possible bug, cdc2 missing from 'signalling' network diagram

vw253 reporter

Hi Dan,

I am seeing cdc2 (SPBC11B10.09) in the current slim under signaling:

See : GO:0023052 signaling 395 5052 7.82% 395 5380 7.34% SPAC1006.06, SPAC1006.08, SPAC1006.09, SPAC1071.12c, SPAC1093.03, SPAC110.01, SPAC110.03, SPAC11E3.06, SPAC11E3.09, SPAC11E3.11c, SPAC11H11.04, SPAC1296.03c, SPAC12B10.14c, SPAC13A11.01c, SPAC13G6.15c, SPAC1420.01c, SPAC144.13c, SPAC1556.03, SPAC1556.08c, SPAC1565.02c, SPAC1565.04c, SPAC1565.06c, SPAC16.01, SPAC167.01, SPAC1687.09, SPAC1687.15, SPAC16A10.04, SPAC16C9.07, SPAC16E8.09, SPAC1705.03c, SPAC1782.05, SPAC1782.09c, SPAC17A5.09c, SPAC17C9.10, SPAC17G8.10c, SPAC17G8.14c, SPAC17H9.09c, SPAC1805.01c, SPAC1805.05, SPAC1834.08, SPAC1851.03, SPAC1851.04c, SPAC186.06, SPAC18B11.04, SPAC18B11.07c, SPAC18B11.11, SPAC18G6.03, SPAC1952.16, SPAC1952.17c, SPAC19A8.01c, SPAC19A8.03, SPAC19D5.01, SPAC19E9.02, SPAC19E9.03, SPAC19G12.06c, SPAC1A6.04c, SPAC1B3.11c, SPAC1B9.02c, SPAC1D4.02c, SPAC1D4.06c, SPAC1D4.11c, SPAC1D4.13, SPAC1F3.02c, SPAC1F3.03, SPAC1F5.09c, SPAC1F5.11c, SPAC1F7.04, SPAC20H4.08, SPAC20H4.11c, SPAC21E11.03c, SPAC222.10c, SPAC227.07c, SPAC227.15, SPAC22E12.07, SPAC22E12.14c, SPAC22E12.16c, SPAC22E12.17c, SPAC22F3.05c, SPAC22F3.12c, SPAC22F3.13, SPAC22F8.11, SPAC22G7.08, SPAC22H10.04, SPAC22H10.07, SPAC22H10.11c, SPAC22H10.12c, SPAC23A1.06c, SPAC23C11.11, SPAC23C11.16, SPAC23C4.08, SPAC23C4.12, SPAC23D3.03c, SPAC23E2.03c, SPAC23G3.05c, SPAC23H3.03c, SPAC23H3.08c, SPAC23H3.13c, SPAC23H4.02, SPAC23H4.14, SPAC24B11.06c, SPAC24B11.11c, SPAC24H6.05, SPAC24H6.09, SPAC25A8.01c, SPAC25B8.13c, SPAC26A3.09c, SPAC26A3.10, SPAC26F1.01, SPAC26F1.09, SPAC26F1.10c, SPAC26H5.07c, SPAC27D7.14c, SPAC27E2.09, SPAC29A4.11, SPAC2C4.05, SPAC2C4.10c, SPAC2F3.12c, SPAC2F3.15, SPAC2F7.02c, SPAC2F7.03c, SPAC2F7.16c, SPAC2G11.07c, SPAC30.01c, SPAC30C2.05, SPAC31A2.10, SPAC31A2.12, SPAC31A2.16, SPAC31F12.01, SPAC31G5.09c, SPAC31G5.11, SPAC343.19, SPAC3C7.06c, SPAC3C7.11c, SPAC3F10.10c, SPAC3G9.05, SPAC3G9.16c, SPAC3H1.12c, SPAC3H1.13, SPAC458.03, SPAC458.05, SPAC4A8.03c, SPAC4A8.07c, SPAC4A8.12c, SPAC4C5.02c, SPAC4D7.01c, SPAC4F10.04, SPAC4F8.13c, SPAC4G8.04, SPAC4G8.05, SPAC4G8.13c, SPAC4H3.11c, SPAC513.03, SPAC56F8.16, SPAC57A10.02, SPAC57A10.04, SPAC57A7.08, SPAC57A7.11, SPAC5D6.07c, SPAC5D6.13, SPAC630.05, SPAC630.12, SPAC630.13c, SPAC637.13c, SPAC644.06c, SPAC644.18c, SPAC694.06c, SPAC6B12.13, SPAC6B12.15, SPAC6F12.06, SPAC6F12.12, SPAC6F6.01, SPAC6F6.08c, SPAC6F6.15, SPAC6G9.04, SPAC821.12, SPAC823.03, SPAC823.15, SPAC824.09c, SPAC890.03, SPAC8C9.03, SPAC8C9.14, SPAC8E11.02c, SPAC9.07c, SPAC9E9.07c, SPAC9G1.02, SPAC9G1.09, SPAC9G1.10c, SPACUNK12.02c, SPAP8A3.09c, SPAPB18E9.02c, SPAPB1A10.10c, SPAPB2B4.03, SPAPYUG7.02c, SPBC106.01, SPBC106.10, SPBC119.07, SPBC119.08, SPBC119.15, SPBC11B10.07c, SPBC11B10.09, ......

