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biometadata-01.bib
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biometadata-01.bib
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@book{leonelli_data-centric_2016,
address = {Chicago ; London},
title = {Data-centric biology: a philosophical study},
isbn = {978-0-226-41633-5 978-0-226-41647-2},
shorttitle = {Data-centric biology},
publisher = {The University of Chicago Press},
author = {Leonelli, Sabina},
year = {2016},
keywords = {Biology, Data processing Philosophy, Knowledge, Theory of, Philosophy, Research, Research Philosophy, Research Sociological aspects},
}
@misc{rocca-serra_selecting_2023,
title = {Selecting terminologies and ontologies},
url = {https://w3id.org/faircookbook/FCB020},
abstract = {An online, open and live resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable and Reusable; in one word FAIR.},
urldate = {2023-08-22},
author = {Rocca-Serra, Philippe and Sansone, Susanna-Assunta and Welter, Danielle and Gray, Alasdair J. G.},
month = jun,
year = {2023},
note = {Publication Title: The FAIR Cookbook},
}
@article{rhee_carpe_2004,
title = {Carpe {Diem}. {Retooling} the “{Publish} or {Perish}” {Model} into the “{Share} and {Survive}” {Model}},
volume = {134},
issn = {1532-2548, 0032-0889},
url = {https://academic.oup.com/plphys/article/134/2/543/6112207},
doi = {10.1104/pp.103.035907},
language = {en},
number = {2},
urldate = {2023-08-22},
journal = {Plant Physiology},
author = {Rhee, Seung Yon},
month = feb,
year = {2004},
pages = {543--547},
file = {Full Text:/home/cpauvert/snap/zotero-snap/common/Zotero/storage/Z79X3BIZ/Rhee - 2004 - Carpe Diem. Retooling the “Publish or Perish” Mode.pdf:application/pdf},
}
@misc{vasilevsky_ontology_nodate,
title = {Ontology {Term} {Use}},
url = {https://oboacademy.github.io/obook/lesson/ontology-term-use/#what-is-delivered-as-part-of-the-course},
urldate = {2023-09-23},
author = {Vasilevsky, Nicole},
note = {OBO Semantic Engineering Training},
}
@misc{mungall_how_2021,
title = {How to select and request terms from ontologies},
url = {https://douroucouli.wordpress.com/2021/07/03/how-select-and-request-terms-from-ontologies/},
abstract = {Background Ontologies, knowledge models, and other kinds of standards are generally not static artefacts. They are created to serve a community, which likely includes you, and they should respond d…},
language = {en},
urldate = {2023-09-23},
journal = {Monkeying around with OWL},
author = {Mungall, Chris},
month = jul,
year = {2021},
file = {Snapshot:/home/cpauvert/snap/zotero-snap/common/Zotero/storage/ZYDLC893/how-select-and-request-terms-from-ontologies.html:text/html},
}
@article{malone_ten_2016,
title = {Ten {Simple} {Rules} for {Selecting} a {Bio}-ontology},
volume = {12},
issn = {1553-7358},
url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004743},
doi = {10.1371/journal.pcbi.1004743},
language = {en},
number = {2},
urldate = {2023-09-23},
journal = {PLOS Computational Biology},
author = {Malone, James and Stevens, Robert and Jupp, Simon and Hancocks, Tom and Parkinson, Helen and Brooksbank, Cath},
month = feb,
year = {2016},
note = {Publisher: Public Library of Science},
pages = {e1004743},
file = {Full Text PDF:/home/cpauvert/snap/zotero-snap/common/Zotero/storage/BBWN57RK/Malone et al. - 2016 - Ten Simple Rules for Selecting a Bio-ontology.pdf:application/pdf},
}
@article{perkel_how_2023,
title = {How to make your scientific data accessible, discoverable and useful},
volume = {618},
issn = {0028-0836, 1476-4687},
url = {https://www.nature.com/articles/d41586-023-01929-7},
doi = {10.1038/d41586-023-01929-7},
language = {en},
number = {7967},
urldate = {2023-09-23},
