# HG changeset patch
# User nathandunn
# Date 1512434112 18000
# Node ID 49b46f044d487a2a23f65c23e3b5d82219625cee
# Parent  d40860663861323595ccae6d24dda36ea99b1e55
planemo upload commit 0dbcda86caba8f8fead7cb6fde0ae3e73d398f1e

diff -r d40860663861 -r 49b46f044d48 README.md
--- a/README.md	Sat Dec 02 16:41:34 2017 -0500
+++ b/README.md	Mon Dec 04 19:35:12 2017 -0500
@@ -14,6 +14,9 @@
 
 
 
-![Screen Shot](images/ScreenShot1.png)
+![Screen Shot](images/ScreenShot2.png)
 
 
+Upload new tool.
+
+    planemo shed_upload --shed_target toolshed
\ No newline at end of file
diff -r d40860663861 -r 49b46f044d48 bioentityset-overrepresentation.xml
--- a/bioentityset-overrepresentation.xml	Sat Dec 02 16:41:34 2017 -0500
+++ b/bioentityset-overrepresentation.xml	Mon Dec 04 19:35:12 2017 -0500
@@ -21,7 +21,15 @@
 #set $background_string += '&background='+str($word)
 #end for
 
-curl --silent -X GET --header 'Accept: application/json' 'https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/?object_category=$object_category$subject_string&background=$background_string&ontology=$ontology&subject_category=$subject_category&taxon=$taxon&object_category=$object_category&max_p_value=$max_p_value' > $output
+curl --silent -X GET --header 'Accept: application/json' 'https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/?object_category=$object_category$subject_string&background=$background_string&ontology=$ontology&subject_category=$subject_category&taxon=$taxon&object_category=$object_category&max_p_value=$max_p_value' > $output_json
+
+&&
+
+echo -e "p\tn\tp_uncorrected\tc" > $output_tsv
+
+&&
+
+cat $output_json | jq -r '.results[] | flatten | @tsv ' >> $output_tsv
 	]]></command>
 	<inputs>
 		<param  name="object_category" type="text" format="txt" multiple="false" label="CATEGORY of entity at link OBJECT (target), e.g. function, phenotype, disease" />
@@ -34,9 +42,19 @@
 		<param  name="object_category" type="text" format="txt" multiple="false" label="E.g. phenotype, function" value="phenotype" />
 		<param name="max_p_value" type="text" format="txt" multiple="false" value="0.05" label="Exclude results with p-value greater than this"/>
 	</inputs>
-	<expand macro="outputs" />
+	<outputs>
+		<data name="output_json" format="json"/>
+		<data 
+			name="output_tsv" 
+			format="tsv"
+			header_row="1"
+			>
+		</data>
+	</outputs>
 	<tests>
-		<!--emulate: https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/
+		<!--
+
+		emulate: https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/
 		?object_category=phenotype
 subject=NCBIGene%3A6295
 subject=NCBIGene%3A1258
@@ -61,7 +79,8 @@
 			<param name="taxon" value="NCBITaxon:9606"/>
 			<param name="object_category" value="phenotype"/>
 			<param name="max_p_value" value="0.05"/>
-			<output name="output" file="bioentityset-overrepresentation.json"/>
+			<output name="output_json" file="bioentityset-overrepresentation.json"/>
+			<output name="output_tsv" file="bioentityset-overrepresentation.tsv"/>
 		</test>
 	</tests>
 	<expand macro="citations" />
diff -r d40860663861 -r 49b46f044d48 images/ScreenShot2.png
Binary file images/ScreenShot2.png has changed
diff -r d40860663861 -r 49b46f044d48 macros.xml
--- a/macros.xml	Sat Dec 02 16:41:34 2017 -0500
+++ b/macros.xml	Mon Dec 04 19:35:12 2017 -0500
@@ -1,6 +1,7 @@
 <macros>
     <xml name="frontmatter">
         <requirements>
+                <requirement type="package" version="1.5">jq</requirement>
         </requirements>
         <stdio>
             <exit_code range="1:"/>
diff -r d40860663861 -r 49b46f044d48 run_server.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_server.sh	Mon Dec 04 19:35:12 2017 -0500
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+planemo s `cat tools.txt`
+
+
diff -r d40860663861 -r 49b46f044d48 run_tests.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_tests.sh	Mon Dec 04 19:35:12 2017 -0500
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+planemo t `cat tools.txt`
+
+
diff -r d40860663861 -r 49b46f044d48 test-data/bioentityset-overrepresentation.json
--- a/test-data/bioentityset-overrepresentation.json	Sat Dec 02 16:41:34 2017 -0500
+++ b/test-data/bioentityset-overrepresentation.json	Mon Dec 04 19:35:12 2017 -0500
@@ -1,1 +1,1 @@
-{"results": [{"p": 6.830958069760975e-17, "p_uncorrected": 2.2250677751664415e-19, "n": "Peripheral retinal degeneration", "c": "HP:0007769"}, {"p": 6.830958069760975e-17, "p_uncorrected": 2.2250677751664415e-19, "n": "Hypoplasia of the retina", "c": "HP:0007770"}, {"p": 7.89829526810427e-17, "p_uncorrected": 2.572734615017678e-19, "n": "Subretinal exudate", "c": "HP:0011532"}, {"p": 7.89829526810427e-17, "p_uncorrected": 2.572734615017678e-19, "n": "Progressive night blindness", "c": "HP:0007675"}, {"p": 7.89829526810427e-17, "p_uncorrected": 2.572734615017678e-19, "n": "Retinal hole", "c": "HP:0011530"}, {"p": 7.89829526810427e-17, "p_uncorrected": 2.572734615017678e-19, "n": "Progressive cone degeneration", "c": "HP:0008020"}, {"p": 1.0494238468181382e-16, "p_uncorrected": 3.418318719277323e-19, "n": "Progressive retinal degeneration", "c": "HP:0007893"}, {"p": 1.206054271707303e-16, "p_uncorrected": 3.928515543020531e-19, "n": "Age-related macular degeneration", "c": "HP:0007868"}, {"p": 1.206054271707303e-16, "p_uncorrected": 3.928515543020531e-19, "n": "Abnormal dark-adapted bright flash electroretinogram", "c": "HP:0030470"}, {"p": 1.206054271707303e-16, "p_uncorrected": 3.928515543020531e-19, "n": "Exudative retinopathy", "c": "HP:0007898"}, {"p": 1.206054271707303e-16, "p_uncorrected": 3.928515543020531e-19, "n": "Severe hearing impairment", "c": "HP:0012714"}, {"p": 1.206054271707303e-16, "p_uncorrected": 3.928515543020531e-19, "n": "Severe sensorineural hearing impairment", "c": "HP:0008625"}, {"p": 1.206054271707303e-16, "p_uncorrected": 3.928515543020531e-19, "n": "Abnormal amplitude of dark-adapted bright flash electroretinogram", "c": "HP:0030478"}, {"p": 1.206054271707303e-16, "p_uncorrected": 3.928515543020531e-19, "n": "Abnormal dark-adapted electroretinogram", "c": "HP:0030469"}, {"p": 1.206054271707303e-16, "p_uncorrected": 3.928515543020531e-19, "n": "Electronegative electroretinogram", "c": "HP:0007984"}, {"p": 1.5839101496752315e-16, "p_uncorrected": 5.159316448453523e-19, "n": "Abetalipoproteinemia", "c": "HP:0008181"}, {"p": 2.0651383842794574e-16, "p_uncorrected": 6.726835127946115e-19, "n": "Mottled pigmentation", "c": "HP:0001070"}, {"p": 2.0651383842794574e-16, "p_uncorrected": 6.726835127946115e-19, "n": "Tapetoretinal degeneration", "c": "HP:0000547"}, {"p": 2.0651383842794574e-16, "p_uncorrected": 6.726835127946115e-19, "n": "Decreased light- and dark-adapted electroretinogram amplitude", "c": "HP:0000654"}, {"p": 3.0355215014437025e-16, "p_uncorrected": 9.887692187113037e-19, "n": "Vitreoretinal degeneration", "c": "HP:0000655"}, {"p": 3.440257701614546e-16, "p_uncorrected": 1.1206051145324254e-18, "n": "Abnormal light- and dark-adapted electroretinogram", "c": "HP:0008323"}, {"p": 4.398497628785198e-16, "p_uncorrected": 1.4327353839691198e-18, "n": "Chorioretinal atrophy", "c": "HP:0000533"}, {"p": 5.5905604395766495e-16, "p_uncorrected": 1.8210294591454885e-18, "n": "Chorioretinal degeneration", "c": "HP:0200065"}, {"p": 5.5905604395766495e-16, "p_uncorrected": 1.8210294591454885e-18, "n": "Pigmentary retinal degeneration", "c": "HP:0001146"}, {"p": 6.289380494506863e-16, "p_uncorrected": 2.0486581415331802e-18, "n": "Abnormal full-field electroretinogram", "c": "HP:0030466"}, {"p": 6.289380494506863e-16, "p_uncorrected": 2.0486581415331802e-18, "n": "Decreased circulating low-density lipoprotein levels", "c": "HP:0003563"}, {"p": 8.882660716055608e-16, "p_uncorrected": 2.893374826076745e-18, "n": "Macular dystrophy", "c": "HP:0007754"}, {"p": 1.382679693118587e-15, "p_uncorrected": 4.503842648594746e-18, "n": "Hypopigmentation of the fundus", "c": "HP:0007894"}, {"p": 1.9031265438999284e-15, "p_uncorrected": 6.1991092635176825e-18, "n": "Undetectable electroretinogram", "c": "HP:0000550"}, {"p": 2.1122613289451027e-15, "p_uncorrected": 6.880330061710433e-18, "n": "Cystoid macular edema", "c": "HP:0011505"}, {"p": 2.3418549516569064e-15, "p_uncorrected": 7.628192024941062e-18, "n": "Macular edema", "c": "HP:0040049"}, {"p": 2.593667312051605e-15, "p_uncorrected": 8.44842772655246e-18, "n": "Hypolipoproteinemia", "c": "HP:0010981"}, {"p": 2.593667312051605e-15, "p_uncorrected": 8.44842772655246e-18, "n": "Retinal exudate", "c": "HP:0001147"}, {"p": 2.593667312051605e-15, "p_uncorrected": 8.44842772655246e-18, "n": "Acanthocytosis", "c": "HP:0001927"}, {"p": 2.8695893665276034e-15, "p_uncorrected": 9.347196633640402e-18, "n": "Macular thickening", "c": "HP:0030498"}, {"p": 3.1716514051110723e-15, "p_uncorrected": 1.0331112068765708e-17, "n": "Aplasia/Hypoplasia of the retina", "c": "HP:0008061"}, {"p": 3.50203175980966e-15, "p_uncorrected": 