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User-Centric Annotation Management for Biological Data [chapter]

Qinglan Li, Alexandros Labrinidis, Panos K. Chrysanthis
2008 Lecture Notes in Computer Science  
In this paper, we propose to treat annotations as first-class citizens for biological data management by presenting a user-centric, view-based annotation framework, called ViP.  ...  Although all such systems are implemented to take user input (i.e., the annotations themselves), very few systems are user-centric, taking into account user preferences on how annotations should propagate  ...  We would like to thank Chad Spensky for his help in designing the user interface.  ... 
doi:10.1007/978-3-540-89965-5_7 fatcat:v7wy3sfvq5eunp5vxpo3pi7hpa

PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data

Steven N. Hart, Raymond M. Moore, Michael T. Zimmermann, Gavin R. Oliver, Jan B. Egan, Alan H. Bryce, Jean-Pierre A. Kocher
2015 PeerJ  
PANDA represents 34 data/annotations as icons in the graph while maintaining the other data elements (i.e. other columns for 35 the table of annotations).  ...  Annotation) Explorer, a 31 visualization tool that integrates gene-level annotation in the context of biological pathways to help 32 interpret complex data from disparate sources.  ...  PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data Steven N Hart, Raymond M Moore, Michael T Zimmermann, Gavin R Oliver, Jan B Egan, Alan H Bryce, Jean-Pierre A  ... 
doi:10.7717/peerj.970 pmid:26038725 pmcid:PMC4451017 fatcat:zexukr4wlzejlav3b3edcsjx5i

WebLab: a data-centric, knowledge-sharing bioinformatic platform

Xiaoqiao Liu, Jianmin Wu, Jun Wang, Xiaochuan Liu, Shuqi Zhao, Zhe Li, Lei Kong, Xiaocheng Gu, Jingchu Luo, Ge Gao
2009 Nucleic Acids Research  
Dedicated space is provided for users to store their input data and analysis results.  ...  To fulfill such requirements, we have developed a data-centric knowledge-sharing platform WebLab for biologists to fetch, analyze, manipulate and share data under an intuitive web interface.  ...  Data management As a data-centric platform, WebLab provides a powerful data management system for users to store and manage their data and scientific literatures online.  ... 
doi:10.1093/nar/gkp428 pmid:19465388 pmcid:PMC2703900 fatcat:fjzepwjmvfbw5cpu7m2ylwe4pq

Pathway Palette: A rich internet application for peptide-, protein- and network-oriented analysis of MS data

Manor Askenazi, Shaojuan Li, Saurav Singh, Jarrod A. Marto
2010 Proteomics  
Unfortunately, tools designed to leverage the "peptide-centric" content of mass spectrometry-based proteomics lag the current rate of data production.  ...  In addition to sheer quantity, the diversity of relevant information which needs to be integrated in order to glean biological insight from the data poses an enduring challenge to practitioners [2] .  ...  Acknowledgments The authors thank Eric Smith for preparation of figures, and also members of the Marto Lab for valuable discussions and testing of Pathway Palette.  ... 
doi:10.1002/pmic.200900723 pmid:20198642 pmcid:PMC3139977 fatcat:2aoi6n2u3nc7jijjqej3wfkwaq

BarleyBase--an expression profiling database for plant genomics

L. Shen
2004 Nucleic Acids Research  
Users can perform cross-experiment queries on probe sets based on observed expression profiles and/or based on known biological information.  ...  Controlled vocabularies for gene and plant ontologies, as well as interconnecting links to physical or genetic map and other genomic data in PlantGDB, Gramene and GrainGenes, allow users to perform EST  ...  Instructive data visualization and presentation of the data are indispensable for users to efficiently mine the data and derive meaningful biological interpretations.  ... 
doi:10.1093/nar/gki123 pmid:15608273 pmcid:PMC540077 fatcat:a7wwql2dxjfcfggnsgw3xx5h5u

Genomic pathways database and biological data management

Z. M. Ozsoyoglu, G. Ozsoyoglu, J. Nadeau
2006 Animal Genetics  
In this paper we discuss the properties of biological data, and challenges it poses for data management, and argue that, in order to meet the data management requirements for "digital biology", careful  ...  integration of the existing technologies and the development of new data management techniques for biological data are needed.  ...  technologies for biological data as well as the development of new data management techniques are needed.  ... 
doi:10.1111/j.1365-2052.2006.01477.x pmid:16887001 fatcat:v3uph3nkyvbmvdennnpfkrecsy

HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency

Chen Li, Sri H. Ramarathinam, Jerico Revote, Georges Khoury, Jiangning Song, Anthony W. Purcell
2017 Scientific Reports  
With the goal of benefiting HIV related research, we collected a number of biological annotations for all the entries in HIVed besides their expression profile, including basic protein information, Gene  ...  We manually curated a variety of third-party databases for structural and functional annotations of the protein entries in HIVed.  ...  Acknowledgements The authors would like to thank all the authors whose experimental data have been included in the database and the curators of several public databases, for making this work possible.  ... 
doi:10.1038/srep45509 pmid:28358052 pmcid:PMC5371986 fatcat:z4zjshuoo5bv5elufi4c3qtude

An ontology-centric architecture for extensible scientific data management systems

