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Names are key to the big new biology
2010
Trends in Ecology & Evolution
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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
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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
2020
Nature Communications
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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
2013
Bulletin of Science, Technology & Society
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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
2012
BMC Genomics
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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
2000
Briefings in Bioinformatics
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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
2008
PLoS Computational Biology
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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
2013
Molecular Cell
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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
2012
Biochimica et Biophysica Acta - Molecular Basis of Disease
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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
2012
Social Studies of Science
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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
2018
Database: The Journal of Biological Databases and Curation
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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
2010
ZooKeys
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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
2008
Journal of Biomedical Informatics
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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
2004
IMIA Yearbook of Medical Informatics
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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
2020
Briefings in Bioinformatics
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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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