1.1407269575927232e-17, "n": "Progressive sensorineural hearing impairment", "c": "HP:0000408"}, {"p": 3.50203175980966e-15, "p_uncorrected": 1.1407269575927232e-17, "n": "Congenital blindness", "c": "HP:0007875"}, {"p": 4.25725636613049e-15, "p_uncorrected": 1.3867284580229608e-17, "n": "Keratoconus", "c": "HP:0000563"}, {"p": 4.25725636613049e-15, "p_uncorrected": 1.3867284580229608e-17, "n": "Increased corneal curvature", "c": "HP:0100692"}, {"p": 4.6872822616738014e-15, "p_uncorrected": 1.52680203963316e-17, "n": "Decreased corneal thickness", "c": "HP:0100689"}, {"p": 5.6665065757932175e-15, "p_uncorrected": 1.8457676142648916e-17, "n": "Congenital sensorineural hearing impairment", "c": "HP:0008527"}, {"p": 6.22204643614839e-15, "p_uncorrected": 2.0267252235011042e-17, "n": "Abnormality of corneal thickness", "c": "HP:0011486"}, {"p": 6.22204643614839e-15, "p_uncorrected": 2.0267252235011042e-17, "n": "Constriction of peripheral visual field", "c": "HP:0001133"}, {"p": 6.826128614391264e-15, "p_uncorrected": 2.2234946626681643e-17, "n": "Retinal perforation", "c": "HP:0011958"}, {"p": 9.806380222363747e-15, "p_uncorrected": 3.194260658750406e-17, "n": "Yellow/white lesions of the retina", "c": "HP:0030506"}, {"p": 1.0714378391101258e-14, "p_uncorrected": 3.49002553456067e-17, "n": "Abnormality of the level of lipoprotein cholesterol", "c": "HP:0010979"}, {"p": 1.1697348885694248e-14, "p_uncorrected": 3.810211363418322e-17, "n": "Macular degeneration", "c": "HP:0000608"}, {"p": 1.2760744238882322e-14, "p_uncorrected": 4.156594214619649e-17, "n": "Hyperinsulinemia", "c": "HP:0000842"}, {"p": 1.3910360837022003e-14, "p_uncorrected": 4.531062161896418e-17, "n": "Cone/cone-rod dystrophy", "c": "HP:0000548"}, {"p": 1.5152357340328436e-14, "p_uncorrected": 4.9356212834946045e-17, "n": "Abnormal insulin level", "c": "HP:0040214"}, {"p": 1.5152357340328436e-14, "p_uncorrected": 4.9356212834946045e-17, "n": "Abnormal circulating insulin level", "c": "HP:0040215"}, {"p": 1.9500056883908283e-14, "p_uncorrected": 6.351810059904978e-17, "n": "Progressive hearing impairment", "c": "HP:0001730"}, {"p": 2.4939874038128746e-14, "p_uncorrected": 8.123737471703174e-17, "n": "Nephronophthisis", "c": "HP:0000090"}, {"p": 2.7035661772422384e-14, "p_uncorrected": 8.80640448613107e-17, "n": "Atypical scarring of skin", "c": "HP:0000987"}, {"p": 4.008932828040028e-14, "p_uncorrected": 1.3058413120651556e-16, "n": "Retinal atrophy", "c": "HP:0001105"}, {"p": 1.5770726338521152e-13, "p_uncorrected": 5.137044409941743e-16, "n": "Abnormality of the renal medulla", "c": "HP:0100957"}, {"p": 5.259073285790678e-13, "p_uncorrected": 1.7130531875539669e-15, "n": "Chorioretinal abnormality", "c": "HP:0000532"}, {"p": 6.659349463318531e-13, "p_uncorrected": 2.1691692062926814e-15, "n": "Poikilocytosis", "c": "HP:0004447"}, {"p": 6.659349463318531e-13, "p_uncorrected": 2.1691692062926814e-15, "n": "Nyctalopia", "c": "HP:0000662"}, {"p": 7.058112904256892e-13, "p_uncorrected": 2.299059577933841e-15, "n": "Progressive visual loss", "c": "HP:0000529"}, {"p": 7.478238672358695e-13, "p_uncorrected": 2.4359083623318224e-15, "n": "Type II diabetes mellitus", "c": "HP:0005978"}, {"p": 1.050722902848435e-12, "p_uncorrected": 3.4225501721447396e-15, "n": "Abnormality of the retinal vasculature", "c": "HP:0008046"}, {"p": 1.050722902848435e-12, "p_uncorrected": 3.4225501721447396e-15, "n": "Abnormal electroretinogram", "c": "HP:0000512"}, {"p": 1.050722902848435e-12, "p_uncorrected": 3.4225501721447396e-15, "n": "Abnormality of the choroid", "c": "HP:0000610"}, {"p": 1.1738758145094465e-12, "p_uncorrected": 3.823699721529142e-15, "n": "Aplasia/Hypoplasia affecting the fundus", "c": "HP:0008057"}, {"p": 1.2401964820000423e-12, "p_uncorrected": 4.039727954397532e-15, "n": "Retinal neoplasm", "c": "HP:0012777"}, {"p": 1.2401964820000423e-12, "p_uncorrected": 4.039727954397532e-15, "n": "Retinoblastoma", "c": "HP:0009919"}, {"p": 1.8071448747244773e-12, "p_uncorrected": 5.8864653899820104e-15, "n": "Rod-cone dystrophy", "c": "HP:0000510"}, {"p": 2.4683037784772113e-12, "p_uncorrected": 8.040077454323164e-15, "n": "Neurodegeneration", "c": "HP:0002180"}, {"p": 4.478830903968583e-12, "p_uncorrected": 1.4589025745826002e-14, "n": "Visual field defect", "c": "HP:0001123"}, {"p": 6.241419062480174e-12, "p_uncorrected": 2.0330355252378417e-14, "n": "Photophobia", "c": "HP:0000613"}, {"p": 8.224646178578066e-12, "p_uncorrected": 2.679037843185038e-14, "n": "Neoplasm of the eye", "c": "HP:0100012"}, {"p": 9.414914677027705e-12, "p_uncorrected": 3.0667474518005555e-14, "n": "Abnormal visual electrophysiology", "c": "HP:0030453"}, {"p": 1.1746775963207132e-11, "p_uncorrected": 3.8263113886668185e-14, "n": "Retinal degeneration", "c": "HP:0000546"}, {"p": 1.1746775963207132e-11, "p_uncorrected": 3.8263113886668185e-14, "n": "Abnormality of cholesterol metabolism", "c": "HP:0003107"}, {"p": 1.2271185604454866e-11, "p_uncorrected": 3.99712886138595e-14, "n": "Abnormality of the curvature of the cornea", "c": "HP:0100691"}, {"p": 1.2816571631169346e-11, "p_uncorrected": 4.174779032954184e-14, "n": "Gliosis", "c": "HP:0002171"}, {"p": 1.588495014454129e-11, "p_uncorrected": 5.174250861414101e-14, "n": "Abnormal macular morphology", "c": "HP:0001103"}, {"p": 1.588495014454129e-11, "p_uncorrected": 5.174250861414101e-14, "n": "Conductive hearing impairment", "c": "HP:0000405"}, {"p": 1.802887603054271e-11, "p_uncorrected": 5.872598055551371e-14, "n": "Blindness", "c": "HP:0000618"}, {"p": 2.5076918624406142e-11, "p_uncorrected": 8.168377402086691e-14, "n": "Functional abnormality of the middle ear", "c": "HP:0011452"}, {"p": 3.732511675833473e-11, "p_uncorrected": 1.2158018488056917e-13, "n": "Ophthalmoplegia", "c": "HP:0000602"}, {"p": 4.192831051586348e-11, "p_uncorrected": 1.3657430135460415e-13, "n": "Embryonal neoplasm", "c": "HP:0002898"}, {"p": 7.091426267827702e-11, "p_uncorrected": 2.3099108364259617e-13, "n": "Retinopathy", "c": "HP:0000488"}, {"p": 7.355048062205055e-11, "p_uncorrected": 2.3957811277540893e-13, "n": "Ophthalmoparesis", "c": "HP:0000597"}, {"p": 8.810257081441287e-11, "p_uncorrected": 2.869790580274035e-13, "n": "Pigmentary retinopathy", "c": "HP:0000580"}, {"p": 8.810257081441287e-11, "p_uncorrected": 2.869790580274035e-13, "n": "Polydactyly", "c": "HP:0010442"}, {"p": 1.388190595549975e-10, "p_uncorrected": 4.5217934708468243e-13, "n": "Microphthalmia", "c": "HP:0000568"}, {"p": 1.388190595549975e-10, "p_uncorrected": 4.5217934708468243e-13, "n": "Abnormality of the vasculature of the eye", "c": "HP:0008047"}, {"p": 1.700756278473561e-10, "p_uncorrected": 5.539922731184238e-13, "n": "Upper limb undergrowth", "c": "HP:0009824"}, {"p": 2.075293589422645e-10, "p_uncorrected": 6.759913972060733e-13, "n": "Retinal dystrophy", "c": "HP:0000556"}, {"p": 2.3646302288247017e-10, "p_uncorrected": 7.702378595520201e-13, "n": "Abnormality of globe size", "c": "HP:0100887"}, {"p": 5.981776395427826e-10, "p_uncorrected": 1.9484613665888684e-12, "n": "Abnormality of the glial cells", "c": "HP:0100705"}, {"p": 6.727486481875538e-10, "p_uncorrected": 2.1913636748780254e-12, "n": "Hypogonadism", "c": "HP:0000135"}, {"p": 6.926524543477764e-10, "p_uncorrected": 2.2561969196995973e-12, "n": "Abnormality of circulating hormone level", "c": "HP:0003117"}, {"p": 7.776774899705444e-10, "p_uncorrected": 2.5331514331288093e-12, "n": "Hypoplasia of penis", "c": "HP:0008736"}, {"p": 8.474892365194142e-10, "p_uncorrected": 2.760551259020893e-12, "n": "Neuroepithelial neoplasm", "c": "HP:0030063"}, {"p": 9.228914326532511e-10, "p_uncorrected": 3.0061610184144985e-12, "n": "Neuroectodermal neoplasm", "c": "HP:0030061"}, {"p": 9.228914326532511e-10, "p_uncorrected": 3.0061610184144985e-12, "n": "Nervous tissue neoplasm", "c": "HP:0030060"}, {"p": 1.1543718428324624e-09, "p_uncorrected": 3.760168869161115e-12, "n": "Glaucoma", "c": "HP:0000501"}, {"p": 1.2198554340554865e-09, "p_uncorrected": 3.973470469236112e-12, "n": "Wide nasal bridge", "c": "HP:0000431"}, {"p": 1.3984366259310385e-09, "p_uncorrected": 4.555168162641819e-12, "n": "Visual loss", "c": "HP:0000572"}, {"p": 1.6879988822761898e-09, "p_uncorrected": 5.498367694710716e-12, "n": "Abnormality of lipid metabolism", "c": "HP:0003119"}, {"p": 1.7334975044422942e-09, "p_uncorrected": 5.646571675707799e-12, "n": "Metrorrhagia", "c": "HP:0100608"}, {"p": 1.9779810642388804e-09, "p_uncorrected": 6.4429350626673635e-12, "n": "Scarring", "c": "HP:0100699"}, {"p": 2.0304474054716845e-09, "p_uncorrected": 6.613835196976171e-12, "n": "Abnormality of retinal pigmentation", "c": "HP:0007703"}, {"p": 2.628331383770522e-09, "p_uncorrected": 8.561340012281831e-12, "n": "Limb undergrowth", "c": "HP:0009826"}, {"p": 3.7316154453488525e-09, "p_uncorrected": 1.2155099170517434e-11, "n": "Obesity", "c": "HP:0001513"}, {"p": 3.919340997996726e-09, "p_uncorrected": 1.2766583055363929e-11, "n": "Hypoplastic