Coremine Medical    www.coremine.com Build Your Biomedical Mind-Map                  by   Dag Are S. Hov (PubGene AS)Karl ...
PubGene Background• PubGene was founded in 2001• Founders from NRH - Norwegian Radium Hospital and NTNU -  Norwegian Unive...
Coremine Medical• Powerful and flexible biomedical search tool• Finds relevant connections between medical concepts such a...
Case study• You are a surgical resident taking part in a  group of colleagues working with the subject  ‘pancreatic diseas...
Goal for the day• You want to find, explore and share  information using the advantages of Coremine  Medical.• Also, you w...
Enter the name of thedisease ’PancreaticDiseases’ and pick from thesuggestions provided byCoremine.
1) Continue to build your   input list,2) deselect any categories you   are not interested in or3) click ’Explore’ to crea...
•Categories of conceptsrelated to your inputthrough PubMed recordsare gathered in stacks•Click a stack to viewrelated conc...
…MeSH (Medical SubjectHeadings)...
…procedure...
…and drug.
•Bookmark the diseaseconcept into ’My Page’ tokeep it for later•Login needed
•Not a user yet?•A quick register will suffice(no charge)•Staying logged in willenable complete searchhistory
utGTbHggwN             •Bookmark set after             registration completed             •All bookmarks are stored       ...
Logging in also enablessetting the email alert onnew articles
All ten synonyms are usedwhen linking the disease toarticles, as is the case withall concepts in Coremine.
General info on the diseaseis fetched from the U.S.National Library ofMedicine.
Hierarchy info provideshyperlinks to generatenetworks on similardiseases.
’Extracted knowledge’section shows you morecomplete lists of theconcepts related to youquery.
’Biomedical experts’contains clickable names ofPubMed authors mostoften appearing in articleswhere Coremine finds’Pancreat...
’Drugs’ shows relateddrugs and the ’Load more’link opens a continousmore complete list of drugsin a falling degree ofrelev...
•The related concepts from’Extracted knowledge’ canbe added to the network.•Interact by mouse-click
Read the general drug infoand click ’Add to network’to mix the drug with thedisease network on theleft.
•You may add to thenetwork as many relatedconcepts as you want.•Here, concepts fromprocedure and anatomyare also added.
After spending time onmodifying thenetwork, you may want tosave it with its excactlayout.
You find the saved networkunder My Page >Bookmarks
•You can also click aconnection to focus on twoconcepts.•The right part of thescreen now displays inforelevant to both con...
To create a network wherethe added concepts areused as normal input alongwith the disease, click’Click to modify yoursearc...
If nothing more needstweaking, hit ’Explore’.
The related concepts in thenetwork are nowimportant to all four inputitems.           •The network has now           becom...
Selecting Twitter, the URLto the result network issent to your followers.
Your followers can click theTwitter link to create thesame network you justviewed.
Clicking the Twitter link willopen a new window/tab ina browser with the sameresult network you justshared.
•In your own resultview, you can use thesession history below thenetwork to get back to aprevious search result.•Let’s go ...
•Below the relatedconcepts, you find ’Relatedarticles and hits’ whereCoremine gets informationfrom external sources.•Of th...
•You can bookmark any ofthe articles.•As for the bookmarks youset for the disease and thenetwork earlier, the onesfor docu...
•Another authorativesource is Clinical Trials
•The heading of any hitunder ’Related articles andhits’ is hyperlinked to thesource.•Bookmark any trial youwant to get bac...
•Bookmark any hit fromany supported source, likeWikipedia, Google Imageand YouTube…
