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@article{liew2016reefgenomics,
author = {Liew, Y. J. and Aranda, M. and Voolstra, C. R.},
title = "{Reefgenomics.Org - a repository for marine genomics
data}",
journal = {Database},
volume = {2016},
year = {2016},
month = {12},
abstract = "{Over the last decade, technological advancements have substantially decreased the
cost and time of obtaining large amounts of sequencing data. Paired with the
exponentially increased computing power, individual labs are now able to
sequence genomes or transcriptomes to investigate biological questions of
interest. This has led to a significant increase in available sequence data.
Although the bulk of data published in articles are stored in public sequence
databases, very often, only raw sequencing data are available; miscellaneous
data such as assembled transcriptomes, genome annotations etc. are not easily
obtainable through the same means. Here, we introduce our website (http://reefgenomics.org) that aims to centralize genomic and
transcriptomic data from marine organisms. Besides providing convenient means to
download sequences, we provide (where applicable) a genome browser to explore
available genomic features, and a BLAST interface to search through the hosted
sequences. Through the interface, multiple datasets can be queried
simultaneously, allowing for the retrieval of matching sequences from organisms
of interest. The minimalistic, no-frills interface reduces visual clutter,
making it convenient for end-users to search and explore processed sequence
data.Database URL: http://reefgenomics.org}",
issn = {1758-0463},
doi = {10.1093/database/baw152},
url = {https://doi.org/10.1093/database/baw152},
note = {baw152},
}
@article{deck2017geome,
author = {Deck, J. AND Gaither, M. AND Ewing, R. and others},
journal = {PLOS Biology},
publisher = {Public Library of Science},
title = {The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples},
year = {2017},
month = {08},
volume = {15},
url = {https://doi.org/10.1371/journal.pbio.2002925},
pages = {1-7},
abstract = {The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information’s (NCBI’s) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science.},
number = {8},
doi = {10.1371/journal.pbio.2002925}
}
@article{yu2020sager,
author = {Yu, L. and Li, T. and Li, L. and others},
title = "{{SAGER}: a database of {S}ymbiodiniaceae and Algal Genomic Resource}",
journal = {Database},
volume = {2020},
year = {2020},
month = {07},
abstract = "{Symbiodiniaceae dinoflagellates are essential endosymbionts of reef building corals and some other invertebrates. Information of their genome structure and function is critical for understanding coral symbiosis and bleaching. With the rapid development of sequencing technology, genome draft assemblies of several Symbiodiniaceae species and diverse marine algal genomes have become publicly available but spread in multiple separate locations. Here, we present a Symbiodiniaceae and Algal Genomic Resource Database (SAGER), a user-friendly online repository for integrating existing genomic data of Symbiodiniaceae species and diverse marine algal gene sets from MMETSP and PhyloDB databases. Relevant algal data are included to facilitate comparative analyses. The database is freely accessible at http://sampgr.org.cn. It provides comprehensive tools for studying gene function, expression and comparative genomics, including search tools to identify gene information from Symbiodiniaceae species, and BLAST tool to find orthologs from marine algae and protists. Moreover, SAGER integrates transcriptome datasets derived from diverse culture conditions of corresponding Symbiodiniaceae species. SAGER was developed with the capacity to incorporate future Symbiodiniaceae and algal genome and transcriptome data, and will serve as an open-access and sustained platform providing genomic and molecular tools that can be conveniently used to study Symbiodiniaceae and other marine algae.Database URL: http://sampgr.org.cn}",
issn = {1758-0463},
doi = {10.1093/database/baaa051},
url = {https://doi.org/10.1093/database/baaa051},
note = {baaa051},
eprint = {https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaa051/33462333/baaa051.pdf},
