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P2G report request #7

Open rachhuntley opened 8 years ago

rachhuntley commented 8 years ago

Hello,

Would it be possible to extend the first Common P2GO report "Summary of annotations created or updated (by user)" to have a taxon option?

Secondly, is there any way to extend/duplicate this same report (and possibly others such as the "Summary of annotations created or updated by group/source") but where you unroll the annotations if there are pipe-separated values in the annotation extension? The purpose of this is to get a "true" count of annotations, since each pipe-separated extension could be counted as a separate annotation.

For example, if you have one annotation with 2 AE statements separated by a pipe, this can get counted as two annotations.

David OS has done a similar thing when he unrolls annotation extensions to produce a report of annotations using each relation, so he might be able to share his ideas.

The second one is not urgent, but would be a great way of getting a more accurate count of annotations for grant reporting.

Thanks, Rachael.

tonysawfordebi commented 8 years ago

Hi Rachael,

I've created a JIRA issue for this.

Cheers, Tony

tonysawfordebi commented 8 years ago

Hi Rachael,

With regard to the first report, would a taxonomic division selector (as in the "List PubMed IDs referenced in GOA annotations but not in UniProt" report) be sufficient, or do you need the ability to search based on any arbitrary taxon ID?

Cheers, Tony

On 15/10/15 10:10, rachhuntley wrote:

Hello,

Would it be possible to extend the first Common P2GO report "Summary of annotations created or updated (by user)" to have a taxon option?

Secondly, is there any way to extend/duplicate this same report (and possibly others such as the "Summary of annotations created or updated by group/source") but where you unroll the annotations if there are pipe-separated values in the annotation extension? The purpose of this is to get a "true" count of annotations, since each pipe-separated extension could be counted as a separate annotation.

For example, if you have one annotation with 2 AE statements separated by a pipe, this can get counted as two annotations.

David OS has done a similar thing when he unrolls annotation extensions to produce a report of annotations using each relation, so he might be able to share his ideas.

The second one is not urgent, but would be a great way of getting a more accurate count of annotations for grant reporting.

Thanks, Rachael.

— Reply to this email directly or view it on GitHub https://github.com/ebi-uniprot/Protein2GO/issues/7.

rachhuntley commented 8 years ago

Hi Tony,

So what I'm aiming for is to get a count of annotations per species, e.g. mouse, rat, human - not for a taxonomic division.

By the way, are you intending to display RNA annotations in the new QuickGO? This seems like an obvious question that I may not have asked yet (or already forgotten the answer to!).

Thanks, Rachael.

tonysawfordebi commented 8 years ago

Hi Rachael,

On 15/10/15 11:49, rachhuntley wrote:

Hi Tony,

So what I'm aiming for is to get a count of annotations per species, e.g. mouse, rat, human - not for a taxonomic division.

OK. That means that I can't just re-use the existing parameter widget; I'll actually have to do some work...

By the way, are you intending to display RNA annotations in the new QuickGO? This seems like an obvious question that I may not have asked yet (or already forgotten the answer to!).

Yes.

Cheers, Tony

Thanks, Rachael.

— Reply to this email directly or view it on GitHub https://github.com/ebi-uniprot/Protein2GO/issues/7#issuecomment-148349676.

rachhuntley commented 8 years ago

Hi Tony,

If it's too much work then don't worry because, as your second answer confirms, I'll be able to get what I want from the new QuickGO.

Rachael.

tonysawfordebi commented 8 years ago

Hi Rachael,

The "Summary of annotations created or updated (by user)" report now has an optional taxon parameter.

Please give it a whirl & see whether it gives you anything like the numbers you expect...

Cheers, Tony

On 15/10/15 12:19, rachhuntley wrote:

Hi Tony,

If it's too much work then don't worry because, as your second answer confirms, I'll be able to get what I want from the new QuickGO.

Rachael.

— Reply to this email directly or view it on GitHub https://github.com/ebi-uniprot/Protein2GO/issues/7#issuecomment-148357479.

rachhuntley commented 8 years ago

Pretty much spot on - thanks very much! Rachael.

tonysawfordebi commented 8 years ago

Hi Rachael,

There are three new reports - "Summary of annotations created or updated (by user|group|source) - annotation_extensions unrolled" - that do what (I think) you asked for - can you give them a bit of a shakedown, please?

Cheers, Tony

tonysawfordebi commented 8 years ago

I forgot to say - these "unrolled" reports take quite a lot longer than the "rolled-up" versions to run.

rachhuntley commented 8 years ago

Hi Tony,

This is great, thanks. I am starting to look at the reports, but it's quite difficult to see if it's giving the expected number - I will try to pull out my annotations from the GAF to see how many pipe-separated statements I've made, but it would be super useful if you could extend the "Annotation history (by user)" report to include extension information. I guess this might cause the query to take a lot longer as well, but could it be an option to include extension data?

Thanks, Rachael.

tonysawfordebi commented 8 years ago

Hi Rachael,

Done.

Cheers, Tony

On 19/10/15 11:04, rachhuntley wrote:

Hi Tony,

This is great, thanks. I am starting to look at the reports, but it's quite difficult to see if it's giving the expected number - I will try to pull out my annotations from the GAF to see how many pipe-separated statements I've made, but it would be super useful if you could extend the "Annotation history (by user)" report to include extension information. I guess this might cause the query to take a lot longer as well, but could it be an option to include extension data?

Thanks, Rachael.

— Reply to this email directly or view it on GitHub https://github.com/ebi-uniprot/Protein2GO/issues/7#issuecomment-149172708.

rachhuntley commented 8 years ago

Great, you're a star! By the way, what is the final column on the new reports; "R" ?

Thanks, Rachael.

tonysawfordebi commented 8 years ago

Oops... That's what's technically known as "a mistake" - the database didn't have the correct report definition in it. Now fixed.

Cheers, Tony

On 19/10/15 11:22, rachhuntley wrote:

Great, you're a star! By the way, what is the final column on the new reports; "R" ?

Thanks, Rachael.

— Reply to this email directly or view it on GitHub https://github.com/ebi-uniprot/Protein2GO/issues/7#issuecomment-149175842.

rachhuntley commented 8 years ago

Hi Tony,

After a few crude tests, I think the unrolled reports are working as I expected. Thanks for doing this so quickly! Rachael.

tonysawfordebi commented 8 years ago

No problem; the invoice is in the post.

On 19/10/15 13:44, rachhuntley wrote:

Hi Tony,

After a few crude tests, I think the unrolled reports are working as I expected. Thanks for doing this so quickly! Rachael.

— Reply to this email directly or view it on GitHub https://github.com/ebi-uniprot/Protein2GO/issues/7#issuecomment-149203003.