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Wrapping up 2016 in the Su Lab

Posted by on Dec 29, 2016 in research, staff-scientist, Su lab, Su lab members | 0 comments


There are a LOT of projects going on in the Su Lab–so many, that it’s hard to keep track of them all.

By now, I’ve posted year-end summaries for some of the major projects in the lab including:
MyGene.info: MyGene.info 2016 Year-end review
MyVariant.info: 2016–More incredible for MyVariant.info than MyGene.info
Gene Wiki / WikiData: 2016–A busy year for Gene Wiki and WikiData

And additional summaries are expected to come soon. The year-end summary for Mark2Cure will be posted tomorrow, and the BioGPS 2016 summary will be shared early in January.

But those are our major projects. Our lab has its fair share of collaborative projects, newer & not-yet-as-popular research tools. As with any academic research lab, we’ve also had our fair share of member changes in 2016.

Member changes in 2016
Moved on 2016.06.21 – Jennifer Fouquier
Moved on 2016.07.01 – Sandip Chatterjee
New member 2016.04.04 – Sebastien Lelong
New member 2016.05.01 – Mike Mayers
New member 2016.06.07 – Núria Queralt Rosinach
Member Upgrade 2016.12.01 – Greg Stupp has been promoted from postdoctoral research associate to staff scientist! Congratulations, Greg!
(plug alert) If you think what we do is cool, have some serious programming chops and want to join our team, ping us! (end plug)

Milestones reached by other projects in the lab
Branch
-2016.06.24: Branch Paper published (Branch: an interactive, web-based tool for testing hypotheses and developing predictive models)
 
CryoEM
-2016.04.04: Jake’s CryoEM project officially launches on the Zooniverse
 
Knowledge.bio
-2016.02.26: Implicitome paper accepted (The Implicitome: A Resource for Rationalizing Gene-Disease Associations)
-2016.05.26: Knowledge.bio paper on biorxiv: Knowledge.Bio: A Web application for exploring, building and sharing webs of biomedical relationships mined from PubMed
 
Science Game Lab
-2016.06.21 – Press release: Solving science questions by playing games
-2016.06.21 – News article: Science Game Lab to be a central hub for scientists and gamers
-2016.06.21 – Science News Release
-2016.06.23-24 – Ben at Games for Change Conference
-2016.09.16 – Margaret on Science Friday mentioned SciGameLab

Looking forward to how these projects and more develop in 2017. If you have time, try them out and let us know what you think! Feedback is a crucial part of the improvement process.

2016–More incredible for MyVariant.info than MyGene.info

Posted by on Dec 28, 2016 in myvariant.info, myvariant.py | 0 comments

As mentioned in MyGene.info’s year-end review, the team behind both services have been very productive. In addition to all the work they did on MyGene.info (and the back-end/BioThings services behind both MyGene.info and MyVariant.info, they made the following improvements to MyVariant.info this year:
-2016.01.06: ClinVar data structure overhauled

-2016.01.18: ClinVar data updated
-2016.07.18: Support for GRCh38/hg38 added

-2016.08.22: Python client updated to v0.3.1
-2016.08.25: Additional ExAC data added/updated

-2016.09: Starting this month, ClinVar data is updated on MyVariant.info on a regular basis.
-2016.10.03: https enabled

-2016.11.30: API status added to site

Also as mentioned in the year-end post for MyGene.info, there were two particular resources that we very excited about:

First, CIViC, which had been using MyGene.info, but recently incorporated MyVariant.info
img http://sulab.org/wp-content/uploads/2016/12/Obi-tweet.png

Second, MyGene2, which is one of six finalists for the Open Science Prize and will potentially impact researcher work and rare disease patient lives alike. Note- Voting for the Open Science Prize is open until January 6th, so you can still vote for MyGene2.

