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PubMed Labs: An experimental platform for improving biomedical literature search [article]

Nicolas Fiorini, Kathi Canese, Rostyslav Bryzgunov, Ievgeniia Radetska, Asta Gindulyte, Martin Latterner, Vadim Miller, Maxim Osipov, Michael Kholodov, Grisha Starchenko, Evgeny Kireev, Zhiyong Lu
2018 arXiv   pre-print
PubMed is a freely accessible system for searching the biomedical literature, with approximately 2.5 million users worldwide on an average workday.  ...  We have recently developed PubMed Labs (, an experimental platform for users to test new features/tools and provide feedback, which enables us to make more informed decisions about  ...  Acknowledgment We would like to thank NCBI/NLM leadership for their support and many others (including our users) for their feedback and helpful discussion on the project.  ... 
arXiv:1806.04004v1 fatcat:wbwfiqdxafbhzkkr2epmwsn5nu

Towards PubMed 2.0

Nicolas Fiorini, David J Lipman, Zhiyong Lu
2017 eLife  
Staff from the National Center for Biotechnology Information in the US describe recent improvements to the PubMed search engine and outline plans for the future, including a new experimental site called  ...  PubMed Labs.  ...  , Asta Gindulyte and Martin Latterner for their work on PubMed Labs; Won Kim, Kathi Canese and Sharmin Hussain for their help with online experiments and log analysis; Jim Ostell, John Wilbur, Udi Manber  ... 
doi:10.7554/elife.28801 pmid:29083299 pmcid:PMC5662282 fatcat:mt6eim7gz5eurbjl2pgj74is6u

Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis

Phillip G Febbo, Mike G Mulligan, David A Slonina, Kimberly Stegmeir, Dolores Di Vizio, Paul R Martinez, Massimo Loda, Stephen C Taylor
2007 BMC Genomics  
Lab were derived.  ...  All analysis of data by investigators supported by Acumenta was performed in a blinded fashion; Acumenta supported investigators were unaware of the experiments from which the gene lists uploaded into Literature  ...  For each experimentally derived gene set, Literature Lab performs an automated literature search to determine the number of abstracts listing any of the identified genes and each term within the term list  ... 
doi:10.1186/1471-2164-8-461 pmid:18088408 pmcid:PMC2244637 fatcat:z4akucjbofaufnq3a3yfz7iq54

Indicators for the use of robotic labs in basic biomedical research: a literature analysis

Paul Groth, Jessica Cox
2017 PeerJ  
Robotic labs, in which experiments are carried out entirely by robots, have the potential to provide a reproducible and transparent foundation for performing basic biomedical laboratory experiments.  ...  In this article, we investigate whether these labs could be applicable in current experimental practice.  ...  Competing Interests Paul Groth and Jessica Cox are employees of Elsevier Labs, Amsterdam, Netherlands.  ... 
doi:10.7717/peerj.3997 pmid:29134146 pmcid:PMC5681851 fatcat:gnkvbapjzjcc3atpaku7bkahma

Overview of LiLAS 2021 – Living Labs for Academic Search [chapter]

Philipp Schaer, Timo Breuer, Leyla Jael Castro, Benjamin Wolff, Johann Schaible, Narges Tavakolpoursaleh
2021 Lecture Notes in Computer Science  
The Living Labs for Academic Search (LiLAS) lab aims to strengthen the concept of user-centric living labs for academic search.  ...  The methodological gap between real-world and lab-based evaluation should be bridged by allowing lab participants to evaluate their retrieval approaches in two real-world academic search systems from life  ...  Introduction The Living Labs for Academic Search (LiLAS) lab aims to strengthen the concept of user-centric living labs for the domain of academic search.  ... 
doi:10.1007/978-3-030-85251-1_25 fatcat:57decx3zzfc3vox6damwe2x62u

EMEN2: An Object Oriented Database and Electronic Lab Notebook

Ian Rees, Ed Langley, Wah Chiu, Steven J. Ludtke
2013 Microscopy and Microanalysis  
for use in virtually any experimental science.  ...  Object-oriented databases present an attractive alternative to traditional relational databases for situations where the experiments themselves are continually evolving.  ...  Acknowledgments We would like to thank NCMI users and collaborators for feedback to drive improvements and development of EMEN2.  ... 
doi:10.1017/s1431927612014043 pmid:23360752 pmcid:PMC3907281 fatcat:t2m6obgetfbxlfqku4o6ms6zva

An inexpensive and easy-to-implement approach to a Quality Management System for an academic research lab

Michael Hewera, Ann-Christin Nickel, Nina Knipprath, Sajjad Muhammad, Xiaolong Fan, Hans-Jakob Steiger, Daniel Hänggi, Ulf Dietrich Kahlert
2020 F1000Research  
For this we used eLabFTW, an electronic lab book, as hub for all other components of our Quality Management System (QMS) and digital storage of lab journals.  ...  Finally, we implemented an automated pipeline to be used for example for drug screens.  ...  It is an interesting manuscript that shows that research groups can improve the quality of their experimental work without spending lots of money.  ... 
doi:10.12688/f1000research.24494.2 fatcat:gnfvus7epzdcpixdkcatfjnmua

Measures to increase value of preclinical research - an inexpensive and easy-to-implement approach to a QMS for an academic research lab

Michael Hewera, Ann-Christin Nickel, Nina Knipprath, Sajjad Muhammad, Xiaolong Fan, Hans-Jakob Steiger, Daniel Hänggi, Ulf Dietrich Kahlert
2020 F1000Research  
For this we used eLabFTW, an electronic lab book, as hub for all other components of our quality management system (QMS). Storage of lab journals and project management will be done there as well.  ...  In a final step we implemented an automated pipeline to be used for example for drug screens.  ...  By establishing our lab bio bank, we aimed to provide a centralized storage facility for bio samples both for experimental and clinical research projects.  ... 
doi:10.12688/f1000research.24494.1 pmid:32765843 pmcid:PMC7385541 fatcat:rlohmhrqxvbr3mmf56xkmmfjpy

