Add files using upload-large-folder tool

.gitattributes

@@ -58,3 +58,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+manual_dics/global_all_column_remaps_WITH_ONTOLOGY_MAPPING_VALUE_ONLY.tsv filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -0,0 +1,218 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
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+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
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+
+# Streamlit
+.streamlit/secrets.toml

800k_completed_metadata.csv.gz

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+oid sha256:a57c080d25c51bfec094263d1d52a53c00ccf66e6a5b795c0ff356c184aa3809
+size 14713461

800k_rnaseq_metappuccino_labels.db.gz

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+version https://git-lfs.github.com/spec/v1
+oid sha256:6aa48ccdd3d378467cf37073a85cbdfb431d307a43d784ffeb0fce092eae605d
+size 1895052372

LICENSE

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README.md

@@ -1,3 +1,9 @@
----
-license: apache-2.0
----
+# 1M RNAseq SRA samples annotations
+
+- 800k_completed_metadata.csv: main metadata table for approximately 800k annotated RNA-seq/SRA samples.
+- 800k_rnaseq_metappuccino_labels.db: SQLite database containing Metappuccino labels and associated structured metadata.
+- manual_dics/: folder containing manual normalization and cross-column remapping dictionaries.
+  - FINAL_pass_unique_biopsy_site_values_mapped_to_uberon_with_cosine.tsv: maps raw biopsy_site values to normalized UBERON anatomical terms.
+  - FINAL_pass_unique_organ_values_mapped_to_uberon_with_cosine.tsv: maps raw organ values to normalized UBERON anatomical terms.
+  - FINAL_pass_unique_disease_values_mapped_to_dot_with_cosine.tsv: maps raw disease values to normalized DOT/DOID disease terms.
+  - global_all_column_remaps_WITH_ONTOLOGY_MAPPING_VALUE_ONLY.tsv: defines cross-column remapping rules for values found in the wrong metadata field.

manual_dics/FINAL_pass_unique_biopsy_site_values_mapped_to_uberon_with_cosine.tsv

