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Ranking Clinical Trials Using Elasticsearch

Ajinkya Yogesh Thorve, Haimonti Dutta
2017 Text Retrieval Conference  
This paper presents an approach to solving the problem by first preparing an index for the clinical trial descriptions based on specific tags in the XML files and querying them using Elasticsearch.  ...  Participants were challenged with the task of retrieving appropriate clinical trials from ClinicalTrials.gov for which a patient is eligible.  ...  These default values of k1 and b are used in the retrieval process. Figure 3 : 3 Figure 3: Performance of 30 topic queries on the clinical trials text corpus using Elasticsearch.  ... 
dblp:conf/trec/ThorveD17 fatcat:ya4rfzcxozecrbmug2rarryzom

DUTIR at TREC 2019: Precision Medicine Track

Jingkun Feng, Zhihao Yang, Zhiqiang Liu, Ling Luo, Hongfei Lin, Jian Wang
2019 Text Retrieval Conference  
The performance of our system is above the median for the scientific abstracts subtask and below median for the clinical trials subtask.  ...  First, we used Elasticsearch, an open-source Lucene-based full-text search engine, to obtain the initial retrieval results. Then we trained several deep models using TREC 2017 PM data.  ...  For clinical trials task, we only used Elasticsearch to search relevant articles. Experimental results show that only using Elasticsearch is not a good method. Figure 1 . 1 Figure 1.  ... 
dblp:conf/trec/FengYLLLW19 fatcat:aiarmr7kljgpthvtqaewosfvra

IBI at TREC 2018: Precision Medicine Track

Francesco Ronzano, Emilio Centeno, Judith Pérez-Granado, Laura I. Furlong
2018 Text Retrieval Conference  
to refine the ranking of search results proposed by Elasticsearch.  ...  To this purpose we rely on the query formulation capabilities provided by Elasticsearch, a full-text search engine, complemented by data processing steps useful both to properly build search queries and  ...  For each clinical case, participants have been required to deal with the following two subtasks: retrieve a ranked list of relevant scientific abstracts and a ranked list of clinical trials of interest  ... 
dblp:conf/trec/RonzanoCPF18 fatcat:73s3iqgjqza7bi4jkktv4cr5uu

PhenCards: a data resource linking human phenotype information to biomedical knowledge

James M. Havrilla, Cong Liu, Xiangchen Dong, Chunhua Weng, Kai Wang
2021 Genome Medicine  
Users can query human phenotype terms or clinical notes.  ...  PhenCards recommends the most probable genetic diseases and candidate genes based on phenotype terms from clinical notes.  ...  Data, PubMed, the IRS, openFDA, ClinicalTrials.gov, and DrugCentral for continuous development of their respective databases over the past several years, which have greatly facilitated and standardized clinical  ... 
doi:10.1186/s13073-021-00909-8 pmid:34034817 pmcid:PMC8147460 fatcat:z6btyzno7ze2xbvmbtdmjvoyem

Team UVA_ART at TREC 2018 Precision Medicine Track: Graph-based Concept Expansion and NLP for Document Relevance Boosting

Sean Mullane, Kasi Vegesana, Valentina Baljak
2018 Text Retrieval Conference  
We used Elasticsearch as our ranking and query engine with different query templates for each run.  ...  Our efforts demonstrate that the existing medical ontologies can be leveraged to achieve moderate results with little to no other clinical input.  ...  ranked and submitted clinical trials from a set of clinical trials listed on Clini-calTrials.gov.  ... 
dblp:conf/trec/MullaneVB18 fatcat:w3ww6mvhozhhdbdmdqzse3fveq

KlickLabs at TREC 2018 Precision Medicine track

Lediona Nishani, Maheedhar Kolla, Gaurav Baruah
2018 Text Retrieval Conference  
Utilizing demographic information in queries improves the performance for clinical trial retrieval.  ...  The 2018 Precision Medicine (PM) track aims to build systems, that sift through biomedical articles to find relevant cancer treatments for patients, as well as search for clinical trials for which a patient  ...  Indexing For both tasks (scientific articles and clinical trials) the available documents in the corpus have been indexed by making use of ElasticSearch [3] .  ... 
dblp:conf/trec/NishaniKB18 fatcat:t5yprrbysvffjh7dmgnhckerjm

LAMDA at TREC CDS track 2015 - Clinical Decision Support Track

Moon Soo Cha, Woo-Jin Han, Garam Lee, Minsung Kim, Kyung-Ah Sohn
2015 Text Retrieval Conference  
In TREC 2015 Clinical Decision Support Track, our goal is to retrieve the relevant medical articles for the questions about medical statement.  ...  Elasticsearch supports the similarity module that defines how matching documents are scored.  ...  Fig. 1 shows the overview of our system that consists of both our clinical decision support system and Elasticsearch framework [4] .  ... 
dblp:conf/trec/ChaHLKS15 fatcat:humxpafep5dulamniudofmucfy

TREC 2017 Precision Medicine - Medical University of Graz

Pablo López-García, Michel Oleynik, Zdenko Kasác, Stefan Schulz
2017 Text Retrieval Conference  
We submitted 5 fully automatic runs to both the biomedical articles and clinical trials subtasks, focusing strongly on the former.  ...  Our system was based on Elasticsearch, whose queries were generated modularly via our own open source framework.  ...  Acknowledgments We thank Marcus Bloice for proofreading the manuscript, and Lexigram, Inc. for providing us with an API key to access their medical knowledge graph.  ... 
dblp:conf/trec/Lopez-GarciaOK017 fatcat:bkofgcobhnfopnw6lj5azg3td4

