Complete family curation and update exports

sorgerlab · Jun 10, 2023 · 8c846ba · 8c846ba
1 parent bf9dc39
commit 8c846ba
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Showing 6 changed files with 68 additions and 23 deletions.
diff --git a/entities.csv b/entities.csv
@@ -383,6 +383,7 @@ HTR
 HTR1
 HTR2
 HVCN
+ICAM
 IFITM
 IFNA
 IFNAR
@@ -736,6 +737,7 @@ TIAM
 TIF_IB
 TIM22_complex
 TK
+TLE
 TLR
 TN
 TNF

diff --git a/export/famplex.belns b/export/famplex.belns
@@ -2,8 +2,8 @@
 Keyword=FPLX
 NameString=FamPlex
 DomainString=Gene and Gene Products
-VersionString=20230501
-CreatedDateTime=2023-05-01T13:27:38
+VersionString=20230610
+CreatedDateTime=2023-06-10T15:49:48
 DescriptionString=FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.
 QueryValueURL=http://identifiers.org/fplx/
 
@@ -405,6 +405,7 @@ Histone_H2A|CGPR
 Histone_H2B|CGPR
 Histone_H3|CGPR
 Histone_H4|CGPR
+ICAM|CGPR
 IFITM|CGPR
 IFNA|CGPR
 IFNAR|CGPR
@@ -752,6 +753,7 @@ TIAM|CGPR
 TIF_IB|CGPR
 TIM22_complex|CGPR
 TK|CGPR
+TLE|CGPR
 TLR|CGPR
 TN|CGPR
 TNF|CGPR

diff --git a/export/famplex.obo b/export/famplex.obo
@@ -1,5 +1,5 @@
 format-version: 1.2
-date: 01:05:2023 13:27
+date: 10:06:2023 15:49
 
 [Term]
 id: FPLX:5_hydroxytryptamine_receptors_G_protein_coupled
@@ -653,7 +653,7 @@ id: FPLX:ALG1_family
 name: ALG1-family
 is_a: FPLX:Glycosyltransferase
 inverse_is_a: HGNC:ALG1
-inverse_is_a: HGNC:ALG1L
+inverse_is_a: HGNC:ALG1L1P
 inverse_is_a: HGNC:ALG1L2
 inverse_is_a: HGNC:ALG2
 inverse_is_a: HGNC:ALG11
@@ -6442,7 +6442,7 @@ xref: RE:R-HSA-8936837
 part_of: FPLX:HIF
 inverse_is_a: HGNC:ARNT
 inverse_is_a: HGNC:ARNT2
-inverse_is_a: HGNC:ARNTL
+inverse_is_a: HGNC:BMAL1
 
 [Term]
 id: FPLX:Histone
@@ -6513,7 +6513,7 @@ inverse_is_a: HGNC:H2AC12
 inverse_is_a: HGNC:H2AC14
 inverse_is_a: HGNC:H2AC21
 inverse_is_a: HGNC:H2AC20
-inverse_is_a: HGNC:H2AW
+inverse_is_a: HGNC:H2AC25
 inverse_is_a: UP:P04908
 inverse_is_a: UP:Q6FI13
 
@@ -6542,7 +6542,7 @@ inverse_is_a: HGNC:H2BC18
 inverse_is_a: HGNC:H2BC19P
 inverse_is_a: HGNC:H2BC20P
 inverse_is_a: HGNC:H2BC21
-inverse_is_a: HGNC:H2BU1
+inverse_is_a: HGNC:H2BC26
 inverse_is_a: HGNC:H2BC12L
 inverse_is_a: HGNC:H2BW2
 inverse_is_a: HGNC:H2BW1
@@ -6803,6 +6803,17 @@ xref: HGNC_GROUP:254
 is_a: FPLX:Voltage_gated_ion_channels
 inverse_is_a: HGNC:HVCN1
 
+[Term]
+id: FPLX:ICAM
+name: ICAM
+synonym: "ICAM" EXACT []
+is_a: FPLX:root
+inverse_is_a: HGNC:ICAM1
+inverse_is_a: HGNC:ICAM2
+inverse_is_a: HGNC:ICAM3
+inverse_is_a: HGNC:ICAM4
+inverse_is_a: HGNC:ICAM5
+
 [Term]
 id: FPLX:IFITM
 name: IFITM
@@ -8563,7 +8574,7 @@ inverse_is_a: HGNC:MYL2
 inverse_is_a: HGNC:MYL5
 inverse_is_a: HGNC:MYL7
 inverse_is_a: HGNC:MYL9
-inverse_is_a: HGNC:MYLPF
+inverse_is_a: HGNC:MYL11
 