male external genitalia", "c": "HP:0000050"}, {"p": 6.321359545900789e-09, "p_uncorrected": 2.0590747706517226e-11, "n": "Abnormality of the middle ear", "c": "HP:0000370"}, {"p": 7.098972376183352e-09, "p_uncorrected": 2.3123688521769875e-11, "n": "Anteverted nares", "c": "HP:0000463"}, {"p": 7.433390275858353e-09, "p_uncorrected": 2.4212997641232422e-11, "n": "Aplasia/Hypoplasia affecting the eye", "c": "HP:0008056"}, {"p": 7.433390275858353e-09, "p_uncorrected": 2.4212997641232422e-11, "n": "External genital hypoplasia", "c": "HP:0003241"}, {"p": 8.145089250918333e-09, "p_uncorrected": 2.6531235345010855e-11, "n": "Increased body weight", "c": "HP:0004324"}, {"p": 9.75530240286726e-09, "p_uncorrected": 3.1776229325300524e-11, "n": "Abnormality of the nares", "c": "HP:0005288"}, {"p": 1.6103309897109546e-08, "p_uncorrected": 5.2453778166480606e-11, "n": "Optic atrophy", "c": "HP:0000648"}, {"p": 1.9060793562044177e-08, "p_uncorrected": 6.208727544639797e-11, "n": "Diabetes mellitus", "c": "HP:0000819"}, {"p": 2.987920944013083e-08, "p_uncorrected": 9.732641511443266e-11, "n": "Abnormality of the nasal alae", "c": "HP:0000429"}, {"p": 5.248020807817572e-08, "p_uncorrected": 1.7094530318624013e-10, "n": "Amyotrophic lateral sclerosis", "c": "HP:0007354"}, {"p": 5.658236502116998e-08, "p_uncorrected": 1.8430737791912046e-10, "n": "Abnormality of the menstrual cycle", "c": "HP:0000140"}, {"p": 5.984595800281632e-08, "p_uncorrected": 1.9493797395054177e-10, "n": "Motor neuron atrophy", "c": "HP:0007373"}, {"p": 6.327799953364802e-08, "p_uncorrected": 2.0611726232458636e-10, "n": "Menstrual irregularities", "c": "HP:0000858"}, {"p": 7.198491237736304e-08, "p_uncorrected": 2.3447854194580793e-10, "n": "Abnormal motor neuron morphology", "c": "HP:0002450"}, {"p": 7.466319549291483e-08, "p_uncorrected": 2.4320259118213297e-10, "n": "Abnormal neuron morphology", "c": "HP:0012757"}, {"p": 7.884897789335068e-08, "p_uncorrected": 2.568370615418589e-10, "n": "Abnormality of the optic disc", "c": "HP:0012795"}, {"p": 1.228397756115146e-07, "p_uncorrected": 4.0012956225249056e-10, "n": "Aplasia/hypoplasia involving bones of the upper limbs", "c": "HP:0006496"}, {"p": 1.483975077425636e-07, "p_uncorrected": 4.833795040474385e-10, "n": "Hyperreflexia", "c": 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0.001310620639930439, "p_uncorrected": 4.269122605636609e-06, "n": "Intellectual disability", "c": "HP:0001249"}, {"p": 0.0013287166742452364, "p_uncorrected": 4.32806734281836e-06, "n": "Global developmental delay", "c": "HP:0001263"}, {"p": 0.001393837501355185, "p_uncorrected": 4.540187300831222e-06, "n": "Seizures", "c": "HP:0001250"}, {"p": 0.00144209606825589, "p_uncorrected": 4.697381329823746e-06, "n": "Abnormal appendicular skeleton morphology", "c": "HP:0011844"}, {"p": 0.0015535980630793837, "p_uncorrected": 5.060580010030566e-06, "n": "Behavioral abnormality", "c": "HP:0000708"}, {"p": 0.0015853247689068327, "p_uncorrected": 5.163924328686751e-06, "n": "Abnormality of the vasculature", "c": "HP:0002597"}, {"p": 0.0016953367076601303, "p_uncorrected": 5.522269406059057e-06, "n": "Abnormality of body weight", "c": "HP:0004323"}, {"p": 0.001848609048286737, "p_uncorrected": 6.021527844582205e-06, "n": "Abnormality of blood and blood-forming tissues", "c": "HP:0001871"}, {"p": 0.0020950978592187467, "p_uncorrected": 6.8244229941978716e-06, "n": "Growth delay", "c": "HP:0001510"}, {"p": 0.0030266555423608833, "p_uncorrected": 9.858812841566396e-06, "n": "Bone spicule pigmentation of the retina", "c": "HP:0007737"}, {"p": 0.004174007346542459, "p_uncorrected": 1.3596115135317457e-05, "n": "Abnormality of the urinary system", "c": "HP:0000079"}, {"p": 0.005126939374012541, "p_uncorrected": 1.6700128254112513e-05, "n": "Abnormality of central motor function", "c": "HP:0011442"}, {"p": 0.00540995350440465, "p_uncorrected": 1.76219983856829e-05, "n": "Neurodevelopmental delay", "c": "HP:0012758"}, {"p": 0.00608983167308619, "p_uncorrected": 1.9836585254352408e-05, "n": "Abnormality of skin morphology", "c": "HP:0011121"}, {"p": 0.006688071979710432, "p_uncorrected": 2.178525074824245e-05, "n": "Abnormality of the ear", "c": "HP:0000598"}, {"p": 0.012588335067972373, "p_uncorrected": 4.100434875561034e-05, "n": "Abnormality of limbs", "c": "HP:0040064"}, {"p": 0.013734914174553314, "p_uncorrected": 4.473913411906617e-05, "n": "Abnormality of the skin", "c": "HP:0000951"}, {"p": 0.024146525032660786, "p_uncorrected": 7.86531760021524e-05, "n": "Abnormal eye physiology", "c": "HP:0012373"}, {"p": 0.03252935640175157, "p_uncorrected": 0.00010595881564088459, "n": "Abnormality of the globe", "c": "HP:0012374"}, {"p": 0.03334787037817537, "p_uncorrected": 0.00010862498494519663, "n": "Abnormal eye morphology", "c": "HP:0012372"}, {"p": 0.034524935406332564, "p_uncorrected": 0.00011245907298479663, "n": "Abnormality of the genitourinary system", "c": "HP:0000119"}, {"p": 0.039139246044852014, "p_uncorrected": 0.00012748940079756357, "n": "Undetectable light- and dark-adapted electroretinogram", "c": "HP:0007688"}, {"p": 0.039139246044852014, "p_uncorrected": 0.00012748940079756357, "n": "Peripheral visual field loss", "c": "HP:0007994"}, {"p": 0.043868013802690724, "p_uncorrected": 0.0001428925531032271, "n": "Neurodevelopmental abnormality", "c": 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+{"results": [{"p": 6.830958069760975e-17, "n": "Peripheral retinal degeneration", "p_uncorrected": 2.2250677751664415e-19, "c": "HP:0007769"}, {"p": 6.830958069760975e-17, "n": "Hypoplasia of the retina", "p_uncorrected": 2.2250677751664415e-19, "c": "HP:0007770"}, {"p": 7.89829526810427e-17, "n": "Retinal hole", "p_uncorrected": 2.572734615017678e-19, "c": "HP:0011530"}, {"p": 7.89829526810427e-17, "n": "Progressive cone degeneration", "p_uncorrected": 2.572734615017678e-19, "c": "HP:0008020"}, {"p": 7.89829526810427e-17, "n": "Progressive night blindness", "p_uncorrected": 2.572734615017678e-19, "c": "HP:0007675"}, {"p": 7.89829526810427e-17, "n": "Subretinal exudate", "p_uncorrected": 2.572734615017678e-19, "c": "HP:0011532"}, {"p": 1.0494238468181382e-16, "n": "Progressive retinal degeneration", "p_uncorrected": 3.418318719277323e-19, "c": "HP:0007893"}, {"p": 1.206054271707303e-16, "n": "Abnormal dark-adapted bright flash electroretinogram", "p_uncorrected": 3.928515543020531e-19, "c": "HP:0030470"}, {"p": 1.206054271707303e-16, "n": "Severe sensorineural hearing impairment", "p_uncorrected": 3.928515543020531e-19, "c": "HP:0008625"}, {"p": 1.206054271707303e-16, "n": "Severe hearing impairment", "p_uncorrected": 3.928515543020531e-19, "c": "HP:0012714"}, {"p": 1.206054271707303e-16, "n": "Electronegative electroretinogram", "p_uncorrected": 3.928515543020531e-19, "c": "HP:0007984"}, {"p": 1.206054271707303e-16, "n": "Age-related macular degeneration", "p_uncorrected": 3.928515543020531e-19, "c": "HP:0007868"}, {"p": 1.206054271707303e-16, "n": "Abnormal dark-adapted electroretinogram", "p_uncorrected": 3.928515543020531e-19, "c": "HP:0030469"}, {"p": 1.206054271707303e-16, "n": "Abnormal amplitude of dark-adapted bright flash electroretinogram", "p_uncorrected": 3.928515543020531e-19, "c": "HP:0030478"}, {"p": 1.206054271707303e-16, "n": "Exudative retinopathy", "p_uncorrected": 3.928515543020531e-19, "c": "HP:0007898"}, {"p": 1.5839101496752315e-16, "n": "Abetalipoproteinemia", "p_uncorrected": 5.159316448453523e-19, "c": "HP:0008181"}, {"p": 2.0651383842794574e-16, "n": "Mottled pigmentation", "p_uncorrected": 6.726835127946115e-19, "c": "HP:0001070"}, {"p": 2.0651383842794574e-16, "n": "Decreased light- and dark-adapted electroretinogram amplitude", "p_uncorrected": 6.726835127946115e-19, "c": "HP:0000654"}, {"p": 2.0651383842794574e-16, "n": "Tapetoretinal degeneration", "p_uncorrected": 6.726835127946115e-19, "c": "HP:0000547"}, {"p": 3.0355215014437025e-16, "n": "Vitreoretinal degeneration", "p_uncorrected": 9.887692187113037e-19, "c": "HP:0000655"}, {"p": 3.440257701614546e-16, "n": "Abnormal light- and dark-adapted electroretinogram", "p_uncorrected": 1.1206051145324254e-18, "c": "HP:0008323"}, {"p": 4.398497628785198e-16, "n": "Chorioretinal atrophy", "p_uncorrected": 1.4327353839691198e-18, "c": "HP:0000533"}, {"p": 5.5905604395766495e-16, "n": "Chorioretinal degeneration", "p_uncorrected": 1.8210294591454885e-18, "c": "HP:0200065"}, {"p": 5.5905604395766495e-16, "n": "Pigmentary retinal degeneration", "p_uncorrected": 1.8210294591454885e-18, "c": "HP:0001146"}, {"p": 6.289380494506863e-16, "n": "Decreased circulating low-density lipoprotein levels", "p_uncorrected": 2.0486581415331802e-18, "c": "HP:0003563"}, {"p": 6.289380494506863e-16, "n": "Abnormal full-field electroretinogram", "p_uncorrected": 2.0486581415331802e-18, "c": "HP:0030466"}, {"p": 8.882660716055608e-16, "n": "Macular dystrophy", "p_uncorrected": 2.893374826076745e-18, "c": "HP:0007754"}, {"p": 