}
@article{lassila1998resource,
title={Resource description framework ({RDF}) model and syntax specification},
author={Lassila, Ora and Swick, Ralph R and others},
year={1998},
publisher={Citeseer}
}
@article{wilkinson2016fair,
title={The {FAIR} Guiding Principles for scientific data management and stewardship},
author={Wilkinson, M. D. and Dumontier, M. and others},
journal={Scientific data},
volume={3},
number={1},
pages={1--9},
year={2016},
publisher={Nature Publishing Group}
}
@article{young2018worldwide,
title={Worldwide Protein Data Bank biocuration supporting open access to high-quality 3{D} structural biology data},
author={Young, Jasmine Y and Westbrook, John D and Feng, Zukang and Peisach, Ezra and Persikova, Irina and Sala, Raul and Sen, Sanchayita and Berrisford, John M and Swaminathan, G Jawahar and Oldfield, Thomas J and others},
journal={Database},
volume={2018},
year={2018},
publisher={Oxford Academic}
}
@article{berman2000pdb,
author = {Berman, Helen M. and Westbrook, John and Feng, Zukang and Gilliland, Gary and Bhat, T. N. and Weissig, Helge and Shindyalov, Ilya N. and Bourne, Philip E.},
title = "{The Protein Data Bank}",
journal = {Nucleic Acids Research},
volume = {28},
number = {1},
pages = {235-242},
year = {2000},
month = {01},
abstract = "{The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.}",
issn = {0305-1048},
doi = {10.1093/nar/28.1.235},
url = {https://doi.org/10.1093/nar/28.1.235},
eprint = {https://academic.oup.com/nar/article-pdf/28/1/235/9895144/280235.pdf},
}
@article{CoralReefLTER,
author = {Edmunds, P and Moorea Coral Reef LTER},
title = {{MCR LTER}: Coral Reef: Long-term Population and Community Dynamics: Corals, ongoing since 2005},
doi = {10.6073/pasta/10ee808a046cb63c0b8e3bc3c9799806}
}
@inproceedings{fountain2009digital,
title={Digital {M}oorea cyberinfrastructure for coral reef monitoring},
author={Fountain, T. and Tilak, S. and Shin, P. and others},
booktitle={2009 International Conference on Intelligent Sensors, Sensor Networks and Information Processing (ISSNIP)},
pages={243--248},
year={2009},
organization={IEEE}
}
@techreport{kunze2018bagit,
title={The bagIt file packaging format (V1. 0)},
author={Kunze, John and Littman, Justin and Madden, Elizabeth and Scancella, John and Adams, Chris},
year={2018}
}
@article{chandler2016bco,
title={{BCO-DMO}: Stewardship of Marine Research Data from Proposal to Preservation},
author={Chandler, C. L. and Groman, R. C. and Kinkade, D. and others},
journal={American Geophysical Union},
volume={2016},
pages={OD24B--2457},
year={2016}
}
@article{DBLP:journals/corr/abs-2006-08589,
author = {Jeremy Leipzig and
Daniel N{\"{u}}st and
Charles Tapley Hoyt and
Stian Soiland{-}Reyes and
Karthik Ram and
Jane Greenberg},
title = {The role of metadata in reproducible computational research},
journal = {CoRR},
volume = {abs/2006.08589},
year = {2020},
url = {https://arxiv.org/abs/2006.08589},
archivePrefix = {arXiv},
eprint = {2006.08589},
timestamp = {Wed, 17 Jun 2020 14:28:54 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2006-08589.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{ball2016rda,
title={{RDA} Metadata Standards Directory Working Group},
author={Ball, Alex and Greenberg, Jane and Jeffery, Keith and Koskela, Rebecca},
year={2016}
}
@inproceedings{qin2012functional,
title={Functional and architectural requirements for metadata: Supporting discovery and management of scientific data},
author={Qin, Jian and Ball, Alex and Greenberg, Jane},
booktitle={International Conference on Dublin Core and Metadata Applications},
pages={62--71},
year={2012}
}
@article{fegraus2005maximizing,
title={Maximizing the value of ecological data with structured metadata: an introduction to ecological metadata language ({EML}) and principles for metadata creation.},
author={Fegraus, Eric H and Andelman, Sandy and Jones, Matthew B and Schildhauer, Mark},
journal={Bulletin of the Ecological Society of America},
volume={86},
number={3},
pages={158--168},
year={2005},
publisher={JSTOR}
}
@article{weibel2000dublin,
title={The {D}ublin core metadata initiative},
author={Weibel, Stuart L and Koch, Traugott},
journal={D-lib magazine},
volume={6},
number={12},
