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#WoodsholeBMI Day #5: Visual Semantic Medline

Oh the possibilities with using Semantic Medline. The demonstration of Semantic Medline really engaged the class. I now remember why I LOVE research. You could say it was the pretty colors or just the complete cool geeky way of correlating research. I wish it would have started with the visualization first then went into the details.

So what is Semantic Medline?

“Semantic MEDLINE is a prototype Web application that integrates PubMed searching, advanced natural language processing, automatic summarization, and visualization into a single Web portal. The application is intended to help manage the results of PubMed searches by identifying semantic predications in the citations retrieved.”

And here is what it looks like:


You may not be able to see it from this still photo, but you can actually click into each color line and term to see why it was linked to the original term. This is all done based on the MeSH terms.
In addition to getting the visual image, you can also see the abstract of the article:

This allows you to look at the visual picture of the connection and then go into the details and the data of why it is connected. Now why is this so awesome besides the pretty colors and patterns?

Imagine all the possibilities and the new heights research could reach……

Think of teaching. How this can be used to help students who are more visual learners grasp what cases Alzheimer’s Disease.The professor could do the search and then lead a discussion into the specific nodes, pulling up the literature that supports why it is related to the topic. It could even go into why the literature is reliable or not.

It access an extremely rich data mine of information and extracts it into a visual presentation. It could lead to new discovers of diagnosis, treatment, management, etc.

Genetics. It can show the connection between a gene and a specific disease. For instance, obesity alters the CLOCK gene, the alterations of to the CLOCK gene have the potential to cause cancer. This can be easily shown through the visualization of the MeSH terms in Semantic Medline.

MeSH. I am going to start teaching MeSH using Semantic Medline. Why? People respond extremely well to the visualization. It reminded me of why I enjoy research. It is piecing together a puzzle, and Semantic Medline pieces it together in a gorgeous data rich way. It makes me want to review terms all day long to find connections, determine if it has been written about before, and write articles. It makes me want to long to research (yes I am an odd duckling).

The only sad part is it is not available to all users yet. It is limited to those with a license to UMLS. It is also important to note that it is still in beta testing. So there are still some issues being worked out before it goes live. If you want to have access you will need to request a license to UMLS. It is free, all you have to do is complete a report once a year. So if you want to use this to teach students, do research, or just have fun with the graphics then you will need to sign-up first.
Can you imagine other ways it can be used? My head is still reeling with all the possibilities.

Of course this is all possible thanks to genius people like Marcelo Fiszman, M.D., who is also an excellent presenter. Excellent job!

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