Merge pull request #192 from bgyori/signor

Curate protein families from SIGNOR

.github/workflows/tests.yml

@@ -11,7 +11,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.6
+        python-version: 3.9
     - name: Install dependencies
       run: |
         sudo apt-get install libstdc++6 python3-dev graphviz libgraphviz-dev pkg-config

entities.csv

@@ -149,6 +149,7 @@ CNG
 CNKSR
 Cofilin
 Cohesin
+Collagen
 COL1
 COL4
 COL5
@@ -201,6 +202,7 @@ Desumoylase
 Deubiquitinase
 DGC
 DGK
+Deiodinase
 DNA_polymerase_alpha
 DNA_polymerase_delta
 DNM
@@ -230,6 +232,7 @@ EIF4E
 EIF4EBP
 EIF4G
 ELA
+ELOVL
 ENO
 Eotaxin
 EPHA
@@ -283,6 +286,7 @@ FPR
 FSH
 FUT
 FZD
+G6Pase
 G_12
 G_12_alpha
 GABBR
@@ -316,6 +320,7 @@ G_protein
 GPX
 G_q
 G_q_alpha
+Growth_factor
 GRI
 GRIA
 GRID
@@ -338,13 +343,16 @@ GUCY
 GUCY1A
 GUCY1B
 GYS
+HACD
 hCG
 HDAC
 HDAC_I
 HDAC_II
 HDAC_III
 HDAC_IV
 HDL
+HECT_E3_ligase
+Hexokinase
 Hedgehog
 Hemoglobin
 HES
@@ -359,8 +367,12 @@ Histone_H2A
 Histone_H2B
 Histone_H3
 Histone_H4
+HLA1
+HLA2_alpha
+HLA2_beta
 HLA_DR
 HMOX
+HOMER
 HRH
 HSP90
 HSP90A
@@ -420,6 +432,7 @@ LDH
 LFA_1
 LH
 Ligand_gated_ion_channels
+Liprin_alpha
 LPAR
 LRRC8
 LXR
@@ -482,6 +495,7 @@ Natriuretic_peptide
 NCOA
 NCOR
 NDRG
+Netrin
 Neurexins
 Neuropeptide_receptor
 Neuropeptides
@@ -562,6 +576,8 @@ PDGFR_BB
 PDH
 PDK
 Pertussis_toxin
+PGAM
+PFK
 PFN
 PhK
 Phosphatase
@@ -574,6 +590,7 @@ PIM
 PKA
 PKC
 PKI
+PKM2
 PKN
 PLA2
 PLA2G2
@@ -611,6 +628,8 @@ PRMT
 Propionyl_CoA_carboxylase
 Protease
 Proteasome
+Protocadherin_alpha
+Protocadherin_beta
 PTGER
 Purinergic_receptors
 PYG
@@ -628,11 +647,13 @@ RasGAP
 RASGRF
 RASGRP
 RASSF
+RBR_E3_ligase
 RFC
 RFX
 RGL
 RHO
 RhoGDI
+RING_E3_ligase
 RIPK
 RLR
 RNApo_I
@@ -685,10 +706,13 @@ SP
 SPHK
 SPRED
 SPRY
+SPTB
 SRC
 SREBF
+STAG
 STAT
 STAT5
+STK3_4
 STT3
 Sulfonylurea_receptor
 SWI_SNF
@@ -739,6 +763,7 @@ Ubiquitin
 UCHL
 UGGT
 UGT
+UNC5
 USP
 USPL
 USP9