Share the bookmarks youhave gathered from MyPage to the Coreminegroup ’Pancreasgroup’, where you are amember.
Bookmarks you share tothe Pancreas group can befound and launched by theother group members.
Another way you cangather and share info fromresult pages into groups isusing Context Notes under’User updated content’.
•Your note will stick to thedisease in focus.•Visability set to only agroup of users will ensureprivacy and notify theothe...
•Inside the group, you seethe note under the’Context notes’ tab.•Other members can replyto the note inside thegroup and in...
Under ’Groupmanagement’ you caninvite others to the groupby Coremine nick name orany email address.
For any hit under ’Relatedarticles and hits’ you canalso leave a comment.
•The comment will followthe hit/document.•Visibility can be set to thesame group as earlier.
The note on the documentis then also seen inside thegroup ’Context Notes’ tab.
Specializing in Pancreatectomy• Using the Coremine Library tool you want to  quickly get an overview of a large set of  do...
21                                                   3    To perform the clustering inside the Library    tool in Coremine...
•In this test example, 1000articles has been selectedfrom the search result.•You hit ’Cluster’ to startthe clustering of t...
The algorithm needs anumber of clusters todivide the documentsinto, and a name for therun.
•The result shows a quickoverview of what articleswas put into the samecluster and what sentencesand keywords are the most...
You save the time to read thearticles to find what is the mostimportant content for you:•Key sentences      •The top ranke...
•Returning to the network of ’PancreaticDiseases’, you open the procedure stack andclick ’pancreatectomy’.•As the focus is...
•The author network showsPubMed authors working withsimilar subjects as Büchler MW.•Basis for the similarity isoverlapping...
•For this expert on’pancreatectomy’ you get       •Keyword profile – the basis       for comparing this author       with ...
•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...
•For this expert on’pancreatectomy’ you get       •Extracted knowledge – the       keyword profile sorted in the       Cor...
Return to the network for’Pancreatic Diseases’ using thesession search history below thenetwork.
Enterprise Clinical Warehouse Support• In the following example we show how  internal enterprise data can be integrated.• ...
Focus is now on ’Pancreas’
•After scrolling down, you openthe section for the hits into patientjournals (electronic medicalrecords).•This section wil...
•All patient journals where thephrase ’pancreas’ is mentioned areshown.•You can bookmark journals.•You enter a journal by ...
Opening the electronic journal youcan read about the patient and, inthis example, further follow a linkto a surgical proce...
•The page opened shows a uniquepresentation from separate globalhospital applications in one contextbased screen.•By this ...
*•’Micro/atomic data’ are also included exemplified by molecular biology data containing gene sequencing and genome analys...
www.coremine.com - Summary• Sophisticated search application in the public  domain facilitating immediate gathering and  i...
Coremine Medical - Build Your Biomedical Mind Map
Coremine Medical - Build Your Biomedical Mind Map
Coremine Medical - Build Your Biomedical Mind Map
Coremine Medical - Build Your Biomedical Mind Map
Coremine Medical - Build Your Biomedical Mind Map
Coremine Medical - Build Your Biomedical Mind Map
Coremine Medical - Build Your Biomedical Mind Map
Coremine Medical - Build Your Biomedical Mind Map
Coremine Medical - Build Your Biomedical Mind Map
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Coremine Medical - Build Your Biomedical Mind Map

