The anniversary of Mark2Cure’s official launch is coming soon

Posted on by ginger

Mark2Cure's 3rd anniversary is coming up, and we are extremely grateful for the opportunity to have interacted and learned from you over the last few years! You make this project interesting. You make this project interesting and exciting. You make this project educational and humbling. You make this project useful and valuable. Although our research team has shrunk two half of what it was when we first started, we have been able to continue to move forward only because of you! We cannot thank you enough!

As a citizen science effort, Mark2Cure is primarily driven by volunteers--and volunteers like you have brought us to where we are today. As of today, we have over 1.3 million annotations!!! We are currently busy with the analysis, so please accept my apologies for being a bit more slow to respond to your inquiries. Fortunately, you and your fellow volunteers continue to help us move forward. In fact, we are excited to share a new preprint on aligning citizen science opportunities with the needs of students fulfilling community service and service learning requirements. The research on these requirements was primarily performed by a volunteer with a marketing/business background and was inspired by a few high school Mark2Curators who have been kind enough to share their experience and needs as students and volunteers.

You can find the preprint on bioarxiv here, and it has been submitted for peer review in the journal Citizen Science Theory and Practice.

A designer has also wrapped up her work on making Mark2Cure more intuitive and user-friendly. A huge thanks to those of you who took the time to provide feedback on individual parts of her designs--although your feedback may not necessarily be incorporated in them here, we will definitely take your detailed and valuable suggestions into consideration.

Since this is citizen science and your voices are important--I'd like to share the designs with all of you. You can find the wire frames here. Note that the actual wording/content is subject to change (especially since we've received detailed content recommendations from some of you), and that the focus is more about the layout of the content. Please feel free to share your opinions about it with us!

For those of you who have joined us in last year's #MedLitBlitz or this year's #CitSciMedBlitz, you may be familiar with our friends at Cochrane Crowd. Like Mark2Cure, Cochrane Crowd is a citizen science project where volunteers help inspect biomedical abstracts. Cochrane crowd was also launched in May and are celebrating their anniversary with the #showyourscreen 2 Million annotations challenge. Learn more about the challenge here.

CitSciMedBlitz Recap and Results

Posted on by ginger

Hopefully, you'll all forgive us for the delay in announcing the results of #CitSciMedBlitz. Our partners at EyesOnAlz, Cochrane crowd, and ourselves were a little tired after the blitz and we gave ourselves a short break. Since the blitz, the EyesOnAlz team has generated the #CitSciMedBlitz digital badge for participants of all three challenges and has been working on creating the trophies; meanwhile, the Cochrane crowd team has contacted the overall #CitSciMedBlitz event winners.

look alive now! We're all up and active now and looking forward to sharing a recap and the results of #CitSciMedBlitz with you.

First, a Recap

On February 21st, CitSciMedBlitz was kicked off with a webinar to introduce the three platforms that would be participating in CitSciMedBlitz
You can watch the webinar here

The first challenge, the StallCatchers challenge, was launched on February 26th at 7am PST. Within minutes of the launch, StallCatchers were hammering away at StallCatchers, including Cochrane Crowd's Anna.
first 10 min

Anna managed to get on the leaderboard but wasn't able to stay on there for very long because the competition was just too tough. At least she placed, though-- I never even made it!

By the end of the challenge, StallCatchers analyzed a whopping 18,348 real videos--the equivalent of two weeks worth of laboratory analysis!
first 10 min

While the EyesOnAlz team was still cooling off from their intense challenge, we were gearing up for the Mark2Cure arm--and NOT without a huge set of worries.
i am worried

You can read more about the hiccups and snafu's that happened during the Mark2Cure 24hr challenge here. By the end of the challenge, CitSciMedBlitzers managed to submit ~300 doc annotations, and ~3000 relationship annotations--an impressive feat considering the increase in task difficulty, and the bugs and other technical issues that made the challenge--well, even more challenging!

While we were busy analyzing the results of our challenge, Cochrane crowd was preparing the last challenge of CitSciMedBlitz. This challenge started off right with 50 assessments within the first 2 minutes, and over 5000 in just the first 4 hours! This arm of the challenge would determine which of the top contenders from the previous challenges would win the trophy so the competition was intense! By the end of this challenge, over 46,000 classifications would be made--allowing our teams to determine the overall winner of #CitSciMedBlitz.

