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Guidelines for annotating papers containing High ThroughPut (HTP) experiments #1469

Closed vanaukenk closed 3 years ago

vanaukenk commented 7 years ago

This working group will develop guidelines for curators on how to annotate results from high throughput experiments.

krchristie commented 6 years ago

I am not in favor of HBA or HSS since I think it is not a good idea to have high throughput codes for phylogenetic analysis that mean a really different type of thing than the high throughput experimental codes.

krchristie commented 6 years ago

I would not propagate a single HTP annotation in PAINT if that is all that is there. I have occasionally propagated an annotation in PAINT that was based on two HTP annotations to CC terms where they were consistent with each other, and the choice was either propagate this or propagate nothing.

hattrill commented 6 years ago

A few issues with annotating with HTP codes have come up:

  1. sequence-based transfer of annotations,
  2. forward genetic screens (not sure who raised that?)
  3. proteomics experiments.

We be good to move forward on these. Can those would are interested in discussing these items make a call on Tuesday 6th or 20th Feb at 4pm GMT?

We should do some prep for this as we need to make some firm decisions.

srengel commented 6 years ago

i can do either Feb6 or Feb20 at 8am Pacific, 4pm GMT.

vanaukenk commented 6 years ago

Either Tuesday works for me, as well.

I raised the issue on forward genetic screens because I have seen some annotations from those types of experiments given an HTP evidence code that I didn't think was warranted and so I'd like to discuss those guidelines more to see if we can clarify at all.

Thx.

ValWood commented 6 years ago

I'd like to join because I'm still quite confused ;) Those dates work for me.

krchristie commented 6 years ago

I am willing to participate since I have a strong opinion on the idea of HBA and HSS. The Feb 6th date is fine for me. I am not sure if I am available on Feb 20th.

sylvainpoux commented 6 years ago

Both dates are fine for me

Thanks

Sylvain

On 1/16/2018 9:45 AM, Helen Attrill wrote:

A few issues with annotating with HTP codes have come up:

  1. sequence-based transfer of annotations,
  2. forward genetic screens (not sure who raised that?)
  3. proteomics experiments.

We be good to move forward on these. Can those would are interested in discussing these items make a call on Tuesday 6th or 20th Feb at 4pm GMT?

We should do some prep for this as we need to make some firm decisions.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/geneontology/go-annotation/issues/1469#issuecomment-357890816, or mute the thread https://github.com/notifications/unsubscribe-auth/ATEYwedIZzo02ThhHALAwYh-o4JB1s25ks5tLGGMgaJpZM4K27fK.Web Bug from https://github.com/notifications/beacon/ATEYwbnJF-LHV6IQoMnAVSPoeWlDYOibks5tLGGMgaJpZM4K27fK.gif

-- Sylvain Poux, PhD Swiss-Prot group SIB Swiss Institute of Bioinformatics 1, rue Michel Servet CH-1211 Geneva 4 Switzerland

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pgaudet commented 6 years ago

Both dates should also work for me. Feb 6th for sure.

Thanks, Pascale

rachhuntley commented 6 years ago

Either is good for me too.

RLovering commented 6 years ago

either is good for me too

tberardini commented 6 years ago

I can join the call at about 8:20 am on either day.

hattrill commented 6 years ago

Thanks, let's go for the 6th then.

In order to make this as efficient as possible, let's divide the tasks into separate tickets and try to get some proposals before the meeting or at least flesh out the issues so we can fully appreciate the problems. It would be good if someone could take the lead on each of the points:

  1. sequence-based transfer of annotations #1775
  2. forward genetic screens. #1774
  3. proteomics experiments. #1773

I can take the lead on "proteomics experiments", as the guidance doc doesn't seem to be working for groups.

Could I ask for volunteers to lead the other two?