Before we get to the best thing about 2016 for MyVariant.info, here’s what the MyVariant team has been up to in terms of spreading the word about this service.
-2016.01.22: Chunlei gave an update for Heart BD2K technical conference call

-2016.03.29: The paper for Mygene.info/MyVariant.info was accepted to Genome Biology
-2016.04.05: Kevin presented at ISCB’s NGS 2016 conference

-2016.05.10: Corresponding press releases were published to Eureka Alert and Science Daily
-2016.05.25: MyGene and MyVariant were featured in a post on the Genome Biology blog
-2016.05.30: Chunlei was interviewed for Rarecast podcast about the services

-2016.06.09: The MyGene/MyVariant services were invited for a guest post on the Elasticsearch blog
-2016.07.10: Kevin did a poster presentation at ISMB 2016

-2016.07.12: Chunlei also presented at ISMB 2016
-2016.11.29: Chunlei presented at BD2K AHM 2016

-2016.11.28-30: Kevin presented a poster at the same meeting

Finally…MyVariant.info broke the record on usage. In just two years, MyVariant.info went from having just a fraction of the usage that MyGene.info had, to having about double MyGene’s traffic. For 2016 (as of December 22nd), MyVariant.info had almost 116 Million sessions according to google analytics.

MyGene.info 2016 Year-end review

Posted by on Dec 27, 2016 in BD2K, BioGPS, mygene.info, mygene.py, publications | 0 comments

It has been a busy year for the MyGene.info team as they worked to apply the lessons they learned in building MyGene.info and MyVariant.info towards a BioThings framework, and the generation of additional services. At this rate, 2017 is on track to be a very interesting year.

In 2016, aside from all the BioThings improvements happening behind-the-scenes, MyGene.info saw a number of improvements including:
-2016.07.07: API updated to v3

-2016.08.18: Python Client Updated to v.3.0.0
-2016.08.25: ExAC functional constraint scores added

-2016.11.30: API status added to site

Even more exciting was the incredible progress made by other groups that use MyGene.info’s service, especially CIViC and MyGene2.

Clinical Interpretations of Variants in Cancer (CIViC) is an open data resource which demonstrates the power/utility of open data and crowdsourcing for cancer variant annotations. In addition to having a user-friendly interface that encourages community cancer variant annotation, the brains behind this valuable bioinformatics resource also committed to open data by switching to public licensing.

MyGene2 is simultaneously a means for crowdsourcing information on gene variants and a valuable matchmaking tool for the rare disease community. The site’s ingenious use of open data for both researchers and patients alike have made it a finalist for the Open Science Prize (and if you can vote for it to win here)

2016 saw a large increase in MyGene.info usage which happily means that other researchers are finding the service useful and hopefully making progress in their important work. According to google analytics, MyGene.info’s user increased to ~51 Million requests this year–over double the 19.2 Million recorded.

Other than the incredible work (done by others) using MyGene.info, the team has been busy this year sharing about their efforts:
-2016.01.22: Chunlei presents update for Heart BD2K technical conference call

-2016.03.29: MyGene.info/MyVariant.info paper accepted to Genome Biology
-2016.04.05: Kevin presents at ISCB’s NGS 2016 conference

-2016.05.10: Corresponding press release to Eureka Alert and Science Daily
-2016.05.25: Genome Biology blog post

-2016.05.30: Rarecast podcast about mygene.info
-2016.06.09: Elasticsearch blog post

-2016.07.10: Kevin’s poster presentation at ISMB 2016
-2016.07.12: Chunlei’s presentation at ISMB 2016

-2016.11.29: Chunlei’s presentation at BD2K AHM 2016
-2016.11.28-30: Kevin’s poster presentation at BD2K AHM 2016

Here’s looking forward to an exciting 2017…we can’t wait to see what you do!

