Happy Halloween

Posted on by ginger

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

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!

Posted on by ginger

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/.

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

Upcoming #CitSciChat on Biomedical Citizen Science

Posted on by ginger
New Mark2Cure Video added to our youtube playlist!

The Citizen Science Conference in May was very productive, and the last of Mark2Cure's recorded talks is now available on our youtube channel. As previously mentioned, Max delivered the project slam for Mark2Cure and was selected as one of the top three to deliver an abbreviated version during the 'Night in the Clouds' event.

View the two-minute talk here:

Biomedical CitSciChat on Wed. July 19th, at 11:00am PT

Speaking of the conference, we were able to connect in person with a lot of lovely people in the citizen science arena, especially the amazing people from @EyesOnAlz, @CitSciBio, and @CochraneCrowd. Because we're all passionate about bringing citizen science to biomedical research, we organized a panel for a biomedical #citscichat. Caren Cooper (@CoopSciScoop) kindly agreed to moderate the chat as usual, and Pietro (@pmichelu, @EyezOnAlz) was able to convince @foldit's Seth Cooper to join the panel.

What: Hour long chat on biomedical citizen science (#CitSciChat)

Where: online via twitter

When: Wed July 19 2:00pm ET (11:00am PT)

Why: Because citizen science is used in biomedical research too

Who: Everyone interested in citizen science is welcome to join this chat which will be moderated by citizen science expert and author, Caren Cooper. The panel so far includes:

  • Mark2Cure of course! Mark2Cure is a citizen science project for addressing the big data issue of biomedical literature. Citizen scientists help look for clues about NGLY1-deficiency in curated literature. (@Mark2Cure/@gtsueng, @x0xmaximus, @AndrewSu)

  • Cochrane Crowd is a citizen science project from the Cochrane Collaborative, and also looks to make biomedical literature more useful. Citizen Scientists help identify randomized controlled trials so that Cochrane Reviewers can use them to answer important medical questions. (@Cochrane_Crowd, @annanoelstorr)

  • EyesOnAlz/Stall Catchers is a citizen science project from the Human Computation Institute to identify blood blockages in short videos of the brain. Their game is super fun, helps with Alzheimer's research AND they have a major event (Catchathon) coming up. If you would like to host a local catchathon, check out this post. (@EyesOnAlz, @seplute, @Clair_csg, @pmichelu)

  • CitSciBio is NIH's new biomedical citizen science hub. It is sponsored by the Division of Cancer Biology at the National Cancer Institute. There are tools for collaborating, creating projects, and now you can login via your scistarter account. (@citscibio)

  • Fold.it is a long standing, and very successful citizen science game which empowers gamers and volunteers to help determine the structure of proteins important to biomedical research. Seth Cooper from Northeastern University has agreed to join the panel to share about this wildly successful project. (@UWGameScience)

    • Beat the heat and help science!

    Need an excuse to stay indoors, avoid chores, and avoid the summer heat? Look no further! One of our current missions is over 80% complete. Help us finish it!

    Happy Fathers Day!

    Posted on by ginger

    A HUGE thanks to all the dads (and EVERYONE) who has been contributing to make a difference for the NGLY1 families.

    Shipping delays Apologies to international prize and drawing winners who were waiting for their prizes. Most of the international packages that we shipped out in May/June have been returned to us due to customs issues (fortunately, this happened at some point prior to shipping so the postage on these is still good, unfortunately, it took a long time for these to get back to us so we can address the issue). We’ll be trying again to get these out ASAP.

    Max’s original project slam now online As mentioned in our previous newsletter, Max delivered the project slam for Mark2Cure at the Citizen Science Conference in Minnesota. The project slam talks were supposed to have been recorded and still may be released by the Citizen Science Association someday, but we couldn’t wait. Here’s our recording of Max’s project slam. He finished within his allotted four minutes, and was engaging enough to win one of three invitations to deliver an even shorter version of the slam at an even the following day.
    You can check it out here: https://www.youtube.com/watch?v=7kxlhhFLdmM

    You be the scientist! One thing we’ve heard (and quite agree with) at the Citizen Science Conference is that trained volunteers are capable of doing more than simple tasks. Mark2Curators have very much fed into the tutorial process, and played an important role in testing and improving the design of the interface. The entities our users have identified from the text have already yielded interesting clues which we’ve used to expand the set of documents to investigate, and by now, there are users who have read a lot of abstracts—A LOT! If you’ve read something that sticks out in your mind as being potentially related to NGLY1-deficiency, share it with us! We’d love to hear YOUR hypothesis on what might be an interesting term to explore and why.

    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!!!