Thanks

hattrill commented 6 years ago

I am starting an agenda for the VC on the 6th tagged onto the meeting doc in the GO folder: https://docs.google.com/document/d/1Gd6cRQh67QZQ2_T7kQjqYMpkfJ_Wqm0baVpyMdFPRHs/edit

Please flesh out any areas that you have a specific proposal or issue with. Hopefully, we can solve the issues within the hour. We shall only have 20 min/topic - 15 discussion, 5 min decision.

hattrill commented 6 years ago

Hello! Just a quick reminder that in 1h and 10 min we'll be having a lovely chat on the usual GO zoom number about HTP annotations.

sylvainpoux commented 6 years ago

On 2/6/2018 3:50 PM, Helen Attrill wrote:

Hello! Just a quick reminder that in 1h and 10 min we'll be having a lovely chat on the usual GO zoom number about HTP annotations.

Thanks Helen,

could you provide the link? It is probably somewhere in the document but I cannot find it

Thanks

Sylvain

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-- Sylvain Poux, PhD Swiss-Prot group SIB Swiss Institute of Bioinformatics 1, rue Michel Servet CH-1211 Geneva 4 Switzerland

sylvain.poux@sib.swiss - www.sib.swiss

hattrill commented 6 years ago

https://stanford.zoom.us/j/976175422

hattrill commented 6 years ago

Hello - just repeating what I said before on the review HTP ticket, as I can see that there isn't complete over lap:

First draft of ISB DATABASE Journal Biocuration HTP paper can be found here https://docs.google.com/document/d/1UGXWy38134Lvq22qb2tVizIgNUhZKQC1x5-docMb-ro/edit in the GO google drive. Bit later than I anticipated (insert excuse). If you feel like beating it with a stick, that would be appreciated. Deadline for submission is 31st, so I would appreciate it if you could look at it as soon as possible.

Doc adding your name as author is here - I will go through the various lists, etc and add folk, but I don't want to miss anyone. If you had anything to do with the working group, review, ECO codes, and Devs put your name down - https://docs.google.com/document/d/16XW-iKZauIN9wisQDX77_fRt5adSyuGRoIF19eSjmWM/edit

If you need access, just shout.

sylvainpoux commented 6 years ago

On 10/22/2018 3:50 PM, Helen Attrill wrote:

Hello - just repeating what I said before on the review HTP ticket, as I can see that there isn't complete over lap:

First draft of ISB DATABASE Journal Biocuration HTP paper can be found here https://docs.google.com/document/d/1UGXWy38134Lvq22qb2tVizIgNUhZKQC1x5-docMb-ro/edit in the GO google drive. Bit later than I anticipated (insert excuse). If you feel like beating it with a stick, that would be appreciated. Deadline for submission is 31st, so I would appreciate it if you could look at it as soon as possible.

Thanks Helen,

 I had a very quick look and it looks great! I will read the paper and get back to you as soon as possible.

Sylvain

Doc adding your name as author is here - I will go through the various lists, etc and add folk, but I don't want to miss anyone. If you had anything to do with the working group, review, ECO codes, and Devs put your name down - https://docs.google.com/document/d/16XW-iKZauIN9wisQDX77_fRt5adSyuGRoIF19eSjmWM/edit

If you need access, just shout.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/geneontology/go-annotation/issues/1469#issuecomment-431841457, or mute the thread https://github.com/notifications/unsubscribe-auth/ATEYwV6sXio38A8o1Q73mL2VJwn8bWnSks5unc0ogaJpZM4K27fK.Web Bug from https://github.com/notifications/beacon/ATEYwYAP2diEQ0nM3b-BqhWbwlkX3atqks5unc0ogaJpZM4K27fK.gif

-- Sylvain Poux, PhD Swiss-Prot group SIB Swiss Institute of Bioinformatics 1, rue Michel Servet CH-1211 Geneva 4 Switzerland

sylvain.poux@sib.swiss - www.sib.swiss

sylvainpoux commented 6 years ago

On 10/22/2018 3:50 PM, Helen Attrill wrote:

Hello - just repeating what I said before on the review HTP ticket, as I can see that there isn't complete over lap:

Hi Helen,

thanks a lot! I had a quick look and it looks great.