equivalences.csv

@@ -2169,7 +2169,10 @@ SIGNOR,SIGNOR-PF34,PIM
 SIGNOR,SIGNOR-PF35,SMAD1_5_9
 SIGNOR,SIGNOR-PF36,ERBB
 SIGNOR,SIGNOR-PF37,NRG
+SIGNOR,SIGNOR-PF38,RTK
+SIGNOR,SIGNOR-PF39,Growth_factor
 SIGNOR,SIGNOR-PF40,Wnt
+SIGNOR,SIGNOR-PF41,STK3_4
 SIGNOR,SIGNOR-PF42,MOB1
 SIGNOR,SIGNOR-PF43,LATS
 SIGNOR,SIGNOR-PF44,RXR
@@ -2178,6 +2181,53 @@ SIGNOR,SIGNOR-PF46,Tubulin
 SIGNOR,SIGNOR-PF48,FERMT
 SIGNOR,SIGNOR-PF49,IFITM
 SIGNOR,SIGNOR-PF50,Interferon
+SIGNOR,SIGNOR-PF52,STAG
+SIGNOR,SIGNOR-PF53,PKC
+SIGNOR,SIGNOR-PF54,PPP1
+SIGNOR,SIGNOR-PF55,GRM
+SIGNOR,SIGNOR-PF56,GRIN
+SIGNOR,SIGNOR-PF57,Kainate_family
+SIGNOR,SIGNOR-PF58,GRIA
+SIGNOR,SIGNOR-PF59,HOMER
+SIGNOR,SIGNOR-PF61,GABR
+SIGNOR,SIGNOR-PF62,GLRA_GLRB
+SIGNOR,SIGNOR-PF66,Axonemal_dynein
+SIGNOR,SIGNOR-PF67,Cytoplasmic_dynein
+SIGNOR,SIGNOR-PF68,Histone_H2B
+SIGNOR,SIGNOR-PF69,Histone_H3
+SIGNOR,SIGNOR-PF70,Histone_H2A
+SIGNOR,SIGNOR-PF71,Cadherin
+SIGNOR,SIGNOR-PF72,CTNNA
+SIGNOR,SIGNOR-PF73,SPTB
+SIGNOR,SIGNOR-PF74,ENO
+SIGNOR,SIGNOR-PF75,ALDO
+SIGNOR,SIGNOR-PF76,Hexokinase
+SIGNOR,SIGNOR-PF77,PRKG
+SIGNOR,SIGNOR-PF78,PGAM
+SIGNOR,SIGNOR-PF79,PFK
+SIGNOR,SIGNOR-PF80,PKM2
+SIGNOR,SIGNOR-PF81,G6Pase
+SIGNOR,SIGNOR-PF82,Liprin_alpha
+SIGNOR,SIGNOR-PF83,Deiodinase
+SIGNOR,SIGNOR-PF84,THR
+SIGNOR,SIGNOR-PF86,HACD
+SIGNOR,SIGNOR-PF87,HLA1
+SIGNOR,SIGNOR-PF89,Ubiquitin
+SIGNOR,SIGNOR-PF90,HLA2_beta
+SIGNOR,SIGNOR-PF91,HLA2_alpha
+SIGNOR,SIGNOR-PF92,ADCY
+SIGNOR,SIGNOR-PF93,ELOVL
+SIGNOR,SIGNOR-PF95,GTF_family_8
+SIGNOR,SIGNOR-PF96,PYG
+SIGNOR,SIGNOR-PF97,Netrin
+SIGNOR,SIGNOR-PF98,UNC5
+SIGNOR,SIGNOR-PF100,Protocadherin_alpha
+SIGNOR,SIGNOR-PF102,Protocadherin_beta
+SIGNOR,SIGNOR-PF103,Collagen
+SIGNOR,SIGNOR-PF104,HECT_E3_ligase
+SIGNOR,SIGNOR-PF105,UBE2
+SIGNOR,SIGNOR-PF106,RING_E3_ligase
+SIGNOR,SIGNOR-PF107,RBR_E3_ligase
 MIRBASE_FAMILY,MIPF0000002,MIRLET7
 SFAM,F0001,p14_3_3
 SCOMP,C0001,9_1_1

export/famplex.belns

@@ -2,8 +2,8 @@
 Keyword=FPLX
 NameString=FamPlex
 DomainString=Gene and Gene Products
-VersionString=20211030
-CreatedDateTime=2021-10-30T16:56:41
+VersionString=20230501
+CreatedDateTime=2023-05-01T13:27:38
 DescriptionString=FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.
 QueryValueURL=http://identifiers.org/fplx/
 
