Happy Halloween

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M2C Halloween movie parody poster

If you love science and enjoy learning, you're in for a treat! Andrew (the brains behind Mark2Cure) will be holding a webinar using two case studies (the Gene Wiki Project and Mark2Cure) to illustrate the use of crowdsourcing as it applies to knowledge management for translational research. Registration is free and open to anyone (we checked first). There may be some required questions on the registration form which may not necessarily be applicable to you, but they're only meant to inform, not exclude. So, if you're interested in the webinar but don't have an affiliation with an institute or department, feel free to select 'other' and type in 'Mark2Cure'.

Event Details

(View the original announcement)

Speaker: Andrew Su, PhD, Professor, Department of Integrative, Structural and Computational Biology, The Scripps Research Institute

Overview: Crowdsourcing involves the engagement of large communities of individuals to collaboratively accomplish tasks at massive scale. These tasks could be online or offline, paid or for free. But how can crowdsourcing science help your research? This webinar will describe two crowdsourcing projects for translational research, both of which aim to better organize biomedical information so that it can be more easily accessed, integrated, and queried:

First, the goal of the Gene Wiki project is to create a community-maintained knowledge base of all relationships between biological entities, including genes, diseases, drugs, pathways, and variants. This project draws on the collective efforts of informatics researchers from a wide range of disciplines, including bioinformatics, cheminformatics, and medical informatics.

Second, the Mark2Cure project partners with the citizen scientist community to extract structured content from biomedical abstracts with an emphasis on rare disease. Although citizen scientists do not have any specialized expertise, after receiving proper training, Mark2Cure has shown that in aggregate they perform bio-curation at an accuracy comparable to professional scientists.

The Digital Scholar Webinar Series introduces health researchers at USC, CHLA and beyond to digital approaches and tools relevant to their research. The series showcases the potential and limitations of digital approaches health researchers need to be aware of. All webinars will be accessible afterward on the Digital Scholar Program page.

Register for the webinar

Precision medicine hackathon and curation coming

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Preliminary analysis or your work on the Relationship Extraction task

We have been working on a preliminary analysis of the relationship extraction data generated by our fantastic Mark2Curators. This analysis is in the process of being written up into an academic paper and if your data was used for this paper, you will be given option of being credited on a page on our site dedicated to the contributors for this paper. We expect to have an email notifying contributors to the data set out by early next week, so keep an eye out for it.

San Diego Hackathon / Curation Jamboree

If you are in San Diego the week of October 14th, and have a background in software development, engineering, computational biology, bioinformatics, pathology, oncology, genomics, or biocuration--there is a hackathon/curation jamboree happening on October 15th-October 16th. The event is a joint event between the Griffith Labs, Su and Wu Labs and will cost $25 to register. Mark2Cure is a project of the Su Lab focusing on biomedical literature curation; while, the hackathon is focused on the CIViC resource from the Griffith labs. CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer which aims to enable precision medicine by providing an educational forum for dissemination of knowledge and active discussion of the clinical significance of cancer genome alterations. You can learn more about this event at: https://www.eventbrite.com/e/cancer-variant-interpretation-hackathon-and-curation-jamboree-tickets-48287431006?aff=General

World Alzheimer Day

In case you missed it, September 21st is World Alzheimer’s day, and our friends at EyesOnAlz will be holding a world-wide Catchathon. Our very own TAdams organized a local team to participate in a previous Catchathon. If members of the Mark2Cure community are interested in teaming up and contributing with other Mark2Curators for this Catchathon, we would be happy to organize a Mark2Cure team for the event. Otherwise, if you are interested in contributing to Alzheimer’s research from the comfort of your own computer on an individual basis, we 100% encourage you to do so!

Science by the people and for the people—introducing a new Citizen Science project from the Knight Lab at UCSD

If you’ve ever wished that there was a citizen science project for answering questions about how nutrition and other habits affect health and other outcomes—there’s now a new platform to address your questions. This platform, Galileo, comes from the Knight Lab at the University of California, San Diego—the same lab that is responsible for the American Gut project!

Here’s how it works:
gutinstinct Learn more at gutinstinct.ucsd.edu/info

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.

Happy Citizen Science Day Hero Badge Hunting!

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Citizen Science Day was April 14th this year, and Mark2Cure partnered with the San Diego Public Library to host a local Citizen Science Expo. Of course, many of our wonderful contributors are not in San Diego and could not attend the event. For those of you who wish to get in on the Citizen Science Day excitement, we've joined the EyesOnAlz Citizen Science Day Hero challenge.

The challenge will run until 9am ET, April 21st and anyone interested in the challenge will have the opportunity to earn digital badges for just trying out (ie- registering or logging into) different citizen science projects. As Mark2Curators, you only need to log into your Mark2Cure account to earn a badge.

