Closed andrewelamb closed 2 years ago
@andrewelamb , the rows in the tables above are truncated, would you please send the whole tables?
@andrewelamb @bswhite This is most likely an error that was introduced when I converted the respective columns to STRING_LIST
, so probably something I'll need to fix. I can grab the data from the table version prior to my update and try to fix from there.
publicationId prod test
1 syn21649049 ["CA182915"] ["CA215845"]
2 syn21645615 ["CA182915", "CA182915"] ["CA182915", "CA215845"]
3 syn21648914 ["CA182915", "CA182915"] ["CA182915", "CA215845"]
4 syn21649120 ["CA182915"] ["CA215845"]
5 syn21645614 ["CA182915", "CA182915"] ["CA182915", "CA215845"]
6 syn21645616 ["CA182915", "CA182915"] ["CA182915", "CA215845"]
7 syn21681504 ["CA182915"] ["CA215845"]
8 syn21648966 ["CA182915", "CA182915"] ["CA182915", "CA215845"]
9 syn21649141 ["CA182915"] ["CA215845"]
10 syn21648986 ["CA182915", "CA182915"] ["CA182915", "CA215845"]
11 syn21649134 ["CA182915", "CA182915"] ["CA182915", "CA215845"]
12 syn21649118 ["CA182915"] ["CA215845"]
13 syn21681822 ["CA182915", "CA182915"] ["CA182915", "CA215845"]
14 syn21681437 ["CA182915", "CA182915"] ["CA182915", "CA215845"]
15 syn21681624 ["CA182915", "CA182915"] ["CA182915", "CA215845"]
16 syn21682010 ["CA182915"] ["CA215845"]
17 syn21649024 ["CA182915"] ["CA215845"]
18 syn21681551 ["CA182915"] ["CA215845"]
19 syn21681626 ["CA182915", "CA182915"] ["CA182915", "CA215845"]
20 syn21645612 ["CA182915", "CA182915"] ["CA182915", "CA215845"]
21 syn21681574 ["CA182915"] ["CA215845"]
22 syn21681963 ["CA182915"] ["CA215845"]
23 syn21645617 ["CA182915", "CA182915"] ["CA182915", "CA215845"]
24 syn21645613 ["CA182915", "CA182915"] ["CA182915", "CA215845"]
25 syn21681559 ["CA182915"] ["CA215845"]
publicationId prod test
1 syn21681375 syn21792857 syn21889704, syn21889789
2 syn21648960 syn21792798, syn21792787 syn21889551, syn21889848
3 syn21645405 syn21790756 syn21889698, syn21889787
4 syn21649049 syn21792696 syn21889611, syn21889887
5 syn21645325 syn21828913 syn21889710, syn21889794
6 syn21648894 syn21792707 syn21889514, syn21889837
7 syn21681723 syn21812634 syn21889633, syn21889905
8 syn21649214 syn13857535 syn21889517, syn21889840
9 syn21681392 syn21796559 syn21889756, syn21889823
10 syn21681382 syn21796537 syn21889515, syn21889838
11 syn21645430 syn21790688 syn21889695, syn21889782
12 syn21648903 syn21790882 syn21889709, syn21889793
13 syn21681737 syn21812642 syn21889569, syn21889864
14 syn21681447 syn21809588 syn21889519, syn21889841
15 syn21681451 syn21809597 syn21889607, syn21889884
16 syn21681618 syn21812565 syn21889640
17 syn21681667 syn21812579 syn21889605, syn21889881
18 syn21649212 syn12976746 syn21889694, syn21889785
19 syn21681441 syn21809465 syn21889589
20 syn21648893 syn21791465 syn21889532
21 syn21645594 syn21790743, syn21889770 syn21889699, syn21889788, syn21889770
22 syn21681851 syn21813759 syn21889622, syn21889900
23 syn21645338 syn21832111, syn21832136, syn21889771 syn21889728, syn21889803, syn21889771
24 syn21645269 syn21791499 syn21889753, syn21889821
25 syn21681890 syn21813804 syn21889660, syn21889917
26 syn21645337 syn21791225 syn21889693, syn21889784
27 syn21648926 syn21792538 syn21889718, syn21889797
28 syn21681814 syn21813525 syn21889637, syn21889907
