Blog RSS https://www.vumc.org/cpm/ en PheMAP–high-throughput Phenotyping by Measured, Automated Profile https://www.vumc.org/cpm/phemap <span class="field field--name-title field--type-string field--label-hidden">PheMAP–high-throughput Phenotyping by Measured, Automated Profile</span> <div class="field field--name-field-barista-posts-category field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/cpm/cpm-blog?cat=64" hreflang="und">Center Resources</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/cpm/users/higbyfme-0" typeof="schema:Person" property="schema:name" datatype="">higbyfme</span></span> <span class="field field--name-created field--type-created field--label-hidden">Mon, 11/04/2019 - 14:42</span> <a href="/cpm/blog-post-rss/612" class="feed-icon" title="Subscribe to PheMAP–high-throughput Phenotyping by Measured, Automated Profile"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-author field--type-string field--label-hidden field__item">Neil Zheng, Wei-Qi Wei</div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>PheMAP is a general, automatic, and portable approach to enable accurate high-throughput phenotyping within electronic health records (EHR). PheMAP quantifies relationships between phenotypes and relevant clinical concepts represented by standard medical terminologies. For each individual, PheMAP assigns a score and probability of having a particular phenotype from identified related concepts within EHRs.</p> <p>We parsed phenotype descriptions from multiple publicly available resources (e.g.,MedlinePlus, MedicineNet, and Wikipedia) using natural language processing (NLP). We mapped the identified concepts to concept unique identifiers (CUIs) from the United Medical Language System (UMLS) and to codes of standard clinical terminologies(e.g., ICD-9-CM, ICD-10-CM, SNOMED CT, CPT, LOINC, and RxNorm). We then weighted each concept relative to a phenotype to reflect how important the concept is to the phenotype in a collection of all phenotype documents.</p> <p>PheMAP is available for free and is ready to be implemented for 1400 unique phenotypes with EHRs in the OMOP Common Data model. The knowledge base is provided for download as well as a Python script for calculating phenotype scores and phenotype probabilities.</p> <p>Please contact <a href="mailto:neil.zheng@vumc.org">neil.zheng@vumc.org</a> or <a href="mailto:wei-qi.wei@vumc.org">wei-qi.wei@vumc.org</a> with any questions.</p> <p><strong>Citation:</strong></p> <p>Zheng NS, Feng QP, Kerchberger VE, Zhao J, Edwards TL, Cox NJ, Stein CM, Roden DM, Denny JC, Wei WQ. PheMap: a Multi-resource Knowledgebase for High-throughput Phenotyping within Electronic Health Records. (Accepted for publication at Journal of American Medical Informatics Associations)</p> <p><strong>PheMap Knowledgebase Downloads<u>:</u></strong></p> <p><a href="https://phewascatalog.org/files/phemap/PheMap_Mapped_Terminologies_1.1.csv">PheMap_Mapped_Terminologies_1.1.csv</a> –The file contains weighted concepts mapped to standard medical terminologies, e.g.,ICDs, SNOMED CT, CPT, LOINC, and RxNorm.</p> <p><a href="https://phewascatalog.org/files/phemap/PheMap_UMLS_Concepts_1.1.csv">PheMap_UMLS_Concepts_1.1.csv</a> - The raw PheMap knowledge base containing weighted concepts mapped toCUIs from UMLS.</p> <p><a href="https://phewascatalog.org/files/phemap/ICD_to_Phecode_mapping.csv">ICD_to_Phecode_mapping.csv</a> - Mapping of ICD9CM and ICD10CM to phecode. Used in phemap_phenotyping.py.</p> <p><a href="https://phewascatalog.org/files/phemap/Phecode_Relationship.csv">Phecode_Relationship.csv</a> - The hierarchical relationship mapping between phecodes.Used in phemap_phenotyping.py.</p> <p><a href="https://phewascatalog.org/files/phemap/README.txt.zip">README.txt</a> –Description of data elements in the above files.</p> <p><strong>Scripts:</strong></p> <p><a href="https://phewascatalog.org/files/phemap/phemap_phenotyping.py.zip">phemap_phenotyping.py</a> – Python script that calculates PheMap phenotype score and probabilities for EHRs structured with OMOP Common Data Model. The script is meant to be run line-by-line.</p> <p><strong>Changelog:</strong></p> <p>PheMap v1.1(07/07/20)</p> <ul> <li>Added Medscape as an additional resource for concept extraction and weighting.