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A look back at 2016 for BioGPS

Posted by on Jan 5, 2017 in annual summary, BioGPS, publication, Su lab, usage stats | 0 comments

BioGPS opened 2016 with a publication in Nucleic Acids Research, right after the New Year holiday. Throughout the year, new designs for the site were being created, reviewed, adjusted, reviewed, adjusted, and more review/adjustments in anticipation of a site redesign for 2017. A Plugin registration Blitz was held in March and April; followed by a Plugin Review Blitz in May. The BioGPS spotlight series was also restarted, with spotlights on BGEE, Intermine, and other Intermine-related plugins.

There were ~910,000 requests made to BioGPS in 2016. Requests to BioGPS peaked in March and at the lowest in December.

Most searches involved human and mouse genes by far, though thousands of requests were also made for other model organisms.

Discarding the default search genes, CDK2, the top 10 most frequently requested genes were:

  1. GAPDH
  2. TP53
  3. Trpm4
  4. EGFR
  5. CD274
  6. KLF6
  7. TNF
  8. ACTB
  9. MYC
  10. AKT1

Given their use as controls, the appearance of GAPDH and ACTB in the top 10 list, wasn’t too surprising. Out of the top 10 genes searched in BioGPS, seven had corresponding Gene Wiki articles that were not stubs. The three genes with incomplete Gene Wiki articles were ACTB, Trpm4, and KLF6. If you feel like sharing what you know about these three genes, consider editing their corresponding Wikipedia articles.

BioGPS users may not have been making as many requests in 2016 as they made in 2015, but in 2016, they still published about 72 articles citing the 2009 paper on BioGPS.

A look back at 2016 with Mark2Cure

Posted by on Dec 30, 2016 in citizen science, community-annotation, mark2cure | 0 comments

Happy New Year!!!

Thank you for contributing to Mark2Cure with your annotations, comments, questions, bug reports–and general feedback. You’ve made the Mark2Cure project an amazing project to work on and we are so grateful that you found us.

Many of you have been kind enough to report bugs and we are definitely trying to fix them. However, we only have one research programmer working on Mark2Cure; hence, many of these issues will take time to resolve. Our programmer will be unavailable in January, so we very much appreciate your patience in the new year. If you have programming experience and would like to help tackle some of these issues, please check out our repository on github (Mark2Cure is open source).

We have some new entity recognition (ER) missions available which you can directly access from the links below:
BiP https://mark2cure.org/group/bip1/
CLN3: https://mark2cure.org/group/CLN3/

We are working to get the relationship module to properly display available tasks again, so hopefully you’ll see the queued relationship docs in your dashboard sometime in the near future.

An abbreviated timeline for Mark2Cure in 2016

-2016.01.27 – Beta experiment paper submitted
-2016.02.26 – The Mark2Cure team meets NGLY1 families.

-2016.04.16 – Citizen Science Day Expo organized by Mark2Cure and the La Jolla Public Library
-2016.04.15 – 2016.04.16: Mark2Curathon

-2016.05.21 – Mark2Cure Campaign for NGLY1 anniversary/launch of relationship app
-2016.06.01 – Mark2Curathon #2
-2016.06.07 – Andrew spoke at library for SD citizen science lecture series at the library

-2016.06.09 – Andrew’s interview on Patient Empowered
-2016.06.16 – Beta experiment paper accepted for publication

-2016.06.21 – Jennifer (research programmer) leaves the Su Lab
-2016.06.22 – Mark2Cure added to NIH-sponsored biomedical citizen science site
-2016.08.15-2016.08.21 – Mark2Cure joins the #dazzle4rare campaign

-2016.09.22 – Andrew speaks at Personalized Health in the Digital Age conference
-2016.10.17 – Andrew presents about Gene Wiki/Wikidata and Mark2Cure at TSRI seminar

-2016.12.04-2016.12.09 – Mark2Cure hosts @IamCitSci on twitter
-2016.12.21 – Beta experiment paper proof submitted

-2016.12.22 – NIH NCATS featured story about Mark2Cure

I really look forward to hearing from, learning from, and growing together with you and the Mark2Cure community in 2017. Be safe and have a happy, healthy, and exciting new year!

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.