Gee-aI-eN-Gee

Misadventures in science


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Max’s Mark2Cure talk at SDBUS, Birthday wishes for Bertrand, and more

Last Wednesday, our lead programmer (Max) was the guest speaker for the San Diego Bioinformatics User Series over at UCSD. We were thrilled to see a Mark2Curator show up for his talk (big shout out to TAdams), and understand that not everyone who wanted to attend could make it. Fortunately, we’ve recorded his presentation, and after editing it (to remove the excessive motion from my poor filming technique), we’ve finally made his talk available. The video processing is one reason why this newsletter was sent today rather than on Friday (when it should have been sent out.)


The other reason is that it’s Bertrand’s birthday! If you’re new to the Mark2Cure community, you might not be familiar with Bertrand Might, whose infectious grin graces our landing page. Bertrand’s birthday serves as a reminder of each unique NGLY1 child that has inspired Mark2Cure and of the rare disease community members who have joined the effort to make sense of the literature.

From all of us on the Mark2Cure development team, HAPPY BIRTHDAY, Bertrand! We’d like to thank ALL of the Mark2Curators who have contributed to the current campaign! Thanks to you, we can proudly tell Bertrand’s parents that the Mark2Cure community has completed five doc sets (over 900 docs), submitting over 400,000 annotations.

5 groups merged zoom out

Knowledge network generated from the completed doc sets: Congenital Disorders of Glycosylation (gray lines), Alacrima (purple lines), FBX2-Engase (orange lines), O-linked glycosylation disorders (red lines), and misfolded and mitochondrial (yellow lines) doc sets.

We’re not done yet and still need your help.

We have three doc sets in need of your contributions. Two of the doc sets are over 70% complete, but we can’t get them done without you. Help finish them by completing a quest today! Just contributing to one quest will make a huge difference. Lastly, please share Mark2Cure with anyone who might be interested. We need to grow our community in order to get these docs done quickly.


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Max to speak about Mark2Cure at SDBUS

Happy Thanksgiving!

 

Thank you all for your contributions and feedback to Mark2Cure. Mark2Cure has changed so much since the beta experiment and it’s all thanks to you! The improvements in Mark2Cure would not have happened without your input.

Our Eeyarestatin doc set now has 1 completed quest and is 70% complete! Check out the network that’s starting to come out of it, and watch the network grow by helping complete the other quests!

If you’re in San Diego on December 2nd (next Wednesday), you can attend Max’s presentation about some of the technical aspects of Mark2Cure! Max will be speaking on behalf of the Su Lab for the San Diego Bioinformatics Users Series. Attendance is free, but it’s at UCSD, so parking might not be. If you’re interested, you can register here: https://www.eventbrite.com/e/san-diego-bioinformatics-users-series-sdbus-tickets-19611662009 .


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Mark2Cure citizen science volunteers finish off another 300 abstracts

The O-linked Glycosylation disorders doc set contained 195 abstracts, while the first misfolded and mitochondrial doc set had 105 abstracts. BOTH doc sets were completed this week by the citizen science participants of Mark2Cure. 300 abstracts is no laughing matter considering that each abstract was read and annotated by at least 15 different users. That’s 4500 doc annotation submissions!

With the completion of these two doc sets, we’ve opened two more doc sets. Our smallest set yet is about Eeyarestatin and is already halfway done!

If you’re curious how your contributions matter, take a good look at the annotation network for Eeyarestatin. Are you seeing just white space? That’s because the computer has no idea what’s in this doc set yet, and needs you to point out what in this doc set. Once a quest reaches 15 completions, the annotations for that quest will appear in the network. Help build the network by finishing a quest today!

This week was also interesting as the citizen science research team at Cancer Research UK (responsible for a number of biomedical citizen science projects) had a twitter takeover. Nice to catch up with other research teams working hard to find solutions in big data challenges surrounding human health.

Oh, and a big, warm welcome to those of you who just joined us this week! We hope you’ll enjoy Mark2Cure and interacting with the wonderful Mark2Curators who comment on the talk pages.


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New feature just in time for Friday the 13th!

It’s Friday the 13th, and we have an exciting new feature to share with you! You will now be able to see the information that you’ve helped to extract for each group. When you go to your dashboard, click on any of the doc-set titles to view the doc-set’s page. You’ll see a description of that doc-set, the progress bar for that set, and the option to ‘Toggle Network.’