I added few suggestions. Feel free to integrate them or not and do not hesitate to contact me if you need help.

Thanks

Sylvain

First draft of ISB DATABASE Journal Biocuration HTP paper can be found here https://docs.google.com/document/d/1UGXWy38134Lvq22qb2tVizIgNUhZKQC1x5-docMb-ro/edit in the GO google drive. Bit later than I anticipated (insert excuse). If you feel like beating it with a stick, that would be appreciated. Deadline for submission is 31st, so I would appreciate it if you could look at it as soon as possible.

Doc adding your name as author is here - I will go through the various lists, etc and add folk, but I don't want to miss anyone. If you had anything to do with the working group, review, ECO codes, and Devs put your name down - https://docs.google.com/document/d/16XW-iKZauIN9wisQDX77_fRt5adSyuGRoIF19eSjmWM/edit

If you need access, just shout.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/geneontology/go-annotation/issues/1469#issuecomment-431841457, or mute the thread https://github.com/notifications/unsubscribe-auth/ATEYwV6sXio38A8o1Q73mL2VJwn8bWnSks5unc0ogaJpZM4K27fK.Web Bug from https://github.com/notifications/beacon/ATEYwYAP2diEQ0nM3b-BqhWbwlkX3atqks5unc0ogaJpZM4K27fK.gif

-- Sylvain Poux, PhD Swiss-Prot group SIB Swiss Institute of Bioinformatics 1, rue Michel Servet CH-1211 Geneva 4 Switzerland

sylvain.poux@sib.swiss - www.sib.swiss

RLovering commented 6 years ago

Hi Helen

This is a great paper. Please take what edits/comments you like.

However I am concerned about the number of apparent HTP datasets that are still associated with a non-HTP evidence code. I have only looked at IEP annotations but there seem to be a lot. Note I have not looked at the full text of papers I have suggested should use the HEP evidence code rather than the IEP code

Is it possible for some groups to review these annotations in the next few weeks, or if the paper is accepted, revise before final proof stage?

Attached are a couple of spreadsheets to back up some of the suggestions I have made.

I have added my name to the author list, I’m not sure everyone appreciates they need to edit this document, as there are currently only 5 authors ;) https://docs.google.com/document/d/16XW-iKZauIN9wisQDX77_fRt5adSyuGRoIF19eSjmWM/edit

Thanks

Ruth

From: Helen Attrill notifications@github.com Reply-To: geneontology/go-annotation reply@reply.github.com Date: Monday, 22 October 2018 at 14:50 To: geneontology/go-annotation go-annotation@noreply.github.com Cc: "Lovering, Ruth" r.lovering@ucl.ac.uk, Assign assign@noreply.github.com Subject: Re: [geneontology/go-annotation] Guidelines for annotating papers containing High ThroughPut (HTP) experiments (#1469)

Hello - just repeating what I said before on the review HTP ticket, as I can see that there isn't complete over lap:

First draft of ISB DATABASE Journal Biocuration HTP paper can be found here https://docs.google.com/document/d/1UGXWy38134Lvq22qb2tVizIgNUhZKQC1x5-docMb-ro/edit in the GO google drive. Bit later than I anticipated (insert excuse). If you feel like beating it with a stick, that would be appreciated. Deadline for submission is 31st, so I would appreciate it if you could look at it as soon as possible.

Doc adding your name as author is here - I will go through the various lists, etc and add folk, but I don't want to miss anyone. If you had anything to do with the working group, review, ECO codes, and Devs put your name down - https://docs.google.com/document/d/16XW-iKZauIN9wisQDX77_fRt5adSyuGRoIF19eSjmWM/edit

If you need access, just shout.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHubhttps://github.com/geneontology/go-annotation/issues/1469#issuecomment-431841457, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ALhTis_Q08NxrGa0fQhdRDc_aGf94p2Nks5unc0lgaJpZM4K27fK.