Learn more about this fun challenge at https://blog.eyesonalz.com/citsciday-hero/.

Citizen Science Day 2018 is just around the corner!

Posted on by ginger

San Diego Citizen Science Day Expo

Citizen Science Day is on April 14th, this year and many citizen science organizations (including yours truly) are hosting citizen science events. Here in San Diego, we've teamed up with the San Diego Public Library and the Wet Lab group to put on the 3rd annual San Diego Citizen Science Day Expo. There are a lot of exciting new entrants into the San Diego citizen science scene, and we hope you will join us in learning about them at the expo. If you're in San Diego, please join us! The details are as follows:

Who: Anyone who wants to do science
What: San Diego Citizen Science Day Expo
When: Saturday, April 14, 2018. 1:00 PM – 5:00 PM
Where: North University Community Library (8820 Judicial Dr, San Diego, CA 92122)

Please note that the location has changed from the previous ones due to the limited availability of parking spots at the La Jolla Library. The North University Community Library has plentiful free parking, so please visit come if you're in the area! For the most up-to-date information about this event, visit SDCitSci.net.

If you're not in San Diego, there is probably an exciting Citizen Science Day event happening near you! To find a Citizen Science Day Event near you, visit Scistarter.com.

San Diego March for Science

The March for Science is also happening on April 14th in San Diego. It starts at the Waterfront park at 10:00am and ends at 1:00pm (right before our event!). If you want to show your love for science consider joining the march! If you want to DO science, be sure to join a Citizen Science Day event near you (or contribute to Mark2Cure, of course!).

Current Status of Mark2Cure

Development status and workarounds

Unfortunately, Mark2Cure no longer has a full time developer working on the project, so a lot of the issues and bugs that have been reported probably will not be fixed for a long, long time. We are very sorry for the frustration our system has caused our users and extremely grateful for the patience, graciousness, and encouragement our users have returned to us. Mark2Cure is really made up of a wonderful bunch of individuals, and we are thankful that this project has introduced us to you. Fortunately, many of you really put the science in the term citizen science and have systematically found ways to contribute productively in spite of all the issues in our system. You are all too amazing!

NER module issues: The most frustrating one has been the inability to highlight certain words, and the random highlighting/un-highlighting of words when users try to mark something. This has been reported by many users (many, many thanks to those of you who took the time to report this issue). Fortunately, one of your fellow volunpeers has found a workaround that appears to be quite robust. To get around a lot of these highlighting issues, AJ_Eckhart highlights the entire paragraph to remove the preannotations. These preannotations seem to be an important factor in this problem, and he has tested this workaround for the 'cannot-highlight-a-specific-term' bug, the 'highlighting-a-term-un-highlights-something-else', and the 'highlighting-a-term-highlights' something else' bugs.

RE module issues: A number of you have kindly taken the time to report issues with the RE module--the most common issue is the seemingly random inability to throw out an annotation. For this issue, two workarounds have been reported by our users. LadySteph has found that returning to the dashboard and then returning to the task will enable you to submit the response you wish (eg- throw out an annotation) and TAdams has reported that many of you have gravitated towards submitting 'Cannot be determined' in lieu of throwing out an annotation. We will take both workarounds into consideration when we analyze the data, so thank you all very much for contributing in spite of all these issues!

Data analysis and research status

Speaking of analyzing the data--we might not yet have enough abstracts annotated in order to generate ground-breaking, new hypotheses on NGLY1 deficiency, but we have enough for some initial analyses on the application of citizen science towards information extraction. We are working towards more scientific publications and look forward to sharing the results of your work and crediting you for your help. Note that many journal submission systems are not made to account for group names or a huge volume of names in the authorship; hence, we will continue to have our Mark2Cure contributors listed on a dedicated page which will be linked in the paper. As with our first paper, this will be an opt-in process because we respect your right to privacy. More details on opting-in will be sent via our mailing list.

CitSciMedBlitz Recap and Results

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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

CitSciMedBlitz Update

Posted on by ginger

The results for Mark2Cure's arm of the CitSciBlitz are now available! Kien Pong Yap took the top spot in this challenge (see ranking at bottom of post).

What's exciting is that several of these names were also in the top 10 for the StallCatchers challenge so it'll be a tough competition in the Cochrane challenge to see who actually wins the CitSciMedBlitz triple challenge trophy.

Here are some random tidbits about the Mark2Cure arm of the CitSciMedBlitz triple challenge:

  • The NER module was broken for the first few hours of the challenge, and we received emails and phone calls about it within the first hour of the challenge. THANK YOU for bringing it to our attention and providing so detailed information about the bugs. Max was able to solve it while on the airplane ride to San Diego for the Future of Genomic Medicine Conference.