1.382679693118587e-15, "n": "Hypopigmentation of the fundus", "p_uncorrected": 4.503842648594746e-18, "c": "HP:0007894"}, {"p": 1.9031265438999284e-15, "n": "Undetectable electroretinogram", "p_uncorrected": 6.1991092635176825e-18, "c": "HP:0000550"}, {"p": 2.1122613289451027e-15, "n": "Cystoid macular edema", "p_uncorrected": 6.880330061710433e-18, "c": "HP:0011505"}, {"p": 2.3418549516569064e-15, "n": "Macular edema", "p_uncorrected": 7.628192024941062e-18, "c": "HP:0040049"}, {"p": 2.593667312051605e-15, "n": "Hypolipoproteinemia", "p_uncorrected": 8.44842772655246e-18, "c": "HP:0010981"}, {"p": 2.593667312051605e-15, "n": "Retinal exudate", "p_uncorrected": 8.44842772655246e-18, "c": "HP:0001147"}, {"p": 2.593667312051605e-15, "n": "Acanthocytosis", "p_uncorrected": 8.44842772655246e-18, "c": "HP:0001927"}, {"p": 2.8695893665276034e-15, "n": "Macular thickening", "p_uncorrected": 9.347196633640402e-18, "c": "HP:0030498"}, {"p": 3.1716514051110723e-15, "n": "Aplasia/Hypoplasia of the retina", "p_uncorrected": 1.0331112068765708e-17, "c": "HP:0008061"}, {"p": 3.50203175980966e-15, "n": "Congenital blindness", "p_uncorrected": 1.1407269575927232e-17, "c": "HP:0007875"}, {"p": 3.50203175980966e-15, "n": "Progressive sensorineural hearing impairment", "p_uncorrected": 1.1407269575927232e-17, "c": "HP:0000408"}, {"p": 4.25725636613049e-15, "n": "Keratoconus", "p_uncorrected": 1.3867284580229608e-17, "c": "HP:0000563"}, {"p": 4.25725636613049e-15, "n": "Increased corneal curvature", "p_uncorrected": 1.3867284580229608e-17, "c": "HP:0100692"}, {"p": 4.6872822616738014e-15, "n": "Decreased corneal thickness", "p_uncorrected": 1.52680203963316e-17, "c": "HP:0100689"}, {"p": 5.6665065757932175e-15, "n": "Congenital sensorineural hearing impairment", "p_uncorrected": 1.8457676142648916e-17, "c": "HP:0008527"}, {"p": 6.22204643614839e-15, "n": "Constriction of peripheral visual field", "p_uncorrected": 2.0267252235011042e-17, "c": "HP:0001133"}, {"p": 6.22204643614839e-15, "n": "Abnormality of corneal thickness", "p_uncorrected": 2.0267252235011042e-17, "c": "HP:0011486"}, {"p": 6.826128614391264e-15, "n": "Retinal perforation", "p_uncorrected": 2.2234946626681643e-17, "c": "HP:0011958"}, {"p": 9.806380222363747e-15, "n": "Yellow/white lesions of the retina", "p_uncorrected": 3.194260658750406e-17, "c": "HP:0030506"}, {"p": 1.0714378391101258e-14, "n": "Abnormality of the level of lipoprotein cholesterol", "p_uncorrected": 3.49002553456067e-17, "c": "HP:0010979"}, {"p": 1.1697348885694248e-14, "n": "Macular degeneration", "p_uncorrected": 3.810211363418322e-17, "c": "HP:0000608"}, {"p": 1.2760744238882322e-14, "n": "Hyperinsulinemia", "p_uncorrected": 4.156594214619649e-17, "c": "HP:0000842"}, {"p": 1.3910360837022003e-14, "n": "Cone/cone-rod dystrophy", "p_uncorrected": 4.531062161896418e-17, "c": "HP:0000548"}, {"p": 1.5152357340328436e-14, "n": "Abnormal circulating insulin level", "p_uncorrected": 4.9356212834946045e-17, "c": "HP:0040215"}, {"p": 1.5152357340328436e-14, "n": "Abnormal insulin level", "p_uncorrected": 4.9356212834946045e-17, "c": "HP:0040214"}, {"p": 1.9500056883908283e-14, "n": "Progressive hearing impairment", "p_uncorrected": 6.351810059904978e-17, "c": "HP:0001730"}, {"p": 2.4939874038128746e-14, "n": "Nephronophthisis", "p_uncorrected": 8.123737471703174e-17, "c": "HP:0000090"}, {"p": 2.7035661772422384e-14, "n": "Atypical scarring of skin", "p_uncorrected": 8.80640448613107e-17, "c": "HP:0000987"}, {"p": 4.008932828040028e-14, "n": "Retinal atrophy", "p_uncorrected": 1.3058413120651556e-16, "c": "HP:0001105"}, {"p": 1.5770726338521152e-13, "n": "Abnormality of the renal medulla", "p_uncorrected": 5.137044409941743e-16, "c": "HP:0100957"}, {"p": 5.259073285790678e-13, "n": "Chorioretinal abnormality", "p_uncorrected": 1.7130531875539669e-15, "c": "HP:0000532"}, {"p": 6.659349463318531e-13, "n": "Poikilocytosis", "p_uncorrected": 2.1691692062926814e-15, "c": "HP:0004447"}, {"p": 6.659349463318531e-13, "n": "Nyctalopia", "p_uncorrected": 2.1691692062926814e-15, "c": "HP:0000662"}, {"p": 7.058112904256892e-13, "n": "Progressive visual loss", "p_uncorrected": 2.299059577933841e-15, "c": "HP:0000529"}, {"p": 7.478238672358695e-13, "n": "Type II diabetes mellitus", "p_uncorrected": 2.4359083623318224e-15, "c": "HP:0005978"}, {"p": 1.050722902848435e-12, "n": "Abnormality of the choroid", "p_uncorrected": 3.4225501721447396e-15, "c": "HP:0000610"}, {"p": 1.050722902848435e-12, "n": "Abnormal electroretinogram", "p_uncorrected": 3.4225501721447396e-15, "c": "HP:0000512"}, {"p": 1.050722902848435e-12, "n": "Abnormality of the retinal vasculature", "p_uncorrected": 3.4225501721447396e-15, "c": "HP:0008046"}, {"p": 1.1738758145094465e-12, "n": "Aplasia/Hypoplasia affecting the fundus", "p_uncorrected": 3.823699721529142e-15, "c": "HP:0008057"}, {"p": 1.2401964820000423e-12, "n": "Retinoblastoma", "p_uncorrected": 4.039727954397532e-15, "c": "HP:0009919"}, {"p": 1.2401964820000423e-12, "n": "Retinal neoplasm", "p_uncorrected": 4.039727954397532e-15, "c": "HP:0012777"}, {"p": 1.8071448747244773e-12, "n": "Rod-cone dystrophy", "p_uncorrected": 5.8864653899820104e-15, "c": "HP:0000510"}, {"p": 2.4683037784772113e-12, "n": "Neurodegeneration", "p_uncorrected": 8.040077454323164e-15, "c": "HP:0002180"}, {"p": 4.478830903968583e-12, "n": "Visual field defect", "p_uncorrected": 1.4589025745826002e-14, "c": "HP:0001123"}, {"p": 6.241419062480174e-12, "n": "Photophobia", "p_uncorrected": 2.0330355252378417e-14, "c": "HP:0000613"}, {"p": 8.224646178578066e-12, "n": "Neoplasm of the eye", "p_uncorrected": 2.679037843185038e-14, "c": "HP:0100012"}, {"p": 9.414914677027705e-12, "n": "Abnormal visual electrophysiology", "p_uncorrected": 3.0667474518005555e-14, "c": "HP:0030453"}, {"p": 1.1746775963207132e-11, "n": "Abnormality of cholesterol metabolism", "p_uncorrected": 3.8263113886668185e-14, "c": "HP:0003107"}, {"p": 1.1746775963207132e-11, "n": "Retinal degeneration", "p_uncorrected": 3.8263113886668185e-14, "c": "HP:0000546"}, {"p": 1.2271185604454866e-11, "n": "Abnormality of the curvature of the cornea", "p_uncorrected": 3.99712886138595e-14, "c": "HP:0100691"}, {"p": 1.2816571631169346e-11, "n": "Gliosis", "p_uncorrected": 4.174779032954184e-14, "c": "HP:0002171"}, {"p": 1.588495014454129e-11, "n": "Conductive hearing impairment", "p_uncorrected": 5.174250861414101e-14, "c": "HP:0000405"}, {"p": 1.588495014454129e-11, "n": "Abnormal macular morphology", "p_uncorrected": 5.174250861414101e-14, "c": "HP:0001103"}, {"p": 1.802887603054271e-11, "n": "Blindness", "p_uncorrected": 5.872598055551371e-14, "c": "HP:0000618"}, {"p": 2.5076918624406142e-11, "n": "Functional abnormality of the middle ear", "p_uncorrected": 8.168377402086691e-14, "c": "HP:0011452"}, {"p": 3.732511675833473e-11, "n": "Ophthalmoplegia", "p_uncorrected": 1.2158018488056917e-13, "c": "HP:0000602"}, {"p": 4.192831051586348e-11, "n": "Embryonal neoplasm", "p_uncorrected": 1.3657430135460415e-13, "c": "HP:0002898"}, {"p": 7.091426267827702e-11, "n": "Retinopathy", "p_uncorrected": 2.3099108364259617e-13, "c": "HP:0000488"}, {"p": 7.355048062205055e-11, "n": "Ophthalmoparesis", "p_uncorrected": 2.3957811277540893e-13, "c": "HP:0000597"}, {"p": 8.810257081441287e-11, "n": "Pigmentary retinopathy", "p_uncorrected": 2.869790580274035e-13, "c": "HP:0000580"}, {"p": 8.810257081441287e-11, "n": "Polydactyly", "p_uncorrected": 2.869790580274035e-13, "c": "HP:0010442"}, {"p": 1.388190595549975e-10, "n": "Abnormality of the vasculature of the eye", "p_uncorrected": 4.5217934708468243e-13, "c": "HP:0008047"}, {"p": 1.388190595549975e-10, "n": "Microphthalmia", "p_uncorrected": 4.5217934708468243e-13, "c": "HP:0000568"}, {"p": 1.700756278473561e-10, "n": "Upper limb undergrowth", "p_uncorrected": 5.539922731184238e-13, "c": "HP:0009824"}, {"p": 2.075293589422645e-10, "n": "Retinal dystrophy", "p_uncorrected": 6.759913972060733e-13, "c": "HP:0000556"}, {"p": 2.3646302288247017e-10, "n": "Abnormality of globe size", "p_uncorrected": 7.702378595520201e-13, "c": "HP:0100887"}, {"p": 5.981776395427826e-10, "n": "Abnormality of the glial cells", "p_uncorrected": 1.9484613665888684e-12, "c": "HP:0100705"}, {"p": 6.727486481875538e-10, "n": "Hypogonadism", "p_uncorrected": 2.1913636748780254e-12, "c": "HP:0000135"}, {"p": 6.926524543477764e-10, "n": "Abnormality of circulating hormone level", "p_uncorrected": 2.2561969196995973e-12, "c": "HP:0003117"}, {"p": 7.776774899705444e-10, "n": "Hypoplasia of penis", "p_uncorrected": 2.5331514331288093e-12, "c": "HP:0008736"}, {"p": 8.474892365194142e-10, "n": "Neuroepithelial neoplasm", "p_uncorrected": 2.760551259020893e-12, "c": "HP:0030063"}, {"p": 9.228914326532511e-10, "n": "Nervous tissue neoplasm", "p_uncorrected": 3.0061610184144985e-12, "c": "HP:0030060"}, {"p": 9.228914326532511e-10, "n": "Neuroectodermal neoplasm", "p_uncorrected": 