 [Term]
 id: FPLX:MYL_slow
@@ -10025,7 +10036,7 @@ has_part: HGNC:CTR9
 has_part: HGNC:LEO1
 has_part: HGNC:PAF1
 has_part: HGNC:RTF1
-has_part: HGNC:WDR61
+has_part: HGNC:SKIC8
 
 [Term]
 id: FPLX:PAK
@@ -11947,7 +11958,7 @@ inverse_is_a: HGNC:CHFR
 inverse_is_a: HGNC:CNOT4
 inverse_is_a: HGNC:COP1
 inverse_is_a: HGNC:CUL9
-inverse_is_a: HGNC:CYHR1
+inverse_is_a: HGNC:ZFTRAF1
 inverse_is_a: HGNC:DCST1
 inverse_is_a: HGNC:DTX1
 inverse_is_a: HGNC:DTX2
@@ -12085,7 +12096,7 @@ inverse_is_a: HGNC:RNF150
 inverse_is_a: HGNC:RNF151
 inverse_is_a: HGNC:RNF152
 inverse_is_a: HGNC:RNF157
-inverse_is_a: HGNC:RNF165
+inverse_is_a: HGNC:ARK2C
 inverse_is_a: HGNC:RNF166
 inverse_is_a: HGNC:RNF167
 inverse_is_a: HGNC:RNF168
@@ -12267,7 +12278,7 @@ synonym: "RLRs" EXACT []
 synonym: "RLR" EXACT []
 synonym: "RIG-I like receptors" EXACT []
 is_a: FPLX:root
-inverse_is_a: HGNC:DDX58
+inverse_is_a: HGNC:RIGI
 inverse_is_a: HGNC:DHX58
 inverse_is_a: HGNC:IFIH1
 
@@ -13516,6 +13527,19 @@ is_a: FPLX:Deoxyribonucleoside_kinases
 inverse_is_a: HGNC:TK1
 inverse_is_a: HGNC:TK2
 
+[Term]
+id: FPLX:TLE
+name: TLE
+synonym: "TLE family" EXACT []
+is_a: FPLX:root
+inverse_is_a: HGNC:TLE1
+inverse_is_a: HGNC:TLE2
+inverse_is_a: HGNC:TLE3
+inverse_is_a: HGNC:TLE4
+inverse_is_a: HGNC:TLE5
+inverse_is_a: HGNC:TLE6
+inverse_is_a: HGNC:TLE7
+
 [Term]
 id: FPLX:TLR
 name: TLR
@@ -14142,7 +14166,7 @@ inverse_is_a: HGNC:USP37
 inverse_is_a: HGNC:USP38
 inverse_is_a: HGNC:USP39
 inverse_is_a: HGNC:USP40
-inverse_is_a: HGNC:USP41
+inverse_is_a: HGNC:USP41P
 inverse_is_a: HGNC:USP42
 inverse_is_a: HGNC:USP43
 inverse_is_a: HGNC:USP44

diff --git a/export/famplex_groundings.tsv b/export/famplex_groundings.tsv
@@ -1213,6 +1213,7 @@ Hsp90	HSP90	fplx	Family
 HuR	Q15717	uniprot	Gene_or_gene_product
 I-R	D015427	mesh	BioProcess
 I/R	D015427	mesh	BioProcess
+ICAM	ICAM	fplx	Family
 ICAM-1	P05362	uniprot	Gene_or_gene_product
 IER3	P46695	uniprot	Gene_or_gene_product
 IFI16	Q16666	uniprot	Gene_or_gene_product
@@ -2446,6 +2447,8 @@ TIF-IB	TIF_IB	fplx	Family
 TIM22 complex	TIM22_complex	fplx	Family
 TIM22-complex	TIM22_complex	fplx	Family
 TK	TK	fplx	Family
+TLE	TLE	fplx	Family
+TLE family	TLE	fplx	Family
 TLR	TLR	fplx	Family
 TLR2	O60603	uniprot	Gene_or_gene_product
 TLR4	O00206	uniprot	Gene_or_gene_product