@@ -0,0 +1,381 @@
+value	uberon_name	cosine_similarity
+Abdomen, skin	skin of abdomen	0.89397323
+adder		0.1896298
+adnexa	uterine adnexa	0.72784257
+air		0.17313093
+antenna	antenna	0.99999994
+anterior cruciate ligament	anterior cruciate ligament	0.99999994
+anterior cul de sac	vesico-uterine pouch	0.17461866
+anterior tibialis	tibialis anterior muscle	0.8526104
+aqueous humor	aqueous humor	1.0
+Arm, skin	skin of upper arm	0.78468335
+Arm, skin, dermis	dermis	0.68117976
+articular capsule	articular capsule	1.0000002
+articular cartilage	articular cartilage	1.0000001
+aryepiglottis	aryepiglottic fold	0.874354
+ascites fluid	ascitic fluid	0.83092123
+ascitic effusion	ascitic fluid	0.8984853
+auricle	auricle	1.0
+axilla	axilla	1.0000001
+axillary	axilla	0.8816522
+axillary LN	axillary lymph node	0.8165453
+axillary node	axillary lymph node	0.9555891
+Back, skin	skin of back	0.914754
+Back, skin, epidermis	epidermis	0.7666265
+Barrett's Oesophagus segment	esophagus	0.5807909
+basal ganglion	basal ganglion	1.0000001
+bile	bile	1.0
+Bile duct, common hepatic duct	common hepatic duct	0.8916615
+biliary organ	biliary tract	0.8826401
+blood, peripheral vein	peripheral blood	0.79244626
+Bone marrow, stroma	bone marrow	0.80276763
+Bone, cranium, clivus	clivus	0.6284603
+Bone, distal femur	femur	0.7665387
+Bone, femur	femur	0.861582
+Bone, fibula	fibula	0.8154766
+Bone, humerus	humerus	0.8096921
+Bone, jaw	jaw	0.7067802
+Bone, jaw, maxilla	maxilla	0.7759691
+Bone, left femur	femur	0.7212278
+Bone, left ilium	ilium	0.6823755
+Bone, left scapula	scapula	0.6399012
+Bone, leg	leg bone	0.9146567
+Bone, pelvis, acetabulum	acetabulum	0.73130864
+Bone, rib	rib	0.7425922
+Bone, right distal femur	femur	0.75684226
+Bone, right femur	femur	0.7717785
+Bone, right humerus	humerus	0.74555564
+Bone, sacrum	sacrum	0.74996936
+Bone, spine	vertebral column	0.48357922
+Bone, tibia	tibia	0.85344094
+Bone, vertebra	vertebra	0.7793418
+Brachialis muscle	brachialis muscle	1.0000002
+brachiocephalic trunk	brachiocephalic artery	0.90650135
+brain stem	brainstem	0.6405661
+Brain, falx cerebri	falx cerebri	0.90487856
+Brain, hippocampus	hippocampus	0.9285996
+Brain, hypothalamus	hypothalamus	0.89444923
+Brain, left frontal lobe	frontal lobe	0.74508595
+Brain, left fronto-parietal lobe	frontoparietal cortex	0.6444911
+Brain, left occipital lobe	occipital lobe	0.8262837
+Brain, left parietal lobe	parietal lobe	0.80000925
+Brain, left temporal lobe	temporal lobe	0.77084875
+Brain, meningeal dura mater	dura mater	0.74843824
+Brain, meninges	meninx	0.43137348
+Brain, optic canal	optic canal	0.8518318
+Brain, parietal lobe	parietal lobe	0.8786379
+Brain, posterior fossa	posterior cranial fossa	0.8612244
+Brain, right frontal cortex	frontal cortex	0.783167
+Brain, right frontal lobe	frontal lobe	0.7773529
+Brain, right frontal parieto-occipital cortex	parieto-occipital cortex	0.84914786
+Brain, right fronto-parietal lobe	frontoparietal cortex	0.6925377
+Brain, right fronto-temporal lobe	frontotemporal cortex	0.7024604
+Brain, right lateral ventricle	lateral ventricle	0.752661
+Brain, right occipital lobe	occipital lobe	0.82977754
+Brain, right parietal lobe	parietal lobe	0.7908889
+Brain, right parieto-occipital lobe	parieto-occipital cortex	0.8406732
+Brain, right temporal cortex	temporal cortex	0.76708686