</li> <li>Improved article text to phecode mapping, increasing available unique phenotypes from 841 to 1400.</li> <li>Improved UMLS CUI to ICD mapping, capturing additional ICD diagnosis codes.</li> </ul> <p>PheMap v1.0 (05/14/20)</p> <ul> <li>First release of PheMap built from information from five publicly available resources: Mayo Clinic, MedlinePlus, MedicineNet, WikiDoc, Wikipedia.</li> <li>Contains PheMap quantified concepts for 841 phenotypes.</li> <li>Please refer to original paper for more details.</li> </ul> </div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Mon, 04 Nov 2019 20:42:04 +0000 higbyfme 612 at https://www.vumc.org/cpm DEB2 https://www.vumc.org/cpm/deb2 <span class="field field--name-title field--type-string field--label-hidden">DEB2</span> <div class="field field--name-field-barista-posts-category field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/cpm/cpm-blog?cat=63" hreflang="und">Software</a>, <a href="/cpm/cpm-blog?cat=64" hreflang="und">Center Resources</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/cpm/users/higbyfme-0" typeof="schema:Person" property="schema:name" datatype="">higbyfme</span></span> <span class="field field--name-created field--type-created field--label-hidden">Fri, 08/23/2019 - 13:16</span> <a href="/cpm/blog-post-rss/606" class="feed-icon" title="Subscribe to DEB2"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p><strong>DEB2</strong> is a medication indication and adverse effect knowledgebase derived from five publicly available sources: the VA’s National Drug File-Reference Terminology, MEDLINE, the US Food and Drug Administration’s drug product labels (via the SIDER2 database), the MedlinePlus consumer health information website, and DrugBank, a manually-curated drug target database. All medications, indications, and adverse effects in DEB2 are represented using the RxNorm and SNOMED-CT terminologies.</p> <p>Indications and adverse effects in DEB2 were extracted from the constituent sources using natural language processing and other ontology methods. The DEB2 knowledgebase requires indications and adverse effects to be corroborated by two or more of its constituent drug information sources, resulting in improved accuracy and precision over the original <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3885918/">DEB1</a>, and other popular medication databases.</p> <p>The DEB2 Dataset contains 6431 indications and 11,539 adverse effects. It includes 1163 distinct drugs and 1601 distinct clinical features (symptoms, findings, diseases, etc.). Based on physician review, DEB2 has an estimated precision of 86% (+/- 3.1%) overall, with indications being slightly more accurate and adverse effects slightly less. Indications and adverse effects for the most commonly-prescribed medications were shown to have a precision of 94% (+/- 3.5%). Drug relationships found in more sources were generally found more likely to be correct.</p> <p>The DEB2 Full Data Superset is also available for download. It includes all drug-indication and drug-adverse effect pairs found in any of the five sources (including those found in only 1 source and therefore not corroborated elsewhere). The DEB2 Full Data Superset includes over 131,000 pairs (consisting of 31,203 indications and 98,745 adverse effects). While it was not reviewed separately, we suspect the superset should have a higher recall and lower precision than the primary DEB2 Dataset.</p> <p>DEB2 is available for free download. It is intended for research and is not a substitute for professional clinical advice. We believe this resource can be useful for research in the areas of pharmacovigilance, clinical data mining, clinical phenotyping, and clinical decision support systems, among others. It can be used unaltered, or as a valuable starting point for developing manually-curated indication and adverse effect datasets.</p> <p>Please cite the reference below when using this resource. Contact <a href="mailto:joshua.smith@vumc.org">joshua.smith@vumc.org</a> with any questions.</p> <p><b>*The DEB2 manuscript has been submitted for publication. If this website has not been updated with the correct reference, please contact me for instructions on how to cite DEB2 in your work.