	medulla of thymus	medulla of thymus
28	UBERON:0003846	thymus lymphoid tissue	thymus lymphoid tissue	UBERON:0002124	medulla of thymus	medulla of thymus
29	UBERON:0001021	nerve	nerve	UBERON:0002125	thymus lobule	thymus lobule
30	UBERON:0001591	thymic vein	thymic vein	UBERON:0002124	medulla of thymus	medulla of thymus
31	UBERON:0003987	Hassall's corpuscle	Hassall's corpuscle	UBERON:0003483	thymus epithelium	thymus epithelium

[dosumis]

Some general notes:

A. Lots of general tissue types as subjects in relationships where an organ specific term is needed for part_of or overlaps to apply: 'connective tissue'; 'nerve', 'adipose tissue'.

• [ ] Decide whether to make organ specific tissue terms for connective and adipose tissue. Add via template.
• [ ] Investigate whether we have a nerve term

B. Lots of vasculature/lymphatic vessels -

• [ ] Check if any (other) relationship applies for all. Consider adding these relationship types to validation/production of CCF.owl.
• [ ] If no relationship is present - check VCCF for relationship and add if found (?)

C. 5 cases that need investigation (numbered here for easy reference)

The log table should be read as:

In Uberon+CL s has no inferred or asserted is_a/part_of/overlaps relationship to o.

n	s	slabel	user_slabel	o	olabel	user_olabel
1	UBERON:0002125	thymus lobule	thymus lobule	UBERON:0005483	thymus lobe	thymus lobe
2	UBERON:0006936	thymus subcapsular epithelium	thymus subcapsular epithelium	UBERON:0002125	thymus lobule	thymus lobule
3	UBERON:0003846	thymus lymphoid tissue	thymus lymphoid tissue	UBERON:0006936	thymus subcapsular epithelium	thymus subcapsular epithelium
4	UBERON:0003483	thymus epithelium	thymus epithelium	UBERON:0006936	thymus subcapsular epithelium	thymus subcapsular epithelium
5	UBERON:0003987	Hassall's corpuscle	Hassall's corpuscle	UBERON:0003483	thymus epithelium	thymus epithelium

The following numbered points refer to n numbers in the table:

1. Absence of relation may reflect species-specific difference. thymus lobule has taxon_notes "in the mouse, the lobes of the thymus are not subdivided into lobules but only in the central medulla and a peripheral cortex (i.e. there is no distinct sublobulation). In humans, the two thymus lobes are composed of many lobules of various sizes which contain follicles, each comprising a medulla and a cortex. in the rat, the thymus is partially subdivided into lobules separated by thin bands of connective tissue which are continuous with the thin connective tissue capsule.[MP]".
   • [x] TBD - is it safe to add the relation to Uberon? It sounds like lobules are always part of lobes, but that lobules not always present? https://github.com/obophenotype/uberon/issues/2099
2. thymus subcapsular epithelium "The epithelial cells lining the capsule and trabeculae of the thymus." Looking at 1. - this may be human-specific as some species. e.g. mice, don't have a lobulated lobes.
   • [ ] TBD do we really need a relationship here? If should we do this via species specific terms, or partonomy terms tailored to this case? Make taxon specific relation (shortcut for GCI?).
3. I strongly doubt that a part relationship applies between an epithelium and lymphoid tissue - perhaps some other relationship is intended.
   • [ ] Ask authors about their intent and decide if needed (and for what use case).
   • [ ] If it is needed consider a different relationship type
4. Relationship is table is reversed: Uberon has thymus subcapsular epithelium subClassOf thymus epithelium
   • [ ] Fix table and inform authors https://github.com/obophenotype/asct-b_validation/issues/44
5. The relationship is in Uberon (checked using names), but wrong ID used in object! UBERON:0003483 = 'thymus lymphoid tissue'.
   • [x] Fix table and inform authors

[emquardokus]

