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An Open-Access Platform for Transparent and Reproducible Structured Searching

Tony Russell-Rose, Jon Chamberlain
2019 Proceedings of the 42nd International ACM SIGIR Conference on Research and Development in Information Retrieval - SIGIR'19  
This eliminates many sources of error, makes the query semantics more transparent, and offers an open-access platform for sharing reproducible search strategies and best practices.  ...  Interactive query suggestions are provided via an NLP services API, and support is offered for optimising, translating and sharing search strategies as executable artefacts.  ...  This eliminates many sources of error, makes their semantics more transparent, and offers an open-access platform for sharing reproducible search templates and best practices.  ... 
doi:10.1145/3331184.3331394 dblp:conf/sigir/Russell-RoseC19 fatcat:3hz2hpugnrcflnbmrnqr7jqb2q

Data accessibility and reproducibility: Moving to transparent publishing in the biosciences

Bernd Pulverer
2015 Information Services and Use  
In what follows, firstly, I will highlight the shift to transparent publishing at EMBO Press, for which open science provides context.  ...  In addition to the published literature, open science policies encourage posting of a vast amount of data in structured and unstructured repositories.  ...  Transparent publishing does not have to change or undermine existing business models, and can be complementary to or, indeed, an alternative to Open Access.  ... 
doi:10.3233/isu-150780 fatcat:qxa4ifbvkffrdacziwu64x473u

Designing the Structured Search Experience: Rethinking the Query-Builder Paradigm

Tony Russell-Rose, Farhad Shokraneh
2020 Weave: Journal of Library User Experience  
Knowledge workers such as healthcare information professionals, legal researchers, and librarians need to create and execute search strategies that are comprehensive, transparent, and reproducible.  ...  This offers a more intuitive user experience (UX) that eliminates many sources of error, makes the query semantics more transparent, and offers new ways to collaborate, share, and optimize search strategies  ...  If that transpires to be a practicable proposition, then such a development could have profound implications for the way in which people teach, learn, and apply professional search skills.  ... 
doi:10.3998/weave.12535642.0003.102 fatcat:ulsdixc4ujckbhjlfglsnf7tma

Orchestrating and sharing large multimodal data for transparent and reproducible research [article]

Anthony Mammoliti, Petr Smirnov, Minoru Nakano, Zhaleh Safikhani, Christopher Eeles, Heewon Seo, Sisira Kadambat Nair, Arvind S Mer, Chantal Ho, Gangesh Beri, Rebecca Kusko, Benjamin Haibe-Kains (+1 others)
2020 bioRxiv   pre-print
Reproducibility is essential to open science, as there is limited relevance for findings that can not be reproduced by independent research groups, regardless of its validity.  ...  To overcome these issues, we created a cloud-based platform called ORCESTRA (orcestra.ca), which provides a flexible framework for the reproducible processing of multimodal biomedical data.  ...  Pachyderm provides a free and open-source version of the tool that contains all the functionalities required to develop a platform ensuring transparent and reproducible processing of multimodal data.  ... 
doi:10.1101/2020.09.18.303842 fatcat:h7vnbidkj5gmjafadpzsbl3dqe

PEERS - an open science "Platform for the Exchange of Experimental Research Standards" in biomedicine [article]

Annesha Sil, Anton Bespalov, Christina Dalla, Chantelle Ferland-Beckham, Arnoud Herremans, Konstantinos Karantzalos, Martien J Kas, Nikolaos Kokras, Michael J Parnham, Pavlina Pavlidi, Kostis Pristouris, Thomas Steckler (+2 others)
2021 biorxiv/medrxiv   pre-print
To address this problem, we present PEERS (Platform for the Exchange of Experimental Research Standards), an open-access online platform that is built to aid scientists in determining which experimental  ...  Most importantly, the platform is based on a structured and transparent system for rating the strength of evidence related to each identified factor and its relevance for a specific method/model.  ...  Guido Steiner for their valuable input and discussions during the conceptualization of PEERS and the initial phase of the project.  ... 
doi:10.1101/2021.07.31.454443 fatcat:xv5vmb2hkvd7dgi6qgqae3lf3y

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

Jeremy Goecks, Anton Nekrutenko, James Taylor, The Galaxy Team
2010 Genome Biology  
Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems.  ...  Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are.  ...  This work was supported by NIH grants HG004909 (AN and JT), HG005133 (JT and AN), and HG005542 (JT and AN), by NSF grant DBI-0850103 (AN and JT) and by funds from the Huck Institutes for the Life Sciences  ... 
doi:10.1186/gb-2010-11-8-r86 pmid:20738864 pmcid:PMC2945788 fatcat:2ahwanuacfb3zo3ktjp3pevf6q

AN APPROACH TO VALUE AGGREGATION IN OPEN GOVERNMENTAL DATA IN BRAZIL

2017 Asia Pacific Journal of Contemporary Education and Communication Technology  
To do so, governments could make a set of tools available, developed on open platform, for a better data treatment and visualization by their users.  ...  a repository with coding in an open platform, to assist in the data analysis available in the Brazilian Open Data Portal, thus adding value to such open data.  ...  The Brazilian Open Data Portal is the central point for the search and access to public data in Brazil.  ... 
doi:10.25275/apjcectv3i2ict6 fatcat:j47hu3eizbbjjkgwe23tenxshe

PEERS — An Open Science "Platform for the Exchange of Experimental Research Standards" in Biomedicine