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'LIVE' demo of a new social search tool, Coremine Medical, by PubGene AS.

Coremine Medical is a powerful and flexible biomedical search tool.

Using Coremine Medical you find relevant connections between medical concepts such as diseases, drugs, procedures, symptoms, genes, and medical experts.

The search tool provides easy visualization and navigation and help save time, explore, comment and share.

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

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Coremine Medical - Build Your Biomedical Mind Map

  1. 1. Coremine Medical www.coremine.com Build Your Biomedical Mind-Map by Dag Are S. Hov (PubGene AS)Karl Øyri (OUS Intervention Centre) Oslo, Norway
  2. 2. 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
  3. 3. 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
  4. 4. Case study• You are a surgical resident taking part in a group of colleagues working with the subject ‘pancreatic diseases’.
  5. 5. 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.
  6. 6. Enter the name of thedisease ’PancreaticDiseases’ and pick from thesuggestions provided byCoremine.
  7. 7. 1) Continue to build your input list,2) deselect any categories you are not interested in or3) click ’Explore’ to create your result network.
  8. 8. •Categories of conceptsrelated to your inputthrough PubMed recordsare gathered in stacks•Click a stack to viewrelated concepts fromcategories like anatomy….
  9. 9. …MeSH (Medical SubjectHeadings)...
  10. 10. …procedure...
  11. 11. …and drug.
  12. 12. •Bookmark the diseaseconcept into ’My Page’ tokeep it for later•Login needed
  13. 13. •Not a user yet?•A quick register will suffice(no charge)•Staying logged in willenable complete searchhistory
  14. 14. utGTbHggwN •Bookmark set after registration completed •All bookmarks are stored under My Page > Bookmarks
  15. 15. Logging in also enablessetting the email alert onnew articles
  16. 16. All ten synonyms are usedwhen linking the disease toarticles, as is the case withall concepts in Coremine.
  17. 17. General info on the diseaseis fetched from the U.S.National Library ofMedicine.
  18. 18. Hierarchy info provideshyperlinks to generatenetworks on similardiseases.
  19. 19. ’Extracted knowledge’section shows you morecomplete lists of theconcepts related to youquery.
  20. 20. ’Biomedical experts’contains clickable names ofPubMed authors mostoften appearing in articleswhere Coremine finds’Pancreatic Diseases’(including synonyms).
  21. 21. ’Drugs’ shows relateddrugs and the ’Load more’link opens a continousmore complete list of drugsin a falling degree ofrelevance.
  22. 22. •The related concepts from’Extracted knowledge’ canbe added to the network.•Interact by mouse-click
  23. 23. Read the general drug infoand click ’Add to network’to mix the drug with thedisease network on theleft.
  24. 24. •You may add to thenetwork as many relatedconcepts as you want.•Here, concepts fromprocedure and anatomyare also added.
  25. 25. After spending time onmodifying thenetwork, you may want tosave it with its excactlayout.
  26. 26. You find the saved networkunder My Page >Bookmarks
  27. 27. •You can also click aconnection to focus on twoconcepts.•The right part of thescreen now displays inforelevant to both concepts
  28. 28. To create a network wherethe added concepts areused as normal input alongwith the disease, click’Click to modify yoursearch’.
  29. 29. If nothing more needstweaking, hit ’Explore’.
  30. 30. The related concepts in thenetwork are nowimportant to all four inputitems. •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.
  31. 31. Selecting Twitter, the URLto the result network issent to your followers.
  32. 32. Your followers can click theTwitter link to create thesame network you justviewed.
  33. 33. Clicking the Twitter link willopen a new window/tab ina browser with the sameresult network you justshared.
  34. 34. •In your own resultview, you can use thesession history below thenetwork to get back to aprevious search result.•Let’s go back to’Pancreatic Diseases’
  35. 35. •Below the relatedconcepts, you find ’Relatedarticles and hits’ whereCoremine gets informationfrom external sources.•Of the more authorativesources, you first find therecent PubMed articles
  36. 36. •You can bookmark any ofthe articles.•As for the bookmarks youset for the disease and thenetwork earlier, the onesfor documents also end upin ’My Page’.
  37. 37. •Another authorativesource is Clinical Trials
  38. 38. •The heading of any hitunder ’Related articles andhits’ is hyperlinked to thesource.•Bookmark any trial youwant to get back to.
  39. 39. •Bookmark any hit fromany supported source, likeWikipedia, Google Imageand YouTube…
  40. 40. Share the bookmarks youhave gathered from MyPage to the Coreminegroup ’Pancreasgroup’, where you are amember.
  41. 41. Bookmarks you share tothe Pancreas group can befound and launched by theother group members.