journal = {Nature},
author = {Perkel, Jeffrey M.},
month = jun,
year = {2023},
pages = {1098--1099},
}
@misc{goldmann_requesting_2023,
title = {Requesting new terms},
url = {https://w3id.org/faircookbook/FCB021},
abstract = {An online, open and live resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable and Reusable; in one word FAIR.},
urldate = {2023-08-22},
author = {Goldmann, Ulrich and Vos, Emma and Rocca-Serra, Philippe},
month = jun,
year = {2023},
note = {Publication Title: The FAIR Cookbook},
}
@article{buttigieg_environment_2013,
title = {The environment ontology: contextualising biological and biomedical entities},
volume = {4},
issn = {2041-1480},
shorttitle = {The environment ontology},
url = {http://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-4-43},
doi = {10.1186/2041-1480-4-43},
language = {en},
number = {1},
urldate = {2023-09-24},
journal = {Journal of Biomedical Semantics},
author = {Buttigieg, Pier and Morrison, Norman and Smith, Barry and Mungall, Christopher J and Lewis, Suzanna E and {the ENVO Consortium}},
year = {2013},
pages = {43},
file = {Full Text:/home/cpauvert/snap/zotero-snap/common/Zotero/storage/GY8H838M/Buttigieg et al. - 2013 - The environment ontology contextualising biologic.pdf:application/pdf},
}
@misc{osumi-sutherland_introduction_2023,
title = {Introduction to {Ontologies}},
url = {https://oboacademy.github.io/obook/explanation/intro-to-ontologies/#key-features-of-well-structured-ontologies},
urldate = {2023-09-24},
author = {Osumi-Sutherland, David and Vasilevsky, Nicole and Diehl, Alex and Matentzoglu, Nico and Brush, Matt and Yoder, Matt and Toriniai, Carlo and Jupp, Simon and Mungall, Chris and Haendal, Melissa and Balhoff, Jim and Overton, James and Meehan, Terry and Parkinson, Helen and Ashburner, Michael},
month = feb,
year = {2023},
note = {OBO Semantic Engineering Training},
}
@misc{scott_metadata_2011,
title = {The {Metadata} {Mania}},
url = {http://ascii.textfiles.com/archives/3181},
abstract = {OK, now that I’ve gone pro with the archiving and I’ve been at it pretty hardcore for a few months, my programmer brain has kicked in and I’m trying to find inefficiencies and kil…},
language = {en-US},
urldate = {2023-09-24},
journal = {ASCII by Jason Scott},
author = {Scott, Jason},
month = jun,
year = {2011},
file = {Snapshot:/home/cpauvert/snap/zotero-snap/common/Zotero/storage/YTTVQFPI/3181.html:text/html},
}
@article{wilkinson_fair_2016,
title = {The {FAIR} {Guiding} {Principles} for scientific data management and stewardship},
volume = {3},
issn = {2052-4463},
url = {https://www.nature.com/articles/sdata201618},
doi = {10.1038/sdata.2016.18},
abstract = {Abstract
There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.},
language = {en},
number = {1},
urldate = {2023-09-24},
journal = {Scientific Data},
author = {Wilkinson, Mark D. and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and Da Silva Santos, Luiz Bonino and Bourne, Philip E. and Bouwman, Jildau and Brookes, Anthony J. and Clark, Tim and Crosas, Mercè and Dillo, Ingrid and Dumon, Olivier and Edmunds, Scott and Evelo, Chris T. and Finkers, Richard and Gonzalez-Beltran, Alejandra and Gray, Alasdair J.G. and Groth, Paul and Goble, Carole and Grethe, Jeffrey S. and Heringa, Jaap and ’T Hoen, Peter A.C and Hooft, Rob and Kuhn, Tobias and Kok, Ruben and Kok, Joost and Lusher, Scott J. and Martone, Maryann E. and Mons, Albert and Packer, Abel L. and Persson, Bengt and Rocca-Serra, Philippe and Roos, Marco and Van Schaik, Rene and Sansone, Susanna-Assunta and Schultes, Erik and Sengstag, Thierry and Slater, Ted and Strawn, George and Swertz, Morris A. and Thompson, Mark and Van Der Lei, Johan and Van Mulligen, Erik and Velterop, Jan and Waagmeester, Andra and Wittenburg, Peter and Wolstencroft, Katherine and Zhao, Jun and Mons, Barend},
