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UniCarbKB: building a knowledge platform for glycoproteomics

Matthew P. Campbell, Robyn Peterson, Julien Mariethoz, Elisabeth Gasteiger, Yukie Akune, Kiyoko F. Aoki-Kinoshita, Frederique Lisacek, Nicolle H. Packer
2013 Nucleic Acids Research  
Here, we introduce a refactored database, supported by substantial new curated data collections and intuitive user-interfaces that improve database searching.  ...  For the first release over 890 references, 3740 glycan structure entries and 400 glycoproteins have been curated.  ...  ACKNOWLEDGEMENTS The authors thank the support provided by many developers and collaborators who have contributed considerable effort to provide tools and resources for the glycosciences.  ... 
doi:10.1093/nar/gkt1128 pmid:24234447 pmcid:PMC3964942 fatcat:t5qv6fey6vdgvol2hwoavgygjy

Site-based data curation based on hot spring geobiology

Carole L. Palmer, Andrea K. Thomer, Karen S. Baker, Karen M. Wickett, Christie L. Hendrix, Ann Rodman, Stacey Sigler, Bruce W. Fouke, Juan A. Añel
2017 PLoS ONE  
The SBDC framework can serve as a global model for the collection and description of hot spring systems field data that can be readily adapted for application to the curation of data from other kinds scientifically  ...  Site-Based Data Curation (SBDC) is an approach to managing research data that prioritizes sharing and reuse of data collected at scientifically significant sites.  ...  Finally, we thank all of the workshop participants for their participation and insights, and An Yan for her assistance with revisions.  ... 
doi:10.1371/journal.pone.0172090 pmid:28253269 pmcid:PMC5333826 fatcat:p5g6qgwo7nbxha6x2cfs4jic3a

A Framework for Applying Data Integration and Curation Pipelines to Support Integration of Migrants and Refugees in Europe [chapter]

Oya Deniz Beyan, Siegfried Handschuh, Adamantios Koumpis, Garyfallos Fragidis, Stefan Decker
2016 IFIP Advances in Information and Communication Technology  
Trustable and high quality data sets will have a positive impact on businesses by improving decision making capabilities based on big data analysis, It will also serve as a collaboration framework for  ...  For this goal, we have developed a framework to provide a systematic transfer of information and technology across different sectors and a developed a data sharing and linking culture.  ... 
doi:10.1007/978-3-319-45390-3_50 fatcat:v6ssaf5dnnej5h2d5nkoluaz5y

Saving Cultural Heritage with Digital Make-Believe: Machine Learning and Digital Techniques to the Rescue

Yasser Mustafa, Kathy Clawson, Chris Bowerman
2017 HCI 2017  
The application of digital methods for content-based curation and dissemination of cultural heritage data offers unique advantages for physical sites at risk of damage.  ...  We propose a framework incorporating computational methods such as: digital image processing, multi-lingual text analysis, and 3D modelling, to facilitate enhanced data archive, federated search, and analysis  ...  the nature of input data, for example objects, buildings, landscapes, and regions.  ... 
doi:10.14236/ewic/hci2017.97 dblp:conf/bcshci/MostafaCB17 fatcat:udkwxhbpb5gkdmg2waxgwo3a7i

Digital Data Practices and the Long Term Ecological Research Program Growing Global

Helena Karasti, Karen S. Baker
2008 International Journal of Digital Curation  
It highlights (1) taking into account the extended temporal horizon of data care, (2) aligning support for data, science and information infrastructure, and (3) integrating site and network-level responsibilities  ...  It describes a number of salient data characteristics that are specific to the LTER program and outlines some central features of the curation approach cultivated within the US LTER network.  ...  We thank Katharina Schleidt for contributions to the earlier version. We offer special thanks to the participants of the LT(S)ER networks with whom we have studied and collaborated.  ... 
doi:10.2218/ijdc.v3i2.57 fatcat:kufvz6a2incojdvmqrgahdyeje

A first RDF implementation of the COSMIC database on mutations in cancer

Achille Zappa, Paolo Romano
2012 EMBnet journal  
This framework is intended to evolve the web into a distributed knowledge-base and a first step in this evolution is the generation of a Web of Data (Bizer et al., 2009) .  ...  For instance, D2RQ generates predicate names which are based on the RDB column names: it has no way to know when a predicate refers to a property for which a shared representation (ontological concept)  ... 
doi:10.14806/ej.18.b.585 fatcat:nx3c2g65xfaoxitpzdndxdkeoi

End User Evaluation of the FAIR4Health Data Curation Tool [chapter]

Mert Gencturk, Alper Teoman, Celia Alvarez-Romero, Alicia Martinez-Garcia, Carlos Luis Parra-Calderon, Beatriz Poblador-Plou, Matthias Löbe, A. Anil Sinaci
2021 Studies in Health Technology and Informatics  
The aim of this study is to build an evaluation framework for the user-centric testing of the Data Curation Tool.  ...  The tool was developed in the scope of the FAIR4Health project to make health data FAIR by transforming them from legacy formats into a Common Data Model based on HL7 FHIR.  ...  We followed a sound and methodological approach to build our evaluation framework which helped us produce systematic and comparable results for different subcomponents and features of the Data Curation  ... 
doi:10.3233/shti210110 pmid:34042695 fatcat:xofo3a3y45g5hmj2i6bvx3c3gi

