Fix capitalization

[cmungall]

cmungall/capital-offence#1

To be capitalized

lieberkuhn

• CL:0002250 ! intestinal crypt stem cell [SYNONYM: "stem cell of intestinal crypt of lieberkuhn " (exact)]
• CL:1000338 ! enterocyte of epithelium of crypt of lieberkuhn of small intestine
• CL:1000345 ! paneth cell of epithelium of crypt of lieberkuhn of small intestine
• UBERON:0001241 ! crypt of Lieberkuhn of small intestine [SYNONYM: "crypt of lieberkuhn of small bowel" (exact)] [SYNONYM: "crypt of lieberkuhn of small intestine" (exact)] [SYNONYM: "intestinal gland of small bowel" (exact)] [SYNONYM: "intestinal gland of small intestine" (exact)] [SYNONYM: " lieberkuhn crypt of small bowel" (exact)] [SYNONYM: " lieberkuhn crypt of small intestine" (exact)] [SYNONYM: "small bowel crypt of lieberkuhn " (exact)] [SYNONYM: "small bowel intestinal gland" (exact)] [SYNONYM: "small bowel lieberkuhn crypt" (exact)] [SYNONYM: "small intestinal crypt of Lieberkuhn" (exact)] [SYNONYM: "small intestine crypt of Lieberkuhn" (exact)] [SYNONYM: "small intestine crypt of lieberkuhn " (exact)] [SYNONYM: "small intestine intestinal gland" (exact)] [SYNONYM: "small intestine lieberkuhn crypt" (exact)]
• UBERON:0001983 ! crypt of Lieberkuhn [SYNONYM: "crypt of lieberkuhn " (exact)] [SYNONYM: "crypt of LieberkC<hn" (exact)] [SYNONYM: "crypts of LieberkC<hn" (exact)] [SYNONYM: "follicles of lieberkuhn " (exact)] [SYNONYM: "intestinal crypt" (exact)] [SYNONYM: "intestinal crypts" (exact)] [SYNONYM: "intestinal gland" (broad)] [SYNONYM: "intestinal gland of Lieberkuhn" (related)] [SYNONYM: "Lieberkuhn crypt" (exact)] [SYNONYM: " lieberkuhn crypt" (exact)] [SYNONYM: "Lieberkuhn gland" (exact)] [SYNONYM: "Lieberkuhn's gland" (exact)] [SYNONYM: "Lieberkuhn's glands" (exact)]
• UBERON:0001984 ! crypt of Lieberkuhn of large intestine [SYNONYM: "intestinal gland of large intestine" (exact)] [SYNONYM: "large intestinal crypt of lieberkuhn " (exact)] [SYNONYM: "large intestine crypt of lieberkuhn " (exact)] [SYNONYM: "large intestine intestinal gland" (exact)] [SYNONYM: "large intestine lieberkuhn crypt" (exact)] [SYNONYM: " lieberkuhn crypt of large intestine" (exact)]
• UBERON:0013485 ! crypt of Lieberkuhn of colon [SYNONYM: "colonic crypt" (exact)] [SYNONYM: "colonic crypt of lieberkuhn " (exact)]
• UBERON:0013486 ! crypt of Lieberkuhn of appendix [SYNONYM: "appendiceal crypt" (exact)] [SYNONYM: "appendiceal crypt of lieberkuhn " (exact)]

