Dataset Open Access
CryoEM Maps and Associated Data Submitted to the 2015/2016 EMDataBank Map Challenge
Lawson, Catherine;
Chiu, Wah;
Carragher, Bridget;
Carazo, Jose-Maria;
Jiang, Wen;
Patwardhan, Ardan;
Rubinstein, John;
Rosenthal, Peter;
Sun, Fei;
Vonck, Janet;
Bai, Xiaochen;
Bell, James;
Caputo, Nick;
Chakraborty, Arka;
Chen, Dong-Hua;
Chen, James;
Diaz-Avalos, Ruben;
Donati, Laurene;
Estrozi, Leandro;
Galaz Montoya, Jesus;
Gati, Cornelius;
Gomez-Blanco, Josue;
Grigorieff, Nikolaus;
Gros, Piet;
Heymann, Bernard;
Leith, ArDean;
Li, Fei;
Ludtke, Steven;
Nans, Andrea;
Nilchian, Masih;
Punjabi, Ali;
Sixma, Titia;
Tegunov, Dimitry;
Yang, Kailu;
Yu, Guimei;
Zhang, Junjie;
Sala, Raul
MARC21 XML Export
<?xml version='1.0' encoding='UTF-8'?>
<record xmlns="http://www.loc.gov/MARC21/slim">
<leader>00000nmm##2200000uu#4500</leader>
<datafield tag="999" ind1="C" ind2="5">
<subfield code="x">Henderson et al (2012) Outcome of the first electron microscopy validation task force meeting. doi:10.1016/j.str.2011.12.014</subfield>
</datafield>
<datafield tag="999" ind1="C" ind2="5">
<subfield code="x">Lawson et al (2016) EMDataBank unified data resource for 3DEM. doi:10.1093/nar/gkv1126</subfield>
</datafield>
<datafield tag="999" ind1="C" ind2="5">
<subfield code="x">Marabini et al (2016) The Electron Microscopy Exchange (EMX) Iniitiative doi:10.1016/j.jsb.2016.02.008</subfield>
</datafield>
<datafield tag="041" ind1=" " ind2=" ">
<subfield code="a">eng</subfield>
</datafield>
<datafield tag="653" ind1=" " ind2=" ">
<subfield code="a">cryo electron microscopy</subfield>
</datafield>
<datafield tag="653" ind1=" " ind2=" ">
<subfield code="a">cryoEM</subfield>
</datafield>
<datafield tag="653" ind1=" " ind2=" ">
<subfield code="a">validation</subfield>
</datafield>
<datafield tag="653" ind1=" " ind2=" ">
<subfield code="a">challenge</subfield>
</datafield>
<datafield tag="653" ind1=" " ind2=" ">
<subfield code="a">benchmark</subfield>
</datafield>
<controlfield tag="005">20190502135917.0</controlfield>
<datafield tag="500" ind1=" " ind2=" ">
<subfield code="a">The 2015/2016 Map Challenge was supported by the US National Institutes of Health / National Institute for General Medical Sciences (NIH/NIGMS) Under Grant Number R01 GM079429 to Wah Chiu (PI). A Directors Award from the UCSD Supercomputer Center provided supercomputer access that was used in 15 of the 66 submitted entries.</subfield>
</datafield>
<controlfield tag="001">1120379</controlfield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Stanford University, USA</subfield>
<subfield code="0">(orcid)0000-0002-8910-3078</subfield>
<subfield code="a">Chiu, Wah</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">New York Structural Biology Center, USA</subfield>
<subfield code="0">(orcid)0000-0002-0624-5020</subfield>
<subfield code="a">Carragher, Bridget</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Centro Nacional de Biotecnología, Madrid, ES</subfield>
<subfield code="0">(orcid)0000-0003-0788-8447</subfield>
<subfield code="a">Carazo, Jose-Maria</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Purdue University, USA</subfield>
<subfield code="a">Jiang, Wen</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">EMBL European Bioinformatics Institute, UK</subfield>
<subfield code="0">(orcid)0000-0001-7663-9028</subfield>
<subfield code="a">Patwardhan, Ardan</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">University of Toronto, CA</subfield>
<subfield code="0">(orcid)0000-0003-0566-2209</subfield>
<subfield code="a">Rubinstein, John</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Francis Crick Institute, UK</subfield>
<subfield code="a">Rosenthal, Peter</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Chinese Academy of Sciences, CN</subfield>
<subfield code="a">Sun, Fei</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Max Planck Institute for Biophysics, DE</subfield>
<subfield code="0">(orcid)0000-0001-5659-8863</subfield>
<subfield code="a">Vonck, Janet</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">MRC Laboratory of Molecular Biology, UK</subfield>
<subfield code="a">Bai, Xiaochen</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Baylor College of Medicine, USA</subfield>
<subfield code="a">Bell, James</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Oregon Health Sciences University, USA</subfield>