  • In spite of the NER module issues (a HUGE thanks to TAdams, JudyE, AJEckhart, and Itwontalwaysbelikethis for helping us troubleshoot), users doing this task still managed to climb the ranks even with the delayed start.

  • A Mark2Curator created an introductory video about the relationship extraction task for the event while we were running around trying to ensure that everything was in place for the M2C challenge. THANK YOU for doing that, TAdams!

  • One of the Mark2Curators joined the challenge as a personal challenge to raise awareness for dystonia on Rare Disease Day. Dystonia = loss of muscle control. There are many types, but you can imagine just how much more challenging that makes things! Read about her efforts here. And if you're curious how well she did--she made it to the top 5!

  • I was worried about following StallCatchers because their task is so visually appealing while ours is text based and quite difficult. Indeed we got questions and suggestions-a-plenty about Mark2Cure on the StallCatchers forum, but there are plenty of very tenacious citizen scientists in stall catchers and they managed to climb pretty high in the ranks.

  • The team behind StallCatchers is AMAZING!!!! Very generous with both support and humor! No wonder the StallCatchers are so ardent!

If you think it's all over--think again! The Cochrane crowd of the challenge has just started, and CitSciMedBlitzers who participate in all THREE challenges will get a digital badge on their StallCatchers profile. It's an awesome badge!

Now go take the cochrane challenge!

citscimedblitz mark2cure rankings

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

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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.

The Sammies award and why it matters to Mark2Cure

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In case you haven't heard, David Lipman and the GenBank team are in the running for the People's Choice Award of the Samuel J. Heyman Service to America Medals (#Sammies2017). Although Lipman and the GenBank team weren't featured in Medium.com or other news sources, they still made it to the final four.

At this point, many of you may be wondering why we're even talking about Lipman and the GenBank team on a discussion venue meant for Mark2Cure. Mark2Cure is a citizen science project that deals in biomedical literature, and doesn't involve BLAST or Lipman or GenBank, right?

But, when you think about how much of scientific progress is incremental, you begin to appreciate the impressive volume of preceding work. This is especially true if you work on a project like Mark2Cure.

Mark2Cure aims to enable citizen scientists to help mine information from the biomedical literature, which means that Mark2Cure would NOT exist if there wasn't a massive volume of preceding and ongoing work in biomedical research. We've been able to build Mark2Cure because key information infrastructure was already in place--PubMed. Lipman launched PubMed in 1997 followed by PubMed Central in 2000. Without PubMed and the subsequent tools built for utilizing PubMed, identifying abstracts and pulling them into Mark2Cure would be more difficult.
As expected, PubMed now has over 27 million articles, up from over 26 million earlier this year Interestingly enough, Lipman's and the GenBank's team nomination for the 2017 Sammies only cursorily mention PubMed Central in favor of focusing on GenBank and his contributions to infectious disease surveillance. Perhaps describing their work this way made it more accessible to anyone not in biomedical research. Unfortunately, their profile description doesn't adequately convey how important the infrastructure they've built is to modern biomedical research in the US, open science, and Mark2Cure.

Because the Mark2Cure community consists of people who've been impacted by Lipman and the GenBank team's work, I'll spell it out here:

For members of our community who like science and like being able to read scientific articles: PubMed Central (PMC) has been a central repository for research articles that ANYONE can access and read. Thanks to NIH leadership, publications resulting from research supported by the NIH must be deposited to PMC.

For members of our community who are afflicted or know someone who is afflicted by a rare genetic disorder: GenBank has been a central repository for DNA sequences and BLAST has been an important means of searching those sequences. Without a central repository for DNA sequences, it would be a lot more difficult for researchers to map and annotate functionality associated with those sequences, to draw comparisons on protein function across the different model organisms, and most importantly, to build on each other's work. Much of what we know (or will know) about rare disease genes or proteins comes from (or will come from) expanding on the work of researchers studying worms (or flies, mice, frogs, fish, and more) thanks to the knowledge sharing enabled by PubMed and GenBank.

For the members of our community who just like to help: Mark2Cure exists because of the sheer volume of incremental progress that is represented by the publication of biomedical research articles. Incremental progress isn't as exciting or fun to talk about as scientific 'breakthroughs', but in science a lot of incremental progress had to happen in order for these 'breakthroughs' to follow.

There is so much to sift through, and every contribution from our citizen scientists unlocks a bit more information buried in the text. The Mark2Cure dream is that in unlocking information from the text, you will be able to help with 'breakthroughs' in disease research.

Although I've been rambling about the importance of Lipman and the GenBank team's work to modern biomedical research, Mark2Cure would be nothing without the community of citizen scientists that contribute to it. In no way should this discussion of Lipman and team detract from this fact.