Coremine Medical

www.coremine.comBuild Your Biomedical Mind-Map

byDag Are S. Hov (PubGene AS)

Karl Øyri (OUS Intervention Centre)Oslo, Norway

PubGene Background• PubGene was founded in 2001

• Founders from NRH - Norwegian Radium Hospital and NTNU - Norwegian University of Science and Technology (Jenssen, TK et al., Nat. Genet., 2001)

• Original problem: Hjelp structure huge data sets in breast cancer microarray research

• Pioneers in the use of text-mining and NLP to index Medline records linking genes and diseases

• US patent for search algorithms and core technology in 2007

Coremine Medical• Powerful and flexible biomedical search tool • Finds relevant connections between medical concepts such as

diseases, drugs, procedures, symptoms, genes, and medical experts

• Easy visualization and navigation

• Help save time, explore, comment and share

• Strong bonds to Oslo University Hospital (OUH) for research and relevant use cases, e.g. The Intervention Centre and integration of clinical data warehouse

Case study

• You are a surgical resident taking part in a group of colleagues working with the subject ‘pancreatic diseases’.

Goal for the day

• You want to find, explore and share information using the advantages of Coremine Medical.

• Also, you would like to search through relevant electronic patient journals from the integrated clinical data warehouse of your hospital.

Enter the name of the disease ’Pancreatic Diseases’ and pick from the suggestions provided by Coremine.

1) Continue to build your input list,

2) deselect any categories you are not interested in or

3) click ’Explore’ to create your result network.

•Categories of concepts related to your input through PubMed records are gathered in stacks

•Click a stack to view related concepts from categories like anatomy….

…MeSH (Medical Subject Headings)...

…procedure...

…and drug.

•Bookmark the disease concept into ’My Page’ to keep it for later

•Login needed

•Not a user yet?

•A quick register will suffice (no charge)

•Staying logged in will enable complete search history

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•Bookmark set after registration completed

•All bookmarks are stored under My Page > Bookmarks

Logging in also enables setting the email alert on new articles

All ten synonyms are used when linking the disease to articles, as is the case with all concepts in Coremine.

General info on the disease is fetched from the U.S. National Library of Medicine.

Hierarchy info provides hyperlinks to generate networks on similar diseases.

’Extracted knowledge’ section shows you more complete lists of the concepts related to you query.

’Biomedical experts’ contains clickable names of PubMed authors most often appearing in articles where Coremine finds ’Pancreatic Diseases’ (including synonyms).

’Drugs’ shows related drugs and the ’Load more’ link opens a continous more complete list of drugs in a falling degree of relevance.

•The related concepts from ’Extracted knowledge’ can be added to the network.

•Interact by mouse-click

Read the general drug info and click ’Add to network’ to mix the drug with the disease network on the left.

•You may add to the network as many related concepts as you want.

•Here, concepts from procedure and anatomy are also added.

After spending time on modifying the network, you may want to save it with its excact layout.

You find the saved network under My Page > Bookmarks

•You can also click a connection to focus on two concepts.

•The right part of the screen now displays info relevant to both concepts

To create a network where the added concepts are used as normal input along with the disease, click ’Click to modify your search’.

If nothing more needs tweaking, hit ’Explore’.

The related concepts in the network are now important to all four input items.

•The network has now become something you might want to spread to your friends or colleagues.

•Using the ’Share’ button on the upper right, you can easily share using email or social media.

Selecting Twitter, the URL to the result network is sent to your followers.

Your followers can click the Twitter link to create the same network you just viewed.

Clicking the Twitter link will open a new window/tab in a browser with the same result network you just shared.

•In your own result view, you can use the session history below the network to get back to a previous search result.

•Let’s go back to ’Pancreatic Diseases’

•Below the related concepts, you find ’Related articles and hits’ where Coremine gets information from external sources.

•Of the more authorative sources, you first find the recent PubMed articles

•You can bookmark any of the articles.

•As for the bookmarks you set for the disease and the network earlier, the ones for documents also end up in ’My Page’.

•Another authorative source is Clinical Trials

•The heading of any hit under ’Related articles and hits’ is hyperlinked to the source.•Bookmark any trial you want to get back to.

•Bookmark any hit from any supported source, like Wikipedia, Google Image and YouTube…

Share the bookmarks you have gathered from My Page to the Coremine group ’Pancreas group’, where you are a member.

Bookmarks you share to the Pancreas group can be found and launched by the other group members.

Another way you can gather and share info from result pages into groups is using Context Notes under ’User updated content’.

•Your note will stick to the disease in focus.

•Visability set to only a group of users will ensure privacy and notify the other group members.

•Inside the group, you see the note under the ’Context notes’ tab.

•Other members can reply to the note inside the group and in the Explorer result page.