@@ -205,6 +205,7 @@ Cholinesterase|CGPR
 Clathrin|CGPR
 Cofilin|CGPR
 Cohesin|CGPR
+Collagen|CGPR
 Creatine_kinase|CGPR
 Cyclin|CGPR
 Cyclin_A|CGPR
@@ -230,6 +231,7 @@ DYNC1|CGPR
 DYNC2|CGPR
 DYRK|CGPR
 Death_receptor|CGPR
+Deiodinase|CGPR
 Deoxyribonucleoside_kinases|CGPR
 Desmoglein|CGPR
 Desumoylase|CGPR
@@ -253,6 +255,7 @@ EIF4E|CGPR
 EIF4EBP|CGPR
 EIF4G|CGPR
 ELA|CGPR
+ELOVL|CGPR
 ENO|CGPR
 EPHA|CGPR
 EPHB|CGPR
@@ -306,6 +309,7 @@ FZD|CGPR
 F_actin|CGPR
 Fibrin|CGPR
 Fibrinogen|CGPR
+G6Pase|CGPR
 GABBR|CGPR
 GABR|CGPR
 GAD|CGPR
@@ -361,20 +365,27 @@ G_s|CGPR
 G_s_alpha|CGPR
 Gamma_secretase|CGPR
 Glycosyltransferase|CGPR
+Growth_factor|CGPR
+HACD|CGPR
 HDAC|CGPR
 HDAC_I|CGPR
 HDAC_II|CGPR
 HDAC_III|CGPR
 HDAC_IV|CGPR
 HDL|CGPR
+HECT_E3_ligase|CGPR
 HES|CGPR
 HEX|CGPR
 HIF|CGPR
 HIF1|CGPR
 HIF_alpha|CGPR
 HIF_beta|CGPR
+HLA1|CGPR
+HLA2_alpha|CGPR
+HLA2_beta|CGPR
 HLA_DR|CGPR
 HMOX|CGPR
+HOMER|CGPR
 HRH|CGPR
 HSP90|CGPR
 HSP90A|CGPR
@@ -387,6 +398,7 @@ HTR2|CGPR
 HVCN|CGPR
 Hedgehog|CGPR
 Hemoglobin|CGPR
+Hexokinase|CGPR
 Histone|CGPR
 Histone_H1|CGPR
 Histone_H2A|CGPR
@@ -445,6 +457,7 @@ LXR|CGPR
 Laminin_111|CGPR
 Laminin_332|CGPR
 Ligand_gated_ion_channels|CGPR
+Liprin_alpha|CGPR
 MAC|CGPR
 MAC_1|CGPR
 MAF|CGPR
@@ -517,6 +530,7 @@ NRG_3_4|CGPR
 NTRK|CGPR
 Na_K_ATPase|CGPR
 Natriuretic_peptide|CGPR
+Netrin|CGPR
 Neurexins|CGPR
 Neuropeptide_receptor|CGPR
 Neuropeptides|CGPR
@@ -577,7 +591,9 @@ PDGF_CC|CGPR
 PDGF_DD|CGPR
 PDH|CGPR
 PDK|CGPR
+PFK|CGPR
 PFN|CGPR
+PGAM|CGPR
 PI3K|CGPR
 PI3K_p110|CGPR
 PI3K_p85|CGPR
@@ -587,6 +603,7 @@ PIM|CGPR
 PKA|CGPR
 PKC|CGPR
 PKI|CGPR
+PKM2|CGPR
 PKN|CGPR
 PLA2|CGPR
 PLA2G2|CGPR
@@ -630,6 +647,8 @@ Potassium_voltage_gated_channels|CGPR
 Propionyl_CoA_carboxylase|CGPR
 Protease|CGPR
 Proteasome|CGPR
+Protocadherin_alpha|CGPR
+Protocadherin_beta|CGPR
 Purinergic_receptors|CGPR
 RAB|CGPR
 RAC|CGPR
@@ -644,10 +663,12 @@ RASAL|CGPR
 RASGRF|CGPR
 RASGRP|CGPR
 RASSF|CGPR
+RBR_E3_ligase|CGPR
 RFC|CGPR
 RFX|CGPR
 RGL|CGPR
 RHO|CGPR
+RING_E3_ligase|CGPR
 RIPK|CGPR
 RLR|CGPR
 RNApo_I|CGPR
@@ -698,10 +719,13 @@ SP|CGPR
 SPHK|CGPR
 SPRED|CGPR
 SPRY|CGPR
+SPTB|CGPR
 SRC|CGPR
 SREBF|CGPR
+STAG|CGPR
 STAT|CGPR
 STAT5|CGPR
+STK3_4|CGPR
 STT3|CGPR
 SWI_SNF|CGPR
 Sarcoglycan_complex|CGPR
@@ -755,6 +779,7 @@ UBE2|CGPR
 UCHL|CGPR
 UGGT|CGPR
 UGT|CGPR
+UNC5|CGPR
 USP|CGPR
 USP17L|CGPR
 USP9|CGPR