29 syn21681435 syn21809435 syn21889705, syn21889790
30 syn21645258 syn12576666 syn21889724, syn21889801
31 syn21681436 syn21809444 syn21889565, syn21889859
32 syn21649154 syn21797922 syn21889580
33 syn21649001 syn18425364 syn21889629, syn21889791
34 syn21649073 syn21796402 syn21889765, syn21889833
35 syn21645383 syn13858908 syn21889762, syn21889824
36 syn21681987 syn21814183 syn21889653, syn21889914
37 syn21681523 syn21791536 syn21889734, syn21889811
38 syn21681403 syn21797924 syn21889545, syn21889849
39 syn21648884 syn21791468 syn21889533, syn21889847
40 syn21648934 syn21796552 syn21889513, syn21889836
41 syn21645422 syn21800136 syn21889752, syn21889819
42 syn21648978 syn21797950 syn21889731, syn21889805
43 syn21681315 syn21790254 syn21889682, syn21889781
44 syn21649209 syn12976694 syn21889722, syn21889800
45 syn21649081 syn21797729 syn21889566, syn21889860
46 syn21681604 syn21812500 syn21889603, syn21889879
47 syn21645389 syn21790831 syn21889708, syn21889792
48 syn21649021 syn21811019 syn21889606, syn21889883
49 syn21649207 syn12976504 syn21889735, syn21889812
50 syn21681517 syn21811363 syn21889575, syn21889867
51 syn21681401 syn21797856 syn21889549, syn21889851
52 syn21681899 syn21814010 syn21889619, syn21889897
53 syn21681801 syn21812998 syn21889620, syn21889895
54 syn21648867 syn12976490 syn21889746
55 syn21645600 syn12976704 syn21889690, syn21889783
56 syn21681783 syn21812940 syn21889638, syn21889908
57 syn21645423 syn12976729 syn21889730, syn21889804
58 syn21681530 syn21811649 syn21889614, syn21889889
59 syn21649211 syn12976725 syn21889744
60 syn21645322 syn21791111 syn21889747, syn21889816
61 syn21645592 syn21800130 syn21889697, syn21889786
62 syn21681547 syn21812436 syn21889628, syn21889902
63 syn21649183 syn21809528 syn21889604, syn21889880
64 syn21645570 syn21790617 syn21889679
65 syn21649039 syn21809454 syn21889590, syn21889856
66 syn21648897 syn21791720 syn21889764, syn21889829
67 syn21681394 syn21797667 syn21889567, syn21889861
68 syn21645339 syn21790813 syn21889725, syn21889802
69 syn21681501 syn21811287 syn21889581, syn21889870
70 syn21645574 syn21789818 syn21889678, syn21889778
71 syn21645266 syn9630031 syn21889740
72 syn21681739 syn21812727 syn21889627, syn21889901
73 syn21645255 syn21791317 syn21889767, syn21889835
74 syn21681865 syn21813770 syn21889617, syn21889890
75 syn21681999 syn21814484 syn21889644, syn21889912
76 syn21645558 syn12685522 syn21889738, syn21889814
77 syn21648977 syn11342978 syn21889520, syn21889842
78 syn21681529 syn21811595 syn21889613, syn21889888
79 syn21681993 syn21814211 syn21889574, syn21889865
80 syn21681772 syn21812746 syn21889562, syn21889858
81 syn21681378 syn21796439 syn21889578
82 syn21681442 syn21809478 syn21889576, syn21889868
83 syn21649210 syn12976723 syn21889755, syn21889822
84 syn21681326 syn21791182 syn21889766, syn21889834
85 syn21681412 syn21797976 syn21889579, syn21889869
86 syn21681486 syn21811223 syn21889683, syn21889777
87 syn21649111 syn21790751 syn21889711, syn21889796
88 syn21645319 syn21790851 syn21889733, syn21889810
89 syn21648885 syn21792744 syn21889524, syn21889844
90 syn21649000 syn21791250 syn21889719
91 syn21649213 syn12976748 syn21889712
OK @jaeddy ... I notice that all of the publicationIds in the first table include the grant "CA215845" either alone or in combination with "CA182915".
