Complex of the month

[bmeldal]

We should start doing this. Via website/Twitter???

Devs discussed how selection could be made by a new function in the Editor which would also work for IntAct DSotM

/cc @sandraorchard @pporrasebi

[tschaka1904]

Maybe you could tweet a new complex once the release has finished ;-)

[bmeldal]

@sandraorchard should be use the amyloid beta ones? It would tie in with Barbara concluding her project on those annotations.

[sandraorchard]

OK, why not. Get the newsletter release date from her and we can coincide.

[bmeldal]

She said she'll release today or tomorrow! I'll email her. Are we going for one specif complex or the set? Search with GO term would bring them all up.

I'm online til 9ish but you can send a slack mgs while I'm on the sports field, that pops up on my phone (email doesn't and webmail interface on my phone is cumbersome!).

[bmeldal]

Search for all amyloid beta complexes with GO:0106003. Only 2 have expt evidence (search for GO:0106003 AND ECO:0000353). But more prominent complex in cell is probably the heterodimer: http://www.ebi.ac.uk/complexportal/complex/EBI-13942506

Max, do you fancy writing the tweet and maybe making another GIF?

[sandraorchard]

Make one a 'Complex of the month' tweet and how to search for the family as a 'tip', which can also be tweeted.

[bmeldal]

Sounds good. And mention @uclgene as provider of info as it was a curation request from them :)

"Complex of the Month: amyloid-beta 40/42 dimer http://www.ebi.ac.uk/complexportal/complex/EBI-13942506. Uncontrolled oligomerisation of the complex results in the typical #alzhmeimers disease plaques. Curated in collaboration with @uclgene" - too long!

"Complex of the Month: amyloid-beta 40/42 dimer http://www.ebi.ac.uk/complexportal/complex/EBI-13942506. Oligomerisation results in typical #alzhmeimers plaques. @uclgene" fits but not as informative.

[sandraorchard]

Something like @uclgene curated Complex of the Month: amyloid-beta 40/42 dimer http://www.ebi.ac.uk/complexportal/complex/EBI-13942506. Role in forming typical #alzhmeimers plaques.

[bmeldal]

Although, I curated, Barbara only sent all the info...

[sandraorchard]

Complex of the Month: amyloid-beta 40/42 dimer http://www.ebi.ac.uk/complexportal/complex/EBI-13942506. Role in forming typical #alzhmeimers plaques. Requested by @uclgene

Also then reminds people curation can be requested.

[bmeldal]

@tschaka1904 please use GO:0106003 as search term and EBI-14348029 as hit when you make the GIF for the search-by-GO-ID hint tweet.

[tschaka1904]

Didn't really think about a gif for that. More something like this:

[bmeldal]

Ah, no, 2 tweets: A) CofM which can have that date image (nice!) B) another 'hint' tweet about the ability to search using a GO term and use the amyloid-bets complex as example so it all ties in :) - this one will have another GIF I would have thought!

Off to school now!

[tschaka1904]

I guess I don't have to wait for the release??

[tschaka1904]

I guess I won't be able to tweet that tomorrow.

[tschaka1904]

[sandraorchard]

To find all amyloid-beta complexes, search on GO:0106003 (amyloid-beta complex) at www.ebi.ac.uk/complexportal - then attach your loop.

[bmeldal]

Good pt about not being able to tweet tomorrow!

Looking at it, the pic for CotM is a little big. Maybe next month we choose a pic of the actual complex? PDB have done that for us today :)

[tschaka1904]

Keep this open, as this is a discussion thread.

[tschaka1904]

Anything for August?

[sandraorchard]

As IL-23 got top hits last month, I'd suggest EBI-9992716 - expand the image in Colins viewer to show binding regions and use that as the attached picture.

[tschaka1904]

Option A:

Option B:

[sandraorchard]

A, as there is not much to look at in the way of multiple proteins or multiple links.

[tschaka1904]

Complex of the Month: Interleukin-23 complex http://www.ebi.ac.uk/complexportal/complex/EBI-9992716.

(still 71 chars left)

[sandraorchard]

Complex of the Month: Interleukin-23 cytokine complex with key role in lymphocyte proliferation http://www.ebi.ac.uk/complexportal/complex/EBI-9992716.

[bmeldal]

CotM September 2017:

Tweet text: CotM: canonical SWI/SNF chromatin remodelling complex in #yeast: http://www.ebi.ac.uk/complexportal/complex/EBI-15100957. Use GO:0090544 to find #human & #mouse variants

There's a partical crystal: 4i6m. Maybe you can use the image from PDBe http://www.ebi.ac.uk/pdbe/entry/pdb/4i6m

[bmeldal]

@tschaka1904 are you able to tweet before or after your hospital appt? You make getter pics or gifs :)

[IntAct-EBI]

If you have the characters, swap 'Use GO:0090544' for 'Search GO:0090544' - sounds better. Not a problem if you have used all 140.

[bmeldal]

used all charachers hence the shortening!