pages={1082--9873},
year={2000}
}
@article{vardigan2014ddi,
title={The {DDI} matures: 1997 to the present},
author={Vardigan, Mary},
journal={IASSIST Quarterly},
volume={37},
number={1-4},
pages={45--45},
year={2014}
}
@article{bosch2011metaorganisms,
title={Metaorganisms as the new frontier},
author={Bosch, Thomas CG and McFall-Ngai, Margaret J},
journal={Zoology},
volume={114},
number={4},
pages={185--190},
year={2011},
publisher={Elsevier}
}
@article{hughes2017coral,
title={Coral reefs in the Anthropocene},
author={Hughes, Terry P and Barnes, Michele L and Bellwood, David R and Cinner, Joshua E and Cumming, Graeme S and Jackson, Jeremy BC and Kleypas, Joanie and Van De Leemput, Ingrid A and Lough, Janice M and Morrison, Tiffany H and others},
journal={Nature},
volume={546},
number={7656},
pages={82--90},
year={2017},
publisher={Nature Publishing Group}
}
@article{woodhead2019coral,
title={Coral reef ecosystem services in the Anthropocene},
author={Woodhead, Anna J and Hicks, Christina C and Norstr{\"o}m, Albert V and Williams, Gareth J and Graham, Nicholas AJ},
journal={Functional Ecology},
volume={33},
number={6},
pages={1023--1034},
year={2019},
publisher={Wiley Online Library}
}
@article{madin2016trait,
title={A trait-based approach to advance coral reef science},
author={Madin, Joshua S and Hoogenboom, Mia O and Connolly, Sean R and Darling, Emily S and Falster, Daniel S and Huang, Danwei and Keith, Sally A and Mizerek, Toni and Pandolfi, John M and Putnam, Hollie M and others},
journal={Trends in Ecology \& Evolution},
volume={31},
number={6},
pages={419--428},
year={2016},
publisher={Elsevier}
}
@article{donner2017new,
title={A new, high-resolution global mass coral bleaching database},
author={Donner, Simon D and Rickbeil, Gregory JM and Heron, Scott F},
journal={PLoS One},
volume={12},
number={4},
pages={e0175490},
year={2017},
publisher={Public Library of Science San Francisco, CA USA}
}
@InProceedings{10.1007/978-3-030-98876-0_18,
author="Shpilker, Polina
and Freeman, John
and McKelvie, Hailey
and Ashey, Jill
and Fonticella, Jay-Miguel
and Putnam, Hollie
and Greenberg, Jane
and Cowen, Lenore
and Couch, Alva
and Daniels, Noah M.",
editor="Garoufallou, Emmanouel
and Ovalle-Perandones, Mar{\'i}a-Antonia
and Vlachidis, Andreas",
title="MEtaData Format for Open Reef Data (MEDFORD)",
booktitle="Metadata and Semantic Research",
year="2022",
publisher="Springer International Publishing",
address="Cham",
pages="206--211",
abstract="Reproducibility of research is critical for science. Computational biology research presents a significant challenge, given the need to track critical details, such as software version or genome draft iteration. Metadata research infrastructures, while greatly improved, often assume a level of programming skills in their user community, or rely on expert curators to ensure that key information is not lost. This paper introduces MEDFORD, a new human-readable, easily-editable and templatable metadata language for scientists to collocate all the details relevant to their experiments. We provide an overview of the underlying design principles, language, and current and planned support infrastructure for parsing and translating MEDFORD into other metadata formats. MEDFORD 0.9 has been specifically designed for the coral research community, with initial metadata generated from RNA-Seq analyses of coral transcriptomes and coral photo collections. Notably, the format is generally applicable and useful for many types of scientific metadata generated by non-computer science experts.",
isbn="978-3-030-98876-0"
}
@inproceedings{bunder2019towards,
title={Towards Multi-editor Support for Domain-Specific Languages Utilizing the Language Server Protocol},
author={B{\"u}nder, Hendrik and Kuchen, Herbert},
booktitle={International Conference on Model-Driven Engineering and Software Development},
pages={225--245},
year={2019},
organization={Springer}
}
@article{daniels2012smurflite,
title={SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone},
author={Daniels, Noah M and Hosur, Raghavendra and Berger, Bonnie and Cowen, Lenore J},
journal={Bioinformatics},
volume={28},
number={9},
pages={1216--1222},
year={2012},
publisher={Oxford University Press}
}