This is the file from http://curation.pombase.org/dumps/latest_build/pombe-embl/supporting_files/ (it is time stamped 8 Nov but the file is identical to the one in the releases directory http://curation.pombase.org/dumps/releases/pombase-chado-v47-2014-10-27/pombe-embl/supporting_files/ on 27th Oct)

Let me know if you still think that there is an issue at our end.

Val

2014-11-26T11:02:54+00:00

Comments (9)

vw253 reporter
I just checked and it is the PomBase GO substrates file SPAC24H6.05 SPBC11B10.09 PMID:1756737
- 2014-11-19T13:42:19+00:00
Dan Bean
It isn't there because cdc2 isn't annotated to signalling in the GO slim file we have
- 2014-11-24T10:22:35+00:00
vw253 reporter
Ah right, it should be, I'll look into that, thanks...
- 2014-11-24T11:18:50+00:00
vw253 reporter
Hi Dan,

I am seeing cdc2 (SPBC11B10.09) in the current slim under signaling:

See : GO:0023052 signaling 395 5052 7.82% 395 5380 7.34% SPAC1006.06, SPAC1006.08, SPAC1006.09, SPAC1071.12c, SPAC1093.03, SPAC110.01, SPAC110.03, SPAC11E3.06, SPAC11E3.09, SPAC11E3.11c, SPAC11H11.04, SPAC1296.03c, SPAC12B10.14c, SPAC13A11.01c, SPAC13G6.15c, SPAC1420.01c, SPAC144.13c, SPAC1556.03, SPAC1556.08c, SPAC1565.02c, SPAC1565.04c, SPAC1565.06c, SPAC16.01, SPAC167.01, SPAC1687.09, SPAC1687.15, SPAC16A10.04, SPAC16C9.07, SPAC16E8.09, SPAC1705.03c, SPAC1782.05, SPAC1782.09c, SPAC17A5.09c, SPAC17C9.10, SPAC17G8.10c, SPAC17G8.14c, SPAC17H9.09c, SPAC1805.01c, SPAC1805.05, SPAC1834.08, SPAC1851.03, SPAC1851.04c, SPAC186.06, SPAC18B11.04, SPAC18B11.07c, SPAC18B11.11, SPAC18G6.03, SPAC1952.16, SPAC1952.17c, SPAC19A8.01c, SPAC19A8.03, SPAC19D5.01, SPAC19E9.02, SPAC19E9.03, SPAC19G12.06c, SPAC1A6.04c, SPAC1B3.11c, SPAC1B9.02c, SPAC1D4.02c, SPAC1D4.06c, SPAC1D4.11c, SPAC1D4.13, SPAC1F3.02c, SPAC1F3.03, SPAC1F5.09c, SPAC1F5.11c, SPAC1F7.04, SPAC20H4.08, SPAC20H4.11c, SPAC21E11.03c, SPAC222.10c, SPAC227.07c, SPAC227.15, SPAC22E12.07, SPAC22E12.14c, SPAC22E12.16c, SPAC22E12.17c, SPAC22F3.05c, SPAC22F3.12c, SPAC22F3.13, SPAC22F8.11, SPAC22G7.08, SPAC22H10.04, SPAC22H10.07, SPAC22H10.11c, SPAC22H10.12c, SPAC23A1.06c, SPAC23C11.11, SPAC23C11.16, SPAC23C4.08, SPAC23C4.12, SPAC23D3.03c, SPAC23E2.03c, SPAC23G3.05c, SPAC23H3.03c, SPAC23H3.08c, SPAC23H3.13c, SPAC23H4.02, SPAC23H4.14, SPAC24B11.06c, SPAC24B11.11c, SPAC24H6.05, SPAC24H6.09, SPAC25A8.01c, SPAC25B8.13c, SPAC26A3.09c, SPAC26A3.10, SPAC26F1.01, SPAC26F1.09, SPAC26F1.10c, SPAC26H5.07c, SPAC27D7.14c, SPAC27E2.09, SPAC29A4.11, SPAC2C4.05, SPAC2C4.10c, SPAC2F3.12c, SPAC2F3.15, SPAC2F7.02c, SPAC2F7.03c, SPAC2F7.16c, SPAC2G11.