From df436d0b2b88a97fe3c228db50fd331d68d7b0b1 Mon Sep 17 00:00:00 2001 From: cmungall Date: Fri, 26 Jun 2020 13:24:05 -0700 Subject: [PATCH 1/6] getting rid of pointless chain for whole pp --- curated/ORFs/uniprot_sars-cov-2.gpi | 2 -- 1 file changed, 2 deletions(-) diff --git a/curated/ORFs/uniprot_sars-cov-2.gpi b/curated/ORFs/uniprot_sars-cov-2.gpi index 366abcd4..ddab81dc 100644 --- a/curated/ORFs/uniprot_sars-cov-2.gpi +++ b/curated/ORFs/uniprot_sars-cov-2.gpi @@ -20,7 +20,6 @@ !Generated: 2020-06-10 13:25 ! UniProtKB P0DTC1 P0DTC1 Replicase polyprotein 1a ORF1a protein taxon:2697049 -UniProtKB P0DTC1-PRO_0000449634 pp1a Replicase polyprotein 1a pp1a|P0DTC1(1-4405)|ORF1a protein taxon:2697049 UniProtKB:P0DTC1 UniProtKB P0DTC1-PRO_0000449635 nsp1 Non-structural protein 1 nsp1|P0DTC1(1-180) protein taxon:2697049 UniProtKB:P0DTC1 UniProtKB P0DTC1-PRO_0000449636 nsp2 Non-structural protein 2 nsp2|P0DTC1(181-818) protein taxon:2697049 UniProtKB:P0DTC1 UniProtKB P0DTC1-PRO_0000449637 nsp3 Non-structural protein 3 nsp3|PL-PRO|P0DTC1(819-2763) protein taxon:2697049 UniProtKB:P0DTC1 @@ -52,7 +51,6 @@ UniProtKB P0DTC8-PRO_0000449655 P0DTC8(16-121) ORF8 protein P0DTC8(16-121) prote UniProtKB P0DTC9 N Nucleoprotein NC|Protein N|P0DTC9(1-419)|N protein taxon:2697049 UniProtKB P0DTC9-PRO_0000449656 N Nucleoprotein NC|Protein N|P0DTC9(1-419)|N protein taxon:2697049 UniProtKB:P0DTC9 UniProtKB P0DTD1 rep Replicase polyprotein 1ab rep|1a-1b|ORF1ab protein taxon:2697049 -UniProtKB P0DTD1-PRO_0000449618 pp1ab Replicase polyprotein 1ab pp1ab|P0DTD1(1-7096)|rep|1a-1b|ORF1ab protein taxon:2697049 UniProtKB:P0DTD1 UniProtKB P0DTD1-PRO_0000449619 nsp1 Host translation inhibitor nsp1 nsp1|P0DTD1(1-180) protein taxon:2697049 UniProtKB:P0DTD1 UniProtKB P0DTD1-PRO_0000449620 nsp2 Non-structural protein 2 nsp2|P0DTD1(181-818) protein taxon:2697049 UniProtKB:P0DTD1 UniProtKB P0DTD1-PRO_0000449621 nsp3 Non-structural protein 3 nsp3|PL-PRO|P0DTD1(819-2763) protein taxon:2697049 UniProtKB:P0DTD1 From 959885ada463c98468b84298fec0b131cffeb568 Mon Sep 17 00:00:00 2001 From: cmungall Date: Fri, 26 Jun 2020 13:25:15 -0700 Subject: [PATCH 2/6] getting rid of duplicates, see Patricks comments in https://github.com/geneontology/go-site/issues/1431 --- curated/ORFs/uniprot_sars-cov-2.gpi | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/curated/ORFs/uniprot_sars-cov-2.gpi b/curated/ORFs/uniprot_sars-cov-2.gpi index ddab81dc..4cce2876 100644 --- a/curated/ORFs/uniprot_sars-cov-2.gpi +++ b/curated/ORFs/uniprot_sars-cov-2.gpi @@ -20,16 +20,6 @@ !Generated: 2020-06-10 13:25 ! UniProtKB P0DTC1 P0DTC1 Replicase polyprotein 1a ORF1a protein taxon:2697049 -UniProtKB P0DTC1-PRO_0000449635 nsp1 Non-structural protein 1 nsp1|P0DTC1(1-180) protein taxon:2697049 UniProtKB:P0DTC1 -UniProtKB P0DTC1-PRO_0000449636 nsp2 Non-structural protein 2 nsp2|P0DTC1(181-818) protein taxon:2697049 UniProtKB:P0DTC1 -UniProtKB P0DTC1-PRO_0000449637 nsp3 Non-structural protein 3 nsp3|PL-PRO|P0DTC1(819-2763) protein taxon:2697049 UniProtKB:P0DTC1 -UniProtKB P0DTC1-PRO_0000449638 nsp4 Non-structural protein 4 nsp4|P0DTC1(2764-3263) protein taxon:2697049 UniProtKB:P0DTC1 -UniProtKB P0DTC1-PRO_0000449639 nsp5 3C-like proteinase nsp5|3CL-PRO|3CLp|Mpro|P0DTC1(3264-3569) protein taxon:2697049 UniProtKB:P0DTC1 -UniProtKB P0DTC1-PRO_0000449640 nsp6 Non-structural protein 6 nsp6|P0DTC1(3570-3859) protein taxon:2697049 UniProtKB:P0DTC1 -UniProtKB P0DTC1-PRO_0000449641 nsp7 Non-structural protein 7 nsp7|P0DTC1(3860-3942) protein taxon:2697049 UniProtKB:P0DTC1 -UniProtKB P0DTC1-PRO_0000449642 nsp8 Non-structural protein 8 nsp8|P0DTC1(3943-4140) protein taxon:2697049 UniProtKB:P0DTC1 -UniProtKB P0DTC1-PRO_0000449643 nsp9 Non-structural protein 9 nsp9|P0DTC1(4141-4253) protein taxon:2697049 UniProtKB:P0DTC1 -UniProtKB P0DTC1-PRO_0000449644 nsp10 Non-structural protein 10 nsp10|GFL|P0DTC1(4254-4392) protein taxon:2697049 UniProtKB:P0DTC1 UniProtKB P0DTC1-PRO_0000449645 nsp11 Non-structural protein 11 nsp11|P0DTC1(4393-4405) protein taxon:2697049 UniProtKB:P0DTC1 UniProtKB P0DTC2 S protein Spike glycoprotein S|2|S protein protein taxon:2697049 UniProtKB P0DTC2-PRO_0000449646 S(13-1273) Spike glycoprotein P0DTC2(13-1273)|S|2|S protein protein taxon:2697049 UniProtKB:P0DTC2 From 09a90e64da2c31f1731b0c2f65b315ee7efd22e0 Mon Sep 17 00:00:00 2001 From: cmungall Date: Fri, 26 Jun 2020 13:32:27 -0700 Subject: [PATCH 3/6] getting rid of pointless chain for whole pp --- curated/ORFs/uniprot_sars-cov-2.gpi | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/curated/ORFs/uniprot_sars-cov-2.gpi b/curated/ORFs/uniprot_sars-cov-2.gpi index 4cce2876..d8cec9de 100644 --- a/curated/ORFs/uniprot_sars-cov-2.gpi +++ b/curated/ORFs/uniprot_sars-cov-2.gpi @@ -22,24 +22,16 @@ UniProtKB P0DTC1 P0DTC1 Replicase polyprotein 1a ORF1a protein taxon:2697049 UniProtKB P0DTC1-PRO_0000449645 nsp11 Non-structural protein 11 nsp11|P0DTC1(4393-4405) protein taxon:2697049 UniProtKB:P0DTC1 UniProtKB P0DTC2 S protein Spike