2015.11.13 mfold-all

If you click on ‘Toggle Network’, you’ll be able to see the concepts that the Mark2Cure community has extracted from this doc-set.  Only concepts from docs that have been marked by 15 users will appear in the network.  If you want to see the network grow, help complete the quests!
2015.11.13 mfold-network
What does this network show?  The network nodes (circles) shows the concepts that have been identified and agreed upon by 15 different users.  They are color-coded based on the concept type.  If there’s an edge (line) between two concepts, it means those two concepts appeared in the same doc, and are probably related somehow.  Note that a big doc-set may take longer to load, and a doc-set with no completed quests will not have anything to display.
2015.11.13 - mfold network zoom
What can you do with this network? Unlike the static network images we’ve generated and shared with you in previous newsletters, this one is interactive.  You can use the + or – buttons, or scroll with your mouse to zoom in on the network so you can inspect its nodes (circles).

You can also use your mouse to drag the network image around so that you’re inspecting the part of the network you’re interested in.  See a particular node/concept term that piques your curiosity?  Clicking on it will open a google search on that concept term.  Want to see more nodes and edges in the network?  Help complete the quests in the doc-set so that the program can find them.

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Just four quests left to go in the O-linked Glycosylation Disorders doc-set. If you have a little time to spare, please help us finish this doc-set.  The Misfolded and Mitochondrial doc-set is nearing completion too!  Just doing one quest will bring this doc-set that much closer to completion.


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FBX2-Engase Doc set…DONE!

With the newest doc set on oxidative stress launched just last week, the Mark2Cure community wrapped up the FBX2-Engase doc set up this week.

FBX 2015.08.14

This set may be done, but our newest set is huge! Help mark it!

In this doc set, 6 users completed almost every doc available in this set (skye, carawgoalie, Isabelle, Ladysteph, ckrypton, and mariomar_it). Following that, five users contributed 40-42 docs (mikulda1, billmcquillan, ReshmaJitesh, and kuhno1980). Seven users contributed at 20-39 docs (vancez, StellaRemnant, daniette, chu2k, mirasume, manabu.torii, and aprilwent). Altogether, users who contributed to at least 20 docs accounted for 85% of the work needed to complete this set. If you are one of the contributors (doesn’t matter how many or how few docs you contributed) to help complete the FBX2-Engase doc set, THANK YOU!

Every doc contributed counts towards our goal. Thank you

Every doc contributed counts towards our goal. Thank you


 

In case you missed last week’s Mark2Cure update, you can find it here:
New Doc Set and a preliminary look at the data generated by Mark2Cure | The Su Lab.


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CDG doc set done!

Composed of ~483 abstracts, the CDG doc set was one of the largest sets in Mark2Cure’s Campaign for NGLY1. This set was completed sometime on Tuesday night (07/28) and is the second doc set to be completed by the Mark2Cure community (the first one being the Alacrima set).

While we work on preparing the next doc set for release, there are still two doc sets available right now to the Mark2Cure community, both of which are over 60% complete.

The FBX/Engase Set

FBX2 description

F-box protein 2 (FBX2) and endo-beta-N-acetylglucosaminidase (ENGASE) are two genes which were identified to be potentially relevant to NGLY1 deficiency. There are very few papers linked to these two genes; but they may hold valuable clues regarding other relevant topics to search. Help finish this set.

The O-linked glycosylation disorders set

O-linked description

Can researchers gain insight on the genes involved in N-linked glycosylated protein degradation and compensatory mechanisms by studying O-linked glycosylation disorders? Are there treatment strategies for O-linked glycosylation disorders that might apply to NGLY1 deficiency? Help finish this set.

We’ll have a big news update for the community next week! Until then, here’s a round of applause for your incredible accomplishment:

applause

A round of applause for you. Image from the Daily Otter.


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Can it be done? Can we finish 15 quests this weekend?

New features and fixes: Earlier, we introduced the document-specific ‘talk pages’, without too much fanfare since we wanted to ensure that it was working properly. Now that we’ve seen a few users jump in and demonstrate that it seems to be working properly, we invite you all to discuss the annotations on the documents you’ve completed. Thank you, bill, klgmd, edward, derosa, and kagaku for trying out the talk pages and posting really useful suggestions, tips, and questions. We can’t tell you how to do every single document, else we’d have already done them! But, with your help, we can all learn and improve with every doc!

As many of you may have noticed, the pre-population of the annotations wasn’t working properly for the last few weeks. Fortunately, this issue has been fixed.

We’ve also added a quick difficulty rating for each doc-set as a whole. Naturally, each set will have a good mix of docs of different difficulty levels.

New Mark2Cure Developer: We have a new developer who will be working to greatly expand the capabilities of Mark2Cure. Like Max, Jennifer will be working stealthily behind the scenes and we are excited to have her join us.

New Goal: It’s just for this weekend, though. The CDG doc set is at 97% and we’re aiming to finish it! Whether or not this happens is completely up to you, so please join us!

It’s Friday so our #WhyMark2Cure pic of the day must be fun! Though the rationale is from one of our awesome Mark2Curators, the pic is from our lab. Shameless plug alert! If you have computational chops, and think you’d like our kind of lab, join us!!!–end of shameless plug