07c, SPAC30.01c, SPAC30C2.05, SPAC31A2.10, SPAC31A2.12, SPAC31A2.16, SPAC31F12.01, SPAC31G5.09c, SPAC31G5.11, SPAC343.19, SPAC3C7.06c, SPAC3C7.11c, SPAC3F10.10c, SPAC3G9.05, SPAC3G9.16c, SPAC3H1.12c, SPAC3H1.13, SPAC458.03, SPAC458.05, SPAC4A8.03c, SPAC4A8.07c, SPAC4A8.12c, SPAC4C5.02c, SPAC4D7.01c, SPAC4F10.04, SPAC4F8.13c, SPAC4G8.04, SPAC4G8.05, SPAC4G8.13c, SPAC4H3.11c, SPAC513.03, SPAC56F8.16, SPAC57A10.02, SPAC57A10.04, SPAC57A7.08, SPAC57A7.11, SPAC5D6.07c, SPAC5D6.13, SPAC630.05, SPAC630.12, SPAC630.13c, SPAC637.13c, SPAC644.06c, SPAC644.18c, SPAC694.06c, SPAC6B12.13, SPAC6B12.15, SPAC6F12.06, SPAC6F12.12, SPAC6F6.01, SPAC6F6.08c, SPAC6F6.15, SPAC6G9.04, SPAC821.12, SPAC823.03, SPAC823.15, SPAC824.09c, SPAC890.03, SPAC8C9.03, SPAC8C9.14, SPAC8E11.02c, SPAC9.07c, SPAC9E9.07c, SPAC9G1.02, SPAC9G1.09, SPAC9G1.10c, SPACUNK12.02c, SPAP8A3.09c, SPAPB18E9.02c, SPAPB1A10.10c, SPAPB2B4.03, SPAPYUG7.02c, SPBC106.01, SPBC106.10, SPBC119.07, SPBC119.08, SPBC119.15, SPBC11B10.07c, SPBC11B10.09, ......

This is the file from http://curation.pombase.org/dumps/latest_build/pombe-embl/supporting_files/ (it is time stamped 8 Nov but the file is identical to the one in the releases directory http://curation.pombase.org/dumps/releases/pombase-chado-v47-2014-10-27/pombe-embl/supporting_files/ on 27th Oct)

Let me know if you still think that there is an issue at our end.

Val
- 2014-11-26T11:02:54+00:00
Dan Bean
The slim file we're using is one you emailed us a quite while ago, I didn't know it was on the pombase server. I'll copy that one across for now, will the urls be stable there (like the interaction data files)? Thanks!
- 2014-11-26T11:09:36+00:00
vw253 reporter
Ah sorry about that:

Yes it will always be in here:

http://curation.pombase.org/dumps/latest_build/pombe-embl/supporting_files/

the file name will change, but it will always be *_slimTab.txt

Is that OK?

Val
- 2014-11-26T11:37:18+00:00
Dan Bean
I'll copy it over manually for now but to do it automatically we really need stable filenames - maybe Kim can create another symbolic link?
- 2014-12-02T15:06:03+00:00
Dan Bean
The slim file we're using is one you emailed us a quite while ago, I didn't know it was on the pombase server. I'll copy that one across for now, will the urls be stable there (like the interaction data files)? Thanks!
- 2014-12-09T00:01:22+00:00
Dan Bean
- changed status to closed
update go slim file automatically - closes ~~#83~~ and ~~#88~~

→ <<cset d2cff4922fda>>
- 2014-12-09T11:17:13+00:00
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