Literature DB >> 30305770

A Corpus with Multi-Level Annotations of Patients, Interventions and Outcomes to Support Language Processing for Medical Literature.

Benjamin Nye1, Junyi Jessy Li2, Roma Patel3, Yinfei Yang4, Iain J Marshall5, Ani Nenkova6, Byron C Wallace7.   

Abstract

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the 'PICO' elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

Entities:  

Year:  2018        PMID: 30305770      PMCID: PMC6174533     

Source DB:  PubMed          Journal:  Proc Conf Assoc Comput Linguist Meet        ISSN: 0736-587X


  18 in total

1.  On the impossibility of being expert.

Authors:  Alan G Fraser; Frank D Dunstan
Journal:  BMJ       Date:  2010-12-14

2.  Modernizing the systematic review process to inform comparative effectiveness: tools and methods.

Authors:  Byron C Wallace; Issa J Dahabreh; Christopher H Schmid; Joseph Lau; Thomas A Trikalinos
Journal:  J Comp Eff Res       Date:  2013-05       Impact factor: 1.744

3.  The automation of systematic reviews.

Authors:  Guy Tsafnat; Adam Dunn; Paul Glasziou; Enrico Coiera
Journal:  BMJ       Date:  2013-01-10

4.  Extracting PICO Sentences from Clinical Trial Reports using Supervised Distant Supervision.

Authors:  Byron C Wallace; Joël Kuiper; Aakash Sharma; Mingxi Brian Zhu; Iain J Marshall
Journal:  J Mach Learn Res       Date:  2016       Impact factor: 3.654

5.  Understanding and using the medical subject headings (MeSH) vocabulary to perform literature searches.

Authors:  H J Lowe; G O Barnett
Journal:  JAMA       Date:  1994-04-13       Impact factor: 56.272

6.  Aggregating and Predicting Sequence Labels from Crowd Annotations.

Authors:  An T Nguyen; Byron C Wallace; Junyi Jessy Li; Ani Nenkova; Matthew Lease
Journal:  Proc Conf Assoc Comput Linguist Meet       Date:  2017

Review 7.  Automating data extraction in systematic reviews: a systematic review.

Authors:  Siddhartha R Jonnalagadda; Pawan Goyal; Mark D Huffman
Journal:  Syst Rev       Date:  2015-06-15

8.  Identifying reports of randomized controlled trials (RCTs) via a hybrid machine learning and crowdsourcing approach.

Authors:  Byron C Wallace; Anna Noel-Storr; Iain J Marshall; Aaron M Cohen; Neil R Smalheiser; James Thomas
Journal:  J Am Med Inform Assoc       Date:  2017-11-01       Impact factor: 4.497

9.  Living systematic reviews: 2. Combining human and machine effort.

Authors:  James Thomas; Anna Noel-Storr; Iain Marshall; Byron Wallace; Steven McDonald; Chris Mavergames; Paul Glasziou; Ian Shemilt; Anneliese Synnot; Tari Turner; Julian Elliott
Journal:  J Clin Epidemiol       Date:  2017-09-11       Impact factor: 6.437

10.  A corpus of potentially contradictory research claims from cardiovascular research abstracts.

Authors:  Abdulaziz Alamri; Mark Stevenson
Journal:  J Biomed Semantics       Date:  2016-06-07
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  23 in total

1.  Identifying main finding sentences in clinical case reports.

Authors:  Mengqi Luo; Aaron M Cohen; Sidharth Addepalli; Neil R Smalheiser
Journal:  Database (Oxford)       Date:  2020-01-01       Impact factor: 3.451

2.  Outcome Prediction from Behaviour Change Intervention Evaluations using a Combination of Node and Word Embedding.

Authors:  Debasis Ganguly; Martin Gleize; Yufang Hou; Charles Jochim; Francesca Bonin; Alessandra Pascale; Pierpaolo Tommasi; Pol Mac Aonghusa; Robert West; Marie Johnston; Mike Kelly; Susan Michie
Journal:  AMIA Annu Symp Proc       Date:  2022-02-21

3.  Generating (Factual?) Narrative Summaries of RCTs: Experiments with Neural Multi-Document Summarization.

Authors:  Byron C Wallace; Sayantan Saha; Frank Soboczenski; Iain J Marshall
Journal:  AMIA Jt Summits Transl Sci Proc       Date:  2021-05-17

4.  Understanding Clinical Trial Reports: Extracting Medical Entities and Their Relations.

Authors:  Benjamin E Nye; Jay DeYoung; Eric Lehman; Ani Nenkova; Iain J Marshall; Byron C Wallace
Journal:  AMIA Jt Summits Transl Sci Proc       Date:  2021-05-17

5.  Data extraction methods for systematic review (semi)automation: A living systematic review.

Authors:  Lena Schmidt; Babatunde K Olorisade; Luke A McGuinness; James Thomas; Julian P T Higgins
Journal:  F1000Res       Date:  2021-05-19

6.  Semi-Automated evidence synthesis in health psychology: current methods and future prospects.

Authors:  Iain J Marshall; Blair T Johnson; Zigeng Wang; Sanguthevar Rajasekaran; Byron C Wallace
Journal:  Health Psychol Rev       Date:  2020-01-29

7.  Toward assessing clinical trial publications for reporting transparency.

Authors:  Halil Kilicoglu; Graciela Rosemblat; Linh Hoang; Sahil Wadhwa; Zeshan Peng; Mario Malički; Jodi Schneider; Gerben Ter Riet
Journal:  J Biomed Inform       Date:  2021-02-26       Impact factor: 6.317

8.  A comprehensive study of mobility functioning information in clinical notes: Entity hierarchy, corpus annotation, and sequence labeling.

Authors:  Thanh Thieu; Jonathan Camacho Maldonado; Pei-Shu Ho; Min Ding; Alex Marr; Diane Brandt; Denis Newman-Griffis; Ayah Zirikly; Leighton Chan; Elizabeth Rasch
Journal:  Int J Med Inform       Date:  2020-12-24       Impact factor: 4.046

9.  A neuro-symbolic method for understanding free-text medical evidence.

Authors:  Tian Kang; Ali Turfah; Jaehyun Kim; Adler Perotte; Chunhua Weng
Journal:  J Am Med Inform Assoc       Date:  2021-05-06       Impact factor: 4.497

10.  UMLS-based data augmentation for natural language processing of clinical research literature.

Authors:  Tian Kang; Adler Perotte; Youlan Tang; Casey Ta; Chunhua Weng
Journal:  J Am Med Inform Assoc       Date:  2021-03-18       Impact factor: 4.497

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