@dosumis Please see google sheet here where authors provided their viewpoint on New term requests with citations, superclass, and all the info needed to add; I had shared this yesterday: NewTermRequests_uberon_CL_ASCT+B https://docs.google.com/spreadsheets/d/1BihrOU9vWrsA_wYjcbdPUr42_Sb22CO3gkBDieiYQPs/edit?usp=sharing Issue obophenotype/ccf-validation-tools#1 thymus lobules as part of lobes. YES, lobules are always part of lobes, but presence of lobules are taxon specific (not in mouse). This paper mentions/documents taxon differences between human and rodent and also some differences between rat, mouse, guinea pig for thymus lobes/lobules. Consensus is 2 lobes, separated by a septum of connective tissue, but formation of lobules differs.
In addition, we already also know there is a huge difference between child, adolescent, adult thymus tissue progression. Adult thymus is largely fat (adipose) tissue and dramatically shrinks in size from child to adult. Differences exist between location of thymus between humans (thoracic cavity near heart) compared to rodents (cervical/neck) Pearse, Gail. 2006. “Normal Structure, Function and Histology of the Thymus.” Toxicologic Pathology 34 (5): 504–14. https://doi.org/10.1080/01926230600865549. Issue obophenotype/ccf-validation-tools#2 The same reference I cited in Issue obophenotype/ccf-validation-tools#1 above goes part by part for thymus so is especially rich in information with respect to capsule and epithelium; it states: "The bulk of the supporting framework in the thymus is composed of the network of epithelial reticular cells. Epithelium-free areas (or “holes”) are compartments lacking stromal elements, which have been identified in the sub-capsular area, extending deep into the cortex (Bruijntjes et al., 1993; Elmore, 2006)." "Immunohistochemically, epithelial cells can be divided into four distinct subtypes: subcapsular cortical, inner cortical, medullary and Hassalls corpuscles. A decrease in the number of different antigenic epithelial populations occurs with age in mice. " Issue 3 Relationship between lymphoid tissue and epithelium does appear to be special in thymus;I found this in literature for thymus: "Differentiating T-cells accumulate between epithelial reticular cells. They can then pass into the venules and efferent lymphatics along the border between the cortex and the medulla." Issue 4 Agree about thymus epithelium <-- thymus subcapsular epithelium; however, I am wondering why the uberon relationship of thymus subcapsular epithelium and thymus capsule is not in table---instead thymus subcapsular epithelium is part of lobule instead, which doesn't make sense to me--did that former relationship "pass" the validation test? Issue 5** I don't understand what this is referring to ? Is this referring to issue 3? See relationship described in paper quoted. "thymus lymphoid tissue" is part_of thymus, but I do not see most of implied relationships from ASCT+B table.

[dosumis]

Issue 5 I don't understand what this is referring to ? s this referring to issue 3?

row n = 5 in the log table. Looks like a typo.

To avoid any confusion, I've added some clarification to my general notes comment on how to read the table and comments. Part of my aim here is to come up with a standard template/SOP for reviewing and actioning. One way to do that might be to automate the generation of tickets via the GitHub API - these can be versioned and dated and include boilerplate text describing how to read the table and document the issues. Feedback on how to improve tables and standardise comments would help. This is also the first time we've really tested this software in any big way. It's entirely possible that there are bugs, so any cases that don't make sense given the original table should be reported as a ticket on this repo and assigned to @anitacaron

As much as I enjoy it, I will have limited time to debate fine details of the biology. Where those impinge on decisions about modifying ontologies, could you discuss with @paolaroncaglia first, and pull me in or bring up on a call if more discussion is needed?

Where there is a clear modification - e.g. 'add 'thymus lobule' part_of some 'thymus lobe' - please make an Uberon ticket and assign it to @paolaroncaglia (or try the edit yourself). Make sure to link the ticket from the review ticket on this repo.

[paolaroncaglia]

FYI, I opened a CL ticket for the thymus new cell type term requests: https://github.com/obophenotype/cell-ontology/issues/1279

[dosumis]

@emquardokus

Issue 5 is pointing to a general error in the Thymus table that needs fixing

thymus epithelium	thymus epithelium	UBERON:0003483				medullary thymic epithelial cell type 1
thymus epithelium	thymus epithelium	UBERON:0003483				medullary thymic epithelial cell type 2
thymus epithelium	thymus epithelium	UBERON:0003483				medullary thymic epithelial cell type 3
thymus epithelium	thymus epithelium	UBERON:0003483	Hassall's corpuscle	Hassall's corpuscle	UBERON:0003987	medullary thymic epithelial cell type 3
thymus epithelium	thymus epithelium	UBERON:0003483				medullary thymic epithelial cell type 4; thymic tuft cells
thymus epithelium	thymus epithelium	UBERON:0003483				myo-medullary thymic epithelial cell
thymus epithelium	thymus epithelium	UBERON:0003483				neuro-medullary thymic epithelial cell

UBERON:0003483 is thymus lymphoid tissue so is clearly used in error in the table where the ID for thymus epithelium should be used.

Please record here when fixed.

Can you make sure there are linked sub-issues for all the other issues in the breakdown/triage here? (We have tickets for at least some)

[emquardokus]

10-28-2021 removed 'Added new term' from ID column in thymus table v1.1 to eliminate error from error logs.

[emquardokus]

10-28-2021 replaced 7 instances of mismatched UBERON label with UBERON ID in ASCT+B thymus table v1.1 UBERON:0003483 is thymus lymphoid tissue

qualifier	author label	UBERON rdfs:label	UBERON ID
mismatch	thymus epithelium	thymus epithelium	UBERON:0003483
corrected	thymus epithelium	thymus epithelium	UBERON:0003846

[anitacaron]

For issue 3 listed here:

As we can see in this commit, all relations related to thymus lymphoid tissue was removed from the table. In some of the cases, it was changed to thymus epithelium.