NLM-Semantic Medline Data Science Data Publication Commons Dr. Brand Niemann Director and Senior Data Scientist/Data Journalist Semantic Community Data Science Data Science for Health Datapalooza 2015 NLM - Semantic Medline Data Science Data Publication June 10,

Overview National Library of Medicine's Web Site: Site Map As Well! Definitions for the National Library of Medicine's Permanence Levels Data Mining: Start With: Databases and Find, Read, Learn Found: All NLM Databases & APIs! Databases, Resources & APIs: Make Linked Data Spreadsheet Table Drill-Down to Inventory and Prioritize Data Science Data Publication: A NIH – Semantic Medline Data Science Data Publication A NIH – Semantic Medline Data Science Data Publication Commons NIH ACD National Library of Medicine (NLM) Working Group Report: PDF-to-MindTouch Presentation Slides 2

National Library of Medicine's Web Site 3 First published: 10 October 1993 Last updated: 29 May 2015 Permanence level: Permanent: Dynamic Content My Note: This is the Site Map as Well!

Definitions for the National Library of Medicine's Permanence Levels Permanence Not Guaranteed: The National Library of Medicine has made no commitment to retain this resource. It could become unavailable at any time. Its identifier could be changed. Permanent: Dynamic Content: The National Library of Medicine has made a commitment to keep this resource permanently available. Its identifier will always provide access to the resource. Its content could be revised, replaced or recaptured. Permanent: Stable Content: The National Library of Medicine has made a commitment to keep this resource permanently available. Its identifier will always provide access to the resource. Its content is subject only to minor corrections or additions. Permanent: Unchanging Content: The National Library of Medicine has made a commitment to keep this resource permanently available. Its identifier will always provide access to the resource. Its content will not change. 4

Data Mining Databases PubMed/MEDLINE MeSH UMLS ClinicalTrials.gov MedlinePlus TOXNET Images from the History of Medicine Digital Collections LocatorPlus All NLM Databases & APIs Find, Read, Learn Search biomedical literature Find medical terminologies Search NLM collections Read about diseases Learn about drugs Explore history Find a clinical trial Use a medical dictionary Find free full-text articles 5

Databases, Resources & APIs 6 APIs: 8 Datasets/XLS/CSV: 9 Downloadable Files (e.g. TXT, PDF): 39 Database: 142 Etc. My Note: See Next Slide for Selected Terms.

NLM-SemMed Data Science Data Publication: Database Linked Data Spreadsheet 7 HDP2015.xlsx

Broad Subject Terms for Indexed Journals 8 Broad Subject Terms are assigned by NLM® to MEDLINE® journals to describe the journal's overall scope. All of these broad subject terms (about 120) are valid MeSH® headings. My Note: This should be a linked dataset! Last reviewed: 9 January 2013 Last updated: 9 January 2013 First published: 15 February 2009

NLM-SemMed Data Science Data Publication: Broad Subject Terms Linked Data Spreadsheet 9 HDP2015.xlsx

NLM-SemMed Data Science Data Publication: Spotfire Data Commons 10 Web Player

NLM-SemMed Data Science Data Publication: LOINC Big Data 11 My Note: 0.5 GB ZIPPED File with Multiple file Formats

NLM-SemMed Data Science Data Publication: LOINC Big Data in Spotfire 12 Web Player

NLM-SemMed Data Science Data Publication: MindTouch Knowledge Base 13 Semantic CommunitySemantic Community Data Science Data Science for Health Datapalooza 2015 NLM - Semantic Medline Data Science Data PublicationData ScienceData Science for Health Datapalooza 2015NLM - Semantic Medline Data Science Data Publication My Note: Use Google Chrome Find

Conclusions and Recommendations National Library of Medicine's Web Site was Data Mined for Sample Databases, Resources & APIs. A NIH – Semantic Medline Data Science Data Publication Was Created For A NIH – Semantic Medline Data Science Data Publication Commons. The NIH ACD National Library of Medicine (NLM) Working Group Report Was Repurposed (PDF-to-MindTouch and Inline Presentation Slides) for the Knowledge Base. This Knowledge Base Was Prepared for July 20th Meetup of the Federal Big Data Working Group Meetup on Data Science for ACA Data and Semantic Medline Precision Medicine. Additional NLM and NIH Institute Open Data Sets Will Be Mined, Integrated, and Federated in a Series of Data Science Data Publications for the Commons for Additional Data Science Tutorials and Meetups. 14