</b></p> <p><a href="#">Browse DEB2 online</a> [coming soon]</p> <p> </p> <p><b>Download links:</b></p> <p> </p> <p><a href="https://phewascatalog.org/files/deb2/DEB2.txt.zip">DEB2.txt</a> - The DEB2 knowledgebase, containing medication indications and adverse effects found in at least two sources. Tab-Separated text file; first line contains column names; double-quotes around any field values with commas.</p> <p><a href="https://phewascatalog.org/files/deb2/DEB2.xlsx.zip">DEB2.xlsx</a> - The DEB2 knowledegbase in Microsoft Excel format. Color-coded for human readability.</p> <p><a href="https://phewascatalog.org/files/deb2/DEB2_full_data_superset.txt.zip">DEB2_full_data_superset.txt</a> - The raw data superset from which DEB2 was constructed, containing medication indications and adverse effects found in any of the sources. The vast majority of drug-CF pairs in this file are from only one source. Tab-Separated text file; first line contains column names; double-quotes around any field values with commas.</p> <p><a href="https://phewascatalog.org/files/deb2/README.zip">README.txt</a> - description of data elements in the above files.</p> <p><br /> DEB2 by Dr. Joshua C. Smith, et al., is licensed under a <a href="http://creativecommons.org/licenses/by-nc-sa/4.0/" rel="license">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>.</p> <p><b>Reference:</b></p> <p>Smith JC, Chen Q, Denny JC, Roden DM, Johnson KB, Miller RA. <i>DEB2: An Improved Drug Evidence Base for Biomedical Research</i>. <b>Manuscript submitted for publication. Currently under review.</b></p> </div> <div> <strong>Tags</strong> <div> <div><a href="/cpm/cpm-blog?tag=11" hreflang="und">phenotyping</a></div> </div> </div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Fri, 23 Aug 2019 18:16:48 +0000 higbyfme 606 at https://www.vumc.org/cpm The Struggle to Build a Massive ‘Biobank’ of Patient Data https://www.vumc.org/cpm/cpm-blog-news/struggle-build-massive-biobank-patient-data <span class="field field--name-title field--type-string field--label-hidden">The Struggle to Build a Massive ‘Biobank’ of Patient Data</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Mon, 03/19/2018 - 00:00</span> <a href="/cpm/blog-post-rss/583" class="feed-icon" title="Subscribe to The Struggle to Build a Massive ‘Biobank’ of Patient Data"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-external-url field--type-link field--label-hidden field__item"><a href="https://www.nytimes.com/2018/03/19/health/nih-biobank-genes.html" target="_blank">https://www.nytimes.com/2018/03/19/health/nih-biobank-genes.html</a></div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Mon, 19 Mar 2018 05:00:00 +0000 Visitor 583 at https://www.vumc.org/cpm What’s Behind Many Mystery Ailments? Genetic Mutations, Study Finds https://www.vumc.org/cpm/cpm-blog-news/whats-behind-many-mystery-ailments-genetic-mutations-study-finds <span class="field field--name-title field--type-string field--label-hidden">What’s Behind Many Mystery Ailments? Genetic Mutations, Study Finds</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 03/15/2018 - 16:08</span> <a href="/cpm/blog-post-rss/498" class="feed-icon" title="Subscribe to What’s Behind Many Mystery Ailments? Genetic Mutations, Study Finds"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-external-url field--type-link field--label-hidden field__item"><a href="https://www.nytimes.com/2018/03/15/health/genetic-mutations-diagnosis.html" target="_blank">https://www.nytimes.com/2018/03/15/health/genetic-mutations-diagnosis.html</a></div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Thu, 15 Mar 2018 21:08:20 +0000 Visitor 498 at https://www.vumc.org/cpm Study reveals safety signal from genes that mimic drugs https://www.vumc.org/cpm/cpm-blog-news/study-reveals-safety-signal-genes-mimic-drugs <span class="field field--name-title field--type-string field--label-hidden">Study reveals safety signal from genes that mimic drugs</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 03/01/2018 - 00:00</span> <a href="/cpm/blog-post-rss/504" class="feed-icon" title="Subscribe to Study reveals safety signal from genes that mimic drugs"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-external-url