3.0061610184144985e-12, "c": "HP:0030061"}, {"p": 1.1543718428324624e-09, "n": "Glaucoma", "p_uncorrected": 3.760168869161115e-12, "c": "HP:0000501"}, {"p": 1.2198554340554865e-09, "n": "Wide nasal bridge", "p_uncorrected": 3.973470469236112e-12, "c": "HP:0000431"}, {"p": 1.3984366259310385e-09, "n": "Visual loss", "p_uncorrected": 4.555168162641819e-12, "c": "HP:0000572"}, {"p": 1.6879988822761898e-09, "n": "Abnormality of lipid metabolism", "p_uncorrected": 5.498367694710716e-12, "c": "HP:0003119"}, {"p": 1.7334975044422942e-09, "n": "Metrorrhagia", "p_uncorrected": 5.646571675707799e-12, "c": "HP:0100608"}, {"p": 1.9779810642388804e-09, "n": "Scarring", "p_uncorrected": 6.4429350626673635e-12, "c": "HP:0100699"}, {"p": 2.0304474054716845e-09, "n": "Abnormality of retinal pigmentation", "p_uncorrected": 6.613835196976171e-12, "c": "HP:0007703"}, {"p": 2.628331383770522e-09, "n": "Limb undergrowth", "p_uncorrected": 8.561340012281831e-12, "c": "HP:0009826"}, {"p": 3.7316154453488525e-09, "n": "Obesity", "p_uncorrected": 1.2155099170517434e-11, "c": "HP:0001513"}, {"p": 3.919340997996726e-09, "n": "Hypoplastic male external genitalia", "p_uncorrected": 1.2766583055363929e-11, "c": "HP:0000050"}, {"p": 6.321359545900789e-09, "n": "Abnormality of the middle ear", "p_uncorrected": 2.0590747706517226e-11, "c": "HP:0000370"}, {"p": 7.098972376183352e-09, "n": "Anteverted nares", "p_uncorrected": 2.3123688521769875e-11, "c": "HP:0000463"}, {"p": 7.433390275858353e-09, "n": "External genital hypoplasia", "p_uncorrected": 2.4212997641232422e-11, "c": "HP:0003241"}, {"p": 7.433390275858353e-09, "n": "Aplasia/Hypoplasia affecting the eye", "p_uncorrected": 2.4212997641232422e-11, "c": "HP:0008056"}, {"p": 8.145089250918333e-09, "n": "Increased body weight", "p_uncorrected": 2.6531235345010855e-11, "c": "HP:0004324"}, {"p": 9.75530240286726e-09, "n": "Abnormality of the nares", "p_uncorrected": 3.1776229325300524e-11, "c": "HP:0005288"}, {"p": 1.6103309897109546e-08, "n": "Optic atrophy", "p_uncorrected": 5.2453778166480606e-11, "c": "HP:0000648"}, {"p": 1.9060793562044177e-08, "n": "Diabetes mellitus", "p_uncorrected": 6.208727544639797e-11, "c": "HP:0000819"}, {"p": 2.987920944013083e-08, "n": "Abnormality of the nasal alae", "p_uncorrected": 9.732641511443266e-11, "c": "HP:0000429"}, {"p": 5.248020807817572e-08, "n": "Amyotrophic lateral sclerosis", "p_uncorrected": 1.7094530318624013e-10, "c": "HP:0007354"}, {"p": 5.658236502116998e-08, "n": "Abnormality of the menstrual cycle", "p_uncorrected": 1.8430737791912046e-10, "c": "HP:0000140"}, {"p": 5.984595800281632e-08, "n": "Motor neuron atrophy", "p_uncorrected": 1.9493797395054177e-10, "c": "HP:0007373"}, {"p": 6.327799953364802e-08, "n": "Menstrual irregularities", "p_uncorrected": 2.0611726232458636e-10, "c": "HP:0000858"}, {"p": 7.198491237736304e-08, "n": "Abnormal motor neuron morphology", "p_uncorrected": 2.3447854194580793e-10, "c": "HP:0002450"}, {"p": 7.466319549291483e-08, "n": "Abnormal neuron morphology", "p_uncorrected": 2.4320259118213297e-10, "c": "HP:0012757"}, {"p": 7.884897789335068e-08, "n": "Abnormality of the optic disc", "p_uncorrected": 2.568370615418589e-10, "c": "HP:0012795"}, {"p": 1.228397756115146e-07, "n": "Aplasia/hypoplasia involving bones of the upper limbs", "p_uncorrected": 4.0012956225249056e-10, "c": "HP:0006496"}, {"p": 1.483975077425636e-07, "n": "Hyperreflexia", "p_uncorrected": 4.833795040474385e-10, "c": "HP:0001347"}, {"p": 1.5352755857272025e-07, "n": "Abnormality of the uvea", "p_uncorrected": 5.00089767337851e-10, "c": "HP:0000553"}, {"p": 1.5352755857272025e-07, "n": "Abnormality of the penis", "p_uncorrected": 5.00089767337851e-10, "c": "HP:0000036"}, {"p": 1.6426921240078137e-07, "n": "Neoplasm by histology", "p_uncorrected": 5.350788677549882e-10, "c": "HP:0011792"}, {"p": 2.25119429172574e-07, "n": "Abnormality of reproductive system physiology", "p_uncorrected": 7.332880429074072e-10, "c": "HP:0000080"}, {"p": 3.0555431964818125e-07, "n": "Abnormality of the cornea", "p_uncorrected": 9.952909434794178e-10, "c": "HP:0000481"}, {"p": 3.2038455159280755e-07, "n": "Visual impairment", "p_uncorrected": 1.0435978879244546e-09, "c": "HP:0000505"}, {"p": 3.9242331225647995e-07, "n": "Aplasia/hypoplasia involving bones of the extremities", "p_uncorrected": 1.278251831454332e-09, "c": "HP:0045060"}, {"p": 4.1098926074512013e-07, "n": "Peripheral neuropathy", "p_uncorrected": 1.3387272336974598e-09, "c": "HP:0009830"}, {"p": 4.238018850191182e-07, "n": "Cataract", "p_uncorrected": 1.3804621661860528e-09, "c": "HP:0000518"}, {"p": 4.78725935631177e-07, "n": "Abnormality of the optic nerve", "p_uncorrected": 1.5593678685054627e-09, "c": "HP:0000587"}, {"p": 4.78725935631177e-07, "n": "Abnormality of skin pigmentation", "p_uncorrected": 1.5593678685054627e-09, "c": "HP:0001000"}, {"p": 5.319518140608289e-07, "n": "Sensorineural hearing impairment", "p_uncorrected": 1.7327420653447194e-09, "c": "HP:0000407"}, {"p": 5.563495931254543e-07, "n": "Abnormality of the external nose", "p_uncorrected": 1.812213658389102e-09, "c": "HP:0010938"}, {"p": 5.647031906221201e-07, "n": "Abnormality of the lens", "p_uncorrected": 1.8394240736876876e-09, "c": "HP:0000517"}, {"p": 5.904457001011749e-07, "n": "Aplasia/hypoplasia of the extremities", "p_uncorrected": 1.923275896095032e-09, "c": "HP:0009815"}, {"p": 7.464471377270939e-07, "n": "Abnormal glucose homeostasis", "p_uncorrected": 2.4314239013911853e-09, "c": "HP:0011014"}, {"p": 8.375817156963961e-07, "n": "Edema", "p_uncorrected": 2.7282792042227886e-09, "c": "HP:0000969"}, {"p": 9.123756391914161e-07, "n": "Abnormality of the nasal bridge", "p_uncorrected": 2.9719076195160134e-09, "c": "HP:0000422"}, {"p": 1.0652736599597843e-06, "n": "Abnormal nasal morphology", "p_uncorrected": 3.469946775113304e-09, "c": "HP:0005105"}, {"p": 1.4816609184875052e-06, "n": "Functional abnormality of the inner ear", "p_uncorrected": 4.826257063477215e-09, "c": "HP:0011389"}, {"p": 1.5018195704310955e-06, "n": "Localized skin lesion", "p_uncorrected": 4.891920424856989e-09, "c": "HP:0011355"}, {"p": 1.8844948396305382e-06, "n": "Abnormality of the inner ear", "p_uncorrected": 6.1384196730636424e-09, "c": "HP:0000359"}, {"p": 1.9348465481391357e-06, "n": "Abnormality of carbohydrate metabolism/homeostasis", "p_uncorrected": 6.302431752896208e-09, "c": "HP:0011013"}, {"p": 2.066065317689044e-06, "n": "Puberty and gonadal disorders", "p_uncorrected": 6.729854455013172e-09, "c": "HP:0008373"}, {"p": 2.1767481626287405e-06, "n": "Abnormality of female internal genitalia", "p_uncorrected": 7.0903848945561585e-09, "c": "HP:0000008"}, {"p": 2.3225926077022225e-06, "n": "Abnormality of fluid regulation", "p_uncorrected": 7.565448233557727e-09, "c": "HP:0011032"}, {"p": 2.5743067328521833e-06, "n": "Abnormality of the testis", "p_uncorrected": 8.385363950658578e-09, "c": "HP:0000035"}, {"p": 2.7438357503096225e-06, "n": "Nystagmus", "p_uncorrected": 8.937575733907565e-09, "c": "HP:0000639"}, {"p": 3.1924265166540625e-06, "n": "Abnormal involuntary eye movements", "p_uncorrected": 1.039878344186991e-08, "c": "HP:0012547"}, {"p": 3.941055199038619e-06, "n": "Abnormal internal genitalia", "p_uncorrected": 1.2837313351917324e-08, "c": "HP:0000812"}, {"p": 4.3982513901891805e-06, "n": "Abnormality of erythrocytes", "p_uncorrected": 1.4326551759573878e-08, "c": "HP:0001877"}, {"p": 4.729009605111635e-06, "n": "Abnormality of the female genitalia", "p_uncorrected": 1.5403940081796854e-08, "c": "HP:0010460"}, {"p": 9.081642576385783e-06, "n": "Ataxia", "p_uncorrected": 2.958189764295043e-08, "c": "HP:0001251"}, {"p": 9.499843448701236e-06, "n": "Abnormal retinal morphology", "p_uncorrected": 3.09441154680822e-08, "c": "HP:0000479"}, {"p": 1.4273095112661205e-05, "n": "Abnormal renal morphology", "p_uncorrected": 4.649216649075311e-08, "c": "HP:0012210"}, {"p": 1.458387749487557e-05, "n": "Abnormality of male external genitalia", "p_uncorrected": 4.750448695399209e-08, "c": "HP:0000032"}, {"p": 1.5888839675674068e-05, "n": "Abnormality of coordination", "p_uncorrected": 5.17551780966582e-08, "c": "HP:0011443"}, {"p": 1.729796819095009e-05, "n": "Atrophy/Degeneration affecting the central nervous system", "p_uncorrected": 5.6345173260423745e-08, "c": "HP:0007367"}, {"p": 1.7854728108751475e-05, "n": "Abnormal external genitalia", "p_uncorrected": 5.8158723481275166e-08, "c": "HP:0000811"}, {"p": 2.2456195406528198e-05, "n": "Abnormality of vision", "p_uncorrected": 7.314721630790944e-08, "c": "HP:0000504"}, {"p": 2.5135309938722395e-05, "n": "Abnormal peripheral nervous system morphology", "p_uncorrected": 8.187397374176675e-08, "c": "HP:0000759"}, {"p": 3.23236138618761e-05, "n": "Abnormality of the male genitalia", "p_uncorrected": 1.0528864450122508e-07, "c": "HP:0010461"}, {"p": 3.2971690409923215e-05, "n": "Aplasia/hypoplasia involving the skeleton", "p_uncorrected": 