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The annotation and the usage of scientific databases could be improved with public issue tracker software

Giovanni Marco Dall'Olio, Jaume Bertranpetit, Hafid Laayouni
2010 Database: The Journal of Biological Databases and Curation  
We would also thank Maria Teresa Rodriguez Plata for valuable feedback and tips. We would like to thank the community at http://biostar.stackexchange.com/ for useful discussion.  ...  Acknowledgements We would like to thank Brandon Invergo and Kevin Keys for grammatical revisions and their nice inputs; and Ludovica Montanucci, Pierre Luisi and Marc Pybus for their helpful discussion  ...  The annotations on public scientific databases could be improved with the help of the community of scientists who use them.  ... 
doi:10.1093/database/baq035 pmid:21186182 pmcid:PMC3011984 fatcat:nitxnn6cnfft3npi54qzo7rgse

D1.5 Incorporation Of Monitoring Statistics And Benchmarking Results In Registry Releases

Jon Ison, Hans Ienasescu, Matus Kalas, Tools Community
2018 Zenodo  
The objective of EXCELERATE Deliverable 1.5 is to review software metrics and assess their usefulness in the context of the bio.tools (https://bio.tools) registry, with view to expose in bio.tools, metrics  ...  The core aim is to provide the end-user with robust, scientifically relevant measures of quality and performance, to guide them in their comparison and selection of tools through: 1) enabling end-users  ...  We identified 9 core aspects of software quality and 61 atomic metrics or indicators, of which 33 are supported by biotoolsSchema and thus calculable from software annotations in bio.tools; the rest could  ... 
doi:10.5281/zenodo.1452909 fatcat:ilpaegdjcfejjehycpuodbo5qi

Community curation of bioinformatics software and data resources

2019 Briefings in Bioinformatics  
The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose.  ...  To address this, the European Infrastructure for Biological Information is supporting a systematic approach towards a comprehensive registry of tools and databases for all domains of bioinformatics, provided  ...  Acknowledgements We acknowledge with gratitude the support of our funders: The Danish Ministry of Higher Education and Science and ELIXIR-EXCELERATE under the European Union's Horizon 2020 research and  ... 
doi:10.1093/bib/bbz075 pmid:31624831 pmcid:PMC7947956 fatcat:sqk4wc3mc5arzomejnmq24qggi

Acknowledging contributions to online expert assistance

Andra Waagmeester, Simon Cockell, Pierre Lindenbaum, Daniel Silvestre, Giovanni Marco Dall'Olio, Andra Waagmeester, Gareth Palidwor, Pawel Szczesny, Istvan Albert, Mary Mangan, Chris Evelo, Chris Miller
2011 Nature Precedings  
The annotation and the usage of scientific databases could be improved with public issue tracker software. Database (Oxford). 2010 Dec 23;2010:baq035. Print 2010.  ...  During the writing we opened some questions on biostar (example) and followed some discussions on the site, to know what was the opinion of the rest of the scientific community about some of the databases  ... 
doi:10.1038/npre.2011.6041 fatcat:tj7z2wa7bbhb7bh3m4mre6cpky

MSR Mining Challenge: The SmartSHARK Repository Mining Data [article]

Alexander Trautsch, Fabian Trautsch, Steffen Herbold
2021 arXiv   pre-print
The SmartSHARK repository mining data is a collection of rich and detailed information about the evolution of software projects.  ...  Moreover, the data does not contain only raw data scraped from repositories, but also annotations in form of labels determined through a combination of manual analysis and heuristics, as well as links  ...  This preprint will then be updated with the final list of projects available for the challenge. differences between the discussions on mailing lists and within issue trackers can be answered without scraping  ... 
arXiv:2102.11540v2 fatcat:smznxa5bkbcmzf2d5gr5pfnspe

Information management system [chapter]

1994 System Software and Software Systems  
The software complies with microarray communication standards and uses an industry standard relational database management system combined with a platform-independent web browser interface for data entry  ...  Finally, a highly flexible reporting tool enables the users and laboratory managers to search the database on the usage history of the platform.  ...  Microarray software should be able to cope with the constant improvements in technology.  ... 
doi:10.1142/9789812814944_0007 fatcat:mut5wvjyergftcon57cav4i5ly

information management system [chapter]

Martin H. Weik
2000 Computer Science and Communications Dictionary  
The software complies with microarray communication standards and uses an industry standard relational database management system combined with a platform-independent web browser interface for data entry  ...  Finally, a highly flexible reporting tool enables the users and laboratory managers to search the database on the usage history of the platform.  ...  Microarray software should be able to cope with the constant improvements in technology.  ... 
doi:10.1007/1-4020-0613-6_8939 fatcat:7nlcguakhze4zbhlvofxazmjby

biotoolsSchema: a formalized schema for bioinformatics software description

Jon Ison, Hans Ienasescu, Emil Rydza, Piotr Chmura, Kristoffer Rapacki, Alban Gaignard, Veit Schwämmle, Jacques van Helden, Matúš Kalaš, Hervé Ménager
2021 GigaScience  
Background Life scientists routinely face massive and heterogeneous data analysis tasks and must find and access the most suitable databases or software in a jungle of web-accessible resources.  ...  . biotoolsSchema results from a series of community-driven workshops and is deployed in the bio.tools registry, providing the scientific community with >17,000 machine-readable and human-understandable  ...  Acknowledgements Jon Ison warmly acknowledges the support of the Institut Franc ¸ais de Bioinformatique.  ... 
doi:10.1093/gigascience/giaa157 pmid:33506265 fatcat:3ds7hqtaxbgqxfjbt3li5fx5q4