field--type-link field--label-hidden field__item"><a href="https://news.vanderbilt.edu/2018/03/01/study-reveals-safety-signal-from-genes-that-mimic-drugs/" target="_blank">https://news.vanderbilt.edu/2018/03/01/study-reveals-safety-signal-from-genes-that-mimic-drugs/</a></div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Thu, 01 Mar 2018 06:00:00 +0000 Visitor 504 at https://www.vumc.org/cpm Personalized drug prescribing program expands, upgrades https://www.vumc.org/cpm/cpm-blog-news/personalized-drug-prescribing-program-expands-upgrades <span class="field field--name-title field--type-string field--label-hidden">Personalized drug prescribing program expands, upgrades</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 01/25/2018 - 00:00</span> <a href="/cpm/blog-post-rss/513" class="feed-icon" title="Subscribe to Personalized drug prescribing program expands, upgrades"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-external-url field--type-link field--label-hidden field__item"><a href="https://news.vanderbilt.edu/2018/01/25/personalized-drug-prescribing-program-expands-upgrades/" target="_blank">https://news.vanderbilt.edu/2018/01/25/personalized-drug-prescribing-program-expands-upgrades/</a></div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Thu, 25 Jan 2018 06:00:00 +0000 Visitor 513 at https://www.vumc.org/cpm Vanderbilt’s Buntin, Denny elected to National Academy of Medicine https://www.vumc.org/cpm/cpm-blog-news/vanderbilts-buntin-denny-elected-national-academy-medicine <span class="field field--name-title field--type-string field--label-hidden">Vanderbilt’s Buntin, Denny elected to National Academy of Medicine</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Mon, 10/16/2017 - 00:00</span> <a href="/cpm/blog-post-rss/505" class="feed-icon" title="Subscribe to Vanderbilt’s Buntin, Denny elected to National Academy of Medicine"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-external-url field--type-link field--label-hidden field__item"><a href="https://news.vanderbilt.edu/2017/10/16/vanderbilts-buntin-denny-elected-to-national-academy-of-medicine/" target="_blank">https://news.vanderbilt.edu/2017/10/16/vanderbilts-buntin-denny-elected-to-national-academy-of-medicine/</a></div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Mon, 16 Oct 2017 05:00:00 +0000 Visitor 505 at https://www.vumc.org/cpm Denny, Wilkins to discuss precision medicine at next Discovery Lecture https://www.vumc.org/cpm/cpm-blog-news/denny-wilkins-discuss-precision-medicine-next-discovery-lecture <span class="field field--name-title field--type-string field--label-hidden">Denny, Wilkins to discuss precision medicine at next Discovery Lecture</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 10/05/2017 - 00:00</span> <a href="/cpm/blog-post-rss/500" class="feed-icon" title="Subscribe to Denny, Wilkins to discuss precision medicine at next Discovery Lecture"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-external-url field--type-link field--label-hidden field__item"><a href="https://news.vanderbilt.edu/2017/10/05/denny-wilkins-to-discuss-precision-medicine-at-next-discovery-lecture/" target="_blank">https://news.vanderbilt.edu/2017/10/05/denny-wilkins-to-discuss-precision-medicine-at-next-discovery-lecture/</a></div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Thu, 05 Oct 2017 05:00:00 +0000 Visitor 500 at https://www.vumc.org/cpm Report identifies IT upgrades needed to enhance cancer care https://www.vumc.org/cpm/cpm-blog-news/report-identifies-it-upgrades-needed-enhance-cancer-care <span class="field field--name-title field--type-string field--label-hidden">Report identifies IT upgrades needed to enhance cancer care</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 08/17/2017 - 00:00</span> <a href="/cpm/blog-post-rss/511" class="feed-icon" title="Subscribe to Report identifies IT upgrades needed to enhance cancer care"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-external-url field--type-link field--label-hidden field__item"><a href="https://news.vanderbilt.edu/2017/08/17/report-identifies-it-upgrades-needed-to-enhance-cancer-care/" target="_blank">https://news.vanderbilt.edu/2017/08/17/report-identifies-it-upgrades-needed-to-enhance-cancer-care/</a></div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Thu, 