Coastal Cleanup Day Site Highlight: Paradise Creek

This year’s Coastal Cleanup Day is set for Saturday, September 16th from 9:00 AM – 12:00 PM. One local wetland has benefitted from the work of a dedicated group of volunteers for the last 25 years, and it is once again set to be a site for the annual volunteer effort.

Paradise Creek Educational Park is a public park in the Old Town neighborhood of National City that was designed to increase environmental stewardship and to provide a place of respite in the busy city. Paradise Creek has flowed out to San Diego Bay as part of the Sweetwater River watershed for thousands of years. In 1999, the non-profit organization, Paradise Creek Educational Park Inc., formed to carry out the mission of advocating for and preserving the salt marsh wetlands. Since that year, a group of community members, teachers, students, families, and others have been holding Creek Day cleanups on the last Saturday of every month. 

On this year’s Coastal Cleanup Day, the park will hold a small celebration of the recent completion of work carried out by the City of National City. Come out and take a walk through the new entry way of native plants at 1815 Hoover Avenue in National City. Also, there is a new schoolyard garden that can be visited. Check out the Paradise Creek Facebook page for more information. 

There is still time to register to volunteer at the Paradise Creek site on Coastal Cleanup Day. Head over to to sign up at Paradise Creek or one of the other 100+ cleanup sites in San Diego County for Coastal Cleanup Day and be a part of this international day of action!

Information extraction and the missing Mark2Cure module

In our previous post, we asked readers, 'What is your preferred moniker?'. Here is the response:

Mark2Curator: 36%
Citizen Scientist: 36%
Contributor: 18%
"Anything BUT volunpeer": 10%

Although it may seem a little strange that researchers have been struggling to find an answer to the "What's in a name?" issue for discussing citizen science, this struggle is a deeply representative of some of the important work biocurators do. "What's in a name? A citizen scientist by any other name still makes important contributions"

Researchers need a common vocabulary to be able to coherently exchange information, but settling on that vocabulary--on how that vocabulary is structured is difficult. Without a common vocabulary, it is easy for scientists to miss research that is valuable to their field of study. Although it has yet to be seen how the citizen science research community will settle this issue, in biomedical research, biocurators help with that sort of determination. Biocurators help standardize terms, define the rules governing how terms are classified and how they are organized. In doing so, they facilitate information quality control and exchange. Biocurators do all this and more.

Given that biocurators do very important, very tedious, and often very difficult work, one question we get quite a bit is:

"How is it possible to train citizen scientists to replace such important, skilled researchers?"

But this question is built on a fundamentally incorrect assumption about the goals of Mark2Cure. We KNOW biocurators do very important work, and that one of the most tedious, and time-consuming things that they do is information extraction.

Information extraction can generally be broken down into three tasks:
1. Named Entity Recognition (identifying and classifying words/phrases in text)
2. Normalization (linking that text to an ontology)
3. Relationship Extraction (identifying the relationship between different entities).

We want to train citizen scientists to help with this task, so that biocurators can apply their unique training towards solving problems in biomedical research analogous to the ones we're seeing in the citizen science field.

Since Mark2Cure is a citizen science project, the "What's in a name?" issue applies to us as well. Although our informal poll was only for fun, I was personally very happy with the results for two reasons:

1. I am a fan of wordplay, and I love that many users liked the term Mark2Curator--a term which blends Mark2Cure and biocurator. I love science puns

2. Even if I'm reading too much into it, I like to think that our users picked 'citizen scientist' or 'contributors' because they feel that the help they provide to Mark2Cure is important--because it is.

If you've gotten this far, you are probably one of our many astute readers and may have noticed that information extraction was divided into THREE tasks, when Mark2Cure only has TWO. Where is the third task? Why is it the missing task is the step in between the first and the last task?

The missing task, 'Normalization', is the task in between NER and Relationship Extraction. We started with NER because NER has been well-investigated so there was a solid foundation for us to build upon. We followed with the relationship extraction task because this would allow us to unlock some of the most difficult to access and valuable information in the text.

As for the Normalization's currently in being built by volunteers. Mark2Curators have been helping us investigate NER mappings to different ontologies, and a very talented programmer and machine learning expert has been busy building the Normalization module. But we could use more help. We need feedback on potential interfaces for how parts of the module might work. If you'd like to help with that, answer the poll in our newsletter.

Of note for our U.S.-based Mark2Curators over 65 years of age.

Did you know? US National Park Services has a lifetime pass for seniors that will allow you to enter or park at US national parks for free or at a discounted rate. These passes only cost $10 now through August 27th. After August 28th, the price will go up to $80.

If you enjoy hiking, nature, or plan to visit any of our beautiful national parks, you may want to get your pass while it's still $10. In San Diego, the closest national park where you can purchase one in person is Cabrillo. To find the national park closest to you, visit the NPS's site. If you don't live near a park, but plan on visiting some in the future, you can purchase a pass by mail or online.