1.0739964302906584e-07, "c": "HP:0009115"}, {"p": 3.464335079920156e-05, "n": "Abnormality of digit", "p_uncorrected": 1.1284479087687803e-07, "c": "HP:0011297"}, {"p": 6.881496226463522e-05, "n": "Short stature", "p_uncorrected": 2.2415297154604308e-07, "c": "HP:0004322"}, {"p": 7.611517703089195e-05, "n": "Muscle weakness", "p_uncorrected": 2.479321727390617e-07, "c": "HP:0001324"}, {"p": 8.259858594747801e-05, "n": "Abnormality of the anterior segment of the globe", "p_uncorrected": 2.690507685585603e-07, "c": "HP:0004328"}, {"p": 0.0001138007728773714, "n": "Upper motor neuron dysfunction", "p_uncorrected": 3.7068655660381564e-07, "c": "HP:0002493"}, {"p": 0.00011888491829110587, "n": "Neoplasm by anatomical site", "p_uncorrected": 3.8724729085050773e-07, "c": "HP:0011793"}, {"p": 0.00012097516293517722, "n": "Abnormality of the fundus", "p_uncorrected": 3.9405590532631017e-07, "c": "HP:0001098"}, {"p": 0.00012417258265780599, "n": "Abnormality of the posterior segment of the globe", "p_uncorrected": 4.044709532827557e-07, "c": "HP:0004329"}, {"p": 0.00015262060533597588, "n": "Hearing impairment", "p_uncorrected": 4.971355222670225e-07, "c": "HP:0000365"}, {"p": 0.00016059211883394877, "n": "Neoplasm", "p_uncorrected": 5.231013642799634e-07, "c": "HP:0002664"}, {"p": 0.00017325315786960351, "n": "Abnormality of the cerebellum", "p_uncorrected": 5.643425337772102e-07, "c": "HP:0001317"}, {"p": 0.00017618587241738414, "n": "Abnormality of the metencephalon", "p_uncorrected": 5.738953498937594e-07, "c": "HP:0011283"}, {"p": 0.00017618587241738414, "n": "Abnormality of hindbrain morphology", "p_uncorrected": 5.738953498937594e-07, "c": "HP:0011282"}, {"p": 0.00017916319029463729, "n": "Hearing abnormality", "p_uncorrected": 5.835934537284602e-07, "c": "HP:0000364"}, {"p": 0.00018218571347576067, "n": "Abnormality of body height", "p_uncorrected": 5.934388061099696e-07, "c": "HP:0000002"}, {"p": 0.00022960204326684703, "n": "Abnormality of the kidney", "p_uncorrected": 7.478893917486874e-07, "c": "HP:0000077"}, {"p": 0.0002391515950095283, "n": "Abnormality of limb bone morphology", "p_uncorrected": 7.789954234838055e-07, "c": "HP:0002813"}, {"p": 0.00024905713587446506, "n": "Abnormal reproductive system morphology", "p_uncorrected": 8.112610289070523e-07, "c": "HP:0012243"}, {"p": 0.00025312164937551113, "n": "Abnormality of eye movement", "p_uncorrected": 8.245004865651829e-07, "c": "HP:0000496"}, {"p": 0.0002699835132109949, "n": "Abnormality of the upper urinary tract", "p_uncorrected": 8.794251244657815e-07, "c": "HP:0010935"}, {"p": 0.0002721607996075025, "n": "Abnormality of the endocrine system", "p_uncorrected": 8.865172625651547e-07, "c": "HP:0000818"}, {"p": 0.000350750188320614, "n": "Abnormality of the nose", "p_uncorrected": 1.142508756744671e-06, "c": "HP:0000366"}, {"p": 0.0006114146839577272, "n": "Abnormality of connective tissue", "p_uncorrected": 1.9915787751066032e-06, "c": "HP:0003549"}, {"p": 0.0006205299480287158, "n": "Abnormality of the genital system", "p_uncorrected": 2.0212701890186184e-06, "c": "HP:0000078"}, {"p": 0.0008069550626492879, "n": "Abnormality of the upper limb", "p_uncorrected": 2.628518119378788e-06, "c": "HP:0002817"}, {"p": 0.0008921120254797562, "n": "Abnormality of limb bone", "p_uncorrected": 2.905902363126242e-06, "c": "HP:0040068"}, {"p": 0.0009992733379070886, "n": "Abnormality of the orbital region", "p_uncorrected": 3.254962012726673e-06, "c": "HP:0000315"}, {"p": 0.001310620639930439, "n": "Intellectual disability", "p_uncorrected": 4.269122605636609e-06, "c": "HP:0001249"}, {"p": 0.0013287166742452364, "n": "Global developmental delay", "p_uncorrected": 4.32806734281836e-06, "c": "HP:0001263"}, {"p": 0.001393837501355185, "n": "Seizures", "p_uncorrected": 4.540187300831222e-06, "c": "HP:0001250"}, {"p": 0.00144209606825589, "n": "Abnormal appendicular skeleton morphology", "p_uncorrected": 4.697381329823746e-06, "c": "HP:0011844"}, {"p": 0.0015535980630793837, "n": "Behavioral abnormality", "p_uncorrected": 5.060580010030566e-06, "c": "HP:0000708"}, {"p": 0.0015853247689068327, "n": "Abnormality of the vasculature", "p_uncorrected": 5.163924328686751e-06, "c": "HP:0002597"}, {"p": 0.0016953367076601303, "n": "Abnormality of body weight", "p_uncorrected": 5.522269406059057e-06, "c": "HP:0004323"}, {"p": 0.001848609048286737, "n": "Abnormality of blood and blood-forming tissues", "p_uncorrected": 6.021527844582205e-06, "c": "HP:0001871"}, {"p": 0.0020950978592187467, "n": "Growth delay", "p_uncorrected": 6.8244229941978716e-06, "c": "HP:0001510"}, {"p": 0.0030266555423608833, "n": "Bone spicule pigmentation of the retina", "p_uncorrected": 9.858812841566396e-06, "c": "HP:0007737"}, {"p": 0.004174007346542459, "n": "Abnormality of the urinary system", "p_uncorrected": 1.3596115135317457e-05, "c": "HP:0000079"}, {"p": 0.005126939374012541, "n": "Abnormality of central motor function", "p_uncorrected": 1.6700128254112513e-05, "c": "HP:0011442"}, {"p": 0.00540995350440465, "n": "Neurodevelopmental delay", "p_uncorrected": 1.76219983856829e-05, "c": "HP:0012758"}, {"p": 0.00608983167308619, "n": "Abnormality of skin morphology", "p_uncorrected": 1.9836585254352408e-05, "c": "HP:0011121"}, {"p": 0.006688071979710432, "n": "Abnormality of the ear", "p_uncorrected": 2.178525074824245e-05, "c": "HP:0000598"}, {"p": 0.012588335067972373, "n": "Abnormality of limbs", "p_uncorrected": 4.100434875561034e-05, "c": "HP:0040064"}, {"p": 0.013734914174553314, "n": "Abnormality of the skin", "p_uncorrected": 4.473913411906617e-05, "c": "HP:0000951"}, {"p": 0.024146525032660786, "n": "Abnormal eye physiology", "p_uncorrected": 7.86531760021524e-05, "c": "HP:0012373"}, {"p": 0.03252935640175157, "n": "Abnormality of the globe", "p_uncorrected": 0.00010595881564088459, "c": "HP:0012374"}, {"p": 0.03334787037817537, "n": "Abnormal eye morphology", "p_uncorrected": 0.00010862498494519663, "c": "HP:0012372"}, {"p": 0.034524935406332564, "n": "Abnormality of the genitourinary system", "p_uncorrected": 0.00011245907298479663, "c": "HP:0000119"}, {"p": 0.039139246044852014, "n": "Undetectable light- and dark-adapted electroretinogram", "p_uncorrected": 0.00012748940079756357, "c": "HP:0007688"}, {"p": 0.039139246044852014, "n": "Peripheral visual field loss", "p_uncorrected": 0.00012748940079756357, "c": "HP:0007994"}, {"p": 0.043868013802690724, "n": "Neurodevelopmental abnormality", "p_uncorrected": 0.0001428925531032271, "c": "HP:0012759"}, {"p": 0.04946207981041838, "n": "Abnormality of muscle physiology", "p_uncorrected": 0.0001611142664834475, "c": "HP:0011804"}]}
diff -r d40860663861 -r 49b46f044d48 test-data/bioentityset-overrepresentation.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bioentityset-overrepresentation.tsv	Mon Dec 04 19:35:12 2017 -0500
@@ -0,0 +1,224 @@
+p	n	p_uncorrected	c
+6.830958069760975e-17	Peripheral retinal degeneration	2.2250677751664415e-19	HP:0007769
+6.830958069760975e-17	Hypoplasia of the retina	2.2250677751664415e-19	HP:0007770
+7.89829526810427e-17	Retinal hole	2.572734615017678e-19	HP:0011530
+7.89829526810427e-17	Progressive cone degeneration	2.572734615017678e-19	HP:0008020
+7.89829526810427e-17	Progressive night blindness	2.572734615017678e-19	HP:0007675
+7.89829526810427e-17	Subretinal exudate	2.572734615017678e-19	HP:0011532
+1.0494238468181382e-16	Progressive retinal degeneration	3.418318719277323e-19	HP:0007893
+1.206054271707303e-16	Abnormal dark-adapted bright flash electroretinogram	3.928515543020531e-19	HP:0030470
+1.206054271707303e-16	Severe sensorineural hearing impairment	3.928515543020531e-19	HP:0008625
+1.206054271707303e-16	Severe hearing impairment	3.928515543020531e-19	HP:0012714
+1.206054271707303e-16	Electronegative electroretinogram	3.928515543020531e-19	HP:0007984
+1.206054271707303e-16	Age-related macular degeneration	3.928515543020531e-19	HP:0007868
+1.206054271707303e-16	Abnormal dark-adapted electroretinogram	3.928515543020531e-19	HP:0030469
+1.206054271707303e-16	Abnormal amplitude of dark-adapted bright flash electroretinogram	3.928515543020531e-19	HP:0030478
+1.206054271707303e-16	Exudative retinopathy	3.928515543020531e-19	HP:0007898
+1.5839101496752315e-16	Abetalipoproteinemia	5.159316448453523e-19	HP:0008181
+2.0651383842794574e-16	Mottled pigmentation	6.726835127946115e-19	HP:0001070
+2.0651383842794574e-16	Decreased light- and dark-adapted electroretinogram amplitude	6.726835127946115e-19	HP:0000654
+2.0651383842794574e-16	Tapetoretinal degeneration	6.726835127946115e-19	HP:0000547
+3.0355215014437025e-16	Vitreoretinal degeneration	9.887692187113037e-19	HP:0000655
+3.440257701614546e-16	Abnormal light- and dark-adapted electroretinogram	1.1206051145324254e-18	HP:0008323
+4.398497628785198e-16	Chorioretinal atrophy	1.4327353839691198e-18	HP:0000533
+5.5905604395766495e-16	Chorioretinal degeneration	1.8210294591454885e-18	HP:0200065
