II-SDV 2016 Michael Iarrobino - Improving Text Mining Results with Access to Full-Text Scientific Articles
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The document discusses the challenges and benefits of text mining full-text scientific articles, emphasizing the need for licensing solutions and rights management for effective access to content. It outlines current obstacles, such as high costs and varying formats, that hinder researchers from utilizing comprehensive data for analysis. CCC's RightFind XML for Mining service aims to facilitate access to full-text articles in XML format, thereby improving text mining efficiency.
II-SDV 2016 Michael Iarrobino - Improving Text Mining Results with Access to Full-Text Scientific Articles
- 1. Improving Text Mining Results with Access to Full-Text Scientific Articles Mike Iarrobino Product Manager, CCC
- 2. Introduction Mike Iarrobino Product Manager RightFind™ XML for Mining Copyright Clearance Center
- 3. Making Copyright Work – CCC and RightsDirect Rightsholders Content Users • Licensing Solutions • Rights Management • Content Delivery • Copyright Education 950+ million rights from: • Publishers • Authors • Agents • Creators • 35,000 companies • Workers worldwide • 1,200 colleges and universities • Publishers and Authors
- 4. CCC and Text Mining Rightsholders Content Users Servicing many text mining license and content requests Managing text mining feeds Negotiating text mining rights with multiple publishers
- 5. “Text mining” is the process of deriving high-quality information from text materials using software.
- 6. Text Mining Non-Patent Literature • Mining limited to abstracts • High cost to obtain formatted full-text content and permission from multiple publishers • Multiple formats • Researchers can’t mine content to which they are not subscribed
- 7. What is the Benefit of Full Text? Volume Timeliness Quality Catherine Blake. “Beyond genes, proteins, and abstracts: Identifying scientific claims from full-text biomedical articles.” Journal of Biomedical Informatics Volume 43, Issue 2, April 2010, Pages 173–189 Elsevier (2015) Harnessing the Power of Content - Extracting value from scientific literature: the power of mining full-text articles for pathway analysis. Available at www.elsevier.com/__data/assets/pdf_file/0016/83005/R _D-Solutions_Harnessing-Power-of-Content_DIGITAL.pdf Elsevier (2015) Harnessing the Power of Content - Extracting value from scientific literature: the power of mining full-text articles for pathway analysis. Available at www.elsevier.com/__data/assets/pdf_file/0016/83005/R _D-Solutions_Harnessing-Power-of-Content_DIGITAL.pdf Enrique Bernal-Delgado and Elliot S Fisher. “Abstracts in high profile journals often fail to report harm.” BMC Medical Research Methodology (2008); 8:14
- 8. Volume and Recall December 20158 (Abstract: "tau hyperphosphorylation" AND Abstract: kinase OR (GSK3β OR (CDK5 OR (MAPK1 OR (MARK1 OR (MARK2 OR (MARK3 OR MARK4))))))) AND (Abstract: alzheimer OR alzheimer's) content:"tau hyperphosphorylation kinase"~25 OR "tau hyperphosphorylation GSK3β "~25 OR "tau hyperphosphorylation CDK5"~25 OR "tau hyperphosphorylation MAPK1"~25 OR "tau hyperphosphorylation MARK1"~25 OR "tau hyperphosphorylation MARK2"~25 OR "tau hyperphosphorylation MARK3"~25 OR "tau hyperphosphorylation MARK4"~25
- 9. Volume and Recall - Results December 20159 0 100 200 300 400 500 600 700 800 BTK Tau hyperphosphorylation NumberArticles Abstract Full text
- 10. Text Mining Today – Example Workflow December 201510 Search Get permission Download PDFs Convert PDFs Import into text mining software Search Get permission Download PDFs Convert PDFs Import into text mining software • Perform search• Obtain permission from publishers to mine full text for commercial use • Requires automated tool or custom software to download in bulk • Requires text mining permission from multiple publishers • Requires content storage and feed management • PDF is converted to a “blob of text” • No tags • Loss of metadata • Low fidelity of content • References induce noise • Requires structuring text into XML • Article text does not have “fields” • Combining content from multiple sources takes time to normalize the metadata Search Get permission Download PDFs Convert PDFs Import into text mining software TEXT MINING TOOLS Run queries View results MANUAL WORKTypically takes 4-8 weeks
- 11. CCC’s RightFind™ XML for Mining Service Build a corpus of full-text articles in XML format for mining Text Mining SoftwareCCC’s Text Mining Service
- 12. XML for Mining • Rapid inventory growth • MEDLINE abstract corpus • Purchase not subscribed articles with cost optimization process • MeSH article tagging and flat synonym list
- 13. Market Observations and Future Vision ACCESS AUTOMATION
- 14. Thank you! Mike Iarrobino Product Manager, CCC +1.978.646.2633 miarrobino@copyright.com