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query about matrix tool #1399

Closed ValWood closed 7 years ago

ValWood commented 8 years ago

I am using this link: http://tomodachi.berkeleybop.org/matrix which version of the GO database does this use.

I am preparing a lab presentation about the MAtrix tool for tomorrow.

I notice that the current version of the data PomBase reports Query: ( GO_ID(GO:0000003 - reproduction) ) AND ( GO_ID(GO:0044281 - small molecule metabolic process) ) This query matches 8 genes.

SPCC550.10 atd3 aldehyde dehydrogenase Atd3 (predicted) SPCC306.09c cap1 adenylyl cyclase-associated protein Cap1 SPCC285.09c cgs2 cAMP-specific phosphodiesterase Cgs2
SPBC19C7.03 cyr1 adenylate cyclase SPBC32H8.07 git5 heterotrimeric G protein beta subunit Git5
SPAC23C4.12 hhp2 serine/threonine protein kinase Hhp2 SPAC6F12.02 rst2 transcription factor Rst2
SPAC17C9.10 stm1 G-protein coupled receptor Stm1

whereas Matrix reports only one? I'll check which one shortly. I want to check whether its due to different versions of the data (seems unlikely because these annotations aren't new?). So, now i'm wondering if not all annotation is included?

cmungall commented 8 years ago

Quick answer as everyone is off today

At the bottom of the screen it says: Last file loaded on 2016-05-22, see full details http://tomodachi.berkeleybop.org/amigo/load_details The PomBase one is 2016-05-29 (which is after 2016-05-22...)

I'm not sure how you're translating your set-logic expression to the matrix interface. Do you calculate the ID lists yourself?

On 30 May 2016, at 9:57, Val Wood wrote:

I am using this link: http://tomodachi.berkeleybop.org/matrix which version of the GO database does this use.

I am preparing a lab presentation about the MAtrix tool for tomorrow.

I notice that the current version of the data PomBase reports Query: ( GO_ID(GO:0000003 - reproduction) ) AND ( GO_ID(GO:0044281 - small molecule metabolic process) ) This query matches 8 genes.

SPCC550.10 atd3 aldehyde dehydrogenase Atd3 (predicted) SPCC306.09c cap1 adenylyl cyclase-associated protein Cap1 SPCC285.09c cgs2 cAMP-specific phosphodiesterase Cgs2
SPBC19C7.03 cyr1 adenylate cyclase
SPBC32H8.07 git5 heterotrimeric G protein beta subunit Git5
SPAC23C4.12 hhp2 serine/threonine protein kinase Hhp2 SPAC6F12.02 rst2 transcription factor Rst2
SPAC17C9.10 stm1 G-protein coupled receptor Stm1

whereas Matrix reports only one? I'll check which one shortly. I want to check whether its due to different versions of the data (seems unlikely because these annotations aren't new?). So, now i'm wondering if not all annotation is included?

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ValWood commented 8 years ago

On 30/05/2016 18:46, Chris Mungall wrote:

Quick answer as everyone is off today Yep me too...

At the bottom of the screen it says: Last file loaded on 2016-05-22, see full details http://tomodachi.berkeleybop.org/amigo/load_details The PomBase one is 2016-05-29 (which is after 2016-05-22...)

OK our live data is from the 12th April. It would have been submitted to GO around 10 MAy so the data should be the same.

I'm not sure how you're translating your set-logic expression to the matrix interface. Do you calculate the ID lists yourself?

I was double checking using PomBase query builder because I wanted to fix any violations...

If I intersect "small molecule metabolic process" and reproduction here http://www.pombase.org/spombe/query/builder

I get the 8 annotations below:

This seems correct? These are annotated to both terms in current dataset....unless something changed in the ontology.....but I could not account for the difference this way when I checked current parentage of some anotations in QuickGO

On 30 May 2016, at 9:57, Val Wood wrote:

I am using this link: http://tomodachi.berkeleybop.org/matrix which version of the GO database does this use.

I am preparing a lab presentation about the MAtrix tool for tomorrow.

I notice that the current version of the data PomBase reports Query: ( GO_ID(GO:0000003 - reproduction) ) AND ( GO_ID(GO:0044281 - small molecule metabolic process) ) This query matches 8 genes.

SPCC550.10 atd3 aldehyde dehydrogenase Atd3 (predicted) SPCC306.09c cap1 adenylyl cyclase-associated protein Cap1 SPCC285.09c cgs2 cAMP-specific phosphodiesterase Cgs2 SPBC19C7.03 cyr1 adenylate cyclase SPBC32H8.07 git5 heterotrimeric G protein beta subunit Git5 SPAC23C4.12 hhp2 serine/threonine protein kinase Hhp2 SPAC6F12.02 rst2 transcription factor Rst2 SPAC17C9.10 stm1 G-protein coupled receptor Stm1

whereas Matrix reports only one? I'll check which one shortly. I want to check whether its due to different versions of the data (seems unlikely because these annotations aren't new?). So, now i'm wondering if not all annotation is included?

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ValWood commented 8 years ago

In matrix only atd3 is included in the intersection GO:0044281/GO:0000003

http://tomodachi.berkeleybop.org/amigo/search/bioentity?q=*:*&fq=taxon_subset_closure_label:%22Schizosaccharomyces%20pombe%22&fq=isa_partof_closure:%22GO:0044281%22&fq=isa_partof_closure:%22GO:0000003%22

I'll confirm one of the missing ones in AmiGO...

ValWood commented 8 years ago

cap1 has

negative regulation of conjugation with cellular fusion which has 'reproduction' parent http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0031138#term=ancchart

regulation of adenylate cyclase activity has "small molecule metabolic process' parent http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0045761#term=ancchart

both annotations are here: http://amigo.geneontology.org/amigo/gene_product/PomBase:SPCC306.09c

ValWood commented 8 years ago

Something else is odd. Our slim has been relatively stable over the last few releases, but the slim totals differ a little between PomBase and GO. (matrix)

protein folding PomBase 103 Matrix 101 carbohydrate metabolic process PomBase 211 Matrix 97 generation of precursor met and energy PomBase 82 Matrix 76 cell wall organisation and bio. PomBase 108 Matrix 85 tRNA metabolic process PomBase 161 Matrix 160 lipid metabolic process PomBase 227 Matrix 214 signalling PomBase 364 Matrix 294

ValWood commented 8 years ago

Ok its 'regulates' relationship...... That's no problem (would be good to be able to toggle on and off).

It just menas that this pass, I won't locate all of the issues. Its probably enough to be going on with. Nothing will be wrong.