paper_resources/paper.bib

@article{ison2015tools,
  title={Tools and data services registry: a community effort to document bioinformatics resources},
  author={Ison, Jon and Rapacki, Kristoffer and M{\'e}nager, Herv{\'e} and Kala{\v{s}}, Mat{\'u}{\v{s}} and Rydza, Emil and Chmura, Piotr and Anthon, Christian and Beard, Niall and Berka, Karel and Bolser, Dan and others},
  journal={Nucleic acids research},
  volume={44},
  number={D1},
  pages={D38--D47},
  year={2015},
  publisher={Oxford University Press},
  doi={10.1093/nar/gkv1116}
}

@article{whetzel2011bioportal,
  title={BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications},
  author={Whetzel, Patricia L and Noy, Natalya F and Shah, Nigam H and Alexander, Paul R and Nyulas, Csongor and Tudorache, Tania and Musen, Mark A},
  journal={Nucleic acids research},
  volume={39},
  number={suppl\_2},
  pages={W541--W545},
  year={2011},
  publisher={Oxford University Press},
  doi={10.1093/nar/gkr469}
}
@inproceedings{jupp2015new,
  title={A new Ontology Lookup Service at EMBL-EBI.},
  author={Jupp, Simon and Burdett, Tony and Leroy, Catherine and Parkinson, Helen E},
  booktitle={SWAT4LS},
  pages={118--119},
  year={2015},
  url={{http://ceur-ws.org/Vol-1546/paper_29.pdf}}
}
@article{ison2013edam,
  title={EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats},
  author={Ison, Jon and Kala{\v{s}}, Mat{\'u}{\v{s}} and Jonassen, Inge and Bolser, Dan and Uludag, Mahmut and McWilliam, Hamish and Malone, James and Lopez, Rodrigo and Pettifer, Steve and Rice, Peter},
  journal={Bioinformatics},
  volume={29},
  number={10},
  pages={1325--1332},
  year={2013},
  publisher={Oxford University Press},
  doi={10.1093/bioinformatics/btt113}
}
@misc{
  d3js,
  author = {Mike Bostock},
  year = 2018,
  title = {{D3 is a JavaScript library for visualizing data with HTML, SVG, and CSS.}},
  howpublished = {https://d3js.org/},
  url = {https://d3js.org/}
}
@article{tudorache2013webprotege,
  title={WebProt{\'e}g{\'e}: A collaborative ontology editor and knowledge acquisition tool for the web},
  author={Tudorache, Tania and Nyulas, Csongor and Noy, Natalya F and Musen, Mark A},
  journal={Semantic web},
  volume={4},
  number={1},
  pages={89--99},
  year={2013},
  publisher={IOS Press},
  doi={10.3233/SW-2012-0057}
}
@article{hoehndorf2015aber,
author="Hoehndorf, Robert
and Slater, Luke
and Schofield, Paul N.
and Gkoutos, Georgios V.",
title="Aber-OWL: a framework for ontology-based data access in biology",
journal="BMC Bioinformatics",
year="2015",
month="Jan",
day="28",
volume="16",
number="1",
pages="26",
abstract="Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within these ontologies relies on the use of automated reasoning.",
issn="1471-2105",
doi="10.1186/s12859-015-0456-9",
url="https://doi.org/10.1186/s12859-015-0456-9"
}
@misc{brancotte2017biosphere,
  TITLE = {{Biosphere Web : un portail haut niveau pour une utilisation bioinformatique des clouds}},
  AUTHOR = {Brancotte, Bryan and Bedri, Mohamed and Lorenzo, Jonathan and Perrin Sandrine and S{\'e}n{\'e}, Fr{\'e}d{\'e}ric and Sepou Nga{\"i}lo, Awa and Blanchet, Christophe and Gibrat, Jean-Fran\c{c}ois},
  URL = {https://www.youtube.com/watch?v=gaopunfIqnc},
  NOTE = {Demo},
  HOWPUBLISHED = {{JOBIM (Journ{\'e}es Ouvertes Biologie Informatique Math{\'e}matiques)}},
  YEAR = {2017},
  MONTH = Jul,
}
@inproceedings{xiang2011ontobee,
  title={Ontobee: A Linked Data Server and Browser for Ontology Terms.},
  author={Xiang, Zuoshuang and Mungall, Chris and Ruttenberg, Alan and He, Yongqun},
  booktitle={ICBO},
  year={2011},
  doi={10.1093/nar/gkw918}
}
@article{afgan2016galaxy,
author = {Afgan, Enis and Baker, Dannon and van den Beek, Marius and Blankenberg, Daniel and Bouvier, Dave and Čech, Martin and Chilton, John and Clements, Dave and Coraor, Nate and Eberhard, Carl and Grüning, Björn and Guerler, Aysam and Hillman-Jackson, Jennifer and Von Kuster, Greg and Rasche, Eric and Soranzo, Nicola and Turaga, Nitesh and Taylor, James and Nekrutenko, Anton and Goecks, Jeremy},
title = {The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update},
journal = {Nucleic Acids Research},
volume = {44},
number = {W1},
pages = {W3-W10},
year = {2016},
doi = {10.1093/nar/gkw343},
URL = {http://dx.doi.org/10.1093/nar/gkw343},
eprint = {/oup/backfile/content_public/journal/nar/44/w1/10.1093_nar_gkw343/3/gkw343.pdf}
}
@article{ashburner2000go, title={Gene Ontology: tool for the unification of biology}, volume={25}, url={http://dx.doi.org/10.1038/75556}, DOI={10.1038/75556}, number={1}, journal={Nature Genetics}, publisher={Springer Nature}, author={Ashburner, Michael and Ball, Catherine A. and Blake, Judith A. and Botstein, David and Butler, Heather and Cherry, J. Michael and Davis, Allan P. and Dolinski, Kara and Dwight, Selina S. and Eppig, Janan T. and et al.}, year={2000}, month={May}, pages={25–29}}
@article{go2016go, title={Expansion of the Gene Ontology knowledgebase and resources}, volume={45}, url={http://dx.doi.org/10.1093/nar/gkw1108}, DOI={10.1093/nar/gkw1108}, number={D1}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, year={2016}, month={Nov}, pages={D331–D338}}
@article{bostock2011d3,
  title={D$^3$ data-driven documents},
  author={Bostock, Michael and Ogievetsky, Vadim and Heer, Jeffrey},
  journal={IEEE transactions on visualization and computer graphics},
  volume={17},
  number={12},
  pages={2301--2309},
  year={2011},
  publisher={IEEE},
  doi={10.1109/TVCG.2011.185}
}
 