17 Aug 2017 05:00:00 +0000 Visitor 511 at https://www.vumc.org/cpm Doris Duke Foundation lauds Van Driest’s research https://www.vumc.org/cpm/cpm-blog/doris-duke-foundation-lauds-van-driests-research <span class="field field--name-title field--type-string field--label-hidden">Doris Duke Foundation lauds Van Driest’s research</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 07/27/2017 - 00:00</span> <a href="/cpm/blog-post-rss/514" class="feed-icon" title="Subscribe to Doris Duke Foundation lauds Van Driest’s research"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-external-url field--type-link field--label-hidden field__item"><a href="https://news.vanderbilt.edu/2017/07/27/doris-duke-foundation-lauds-van-driests-research/" target="_blank">https://news.vanderbilt.edu/2017/07/27/doris-duke-foundation-lauds-van-driests-research/</a></div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Thu, 27 Jul 2017 05:00:00 +0000 Visitor 514 at https://www.vumc.org/cpm Scientists create unique disease ‘catalog’ linked to immune system gene variations https://www.vumc.org/cpm/cpm-blog-news/scientists-create-unique-disease-catalog-linked-immune-system-gene-variations <span class="field field--name-title field--type-string field--label-hidden">Scientists create unique disease ‘catalog’ linked to immune system gene variations</span> <div class="field field--name-field-barista-posts-category field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/cpm/cpm-blog?cat=62" hreflang="und">PheWAS</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Wed, 05/10/2017 - 00:00</span> <a href="/cpm/blog-post-rss/499" class="feed-icon" title="Subscribe to Scientists create unique disease ‘catalog’ linked to immune system gene variations"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-external-url field--type-link field--label-hidden field__item"><a href="https://news.vanderbilt.edu/2017/05/10/scientists-create-unique-disease-catalog-linked-to-immune-system-gene-variations/" target="_blank">https://news.vanderbilt.edu/2017/05/10/scientists-create-unique-disease-catalog-linked-to-immune-system-gene-variations/</a></div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Wed, 10 May 2017 05:00:00 +0000 Visitor 499 at https://www.vumc.org/cpm Children at risk for complications from brown recluse spider bites: study https://www.vumc.org/cpm/cpm-blog-news/children-risk-complications-brown-recluse-spider-bites-study <span class="field field--name-title field--type-string field--label-hidden">Children at risk for complications from brown recluse spider bites: study</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 04/27/2017 - 00:00</span> <a href="/cpm/blog-post-rss/512" class="feed-icon" title="Subscribe to Children at risk for complications from brown recluse spider bites: study"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-external-url field--type-link field--label-hidden field__item"><a href="https://news.vanderbilt.edu/2017/04/27/children-complications-brown-recluse-spider/" target="_blank">https://news.vanderbilt.edu/2017/04/27/children-complications-brown-recluse-spider/</a></div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Thu, 27 Apr 2017 05:00:00 +0000 Visitor 512 at https://www.vumc.org/cpm Study reveals circadian time in a blood sample https://www.vumc.org/cpm/cpm-blog-news/study-reveals-circadian-time-blood-sample <span class="field field--name-title field--type-string field--label-hidden">Study reveals circadian time in a blood sample</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 03/02/2017 - 00:00</span> <a href="/cpm/blog-post-rss/501" class="feed-icon" title="Subscribe to Study reveals circadian time in a blood sample"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-external-url field--type-link field--label-hidden field__item"><a href="https://news.vanderbilt.edu/2017/03/02/study-reveals-circadian-time-in-a-blood-sample/" target="_blank">https://news.vanderbilt.edu/2017/03/02/study-reveals-circadian-time-in-a-blood-sample/</a></div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Thu, 02 Mar 2017 06:00:00 +0000 Visitor 501 at https://www.vumc.org/cpm