<subfield code="a">Caputo, Nick</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Institut de Biologia Molecular de Barcelona, ES</subfield>
<subfield code="0">(orcid)0000-0002-9699-3208</subfield>
<subfield code="a">Chakraborty, Arka</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Stanford University, USA</subfield>
<subfield code="a">Chen, Dong-Hua</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Oregon Health Sciences University, USA</subfield>
<subfield code="a">Chen, James</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">HHMI Janelia Research Campus, USA</subfield>
<subfield code="a">Diaz-Avalos, Ruben</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">École Polytechnique Fédérale de Lausanne, CH</subfield>
<subfield code="a">Donati, Laurene</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Institut de Biologie Structurale Grenoble, FR</subfield>
<subfield code="0">(orcid)0000-0003-2548-2547</subfield>
<subfield code="a">Estrozi, Leandro</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Baylor College of Medicine, USA</subfield>
<subfield code="0">(orcid)0000-0002-0113-9325</subfield>
<subfield code="a">Galaz Montoya, Jesus</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">MRC Laboratory of Molecular Biology, UK</subfield>
<subfield code="a">Gati, Cornelius</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Centro Nacional de Biotecnología, Madrid, ES</subfield>
<subfield code="0">(orcid)0000-0002-6168-3859</subfield>
<subfield code="a">Gomez-Blanco, Josue</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">HHMI Janelia Research Campus, USA</subfield>
<subfield code="0">(orcid)0000-0002-1506-909X</subfield>
<subfield code="a">Grigorieff, Nikolaus</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Utrecht University, NL</subfield>
<subfield code="a">Gros, Piet</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">National Institutes of Health, USA</subfield>
<subfield code="0">(orcid)0000-0002-8872-5326</subfield>
<subfield code="a">Heymann, Bernard</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Wadsworth Laboratories, USA</subfield>
<subfield code="a">Leith, ArDean</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">The Scripps Research Institute La Jolla, USA</subfield>
<subfield code="a">Li, Fei</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Baylor College of Medicine, USA</subfield>
<subfield code="0">(orcid)0000-0002-1903-1574</subfield>
<subfield code="a">Ludtke, Steven</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Francis Crick Institute, UK</subfield>
<subfield code="a">Nans, Andrea</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">École Polytechnique Fédérale de Lausanne, CH</subfield>
<subfield code="a">Nilchian, Masih</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">University of Toronto, CA</subfield>
<subfield code="a">Punjabi, Ali</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Netherlands Cancer Institute, NL</subfield>
<subfield code="a">Sixma, Titia</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Max Planck Institute for Biochemistry, Martinsreid, DE</subfield>
<subfield code="0">(orcid)0000-0001-7019-3221</subfield>
<subfield code="a">Tegunov, Dimitry</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Texas A&M University, USA</subfield>
<subfield code="a">Yang, Kailu</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Purdue University, USA</subfield>
<subfield code="a">Yu, Guimei</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Texas A&M University, USA</subfield>
<subfield code="a">Zhang, Junjie</subfield>
</datafield>
<datafield tag="700" ind1=" " ind2=" ">
<subfield code="u">Rutgers University, USA</subfield>
<subfield code="0">(orcid)0000-0002-6500-6441</subfield>
<subfield code="a">Sala, Raul</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">6031353386</subfield>
<subfield code="z">md5:4b4db43292b158776f93b30f9d5a3174</subfield>
<subfield code="u">https://zenodo.org/record/1120379/files/BetaGal_benchmark.zip</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">5905180854</subfield>
<subfield code="z">md5:00b094bd17e426997b9e3cd6252c4a38</subfield>
<subfield code="u">https://zenodo.org/record/1120379/files/BMV_benchmark.zip</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">706059725</subfield>
<subfield code="z">md5:423d90fa5a063cc6ded975df59fd4027</subfield>