+5.5905604395766495e-16	Pigmentary retinal degeneration	1.8210294591454885e-18	HP:0001146
+6.289380494506863e-16	Decreased circulating low-density lipoprotein levels	2.0486581415331802e-18	HP:0003563
+6.289380494506863e-16	Abnormal full-field electroretinogram	2.0486581415331802e-18	HP:0030466
+8.882660716055608e-16	Macular dystrophy	2.893374826076745e-18	HP:0007754
+1.382679693118587e-15	Hypopigmentation of the fundus	4.503842648594746e-18	HP:0007894
+1.9031265438999284e-15	Undetectable electroretinogram	6.1991092635176825e-18	HP:0000550
+2.1122613289451027e-15	Cystoid macular edema	6.880330061710433e-18	HP:0011505
+2.3418549516569064e-15	Macular edema	7.628192024941062e-18	HP:0040049
+2.593667312051605e-15	Hypolipoproteinemia	8.44842772655246e-18	HP:0010981
+2.593667312051605e-15	Retinal exudate	8.44842772655246e-18	HP:0001147
+2.593667312051605e-15	Acanthocytosis	8.44842772655246e-18	HP:0001927
+2.8695893665276034e-15	Macular thickening	9.347196633640402e-18	HP:0030498
+3.1716514051110723e-15	Aplasia/Hypoplasia of the retina	1.0331112068765708e-17	HP:0008061
+3.50203175980966e-15	Congenital blindness	1.1407269575927232e-17	HP:0007875
+3.50203175980966e-15	Progressive sensorineural hearing impairment	1.1407269575927232e-17	HP:0000408
+4.25725636613049e-15	Keratoconus	1.3867284580229608e-17	HP:0000563
+4.25725636613049e-15	Increased corneal curvature	1.3867284580229608e-17	HP:0100692
+4.6872822616738014e-15	Decreased corneal thickness	1.52680203963316e-17	HP:0100689
+5.6665065757932175e-15	Congenital sensorineural hearing impairment	1.8457676142648916e-17	HP:0008527
+6.22204643614839e-15	Constriction of peripheral visual field	2.0267252235011042e-17	HP:0001133
+6.22204643614839e-15	Abnormality of corneal thickness	2.0267252235011042e-17	HP:0011486
+6.826128614391264e-15	Retinal perforation	2.2234946626681643e-17	HP:0011958
+9.806380222363747e-15	Yellow/white lesions of the retina	3.194260658750406e-17	HP:0030506
+1.0714378391101258e-14	Abnormality of the level of lipoprotein cholesterol	3.49002553456067e-17	HP:0010979
+1.1697348885694248e-14	Macular degeneration	3.810211363418322e-17	HP:0000608
+1.2760744238882322e-14	Hyperinsulinemia	4.156594214619649e-17	HP:0000842
+1.3910360837022003e-14	Cone/cone-rod dystrophy	4.531062161896418e-17	HP:0000548
+1.5152357340328436e-14	Abnormal circulating insulin level	4.9356212834946045e-17	HP:0040215
+1.5152357340328436e-14	Abnormal insulin level	4.9356212834946045e-17	HP:0040214
+1.9500056883908283e-14	Progressive hearing impairment	6.351810059904978e-17	HP:0001730
+2.4939874038128746e-14	Nephronophthisis	8.123737471703174e-17	HP:0000090
+2.7035661772422384e-14	Atypical scarring of skin	8.80640448613107e-17	HP:0000987
+4.008932828040028e-14	Retinal atrophy	1.3058413120651556e-16	HP:0001105
+1.5770726338521152e-13	Abnormality of the renal medulla	5.137044409941743e-16	HP:0100957
+5.259073285790678e-13	Chorioretinal abnormality	1.7130531875539669e-15	HP:0000532
+6.659349463318531e-13	Poikilocytosis	2.1691692062926814e-15	HP:0004447
+6.659349463318531e-13	Nyctalopia	2.1691692062926814e-15	HP:0000662
+7.058112904256892e-13	Progressive visual loss	2.299059577933841e-15	HP:0000529
+7.478238672358695e-13	Type II diabetes mellitus	2.4359083623318224e-15	HP:0005978
+1.050722902848435e-12	Abnormality of the choroid	3.4225501721447396e-15	HP:0000610
+1.050722902848435e-12	Abnormal electroretinogram	3.4225501721447396e-15	HP:0000512
+1.050722902848435e-12	Abnormality of the retinal vasculature	3.4225501721447396e-15	HP:0008046
+1.1738758145094465e-12	Aplasia/Hypoplasia affecting the fundus	3.823699721529142e-15	HP:0008057
+1.2401964820000423e-12	Retinoblastoma	4.039727954397532e-15	HP:0009919
+1.2401964820000423e-12	Retinal neoplasm	4.039727954397532e-15	HP:0012777
+1.8071448747244773e-12	Rod-cone dystrophy	5.8864653899820104e-15	HP:0000510
+2.4683037784772113e-12	Neurodegeneration	8.040077454323164e-15	HP:0002180
+4.478830903968583e-12	Visual field defect	1.4589025745826002e-14	HP:0001123
+6.241419062480174e-12	Photophobia	2.0330355252378417e-14	HP:0000613
+8.224646178578066e-12	Neoplasm of the eye	2.679037843185038e-14	HP:0100012
+9.414914677027705e-12	Abnormal visual electrophysiology	3.0667474518005555e-14	HP:0030453
+1.1746775963207132e-11	Abnormality of cholesterol metabolism	3.8263113886668185e-14	HP:0003107
+1.1746775963207132e-11	Retinal degeneration	3.8263113886668185e-14	HP:0000546
+1.2271185604454866e-11	Abnormality of the curvature of the cornea	3.99712886138595e-14	HP:0100691
+1.2816571631169346e-11	Gliosis	4.174779032954184e-14	HP:0002171
+1.588495014454129e-11	Conductive hearing impairment	5.174250861414101e-14	HP:0000405
+1.588495014454129e-11	Abnormal macular morphology	5.174250861414101e-14	HP:0001103
+1.802887603054271e-11	Blindness	5.872598055551371e-14	HP:0000618
+2.5076918624406142e-11	Functional abnormality of the middle ear	8.168377402086691e-14	HP:0011452
+3.732511675833473e-11	Ophthalmoplegia	1.2158018488056917e-13	HP:0000602
+4.192831051586348e-11	Embryonal neoplasm	1.3657430135460415e-13	HP:0002898
+7.091426267827702e-11	Retinopathy	2.3099108364259617e-13	HP:0000488
+7.355048062205055e-11	Ophthalmoparesis	2.3957811277540893e-13	HP:0000597
+8.810257081441287e-11	Pigmentary retinopathy	2.869790580274035e-13	HP:0000580
+8.810257081441287e-11	Polydactyly	2.869790580274035e-13	HP:0010442
+1.388190595549975e-10	Abnormality of the vasculature of the eye	4.5217934708468243e-13	HP:0008047
+1.388190595549975e-10	Microphthalmia	4.5217934708468243e-13	HP:0000568
+1.700756278473561e-10	Upper limb undergrowth	5.539922731184238e-13	HP:0009824
+2.075293589422645e-10	Retinal dystrophy	6.759913972060733e-13	HP:0000556
+2.3646302288247017e-10	Abnormality of globe size	7.702378595520201e-13	HP:0100887
+5.981776395427826e-10	Abnormality of the glial cells	1.9484613665888684e-12	HP:0100705
+6.727486481875538e-10	Hypogonadism	2.1913636748780254e-12	HP:0000135
+6.926524543477764e-10	Abnormality of circulating hormone level	2.2561969196995973e-12	HP:0003117
+7.776774899705444e-10	Hypoplasia of penis	2.5331514331288093e-12	HP:0008736
+8.474892365194142e-10	Neuroepithelial neoplasm	2.760551259020893e-12	HP:0030063
+9.228914326532511e-10	Nervous tissue neoplasm	3.0061610184144985e-12	HP:0030060
+9.228914326532511e-10	Neuroectodermal neoplasm	3.0061610184144985e-12	HP:0030061
+1.1543718428324624e-09	Glaucoma	3.760168869161115e-12	HP:0000501
+1.2198554340554865e-09	Wide nasal bridge	3.973470469236112e-12	HP:0000431
+1.3984366259310385e-09	Visual loss	4.555168162641819e-12	HP:0000572
+1.6879988822761898e-09	Abnormality of lipid metabolism	5.498367694710716e-12	HP:0003119
+1.7334975044422942e-09	Metrorrhagia	5.646571675707799e-12	HP:0100608
+1.9779810642388804e-09	Scarring	6.4429350626673635e-12	HP:0100699
+2.0304474054716845e-09	Abnormality of retinal pigmentation	6.613835196976171e-12	HP:0007703
+2.628331383770522e-09	Limb undergrowth	8.561340012281831e-12	HP:0009826
+3.7316154453488525e-09	Obesity	1.2155099170517434e-11	HP:0001513
+3.919340997996726e-09	Hypoplastic male external genitalia	1.2766583055363929e-11	HP:0000050
+6.321359545900789e-09	Abnormality of the middle ear	2.0590747706517226e-11	HP:0000370
+7.098972376183352e-09	Anteverted nares	2.3123688521769875e-11	HP:0000463
+7.433390275858353e-09	External genital hypoplasia	2.4212997641232422e-11	HP:0003241
+7.433390275858353e-09	Aplasia/Hypoplasia affecting the eye	2.4212997641232422e-11	HP:0008056
+8.145089250918333e-09	Increased body weight	2.6531235345010855e-11	HP:0004324
+9.75530240286726e-09	Abnormality of the nares	3.1776229325300524e-11	HP:0005288
+1.6103309897109546e-08	Optic atrophy	5.2453778166480606e-11	HP:0000648
+1.9060793562044177e-08	Diabetes mellitus	6.208727544639797e-11	HP:0000819
+2.987920944013083e-08	Abnormality of the nasal alae	9.732641511443266e-11	HP:0000429
+5.248020807817572e-08	Amyotrophic lateral sclerosis	1.7094530318624013e-10	HP:0007354
+5.658236502116998e-08	Abnormality of the menstrual cycle	1.8430737791912046e-10	HP:0000140
+5.984595800281632e-08	Motor neuron atrophy	1.9493797395054177e-10	HP:0007373
+6.327799953364802e-08	Menstrual irregularities	2.0611726232458636e-10	HP:0000858
+7.198491237736304e-08	Abnormal motor neuron morphology	2.3447854194580793e-10	HP:0002450
+7.466319549291483e-08	Abnormal neuron morphology	2.4320259118213297e-10	HP:0012757
+7.884897789335068e-08	Abnormality of the optic disc	2.568370615418589e-10	HP:0012795
+1.228397756115146e-07	Aplasia/hypoplasia involving bones of the upper limbs	4.0012956225249056e-10	HP:0006496
+1.483975077425636e-07	Hyperreflexia	4.833795040474385e-10	HP:0001347
+1.5352755857272025e-07	Abnormality of the uvea	5.00089767337851e-10	HP:0000553
+1.5352755857272025e-07	Abnormality of the penis	5.00089767337851e-10	HP:0000036
+1.6426921240078137e-07	Neoplasm by histology	5.350788677549882e-10	HP:0011792
+2.25119429172574e-07	Abnormality of reproductive system physiology	7.332880429074072e-10	HP:0000080