Registration Open for 33rd Annual Coastal Cleanup Day

Get registered today at!

Registration officially is open for San Diego County’s Coastal Cleanup Day! While the name Coastal Cleanup Day suggests that this cleanup is all about the beach, many of you already know ILACSD’s volunteer efforts reach far beyond the coast. With eighty percent of marine debris originating in inland areas, at ILACSD we have expanded our Coastal Cleanup Day reach to include both inland and coastal territory. This year, sixty-five percent of the cleanup sites are located inland along rivers, creeks, canyons, and urban areas with the aim to stop debris before it makes its way to the ocean. We even have 3 clean ups happening on the water with kayaks! With 114 cleanup sites last year, volunteers removed 185,000 pounds of debris from San Diego County – the equivalent weight of 10 garbage trucks! Help us remove even more trash and debris and beautify our county by getting registered for this year’s Coastal Cleanup Day on September 16, 2017, from 9:00 AM – 12:00 PM! Get registered now at!

Cut back on waste by bringing your own reusable buckets, work gloves, and water bottle if you have them!

In an effort to reduce waste produced by an event of this size, Coastal Cleanup Day volunteers can pledge to bring at least one reusable item to the cleanup. When volunteers bring their own reusable water bottle, work gloves, and bucket to collect litter, they prevent thousands of single-use bags and disposable gloves from entering San Diego’s landfills. When you register, please consider pledging to bring one of these items with you (or all three)! Once again, we will be having our “Bling Your Bucket” competition for Coastal Cleanup Day. Participants have the opportunity to decorate their reusable buckets showing off their creativity and imagination and submit photos for the chance to win fun prizes and have their picture posted on the Coastal Cleanup Day website for one year! Volunteers of all ages are also encouraged to participate!

Participate in the Sony Photo Contest for the chance to win a Point & Shoot Camera!

The Sony Photo Contest is also returning to Coastal Cleanup Day! While you spend the morning helping to preserve our environment, snap some pictures of all of your hard work! After attending Coastal Cleanup Day, participants can submit their best photo from the event into the competition where the top five finalists will be put to a vote on the ILACSD Facebook page. The winner will receive a Sony Point and Shoot Camera!

We also collect valuable data about the debris collection that helps us understand how we can better prevent litter. Instead of using paper data cards, ILACSD is asking volunteers to download the Ocean Conservancy’s user-friendly mobile data collection app, Clean Swell, onto their smartphones as another way to cut back on waste.

Bring the whole family and join us for Coastal Cleanup Day on September 16th!

Not only will we be removing litter on Coastal Cleanup Day, the event also includes beautification projects such as graffiti removal and replacement of invasive species with drought-tolerant alternatives. Volunteers who signup will work with ILACSD to preserve and enhance San Diego for current and future generations to enjoy. Leading the way to a zero waste, litter-free, and environmentally engaged San Diego region, ILACSD encourages all community members to take action in their neighborhood by joining us on September 16th. Registration information and details regarding Coastal Cleanup Day can be found at

Join Mark2Cure and Dazzle4Rare

From August 13th to August 20th, Mark2Cure will be participating in the #Dazzle4Rare campaign to raise awareness for rare diseases. Did you know? About 10% of the population lives with a rare disease, and roughly 50% of rare diseases don’t have any sort of disease-specific foundation to support or research those diseases. See more interesting statistics about rare disease at Global Genes.
If you have a rare disease story you would like us to highlight for the campaign, please get in touch!

What's new in Mark2Cure?
The EDEM1 Entity Recognition mission is over 95% complete, please help us finish it so we can launch the next one. If it seems like we’ve been quiet lately it’s because we’ve been preparing for some major updates. If you’re curious about what’s in the pipeline or would like to preview/provide feedback for potential future interface designs, we’d LOVE to hear from you! Your feedback is how we improve! If not for our many marvelous Mark2Curators providing constructive criticism, Mark2Cure would be a clunky and more difficult to use platform.

Speaking of our volunteers, citizen scientists, participants, contributors, volunpeers, and Mark2Curators…there was an interesting discussion earlier today within the citizen science community on the best way to address the amazing people who help make science happen. In fact, a bunch of researchers even wrote an interesting paper about the pros and cons of different terminology

Which takes us to our current poll.

Lastly, there is an ongoing effort to increase discussion, collaboration, and cooperation within the citizen science (or whatever you wish to call it) community. This has led our friend Alice to introduce #CitSciStories. You may think that your contributions to science in your spare time are no big deal, but from the perspective of the researchers who rely on these are amazing! Inspiring! Awesome beyond words! We love what you do and we love learning from you and getting to know you. If you'd like to share your story and inspire others to help science, please get in touch with Alice (@PenguinGalaxy). You can learn more about the #CitSciStories effort, here.