CA215845 is From Mechanism to Population: Modeling HPV-related Oropharyngeal Carcinogenesis and should have been dropped.
CA182915 is itself problematic, as there were two grants associated with it -- one we agreed to drop.
Thanks @bswhite — that matches what I'm seeing in the table. Not sure what happened (or why it only affected those 2 grants), but should be straightforward enough to fix.
I believe that the dataset IDs are all the result of manual curation at this point? At least, the prod
versions seem to be in the merged publications table dating at least as far back as 5/14. @vpchung / @jaybee84 were these values part of your recent sweep?
This dataset under CA215845 grant was annotated by me, but it seems like the publications were already annotated for this dataset before I started working on this. Don't know if that is helpful to know, but wanted to mention it if that helps tracking down the timeline of the problem.
Sorry for coming to the convo late!
I don't recognize either of the grant numbers on my end, but I can look in more detail tomorrow morning.
@jaeddy @bswhite
It looks like James made some changes to the merged tables last night and the grant number is fixed. The dataset ids are still different:
publication_differences$value_diffs$datasetId %>% data.frame()
publicationId prod test
1 syn21681375 syn21792857 syn21889704, syn21889789
2 syn21648960 syn21792798, syn21792787 syn21889551, syn21889848
3 syn21645405 syn21790756 syn21889698, syn21889787
4 syn21649049 syn21792696 syn21889611, syn21889887
5 syn21645325 syn21828913 syn21889710, syn21889794
6 syn21648894 syn21792707 syn21889514, syn21889837
7 syn21681723 syn21812634 syn21889633, syn21889905
8 syn21649214 syn13857535 syn21889517, syn21889840
9 syn21681392 syn21796559 syn21889756, syn21889823
10 syn21681382 syn21796537 syn21889515, syn21889838
11 syn21645430 syn21790688 syn21889695, syn21889782
12 syn21648903 syn21790882 syn21889709, syn21889793
13 syn21681737 syn21812642 syn21889569, syn21889864
14 syn21681447 syn21809588 syn21889519, syn21889841
15 syn21681451 syn21809597 syn21889607, syn21889884
16 syn21681618 syn21812565 syn21889640
17 syn21681667 syn21812579 syn21889605, syn21889881
18 syn21649212 syn12976746 syn21889694, syn21889785
19 syn21681441 syn21809465 syn21889589
20 syn21648893 syn21791465 syn21889532
21 syn21645594 syn21790743, syn21889770 syn21889699, syn21889788, syn21889770
22 syn21681851 syn21813759 syn21889622, syn21889900
23 syn21645338 syn21832111, syn21832136, syn21889771 syn21889728, syn21889803, syn21889771
24 syn21645269 syn21791499 syn21889753, syn21889821
25 syn21681890 syn21813804 syn21889660, syn21889917
26 syn21645337 syn21791225 syn21889693, syn21889784
27 syn21648926 syn21792538 syn21889718, syn21889797
28 syn21681814 syn21813525 syn21889637, syn21889907
29 syn21681435 syn21809435 syn21889705, syn21889790
30 syn21645258 syn12576666 syn21889724, syn21889801
31 syn21681436 syn21809444 syn21889565, syn21889859
32 syn21649154 syn21797922 syn21889580
33 syn21649001 syn18425364 syn21889629, syn21889791
34 syn21649073 syn21796402 syn21889765, syn21889833