glycoprotein S|2|S protein protein taxon:2697049 -UniProtKB P0DTC2-PRO_0000449646 S(13-1273) Spike glycoprotein P0DTC2(13-1273)|S|2|S protein protein taxon:2697049 UniProtKB:P0DTC2 UniProtKB P0DTC2-PRO_0000449647 S(13-685) Spike protein S1 P0DTC2(13-685)|S|2 protein taxon:2697049 UniProtKB:P0DTC2 UniProtKB P0DTC2-PRO_0000449648 S(686-1273) Spike protein S2 P0DTC2(686-1273)|S|2 protein taxon:2697049 UniProtKB:P0DTC2 UniProtKB P0DTC2-PRO_0000449649 S(816-1273) Spike protein S2' P0DTC2(816-1273)|S|2 protein taxon:2697049 UniProtKB:P0DTC2 UniProtKB P0DTC3 ORF3a ORF3a protein ORF3a|3a protein taxon:2697049 -UniProtKB P0DTC3-PRO_0000449650 3a(1-275) ORF3a protein P0DTC3(1-275)|3a|ORF3a protein taxon:2697049 UniProtKB:P0DTC3 UniProtKB P0DTC4 E protein Envelope small membrane protein E|4|E protein protein taxon:2697049 -UniProtKB P0DTC4-PRO_0000449651 E protein Envelope small membrane protein E protein|sM protein|P0DTC4(1-75)|E|4 protein taxon:2697049 UniProtKB:P0DTC4 UniProtKB P0DTC5 P0DTC5 Membrane protein protein taxon:2697049 -UniProtKB P0DTC5-PRO_0000449652 M protein Membrane protein M protein|P0DTC5(1-222) protein taxon:2697049 UniProtKB:P0DTC5 UniProtKB P0DTC6 ORF6 Non-structural protein 6 ORF6 protein taxon:2697049 -UniProtKB P0DTC6-PRO_0000449653 ns6 ORF6 protein ns6|P0DTC6(1-61)|6 protein taxon:2697049 UniProtKB:P0DTC6 UniProtKB P0DTC7 ORF7a ORF7a protein ORF7a|7a protein taxon:2697049 -UniProtKB P0DTC7-PRO_0000449654 7a(16-121) ORF7a protein P0DTC7(16-121)|7a|ORF7a protein taxon:2697049 UniProtKB:P0DTC7 UniProtKB P0DTC8 P0DTC8 Non-structural protein 8 nsp8 protein taxon:2697049 -UniProtKB P0DTC8-PRO_0000449655 P0DTC8(16-121) ORF8 protein P0DTC8(16-121) protein taxon:2697049 UniProtKB:P0DTC8 UniProtKB P0DTC9 N Nucleoprotein NC|Protein N|P0DTC9(1-419)|N protein taxon:2697049 -UniProtKB P0DTC9-PRO_0000449656 N Nucleoprotein NC|Protein N|P0DTC9(1-419)|N protein taxon:2697049 UniProtKB:P0DTC9 UniProtKB P0DTD1 rep Replicase polyprotein 1ab rep|1a-1b|ORF1ab protein taxon:2697049 UniProtKB P0DTD1-PRO_0000449619 nsp1 Host translation inhibitor nsp1 nsp1|P0DTD1(1-180) protein taxon:2697049 UniProtKB:P0DTD1 UniProtKB P0DTD1-PRO_0000449620 nsp2 Non-structural protein 2 nsp2|P0DTD1(181-818) protein taxon:2697049 UniProtKB:P0DTD1 @@ -57,8 +49,5 @@ UniProtKB P0DTD1-PRO_0000449631 nsp14 Proofreading exoribonuclease nsp14|ExoN|P0 UniProtKB P0DTD1-PRO_0000449632 nsp15 Uridylate-specific endoribonuclease nsp15|P0DTD1(6453-6798) protein taxon:2697049 UniProtKB:P0DTD1 