month = mar,
year = {2016},
pages = {160018},
file = {Full Text:/home/cpauvert/snap/zotero-snap/common/Zotero/storage/EM3CR8UU/Wilkinson et al. - 2016 - The FAIR Guiding Principles for scientific data ma.pdf:application/pdf},
}
@article{gill_dataharmonizer_2023,
title = {The {DataHarmonizer}: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information},
volume = {9},
issn = {2057-5858},
shorttitle = {The {DataHarmonizer}},
url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000908},
doi = {10.1099/mgen.0.000908},
abstract = {Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations as well as research. In order to make use of pathogen genomics data, they must be interpreted using contextual data (metadata). Contextual data include sample metadata, laboratory methods, patient demographics, clinical outcomes and epidemiological information. However, the variability in how contextual information is captured by different authorities and how it is encoded in different databases poses challenges for data interpretation, integration and their use/re-use. The DataHarmonizer is a template-driven spreadsheet application for harmonizing, validating and transforming genomics contextual data into submission-ready formats for public or private repositories. The tool’s web browser-based JavaScript environment enables validation and its offline functionality and local installation increases data security. The DataHarmonizer was developed to address the data sharing needs that arose during the COVID-19 pandemic, and was used by members of the Canadian COVID Genomics Network (CanCOGeN) to harmonize SARS-CoV-2 contextual data for national surveillance and for public repository submission. In order to support coordination of international surveillance efforts, we have partnered with the Public Health Alliance for Genomic Epidemiology to also provide a template conforming to its SARS-CoV-2 contextual data specification for use worldwide. Templates are also being developed for One Health and foodborne pathogens. Overall, the DataHarmonizer tool improves the effectiveness and fidelity of contextual data capture as well as its subsequent usability. Harmonization of contextual information across authorities, platforms and systems globally improves interoperability and reusability of data for concerted public health and research initiatives to fight the current pandemic and future public health emergencies. While initially developed for the COVID-19 pandemic, its expansion to other data management applications and pathogens is already underway.},
language = {en},
number = {1},
urldate = {2023-09-29},
journal = {Microbial Genomics},
author = {Gill, Ivan S. and Griffiths, Emma J. and Dooley, Damion and Cameron, Rhiannon and Savić Kallesøe, Sarah and John, Nithu Sara and Sehar, Anoosha and Gosal, Gurinder and Alexander, David and Chapel, Madison and Croxen, Matthew A. and Delisle, Benjamin and Di Tullio, Rachelle and Gaston, Daniel and Duggan, Ana and Guthrie, Jennifer L. and Horsman, Mark and Joshi, Esha and Kearny, Levon and Knox, Natalie and Lau, Lynette and LeBlanc, Jason J. and Li, Vincent and Lyons, Pierre and MacKenzie, Keith and McArthur, Andrew G. and Panousis, Emily M. and Palmer, John and Prystajecky, Natalie and Smith, Kerri N. and Tanner, Jennifer and Townend, Christopher and Tyler, Andrea and Van Domselaar, Gary and Hsiao, William W. L.},
month = jan,
year = {2023},
file = {Full Text:/home/cpauvert/snap/zotero-snap/common/Zotero/storage/W7UQ3MN5/Gill et al. - 2023 - The DataHarmonizer a tool for faster data harmoni.pdf:application/pdf},
}