ECNU-ICA team at TREC 2019 Precision Medicine Track

Qi Zheng, Yong Li, Jiaying Hu, Yan Yang, Liang He, Yi Xue
2019 Text Retrieval Conference  
After initial retrieval process, We further re-rank the retrieved documents using language model based re-ranker to get the final results. 1 https://www.lexigram.io/  ...  In this paper, we describe our biomedical retrieval system used in TREC 2019 precision medicine track.  ...  The detailed setting used in each runs are listed as follow: cl base: Baseline for clinical trials run, use default retrieval setting. clinic ft: Clinical trials baseline system with fine-tuned parameters  ... 
dblp:conf/trec/ZhengLHYHX19 fatcat:nyxih3qxnvgzfnbzqetzlst23e

A Hybrid Approach to Precision Medicine-related Biomedical Article Retrieval and Clinical Trial Matching

Yuan Ling, Sadid A. Hasan, Michele Filannino, Kevin P. Buchan, Kahyun Lee, Joey Liu, William Boag, Di Jin, Özlem Uzuner, Kathy Lee, Vivek V. Datla, Ashequl Qadir (+1 others)
2017 Text Retrieval Conference  
Evaluation results demonstrate that our best run obtained the 2nd highest precision (P@5) score for the clinical trial matching task and was consistently ranked within top 5 teams in all evaluation metrics  ...  We submitted five runs for biomedical article retrieval and five runs for clinical trial matching. Our approaches combine strict rule matching with an ontology-based solution.  ...  ranked clinical trials for patients.  ... 
dblp:conf/trec/LingHFBLLBJULDQ17 fatcat:6hbwuhnq5zernajc2voulhpihm

Aliababa DAMO Academy at TREC Precision Medicine 2020: State-of-the-art Evidence Retriever for Precision Medicine with Expert-in-the-loop Active Learning

Qiao Jin, Chuanqi Tan, Mosha Chen, Ming Yan, Songfang Huang, Ningyu Zhang, Xiaozhong Liu
2020 Text Retrieval Conference  
We use a two-step approach that includes: 1) a baseline retriever using query expansion with Elasticsearch (ES) and 2) an automatic or expert-in-the-loop reranker: the automatic re-ranker uses features  ...  The focus of the TREC PM Track is to retrieve academic papers that report critical clinical evidence for or against a given treatment in a population specified by its disease and gene mutation.  ...  in the ElasticSearch queries to lower the ranks of rare synonyms.  ... 
dblp:conf/trec/JinJTCYHZL20 fatcat:a3rtcfs7gfd6habzsg73r7zlcm

JULIE Lab & Med Uni Graz @ TREC 2019 Precision Medicine Track

Erik Faessler, Udo Hahn, Michel Oleynik
2019 Text Retrieval Conference  
The 2019 Precision Medicine Track at TREC (TREC-PM) aimed at identifying relevant documents from two collections, namely PubMed (biomedical abstracts) and ClinicalTrials.gov (clinical trials), given 40  ...  Our approach builds upon carefully designed weighted queries based on our experience from last year's participation and explores the usefulness of Learning to Rank (LETOR), trained on either the previous  ...  We also describe our approach to treatment ranking (Section 2.5) and indicate improvements for clinical trials (Section 2.6).  ... 
dblp:conf/trec/FaesslerHO19 fatcat:xshzxnt5t5gfrb2kf3octtne2i

VOH.CoLAB at TREC 2020 Precision Medicine Track

Miguel D. Cardoso, Flávio Martins
2020 Text Retrieval Conference  
We performed experiments with Drugbank-based synonym expansion, Rocchio-based pseudo-relevance feedback, and neural re-ranking using the BioBERT biomedical pre-trained language models.  ...  We present our approach and the methods implemented, including both submitted runs and several post-mortem experiments using different methods.  ...  Track Description In contrast with the 2019 edition, which promoted two tasks, one on Clinical Trials and another on Scientific Abstracts, this years' TREC Precision Medicine track focused only on a Scientific  ... 
dblp:conf/trec/CardosoM20 fatcat:5i5mpfzdufb7towqv4pkaicone

Brown University at TREC Precision Medicine 2018

Prakrit Baruah, Riya Dulepet, Kyle Qian, Carsten Eickhoff
2018 Text Retrieval Conference  
We use this information in the form of cubic rank transformations between initial weak rankers and the final ranking.  ...  Collection Indexing The collections of scholarly abstracts and clinical trials, respectively, are indexed using Apache Lucene [2] and Elasticsearch [3] .  ...  For clinical trial searches, any trials not matching the patient's age and gender were removed.  ... 
dblp:conf/trec/BaruahDQE18 fatcat:uloklguikfbylact3ykawsuctm

LongLife: a Platform for Personalized Search for Health and Life Sciences

Patrick Ernst, Erisa Terolli, Gerhard Weikum
2019 International Semantic Web Conference  
The system supports user-friendly access to entities, categories and free-text phrases in a corpus of 21 million documents, comprising scientific publications, clinical trials, encyclopedic articles, biomedical  ...  Professional Scenario: Doctors and researchers are interested in clinical trials and publications.  ...  LongLife stores the data based on ElasticSearch v.1.7.6.  ... 
dblp:conf/semweb/ErnstTW19 fatcat:okkvlhtecnc7vblwfy4bjxmds4
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