Help us reach our goal so we can help you! | Mark2Cure

Help us reach our goal so we can help you! | Mark2Cure.

Join us now! click here!

If you haven’t seen or don’t have time to watch Andrew’s excellent Tedx talk explaining how Mark2Cure works, here’s a quick summary and brief explanation why we NEED YOU to join us.

It takes about thirty minutes to read one of many articles that get published every thirty seconds! No wonder scientists are struggling to keep up. You can help scientists extract the information they need so they can discover new relationships faster, so they can more quickly move on to test new ideas and find cures for various diseases. Join now!

After this experiment, we will target specific diseases that our beta contributors care about, but our long term goal is to help every domain of disease research that our contributors care about until ALL biomedical research is annotated
After this experiment, we will first target specific diseases that our beta contributors care about, but our long term goal is to help every domain of disease research that our contributors care about until ALL biomedical research is annotated

This post was originally written for Mark2Cure and can be viewed in its entirety here.

How the rare disease community can help Mark2Cure help rare disease research

Join us now! click here!

I used SavingCase’s tweet because it highlights how important the internet has become for connecting people and how people share information. (I might have missed Susannah’s piece if not for that tweet.)

That patient-patient connection is number three in a list by Ilana Jacqueline, who wrote the Global Genes’ Rare Daily piece about empowering moments felt by people living with a rare disease. These patient-patient connections not only provide support, information, and a measure of comfort; they can grow into powerful advocacy groups eventually connecting (and often funding) researchers investigating their disease. In many cases the patient becomes the educator (educating doctors was #4 in Ilana’s list) and expert on what is already known about that disease, but researchers still play an important role in expanding that knowledge base.

This post was originally written for Mark2Cure and can be viewed in its entirety here.

Citizen Scientists Needed to Help Mark2Cure Reach Next Milestone

Mark2Cure letter header

Did you know that a new biomedical research article is published every 30 seconds?! It’s become impossible for researchers to read every paper relevant to their field of research. Mark2Cure allows citizen scientists to help biomedical researchers make research literature more useful. Mark2Cure contributors enable researchers to find the right information faster, uncover new relationships between disparate fields of research, and generate/prioritize new hypothesis faster. We hope to empower citizen scientists to accelerate research on diseases of interest to them. Curious? Join and contribute now!

The Mark2Cure development team has been working hard to get Mark2Cure in shape and have now launched Mark2Cure for our first major beta test. Although Mark2Cure’s current functionality is but a fraction of where we would like it to be, this test is critical to proving that Mark2Cure is worth the development effort. If Mark2Cure does not garner sufficient interest or contributions, it could be dropped before citizen scientists have a chance to make major contributions to biomedical research. For more information on the idea behind Mark2Cure, click here or click here to see the related Tedx Talk

This post was originally written for Mark2Cure and can be viewed in its entirety here.

Wikipedia as a basic scientific reference

Wikipedia is probably the most current, extensive, and accessible knowledge base available. Currently, there are over 10,000 Wikipedia entries for human genes of interest thanks to the Gene Wiki project and the contributions of the dedicated and altruistic Wikipedia community. Unfortunately, many of these articles are out-of-date or are just stubs in desperate need of content. If you are in science and truly believe in open access, why not contribute?

It may be a bit intimidating to edit a scientific Wikipedia article if you’ve never done it before, but it is actually quite easy! In the interest of encouraging wiki contributions from those in STEM disciplines, here’s a 10 step walk-thru for editing a Wikipedia entry:

1. Register/Login – No, it’s not necessary for you to do this step in order to edit a wiki, but you should just so you can be proud of all the wiki pages you improve in the future
2. Go to a wiki page in need of an update. Look up your favorite gene in wikipedia and help improve it!
3. Click on the ‘edit’ tab in the top, right corner of the page
01. Click on Edit
4. Edit the content of the page. To add a section break, use double equal signs (eg- ==Section== )
5. To add a journal reference, click on ‘cite’ in the navigation bar, click on the ‘templates’ drop-down menu and select ‘cite journal’. Enter the PMID of the article into the ‘PMID’ field and click on the search (magnifying glass) icon to auto-populate the other fields.
02. click on PMID search icon.
6. If you plan on using this reference more than once, assign it a reference name so you can insert it again later.
03a. Assign a reference name
7. Click ‘insert’ to insert the reference
8. When using a previously inserted/named reference again just use the ‘Named Reference’ (clipboard) icon.
03b. Use a previous named reference
9. Make a note about your changes in the ‘edit summary’ field, and then preview (optional) and save your edits.
04a. save your edits
10. If you make a mistake, you can easily revert the edits you made. Just go to the ‘view history’ tab. Find the changes you need to revert and click ‘undo’.
04. revert a change

That’s it! What are you waiting for?