+Brain, right temporal lobe	temporal lobe	0.7601615
+Brain, right temporo-occipital lobe	temporo-occipital cortex	0.80114055
+Brain, right temporo-parietal junction	temporoparietal junction	0.72938854
+Brain, temporal lobe	temporal lobe	0.88942236
+Brain, temporal lobe, blood microvessel	brain blood vessel	0.7201049
+Brain, temporo-occipital lobe	temporo-occipital cortex	0.88114786
+Brainstem, pons	pons	0.65734106
+Breast, epithelium	mammary gland epithelium	0.6935687
+Breast, stroma	mammary gland stroma	0.70577186
+Buttock, skin	skin of buttock	0.9381326
+caecum	cecum	0.8849787
+calcus		0.18097189
+Caudal fin	caudal fin	1.0000001
+caudate nucleus	caudate nucleus	1.0000001
+celiac axis	celiac artery	0.82892704
+Celiac axis lymph node	celiac lymph node	0.9614239
+cerebral organ	brain	0.59656405
+cerebral spinal fluid	cerebrospinal fluid	0.7915826
+cervical LN	cervical lymph node	0.74610424
+Cervical, LN	cervical lymph node	0.73898625
+Chest, skin	skin of chest	0.8913643
+clavicle	clavicle	1.0000001
+coecum	cecum	0.83150685
+Colon, ascending	ascending colon	0.93160474
+Colon, mucosa	colonic mucosa	0.9033359
+Colon, sigmoid	sigmoid colon	0.935086
+Colon, transverse	transverse colon	0.9332312
+cucumber		0.08749334
+cul de sac	rectouterine pouch	0.043430615
+Ear, inner ear, cochlea	cochlea	0.81573737
+Ear, skin	skin of ear	0.90114963
+EBV B-CELLS		0.09328094
+effusion		0.17127106
+elbow	elbow	1.0
+Embryonic heart, cardiac muscle	heart	0.5408638
+Embryonic heart, ventricular epicardium	epicardium	0.728783
+Embryonic limb, cartilage	cartilage tissue	0.70816535
+Embryonic liver	liver	0.5487298
+Endometrium, epithelium	endometrium	0.9147095
+Epigastrium	epigastric region	0.7663076
+Esophagus, distal	lower esophagus	0.8000455
+exfolitated human epithelial cells from stool		0.14268358
+eye lid	eyelid	0.852324
+Eye socket	orbit	0.4941814
+Eye, bulbar conjunctiva	bulbar conjunctiva	0.9292534
+Eye, cornea	cornea	0.87704486
+Eye, cornea, epithelium	corneal epithelium	0.8818718
+Eye, globe	eyeball	0.80746317
+Eye, ocular lens	lens of camera-type eye	0.6427158
+Eye, ocular lens, epithelium	lens epithelium	0.8212474
+Eye, retina	retina	0.8427897
+Eye, retina, retinal pigment epithelium	retinal pigment epithelium	0.9038105
+Eye, uvea	uvea	0.86343116
+Face, skin	skin of face	0.9061997
+Face, skin, sebaceous gland	sebaceous gland	0.8298489
+Fallopian tube, ampulla	ampulla of uterine tube	0.7529362
+Fallopian tube, subserosa	uterine tube	0.4443578
+fat pad	adipose tissue	0.6678662
+femur left	femur	0.7816587
+Fetal bone, limb	limb bone	0.79111135
+Fetal brain, cerebral cortex	cerebral cortex	0.6937956
+Fetal brain, choroid plexus	choroid plexus	0.7912245
+Fetal brain, forebrain	forebrain	0.7793399
+Fetal brain, hindbrain	hindbrain	0.7726132
+Fetal brain, ventral mesencephalon	ventral mesencephalon	0.8291587
+Fetal esophagus	esophagus	0.72665066
+Fetal intestine	intestine	0.75718427
+Fetal oral cavity, palate	palate	0.7063023
+Fetal pancreas, islets of Langerhans	islet of Langerhans	0.7844769
+Fetal stomach, epithelium	stomach epithelium	0.77672493
+Fetal testis	testis	0.77123547
+Fetal urinary bladder	urinary bladder	0.6949231
+fimbria	fimbria of uterine tube	0.6540993
+Fin	fin	1.0
+floor of mouth	floor of mouth	1.0000001
+forearm	forearm	1.0000002
+Forearm, skin	skin of forearm	0.9272198
+forehead	forehead	1.0000002