And now...the results of CitSciMedBlitz...

Of course, the biggest winner of the challenge goes to...

...biomedical and health evidence research! Everyone who has contributed (in the past) and continues to contributes to these efforts deserve a round of applause for being generous enough to donate their time towards helping with disease and health research.

Thank you for being amazing

The winner of the CitSciMedBlitz trophy is Michael Landau! Note, it was previously stated that Michael was also the top contributor to the EyesOnAlz challenge of CitSciMedBlitz. This is wrong.

Mike Capraro was the top contributor across all three measures of the EyesOnAlz challenge and the overall top contributor of that challenge for CitSciMedBlitz.

Editor's note #2: If you'd like to read more about CitSciMedBlitz from the EyesOnAlz team, check out their latest recap post here!

The top contributor to the Mark2Cure arm of CitSciMedBlitz was Kien Pong Yap, while the top contributor to the Cochrane Crowd arm of CitSciMedBlitz was Nikolaos. The top contributors to each platform will be receiving a platform-specific trophy.

Each platform will be awarding additional prizes to some of their top contributors and the notifications should be arriving via email (if they haven't already).

Editor's note #3, the recap from the Cochrane Crowd side of things is now available

Now that all the excitement of CitSciMedBlitz is over, I'd like to thank ALL the citizen scientists who contribute to projects like ours and make these platforms great. In citizen science, the people make the platform. And, as you can see--the people contributing to these platforms, do so with:

a collaborative spirit,
sharing is caring

humor,
guilt to the rescue

humility,
struggled and won

good spirit,
positive attitude for the win

and grace,
positive attitude for the win

Thank you all! Much respect for the work that you've done and the character you've shown!

mad respects

Note this post was updated on 2018.03.12 to correct an error and on 2018.03.19 to add a link

CitSciMed Blitz has started!

Posted on by ginger

It's on! The CitSciMedblitz week of challenges have started!

If you missed the webinar detailing the three biomedical/health citizen science research projects, it is available for viewing on youtube.
CitSciMedblitz webinar

You are welcome to participate in as many or as few of the challenges as you'd like, but a trophy will be awarded to the highest ranking participant across all THREE challenges. Read more about CitSciMedblitz from this post at citscibio.org

With regards to the challenges, up first (and going on now!) is the EyesOnAlz 24hr Catchathon. EyesOnAlz is an Alzheimer disease-focused citizen science project investigating stalled blood in brain images. It has a lot of cool images/videos in need of review by citizen scientists and a lot of fun features. The challenge has only just started and will run to 7am PST (3pm GMT) tomorrow (Feb. 28th) so get in on it ASAP!

The Mark2Cure challenge will start at 7am PST (3pm GMT) on Wednesday, February 28th. It is a doubly-special day because the 28th is Rare Disease Day and we have had an incredibly inspirational weekend at the Sanford Burnham Presby Rare Disease Day Symposium. We look forward to sharing rare disease stories from Mark2Curators and bringing awareness about these diseases as we tackle the literature around NGLY1 during this 24hr challenge.

Speaking of literature, our old friends at Cochrane Crowd are back with a lot of new features which you can explore during the Cochrane Screening Challenge. This challenge starts at 7am PST (3pm GMT) on Friday, March 2nd and runs for 24hrs.

CitSciMed Blitz, Rare Disease Day, and more

Posted on by ginger

It's finally February which means it's time to prepare for Rare Disease Day 2018 and CitSciMedBlitz! This year's theme for Rare Disease Day continues off of last year's theme--research. According to RareDiseaseDay.org, patients are not only subjects but also proactive actors in research--and we couldn't agree more! Mark2Cure would not be where it is now without the inspiration, contributions, and drive from our partners and contributors in the rare disease community. Mark2Curators have inspired us with their generosity, perseverance, curiosity, and overall intellectual voraciousness--and for us, Rare Disease Day is an opportunity to share about the diseases that the Mark2Cure community cares about--and not just NGLY1-deficiency. If there is a disease that you care about that you'd like us to highlight for Rare Disease Day, please get in touch.

Patients are not only subjects but also proactive actors in research.
Patients kick start research
Patients drive research
Patients organize research
Patients proactively provide data

The increasing role of patients in research is not limited to Rare Disease
As citizen science becomes increasingly popular in biomedical research, patients and care providers are becoming increasingly important partners for disease research in general. And, as many of you have pointed out--we will all be patients at some point in our lives so it's nice to be able to actively contribute to disease research.