  42. 42. Another way you cangather and share info fromresult pages into groups isusing Context Notes under’User updated content’.
  43. 43. •Your note will stick to thedisease in focus.•Visability set to only agroup of users will ensureprivacy and notify theother group members.
  44. 44. •Inside the group, you seethe note under the’Context notes’ tab.•Other members can replyto the note inside thegroup and in the Explorerresult page.
  45. 45. Under ’Groupmanagement’ you caninvite others to the groupby Coremine nick name orany email address.
  46. 46. For any hit under ’Relatedarticles and hits’ you canalso leave a comment.
  47. 47. •The comment will followthe hit/document.•Visibility can be set to thesame group as earlier.
  48. 48. The note on the documentis then also seen inside thegroup ’Context Notes’ tab.
  49. 49. 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.
  50. 50. 21 3 To perform the clustering inside the Library tool in Coremine, you start by searching for the procedure concept ’pancreatectomy’.
  51. 51. •In this test example, 1000articles has been selectedfrom the search result.•You hit ’Cluster’ to startthe clustering of thedocuments.
  52. 52. The algorithm needs anumber of clusters todivide the documentsinto, and a name for therun.
  53. 53. •The result shows a quickoverview of what articleswas put into the samecluster and what sentencesand keywords are the mostimportant.•A better formattedoverview is found inExplorer by hitting’Network’.
  54. 54. You save the time to read thearticles to find what is the mostimportant 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.
  55. 55. •Returning to the network of ’PancreaticDiseases’, you open the procedure stack andclick ’pancreatectomy’.•As the focus is now on pancreatectomy, thecontent of the section at the right changesaccordingly.•You open ’Biomedical experts’ and click thehighest ranked expert, ’Büchler MW’ andfurther follow the link ’Open as a new search’
  56. 56. •The author network showsPubMed authors working withsimilar subjects as Büchler MW.•Basis for the similarity isoverlapping keyword profile.•Each profile is built looking at allthe concepts found in an author’sarticles and how specific theseconcepts are for these articlescompared with all other PubMedarticles.•Green connections indicate co-authorship
  57. 57. •For this expert on’pancreatectomy’ you get •Keyword profile – the basis for comparing this author with others
  58. 58. •For this expert on’pancreatectomy’ you get •Recent articles – read and bookmark highlights.
  59. 59. •For this expert on’pancreatectomy’ you get •Publishing timeline – when was this author productive?
  60. 60. •For this expert on’pancreatectomy’ you get •Biomedical experts working with similar subjects – complete list of the authors best matching Büchler’s keyword profile.
  61. 61. •For this expert on’pancreatectomy’ you get •Extracted knowledge – the keyword profile sorted in the Coremine categories.
  62. 62. Return to the network for’Pancreatic Diseases’ using thesession search history below thenetwork.
  63. 63. 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.
  64. 64. Focus is now on ’Pancreas’
  65. 65. •After scrolling down, you openthe section for the hits into patientjournals (electronic medicalrecords).•This section will only be visibleinside the specific hospital.
  66. 66. •All patient journals where thephrase ’pancreas’ is mentioned areshown.•You can bookmark journals.•You enter a journal by clicking theheading.
  67. 67. Opening the electronic journal youcan read about the patient and, inthis example, further follow a linkto a surgical procedure where thepatient had a laparoscopicpancreatectomy performed due tocancer.
  68. 68. •The page opened shows a uniquepresentation from separate globalhospital applications in one contextbased screen.•By this you get a unique overview ofinformation associated to the particularcase.•In the laparoscopic pancreatic surgeryexample the main phases, episodes andadverse events of the procedure aretagged. The tags are displayed ashighlights of the surgery, so you get aneasy overview of the procedure that canlast for several hours.•The surgery summary text is alsoindexed, so you can quickly perform asearch for another patient journal orcreate a Coremine network.•You also get ’macro data’ like vital signdata from the computerized order entryand charting system and images from thePACS system.
  69. 69. *•’Micro/atomic data’ are also included exemplified by molecular biology data containing gene sequencing and genome analysis oftumor cells. The molecular data in this example is a result of a pipeline analyzing the output from genome studies on the tumorcells, 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 genesare gained or lost in copy number on chromosome 17) is from real data where the patient got conventional chemo therapy that didnot cover the actual oncogenes eventually killing the patient (* Hjortland et al., BMC Cancer, In Press).
  70. 70. 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.
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