diff --git a/export/hgnc_symbol_map.csv b/export/hgnc_symbol_map.csv
@@ -144,7 +144,7 @@ ALG11,32456
 ALG12,19358
 ALG13,30881
 ALG14,28287
-ALG1L,33721
+ALG1L1P,33721
 ALG1L2,37258
 ALG2,23159
 ALG3,23056
@@ -243,6 +243,7 @@ ARID1A,11110
 ARID1B,18040
 ARIH1,689
 ARIH2,690
+ARK2C,31696
 ARL1,692
 ARL10,22042
 ARL11,24046
@@ -267,7 +268,6 @@ ARL8B,25564
 ARL9,23592
 ARNT,700
 ARNT2,16876
-ARNTL,701
 ARPC1A,703
 ARPC1B,704
 ARPC2,705
@@ -389,6 +389,7 @@ BIRC7,13702
 BIRC8,14878
 BLVRA,1062
 BLVRB,1063
+BMAL1,701
 BMI1,1066
 BMP1,1067
 BMP10,20869
@@ -953,7 +954,6 @@ CXCR6,16647
 CYBA,2577
 CYBB,2578
 CYC1,2579
-CYHR1,17806
 CYLD,2584
 CYP11A1,2590
 CYP11B1,2591
@@ -1023,7 +1023,6 @@ DCST1,26539
 DCTN2,2712
 DDR1,2730
 DDR2,2731
-DDX58,19102
 DESI1,24577
 DESI2,24264
 DGCR2,2845
@@ -1652,10 +1651,10 @@ H2AC12,13671
 H2AC14,4727
 H2AC20,4738
 H2AC21,20508
+H2AC25,20507
 H2AC6,4733
 H2AC7,4729
 H2AJ,14456
-H2AW,20507
 H2AX,4739
 H2AZ1,4741
 H2AZ2,20664
@@ -1671,10 +1670,10 @@ H2BC18,24700
 H2BC19P,20517
 H2BC20P,20516
 H2BC21,4760
+H2BC26,20514
 H2BC3,4751
 H2BC5,4747
 H2BC9,4755
-H2BU1,20514
 H2BW1,27252
 H2BW2,27867
 H3-4,4778
@@ -1826,6 +1825,11 @@ HUWE1,30892
 HVCN1,28240
 HYOU1,16931
 IAPP,5329
+ICAM1,5344
+ICAM2,5345
+ICAM3,5346
+ICAM4,5347
+ICAM5,5348
 IFIH1,18873
 IFITM1,5412
 IFITM10,40022
@@ -2485,6 +2489,7 @@ MYH8,7578
 MYH9,7579
 MYL1,7582
 MYL10,29825
+MYL11,29824
 MYL12A,16701
 MYL12B,29827
 MYL2,7583
@@ -2496,7 +2501,6 @@ MYL6B,29823
 MYL7,21719
 MYL9,15754
 MYLIP,21155
-MYLPF,29824
 MYO10,7593
 MYO15A,7594
 MYO15B,14083
@@ -3730,6 +3734,7 @@ RHOB,668
 RHOC,669
 RHOG,672
 RICTOR,28611
+RIGI,19102
 RING1,10018
 RIPK1,10019
 RIPK2,10020
@@ -3772,7 +3777,6 @@ RNF150,23138
 RNF151,23235
 RNF152,26811
 RNF157,29402
-RNF165,31696
 RNF166,28856
 RNF167,24544
 RNF168,26661
@@ -3978,6 +3982,7 @@ SIRT4,14932
 SIRT5,14933
 SIRT6,14934
 SIRT7,14935
+SKIC8,30300
 SKP1,10899
 SLC27A2,10996
 SLC2A1,11005
@@ -4178,6 +4183,13 @@ TIMM9,11819
 TIPARP,23696
 TK1,11830
 TK2,11831
+TLE1,11837
+TLE2,11838
+TLE3,11839
+TLE4,11840
+TLE5,307
+TLE6,30788
+TLE7,53648
 TLR1,11847
 TLR10,15634
 TLR2,11848
@@ -4521,7 +4533,7 @@ USP38,20067
 USP39,20071
 USP4,12627
 USP40,20069
-USP41,20070
+USP41P,20070
 USP42,20068
 USP43,20072
 USP44,20064
@@ -4566,7 +4578,6 @@ VPS54,18652
 VPS8,29122
 WDCP,26157
 WDR59,25706
-WDR61,30300
 WDSUB1,26697
 WNT1,12774
 WNT10A,13829
@@ -4613,6 +4624,7 @@ ZACN,29504
 ZAP70,12858
 ZBTB12,19066
 ZFPL1,12868
+ZFTRAF1,17806
 ZNF134,12918
 ZNF341,15992
 ZNF511,28445

diff --git a/grounding_map.csv b/grounding_map.csv
@@ -3297,3 +3297,5 @@ HLA2 alpha chain,FPLX,HLA2_alpha,,,,
 ELOVL,FPLX,ELOVL,,,,
 netrin,FPLX,Netrin,,,,
 UNC5,FPLX,UNC5,,,,
+TLE family,FPLX,TLE,,,,
+ICAM,FPLX,ICAM,,,,