UniProtKB P0DTD1-PRO_0000449633 nsp16 2'-O-methyltransferase nsp16|P0DTD1(6799-7096) protein taxon:2697049 UniProtKB:P0DTD1 UniProtKB P0DTD2 P0DTD2 Protein 9b ORF9b protein taxon:2697049 -UniProtKB P0DTD2-PRO_0000449657 P0DTD2(1-97) ORF9b protein P0DTD2(1-97)|ORF9b protein taxon:2697049 UniProtKB:P0DTD2 UniProtKB P0DTD3 ORF14 Uncharacterized protein 14 ORF14 protein taxon:2697049 -UniProtKB P0DTD3-PRO_0000449658 ORF14(1-73) Uncharacterized protein 14 P0DTD3(1-73)|ORF14 protein taxon:2697049 UniProtKB:P0DTD3 UniProtKB P0DTD8 P0DTD8 Protein non-structural 7b ORF7b protein taxon:2697049 -UniProtKB P0DTD8-PRO_0000449799 ns7b Protein non-structural 7b ns7b|P0DTD8(1-43)|ORF7b protein taxon:2697049 UniProtKB:P0DTD8 From 1459f2c915a243082bca5a581f3cb059b70a76d6 Mon Sep 17 00:00:00 2001 From: cmungall Date: Fri, 26 Jun 2020 13:39:53 -0700 Subject: [PATCH 4/6] fixing pp labels --- curated/ORFs/uniprot_sars-cov-2.gpi | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/curated/ORFs/uniprot_sars-cov-2.gpi b/curated/ORFs/uniprot_sars-cov-2.gpi index d8cec9de..f220b0ce 100644 --- a/curated/ORFs/uniprot_sars-cov-2.gpi +++ b/curated/ORFs/uniprot_sars-cov-2.gpi @@ -19,7 +19,7 @@ ! !Generated: 2020-06-10 13:25 ! -UniProtKB P0DTC1 P0DTC1 Replicase polyprotein 1a ORF1a protein taxon:2697049 +UniProtKB P0DTC1 pp1a Replicase polyprotein 1a ORF1a|1a|pp1a protein taxon:2697049 UniProtKB P0DTC1-PRO_0000449645 nsp11 Non-structural protein 11 nsp11|P0DTC1(4393-4405) protein taxon:2697049 UniProtKB:P0DTC1 UniProtKB P0DTC2 S protein Spike glycoprotein S|2|S protein protein taxon:2697049 UniProtKB P0DTC2-PRO_0000449647 S(13-685) Spike protein S1 P0DTC2(13-685)|S|2 protein taxon:2697049 UniProtKB:P0DTC2 @@ -32,7 +32,7 @@ UniProtKB P0DTC6 ORF6 Non-structural protein 6 ORF6 protein taxon:2697049 UniProtKB P0DTC7 ORF7a ORF7a protein ORF7a|7a protein taxon:2697049 UniProtKB P0DTC8 P0DTC8 Non-structural protein 8 nsp8 protein taxon:2697049 UniProtKB P0DTC9 N Nucleoprotein NC|Protein N|P0DTC9(1-419)|N protein taxon:2697049 -UniProtKB P0DTD1 rep Replicase polyprotein 1ab rep|1a-1b|ORF1ab protein taxon:2697049 +UniProtKB P0DTD1 pp1ab Replicase polyprotein 1ab rep|1a-1b|ORF1ab protein taxon:2697049 UniProtKB P0DTD1-PRO_0000449619 nsp1 Host translation inhibitor nsp1 nsp1|P0DTD1(1-180) protein taxon:2697049 UniProtKB:P0DTD1 UniProtKB P0DTD1-PRO_0000449620 nsp2 Non-structural protein 2 nsp2|P0DTD1(181-818) protein taxon:2697049 UniProtKB:P0DTD1 UniProtKB P0DTD1-PRO_0000449621 nsp3 Non-structural protein 