The Sammies award and why it matters to Mark2Cure

Posted on by ginger

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.

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.

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!!!