2016 – A busy year for Gene Wiki and WikiData

Posted by on Dec 26, 2016 in big data, biocuration, conference, Gene Wiki, poster, presentation, publication, semantic wikipedia, wiki, Wikidata, wikipedia | 0 comments

I knew it! Last year, I struggled with the year-end post for the Gene Wiki/WikiData (AKA the Gene WikiData) project because the Gene WikiData team was incredibly active. I learned my lesson, and attempted to better track their activity earlier this year with a running tally. Still, the Gene WikiData team was so productive, I still had trouble keeping up with everything they did! They’ve been busy on this project–so much so, that it makes more sense to list their presentations, papers, slides; as opposed to trying to actually describe everything they’ve done this year. So here it is (and I’m probably missing things here and there), a non-exhaustive list of the Gene WikiData team’s activity (and this is only the activity of the project members here in La Jolla). I can’t even begin to cover the crazy amount of work the team members outside of La Jolla have put into this project.

You can see what they’ve done yourself by inspecting the linked, papers, presentations, slides:

Want to help? Here’s a really quick/easy way to do so: Join the WikiData property proposal discussion on Natural Science properties. The team has been requesting new properties in order to add/expand the information in Wikidata so it can become more useful. Properties need plenty of discussion and refinement in order to be approved, so chime in!

Merry X-mas and Happy Holidays

Posted by on Dec 23, 2016 in citizen science, crowdsourcing, games, mark2cure, press | 0 comments

We just have three quick pieces of news to share:

  1. NIH/NCATS which funds our research has decided to do a feature story on Mark2Cure. This would NEVER have happened without your contributions to the project, so THANK YOU! You can find the feature here: https://ncats.nih.gov/pubs/features/citizen-science
    (For those of you who have sent us bug reports or helped us with Ux testing, THANK YOU many, many times over. We’re still trying to fix the issues you’ve reported, but we’re definitely working on them.)
  2. Mark2Cure has been listed on a new citizen science gaming directory website. The site is a nice new resource for information on citizen science games, and we’ve been very excited about its launch. Hopefully it will integrate with Science Game Lab in the future so that even the act of submitting reviews/sharing about citizen science games will be rewarded/gamified.
  3. A few pictures from our Secret Santa event have come in. If you’ve already received/opened your Secret Santa gift, please be sure to send a captioned picture so we can share it with your Secret Santa.
    http://sulab.org/wp-content/uploads/2016/12/Secret-Santa2.png
    http://sulab.org/wp-content/uploads/2016/12/Secret-Santa-pix01.jpg

Birthday Wishes for Bertrand

Posted by on Dec 9, 2016 in citizen science, community intelligence, crowdsourcing, mark2cure | 0 comments

The Might family has been an incredibly moving proponent of precision medicine, citizen science, and rare disease. Thank you for what you’ve done for Mark2Cure and the fields of health and science. We wish Bertrand and his family health, happiness, and prosperity in the upcoming year.

In case you haven’t noticed, we’ve carved our blog out from our lab’s main blog sulab.org and will serve it up directly on our site at mark2cure.org/blog. If would like to write a post to share with the Mark2Cure community, let us know! If you have recommendations, or if there are things you’d like to see discussed on our blog, contact us!

This week, Mark2Cure hosted the @IamCitSci twitter account to share what we learned to the rest of the citizen science community. For details, see our storify.

Lastly, thank you for your patience and a HUGE THANKS to those of you who have taken the time to report bugs in the system via email, posting on the talk pages etc. We really appreciate it very much, and are working to resolve them as quickly as possible.

Happy Thanksgivings Mark2Curators!

Posted by on Nov 23, 2016 in citizen science, community intelligence, crowdsourcing, games, mark2cure | 0 comments

It’s still a little early, but we wanted to wish you well before the rest of your week got hectic with all the Turkey-day goodness. Since the project started, we’re grateful to have had the chance to learn and be inspired by you. For those of you who have taken the time to write to us, we’re awed by how driven, analytical, humorous, creative, and helpful you are–and we wanted some means of sharing that with you.

If only there was some way to send you a gift for the holiday season…
…given our experience with citizen science, maybe we can crowd-source it?…

And that’s how we came up with the Mark2Cure Secret Santa! Keep an eye out for our newsletter in your email inbox for more details on how to sign-up/participate.

New Mission Available!
When an NGLY1 researcher heard about what you all were doing, she wondered if the community had found anything on her gene of interest. Help search for clues on this gene in our new mission.