Researchers chart new informatics path in tracking disease risk https://www.vumc.org/cpm/cpm-blog-news/researchers-chart-new-informatics-path-tracking-disease-risk <span class="field field--name-title field--type-string field--label-hidden">Researchers chart new informatics path in tracking disease risk</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 02/23/2017 - 00:00</span> <a href="/cpm/blog-post-rss/503" class="feed-icon" title="Subscribe to Researchers chart new informatics path in tracking disease risk"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-external-url field--type-link field--label-hidden field__item"><a href="https://news.vanderbilt.edu/2017/02/23/researchers-chart-new-informatics-path-in-tracking-disease-risk/" target="_blank">https://news.vanderbilt.edu/2017/02/23/researchers-chart-new-informatics-path-in-tracking-disease-risk/</a></div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Thu, 23 Feb 2017 06:00:00 +0000 Visitor 503 at https://www.vumc.org/cpm Rheumatoid subtypes explored by PheWAS https://www.vumc.org/cpm/cpm-blog-news/rheumatoid-subtypes-explored-phewas <span class="field field--name-title field--type-string field--label-hidden">Rheumatoid subtypes explored by PheWAS</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Fri, 10/07/2016 - 00:00</span> <a href="/cpm/blog-post-rss/506" class="feed-icon" title="Subscribe to Rheumatoid subtypes explored by PheWAS"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-external-url field--type-link field--label-hidden field__item"><a href="https://news.vanderbilt.edu/2016/10/07/rheumatoid-subtypes-phewas/" target="_blank">https://news.vanderbilt.edu/2016/10/07/rheumatoid-subtypes-phewas/</a></div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Fri, 07 Oct 2016 05:00:00 +0000 Visitor 506 at https://www.vumc.org/cpm VUMC to Lead Pilot Program for Precision Medicine Initiative Cohort Program https://www.vumc.org/cpm/cpm-blog-news/vumc-lead-pilot-program-precision-medicine-initiative-cohort-program <span class="field field--name-title field--type-string field--label-hidden">VUMC to Lead Pilot Program for Precision Medicine Initiative Cohort Program</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 02/25/2016 - 00:00</span> <a href="/cpm/blog-post-rss/376" class="feed-icon" title="Subscribe to VUMC to Lead Pilot Program for Precision Medicine Initiative Cohort Program"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><h3><strong>VUMC to Lead Pilot Program for Precision Medicine Initiative Cohort Program</strong></h3>&#13; &#13; <p>President Obama and National Institutes of Health (NIH) Director Francis Collins announced today that Vanderbilt University Medical Center (VUMC) will lead the Direct Volunteers Pilot Studies under the first grant to be awarded in the federal <a href="https://www.nih.gov/precision-medicine-initiative-cohort-program">Precision Medicine Initiative Cohort Program</a>.<br />&#13;  <br />&#13; The Precision Medicine Initiative Cohort Program’s objective is to build a broad and diverse national research cohort of 1 million or more U.S. volunteers whose participation will provide the platform for expanding approaches to precision medicine that will benefit the nation and medical science for decades to come.<br />&#13;  <br />&#13; The team of researchers involved with the Direct Volunteers Pilot Studies, whose objective is to create a prototype set of technologies and experiments that will inform the successful approach for such a large research cohort, also includes experts from Verily (formerly Google Life Sciences) as well as the University of Michigan, the Broad Institute of the Massachusetts Institute of Technology and Harvard University.<br />&#13;  <br />&#13; Josh Denny, M.D., M.S., is principal investigator for the effort, which is supported by a one-year grant from the PMI Cohort Program (NIH Award #1-OT2-OD-023132).  He served on the national PMI Working Group of the NIH Advisory Committee to the Director.  <a href="https://www.nih.gov/sites/default/files/research-training/initiatives/pmi/pmi-working-group-report-20150917-2.pdf">The report from the PMI Working Group can be found here</a>.