Need more editing tips? Check out the Gene Wiki portal and learn more ways to help improve Wikipedia as a knowledge base for human genes of interest.

Mark2Cure 1st major experiment to start soon

The results from Mark2Cure’s limited holiday test were promising. Special thanks to all the participants! Mark2Cure is now gearing up for its 1st major experiment to demonstrate that citizen scientists (like yourself) CAN and WILL use Mark2Cure to help biomedical researchers. Every minute you spend, every contribution you make in Mark2Cure will be extremely important for the future of this project. Without your contributions, Mark2Cure cannot move forward!

This post was originally written for Mark2Cure and can be viewed in its entirety here.

Wikidata can change the way citizen scientists contribute

If you’ve been following discussions on citizen science, you’ve probably realized that researchers are generating so much data, that they need extensive help for parsing the data and making it more useful. For many projects, citizen scientists have answered the call for help–making enormous contributions. Sure, there was a recent study which found that “Most participants in citizen science projects give up almost immediately”, but as Caren Cooper pointed out:

Just by trying, citizen scientists made important contributions regardless of whether or not they chose to continue.

But I digress...
But I digress…

What does citizen science have to do with wikidata? On that matter, what the heck is wikidata?

Much of citizen science contributions come in some form of data collection (observations; sample collection; taking measurements, pictures, coordinates, etc) or classification (identification, data entry, etc) but few citizen scientists participate in analyzing the data.

From ‘Surveying the Citizen Science Landscape’ by Andrea Wiggins and Kevin Crowstone (click the figure to read the paper, it’s open access)

Wikidata (a linked, structured database for open data) may serve to change that. Naturally, wikidata relies on the contributions of volunteers; however, the data incorporated into wikidata is open for anyone to use. In fact, wikidata is begging to be used and citizen scientists and citizen data scientists are welcome to use it. An international group of has already put together a grant proposal (open/crowdsourced in the true spirit of wikipedia) to make wikidata an open virtual research environment. Dubbed, Wikidata for Research the proposal aims to establish “Wikidata as a central hub for linked open research data more generally, so that it can facilitate fruitful interactions at scale between professional research institutions and citizen science and knowledge initiatives.”

As exciting as this all is, there is a lot of work that still needs to be done for making wikidata more successful. Although it’s open access, it’s still a bit inaccessible due to the lack of clear documentation for new users. It’s not that the information doesn’t exist–there is a ton of information on wikidata available and a lot of neat tools already available and in development. You just have to look really hard for it. Fortunately, the wikidata community is already aware of the key issues that need to be addressed in order to become more successful.

Researchers have already taken considerable effort to make science more accessible by contributing to science-related articles. There are over 10,000 genes already in wikipedia thanks (in part) to the Gene Wiki initiative! It makes sense that wikidata is next. A lot of progress has been made in this arena, but I’ll save that for later.

BioGPS Featured Article – Chemoproteomics reveals Toll-like receptor fatty acylation | The Su Lab

Here’s what you’ll need to know in order to appreciate and enjoy this week’s BioGPS Featured Article – Chemoproteomics reveals Toll-like receptor fatty acylation | The Su Lab.

Palmitoylation is a kind of fatty acylation where a palmitoyl group (derived from palmitic acid see below) is added to specific amino acid residues on a protein (usually cysteine, but some times serine or threonine) Palmitic acid

This post-transcriptional modification of proteins can play an important regulatory role by affecting where the proteins localize, how they interact with other proteins, etc.

Palmitoylation can affect protein localization
Palmitoylation–depalmitoylation cycles mediate inter-compartment shuttling of proteins. By: Yuko Fukata & Masaki Fukata Nature Reviews Neuroscience 11, 161-175 (March 2010)

In spite of playing an important regulatory role, the palmitoyl proteome has yet to be fully elucidated. The researchers behind this week’s BioGPS featured article used bioinformatics to identified over 200 potential palmitoylation targets, including Toll-Like Receptor 2 which plays an important role in the immune response.

The Immune response-TLR signaling pathways from Thomson-Reuters.

Learn more about the researchers, their work, and how they used BioGPS in the feature post and check out their cool findings in their open access article