emquardokus
commented
2 years ago 1) Corrected 1537 instances of Uberon_ to UBERON: across 12 ASCT+B tables that caused this type of error: Example: WARNING - Unrecognised cell content 'UBERON_0000314'
2) Changed instances of "submucosa of colon" to "submucosa of anal canal" rwos 1211-1227 in ASCT+B table.
3) Several errors are due to lack of synonyms; made notes in review. Examples: a) crypt, intestinal crypt and crypt of Lieberkuhn of colon are the same b) spelling variant caecum vs cecum; both are correct
4) Several errors are resulting from lack of regional specificity in layers throughout large intestine. According to discussion with domain expert with David, these can be added as there are histological and molecular differences that warrant adding new terms for regions of colon for mucosa, submucosa, lamina propria, subserosa, serosa (note distal rectum does NOT have serosa)
5) Errors in general due to lack of specificity or acknowledgement of multiple types of a particular structure: Example taeniae coli---there are 3 distinct types, only generic is in uberon.
6) Error mismatch uberon ID and uberon label; Changed label for anal canal--> epithelium --> to anal canal epithelium UBERON:0015716.
Errors
TONS of errors due to underscore instead of colon used with uberon ID Example: WARNING - Unrecognised cell content 'UBERON_0000314'
This looks like it should result in New term request as there are 3 separate and distinct type of taenia coli: free, mes https://en.wikipedia.org/wiki/Taenia_coli
Oddly only 1 warning is appearing and all 3 are in ASCT+B table with same uberon ID Rows 763-765 of https://docs.google.com/spreadsheets/d/1tK916JyG5ZSXW_cXfsyZnzXfjyoN-8B2GXLbYD6_vF0/edit#gid=512613979
"The taenia libera, is placed anteriorly in the caecum, ascending, descending and sigmoid colon, but is placed inferiorly in the transverse colon. The taenia mesocolica is present on the posteromedial surface of caecum, ascending, descending and sigmoid colon, but is placed posteriorly on transverse colon at the site of attachment of transverse mesocolon. The taenia omentalis is situated posterolaterally in caecum, ascending, descending and sigmoid colon, but is situated on the anterosuperior surface of transverse colon where layers three and four of the greater omentum meet the transverse colon. "
New term requests need to be made to specify different regional differences in mucosa, submucosa, subserosa, serosa , muscularis mucosa, lamina propria along large intestine are needed; many things currently are generic mucosa of colon, which is better than just mucosa etc
This should be mucosa of ileocecal valve ; it was incorrectly chosen as mucosa of appendix
This should be serosa of ileocecal valve ; incorrectly chosen as serosa of appendix
According to literature, there were some discussions about attribution, so now they are called inner (Meissner's) and outer (Schabadasch's or Henle's) submucous nerve plexus, but either way 2 distinct plexus and in humans a 3rd one is present compared to other mammals according to Timmermans 2001.
Timmermans, Jean-Pierre, Jurgen Hens, and Dirk Adriaensen. 2001. “Outer Submucous Plexus: An Intrinsic Nerve Network Involved in Both Secretory and Motility Processes in the Intestine of Large Mammals and Humans.” The Anatomical Record 262 (1): 71–78. https://doi.org/10.1002/1097-0185(20010101)262:1<71::AID-AR1012>3.0.CO;2-A.
https://en.wikipedia.org/wiki/Submucosal_plexus
Hoyle, C H, and G Burnstock. 1989. “Neuronal Populations in the Submucous Plexus of the Human Colon.” Journal of Anatomy 166 (October): 7–22. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1256735/pdf/janat00044-0015.pdf The submucous plexus appeared to contain three identifiable plexuses: Henle's plexus was located adjacent to the circular muscle layer, Meissner's plexus was located adjacent to the muscularis mucosae and a third intermediate plexus was found which lay closer to the muscularis mucosae than to the circular muscle.
New term requests for more specific regional area of large intestine Currently only lamina propria of mucosa of colon exists,
New term request for lamina propria of mucosa of appendix
Changed instances for anal canal
New term requests for other regions of colon:
Table Spoke with table author Teri Longacre, MD together with David OS; much redundancy within large intestine along different sections, but distinct molecular signatures, so should be represented with each section. In the absence of the proper specific term for the region an inappropriate generic term was selected for organ as opposed to region--many new term requests for these to be added as github issues in uberon.
Muscle 1| UBERON:0012489 | muscle layer of colon | muscularis propria | UBERON:0000569 | ileocecal valve | cecum 2|UBERON:0012398 | large intestine smooth muscle circular layer | circular muscle layer | UBERON:0012489 | muscle layer of colon | muscularis propria 3|UBERON:0012399 | large intestine smooth muscle longitudinal layer | longitudinal muscle layer | UBERON:0012489 | muscle layer of colon | muscularis propria 4|UBERON:0007178 | muscularis mucosae of colon | muscularis mucosa | UBERON:0001153 | caecum | cecum 5|UBERON:0012489 | muscle layer of colon | muscularis propria | UBERON:0001153 | caecum | cecum