Your comments matter!
With complex programs, something is bound to get broken when code is updated, and it would be impossible to find and squash all the bugs, if users didn’t report them. If Mark2Cure gets wonky for you, we’d LOVE to know! Post to the talk pages, or send us an email. We can’t improve without you!

Wikiconference North America

Posted by on Oct 8, 2016 in collective wisdom, community intelligence, conference, Gene Wiki, Wikidata, wikipedia | 0 comments

Wikipedia is one of the most widely used and freely accessible knowledgebases. As one of the largest, crowdsourced resources, many researchers are engaged in making the Wikimedia platform more useful in scientific research—including researchers from our lab here at The Scripps Research Institute. If you’re interested in how Wikipedia and Wikidata are being used in science, you should check out the Wikiconference, happening today through Monday. Registration is free (or $10-$25 with food included). More details here.

Three members of the Su Lab will be presenting their work on pushing the boundaries of how Wikidata can be used in academic research.

First up is Tim. Tim will present his work on developing a microbial specific semantic data model in Wikidata modeling bacterial species, genes, proteins, diseases they cause, and drugs that treat them. He’s part of the 1:00-3:00pm session today in the Clark Room at the San Diego Central Library. Learn more.
Tim’s presentation slides can be found on figshare.
Recording of Tim’s presentation on youtube.

Both Greg and Sebastian are scheduled to present during the 3:30-5:00pm session today, at roughly the same time too! Fortunately, the conference organizers have plans to record the talks, unfortunately the quality of the video recordings tend to vary greatly.

Greg will present on a Cytoscape browser he developed using the Wikidata SPARQL endpoint. This allows him to combine a powerful way for pulling more complex information from Wikidata with a useful method of visualization. Greg will be presenting in the Shiley room on the 9th floor of the library. Learn more.
An early version of his slides are available on google drive.
Recording of Greg’s presentation on youtube (pending)

At the same time, Sebastian will be in the Clark room to present his work on adding Drug and chemical compound items in Wikidata as a data source for Wikipedia infoboxes. Sebastian played an important role in adding gene and protein items into Wikidata which allowed Gene Wiki infoboxes to pull from Wikidata. Learn more.
An early version of his slides are available on slideshare.
Recording of Sebastian’s presentation on youtube.
 
2016.10.09 update – links to the slides for their presentations have been added. Video of their talks is pending.
2016.10.12 update – link to recording of Tim’s presentation added.
2016.10.19 update – link to recording of Sebastian’s presentation added.

Mark2Cure Pro-tip #2- Verifying your hunch

Posted by on Oct 7, 2016 in citizen science, crowdsourcing, mark2cure | 0 comments

In Mark2Cure, it’s almost guaranteed that you’ll encounter words you’ve never seen before. Often times, you can use the context to infer whether or not that term should be marked. Other times, the abstract may be just too jargon-laden or poorly written to make that determination. How do you determine whether or not to mark a term under this situation?
Aside from tips you may have picked up from other Mark2Curators via the talk pages (see pro-tip #1), here’s how a few of our Mark2Curators have approached this problem.

#1 – Revisit the rules: The rules for each concept/entity recognition task are linked via the colored boxes at the bottom of the task page.

Clicking on any of the colored boxes (‘Disease Concept’, ‘Genes Concept’, or ‘Treatments Concept’) will take you to the instructions page which details what you should mark

Clicking on any of the colored boxes (‘Disease Concept’, ‘Genes Concept’, or ‘Treatments Concept’) will take you to the instructions page which details what you should mark

Because many things in biomedical research are related it can be tempting to mark terms that are related to the concepts even if they’re not mentioned in the instructions. For example, specific gene variants may appear in the text but gene variants are not listed in the instructions. As tempting as it is, you should refrain from marking the gene variants and try to stay as close to the rules as possible.
genes-instructions

#2 – Use the search button. The last term of phrase you highlight is captured and becomes the default terms for the search button at the bottom of the task page. Once you’ve highlighted something, click on the blue ‘search’ button on the bottom to search the terms you just highlighted. You are also welcome to look up terms for the Concept/entity recognition task—in fact, we encourage you to do so! We’re big fans of learning, and you will often learn from whatever you bother to look up! The instructions page also contains links to concept-specific databases which may be helpful, but Wikipedia is also a great resource to search.