<br />&#13;  <br />&#13; Precision medicine uses advanced approaches to data collection and analysis that rapidly assimilate unprecedented amounts of individuals’ personal health data, as well as behavioral and environmental data. This information, when combined with genetic and other molecular data, will provide a broad platform that can be used extensively for discoveries that will help advance the science of preventive care, as well as new treatments and potentially cures for diseases. The goal of precision medicine is to match individuals with treatments and preventive strategies that are most likely to work for them.<br />&#13;  <br />&#13; As part of the Direct Volunteers Pilot Studies, VUMC will create and optimize a prototype informational website that is engaging to a diverse array of potential volunteers, and develop an interface for obtaining consent and basic enrollment and health information that is efficient, effective and secure.<br />&#13;  <br />&#13; Vanderbilt researchers involved with the Direct Volunteers Pilot Studies also include Paul Harris, Ph.D., director of the Office of Research Informatics; Consuelo Wilkins, M.D., director of the Meharry-Vanderbilt Alliance; and Sunil Kripalani, M.D., director of Vanderbilt’s Effective Health Communication Program. Bradley Malin, Ph.D., founder and director of Vanderbilt’s Health Information Privacy Laboratory, will help construct platforms that protect the privacy of cohort participants. Jill Pulley, MBA, director of Research Support Services in the Office of Research, will oversee program architecture and organization.</p>&#13; &#13; <p>Vanderbilt University press release<br />&#13; <a href="http://news.vanderbilt.edu/2016/02/vumc-to-lead-pilot-program-for-precision-medicine-initiative-cohort-program/">http://news.vanderbilt.edu/2016/02/vumc-to-lead-pilot-program-for-preci…</a></p>&#13; &#13; <p><br />&#13; Video of the Precision Medicine Initiative summit<br />&#13; <a href="https://www.youtube.com/watch?v=3AMq759psUM">https://www.youtube.com/watch?v=3AMq759psUM</a></p>&#13; &#13; <p>​More about the White House's Precision Medicine Inititiative<br />&#13; <a href="https://www.whitehouse.gov/precision-medicine">https://www.whitehouse.gov/precision-medicine</a></p>&#13; &#13; <p>New York Times<br />&#13; <a href="http://www.nytimes.com/aponline/2016/02/25/health/ap-us-med-precision-medicine.html">http://www.nytimes.com/aponline/2016/02/25/health/ap-us-med-precision-m…</a></p>&#13; </div> <div class="field field--name-field-barista-posts-full-image field--type-image field--label-hidden field__item"> <img src="/cpm/sites/default/files/styles/barista_posts_full_image/public/cpm_summit_wh.png?itok=AytgXKKW" width="576" height="299" alt="" typeof="foaf:Image" class="image-style-barista-posts-full-image" /> </div> <div class="field field--name-field-barista-posts-full-caption field--type-string-long field--label-hidden field__item">President Obama and panel at the PMI Summit</div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Thu, 25 Feb 2016 06:00:00 +0000 Visitor 376 at https://www.vumc.org/cpm Neanderthal DNA has subtle but significant impact on human traits https://www.vumc.org/cpm/cpm-blog-news/neanderthal-dna-has-subtle-significant-impact-human-traits <span class="field field--name-title field--type-string field--label-hidden">Neanderthal DNA has subtle but significant impact on human traits</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Fri, 02/12/2016 - 00:00</span> <a href="/cpm/blog-post-rss/377" class="feed-icon" title="Subscribe to Neanderthal DNA has subtle but significant impact on human traits"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><h3>Neanderthal DNA has subtle but significant impact on human traits</h3>&#13; &#13; <p>Since 2010 scientists have known that people of Eurasian origin have inherited anywhere from 1 to 4 percent of their DNA from Neanderthals.  In a study <a href="http://www.ncbi.nlm.nih.gov/pubmed/26912863">published in Science</a>, Tony Capra and Corinne Simonti used phenome-wide association studies to study the impact of Neanderthal alleles on human phenotypes in the <a href="https://emerge.mc.vanderbilt.edu" target="_blank">eMERGE Network</a>. Specific Neanderthal alleles significantly increased risk for nicotine addiction and hypercoagulability  Collectively, Neanderthal alleles were associated with depression and skin lesions.