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Names are key to the big new biology

D.J. Patterson, J. Cooper, P.M. Kirk, R.L. Pyle, D.P. Remsen
2010 Trends in Ecology & Evolution  
The result will be a virtual data commons, expanding as further data are shared, allowing biology to become more of a "big science".  ...  Informatics devices will exploit this 'big new biology', revitalizing comparative biology with a broad perspective to reveal previously inaccessible trends and discontinuities, so helping us to reveal  ...  DJP thanks the NSF for support through the Data Conservancy project and the Alfred P. Sloan and John D. and Catherine T. MacArthur foundations for their support.  ... 
doi:10.1016/j.tree.2010.09.004 pmid:20961649 fatcat:mao7pxajlbfjrjuifqdqtcdsae

The ReFuGe 2020 Consortium—using "omics" approaches to explore the adaptability and resilience of coral holobionts to environmental change

2015 Frontiers in Marine Science  
For instance, the Global Invertebrate Genomics Alliance (GIGA) was formed to coordinate current efforts generating and analyzing invertebrate non-arthropod genomic data (GIGA Community of Scientists, 2014  ...  been linked directly with loss of biodiversity.  ... 
doi:10.3389/fmars.2015.00068 fatcat:yhxcs377frd5jbavhi76zq4k2a

Towards a unified open access dataset of molecular interactions

Pablo Porras, Elisabet Barrera, Alan Bridge, Noemi Del-Toro, Gianni Cesareni, Margaret Duesbury, Henning Hermjakob, Marta Iannuccelli, Igor Jurisica, Max Kotlyar, Luana Licata, Ruth C Lovering (+15 others)
2020 Nature Communications  
Additionally, we provide examples of how IMEx data are being used by biomedical researchers and integrated in other bioinformatic tools and resources.  ...  The International Molecular Exchange (IMEx) Consortium provides scientists with a single body of experimentally verified protein interactions curated in rich contextual detail to an internationally agreed  ...  Examples of uses of the IMEx dataset Building high-quality networks for data analysis.  ... 
doi:10.1038/s41467-020-19942-z pmid:33262342 pmcid:PMC7708836 fatcat:soyrqsypencbrkmqwxzjz6crp4

Why the Current Insistence on Open Access to Scientific Data? Big Data, Knowledge Production, and the Political Economy of Contemporary Biology

Sabina Leonelli
2013 Bulletin of Science, Technology & Society  
Large molecular datasets, often referred to as 'big data', are increasingly incorporated into digital databases, many of which are freely accessible online.  ...  how internet-based communication and the use of online databases impact scientific research and its role within contemporary society. 2  ...  Let us not forget that the vast majority of genomic data made available online over the last ten years have yet to be used in ways that are scientifically meaningful; and that some scientists view much  ... 
doi:10.1177/0270467613496768 fatcat:awfblv55vjhefbqlgplstuz22m

CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes

Enrique Blanco, Montserrat Corominas
2012 BMC Genomics  
in Drosophila.  ...  Conclusions: The CBS platform is a powerful resource that provides tools for data mining individual sequences and groups of co-expressed genes with epigenomics information to conduct regulatory screenings  ...  Abril, Sílvia Pérez-Lluch, Ada Repiso, Natalia Mora, and Marina Ruiz-Romero for helpful discussions on the web server and the manuscript. E. Blanco and M.  ... 
doi:10.1186/1471-2164-13-688 pmid:23228284 pmcid:PMC3564944 fatcat:yukwy5bk3jhatmihapdcxtwme4

Arabidopsis genome analysis as exemplified by analysis of chromosome 4

K. F.X. Mayer
2000 Briefings in Bioinformatics  
Beside an overview on methods and strategies for Arabidopsis genome analysis, a summary of the results from the first analysis is presented.  ...  During the last decade the small cruciferous plant Arabidopsis thaliana has become a model organism for flowering plants. Sequencing and analysis of the Arabidopsis genome is nearing completion.  ...  For each feature analysis data are summarised on a single page and numerous links for in-depth data retrieval and further analysis data are provided.  ... 
doi:10.1093/bib/1.4.389 pmid:11465056 fatcat:df4gtvodtrgalpacjyn3gzfgxm

Bioinformatics in China: A Personal Perspective

Liping Wei, Jun Yu, Philip E. Bourne
2008 PLoS Computational Biology  
Acknowledgments We thank Chuan-Yun Li and Xiaomo Li for help with compiling the references and tables.  ...  We thank Professors Chun-Ting Zhang, Ying Xu, Xiaole Liu, Heping Cheng, Manyuan Long, Louis Tao, Xiaocheng Gu, Jingchu Luo, and the editors for insightful suggestions.  ...  Providing biological data resources and services is still an important part of bioinformatics.  ... 
doi:10.1371/journal.pcbi.1000020 pmid:18437216 pmcid:PMC2291564 fatcat:wknohzfhunetrmagn3gl6s7xde

New Insights from Existing Sequence Data: Generating Breakthroughs without a Pipette