35 syn21645383 syn13858908 syn21889762, syn21889824
36 syn21681987 syn21814183 syn21889653, syn21889914
37 syn21681523 syn21791536 syn21889734, syn21889811
38 syn21681403 syn21797924 syn21889545, syn21889849
39 syn21648884 syn21791468 syn21889533, syn21889847
40 syn21648934 syn21796552 syn21889513, syn21889836
41 syn21645422 syn21800136 syn21889752, syn21889819
42 syn21648978 syn21797950 syn21889731, syn21889805
43 syn21681315 syn21790254 syn21889682, syn21889781
44 syn21649209 syn12976694 syn21889722, syn21889800
45 syn21649081 syn21797729 syn21889566, syn21889860
46 syn21681604 syn21812500 syn21889603, syn21889879
47 syn21645389 syn21790831 syn21889708, syn21889792
48 syn21649021 syn21811019 syn21889606, syn21889883
49 syn21649207 syn12976504 syn21889735, syn21889812
50 syn21681517 syn21811363 syn21889575, syn21889867
51 syn21681401 syn21797856 syn21889549, syn21889851
52 syn21681899 syn21814010 syn21889619, syn21889897
53 syn21681801 syn21812998 syn21889620, syn21889895
54 syn21648867 syn12976490 syn21889746
55 syn21645600 syn12976704 syn21889690, syn21889783
56 syn21681783 syn21812940 syn21889638, syn21889908
57 syn21645423 syn12976729 syn21889730, syn21889804
58 syn21681530 syn21811649 syn21889614, syn21889889
59 syn21649211 syn12976725 syn21889744
60 syn21645322 syn21791111 syn21889747, syn21889816
61 syn21645592 syn21800130 syn21889697, syn21889786
62 syn21681547 syn21812436 syn21889628, syn21889902
63 syn21649183 syn21809528 syn21889604, syn21889880
64 syn21645570 syn21790617 syn21889679
65 syn21649039 syn21809454 syn21889590, syn21889856
66 syn21648897 syn21791720 syn21889764, syn21889829
67 syn21681394 syn21797667 syn21889567, syn21889861
68 syn21645339 syn21790813 syn21889725, syn21889802
69 syn21681501 syn21811287 syn21889581, syn21889870
70 syn21645574 syn21789818 syn21889678, syn21889778
71 syn21645266 syn9630031 syn21889740
72 syn21681739 syn21812727 syn21889627, syn21889901
73 syn21645255 syn21791317 syn21889767, syn21889835
74 syn21681865 syn21813770 syn21889617, syn21889890
75 syn21681999 syn21814484 syn21889644, syn21889912
76 syn21645558 syn12685522 syn21889738, syn21889814
77 syn21648977 syn11342978 syn21889520, syn21889842
78 syn21681529 syn21811595 syn21889613, syn21889888
79 syn21681993 syn21814211 syn21889574, syn21889865
80 syn21681772 syn21812746 syn21889562, syn21889858
81 syn21681378 syn21796439 syn21889578
82 syn21681442 syn21809478 syn21889576, syn21889868
83 syn21649210 syn12976723 syn21889755, syn21889822
84 syn21681326 syn21791182 syn21889766, syn21889834
85 syn21681412 syn21797976 syn21889579, syn21889869
86 syn21681486 syn21811223 syn21889683, syn21889777
87 syn21649111 syn21790751 syn21889711, syn21889796
88 syn21645319 syn21790851 syn21889733, syn21889810
89 syn21648885 syn21792744 syn21889524, syn21889844
90 syn21649000 syn21791250 syn21889719
91 syn21649213 syn12976748 syn21889712
@bswhite @jaeddy
After fixing the grant issue and deleting/fixing the publications I'm now seeing more descrepancies. These test values are correct after taking in account changes made to the merged grants table.