Annesha Sil, Anton Bespalov, Christina Dalla, Chantelle Ferland-Beckham, Arnoud Herremans, Konstantinos Karantzalos, Martien J. Kas, Nikolaos Kokras, Michael J. Parnham, Pavlina Pavlidi, Kostis Pristouris, Thomas Steckler (+2 others)
2021 Frontiers in Behavioral Neuroscience  
To address this problem, we developed "PEERS" (Platform for the Exchange of Experimental Research Standards), an open-access online platform that is built to aid scientists in determining which experimental  ...  The platform is based on a structured and transparent system for rating the strength of evidence related to each identified factor and its relevance for a specific method/model.  ...  Guido Steiner for their valuable input and discussions during the conceptualization of PEERS and the initial phase of the project.  ... 
doi:10.3389/fnbeh.2021.755812 pmid:34744655 pmcid:PMC8567102 fatcat:zjhskqj4v5abnh52zg7qbbcnv4

Exchange of Clinical and Omics Data According to FAIR Principles: A Review of Open Source Solutions

Philipp Pugliese, Christian Knell, Jan Christoph
2020 Methods of Information in Medicine  
Objectives The study aims at identification of platforms by literature search that are suitable for implementation in translational research, in particular with regard to their FAIRness.  ...  Results Platforms have been identified which are suitable for linking with other translational platforms with regard to documentation, long-term archiving, and processing as well as for FAIR handling of  ...  The authors thank the contributors of the Base, Ensembl, Galaxy, GenePattern, ISA-Tools, LabKey Server, openBIS, SABIO-RK and SEEK platforms who answered our request for information.  ... 
doi:10.1055/s-0040-1712968 pmid:32620018 fatcat:o2acklthsbbzlclmfs7xyrpsg4

Tools of discovery

T. Lemberger
2014 Molecular Systems Biology  
Molecular Systems Biology has transitioned to the new EMBO Press publishing platform to offer a richer and more transparent access to high-quality research.  ...  W hen Molecular Systems Biology was launched in 2005 as an Open Access journal, the scientific motivation was to disseminate immediately the results produced by the systems biology community and to make  ...  Improving access to this core component of the paper will be one of the priorities for the development of the EMBO Press platform.  ... 
doi:10.1002/msb.201305048 pmid:24408915 pmcid:PMC4023401 fatcat:eyyj42w2crhdva2ny6ymwqu5de

Item 5 : RDM Workshop

Mareike Christina Harms Buss, Haakon Lund, Katrine Flindt Holmstrand, Katrine Düring Davidsen
2020 Zenodo  
This included an introduction to the FAIR principles and Data Management Plans (DMP).  ...  Buss, Haakon Lund, Katrine Flindt Holmstrand File 5.2: What is Open Science and the library role Author: Katrine Flindt Holmstrand File 5.3: Research Data Life Cycle Author: Haakon Lund File 5.4: FAIR  ...  Transparency: … should provide open and transparent means for judging the credibility of a research result Evaluation: …support fair evaluation Discoverability: ...facilitate search, exploration  ... 
doi:10.5281/zenodo.3773736 fatcat:ih2d7wjd4rglrgdh4ap4thssmi

Open Science. Why and how?

Katja Mayer
2021 Zenodo  
This is intended to intensify transparency, reusability and exchange with industry and society. In the workshop "Open Science - why and how?"  ...  Open Science Workshop, October 20, 2021 Open Science means making research processes and research results - including methods, processes, research data and publications - as accessible as possible.  ...  Ideally, additional rights such as the right to copy, distribute, search, link, crawl and mine should also be provided. Open Access: what's in it for you?  ... 
doi:10.5281/zenodo.5584828 fatcat:x5oom6epbrg3rc5bwya3wje4lq

Removing Barriers to Reproducible Research in Archaeology [article]

Emma Karoune, Esther Plomp
2022 Zenodo  
parts of a research lifecycle such as data collection, data analysis, data archiving, etc, and making all stages reproducible by using a history tracking system (version control) and transparent documation  ...  Finally, in an extensive appendix, we address common questions about reproducible research to remove the stigma about these issues and suggest ways to overcome them.  ...  Many thanks to Yo Yehudi for her work on indexing references on data science and to Ben Marwick for his list of reproducible archaeological articles.  ... 
doi:10.5281/zenodo.6618672 fatcat:7wmhdwdolrhffjkootfkdkho2u

Challenges and Directions in 3D and VR Data Curation

Nathan Frank Hall, Juliet Hardesty, Zack Lischer-Katz, Jennifer Johnson, Matt Cook, Julie Griffin, Andrea Ogier, Tara Carlisle, Zhiwu Xie, Robert McDonald, Jamie Wittenberg
1970 International Journal of Digital Curation  
, and transparency for research integrity and reproducibility; and features for storage, access, and management to facilitate re-use by researchers and educators.  ...  , data dictionaries for 3D research, and aggregation tools for expanding discovery; 2) development of an open source viewer that supports streaming and annotation on archival formats of 3D models and makes  ...  Jamie Wittenberg) for their time, contributions, and cooperation in this study.  ... 
doi:10.2218/ijdc.v14i1.588 fatcat:3z4vng7vvrhxdj7uqluvewjo5e

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

Hannes L Röst, Timo Sachsenberg, Stephan Aiche, Chris Bielow, Hendrik Weisser, Fabian Aicheler, Sandro Andreotti, Hans-Christian Ehrlich, Petra Gutenbrunner, Erhan Kenar, Xiao Liang, Sven Nahnsen (+15 others)
2016 Nature Methods  
., J.P, and T.S. acknowledge funding from BMBF (grants 031A367 and 031A535A). We are deeply grateful for the support of the KNIME team, the Proteome Discoverer team, and the Compound Discoverer team.  ...  for direct access to core data structures and algorithms.  ...  We present OpenMS 2.0 (http://www.openms.org), a robust open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data.  ... 
doi:10.1038/nmeth.3959 pmid:27575624 fatcat:khqavbue6zepvpbsfzmkwcg6ly
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