In addition to helping to organize the knowledge surrounding NGLY1-deficiency, patients and citizen scientists have been making important contributions to Alzheimer's disease research and contributing to health evidence--all of which brings us back to CitSciMed Blitz!

CitSciMed Blitz is coming

Similar to last year's MedLitBlitz, there will be prizes for the top contributors to all THREE platforms. Only participation during the 24hr challenges will count towards the prize, however, you are welcome to register and complete the training for the other platforms prior to the event if you'd like. Learn more about the event and the other platforms here.

Happy Memorial Day weekend!

Posted on by ginger

The last few weeks have been a bit hectic, so we've got plenty of news and info to share with you.

First of all, if you haven't seen it yet, Cochrane Crowd has posted about about our joint webinar and the #MedLitBlitz. If you missed the webinar or had technical difficulties/time zone issues with it, it's available on youtube. The prize packages for the top three participants of #MedLitBlitz are packed and will be shipped either today or early next week (depending on whether or not shipments have been picked up for today or not).

Secondly, Mark2Cure was at the Citizen Science Association conference from 2017.05.15-2017.05.20, and was fortunate enough to share about YOUR work to an audience of scientists who LOVE citizen science! More than a few researchers stopped to introduce themselves to me and spoke highly of our community! Although it's always weird to hear a recording of your own voice, I recorded my presentation because it wouldn't be fair to talk about the amazing work you've done without sharing it with you! You can find my presentation for the biomedical session in our youtube channel. On a side note, I know the audio quality isn't the best which is why I've transcribed it using youtube's captioning software. If you have trouble hearing the presentation (because of the poor audio quality), please turn on the closed captions.

Max also delivered two lightning talks for the event, which I hope to upload soon.
Not available yet, but will be soon In addition to the talks, we had a poster for Mark2Cure and a table at two public events.
Max spreading the love for Mark2Cure

We were especially pleased to be so close to our buddy at Cochrane Crowd for this event
Cochrane Crowd looking good

Lastly, it looks like one of the missions was completed just as I was settling back in after the conference. A HUGE thanks to everyone that helped complete the carpingly mission. A new mission has been launched in its place, so check it out if you have some free time.

MedLit Blitz, Mark2Curathon Results and More

Posted on by ginger

Mark2Curathon Results

MedLit Blitz, Mark2Curathon Results and More

Sorry for the delay, the Mark2Curathon results are finally in! During the Mark2Cure portion of MedLit Blitz, we had 34 participants contribute over 16,000 annotations. Because both the entity recognition and the relationship extraction tasks are very different from Cochrane's screening task, we had to take some additional considerations when tallying the results.

For the Relationship Extraction module, multiple annotations per abstract were possible as each abstract could have any number of concept pairings. Hence, for the relationship extraction module each annotation submitted counted as one task unit

For the Entity Recognition module, only one submission was possible per abstract, but users needed to identify three different types of entities. Hence, each abstract completed counted as three task units (one for each concept type--genes, treatments, diseases). Additionally, a tiered bonus multiplier (of an additional 2% to 15%) was applied for users who submitted high quality annotations.

The RE and ER tasks units were then added together for each user, and sorted from highest to lowest in order to determine user ranking for the event. Without further ado, these were the top 15 participants in the Mark2Curathon:
1. ckrypton
2. Dr-SR
3. TAdams
4. hwiseman
5. Kien Pong Yap
6. skye
7. ScreenerDB
8. priyakorni
9. Judy E
10. pennnursinglib
11. Calico
12. AJ_Eckhart
13. uellis
14. sueandarmani
15. nclairoux

A huge thanks to you all, and everyone who participated for making our first adventure with Cochrane Crowd so successful!

To qualify for the MedLit Blitz prize, Mark2Curators had to have contributed to the Cochrane Screening Challenge as well.

MedLit Blitz Results

We are in the process of contacting the winners and hope to have an update about this soon.

Mark2Cure at Citizen Science Association Conference 2017

Max and I have arrived in Twin Cities, Minnesota for the Citizen Science conference. Mark2Cure was accepted as part of the symposium on biomedical citizen science. Additionally, Mark2Cure was also accepted for a poster presentation and for the project slam. If that doesn't sound busy enough, Mark2Cure was accepted for a table at the 'Night in the Cloud' event (open to the public). If you are in town, please stop by our table!