> publication_differences$value_diffs$themeId %>% data.frame()
publicationId prod test
1 syn21645615 <NA> syn21630076, syn21630075
2 syn21648914 <NA> syn21630076, syn21630075
3 syn21645614 <NA> syn21630076, syn21630075
4 syn21645616 <NA> syn21630076, syn21630075
5 syn21648966 <NA> syn21630076, syn21630075
6 syn21645366 syn21630081, syn21630075, syn21630076, syn21630078, syn21630077 syn21630075, syn21630081, syn21630076, syn21630078, syn21630077
7 syn21648986 <NA> syn21630076, syn21630075
8 syn21645584 syn21630081, syn21630075 syn21630075, syn21630081
9 syn21649001 syn21630081, syn21630075, syn21630076, syn21630078 syn21630075, syn21630081, syn21630076, syn21630078
10 syn21649134 <NA> syn21630076, syn21630075
11 syn21681822 <NA> syn21630076, syn21630075
12 syn21681437 <NA> syn21630076, syn21630075
13 syn21681624 <NA> syn21630076, syn21630075
14 syn21648921 syn21630081, syn21630075 syn21630075, syn21630081
15 syn21681626 <NA> syn21630076, syn21630075
16 syn21645612 <NA> syn21630076, syn21630075
17 syn21645585 syn21630081, syn21630075 syn21630075, syn21630081
18 syn21645586 syn21630081, syn21630075 syn21630075, syn21630081
19 syn21645617 <NA> syn21630076, syn21630075
20 syn21645613 <NA> syn21630076, syn21630075
21 syn21645583 syn21630081, syn21630075 syn21630075, syn21630081
> publication_differences$value_diffs$theme %>% data.frame()
publicationId prod
1 syn21645615 []
2 syn21648914 []
3 syn21645614 []
4 syn21645616 []
5 syn21648966 []
6 syn21645366 ["Evolution", "Heterogeneity", "Drug Resistance/Sensitivity", "Microenvironment", "Tumor-Immune"]
7 syn21648986 []
8 syn21645584 ["Evolution", "Heterogeneity"]
9 syn21649001 ["Evolution", "Heterogeneity", "Drug Resistance/Sensitivity", "Microenvironment"]
10 syn21649134 []
11 syn21681822 []
12 syn21681437 []
13 syn21681624 []
14 syn21648921 ["Evolution", "Heterogeneity"]
15 syn21681626 []
16 syn21645612 []
17 syn21645585 ["Evolution", "Heterogeneity"]
18 syn21645586 ["Evolution", "Heterogeneity"]
19 syn21645617 []
20 syn21645613 []
21 syn21645583 ["Evolution", "Heterogeneity"]
test
1 ["Drug Resistance/Sensitivity", "Heterogeneity"]
2 ["Drug Resistance/Sensitivity", "Heterogeneity"]
3 ["Drug Resistance/Sensitivity", "Heterogeneity"]
4 ["Drug Resistance/Sensitivity", "Heterogeneity"]
5 ["Drug Resistance/Sensitivity", "Heterogeneity"]
6 ["Heterogeneity", "Evolution", "Drug Resistance/Sensitivity", "Microenvironment", "Tumor-Immune"]
7 ["Drug Resistance/Sensitivity", "Heterogeneity"]
8 ["Heterogeneity", "Evolution"]
9 ["Heterogeneity", "Evolution", "Drug Resistance/Sensitivity", "Microenvironment"]
10 ["Drug Resistance/Sensitivity", "Heterogeneity"]
11 ["Drug Resistance/Sensitivity", "Heterogeneity"]
12 ["Drug Resistance/Sensitivity", "Heterogeneity"]
13 ["Drug Resistance/Sensitivity", "Heterogeneity"]
14 ["Heterogeneity", "Evolution"]
15 ["Drug Resistance/Sensitivity", "Heterogeneity"]
16 ["Drug Resistance/Sensitivity", "Heterogeneity"]
17 ["Heterogeneity", "Evolution"]
18 ["Heterogeneity", "Evolution"]
19 ["Drug Resistance/Sensitivity", "Heterogeneity"]
20 ["Drug Resistance/Sensitivity", "Heterogeneity"]
21 ["Heterogeneity", "Evolution"]
@jaeddy @bswhite
the grant number CA215845 popped up again:
> publication_differences$value_diffs$grant
# A tibble: 14 x 3
publicationId prod test