RLovering commented 6 years ago

Thanks for looking at this, Ruth. I really appreciate your input.

Yes, I am aware that there are quite a few that still need to be done and it’s not a complete revision - I think that some are synchrony issues with data releases. I’ve done some cross-referencing and these will help. Others just haven’t been done. I am planning to chase these up. I’ve had to be careful not to say that the review is compete!

I think that I’ve got most folks on my own list - I am going to email them and make sure that they are ok with the author list. I think that I might also just put a notice on the GO mailing list to make sure I’ve not left anyone off.

Thanks,

Helen

.

On 24 Oct 2018, at 17:14, Lovering, Ruth r.lovering@ucl.ac.uk wrote:

Hi Helen

This is a great paper. Please take what edits/comments you like.

However I am concerned about the number of apparent HTP datasets that are still associated with a non-HTP evidence code. I have only looked at IEP annotations but there seem to be a lot. Note I have not looked at the full text of papers I have suggested should use the HEP evidence code rather than the IEP code

Is it possible for some groups to review these annotations in the next few weeks, or if the paper is accepted, revise before final proof stage?

Attached are a couple of spreadsheets to back up some of the suggestions I have made.

I have added my name to the author list, I’m not sure everyone appreciates they need to edit this document, as there are currently only 5 authors ;) https://docs.google.com/document/d/16XW-iKZauIN9wisQDX77_fRt5adSyuGRoIF19eSjmWM/edit https://docs.google.com/document/d/16XW-iKZauIN9wisQDX77_fRt5adSyuGRoIF19eSjmWM/edit

Thanks

Ruth

From: Helen Attrill <notifications@github.com mailto:notifications@github.com> Reply-To: geneontology/go-annotation <reply@reply.github.com mailto:reply@reply.github.com> Date: Monday, 22 October 2018 at 14:50 To: geneontology/go-annotation <go-annotation@noreply.github.com mailto:go-annotation@noreply.github.com> Cc: "Lovering, Ruth" <r.lovering@ucl.ac.uk mailto:r.lovering@ucl.ac.uk>, Assign <assign@noreply.github.com mailto:assign@noreply.github.com> Subject: Re: [geneontology/go-annotation] Guidelines for annotating papers containing High ThroughPut (HTP) experiments (#1469)

Hello - just repeating what I said before on the review HTP ticket, as I can see that there isn't complete over lap: First draft of ISB DATABASE Journal Biocuration HTP paper can be found here https://docs.google.com/document/d/1UGXWy38134Lvq22qb2tVizIgNUhZKQC1x5-docMb-ro/edit https://docs.google.com/document/d/1UGXWy38134Lvq22qb2tVizIgNUhZKQC1x5-docMb-ro/edit in the GO google drive. Bit later than I anticipated (insert excuse). If you feel like beating it with a stick, that would be appreciated. Deadline for submission is 31st, so I would appreciate it if you could look at it as soon as possible. Doc adding your name as author is here - I will go through the various lists, etc and add folk, but I don't want to miss anyone. If you had anything to do with the working group, review, ECO codes, and Devs put your name down -https://docs.google.com/document/d/16XW-iKZauIN9wisQDX77_fRt5adSyuGRoIF19eSjmWM/edit https://docs.google.com/document/d/16XW-iKZauIN9wisQDX77_fRt5adSyuGRoIF19eSjmWM/edit If you need access, just shout.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/geneontology/go-annotation/issues/1469#issuecomment-431841457, or mute the thread https://github.com/notifications/unsubscribe-auth/ALhTis_Q08NxrGa0fQhdRDc_aGf94p2Nks5unc0lgaJpZM4K27fK.