<subfield code="u">https://zenodo.org/record/1120379/files/Ferritin_benchmark.zip</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">1147598874</subfield>
<subfield code="z">md5:6a426054a1c07e4b1a3d407ad09f3ea6</subfield>
<subfield code="u">https://zenodo.org/record/1120379/files/GroEL_benchmark.zip</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">707155976</subfield>
<subfield code="z">md5:41285fd0792235e5dd30c65c0ee34cfe</subfield>
<subfield code="u">https://zenodo.org/record/1120379/files/Images_for_all_benchmarks.zip</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">286720</subfield>
<subfield code="z">md5:c3addaa28698174757c5fa137d3e7cfe</subfield>
<subfield code="u">https://zenodo.org/record/1120379/files/map-challenge-metadata.xls</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">1504152</subfield>
<subfield code="z">md5:f9099f2959fadfdb7be3587766d31ce2</subfield>
<subfield code="u">https://zenodo.org/record/1120379/files/Map Challenge Web Contents Archive.pdf</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">2716286442</subfield>
<subfield code="z">md5:de1d58f7854c6bdbbf2533f42700ec03</subfield>
<subfield code="u">https://zenodo.org/record/1120379/files/Proteasome_benchmark.zip</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">1549</subfield>
<subfield code="z">md5:f34353e9b357b878481d133349077808</subfield>
<subfield code="u">https://zenodo.org/record/1120379/files/README.txt</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">8361337285</subfield>
<subfield code="z">md5:1f51ea2a89defca85e64402a5bc4d04f</subfield>
<subfield code="u">https://zenodo.org/record/1120379/files/Ribosome_benchmark.zip</subfield>
</datafield>
<datafield tag="856" ind1="4" ind2=" ">
<subfield code="s">3332348251</subfield>
<subfield code="z">md5:23ce888932ad212625b5df7c18bbf335</subfield>
<subfield code="u">https://zenodo.org/record/1120379/files/TRPVI_benchmark.zip</subfield>
</datafield>
<datafield tag="542" ind1=" " ind2=" ">
<subfield code="l">open</subfield>
</datafield>
<datafield tag="260" ind1=" " ind2=" ">
<subfield code="c">2017-12-21</subfield>
</datafield>
<datafield tag="909" ind1="C" ind2="O">
<subfield code="p">openaire_data</subfield>
<subfield code="p">user-3dcryoemchallenges</subfield>
<subfield code="o">oai:zenodo.org:1120379</subfield>
</datafield>
<datafield tag="100" ind1=" " ind2=" ">
<subfield code="u">Rutgers University, USA</subfield>
<subfield code="0">(orcid)0000-0002-3261-7035</subfield>
<subfield code="a">Lawson, Catherine</subfield>
</datafield>
<datafield tag="245" ind1=" " ind2=" ">
<subfield code="a">CryoEM Maps and Associated Data Submitted to the 2015/2016 EMDataBank Map Challenge</subfield>
</datafield>
<datafield tag="980" ind1=" " ind2=" ">
<subfield code="a">user-3dcryoemchallenges</subfield>
</datafield>
<datafield tag="540" ind1=" " ind2=" ">
<subfield code="u">http://creativecommons.org/licenses/by/4.0/legalcode</subfield>
<subfield code="a">Creative Commons Attribution 4.0 International</subfield>
</datafield>
<datafield tag="650" ind1="1" ind2="7">
<subfield code="a">cc-by</subfield>
<subfield code="2">opendefinition.org</subfield>
</datafield>
<datafield tag="650" ind1="1" ind2=" ">
<subfield code="a">Benchmarking</subfield>
<subfield code="0">(url)https://meshb.nlm.nih.gov/record/ui?name=Benchmarking</subfield>
</datafield>
<datafield tag="650" ind1="1" ind2=" ">
<subfield code="a">Databases, Protein</subfield>
<subfield code="0">(url)https://meshb.nlm.nih.gov/record/ui?name=Databases,%20Protein</subfield>
</datafield>
<datafield tag="650" ind1="1" ind2=" ">
<subfield code="a">Cryoelectron Microscopy</subfield>
<subfield code="0">(url)https://meshb.nlm.nih.gov/record/ui?name=Cryoelectron%20Microscopy</subfield>
</datafield>
<datafield tag="650" ind1="1" ind2=" ">
<subfield code="a">Imaging, Three Dimensional</subfield>
<subfield code="0">(url)https://meshb.nlm.nih.gov/record/ui?name=Imaging,%20Three%20Dimensional</subfield>
</datafield>
<datafield tag="650" ind1="1" ind2=" ">
<subfield code="a">Microscopy, Electron</subfield>
<subfield code="0">(url)https://meshb.nlm.nih.gov/record/ui?name=Microscopy,%20Electron</subfield>
</datafield>
<datafield tag="520" ind1=" " ind2=" ">
<subfield code="a"><p>Files and metadata associated with the EMDataBank/Unified Data Resource for 3DEM 2015/2016 Map Challenge hosted at challenges.emdatabank.org are deposited.</p>
