OHDSI MEETINGS THIS WEEK
OHDSI Community Call - Tuesday at 12pm EThttps://meetings.webex.com/collabs/#/meetings/detail?uuid=M59X2V1U61WC9ASID2Z5N3UT95-D1JL&rnd=811649.98682211
Patient-level prediction (Western hemisphere) workgroup meeting - Wednesday at 12pm EThttps://global.gotomeeting.com/join/972917661
Population-Level Estimation (Eastern hemisphere) workgroup meeting - Wednesday at 3pm Hong Kong timehttps://meetings.webex.com/collabs/meetings/join?uuid=M6WE9AOKFETH2VEFPVCZWWBIT0-D1JL
Architecture Working Group - Thursday at 1pm EThttps://jjconferencing.webex.com/mw3100/mywebex/default.do?service=1&main_url=%2Fmc3100%2Fe.do%3Fsiteurl%3Djjconferencing%26AT%3DMI%26EventID%3D283835502%26MTID%3Dmb7e839a762fbdaab0608f27500679223%26Host%3DQUhTSwAAAARK-_S6Kosdv23jLkqgL3r7r2_kmXe14dpWuPX_s-awpxIklc165xpM7OlFBUqACSQve0MmCqdtp1SllwRQjyjj0%26FrameSet%3D2&siteurl=jjconferencing&nomenu=true
GIS working group meeting - Monday (November 20th) at 10am EThttps://tufts.webex.com/mw3200/mywebex/default.do?service=1&siteurl=tufts&nomenu=true&main_url=%2Fmc3200%2Fe.do%3Fsiteurl%3Dtufts%26AT%3DMI%26EventID%3D562301137%26UID%3D528546812%26Host%3DQUhTSwAAAAT_EHuT3Ok-zHVhY1-kVGh78TH62dPsFk0x99qz1E9039sh_Eiepw8CoZeIF2SfnopQ8oAZaLN9PkzIZovRf2kV0%26FrameSet%3D2%26MTID%3Dm243d8e9a9c6c2d42d5182aeb5d30efdb1
ANNOUNCEMENTS
2018 Symposium Planning Committee: We’re looking for volunteers to join next year’s symposium planning committee. Interested? Check out our call for volunteers here:
Thank you to everyone who helped to plan the OHDSI Symposium this year! Once again, we are looking for planning committee members to assist with the 2018 Symposium.
Some of the prerequisites to help plan are: 1) Availability for a planning call every 2 weeks (usually on Fridays) 2) Assisting on the peer-review of the Collaborative Showcase submissions 3) Creating the agenda including panels, sessions, presentations and tutorials 4) Obtaining speakers, if applicable 5) Moderating sessions, if a…
2017 OHDSI Symposium Materials - Presentation slides from this year’s symposium and tutorials have been uploaded here: https://www.ohdsi.org/past-events/
Symposium Videos - Recordings from the symposium are now available here: https://www.ohdsi.org/past-events/2017-ohdsi-symposium-materials/2017-ohdsi-sympoium-videos/
Tutorial videos: https://www.ohdsi.org/past-events/2017-tutorials-population-level-estimation/ https://www.ohdsi.org/past-events/2017-tutorials-ohdsi-development-architecture/ https://www.ohdsi.org/past-events/2017-tutorials-patient-level-prediction/
We are all special cases.
COMMUNITY PUBLICATIONS
Normalizing acronyms and abbreviations to aid patient understanding of clinical texts: ShARe/CLEF eHealth Challenge 2013, Task 2.