<chr> <chr> <chr>
1 syn21645615 "[\"CA182915\", \"CA215845\"]" "[\"CA215845\"]"
2 syn21648914 "[\"CA182915\", \"CA215845\"]" "[\"CA215845\"]"
3 syn21645614 "[\"CA182915\", \"CA215845\"]" "[\"CA215845\"]"
4 syn21645616 "[\"CA182915\", \"CA215845\"]" "[\"CA215845\"]"
5 syn21648966 "[\"CA182915\", \"CA215845\"]" "[\"CA215845\"]"
6 syn21648986 "[\"CA182915\", \"CA215845\"]" "[\"CA215845\"]"
7 syn21649134 "[\"CA182915\", \"CA215845\"]" "[\"CA215845\"]"
8 syn21681822 "[\"CA182915\", \"CA215845\"]" "[\"CA215845\"]"
9 syn21681437 "[\"CA182915\", \"CA215845\"]" "[\"CA215845\"]"
10 syn21681624 "[\"CA182915\", \"CA215845\"]" "[\"CA215845\"]"
11 syn21681626 "[\"CA182915\", \"CA215845\"]" "[\"CA215845\"]"
12 syn21645612 "[\"CA182915\", \"CA215845\"]" "[\"CA215845\"]"
13 syn21645617 "[\"CA182915\", \"CA215845\"]" "[\"CA215845\"]"
14 syn21645613 "[\"CA182915\", \"CA215845\"]" "[\"CA215845\"]"
> publication_differences$value_diffs$grantName %>% as.data.frame()
publicationId prod
1 syn21645615 ["From Mechanism to Population - Modeling HPV-related Oropharyngeal Carcinogenesis", "Phenotype Transitions in Small Cell Lung Cancer"]
2 syn21648914 ["From Mechanism to Population - Modeling HPV-related Oropharyngeal Carcinogenesis", "Phenotype Transitions in Small Cell Lung Cancer"]
3 syn21645614 ["From Mechanism to Population - Modeling HPV-related Oropharyngeal Carcinogenesis", "Phenotype Transitions in Small Cell Lung Cancer"]
4 syn21645616 ["From Mechanism to Population - Modeling HPV-related Oropharyngeal Carcinogenesis", "Phenotype Transitions in Small Cell Lung Cancer"]
5 syn21648966 ["From Mechanism to Population - Modeling HPV-related Oropharyngeal Carcinogenesis", "Phenotype Transitions in Small Cell Lung Cancer"]
6 syn21648986 ["From Mechanism to Population - Modeling HPV-related Oropharyngeal Carcinogenesis", "Phenotype Transitions in Small Cell Lung Cancer"]
7 syn21649134 ["From Mechanism to Population - Modeling HPV-related Oropharyngeal Carcinogenesis", "Phenotype Transitions in Small Cell Lung Cancer"]
8 syn21681822 ["From Mechanism to Population - Modeling HPV-related Oropharyngeal Carcinogenesis", "Phenotype Transitions in Small Cell Lung Cancer"]
9 syn21681437 ["From Mechanism to Population - Modeling HPV-related Oropharyngeal Carcinogenesis", "Phenotype Transitions in Small Cell Lung Cancer"]
10 syn21681624 ["From Mechanism to Population - Modeling HPV-related Oropharyngeal Carcinogenesis", "Phenotype Transitions in Small Cell Lung Cancer"]
11 syn21681626 ["From Mechanism to Population - Modeling HPV-related Oropharyngeal Carcinogenesis", "Phenotype Transitions in Small Cell Lung Cancer"]
12 syn21645612 ["From Mechanism to Population - Modeling HPV-related Oropharyngeal Carcinogenesis", "Phenotype Transitions in Small Cell Lung Cancer"]
13 syn21645617 ["From Mechanism to Population - Modeling HPV-related Oropharyngeal Carcinogenesis", "Phenotype Transitions in Small Cell Lung Cancer"]
14 syn21645613 ["From Mechanism to Population - Modeling HPV-related Oropharyngeal Carcinogenesis", "Phenotype Transitions in Small Cell Lung Cancer"]
test
1 ["Phenotype Transitions in Small Cell Lung Cancer"]
2 ["Phenotype Transitions in Small Cell Lung Cancer"]
3 ["Phenotype Transitions in Small Cell Lung Cancer"]
4 ["Phenotype Transitions in Small Cell Lung Cancer"]