Crowdsourcing biocuration: the Community Assessment of Community Annotation with Ontologies (CACAO) [article]

Jolene Ramsey, Brenley McIntosh, Daniel Renfro, Suzanne A. Aleksander, Sandra LaBonte, Curtis Ross, Adrienne E. Zweifel, Nathan Liles, Shabnam Farrar, Jason J. Gill, Ivan Erill, Sarah Ades (+36 others)
2021 bioRxiv   pre-print
This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions.  ...  Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace.  ...  Acknowledgments Funding was provided by the National Institutes of Health (awards GM088849 and GM089636 to J.C.H.) and the National Science Foundation (awards EF-0949351 and DBI-1565146 to J.C.H.) and  ... 
doi:10.1101/2021.04.30.440339 fatcat:ni6k25anrnb7nlfgkqp46tlixq

The Data Use Ontology to streamline responsible access to human biomedical datasets

Jonathan Lawson, Moran N. Cabili, Giselle Kerry, Tiffany Boughtwood, Adrian Thorogood, Pinar Alper, Sarion R. Bowers, Rebecca R. Boyles, Anthony J. Brookes, Matthew Brush, Tony Burdett, Hayley Clissold (+45 others)
2021 Cell Genomics  
Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions.  ...  DUO annotations increase the FAIRness of datasets and support data linkages using common data use profiles when integrating the data for secondary analyses.  ...  National Cancer Institute have all contributed to the establishment and review of DUO terms, which are aligned with data use terms or phrasing of their respective consent forms.  ... 
doi:10.1016/j.xgen.2021.100028 pmid:34820659 pmcid:PMC8591903 fatcat:2eqm5raidnfvpbljfi5g3idx5e

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Lisa Harper, Jacqueline Campbell, Ethalinda K S Cannon, Sook Jung, Monica Poelchau, Ramona Walls, Carson Andorf, Elizabeth Arnaud, Tanya Z Berardini, Clayton Birkett, Steve Cannon, James Carson (+40 others)
2018 Database: The Journal of Biological Databases and Curation  
, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable.  ...  The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential.  ...  Acknowledgements We acknowledge with thanks The National Science Foundation Plant Genome Research Program Award # 1444573 for funding the AgBioData Workshop and development and hosting of the AgBio-Data  ... 
doi:10.1093/database/bay088 pmid:30239679 pmcid:PMC6146126 fatcat:spcxmd66qrgdnos4larqfvf6ai

Ontology application and use at the ENCODE DCC

Venkat S. Malladi, Drew T. Erickson, Nikhil R. Podduturi, Laurence D. Rowe, Esther T. Chan, Jean M. Davidson, Benjamin C. Hitz, Marcus Ho, Brian T. Lee, Stuart Miyasato, Gregory R. Roe, Matt Simison (+6 others)
2015 Database: The Journal of Biological Databases and Curation  
Additionally, we provide examples of how ontologies are used to annotate ENCODE metadata and how the annotations can be identified via ontology-driven searches at the ENCODE portal.  ...  and the scientific community.  ...  Acknowledgements We thank all participants in the ENCODE Consortium for collaborations that have enhanced the metadata definitions and the ENCODE Portal users for their useful feedback.  ... 
doi:10.1093/database/bav010 pmid:25776021 pmcid:PMC4360730 fatcat:7ccxq7rgmje7nffans7edld5da

Tools and collaborative environments for bioinformatics research

P. Romano, R. Giugno, A. Pulvirenti
2011 Briefings in Bioinformatics  
We then review the principles and some of the most relevant applications of social networking, with a special attention to networks supporting scientific collaboration, by also highlighting some critical  ...  issues, such as identification of users and standardization of formats.  ...  Acknowledgements Authors wish to thank Tom Wiley for his precious support in the preparation of the final version of the article.  ... 
doi:10.1093/bib/bbr055 pmid:21984743 pmcid:PMC3220874 fatcat:nsemkrp6yjgx5biyjwvrlyz534

Technical requirements on the ENES Climate Data Infrastructure software stack (M10.1) [article]

Sandro Fiore, Paola Nassisi, Fabrizio Antonio, Lars Bärring, Katharina Berger, David Hassel, Martin Juckes, Philip Kershaw, Stephan Kindermann, Guillaume Levavasseur, Alessandra Nuzzo, Christian Pagé (+4 others)
2020 Zenodo  
This report addresses the milestone M10.1 "Technical requirements on the software stack" of the IS-ENES3 project and provides a comprehensive list of technical requirements driven by the work done in WP5  ...  The document adopts the concepts of user stories and use cases to translate them into functional and non-functional requirements for the whole ENES CDI software stack.  ...  Python library for accessing the compiled database; Web site providing navigable view of the database; Issue tracker; Database as XML file, with XSD schema; Documentation about software and schema; Provide  ... 
doi:10.5281/zenodo.3731018 fatcat:eb364luiyjbwphiv3q7puxm5da

PDBWiki: added value through community annotation of the Protein Data Bank

H. Stehr, J. M. Duarte, M. Lappe, J. Bhak, D. M. Bolser
2010 Database: The Journal of Biological Databases and Curation  
The authors would like to thank Maryana Bhak for help proofreading and correcting a draft of the article.  ...  Acknowledgements The article was collaboratively written using the MediaWiki software package http://www.mediawiki.org.  ...  We address the issues of data integrity and trust by clearly separating the original database content from the user annotations.  ... 
doi:10.1093/database/baq009 pmid:20624717 pmcid:PMC2911844 fatcat:wfjmw6seavb3lghiegphrrvhg4
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