Under ’Group management’ you can invite others to the group by Coremine nick name or any email address.

For any hit under ’Related articles and hits’ you can also leave a comment.

•The comment will follow the hit/document.

•Visibility can be set to the same group as earlier.

The note on the document is then also seen inside the group ’Context Notes’ tab.

Specializing in Pancreatectomy

• Using the Coremine Library tool you want to quickly get an overview of a large set of documents by clustering them (feature in development).

• You will also like to find focused information on an expert in the field.

To perform the clustering inside the Library tool in Coremine, you start by searching for the procedure concept ’pancreatectomy’.

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•In this test example, 1000 articles has been selected from the search result.

•You hit ’Cluster’ to start the clustering of the documents.

The algorithm needs a number of clusters to divide the documents into, and a name for the run.

•The result shows a quick overview of what articles was put into the same cluster and what sentences and keywords are the most important.

•A better formatted overview is found in Explorer by hitting ’Network’.

You save the time to read the articles to find what is the most important content for you:

•Key sentences• The top ranked sentences,

based on the words inside the sentences.

•Keywords• The top five most important

•Cluster articles (121)• The cluster articles can be

bookmarked and commented.

•Extracted knowledge• Coremine supported

concepts found in the cluster articles sorted in categories.

•Returning to the network of ’Pancreatic Diseases’, you open the procedure stack and click ’pancreatectomy’.

•As the focus is now on pancreatectomy, the content of the section at the right changes accordingly.

•You open ’Biomedical experts’ and click the highest ranked expert, ’Büchler MW’ and further follow the link ’Open as a new search’

•The author network shows PubMed authors working with similar subjects as Büchler MW.

•Basis for the similarity is overlapping keyword profile.

•Each profile is built looking at all the concepts found in an author’s articles and how specific these concepts are for these articles compared with all other PubMed articles.

•Green connections indicate co-authorship

•For this expert on ’pancreatectomy’ you get

• Keyword profile – the basis for comparing this author with others

•For this expert on ’pancreatectomy’ you get

• Recent articles – read and bookmark highlights.

•For this expert on ’pancreatectomy’ you get

• Publishing timeline – when was this author productive?

•For this expert on ’pancreatectomy’ you get

• Biomedical experts working with similar subjects – complete list of the authors best matching Büchler’s keyword profile.

•For this expert on ’pancreatectomy’ you get

• Extracted knowledge – the keyword profile sorted in the Coremine categories.

Return to the network for ’Pancreatic Diseases’ using the session search history below the network.

Enterprise Clinical Warehouse Support

• In the following example we show how internal enterprise data can be integrated.

• You reopened the network of ’pancreatic diseases’ from the session history, opened the anatomy stack and clicked the concept ’pancreas’ to focus and search for it in electronic patient journals.

Focus is now on ’Pancreas’

•After scrolling down, you open the section for the hits into patient journals (electronic medical records).

•This section will only be visible inside the specific hospital.

•All patient journals where the phrase ’pancreas’ is mentioned are shown.

•You can bookmark journals.

•You enter a journal by clicking the heading.

Opening the electronic journal you can read about the patient and, in this example, further follow a link to a surgical procedure where the patient had a laparoscopic pancreatectomy performed due to cancer.

•The page opened shows a unique presentation from separate global hospital applications in one context based screen.

•By this you get a unique overview of information associated to the particular case.

•In the laparoscopic pancreatic surgery example the main phases, episodes and adverse events of the procedure are tagged. The tags are displayed as highlights of the surgery, so you get an easy overview of the procedure that can last for several hours.

•The surgery summary text is also indexed, so you can quickly perform a search for another patient journal or create a Coremine network.

•You also get ’macro data’ like vital sign data from the computerized order entry and charting system and images from the PACS system.

•’Micro/atomic data’ are also included exemplified by molecular biology data containing gene sequencing and genome analysis of tumor cells. The molecular data in this example is a result of a pipeline analyzing the output from genome studies on the tumor cells, like the output from 23andme, decodeme etc. The molecular data can be combined with other sources of information (eg. drugs) and provide decision support for individualized chemo therapeutic drugs.

•This bridges the gap between clinic medicine and genomics in a novel way. The case shown here (figure on what tumor cell genes are gained or lost in copy number on chromosome 17) is from real data where the patient got conventional chemo therapy that did not cover the actual oncogenes eventually killing the patient (* Hjortland et al., BMC Cancer, In Press).

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www.coremine.com - Summary

• Sophisticated search application in the public domain facilitating immediate gathering and intuitive presentation of multimedia-based information from substantial publicly available resources.

• Coremine can be integrated with complex clinical enterprise data. The synergy facilitates tailored individualized therapy based on phenotype in a novel way. This contributes to bridge the gap between applied clinical medicine and genomics.