henle

• CL:1000909 ! kidney loop of henle epithelial cell
• CL:1001016 ! kidney loop of henle ascending limb epithelial cell
• CL:1001021 ! kidney loop of henle descending limb epithelial cell
• CL:1001106 ! kidney loop of henle thick ascending limb epithelial cell
• CL:1001107 ! kidney loop of henle thin ascending limb epithelial cell
• CL:1001108 ! kidney loop of henle medullary thick ascending limb epithelial cell
• CL:1001109 ! kidney loop of henle cortical thick ascending limb epithelial cell
• CL:1001111 ! kidney loop of henle thin descending limb epithelial cell
• UBERON:0001288 ! loop of Henle [SYNONYM: "ansa nephroni" (exact)] [SYNONYM: "Henle loop" (exact)] [SYNONYM: " henle 's loop" (exact)]
• UBERON:0003455 ! inner renal medulla loop of henle [SYNONYM: "Henle loop of inner medulla of kidney" (exact)] [SYNONYM: "Henle loop of inner renal medulla" (exact)] [SYNONYM: "Henle loop of inner zone of medulla of kidney" (exact)] [SYNONYM: "Henle loop of inner zone of renal medulla" (exact)] [SYNONYM: " henle 's loop of inner medulla of kidney" (exact)] [SYNONYM: " henle 's loop of inner renal medulla" (exact)] [SYNONYM: " henle 's loop of inner zone of medulla of kidney" (exact)] [SYNONYM: " henle 's loop of inner zone of renal medulla" (exact)] [SYNONYM: "inner medulla of kidney Henle loop" (exact)] [SYNONYM: "inner medulla of kidney henle 's loop" (exact)] [SYNONYM: "inner medulla of kidney loop of Henle" (exact)] [SYNONYM: "inner renal medulla Henle loop" (exact)] [SYNONYM: "inner renal medulla henle 's loop" (exact)] [SYNONYM: "inner renal medulla loop of Henle" (exact)] [SYNONYM: "inner zone of medulla of kidney Henle loop" (exact)] [SYNONYM: "inner zone of medulla of kidney henle 's loop" (exact)] [SYNONYM: "inner zone of medulla of kidney loop of Henle" (exact)] [SYNONYM: "inner zone of renal medulla Henle loop" (exact)] [SYNONYM: "inner zone of renal medulla henle 's loop" (exact)] [SYNONYM: "inner zone of renal medulla loop of Henle" (exact)] [SYNONYM: "kidney inner medulla loop of henle " (exact)] [SYNONYM: "loop of Henle of inner medulla of kidney" (exact)] [SYNONYM: "loop of Henle of inner renal medulla" (exact)] [SYNONYM: "loop of Henle of inner zone of medulla of kidney" (exact)] [SYNONYM: "loop of Henle of inner zone of renal medulla" (exact)]
• UBERON:0005096 ! descending thin limb [SYNONYM: "descending limb of henle %27s loop" (related)] [SYNONYM: "descending limb of loop of henle " (related)] [SYNONYM: "descending thin limb of loop of Henle" (exact)] [SYNONYM: "loop of Henle descending thin limb" (exact)] [SYNONYM: "loop of henle thin descending limb" (exact)] [SYNONYM: "pars descendens (tubulus attenuatus)" (exact)] [SYNONYM: "thin descending limb" (exact)] [SYNONYM: "thin descending limb of loop of henle " (related)] [SYNONYM: "thin descending limb of the loop of henle " (related)] [SYNONYM: "thin descending loop of henle " (related)]
• UBERON:0006541 ! outer medulla inner stripe loop of henle
• UBERON:0006542 ! outer medulla outer stripe loop of henle
• UBERON:0034996 ! outer renal medulla loop of henle [SYNONYM: "loop of Henle, outer medullary portion" (exact)]
• UBERON:0034997 ! renal medulla loop of henle [SYNONYM: "loop of Henle of renal medulla" (exact)] [SYNONYM: "loop of Henle, medullary portion" (exact)]

Lugaro

• CL:0011006 ! lugaro cell [SYNONYM: "Lugaro cell" (exact)]

Purkinje

• CL:1000376 ! purkinje myocyte of interventricular septum
  • CL:1000479 ! purkinje myocyte of atrioventricular node
  • CL:1000483 ! purkinje myocyte of internodal tract
  • CL:1000484 ! purkinje myocyte of atrioventricular bundle

Peyer

• CL:1000411 ! endothelial cell of peyer 's patch
• UBERON:0004693 ! Peyer's patch epithelium [SYNONYM: " peyer 's patch epithelium" (exact)]
• UBERON:0010386 ! Peyer's patch follicle [SYNONYM: " peyer 's patch follicle" (exact)]

[nicolevasilevsky]

I can fix these manually, does that work?

[cmungall]

Go for it - I assume you will just do in a text editor?

obv. the uberon ones will be fixed at src

[nicolevasilevsky]

Do you just want the labels to have proper capitalization? So the synonym in the first example would be 'stem cell of intestinal crypt of Lieberkuhn'

I would just do this in Protege, right?

[cmungall]

On 6 Sep 2016, at 14:10, nicolevasilevsky wrote:

Do you just want the labels to have proper capitalization? So the
synonym in the first example would be 'stem cell of intestinal crypt
of Lieberkuhn'

labels and synonyms, and yes that's the correct capitalization for the
synonym

I would just do this in Protege, right?

if that's the way you really want to do it. I mean this is designed so
that we can just run the script to do it but I won't have time to do it

[nicolevasilevsky]

Ah, I see. I can just fix it via Protege, it shouldn't take me too long.

[nicolevasilevsky]

I fixed all the CL terms except
CL:0011006 ! lugaro cell [SYNONYM: "Lugaro cell" (exact)]

If I change the label to Lugaro cell, it will then match the synonym. Should I do that and remove the synonym?

[cmungall]

Yes, remove it

On 6 Sep 2016, at 16:43, nicolevasilevsky wrote:

I fixed all the CL terms except
CL:0011006 ! lugaro cell [SYNONYM: "Lugaro cell" (exact)]

If I change the label to Lugaro cell, it will then match the synonym.
Should I do that and remove the synonym?

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