</p>&#13; &#13; <p> </p>&#13; &#13; <p><strong>PheWAS Catalog of Neanderthal variants </strong>(all tested Neanderthal variants and their phenotype associations):</p>&#13; &#13; <p><a href="https://phewas.mc.vanderbilt.edu/neanderthal">https://phewas.mc.vanderbilt.edu/neanderthal</a></p>&#13; &#13; <p> </p>&#13; &#13; <p>​<strong>Vanderbilt University press release:</strong></p>&#13; &#13; <p><a href="http://news.vanderbilt.edu/2016/02/neanderthal-dna-has-subtle-but-significant-impact-on-human-traits/">http://news.vanderbilt.edu/2016/02/neanderthal-dna-has-subtle-but-signi…</a> </p>&#13; </div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Fri, 12 Feb 2016 06:00:00 +0000 Visitor 377 at https://www.vumc.org/cpm Warner named medical director of Cancer Registry https://www.vumc.org/cpm/cpm-blog-news/warner-named-medical-director-cancer-registry <span class="field field--name-title field--type-string field--label-hidden">Warner named medical director of Cancer Registry</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Thu, 02/11/2016 - 00:00</span> <a href="/cpm/blog-post-rss/510" class="feed-icon" title="Subscribe to Warner named medical director of Cancer Registry"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-external-url field--type-link field--label-hidden field__item"><a href="https://news.vanderbilt.edu/2016/02/11/warner-named-medical-director-of-cancer-registry/" target="_blank">https://news.vanderbilt.edu/2016/02/11/warner-named-medical-director-of-cancer-registry/</a></div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Thu, 11 Feb 2016 06:00:00 +0000 Visitor 510 at https://www.vumc.org/cpm AMIA 2015 NLP Application Tutorial https://www.vumc.org/cpm/cpm-blog/amia-2015-nlp-application-tutorial <span class="field field--name-title field--type-string field--label-hidden">AMIA 2015 NLP Application Tutorial</span> <div class="field field--name-field-barista-posts-category field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/cpm/cpm-blog?cat=63" hreflang="und">Software</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Sun, 11/15/2015 - 13:46</span> <a href="/cpm/blog-post-rss/366" class="feed-icon" title="Subscribe to AMIA 2015 NLP Application Tutorial"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p><strong>AMIA 2015 NLP Application Tutorial</strong></p> <p>Below are the slides from the AMIA 2015 NLP Tutorial.  </p> <p> </p> <p>Josh Denny:  NLP applied to EHR phenotyping and medical education: </p> <p><a href="https://vumc.org/cpm/sites/vumc.org.cpm/files/public_files/josh%20amia%20NLP%20tutorial%202015.pdf">josh amia NLP tutorial 2015.pdf</a></p> <p> </p> <p>Hua Xu:  Introduction to pipeline NLP and Clinical Language Annotation, Modeling, and Processing Toolkit (CLAMP) </p> <p><a href="https://vumc.org/cpm/sites/vumc.org.cpm/files/public_files/2015_AMIA_NLP_Tutorial_CLAMP.pdf">2015_AMIA_NLP_Tutorial_CLAMP.pdf</a></p> <p> </p> </div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Sun, 15 Nov 2015 19:46:35 +0000 Visitor 366 at https://www.vumc.org/cpm Data diving for health https://www.vumc.org/cpm/cpm-blog-news/data-diving-health <span class="field field--name-title field--type-string field--label-hidden">Data diving for health</span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" typeof="schema:Person" property="schema:name" datatype="">Visitor</span></span> <span class="field field--name-created field--type-created field--label-hidden">Wed, 09/23/2015 - 00:00</span> <a href="/cpm/blog-post-rss/502" class="feed-icon" title="Subscribe to Data diving for health"> RSS: <i class="fa fa-rss-square"></i> </a> <div class="field field--name-field-barista-posts-external-url field--type-link field--label-hidden field__item"><a href="https://news.vanderbilt.edu/2015/09/23/data-diving-for-health/" target="_blank">https://news.vanderbilt.edu/2015/09/23/data-diving-for-health/</a></div> <div class="field field--name-field-lockdown-auth field--type-string field--label-above"> <div class="field__label">Lockdown Auth</div> <div class="field__item">1</div> </div> Wed, 23 Sep 2015 05:00:00 +0000 Visitor 502 at https://www.vumc.org/cpm