3 nsp3|PL-PRO|P0DTD1(819-2763) protein taxon:2697049 UniProtKB:P0DTD1 From 680b5ae38b6d3ba14bc3ad12d7a195b0a02cdb3a Mon Sep 17 00:00:00 2001 From: cmungall Date: Fri, 26 Jun 2020 13:43:28 -0700 Subject: [PATCH 5/6] fixing ORF8. https://github.com/geneontology/go-site/issues/1431 --- curated/ORFs/uniprot_sars-cov-2.gpi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/curated/ORFs/uniprot_sars-cov-2.gpi b/curated/ORFs/uniprot_sars-cov-2.gpi index f220b0ce..b12e0e3a 100644 --- a/curated/ORFs/uniprot_sars-cov-2.gpi +++ b/curated/ORFs/uniprot_sars-cov-2.gpi @@ -30,7 +30,7 @@ UniProtKB P0DTC4 E protein Envelope small membrane protein E|4|E protein protein UniProtKB P0DTC5 P0DTC5 Membrane protein protein taxon:2697049 UniProtKB P0DTC6 ORF6 Non-structural protein 6 ORF6 protein taxon:2697049 UniProtKB P0DTC7 ORF7a ORF7a protein ORF7a|7a protein taxon:2697049 -UniProtKB P0DTC8 P0DTC8 Non-structural protein 8 nsp8 protein taxon:2697049 +UniProtKB P0DTC8 ORF8 ORF8 ns8 protein taxon:2697049 UniProtKB P0DTC9 N Nucleoprotein NC|Protein N|P0DTC9(1-419)|N protein taxon:2697049 UniProtKB P0DTD1 pp1ab Replicase polyprotein 1ab rep|1a-1b|ORF1ab protein taxon:2697049 UniProtKB P0DTD1-PRO_0000449619 nsp1 Host translation inhibitor nsp1 nsp1|P0DTD1(1-180) protein taxon:2697049 UniProtKB:P0DTD1 From cf7f4d523bb2f931d674961d8027e9c899270c3f Mon Sep 17 00:00:00 2001 From: cmungall Date: Fri, 26 Jun 2020 13:43:48 -0700 Subject: [PATCH 6/6] Renaming M. https://github.com/geneontology/go-site/issues/1431 --- curated/ORFs/uniprot_sars-cov-2.gpi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/curated/ORFs/uniprot_sars-cov-2.gpi b/curated/ORFs/uniprot_sars-cov-2.gpi index b12e0e3a..8b34d7bd 100644 --- a/curated/ORFs/uniprot_sars-cov-2.gpi +++ b/curated/ORFs/uniprot_sars-cov-2.gpi @@ -27,7 +27,7 @@ UniProtKB P0DTC2-PRO_0000449648 S(686-1273) Spike protein S2 P0DTC2(686-1273)|S| UniProtKB P0DTC2-PRO_0000449649 S(816-1273) Spike protein S2' P0DTC2(816-1273)|S|2 protein taxon:2697049 UniProtKB:P0DTC2 UniProtKB P0DTC3 ORF3a ORF3a protein ORF3a|3a protein taxon:2697049 UniProtKB P0DTC4 E protein Envelope small membrane protein E|4|E protein protein taxon:2697049 -UniProtKB P0DTC5 P0DTC5 Membrane protein protein taxon:2697049 +UniProtKB P0DTC5 M protein Membrane protein protein taxon:2697049 UniProtKB P0DTC6 ORF6 Non-structural protein 6 ORF6 protein taxon:2697049 UniProtKB P0DTC7 ORF7a ORF7a protein ORF7a|7a protein taxon:2697049 UniProtKB P0DTC8 ORF8 ORF8 ns8 protein taxon:2697049