Yuan-Fang Li, Gavin Kennedy, Faith Ngoran, Philip Wu, Jane Hunter
2013 Future generations computer systems  
In this paper we present an ontologycentric architecture for data management systems that is extensible and domain independent.  ...  Data management has become a critical challenge faced by a wide array of scientific disciplines in which the provision of sound data management is pivotal to the achievements and impact of research projects  ...  Finally we wish to thank Dr Xavier Sirault and Dr Kai Xu for their assistance in developing the domain models.  ... 
doi:10.1016/j.future.2011.06.007 fatcat:xswbe7m46nfq7hyrvvmc3czjgu

C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms

Balaguru Ravikumar, Zaid Alam, Gopal Peddinti, Tero Aittokallio
2017 Nucleic Acids Research  
Most of the existing compound-centric chemoinformatics tools lack interactive options and user interfaces that are critical for the real-time needs of chemical biologists carrying out compound screening  ...  Toward that end, we introduce C-SPADE, an opensource exploratory web-tool for interactive analysis and visualization of drug profiling assays (biochemical, cell-based or cell-free) using compound-centric  ...  We thank Disha Malani and her colleagues for providing and explaining the example drug screening data.  ... 
doi:10.1093/nar/gkx384 pmid:28472495 pmcid:PMC5570255 fatcat:izk4ce5ggbgg3gtfim3zpnclqm

Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB

Zhi-Liang Hu, Carissa A Park, James M Reecy
2018 Nucleic Acids Research  
Our ultimate goals of database development are to provide infrastructure for data collection, curation, and annotation, and more importantly, to support innovated data structure for new types of data mining  ...  We have focused our efforts on data curation, improved data quality maintenance, new tool developments, and database co-developments, in order to provide convenient platforms for users to query and analyze  ...  A strategy for unambiguous management of these data during database development is the use of biological ontologies.  ... 
doi:10.1093/nar/gky1084 pmid:30407520 pmcid:PMC6323967 fatcat:at6wmjfuhjdmnfnuvw5ado65wq

PiHelper: an open source framework for drug-target and antibody-target data

B. A. Aksoy, J. Gao, G. Dresdner, W. Wang, A. Root, X. Jing, E. Cerami, C. Sander
2013 Bioinformatics  
in many biological systems.  ...  PiHelper has utilities to (i) import drug-and antibody-target information; (ii) search the associations either programmatically or through a web user interface (UI); (iii) visualize the data interactively  ...  ACKNOWLEDGEMENTS We gratefully acknowledge Emek Demir, Ö zgu¨n Babur, Anil Korkut and Nikolaus Schultz (MSKCC, cBio) for their helpful comments on the article and the framework.  ... 
doi:10.1093/bioinformatics/btt345 pmid:23766416 pmcid:PMC3722529 fatcat:vfmtith3gzfajlg7tvtlodhtp4

dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more

Hai Fang, Julian Gough
2012 Nucleic Acids Research  
All ontological terms have probabilistic scores for their associations.  ...  Domain-centric GO, 'dcGO', provides associations between ontological terms and protein domains at the superfamily and family levels.  ...  The automatically generated slim version of each ontology is based on annotation frequency (4) , and it provides the user with a manageable and more coarse-grained list.  ... 
doi:10.1093/nar/gks1080 pmid:23161684 pmcid:PMC3531119 fatcat:hfk5fqktlnbttoxb5g7gic6iqa

Plant-Based Microarray Data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a Submission Tool for Arabidopsis Gene Expression Data to ArrayExpress

G. Mukherjee
2005 Plant Physiology  
Plant data are queryable both in ArrayExpress and in the Data Warehouse databases, which support queries based on gene-centric and sample-centric annotation.  ...  It was designed as a tool for users with minimal bioinformatics expertise, has comprehensive help and user support, and represents a simple solution to meeting the MIAME guidelines for the Arabidopsis  ...  public curated normalized data that supports gene-centric queries.  ... 
doi:10.1104/pp.105.063156 pmid:16219923 pmcid:PMC1255982 fatcat:ylj2obzlzjho7pratwpr2btcba

HTS-DB: an online resource to publish and query data from functional genomics high-throughput siRNA screening projects

Rebecca E. Saunders, Rachael Instrell, Rossella Rispoli, Ming Jiang, Michael Howell
2013 Database: The Journal of Biological Databases and Curation  
It also provides a repository for additional measurements obtained from screens that were not the focus of the project, such as cell viability, and groups these data so that it can provide a gene-centric  ...  This format allows users to browse and search data from large-scale studies in an informative and intuitive way.  ...  Acknowledgements The authors thank their colleagues at the LRI for allowing to make their hard-won data public before publication, and Ilaria Gori and Nicholas McGranahan for helpful comments on the manuscript  ... 
doi:10.1093/database/bat072 pmid:24122843 pmcid:PMC3796064 fatcat:jqb6t7zjdzcq3pri6r462fyku4

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

Jessica Severin, Andrew M Waterhouse, Hideya Kawaji, Timo Lassmann, Erik van Nimwegen, Piotr J Balwierz, Michiel JL de Hoon, David A Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten O Daub (+1 others)
2009 Genome Biology  
EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets that requires minimal development for new data types  ...  http://fantom.gsc.riken.jp/4/ edgeexpress summarizes gene expression patterns in the context of alternative promoter structures and regulatory transcription factors and microRNAs using intuitive gene-centric  ...  Acknowledgements This work was supported by a Research Grant for RIKEN Omics Science Center from MEXT to YH and a grant of the Genome Network Project [2] from the Ministry of Education, Culture, Sports  ... 
doi:10.1186/gb-2009-10-4-r39 pmid:19374773 pmcid:PMC2688930 fatcat:hdvyvljpfzeqbjynzkac7aejry
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