Review Lung v1.1 table

[emquardokus]

Error log: 9969 entries!

Mainly redundant errors with easy fixes in ASCT+B tables: 1) TONS of UBERON: space number Example: WARNING - Unrecognised cell content 'UBERON: 0010368' 2) TONS of blank spaces Example: WARNING - Unrecognised cell content '' 3) Wondering if there is a match case issue? TONS of errors that appear like font case issues. Example: WARNING - Unrecognised cell content 'Uberon:0008953' this checks correctly to content of cell but Uberon, not UBERON.

New Error Log run 10-27-2021 1)Main errors are now reduced to FMA and LungMAP ontology specific LMHA ids, plus the specific handful of errors from before. Example lungMAP ontology IDs: WARNING - Unrecognised cell content 'LMHA:00142' 2) Looks like conflicts with font case (capital vs lowercase) for the remaining errors.

FMA entries as opposed to UBERON 1) TONS of FMA entries because supposedly not found in UBERON (some due to laterality R/L) 2) Inconsistent entry with no space, with colon or 2 colon WARNING - Unrecognised cell content 'fma31933' WARNING - Unrecognised cell content 'fma:7380' WARNING - Unrecognised cell content 'fma::7401'

Different labels found in Uberongraph vs ASCT+B table--triaged categories. Legitimate errors: that warrant attention Are these errors due to font case issue? uberon all lower case, ASCT+B table case each word capitalized first letter? WARNING - Different labels found for UBERON:0002177. Uberongraph: right main bronchus ; ASCT+b table: Right Main Bronchus WARNING - Different labels found for UBERON:0002171. Uberongraph: lower lobe of right lung ; ASCT+b table: Lower Lobe of Right Lung WARNING - Different labels found for UBERON:0002178. Uberongraph: left main bronchus ; ASCT+b table: Left Main Bronchus WARNING - Different labels found for UBERON:0002048. Uberongraph: lung ; ASCT+b table: Lung WARNING - Different labels found for UBERON:0002168. Uberongraph: left lung ; ASCT+b table: Left Lung WARNING - Different labels found for UBERON:0001004. Uberongraph: respiratory system ; ASCT+b table: Respiratory System WARNING - Different labels found for UBERON:0003126. Uberongraph: trachea ; ASCT+b table: Trachea WARNING - Different labels found for UBERON:0005317. Uberongraph: pulmonary artery endothelium ; ASCT+b table: Pulmonary artery endothelium WARNING - Different labels found for UBERON:0008874. Uberongraph: pulmonary acinus ; ASCT+b table: Pulmonary Acinus WARNING - Different labels found for UBERON:0002167. Uberongraph: right lung ; ASCT+b table: Right Lung

laterality specified in ASCT+B but not in uberon WARNING - Different labels found for UBERON:0002184. Uberongraph: segmental bronchus ; ASCT+b table: Right Apical Segmental Bronchus

lung instead of respiratory system used in label WARNING - Different labels found for UBERON:0012418. Uberongraph: respiratory system venous smooth muscle ; ASCT+b table: lung venous smooth muscle WARNING - Different labels found for UBERON:0012416. Uberongraph: respiratory system arterial smooth muscle ; ASCT+b table: lung arterial smooth muscle

misspelling of capillary with 3 "l" in ASCT+B table WARNING - Different labels found for UBERON:0016405. Uberongraph: pulmonary capillary ; ASCT+b table: pulmonary capilllary

Tables n	s	slabel	user_slabel	o	olabel	user_olabel
1	UBERON:0002339	epithelium of lobar bronchus	bronchial epithelium	UBERON:0002177	right main bronchus	Right Main Bronchus
2	UBERON:0004242	bronchus smooth muscle	bronchial smooth muscle	UBERON:0002177	right main bronchus	Right Main Bronchus
3	UBERON:0001102	cartilage of main bronchus	cartilagenous plate	UBERON:0002177	right main bronchus	Right Main Bronchus
4	UBERON:0004889	lobar bronchus vasculature	bronchial vessels	UBERON:0002177	right main bronchus	Right Main Bronchus
5	UBERON:0019190	mucous gland of lung	bronchial submucosal gland	UBERON:0002177	right main bronchus	Right Main Bronchus
6	UBERON:0002339	epithelium of lobar bronchus	bronchial epithelium	UBERON:0002178	left main bronchus	Left Main Bronchus
7	UBERON:0004242	bronchus smooth muscle	bronchial smooth muscle	UBERON:0002178	left main bronchus	Left Main Bronchus
8	UBERON:0001102	cartilage of main bronchus	cartilagenous plate	UBERON:0002178	left main bronchus	Left Main Bronchus
9	UBERON:0019190	mucous gland of lung	bronchial submucosal gland	UBERON:0002178	left main bronchus	Left Main Bronchus
10	UBERON:0002339	epithelium of lobar bronchus	bronchial epithelium	UBERON:0002184	segmental bronchus	Right Apical Segmental Bronchus
11	UBERON:0004242	bronchus smooth muscle	bronchial smooth muscle	UBERON:0002184	segmental bronchus	Right Apical Segmental Bronchus
12	UBERON:0004884	lobar bronchus mesenchyme	bronchial mesenchyme	UBERON:0002184	segmental bronchus	Right Apical Segmental Bronchus
13	UBERON:0001102	cartilage of main bronchus	cartilagenous plate	UBERON:0002184	segmental bronchus	Right Apical Segmental Bronchus
14	UBERON:0019190	mucous gland of lung	bronchial submucosal gland	UBERON:0002184	segmental bronchus	Right Apical Segmental Bronchus
15	UBERON:0004903	bronchoalveolar duct junction	Bronchoalveolar duct junction	UBERON:0002187	terminal bronchiole	Terminal/ Transitional Bronchioles
16	UBERON:0002173	pulmonary alveolar duct	Alveolar Ducts	UBERON:0008874	pulmonary acinus	Pulmonary Acinus