Payao: a community platform for SBML pathway model curation

Y. Matsuoka, S. Ghosh, N. Kikuchi, H. Kitano
2010 Bioinformatics  
Payao is a community-based, collaborative web service platform for gene-regulatory and biochemical pathway model curation.  ...  Web site implemented in Seaser Framework 2.0 with S2Flex2, MySQL 5.0 and Tomcat 5.5, with all major browsers supported.  ...  What is needed is a framework to facilitate tracking and update mechanism for modelers and researchers in the community to contribute to the collaborative model building and curation process.  ... 
doi:10.1093/bioinformatics/btq143 pmid:20371497 pmcid:PMC2865864 fatcat:lw7srogqnjbvtn2yensatqec7a

A Multiple Perspective Account of Digital Curation for Cultural Heritage: Tasks, Disciplines and Institutions

Tugce Karatas, Vincenzo Lombardo
2020 Adjunct Publication of the 28th ACM Conference on User Modeling, Adaptation and Personalization  
In particular, the innumerable initiatives for providing access to cultural heritage data are ideally coordinated by digital curation and are part of the process since the beginning.  ...  Digital data in support of cultural heritage management are addressed by the digital curation process, which has been emerging to account for the diversity of disciplinary communities and cultural heritage  ...  ., a container with a cup shape in a trench of an archaeological site) 5 , the digital curation process builds some digital assets; these can be acquired from the asset (e.g., by photograph) or created  ... 
doi:10.1145/3386392.3399277 dblp:conf/um/KaratasL20 fatcat:bddfjl5qjvecxna27r3kpf2ada

WormBase 2014: new views of curated biology

Todd W. Harris, Joachim Baran, Tamberlyn Bieri, Abigail Cabunoc, Juancarlos Chan, Wen J. Chen, Paul Davis, James Done, Christian Grove, Kevin Howe, Ranjana Kishore, Raymond Lee (+21 others)
2013 Nucleic Acids Research  
The Perl web framework Catalyst (www.catalystframe work.org) provides the core of the new site.  ...  FUTURE DIRECTIONS The WormBase curation strategy, build process and Web site continue to evolve in response to user feedback and technical requirements.  ... 
doi:10.1093/nar/gkt1063 pmid:24194605 pmcid:PMC3965043 fatcat:lh2mkgbydvfwrdngdv7nz3icme

Community-Enhanced Repository for Engaged Scholarship: A case study on supporting digital humanities research

Sarah J. Sweeney, Julia Flanders, Abbie Levesque
2017 College & Undergraduate Libraries  
Building digital curation and sustainability into digital humanities project development is challenging, and engaging digital humanities researchers fully as partners in curation practices with the library  ...  , and enable the library and its partners to work together to build sustainable digital projects.  ...  'the faculty Web site problem' --an ever-growing number of requests for Web-based spaces and tools to collaborate on scholarly research and share the results" (28), a challenge that they suggest could  ... 
doi:10.1080/10691316.2017.1336144 fatcat:ul5nm2mwsbbt3dddgfictught4

DISC-UK DataShare Project

Robin Rice
2020 Zenodo  
• Not to be confused with 'open data definition' used for copying personal data from one social networking site to another.  ...  DISC-UK DataShare State of the Art Review (H Gibbs, 2007) • Data Audit Framework -a JISC project led by DCC at University of Glasgow to carry out the recommendation in Liz Lyon's 2007 report: 'A framework  ... 
doi:10.5281/zenodo.3782038 fatcat:3vvdpvbekvhybimsf7deohttpu

Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint

Karen E. Ross, Cecilia N. Arighi, Jia Ren, Hongzhan Huang, Cathy H. Wu
2013 Database: The Journal of Biological Databases and Curation  
In this article, we evaluate the current state of phosphorylation event curation and then present a bioinformatics framework for the annotation and representation of phosphorylated proteins and construction  ...  The integrated approach involves (i) text mining guided by RLIMS-P, a tool that identifies phosphorylation-related information in scientific literature; (ii) data mining from curated PPI databases; (iii  ...  Acknowledgements The authors would like to thank Peter D'Eustachio for assistance with searching Reactome and Natalia Roberts for providing phosphorylation site information from PRO.  ... 
doi:10.1093/database/bat038 pmid:23749465 pmcid:PMC3675891 fatcat:utjrqnq6wngbvjgni5tf6bhmaq

Mining Biological Pathways Using WikiPathways Web Services

Thomas Kelder, Alexander R. Pico, Kristina Hanspers, Martijn P. van Iersel, Chris Evelo, Bruce R. Conklin, Winston Hide
2009 PLoS ONE  
Exposing WikiPathways through a web service opens up new ways of utilizing pathway information and assisting the community curation process.  ...  WikiPathways is a platform for creating, updating, and sharing biological pathways [1] . Pathways can be edited and downloaded using the wiki-style website.  ...  The WikiPathways web service could be used as framework for building data analysis tools that make use of pathway information.  ... 
doi:10.1371/journal.pone.0006447 pmid:19649250 pmcid:PMC2714472 fatcat:w2ed245xnfavjbwkgcooib6qie

Toward interoperable bioscience data

Susanna-Assunta Sansone, Philippe Rocca-Serra, Dawn Field, Eamonn Maguire, Chris Taylor, Oliver Hofmann, Hong Fang, Steffen Neumann, Weida Tong, Linda Amaral-Zettler, Kimberly Begley, Tim Booth (+38 others)
2012 Nature Genetics  
At the heart of the ISA framework is the extensible, hierarchical 'ISA-Tab' file format 20 that can be used alone or as a template for a variety of spreadsheet-based formats for data sharing 21 .  ...  The SEEK is a web-based registry and repository for systems biology data, models and experiments.  ... 
doi:10.1038/ng.1054 pmid:22281772 pmcid:PMC3428019 fatcat:wfg3czxhjncylphgdtlzpvr26u
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