+forelimb stylopod	forelimb stylopod	1.0
+Foreskin, skin	skin of prepuce of penis	0.41732663
+Foreskin, skin, dermis	dermis	0.6626989
+Foreskin, skin, dermis, microvascular endothelium	microvascular endothelium	0.7240523
+Foreskin, skin, epidermis	epidermis	0.67021227
+frontal bone	frontal bone	1.0000001
+GA		0.2630852
+ganglion	ganglion	1.0
+gastrocnemius muscle	gastrocnemius muscle	1.0
+Gastrula	gastrula	1.0000001
+GB		0.2332956
+Gill	gill	1.0
+Groin	groin	1.0000001
+Groin, skin	skin of groin	0.9380174
+hamstring	hamstring muscle	0.93408644
+Hand, skin	skin of hand	0.9206213
+Head kidney	head kidney	1.0000001
+heel	heel	1.0
+hind limb	hindlimb	0.8985489
+hindlimb	hindlimb	1.0
+Hypodermis	hypodermis	1.0
+ileo-inguinal node	inguinal lymph node	0.88150233
+iliac bone	ilium	0.74951595
+Iliac lymph node	iliac lymph node	1.0
+iliac vein	iliac vein	1.0000002
+ilium right	ilium	0.8533598
+inferior turbinate	inferior nasal concha	0.70622706
+infrarenal lymph node	retroperitoneal lymph node	0.7761977
+inguinal gland	inguinal lymph node	0.7690822
+inguinal LN	inguinal lymph node	0.79290867
+internal capsule	internal capsule of telencephalon	0.7024829
+Intestine, ileocecal valve	ileocecal valve	0.8637368
+jawbone	jaw	0.8316852
+jejunum_1	jejunum	0.8589622
+jejunum_2	jejunum	0.81619656
+jejunum_3	jejunum	0.6951437
+jejunum_4	jejunum	0.74616694
+Kidney, epithelium	kidney epithelium	0.92655635
+Kidney, glomerulus	glomerulus	0.89457816
+Kidney, proximal tubule	proximal tubule	0.9256049
+Kidney, renal pelvis	renal pelvis	0.91787636
+LA		0.26169294
+labial salivary gland	labial gland	0.8418175
+Larynx, supraglottis	supraglottis	0.860058
+lateral septum	lateral septal nucleus	0.8155811
+LB		0.11535665
+leaf		0.20418368
+Left axillary lymph node	axillary lymph node	0.919783
+Left calf, skin	skin of calf	0.8294084
+left common carotid artery	common carotid artery	0.86581194
+Left inguinal lymph node	inguinal lymph node	0.9061039
+Left leg, skeletal muscle	skeletal muscle tissue	0.60216045
+Left shin, skin	skin of lower leg	0.43416804
+Left supraclavicular lymph node	supraclavicular lymph node	0.9123231
+Leg, skin	skin of lower leg	0.79844356
+Liver, intrahepatic bile duct	intrahepatic bile duct	0.9302899
+lower back	lower back	1.0
+lower leg	lower leg	1.0000001
+Lung, bronchus, epithelium	bronchus epithelium	0.86419874
+Lung, endothelium	lung endothelium	0.93003494
+Lung, left upper lobe	upper lobe of left lung	0.93947995
+Lung, pleura	pleura	0.8769353
+Lung, right lower lobe	lower lobe of right lung	0.91794634
+Lung, right upper lobe	upper lobe of right lung	0.94559526
+lung_small_cell	lung	0.55603415
+lung_squamous	lung	0.5833643
+mammary fat pad	mammary fat pad	1.0000001
+Mammary placode	mammary placode	1.0000001
+membrane		0.3146323
+middle turbinate	middle nasal concha	0.72329575
+Midgut	midgut	1.0000001
+Morula	morula	1.0000001
+Muscle, pectoralis major	pectoralis major muscle	0.9654458
+Muscle, triceps brachii	triceps brachii muscle	0.9735701
+Muscle, vastus lateralis	vastus lateralis muscle	0.97360116
+nasal passage	nasal cavity	0.81223
+nasal passages	nasal cavity	0.85694456
+nasal tissue	nasal cavity	0.82623994
+nasal turbinates	nasal concha	0.71538514
+Neck, hypodermis	hypodermis	0.83015
+Nose, nasal cavity	nasal cavity	0.91287565
+Nose, nasal cavity, epithelium	nasal cavity epithelium	0.89541566