DL Mowery, BR South, L Christensen, J Leng, LM Peltonen, S Salanterä, H Suominen, D Martinez, S Velupillai, N Elhadad, G Savova, S Pradhan and WW Chapman,
Journal of biomedical semantics , Jul 2016 01
The ShARe/CLEF eHealth challenge lab aims to stimulate development of natural language processing and information retrieval technologies to aid patients in understanding their clinical reports. In clinical text, acronyms and abbreviations, also referenced as short forms, can be difficult for patients to understand. For one of three shared tasks in 2013 (Task 2), we generated a reference standard of clinical short forms normalized to the Unified Medical Language System. This reference standard can be used to improve patient understanding by linking to web sources with lay descriptions of annotated short forms or by substituting short forms with a more simplified, lay term.In this study, we evaluate 1) accuracy of participating systems' normalizing short forms compared to a majority sense baseline approach, 2) performance of participants' systems for short forms with variable majority sense distributions, and 3) report the accuracy of participating systems' normalizing shared normalized concepts between the test set and the Consumer Health Vocabulary, a vocabulary of lay medical terms.The best systems submitted by the five participating teams performed with accuracies ranging from 43 to 72 %. A majority sense baseline approach achieved the second best performance. The performance of participating systems for normalizing short forms with two or more senses with low ambiguity (majority sense greater than 80 %) ranged from 52 to 78 % accuracy, with two or more senses with moderate ambiguity (majority sense between 50 and 80 %) ranged from 23 to 57 % accuracy, and with two or more senses with high ambiguity (majority sense less than 50 %) ranged from 2 to 45 % accuracy. With respect to the ShARe test set, 69 % of short form annotations contained common concept unique identifiers with the Consumer Health Vocabulary. For these 2594 possible annotations, the performance of participating systems ranged from 50 to 75 % accuracy.Short form normalization continues to be a challenging problem. Short form normalization systems perform with moderate to reasonable accuracies. The Consumer Health Vocabulary could enrich its knowledge base with missed concept unique identifiers from the ShARe test set to further support patient understanding of unfamiliar medical terms.
Patient Experiences Using an Inpatient Personal Health Record.
J Woollen, J Prey, L Wilcox, A Sackeim, S Restaino, ST Raza, S Bakken, S Feiner, G Hripcsak and D Vawdrey,
Applied clinical informatics , 2016
To investigate patients' experience using an inpatient personal health record (PHR) on a tablet computer to increase engagement in their hospital care.We performed observations and conducted semi-structured interviews with 14 post-operative cardiac surgical patients and their family members who received an inpatient PHR. Themes were identified using an inductive coding scheme.All participants responded favorably to having access to view their clinical information. A majority (85.7%) of participants used the application following an initial training session. Patients reported high satisfaction with being able to view their hospital medications and access educational materials related to their medical conditions. Patients reported a desire to view daily progress reports about their hospital stay and have access to educational information about their post-acute recovery. In addition, patients expressed a common desire to view their diagnoses, laboratory test results, radiology reports, and procedure notes in language that is patient-friendly.Patients have unmet information needs in the hospital setting. Our findings suggest that for some inpatients and their family members, providing personalized health information through a tablet computer may improve satisfaction, decrease anxiety, increase understanding of their health conditions, and improve safety and quality of care.
Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop.
K Verspoor, A Oellrich, N Collier, T Groza, P Rocca-Serra, L Soldatova, M Dumontier and N Shah,
Journal of biomedical semantics , 2016 12 12
This special issue covers selected papers from the 18th Bio-Ontologies Special Interest Group meeting and Phenotype Day, which took place at the Intelligent Systems for Molecular Biology (ISMB) conference in Dublin in 2015. The papers presented in this collection range from descriptions of software tools supporting ontology development and annotation of objects with ontology terms, to applications of text mining for structured relation extraction involving diseases and phenotypes, to detailed proposals for new ontologies and mapping of existing ontologies. Together, the papers consider a range of representational issues in bio-ontology development, and demonstrate the applicability of bio-ontologies to support biological and clinical knowledge-based decision making and analysis.The full set of papers in the Thematic Issue is available at http://www.biomedcentral.com/collections/sig .
Toward multimodal signal detection of adverse drug reactions
FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.
JT Bolleman, CJ Mungall, F Strozzi, J Baran, M Dumontier, RJ Bonnal, R Buels, R Hoehndorf, T Fujisawa, T Katayama and PJ Cock,
Journal of biomedical semantics , Jun 2016 13
Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples.We have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned "omics" areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations.Our ontology allows users to uniformly describe - and potentially merge - sequence annotations from multiple sources. Data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.
Electronic Health Records-Based Phenotyping
Electronic Health Records-Based Phenotyping Contributors Rachel Richesson, PhD, MPH Michelle Smerek Shelley Rusincovitch Meredith Nahm Zozus, PhD Paramita Saha Chaudhuri, PhD W. Ed Hammond, PhD Robert M. Califf, MD Greg Simon, MD Beverly Green, MD,...
A Data Quality Assessment Guideline for Electronic Health Record Data Reusehttps://egems.academyhealth.org/articles/abstract/10.13063/egems.1280/
The impact of different surgical procedures on hypoparathyroidism after thyroidectomy: A population-based study.