The rest are blood or lymph vasculature related

n	s	slabel	user_slabel	o	olabel	user_olabel
1	UBERON:0007149	inferior thyroid artery	inferior thyroid artery	UBERON:0003505	trachea blood vessel	trachea blood vessel
2	UBERON:0002040	bronchial artery	bronchial artery	UBERON:0003505	trachea blood vessel	trachea blood vessel
3	UBERON:0004848	respiratory system arterial endothelium	respiratory system arterial endothelium	UBERON:0002040	bronchial artery	bronchial artery
4	UBERON:0012416	respiratory system arterial smooth muscle	respiratory system arterial smooth muscle	UBERON:0002040	bronchial artery	bronchial artery
5	UBERON:0007156	inferior thyroid vein	inferior thyroid vein	UBERON:0003505	trachea blood vessel	trachea blood vessel
6	UBERON:0001592	bronchial vein	bronchial vein	UBERON:0003505	trachea blood vessel	trachea blood vessel
7	UBERON:0004849	respiratory system venous endothelium	respiratory system venous endothelium	UBERON:0001592	bronchial vein	bronchial vein
8	UBERON:0012418	respiratory system venous smooth muscle	respiratory system venous smooth muscle	UBERON:0001592	bronchial vein	bronchial vein
9	UBERON:0005317	pulmonary artery endothelium	Pulmonary arterial endothelium	UBERON:0001651	right pulmonary artery	Right Main Pulmonary Artery
10	UBERON:0004889	lobar bronchus vasculature	bronchial vessels	UBERON:0002178	left main bronchus	Left Main Bronchus
11	UBERON:0002040	bronchial artery	bronchial artery	UBERON:0004889	lobar bronchus vasculature	bronchial vessels
12	UBERON:0004695	arterial system smooth muscle	arterial system smooth muscle	UBERON:0002040	bronchial artery	bronchial artery
13	UBERON:0001592	bronchial vein	bronchial vein	UBERON:0004889	lobar bronchus vasculature	bronchial vessels
14	UBERON:0004696	venous system smooth muscle	venous system smooth muscle	UBERON:0001592	bronchial vein	bronchial vein
15	UBERON:0005317	pulmonary artery endothelium	Pulmonary arterial endothelium	UBERON:0001652	left pulmonary artery	Left Main Pulmonary Artery
16	UBERON:0004889	lobar bronchus vasculature	bronchial vessels	UBERON:0002184	segmental bronchus
17	UBERON:0016405	pulmonary capillary	Alveolar capillaries	UBERON:0008870	pulmonary alveolar parenchyma	Alveoli
18	UBERON:0003529	respiratory system lymphatic vessel endothelium	respiratory system lymphatic vessel endothelium	UBERON:0018227	pulmonary lymphatic vessel	pulmonary lymphatic vessel
19	UBERON:0004296	respiratory system lymphatic vessel smooth muscle	respiratory system lymphatic vessel smooth muscle	UBERON:0018227	pulmonary lymphatic vessel	pulmonary lymphatic vessel

[emquardokus]

Resolved in ASCT+B tables directly errors associated with spaces, capitalization, single, double colon within uberon ID 3258 instances of Uberon: space number replaced across 2 sheets; 76 instances of capilllary misspelled with 3 l's across 2 sheets; 2011 instances of no space, one colon or 2 colons fma, convert to all fma: one colon. 81 instance of lower case uberon, substitute upper case UBERON.

[emquardokus]

1) Reviewed new errors file 10-27-2021 reduced to FMA and LMHA ID instances---these represent some laterality, but remember Lung Right is different than Lung Left. LMHA ontology has relationships that should be updated in uberon, but this is a much larger endeavor beyond scope of Year 4 Q2 of MC-IU team. 2) Still noticing the remainder of errors mostly look like a case sensitive flagging as opposed to content errors.