Measuring handrim wheelchair propulsion in the lab: a critical analysis of stationary ergometers

R. De Klerk, R. J. K. Vegter, V. L. Goosey-Tolfrey, B. S. Mason, J. P. Lenton, H. E. J. Veeger, L. H. V. Van Der Woude
2019 IEEE Reviews in Biomedical Engineering  
This narrative review provides an overview of the lab-based equipment used in published research and critically assesses their ability to simulate and measure wheelchair propulsion performance.  ...  Lab-based testing is either performed on a treadmill or a wheelchair ergometer (WCE). For this study WCEs were divided into three categories: roller, flywheel, and integrated ergometers.  ...  SEARCH STRATEGY For this narrative review, an overview of the existing literature was made by performing a semi-structured search using the PubMed, CINAHL, and Web of Science internet databases with the  ... 
doi:10.1109/rbme.2019.2942763 pmid:31675342 fatcat:a325tiujdvbahp5ulhp3awbuqe

User Interface Design for Searching Biomedical Literature

Carlos Iñiguez-Jarrín, José Ignacio Panach, Oscar Pastor López
2018 Information Systems Development  
This paper presents a UI design for the search of biomedical bibliography that incorporates solutions to the usability problems documented and detected by a study of the literature.  ...  Biomedical bibliographic sources are crucial resources for the work of physicians, biologists, and bioinformatics.  ...  Acknowledgments The authors thank the members of the PROS Center's Genome group for fruitful discussions.  ... 
dblp:conf/isdevel/Iniguez-JarrinP18a fatcat:wplheytjjffezdi7g6innourvy

Information retrieval and literature searching in today's information landscape

Bianca Kramer
2009 Hypothesis  
Recently, an experimental biomedical search engine was launched that makes use of semantic search algorithms (23) .  ...  Although PubMed, with over 19 million references from 5200 biomedical journals, is often used as the starting point for literature searching in the biomedical sciences (13), there are other databases that  ... 
doi:10.5779/hypothesis.v8i1.182 fatcat:nijcyqvpvve67mvi5nf24foqnm

Database resources of the National Center for Biotechnology Information

Eric W Sayers, Richa Agarwala, Evan E Bolton, J Rodney Brister, Kathi Canese, Karen Clark, Ryan Connor, Nicolas Fiorini, Kathryn Funk, Timothy Hefferon, J Bradley Holmes, Sunghwan Kim (+11 others)
2018 Nucleic Acids Research  
New resources released in the past year include PubMed Labs and a new sequence database search.  ...  The Entrez system provides search and retrieval operations for most of these data from 38 distinct databases. The E-utilities serve as the programming interface for the Entrez system.  ...  In particular, the authors would like to thank these individuals for their contributions to the resources described in  ... 
doi:10.1093/nar/gky1069 pmid:30395293 fatcat:6myevv752rbsjkfofodo4lo3gu

A2A: a platform for research in biomedical literature search

Maciej Rybinski, Sarvnaz Karimi, Vincent Nguyen, Cecile Paris
2020 BMC Bioinformatics  
Search engines such as PubMed provide a means to search and retrieve published literature, given a query.  ...  To give this control to both biomedical researchers and computer scientists working in biomedical information retrieval, we introduce a public online tool for searching over biomedical literature.  ...  For users looking for a literature search and browsing functionality on an up-to-date collection of documents, in most cases PubMed is a better choice.  ... 
doi:10.1186/s12859-020-03894-8 pmid:33349237 fatcat:dy45nsg2mvf3nlwrxf4s5wpe3a

Evaluation Infrastructures for Academic Shared Tasks

Johann Schaible, Timo Breuer, Narges Tavakolpoursaleh, Bernd Müller, Benjamin Wolff, Philipp Schaer
2020 Datenbank-Spektrum  
In addition, we introduce an evaluation infrastructure concept design aiming at reducing the shortcomings in shared tasks for search and recommender systems.  ...  An increasing amount of requirements for producing accurate retrieval results have to be considered, e.g., close integration of the system's users.  ...  The challenge on biomedical semantic indexing and question answering (BioASQ) [27] aims to improve the indexing process of PubMed 6 articles with the annotation of terms from the Medical Subject Headings  ... 
doi:10.1007/s13222-020-00335-x fatcat:f7lj6fr4n5hazoqtywrulw7b4u

Applications of the microphysiology systems database for experimental ADME-Tox and disease models

Mark Schurdak, Lawrence Vernetti, Luke Bergenthal, Quinn K Wolter, Tong Ying Shun, Sandra Karcher, D Lansing Taylor, Albert Gough
2020 Lab on a Chip  
We have previously implemented an open source Microphysiology Systems Database (MPS-Db), with a simple icon driven interface, as a resource for MPS researchers and drug discovery/development scientists  ...  We introduce the Disease Portal module with links to resources for the design of MPS disease models and studies and discuss the integration of computational models for the prediction of PK/PD and disease  ...  Acknowledgements The authors wish to thank members of the UPDDI for experimental and IT support: Richard DeBiasio, Dillon Gavlock, Xiang Li, Celeste Reese, Michael Castiglione, and Harold Takyi.  ... 
doi:10.1039/c9lc01047e pmid:32211684 pmcid:PMC7497411 fatcat:yyekndbitzgshfbkuc4xppgwom
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