+3.0555431964818125e-07	Abnormality of the cornea	9.952909434794178e-10	HP:0000481
+3.2038455159280755e-07	Visual impairment	1.0435978879244546e-09	HP:0000505
+3.9242331225647995e-07	Aplasia/hypoplasia involving bones of the extremities	1.278251831454332e-09	HP:0045060
+4.1098926074512013e-07	Peripheral neuropathy	1.3387272336974598e-09	HP:0009830
+4.238018850191182e-07	Cataract	1.3804621661860528e-09	HP:0000518
+4.78725935631177e-07	Abnormality of the optic nerve	1.5593678685054627e-09	HP:0000587
+4.78725935631177e-07	Abnormality of skin pigmentation	1.5593678685054627e-09	HP:0001000
+5.319518140608289e-07	Sensorineural hearing impairment	1.7327420653447194e-09	HP:0000407
+5.563495931254543e-07	Abnormality of the external nose	1.812213658389102e-09	HP:0010938
+5.647031906221201e-07	Abnormality of the lens	1.8394240736876876e-09	HP:0000517
+5.904457001011749e-07	Aplasia/hypoplasia of the extremities	1.923275896095032e-09	HP:0009815
+7.464471377270939e-07	Abnormal glucose homeostasis	2.4314239013911853e-09	HP:0011014
+8.375817156963961e-07	Edema	2.7282792042227886e-09	HP:0000969
+9.123756391914161e-07	Abnormality of the nasal bridge	2.9719076195160134e-09	HP:0000422
+1.0652736599597843e-06	Abnormal nasal morphology	3.469946775113304e-09	HP:0005105
+1.4816609184875052e-06	Functional abnormality of the inner ear	4.826257063477215e-09	HP:0011389
+1.5018195704310955e-06	Localized skin lesion	4.891920424856989e-09	HP:0011355
+1.8844948396305382e-06	Abnormality of the inner ear	6.1384196730636424e-09	HP:0000359
+1.9348465481391357e-06	Abnormality of carbohydrate metabolism/homeostasis	6.302431752896208e-09	HP:0011013
+2.066065317689044e-06	Puberty and gonadal disorders	6.729854455013172e-09	HP:0008373
+2.1767481626287405e-06	Abnormality of female internal genitalia	7.0903848945561585e-09	HP:0000008
+2.3225926077022225e-06	Abnormality of fluid regulation	7.565448233557727e-09	HP:0011032
+2.5743067328521833e-06	Abnormality of the testis	8.385363950658578e-09	HP:0000035
+2.7438357503096225e-06	Nystagmus	8.937575733907565e-09	HP:0000639
+3.1924265166540625e-06	Abnormal involuntary eye movements	1.039878344186991e-08	HP:0012547
+3.941055199038619e-06	Abnormal internal genitalia	1.2837313351917324e-08	HP:0000812
+4.3982513901891805e-06	Abnormality of erythrocytes	1.4326551759573878e-08	HP:0001877
+4.729009605111635e-06	Abnormality of the female genitalia	1.5403940081796854e-08	HP:0010460
+9.081642576385783e-06	Ataxia	2.958189764295043e-08	HP:0001251
+9.499843448701236e-06	Abnormal retinal morphology	3.09441154680822e-08	HP:0000479
+1.4273095112661205e-05	Abnormal renal morphology	4.649216649075311e-08	HP:0012210
+1.458387749487557e-05	Abnormality of male external genitalia	4.750448695399209e-08	HP:0000032
+1.5888839675674068e-05	Abnormality of coordination	5.17551780966582e-08	HP:0011443
+1.729796819095009e-05	Atrophy/Degeneration affecting the central nervous system	5.6345173260423745e-08	HP:0007367
+1.7854728108751475e-05	Abnormal external genitalia	5.8158723481275166e-08	HP:0000811
+2.2456195406528198e-05	Abnormality of vision	7.314721630790944e-08	HP:0000504
+2.5135309938722395e-05	Abnormal peripheral nervous system morphology	8.187397374176675e-08	HP:0000759
+3.23236138618761e-05	Abnormality of the male genitalia	1.0528864450122508e-07	HP:0010461
+3.2971690409923215e-05	Aplasia/hypoplasia involving the skeleton	1.0739964302906584e-07	HP:0009115
+3.464335079920156e-05	Abnormality of digit	1.1284479087687803e-07	HP:0011297
+6.881496226463522e-05	Short stature	2.2415297154604308e-07	HP:0004322
+7.611517703089195e-05	Muscle weakness	2.479321727390617e-07	HP:0001324
+8.259858594747801e-05	Abnormality of the anterior segment of the globe	2.690507685585603e-07	HP:0004328
+0.0001138007728773714	Upper motor neuron dysfunction	3.7068655660381564e-07	HP:0002493
+0.00011888491829110587	Neoplasm by anatomical site	3.8724729085050773e-07	HP:0011793
+0.00012097516293517722	Abnormality of the fundus	3.9405590532631017e-07	HP:0001098
+0.00012417258265780599	Abnormality of the posterior segment of the globe	4.044709532827557e-07	HP:0004329
+0.00015262060533597588	Hearing impairment	4.971355222670225e-07	HP:0000365
+0.00016059211883394877	Neoplasm	5.231013642799634e-07	HP:0002664
+0.00017325315786960351	Abnormality of the cerebellum	5.643425337772102e-07	HP:0001317
+0.00017618587241738414	Abnormality of the metencephalon	5.738953498937594e-07	HP:0011283
+0.00017618587241738414	Abnormality of hindbrain morphology	5.738953498937594e-07	HP:0011282
+0.00017916319029463729	Hearing abnormality	5.835934537284602e-07	HP:0000364
+0.00018218571347576067	Abnormality of body height	5.934388061099696e-07	HP:0000002
+0.00022960204326684703	Abnormality of the kidney	7.478893917486874e-07	HP:0000077
+0.0002391515950095283	Abnormality of limb bone morphology	7.789954234838055e-07	HP:0002813
+0.00024905713587446506	Abnormal reproductive system morphology	8.112610289070523e-07	HP:0012243
+0.00025312164937551113	Abnormality of eye movement	8.245004865651829e-07	HP:0000496
+0.0002699835132109949	Abnormality of the upper urinary tract	8.794251244657815e-07	HP:0010935
+0.0002721607996075025	Abnormality of the endocrine system	8.865172625651547e-07	HP:0000818
+0.000350750188320614	Abnormality of the nose	1.142508756744671e-06	HP:0000366
+0.0006114146839577272	Abnormality of connective tissue	1.9915787751066032e-06	HP:0003549
+0.0006205299480287158	Abnormality of the genital system	2.0212701890186184e-06	HP:0000078
+0.0008069550626492879	Abnormality of the upper limb	2.628518119378788e-06	HP:0002817
+0.0008921120254797562	Abnormality of limb bone	2.905902363126242e-06	HP:0040068
+0.0009992733379070886	Abnormality of the orbital region	3.254962012726673e-06	HP:0000315
+0.001310620639930439	Intellectual disability	4.269122605636609e-06	HP:0001249
+0.0013287166742452364	Global developmental delay	4.32806734281836e-06	HP:0001263
+0.001393837501355185	Seizures	4.540187300831222e-06	HP:0001250
+0.00144209606825589	Abnormal appendicular skeleton morphology	4.697381329823746e-06	HP:0011844
+0.0015535980630793837	Behavioral abnormality	5.060580010030566e-06	HP:0000708
+0.0015853247689068327	Abnormality of the vasculature	5.163924328686751e-06	HP:0002597
+0.0016953367076601303	Abnormality of body weight	5.522269406059057e-06	HP:0004323
+0.001848609048286737	Abnormality of blood and blood-forming tissues	6.021527844582205e-06	HP:0001871
+0.0020950978592187467	Growth delay	6.8244229941978716e-06	HP:0001510
+0.0030266555423608833	Bone spicule pigmentation of the retina	9.858812841566396e-06	HP:0007737
+0.004174007346542459	Abnormality of the urinary system	1.3596115135317457e-05	HP:0000079
+0.005126939374012541	Abnormality of central motor function	1.6700128254112513e-05	HP:0011442
+0.00540995350440465	Neurodevelopmental delay	1.76219983856829e-05	HP:0012758
+0.00608983167308619	Abnormality of skin morphology	1.9836585254352408e-05	HP:0011121
+0.006688071979710432	Abnormality of the ear	2.178525074824245e-05	HP:0000598
+0.012588335067972373	Abnormality of limbs	4.100434875561034e-05	HP:0040064
+0.013734914174553314	Abnormality of the skin	4.473913411906617e-05	HP:0000951
+0.024146525032660786	Abnormal eye physiology	7.86531760021524e-05	HP:0012373
+0.03252935640175157	Abnormality of the globe	0.00010595881564088459	HP:0012374
+0.03334787037817537	Abnormal eye morphology	0.00010862498494519663	HP:0012372
+0.034524935406332564	Abnormality of the genitourinary system	0.00011245907298479663	HP:0000119
+0.039139246044852014	Undetectable light- and dark-adapted electroretinogram	0.00012748940079756357	HP:0007688
+0.039139246044852014	Peripheral visual field loss	0.00012748940079756357	HP:0007994
+0.043868013802690724	Neurodevelopmental abnormality	0.0001428925531032271	HP:0012759
+0.04946207981041838	Abnormality of muscle physiology	0.0001611142664834475	HP:0011804
diff -r d40860663861 -r 49b46f044d48 test-data/participatant_in-for-substance.json
--- a/test-data/participatant_in-for-substance.json	Sat Dec 02 16:41:34 2017 -0500
+++ b/test-data/participatant_in-for-substance.json	Mon Dec 04 19:35:12 2017 -0500
@@ -1,1 +1,1 @@
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diff -r d40860663861 -r 49b46f044d48 test-data/roles-for-substance.json
--- a/test-data/roles-for-substance.json	Sat Dec 02 16:41:34 2017 -0500
+++ b/test-data/roles-for-substance.json	Mon Dec 04 19:35:12 2017 -0500
@@ -1,1 +1,1 @@
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diff -r d40860663861 -r 49b46f044d48 tools.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools.txt	Mon Dec 04 19:35:12 2017 -0500
@@ -0,0 +1,1 @@
+associations.xml bioentity-associations.xml bioentityset-overrepresentation.xml bulk-operations.xml disease-associations.xml gene-associations.xml genotype-associations.xml get-object.xml phenotype-gene-associations.xml search-operations.xml substance-associations.xml variant-associations.xml
diff -r d40860663861 -r 49b46f044d48 upload_tool.sh