5 ["Phenotype Transitions in Small Cell Lung Cancer"]
6 ["Phenotype Transitions in Small Cell Lung Cancer"]
7 ["Phenotype Transitions in Small Cell Lung Cancer"]
8 ["Phenotype Transitions in Small Cell Lung Cancer"]
9 ["Phenotype Transitions in Small Cell Lung Cancer"]
10 ["Phenotype Transitions in Small Cell Lung Cancer"]
11 ["Phenotype Transitions in Small Cell Lung Cancer"]
12 ["Phenotype Transitions in Small Cell Lung Cancer"]
13 ["Phenotype Transitions in Small Cell Lung Cancer"]
14 ["Phenotype Transitions in Small Cell Lung Cancer"]
This seems to be coming from a change made in the merged grants
In the source grant table the grant number is CA182915. Is this the correct number?
Finnaly there are some issues with some of the datasets:
$datasetId
# A tibble: 94 x 3
publicationId prod test
<chr> <chr> <chr>
1 syn21681375 syn21792857 syn21889704, syn21889789
2 syn21648960 syn21792798, syn21792787 syn21889551, syn21889848
3 syn21645405 syn21790756 syn21889698, syn21889787
4 syn21649049 syn21792696 syn21889611, syn21889887
5 syn21645325 syn21828913 syn21889710, syn21889794
6 syn21648894 syn21792707 syn21889514, syn21889837
7 syn21681723 syn21812634 syn21889633, syn21889905
8 syn21649214 syn13857535 syn21889517, syn21889840
9 syn21681392 syn21796559 syn21889756, syn21889823
10 syn21681382 syn21796537 syn21889515, syn21889838
# … with 84 more rows
$dataset
# A tibble: 135 x 3
publicationId prod test
<chr> <chr> <chr>
1 syn21681375 PRJNA312905 NA
2 syn21648960 PRJNA429647, PRJNA429648 NA
3 syn21648963 GSE93765, SRP096964 NA
4 syn21645405 PRJNA312218 NA
5 syn21681836 GSE125609, SRP181911 NA
6 syn21649049 PRJNA503257 NA
7 syn21681409 GSE114438 NA
8 syn21645325 PRJNA325519 NA
9 syn21648894 PRJNA393881 NA
10 syn21681723 PRJNA527110 NA
# … with 125 more rows
I think this is more due to how we are dealing with datasets being in flux, so I'll come back to those discrepancies later.
@andrewelamb , I think there are a few issues here. I'm just responding to CA182915 vs CA215845. Finally we have a resolution to why these two grants are always showing up together -- nice!
CA182915 is From Mechanism to Population: Modeling HPV-related Oropharyngeal Carcinogenesis It should be dropped.
CA215845 is Phenotype Transitions in Small Cell Lung Cancer. It should be kept.
This two grants are being incorrectly mixed in the source grants table, which incorrectly says that CA182915 is Phenotype Transitions in Small Cell Lung Cancer.
The merged grants table correctly links CA215845 to Phenotype Transitions in Small Cell Lung Cancer.
Can you fix that and see how that affects the other issue(s) above?
@bswhite it looks like it was indeed just the publications associated with the mixed up grant numbers that were the issue. Deleting them fixed all the issues except the dataset ones above. I'm keeping this open as a reminder to fix once we have datasets sorted out.
I think the issue is stems from this issue
Closing this ticket for now, as I don't think it's related anymore.
Will re-open if necessary.
The grant (grant number) and datasetId columns have some values that don't agree with what they should be. In addition, some of the grant numbers are duplicated. Unless the values in the test column are wrong this will be fixed automatically.