Wednesday, 18 November 2015

Mark 2 cure

I found the website the other week, and I finally found a few minutes to give this a try. The basic premise of the site is that it shows you a paragraph from a medical paper and you have to highlight terms to do with;

  • Diseases
  • Genes
  • Treatments

They give you a bit of on-line training, and then you're off, headlong into reading text and marking them up. The objective is to allow researchers to seek out common connections between papers in order to examine potential relationships. Their focus is on rare disease literature, hence my interest in this. I really like this idea.

Essentially I've been reading the abstracts from exactly this type of paper in order to inform me (and this blog) about HSP, so it struck me as a good idea to use that skill to better use. Now, the issue will be finding the time to do this. I suspect I'll be in-and-out for short times here and there. My first paper took some 5mins to do, but I think its the kind of task which will get easier with repetition.

This text, from their website says what they're on to:

"Mark2Cure works by teaching citizen scientists to precisely identify concepts and concept relationships in biomedical text. This is a task that anyone can learn to do and can perform better than any known computer program. Once these tasks are completed, advanced statistical algorithms take the data provided by the volunteers and use it to provide scientists with new tools for finding the information that they require within the sea of biomedical knowledge.
For example, scientists often have questions like “How might one disease, say Ebola, be related to another disease, say Dengue Fever?”. Such connections may not exist in any one scientific article. By specifically identifying what diseases (and perhaps other concepts) are represented in each article, it may be possible to find hidden connections. These hidden connections form the basis for most important new discoveries.
Mark2Cure is currently on its NGLY1 Campaign. The goal of this campaign is to organize information for researchers studying NGLY1 deficiency. Mark2Curators already demonstrated in the beta experiment that citizen scientists and volunteers can and are willing to help. Now we must demonstrate that the help given by Mark2Curators can make a difference for researchers studying NGLY1.
N-Glycanase 1 deficiency is an extremely rare genetic disorder with less than 40 known cases worldwide. As of April 2015, there were less than 15 articles on this disease indexed in pubmed; hence, researchers need to investigate potentially related literature in order to find more information. Since many of the symptoms of NGLY1 are observed in other disorders the number of potential related articles can easily balloon into an unmanageable number. Working with and NGLY1 researchers, Mark2Cure has identified a set of 10,000 documents of interest. Your help is needed to organize information in this set of docs. Visit to learn more about this extremely rare disease."

Friday, 6 November 2015

Spatax Network Map

My first venture into online HSP mapping...

I wanted to see the spread of researchers in HSP. I thought it would be reasonably straightforward to create a map of the members of the Spatax Network, and here is that map!

So, this takes the info from here: and by a process of looking up addresses through Google, popping those addresses here and then importing that data to the ArcGIS online system here

I was able to create this map in a couple of hours. Caveats - I believe those locations to be roughly right, based on that data route.

I like the heatmap way of looking at things, and it is immediately obvious that:

  • There's a large chunk of expertise in Paris
  • No-one in the USA, Australia or the far east are involved in the network.
I have plans to expand this map according to the PubMed database of papers, but thats going to be a fair way away as there will be many more addresses to process.