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17 Research products

  • Digital Humanities and Cultural Heritage
  • 2019-2023
  • Open Access
  • Research data
  • Image
  • Digital Humanities and Cultural Heritage
  • Knowmad Institut

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Peng, Jacqueline; Mengge Zhao; Havrilla, James; Liu, Cong; +5 Authors

    Additional file 2: Fig. 2. Frequency of FP terms predicted by CLAMP, cTAKES, and MetaMap. The frequencies of FP terms predicted by the three tools were combined and are shown as a pie graph. Prioritized CUIs represent the set of CUIs from CUI predictions shared by the three tools in the same sentence and co-occurring with a general BM term; non-prioritized CUIs represent all other CUIs. The normalized entity name for the CUI is displayed in square brackets beside the CUI. The number in each section of the pie graph, which the size of the section is scaled to, represents the frequency as a percentage of all FP predictions from CLAMP, cTAKES, and MetaMap combined, and only percentages greater than 2 are labelled.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Walker, Ruth; Stewart, Lesley; Simmonds, Mark;

    Additional file 5: Supplementary Material Figure 3. Estimates of treatment-covariate interaction for the outcome serious adverse outcome small for.

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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Falissard, Bruno; Simpson, Eric L.; Guttman-Yassky, Emma; Papp, Kim A.; +6 Authors

    Provide enhanced digital features for this article This Figshare page contains a Summary Slide. If you are an author of this publication and would like to provide additional enhanced digital features for your article then please contact adisrapidplus@springer.com. The journal offers a range of additional features designed to increase visibility and readership. All features will be thoroughly peer reviewed to ensure the content is of the highest scientific standard and all features are marked as ‘peer reviewed’ to ensure readers are aware that the content has been reviewed to the same level as the articles they are being presented alongside. Moreover, all sponsorship and disclosure information is included to provide complete transparency and adherence to good publication practices. This ensures that however the content is reached the reader has a full understanding of its origin. No fees are charged for hosting additional open access content. Other enhanced features include, but are not limited to: • Slide decks • Videos and animations • Audio abstracts • Audio slides

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Tamames, Javier; Cobo-Simón, Marta; Puente-Sánchez, Fernando;

    Additional file 1: Figure S1. Taxonomic assignments for the mock communities, at the family rank. Ac, Megahit assembly and mapping reads to contigs. Ag, Same but mapping reads to genes. Am, same but mapping genes first to contigs, then to genes. RR, raw reads assignment. KR: Kraken. MP: Metaphlan2. Left: All reads considered. Right: Discounting unclassified reads. Numbers above the bars in the right panels correspond to the Bray-Curtis dissimilarity to the composition of the original microbiome.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    Authors: Tamames, Javier; Cobo-Simón, Marta; Puente-Sánchez, Fernando;

    Additional file 2: Figure S2. Bray-Curtis dissimilarity between assignment methods for mock metagenomes. The “real” column indicated the distance to the real composition of the mock metagenome.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    Authors: Tamames, Javier; Cobo-Simón, Marta; Puente-Sánchez, Fernando;

    Additional file 4: Figure S4. Bray-Curtis dissimilarity to the real composition of the mock community, at family taxonomic rank. For several sample sizes, at phylum rank. Ac, Assembly and mapping reads to contigs. Ag, Same but mapping reads to genes. Am, same but mapping genes first to contigs, then to genes. RR, raw reads assignment. KR: Kraken2. MP: Metaphlan2.

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    Authors: Walker, Ruth; Stewart, Lesley; Simmonds, Mark;

    Additional file 3: Supplementary Material Figure 1. Estimates of treatment-covariate interaction for the outcome serious adverse outcome.

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    Authors: Walker, Ruth; Stewart, Lesley; Simmonds, Mark;

    Additional file 4: Supplementary Material Figure 2. Estimates of treatment-covariate interaction for the outcome preterm birth before 34 weeks.

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    Authors: Chen, Robert; Ho, Joyce C.; Lin, Jin-Mann S.;

    Additional file 1 Appendix Figure A.1. An end-to-end illustration of each module of the medication processing (A) and reason processing (B) algorithms. For each type of input, raw strings are provided as input to the algorithm, and subsequently transformed through successive modules. The final result is a string representing the category. Each module is labeled accordingly in the code, provided at https://github.com/rchen25/medication_natural_language_processing .

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    Authors: Tamames, Javier; Cobo-Simón, Marta; Puente-Sánchez, Fernando;

    Additional file 5: Figure S5. Taxonomic assignments for the real communities, at the family rank. Ac, Megahit assembly and mapping reads to contigs. Ag, Same but mapping reads to genes. Am, same but mapping genes first to contigs, then to genes. RR, raw reads assignment. KR: Kraken. MP: Metaphlan2. Left: All reads considered. Right: Discounting unclassified reads.

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    Authors: Peng, Jacqueline; Mengge Zhao; Havrilla, James; Liu, Cong; +5 Authors

    Additional file 2: Fig. 2. Frequency of FP terms predicted by CLAMP, cTAKES, and MetaMap. The frequencies of FP terms predicted by the three tools were combined and are shown as a pie graph. Prioritized CUIs represent the set of CUIs from CUI predictions shared by the three tools in the same sentence and co-occurring with a general BM term; non-prioritized CUIs represent all other CUIs. The normalized entity name for the CUI is displayed in square brackets beside the CUI. The number in each section of the pie graph, which the size of the section is scaled to, represents the frequency as a percentage of all FP predictions from CLAMP, cTAKES, and MetaMap combined, and only percentages greater than 2 are labelled.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Walker, Ruth; Stewart, Lesley; Simmonds, Mark;

    Additional file 5: Supplementary Material Figure 3. Estimates of treatment-covariate interaction for the outcome serious adverse outcome small for.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Falissard, Bruno; Simpson, Eric L.; Guttman-Yassky, Emma; Papp, Kim A.; +6 Authors

    Provide enhanced digital features for this article This Figshare page contains a Summary Slide. If you are an author of this publication and would like to provide additional enhanced digital features for your article then please contact adisrapidplus@springer.com. The journal offers a range of additional features designed to increase visibility and readership. All features will be thoroughly peer reviewed to ensure the content is of the highest scientific standard and all features are marked as ‘peer reviewed’ to ensure readers are aware that the content has been reviewed to the same level as the articles they are being presented alongside. Moreover, all sponsorship and disclosure information is included to provide complete transparency and adherence to good publication practices. This ensures that however the content is reached the reader has a full understanding of its origin. No fees are charged for hosting additional open access content. Other enhanced features include, but are not limited to: • Slide decks • Videos and animations • Audio abstracts • Audio slides

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Tamames, Javier; Cobo-Simón, Marta; Puente-Sánchez, Fernando;

    Additional file 1: Figure S1. Taxonomic assignments for the mock communities, at the family rank. Ac, Megahit assembly and mapping reads to contigs. Ag, Same but mapping reads to genes. Am, same but mapping genes first to contigs, then to genes. RR, raw reads assignment. KR: Kraken. MP: Metaphlan2. Left: All reads considered. Right: Discounting unclassified reads. Numbers above the bars in the right panels correspond to the Bray-Curtis dissimilarity to the composition of the original microbiome.

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    Authors: Tamames, Javier; Cobo-Simón, Marta; Puente-Sánchez, Fernando;