+Nose, nasal cavity, nasal turbinate	nasal concha	0.6913282
+Nose, skin	skin of nose	0.90369296
+nucleus		0.273911
+Obturator lymph node	obturator lymph node	1.0
+occipital bone	occipital bone	0.99999994
+Oral cavity, alveolar ridge	alveolar ridge	0.8804753
+Oral cavity, buccal mucosa	buccal mucosa	0.88480693
+Oral cavity, floor of mouth	floor of mouth	0.90125924
+Oral cavity, gingiva	gingiva	0.8511558
+Oral cavity, gingiva, epithelium	gingival epithelium	0.8648495
+Oral cavity, retromolar trigone	retromolar trigone	0.80234027
+Oral cavity, soft palate, hypodermis	soft palate	0.62246203
+Oral cavity, tongue	tongue	0.7817873
+Oral cavity, tongue, anterior part	anterior part of tongue	0.8694002
+Oral cavity, tongue, lateral border	tongue	0.5628434
+Oral cavity, tonsil	palatine tonsil	0.72200775
+Oral cavity, tonsil, tonsillar fossa	tonsillar fossa	0.8587235
+Oral cavity, tonsil, tonsillar pillar	palatine tonsil	0.6889178
+Orbital region	orbital region	1.0
+Ovary, ovarian follicle, granulosa cell layer	granulosa cell layer	0.74124295
+Ovary, surface epithelium	ovarian surface epithelium	0.9230838
+palmer fascia	palmar fascia	0.94681156
+Pancreas, ampulla of Vater	hepatopancreatic ampulla	0.70993006
+Pancreas, islets of Langerhans	islet of Langerhans	0.8610744
+Paragastric lymph node	gastric lymph node	0.8029991
+parapharyngeal gland		0.13144527
+paraspinal	paraspinal region	0.9289522
+parasternum	sternum	0.27208057
+parietal bone	parietal bone	1.0000001
+parietal occipital	parieto-occipital cortex	0.90160227
+parieto occipital	parieto-occipital cortex	0.9185189
+Parotid lymph node	parotid lymph node	0.99999994
+patella	patella	1.0
+patellar tendon	patellar ligament	0.8877057
+pectoralis	pectoralis major muscle	0.82914317
+pectoralis major	pectoralis major muscle	0.92543906
+pelvic bone	pelvic bone	1.0
+Pelvic wall	pelvic wall	0.99999994
+Pelvis, innominate bone	hip bone	0.49968904
+Pelvis, muscle	pelvic muscle	0.86806846
+pericardial adipose tissue	pericardial adipose tissue	1.0000001
+periesophagus	esophagus	0.6129679
+Perineus, muscle	perineal muscle	0.90522903
+Peripheral nervous system, cranial nerve, hypoglossal nerve	hypoglossal nerve	0.81103975
+Peripheral nervous system, lower leg nerve	peripheral nerve	0.73821306
+Peripheral nervous system, nerve	peripheral nerve	0.84410965
+Peripheral nervous system, sural nerve	sural nerve	0.8586925
+peritoneal cavity	peritoneal cavity	1.0
+peritoneal nodule	peritoneum	0.735579
+Pharynx, hypopharynx	hypopharynx	0.89016247
+Pharynx, nasopharynx	nasopharynx	0.83675003
+Pharynx, nasopharynx, epithelium	nasopharyngeal epithelium	0.846358
+Pharynx, oropharynx	oropharynx	0.90541357
+Placenta, arterial endothelium	placenta	0.6803268
+portal vein	portal vein	1.0000001
+posterior vena cava	inferior vena cava	0.68027085
+prepuce	prepuce of penis	0.70985246
+Pretracheal lymph node	pretracheal lymph node	1.0
+Prostate, epithelium	prostate gland epithelium	0.86636895
+Prostate, stroma	prostate gland stroma	0.8781293
+psoas	psoas muscle	0.8236657
+Pyloric lymph node	pyloric lymph node	0.99999994
+quadricep	quadriceps femoris muscle	0.82411134
+radial		0.25531158
+radius	radius bone	0.69847167
+rectus abdominis	rectus abdominis muscle	0.96967995
+rectus femoris	rectus femoris muscle	0.95899
+respiratory epithelium	respiratory epithelium	1.0
