updated data example for terminology

ivanwilliammd · May 2, 2024 · 75b0f94 · 75b0f94
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Showing 10 changed files with 13,358 additions and 13,361 deletions.
diff --git a/Playbook.ipynb b/Playbook.ipynb
diff --git a/output/differential_diagnosis_similarity.tsv b/output/differential_diagnosis_similarity.tsv
@@ -1,38 +1,38 @@
 rank	id	name	score
-1	227810	Fanconi-Bickel syndrome	0.3851177990436554
-2	611881	Glycogen storage disease XII	0.3723735809326172
-3	603902	Thalassemia-beta, dominant inclusion-body	0.3528570234775543
-4	232500	Glycogen storage disease IV	0.3311641216278076
-5	613027	Glycogen storage disease IXc	0.3222183883190155
-6	232700	Glycogen storage disease VI	0.32113826274871826
-7	615895	Polyglucosan body myopathy 1 with or without immunodeficiency	0.3190052807331085
-8	610539	Gaucher disease, atypical	0.3134368658065796
-9	230800	Gaucher disease, type I	0.2948063015937805
-10	257220	Niemann-pick disease, type C1	0.2887139916419983
-11	231000	Gaucher disease, type III	0.28795626759529114
-12	232200	Glycogen storage disease Ia	0.2799232304096222
-13	230900	Gaucher disease, type II	0.2669340968132019
-14	608013	Gaucher disease, perinatal lethal	0.2648431360721588
-15	261750	Glycogen storage disease type IXb	0.25858327746391296
-16	232220	Glycogen storage disease Ib	0.25592923164367676
-17	607625	Niemann-pick disease, type C2	0.2328203171491623
-18	232800	Glycogen storage disease VII	0.21963520348072052
-19	232240	Glycogen storage disease Ic	0.21480496227741241
-20	306000	Glycogen storage disease, type IXa1	0.2114570587873459
-21	231005	Gaucher disease, type IIIC	0.19200804829597473
-22	240600	Glycogen storage disease 0, liver	0.18373343348503113
-23	232300	Glycogen storage disease II	0.17807894945144653
-24	232400	Glycogen storage disease III	0.17743338644504547
-25	612933	Glycogen storage disease XI	0.16075573861598969
-26	612932	Glycogen storage disease XIII	0.12607280910015106
-27	232600	Glycogen storage disease V	0.11939386278390884
-28	263570	Polyglucosan body neuropathy, adult form	0.11525966227054596
-29	261670	Phosphoglycerate mutase, muscle, deficiency of	0.10096176713705063
-30	611556	Glycogen storage disease 0, muscle	0.10010755807161331
-31	613507	Glycogen storage disease XV	0.08989541977643967
-32	300653	Phosphoglycerate kinase 1 deficiency	0.08972006291151047
-33	616199	Polyglucosan body myopathy 2	0.08133861422538757
-34	614128	Lactate dehydrogenase B deficiency	0.07455503195524216
-35	613985	BETA-THALASSEMIA	0.07443328201770782
-36	300257	Danon disease	0.06328766793012619
-37	300559	Muscle glycogenosis, X-linked	0.06328236311674118
+1	227810	Fanconi-Bickel syndrome	0.3851173520088196
+2	611881	Glycogen storage disease XII	0.3722228407859802
+3	603902	Thalassemia-beta, dominant inclusion-body	0.3526041507720947
+4	232500	Glycogen storage disease IV	0.3303186297416687
+5	613027	Glycogen storage disease IXc	0.32203608751296997
+6	232700	Glycogen storage disease VI	0.3211374878883362
+7	230800	Gaucher disease, type I	0.31730157136917114
+8	615895	Polyglucosan body myopathy 1 with or without immunodeficiency	0.3143061399459839
+9	610539	Gaucher disease, atypical	0.31325531005859375
+10	257220	Niemann-pick disease, type C1	0.28857144713401794
+11	231000	Gaucher disease, type III	0.2877655029296875
+12	232200	Glycogen storage disease Ia	0.27772560715675354
+13	230900	Gaucher disease, type II	0.26679158210754395
+14	608013	Gaucher disease, perinatal lethal	0.26405036449432373
+15	261750	Glycogen storage disease type IXb	0.25837698578834534
+16	232220	Glycogen storage disease Ib	0.2537723183631897
+17	607625	Niemann-pick disease, type C2	0.23268966376781464
+18	232800	Glycogen storage disease VII	0.21963471174240112
+19	231005	Gaucher disease, type IIIC	0.2128029763698578
+20	232240	Glycogen storage disease Ic	0.21218885481357574
+21	306000	Glycogen storage disease, type IXa1	0.2112610787153244
+22	240600	Glycogen storage disease 0, liver	0.18373245000839233
+23	232400	Glycogen storage disease III	0.1760760098695755
+24	232300	Glycogen storage disease II	0.17487147450447083
+25	612933	Glycogen storage disease XI	0.16075505316257477
+26	612932	Glycogen storage disease XIII	0.1260719746351242
+27	263570	Polyglucosan body neuropathy, adult form	0.11429351568222046
+28	232600	Glycogen storage disease V	0.11259487271308899
+29	261670	Phosphoglycerate mutase, muscle, deficiency of	0.10096098482608795
+30	611556	Glycogen storage disease 0, muscle	0.09868407994508743
+31	300653	Phosphoglycerate kinase 1 deficiency	0.08971938490867615
+32	613507	Glycogen storage disease XV	0.08390989899635315
+33	616199	Polyglucosan body myopathy 2	0.08133801072835922
+34	614128	Lactate dehydrogenase B deficiency	0.07455464452505112
+35	613985	BETA-THALASSEMIA	0.07443299144506454
+36	300559	Muscle glycogenosis, X-linked	0.06328175961971283
+37	300257	Danon disease	0.051653873175382614
diff --git a/output/iderare.yml b/output/iderare.yml
@@ -19,7 +19,7 @@ analysis:
   - HP:0002910
   - HP:0001399
   - HP:0000938
-  - HP:0001642
+  - HP:0001653
   - HP:0200114
   - HP:0003073
   - HP:0003233

diff --git a/output/linkage_all_ddx.png b/output/linkage_all_ddx.png
diff --git a/output/linkage_disease.png b/output/linkage_disease.png
diff --git a/output/linkage_filt_ddx.png b/output/linkage_filt_ddx.png
diff --git a/output/linkage_gene.png b/output/linkage_gene.png