<p>All members of the Scientific Community--at all levels of experience--were invited to participate as Challengers, and/or as Assessors.</p>
<p>Seven benchmark raw image datasets were selected for the challenge. Six are selected from recently described single particle structure determinations with image data collected as multi-frame movies; one is based on simulated (in silico) images. All of the raw image datasets are archived at pdbe.org/empiar.</p>
<p>27 Challengers created 66 single particle reconstructions from the targets, and then uploaded their results with associated details.&nbsp; 15 of the reconstructions were calculated using the SDSC Gordon supercomputer.</p>
<p>This map challenge was one of two community-wide challenges sponsored by EMDataBank in 2015/2016 to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model.</p>
<p>&nbsp;</p></subfield>
</datafield>
<datafield tag="773" ind1=" " ind2=" ">
<subfield code="n">doi</subfield>
<subfield code="i">cites</subfield>
<subfield code="a">10.1093/nar/gkv1126</subfield>
</datafield>
<datafield tag="773" ind1=" " ind2=" ">
<subfield code="n">doi</subfield>
<subfield code="i">cites</subfield>
<subfield code="a">10.1016/j.str.2011.12.014</subfield>
</datafield>
<datafield tag="773" ind1=" " ind2=" ">
<subfield code="n">doi</subfield>
<subfield code="i">references</subfield>
<subfield code="a">10.6019/EMPIAR-10010</subfield>
</datafield>
<datafield tag="773" ind1=" " ind2=" ">
<subfield code="n">doi</subfield>
<subfield code="i">references</subfield>
<subfield code="a">10.6019/EMPIAR-10012</subfield>
</datafield>
<datafield tag="773" ind1=" " ind2=" ">
<subfield code="n">doi</subfield>
<subfield code="i">references</subfield>
<subfield code="a">10.6019/EMPIAR-10013</subfield>
</datafield>
<datafield tag="773" ind1=" " ind2=" ">
<subfield code="n">doi</subfield>
<subfield code="i">references</subfield>
<subfield code="a">10.6019/EMPIAR-10026</subfield>
</datafield>
<datafield tag="773" ind1=" " ind2=" ">
<subfield code="n">doi</subfield>
<subfield code="i">references</subfield>
<subfield code="a">10.6019/EMPIAR-10029</subfield>
</datafield>
<datafield tag="773" ind1=" " ind2=" ">
<subfield code="n">doi</subfield>
<subfield code="i">references</subfield>
<subfield code="a">10.6019/EMPIAR-10025</subfield>
</datafield>
<datafield tag="773" ind1=" " ind2=" ">
<subfield code="n">doi</subfield>
<subfield code="i">references</subfield>
<subfield code="a">10.6019/EMPIAR-10028</subfield>
</datafield>
<datafield tag="773" ind1=" " ind2=" ">
<subfield code="n">doi</subfield>
<subfield code="i">references</subfield>
<subfield code="a">10.6019/EMPIAR-10005</subfield>
</datafield>
<datafield tag="773" ind1=" " ind2=" ">
<subfield code="n">doi</subfield>
<subfield code="i">references</subfield>
<subfield code="a">10.6019/EMPIAR-10011</subfield>
</datafield>
<datafield tag="773" ind1=" " ind2=" ">
<subfield code="n">url</subfield>
<subfield code="i">documents</subfield>
<subfield code="a">http://challenges.emdatabank.org</subfield>
</datafield>
<datafield tag="773" ind1=" " ind2=" ">
<subfield code="n">doi</subfield>
<subfield code="i">cites</subfield>
<subfield code="a">10.1016/j.jsb.2016.02.008</subfield>
</datafield>
<datafield tag="773" ind1=" " ind2=" ">
<subfield code="n">doi</subfield>
<subfield code="i">isVersionOf</subfield>
<subfield code="a">10.5281/zenodo.1120378</subfield>
</datafield>
<datafield tag="024" ind1=" " ind2=" ">
<subfield code="a">10.5281/zenodo.1120379</subfield>
<subfield code="2">doi</subfield>
</datafield>
<datafield tag="980" ind1=" " ind2=" ">
<subfield code="a">dataset</subfield>
</datafield>
</record>
244
199
views
downloads
| All versions | This version | |
|---|---|---|
| Views | 244 | 105 |
| Downloads | 199 | 104 |
| Data volume | 349.7 GB | 121.7 GB |
| Unique views | 218 | 101 |
| Unique downloads | 92 | 58 |
Indexed in
- Publication date:
- December 21, 2017
- DOI:
-
- Keyword(s):
- cryo electron microscopy cryoEM validation challenge benchmark
- Subject(s):
- Related identifiers:
- Cites:
10.1093/nar/gkv1126, 10.1016/j.str.2011.12.014, 10.1016/j.jsb.2016.02.008 - Documents:
http://challenges.emdatabank.org - References:
10.6019/EMPIAR-10010, 10.6019/EMPIAR-10012, 10.6019/EMPIAR-10013, 10.6019/EMPIAR-10026, 10.6019/EMPIAR-10029, 10.6019/EMPIAR-10025, 10.6019/EMPIAR-10028, 10.6019/EMPIAR-10005, 10.6019/EMPIAR-10011 - Communities:
- License (for files):
- Creative Commons Attribution 4.0 International