KC Chen, U Iqbal, PA Nguyen, CH Hsu, CL Huang, YE Hsu, S Atique, MM Islam, YJ Li and WS Jian,
Medicine , Oct 2017
The main objective of this study is to investigate the outcome between surgical procedures and the risk of development of hypoparathyroidism followed by surgical procedure in patients with thyroid disorders.We analyzed the data acquired from Taiwan's Bureau of National Health Insurance (BNHI) research database from 1998 to 2011 and found 9316 patients with thyroid surgery. Cox regression model was used to calculate the hazard ratio (HR).A count of 314 cases (3.4%) of hypoparathyroidism was identified. The 9 years cumulated incidence of hypoparathyroidism was the highest in patient undergone bilateral total thyroidectomy (13.5%) and the lowest in the patient with unilateral subtotal thyroidectomy (1.2%). However, in the patients who had undergone unilateral subtotal, the risk was the highest in bilateral total (HR: 11.86), followed by radical thyroidectomy with unilateral neck lymph node dissection (HR: 8.56), unilateral total (HR, 4.39), and one side total and another side subtotal (HR: 2.80).The extent of thyroid resection determined the risk of development of hypoparathyroidism. It is suggested that the association of these factors is investigated in future studies.
Gender-based personalized pharmacotherapy: a systematic review.
MM Islam, U Iqbal, BA Walther, PA Nguyen, YJ Li, NK Dubey, TN Poly, JHB Masud, S Atique and S Syed-Abdul,
Archives of gynecology and obstetrics , Jun 2017
In general, male and female are prescribed the same amount of dosage even if most of the cases female required less dosage than male. Physicians are often facing problem on appropriate drug dosing, efficient treatment, and drug safety for a female in general. To identify and synthesize evidence about the effectiveness of gender-based therapy; provide the information to patients, providers, and health system intervention to ensure safety treatment; and minimize adverse effects.We performed a systematic review to evaluate the effect of gender difference on pharmacotherapy. Published articles from January 1990 to December 2015 were identified using specific term in MEDLINE (PubMed), EMBASE, and the Cochrane library according to search strategies that strengthen the reporting of observational and clinical studies.Twenty-six studies fulfilled the inclusion criteria for this systematic review, yielding a total of 6309 subjects. We observed that female generally has a lower the gastric emptying time, gastric PH, lean body mass, and higher plasma volume, BMI, body fat, as well as reduce hepatic clearance, difference in activity of Cytochrome P450 enzyme, and metabolize drugs at different rate compared with male. Other significant factors such as conjugation, protein binding, absorption, and the renal elimination could not be ignored. However, these differences can lead to adverse effects in female especially for the pregnant, post-menopausal, and elderly women.This systematic review provides an evidence for the effectiveness of dosage difference to ensure safety and efficient treatment. Future studies on the current topic are, therefore, recommended to reduce the adverse effect of therapy.
Comparison of Utilization and Clinical Outcomes for Belatacept- and Tacrolimus-Based Immunosuppression in Renal Transplant Recipients.
X Wen, MJ Casey, AH Santos, A Hartzema and KL Womer,
American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons , 2016 11
The performance of belatacept in a real clinical setting has not been reported. A retrospective cohort study was conducted using registry data comparing 1-year clinical outcomes between belatacept- and tacrolimus-treated adult kidney transplant recipients (KTRs) from January 6, 2011, through January 12, 2014. Of 50 244 total patients, 417 received belatacept plus tacrolimus, 458 received belatacept alone, and 49 369 received tacrolimus alone at discharge. In the overall study cohort, belatacept alone was associated with a higher risk of 1-year acute rejection, with the highest rates associated with non-lymphocyte-depleting induction (adjusted hazard ratio 2.65, 95% confidence interval 1.90-3.70, p < 0.0001). There was no significant difference in rejection rates between belatacept plus tacrolimus and tacrolimus alone. In KTRs who met inclusion criteria for the Belatacept Evaluation of Nephroprotection and Efficacy as First-line Immunosuppression Trial-Extended Criteria Donors (BENEFIT-EXT), 1-year kidney function was higher with belatacept plus tacrolimus and belatacept alone versus tacrolimus alone (mean estimated GFR 65.6, 60.4 and 54.3 mL/min per 1.73 m2 , respectively; p < 0.001). The incidence of new-onset diabetes after transplantation was significantly lower with belatacept plus tacrolimus and belatacept alone versus tacrolimus alone (1.7%, 2.2%, and 3.8%, respectively; p = 0.01). Despite improved graft function and metabolic complications with belatacept alone, it may be advisable to add short-term tacrolimus in the first year after transplant and to consider lymphocyte-depleting induction in patients with high rejection risk, as the risk-benefit ratio allows.