#3 – Reach out. Talk pages are a great place to have doc-specific questions answered, and posting your questions to the talk pages helps the entire community so we can learn together! You can also contact us by posting on twitter, facebook, Wikia, or via email. Please note, facebook and Wikia are currently the slowest way to reach us, though we’ll try to be better with them. Although we may not have definitive answers for all your questions (by nature, language has ambiguity, and sometimes that makes it possible for multiple choices to be correct), we’ll try to at least provide guidance wherever you’re stuck.

Mark2Cure Pro-tip #1

Posted by on Sep 23, 2016 in citizen science, collective intelligence, crowdsourcing, mark2cure | 0 comments

As a citizen science project, Mark2Cure has been very fortunate to recruit a number of volunpeers who have grown to become experts at the concept recognition task and provide a lot of useful feedback, comments, and suggestions. While we encourage you to explore and use the site in the ways that work best for you, we would like to share some of the great tips that users have shared with us. Without further ado, here is our first user pro-tip.

Pro-tip #1 – Using the talk pages to learn together
Upon the completion of a doc, you will be presented with a feedback screen which shows what your partner has marked, and the option to visit the talk page for that doc.

The talk page button is right next to the 'Next Doc' button on the feedback screen.

The talk page button is right next to the ‘Next Doc’ button on the feedback screen.

If there was anything in the document that you felt was confusing or unclear (in terms of whether or not it should be marked), someone else probably felt the same way you did. If you click on ‘Yes, Let’s Talk’, you may find that your question has been asked and learn from the answer; or you can post your question there so that others will learn from your question.

If you’re worried that your question has been asked elsewhere, DON’T worry about that! Each talk page is viewable only by users who have contributed to that doc. This means that duplicate questions are welcome as they increase the likelihood new users will encounter them.
On the talk page itself, there are several ways to check your work.

First is in the comments that users submitted:

Comments and questions submitted by users may have very useful info!

Comments and questions submitted by users may have very useful info!

As seen here, this user has offered some very useful background information about some terms in the text.

Secondly, you can see how other users marked this doc and learn off them by scrolling over the numbers at the top of the talk page.

Different users may mark different terms in the text. Pay special attention to terms marked the same way by multiple users.

Different users may mark different terms in the text. Pay special attention to terms marked the same way by multiple users.

By looking at how other users marked the doc, you can get an idea on what annotations the community agrees should be marked.

If you dislike scrolling through the user annotations, you can also get a feel for what the community marked by looking at the frequency table below. The table exhibits the top 20-25 most frequently marked terms for each concept type.

The frequency table gives you a quick way to see the terms that were marked by people who have also completed this doc.

The frequency table gives you a quick way to see the terms that were marked by people who have also completed this doc.

Lastly, if you’re wondering why the majority of users marked something differently than you did, or if you just have doubts about what you’re doing, you are welcome to post about it! We will always try to respond in a timely fashion, but an amazing Mark2Curator may just beat us to it!

A big thanks to everyone who has posted to the talk pages for helping to improve the learning opportunities in Mark2Cure

A big thanks to everyone who has posted to the talk pages for helping to improve the learning opportunities in Mark2Cure

If you’d like to chime in on a discussion about a document you’ve contributed to before, click on the ‘Talk’ link at the top right corner of your dashboard header. This will show you the docs that you’ve done which are under discussion. If a doc you’ve done doesn’t appear, it’s likely because no one has discussed the doc. If another users begins a discussion on a doc that you’ve completed, it will appear in your list.

Special thanks to ckrypton for responding faster than I do on some of these, and for giving us the idea of this pro-tip!