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Literature Mining Effectiveness in Today’s Economy
Challenges in Literature mining ,[object Object],[object Object],[object Object],[object Object],[object Object],PubMed Publication rate 2008
More Time consuming = More Cost   To annotate 30 days of data on breast neoplasm = 1 man day  So to annotate 50,000 abstracts = 500,000 mins or 1,041 man-days or ~ 3 man years to annotate 1 month of literature findings Increase in Publications Time Cost Keywords searched across PUBMED Dates of Addition in PUBMED Number of Abstracts Approx time taken for manual annotation & extraction (10 min per abstract) Breast  Neoplasm Last 90 days 621 6210 min OR  103 hrs OR  11 working days Last 60 Days 271 2710 min OR  45 hrs OR  5 working days Last 30 Days 56 560 mins OR  9 hrs OR  1 working day It takes at least one working day to extract all the possible relations from 56 abstracts Analysis conducted as on 28 Apr 08 on PubMed
Low Precision of NLP v/s Manual Analysis of  the “standard NLP” v/s manual curation efforts revealed that…..  12-35% false positive picks were found with NLP  in comparison to our manual approach
Low Precision of NLP  v/s Manual  ..contd ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],An ideal Solution should ensure High Precision on annotations for Proteins, Diseases, Drugs and Biological Processes
Our Approach to Literature Mining Manual Annotation Manual Categorization Multiple Categories-  Biomarkers, Clinical Trials,  knockout studies, toxicity, disease mechanisms, pathways etc.. The major bottleneck with manual curation as demonstrated involves considerable time and cost. In XTractor, we have reduced the time involved in the manual annotation effort - by significantly cutting down the process steps to boost our internal productivity and turnaround time.  Therefore, in almost real-time basis we are able to serve you with the latest manually annotated scientific facts. Swiss Prot for Proteins PubChem for Drugs MeSH for Diseases  Gene Ontology (GO) for Biological Process 100% expert annotated
Solution = XTractor Premium ,[object Object],[object Object],Share your findings Export  results Track your research entities Know the  competition Hypothesize your findings Ontology based  Searching Generate  Reports Discover newer relationships XTractor Premium
XTractor Knowledgebase ,[object Object],[object Object],[object Object],[object Object]
XTractor Knowledgebase  Key Features Accuracy:  Manually annotated content Semantic Consistency: Standard ontologies followed including MeSH, GO, Swiss Prot, PubChem, Protein isoform based mapping Comprehensiveness: Covers a large % of all the major protein, disease and drug databases Up-to-Date & Current: Updated on a weekly basis with the latest information  Accuracy Semantic  Consistency Up-to-date  & Current Comprehensive
Solution for Discovery Target  Validation Target  Discovery Toxicity Clinical  Trials Drug  Studies Complete solutions for your Drug Discovery data needs  Disease markers Target  Discovery Biomarkers Drug effects Clinical trials RNAi studies Knockout studies Mutations Pathways Disease mechanisms Biological Process Target information Prognosis
XTractor Premium: Search & Analytics More insights of Scientific Data with XTractor Search Features Semantic Search Bibliographic Search Summary Search Concept Linking WatchList
What does XTractor answer? Knockout/RNAi studies, pertaining to Rheumatoid arthritis Drug- toxicity studies in Alzheimer’ s patients PK & PD studies of drug tamoxifen Pathways involving apoptosis and breast cancer Disease prognosis and diagnosis for Diabetes type 2 Marker/ Biomarker studies in colon cancer Drugs against colon cancer Route of administration studies  For  insulin Dose related  and clearance  Studies for  doxorubicin Cisplatin Clinical Trials  Major disease classes that are associated with PDGFR All this  And Much  more..
[object Object],[object Object],For a free trial access  contact:  [email_address] Click Here  To Register for a Webinar

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Literature Mining Effectiveness in Today’s Economy

  • 1. Literature Mining Effectiveness in Today’s Economy
  • 2.
  • 3. More Time consuming = More Cost   To annotate 30 days of data on breast neoplasm = 1 man day So to annotate 50,000 abstracts = 500,000 mins or 1,041 man-days or ~ 3 man years to annotate 1 month of literature findings Increase in Publications Time Cost Keywords searched across PUBMED Dates of Addition in PUBMED Number of Abstracts Approx time taken for manual annotation & extraction (10 min per abstract) Breast Neoplasm Last 90 days 621 6210 min OR 103 hrs OR 11 working days Last 60 Days 271 2710 min OR 45 hrs OR 5 working days Last 30 Days 56 560 mins OR 9 hrs OR 1 working day It takes at least one working day to extract all the possible relations from 56 abstracts Analysis conducted as on 28 Apr 08 on PubMed
  • 4. Low Precision of NLP v/s Manual Analysis of the “standard NLP” v/s manual curation efforts revealed that….. 12-35% false positive picks were found with NLP in comparison to our manual approach
  • 5.
  • 6. Our Approach to Literature Mining Manual Annotation Manual Categorization Multiple Categories- Biomarkers, Clinical Trials, knockout studies, toxicity, disease mechanisms, pathways etc.. The major bottleneck with manual curation as demonstrated involves considerable time and cost. In XTractor, we have reduced the time involved in the manual annotation effort - by significantly cutting down the process steps to boost our internal productivity and turnaround time. Therefore, in almost real-time basis we are able to serve you with the latest manually annotated scientific facts. Swiss Prot for Proteins PubChem for Drugs MeSH for Diseases Gene Ontology (GO) for Biological Process 100% expert annotated
  • 7.
  • 8.
  • 9. XTractor Knowledgebase Key Features Accuracy: Manually annotated content Semantic Consistency: Standard ontologies followed including MeSH, GO, Swiss Prot, PubChem, Protein isoform based mapping Comprehensiveness: Covers a large % of all the major protein, disease and drug databases Up-to-Date & Current: Updated on a weekly basis with the latest information Accuracy Semantic Consistency Up-to-date & Current Comprehensive
  • 10. Solution for Discovery Target Validation Target Discovery Toxicity Clinical Trials Drug Studies Complete solutions for your Drug Discovery data needs Disease markers Target Discovery Biomarkers Drug effects Clinical trials RNAi studies Knockout studies Mutations Pathways Disease mechanisms Biological Process Target information Prognosis
  • 11. XTractor Premium: Search & Analytics More insights of Scientific Data with XTractor Search Features Semantic Search Bibliographic Search Summary Search Concept Linking WatchList
  • 12. What does XTractor answer? Knockout/RNAi studies, pertaining to Rheumatoid arthritis Drug- toxicity studies in Alzheimer’ s patients PK & PD studies of drug tamoxifen Pathways involving apoptosis and breast cancer Disease prognosis and diagnosis for Diabetes type 2 Marker/ Biomarker studies in colon cancer Drugs against colon cancer Route of administration studies For insulin Dose related and clearance Studies for doxorubicin Cisplatin Clinical Trials Major disease classes that are associated with PDGFR All this And Much more..
  • 13.