Alex M. Plocik, Brenton R. Graveley
2013 Molecular Cell  
Here, we discuss resources of publicly available sequencing data most useful for interrogating the mechanisms of gene expression.  ...  With the rapidly declining cost of data generation, and the accumulation of massive datasets, molecular biology is entering an era in which incisive analysis of existing data will play an increasingly  ...  Kirschstein National Research Service Award (F32GM105264) to A.M.P.  ... 
doi:10.1016/j.molcel.2013.01.031 pmid:23438857 pmcid:PMC3590807 fatcat:k5edvke5vradljjpux7lewcrzu

The bioinformatics tool box for reproductive biology

Michael Primig
2012 Biochimica et Biophysica Acta - Molecular Basis of Disease  
This review outlines database projects and online analysis tools useful for life scientists in general and discusses in detail selected projects that have specifically been developed for researchers and  ...  These technologies have spawned a thriving discipline within the bioinformatics field that employs information technology for managing and interpreting biological highthroughput data.  ...  Roult at Genouest for GermOnline and GPSy system administration.  ... 
doi:10.1016/j.bbadis.2012.05.018 pmid:22687534 fatcat:rjlfosfypndzladmwg5dcp3444

When humans are the exception: Cross-species databases at the interface of biological and clinical research

Sabina Leonelli
2012 Social Studies of Science  
for the dissemination of data on humans and as a tool for comparing results of medical significance across the human-animal boundary.  ...  Postgenomic medicine has made cross-species comparison crucial in another respect: the 'community databases' developed to collect and disseminate data on model organisms are now often used as a template  ...  I am grateful to Alberto Cambrosio for helpful comments on an early draft and to my colleagues in Egenis for their support and feedback. Also, I benefited from comments by audiences at a CRASSH  ... 
doi:10.1177/0306312711436265 pmid:22848998 fatcat:qpazntpt4negbda4ev2t4qswbq

SPRENO: a BioC module for identifying organism terms in figure captions

Hong-Jie Dai, Onkar Singh
2018 Database: The Journal of Biological Databases and Curation  
The abbreviated term 'SIN' exemplifies such issue as it may stand for Sindbis virus or the sexlethal interactor gene (Drosophila melanogaster).  ...  In this study, we present our species identification tool SPRENO (Species Recognition and Normalization), which is established for recognizing organism terms mentioned in figure captions and linking them  ...  For cases without matched IDs in the compiled dictionary, they used the NCBI Entrez web service to search the NCBI taxonomy database for candidate IDs.  ... 
doi:10.1093/database/bay048 pmid:29873706 pmcid:PMC6007219 fatcat:leki4amzwrehrajfb56vrwugzy

Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples

Lyubomir Penev, Donat Agosti, Teodor Georgiev, Terry Catapano, Jeremy Miller, Vladimir Blagoderov, David Roberts, Vincent Smith, Irina Brake, Simon Ryrcroft, Ben Scott, Norman Johnson (+11 others)
2010 ZooKeys  
le (PTP) to large international database services and indexers such as Global and others; (vi) GenBank accession numbers autotagged and linked to NCBI; (vii) external links of taxon names to references  ...  XML tagging and semantic enhancements were implemented during the editorial process of ZooKeys using the Pensoft Mark Up Tool (PMT), specially designed for this purpose.  ...  Acknowledgments Our thanks are due to a number of institutions and persons for the encouragement, valuable comments and useful discussions on the process of semantic tagging and en-  ... 
doi:10.3897/zookeys.50.538 pmid:21594113 pmcid:PMC3088020 fatcat:j5snxmi2qbbfll77jdon2hluce

An ontology-driven semantic mashup of gene and biological pathway information: Application to the domain of nicotine dependence

Satya S. Sahoo, Olivier Bodenreider, Joni L. Rutter, Karen J. Skinner, Amit P. Sheth
2008 Journal of Biomedical Informatics  
The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created.  ...  Methods: We use an ontology-driven approach to integrate two gene resources (Entrez Gene and Homol-oGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans.  ...  Cytoscape was used to visualize the interaction networks.  ... 
doi:10.1016/j.jbi.2008.02.006 pmid:18395495 pmcid:PMC2766186 fatcat:2pyc76cacvfl5npklwhksksb7a

Curated databases and their role in clinical bioinformatics

C.C. Englbrecht, M. Han, M.T. Mader, A. Osanger, K.F.X. Mayer
2004 IMIA Yearbook of Medical Informatics  
In the fruit fly Drosophila melanogaster, ab initio gene prediction methods correctly predicted about 79% of individual exons [30] , in contrast to about 70% in human [31] .  ...  In 2000, the genome sequence of another important invertebrate model, the fruit fly Drosophila melanogaster, was published [8] , and as a culmination the draft sequences of man [9, 10] and mouse [11  ... 
doi:10.1055/s-0038-1638188 fatcat:ziahknl6kjdu7jz5oabyvtvbui

The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling

Vasundra Touré, Åsmund Flobak, Anna Niarakis, Steven Vercruysse, Martin Kuiper
2020 Briefings in Bioinformatics  
This review lists the different types of public resources with causal interactions, the different views on biological processes that they represent, the various data formats they use for data representation  ...  It can therefore be challenging to efficiently explore various resources of causal interaction and maintain an overview of recorded contextual information that ensures valid use of the data.  ...  Data Availability Statement No new data were generated or analysed in support of this research.  ... 
doi:10.1093/bib/bbaa390 pmid:33378765 pmcid:PMC8294520 fatcat:tevslhoc2rgarjhzrcxdljzaea
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