[IntAct-EBI]

Is there any point is starting with CotM: - I don't suppose anyone knows what it means, and it uses 5 characters up. Just feature a monthly complex without that label.

[bmeldal]

Ensembl do it...

But let's go for: CotM: canonical SWI/SNF chromatin remodelling complex in #yeast: http://www.ebi.ac.uk/complexportal/complex/EBI-15100957. Search GO:0090544 to find #human & #mouse variants

[tschaka1904]

Can I just throw in that we already use #ComplexOfTheMonth I don't have any strong feelings about it, but just to let you know.

[bmeldal]

too long... :(

[pporrasebi]

You can use #FeaturedComplex instead, if you prefer.

On 12/09/2017 09:37, Birgit Meldal wrote:

too long... :(

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Complex-Portal/complex-portal-view/issues/126#issuecomment-328783467, or mute the thread https://github.com/notifications/unsubscribe-auth/APJwL-cqpTHzCUau77Fo6tm-mqrHNc9Rks5shkLEgaJpZM4N7EDJ.

--

Pablo Porras Millán, Ph.D. Molecular Interactions Project Leader European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 1223 494482 email: pporras@ebi.ac.uk URL: http://www.ebi.ac.uk/intact/main.xhtml

[tschaka1904]

CotM leads you to 'Church on the move' ;-) At the time I just copied it from here.

I like Pablo's idea.

[bmeldal]

That was in a comment without thought about the pracrticalities ;-)

CotM is better than my retweeting the petition to save the Model Organism DBs = MODs: I tagged it #SaveTheMods only to remember afterwards that I just linked it to the black-and-white-checkered vespa & music 'cult culture' of the 80s!!! Could have been worse I guess, they are kind people - I knew a few in my school days :) (actually, not long ago I spotted a vespa with the classic checkered pattern!)

[tschaka1904]

Okay, as long as we are consistent with that. I think it is important to have a hashtag, as we can search/filter them and maybe make a dedicated page for it. Otherwise they are very difficult to distinguish from all the others. I'll make the tweet in a few minutes.

[bmeldal]

I take your point about consistency :)

[tschaka1904]

Is out! Maybe Monday we can retweet it with the other accounts.

[tschaka1904]

Also, CotM should be a # to. I squeezed it in. This way we can make #-searches.

[tschaka1904]

October?

[tschaka1904]

The most searched term in September was: 'syntenin' (apart from the usual examples).

[bmeldal]

I'm suggesting to use one of the first Arabidopsis complexes after the next release. One is ready for release and another one should be ready as well by the time we release.

[bmeldal]

As the next release is now not going to be out til the end of the month let's feature another complex this month. Syntenin hasn't got a lot of linked data but related escrt-iii does. It's linked to autophagy and virus budding and Reactome have a nice diagram for the HIV reactions that we could use as the pic. https://www.ebi.ac.uk/complexportal/complex/EBI-11509704

Tweet:

CotM: ESCRT-III https://www.ebi.ac.uk/complexportal/complex/EBI-11509704, involved in #autophagy and #HIV #VirionBudding. Search 4 more autophagy complexes with GO:0006914

[bmeldal]

@sandraorchard @pporrasebi Max is working on this, speak now or forever hold your peace ;-)

[pporrasebi]

Sounds fine to me.

Pablo.

On 09/10/2017 11:54, Birgit Meldal wrote:

@sandraorchard https://github.com/sandraorchard @pporrasebi https://github.com/pporrasebi Max is working on this, speak now or forever hold your peace ;-)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Complex-Portal/complex-portal-view/issues/126#issuecomment-335124268, or mute the thread https://github.com/notifications/unsubscribe-auth/APJwLzMwr4FicwOpEgvIBHvB8LHql33jks5sqftKgaJpZM4N7EDJ.

--

Pablo Porras Millán, Ph.D. Molecular Interactions Project Leader European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 1223 494482 email: pporras@ebi.ac.uk URL: http://www.ebi.ac.uk/intact/main.xhtml

[pporrasebi]

In any case, you should consider changing "complex of the month" to "featured complex". Saves us the trouble caused by having releases in the middle of the month...

Cheers,

Pablo.

On 09/10/2017 11:54, Birgit Meldal wrote:

@sandraorchard https://github.com/sandraorchard @pporrasebi https://github.com/pporrasebi Max is working on this, speak now or forever hold your peace ;-)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Complex-Portal/complex-portal-view/issues/126#issuecomment-335124268, or mute the thread https://github.com/notifications/unsubscribe-auth/APJwLzMwr4FicwOpEgvIBHvB8LHql33jks5sqftKgaJpZM4N7EDJ.

--

Pablo Porras Millán, Ph.D. Molecular Interactions Project Leader European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 1223 494482 email: pporras@ebi.ac.uk URL: http://www.ebi.ac.uk/intact/main.xhtml

[bmeldal]

We debated it and it uses lots of characters... I don't think we'll have too many months with 2 featured complexes.

Or have a go at loosing 1 characters :)

[sandraorchard]

Holding peace - sounds good to me.

[tschaka1904]

We can also use a new hashtag every month ;-)