+retromolar trigone	retromolar trigone	1.0000001
+Retroperitoneal lymph node	retroperitoneal lymph node	1.0000002
+Retroperitoneal space	retroperitoneal space	1.0
+retropitoneum	retroperitoneum	0.5869338
+retropperitoneum	retroperitoneum	0.85673785
+Rib, costal cartilage	costal cartilage	0.8905544
+Right anterior leg, skin	skin of lower leg	0.57244754
+Right axillary lymph node	axillary lymph node	0.8977654
+Right buttock, hypodermis	hypodermis	0.68216354
+Right ear, skin	skin of ear	0.66422313
+Right pararenal lymph node	pararenal lymph node	0.9169978
+Right temple, skin	skin of temple	0.7664919
+Right thigh, skin	skin of thigh	0.8242299
+root		0.25094566
+Salivary gland, sublingual gland	sublingual gland	0.8653391
+Salivary gland, submandibular gland	submandibular gland	0.9086324
+saphenous vein	saphenous vein	1.0000001
+Seedling		0.13669565
+Semitendinosus tendon	semitendinosus tendon	1.0
+shoulder joint	shoulder joint	0.9999999
+Shoulder, skin	skin of shoulder	0.91628134
+shoulder/back	skin of back	0.51655746
+sinus	paranasal sinus	0.68257076
+skin, unspecified	skin	0.46389174
+skin, upper arm	skin of upper arm	0.96127737
+small bowel	small intestine	0.9144154
+Small intestine, duodenum	duodenum	0.7765962
+Small intestine, jejunum	jejunum	0.87848866
+Snout	snout	1.0
+spermatic cord	spermatic cord	1.0000001
+Stem		0.20665768
+Stomach, fundus	fundus of stomach	0.89701843
+stomach_1	stomach	0.7575322
+stomach_2	stomach	0.6916539
+stomach_3	stomach	0.64318377
+stomach_4	stomach	0.61599606
+stomach_5	stomach	0.60239375
+subclavicular	subclavian region	0.8458588
+superior vena cava	superior vena cava	0.9999999
+Supraclavicular lymph node	supraclavicular lymph node	1.0
+supraglottis	supraglottis	1.0000001
+synovial membrane	synovial membrane	1.0000002
+tail	tail	1.0000001
+talus	talus	1.0
+tear	lacrimal fluid	0.26168734
+Temple, skin	skin of temple	0.9438474
+temporoparietal	temporoparietal junction	0.9188652
+teres major	teres major muscle	0.8449147
+Thigh, quadriceps skeletal muscle	quadriceps femoris muscle	0.8646847
+Thigh, skeletal muscle	skeletal muscle tissue	0.68212354
+Thigh, skin	skin of thigh	0.92669845
+Thoracic cavity	thoracic cavity	1.0
+Thoracic lymph duct	thoracic duct	0.8072634
+thoracic spinal ligament	spinal ligament	0.82314414
+tibialis anterior muscle	tibialis anterior muscle	1.0
+Tooth, dental pulp	dental pulp	0.88605726
+tricep	triceps brachii muscle	0.7229292
+Trophoblast, cytotrophoblast	cytotrophoblast	0.9131254
+Trunk, skin	skin of trunk	0.90851593
+Upper arm	upper arm	1.0000001
+upper limb	upper limb	1.0000001
+urethra	urethra	1.0000002
+Urinary bladder, bladder dome	dome of urinary bladder	0.927925
+Urinary bladder, urothelium	urothelium of urinary bladder	0.94977003
+Uterus, cervix, ectocervical epithelium	ectocervical epithelium	0.8556006
+Uterus, cervix, endocervical epithelium	endocervical epithelium	0.8389935
+Uterus, myometrium	myometrium	0.87591445
+Vagina, mucosa	vaginal mucosa	0.92024803
+vascular tissue		0.24078839
+ventricles		0.24028896
+vertebra	vertebra	1.0000001
+viscera		0.20023066
+vitelline artery	vitelline artery	1.0
+vitreous	vitreous humor	0.89124155
+wall		0.2526618
+Whole embryo	embryo	0.832602

manual_dics/global_all_column_remaps_WITH_ONTOLOGY_MAPPING_VALUE_ONLY.tsv

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