About the prizes

Winners will receive a Mark2Cure mug, marker, novelty item, in addition to any prizes that Cochrane has prepared for this event.

The Mark2Curathon starts now!

Posted on by ginger
The Mark2Curathon starts now!

Our anniversary celebration with Cochrane Crowd is well under way. #MedLitBlitz started with a webinar on Monday, and was followed by the Cochrane screening challenge from Tuesday to Wednesday. During that challenge, over 100 MedLit Blitzers screened 29,494 citations--over nine THOUSAND more than the initial goal of 20,000!

But the celebrations aren't over yet. It's now time for the Mark2Curathon portion of #MedLitBlitz!

For this part, we've launched 3 new missions in the Entity Recognition module. To be clear, all annotations (regardless of whether they were submitted via the Entity Recognition or Relationship Extraction module) will count towards #MedLitBlitz as long as they fall within the time frame of the event. If you don't see the new ER missions, log out, clear your cache and log back in.

As with Cochrane Crowd, we will be active on twitter; however, we know that many of our most ardent Mark2Curators do not use twitter. For this reason, we will also be sharing updates via our chat channel. As with our previous Mark2Curathons, no sign up is required to chat on this channel, and we encourage you to join us there.

For ease of tracking, here's the countdown till the end of the event:

If you participated in the Cochrane screening challenge as part of #MedLitBlitz we'd love to hear about it! It's been really fun working with Anna and Emily over at Cochrane Crowd, we'll definitely look forward to working with them in the future. If you've enjoyed our collaborative effort, feel free to ping some praise to @AnnaNoelStorr and @cochrane_crowd.

Webinar, Mark2Curathon, and more

Posted on by ginger
Webinar, Mark2Curathon, and more

It’s citizen science season and we’re in the thick of it!

First off, welcome new users! If you found us from the latest SciStarter campaign, feel free ping us on twitter to let us know so we can pass our thanks to the @SciStarter team! We’re very excited to be featured as part of SciStarter’s recent focus/feature on biomedical citizen science! Note, if you complete your SciStarter profile this month, the SciStarter team will send you a free digital copy of The Rightful Place of Science: Citizen Science. See their post for more details

Citizen science has enormous potential, and we’re glad that Mark2Curators are helping us explore its application towards biomedical discovery.

As mentioned last week, we’re not the only ones who need your help for dealing with the biomedical literature. Cochrane Crowd is reaching its first anniversary in joining this domain of citizen science, and we’re celebrating together! We will be jointly hosting a webinar on May 8th and there will be two 24hr screening challenges. There will be prizes for the top three contributors who take part in both the Cochrane Crowd and Mark2Cure screening challenges. Here are the details:

Mark2Cure/Cochrane Crowd Webinar:

Date/Time: May 08, 2017, 9:00am – 10:00am PDT

Tentative agenda:

  1. Intro (5 minutes)
  2. Mark2Cure presentation (15 mins)
  3. Cochrane Crowd presentation (15 mins)
  4. MedLit Blitz (5 minutes)
  5. Audience Q&A (15-20 mins)

Interested in participating in the webinar? You’ll need to register first! Hurry, space is limited (due to limitations/licensing restrictions) of the webinar software. Register here

Medlit Blitz (2 x 24 hr screening challenges):

Cochrane Challenge: Help Cochrane Crowd identify studies that provide the best possible evidence of the effectiveness of a health treatment. Once identified by the Crowd the studies go into a central register where health researchers and practitioners can access them. The more studies identified by the Crowd, the more high-quality evidence is available to help health practitioners treat their clients.

Challenge Start: May 9th, 2017 10am GMT + 1 (UK time zone) / 2am (PDT)

Challenge Finish: May 10th, 2017 10am GMT + 1 (UK time zone) / 2am (PDT)

Mark2Curathon: Join the search for clues on a rare disease by identifying genes, diseases, drugs, and the relationships between these based on literature surrounding the NGLY1.

Challenge Start: May 11th, 2017 7pm GMT + 1 (UK time zone) / 11am (PDT)

Challenge Finish: May 12th, 2017 7pm GMT + 1 (UK time zone) / 11am (PDT)

Get ready to use your reading skills to make a difference in biomedical science and health!!!