cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12928136.v1
title: Non-English database version of InvaCost

description: The ‘Non-English database’ is part of the InvaCost project (1) that compiles cost information associated with biological invasions. These records describe cost estimates reported in documents written in ten languages other than English (i.e. Chinese, French, German, Greek, Japanese, Portuguese, Russian, Spanish, Dutch, and Ukrainian). An updated version of this database is now incorporated within the core InvaCost Database (3).CONTENT: This page contains (a) the original version of the 'InvaCost_Non-English database' and (b) full definition and details about the descriptive columns used in this database (‘Descriptors’ file).METHODOLOGY: The methodology was similar to the one used to compile the original version of InvaCost (2), but targeting more national webpages and specific literature databases, as well as directly contacting stakeholders that could provide data. The search was carried out by native speakers. Entries were checked by two contributors, except for the entries in Ukrainian and Greek. These ‘non-English’ searches originally resulted in 356 documents and 5,212 entries.UPDATES, RECOMMENDATIONS & CAUTION: Please consider information already described elsewhere (3) for the original InvaCost database. RELATED LINKS AND PUBLICATIONS:1. Diagne C, Catford JA, Essl F, Nuñez MA, Courchamp F (2020) What are the economic costs of biological invasions? A complex topic requiring international and interdisciplinary expertise. NeoBiota 63: 25–37. https://doiorg/10.3897/neobiota.63.552602. Diagne, C., Leroy, B., Gozlan, R.E. et al. InvaCost, a public database of the economic costs of biological invasions worldwide. Sci Data 7, 277 (2020). https://doi.org/10.1038/s41597-020-00586-z3.Database: https://figshare.com/articles/dataset/InvaCost_References_and_description_of_economic_cost_estimates_associated_with_biological_invasions_worldwide_/12668570 4. Researchgate page: https://www.researchgate.net/project/InvaCost-assessing-the-economic-costs-of-biological-invasions5. InvaCost workshop: https://www.biodiversitydynamics.fr/invacost-workshop/
DOI: 10.6084/m9.figshare.12928145
title: Complementary search database for Invacost

description: This database is complementary to the original version of Invacost<sup>[1]</sup>. An updated version of this database is now incorporated within this core database.<b>CONTENT</b>: This page contains (a) the original version of the 'Complementary Search’ database' ('InvaCost_SC database') and (b) full definition and details about the descriptive columns used in this database (‘Descriptors’ file). <b>METHODOLOGY</b>: The construction of this complementary database results from a collective work made by members of the <i>InvaCost</i> consortium<sup>[2]</sup> following the InvaCost workshop<sup>[3,4].</sup> We have screened a total of 304 new references (collected but not processed in the building process of original InvaCost) from which we extracted 2,374 cost entries. Most of the screened references belong to plants; however, they also contain costs for other invasive organisms (animals and pathogens). All cost entries have been standardized for both costs and text, however not all have been yet double-checked (i.e. process to ensure quality of the integrated information, usually made by one or two independent researchers) as the other parts of the Invacost database (i.e. original InvaCost_1.0 and Non-English).<b>UPDATES, RECOMMENDATIONS & CAUTION: </b>Please consider information already described elsewhere<sup>[5]</sup> for the original InvaCost database. <b> </b><b>RELATED LINKS AND PUBLICATIONS</b>: [1]Database: https://figshare.com/articles/dataset/InvaCost_References_and_description_of_economic_cost_estimates_associated_with_biological_invasions_worldwide_/12668570 [2] Researchgate page: https://www.researchgate.net/project/InvaCost-assessing-the-economic-costs-of-biological-invasions[3] InvaCost workshop: https://www.biodiversitydynamics.fr/invacost-workshop/ [4] Diagne C, Catford JA, Essl F, Nuñez MA, Courchamp F (2020) What are the economic costs of biological invasions? A complex topic requiring international and interdisciplinary expertise. NeoBiota 63: 25–37.https://doi.org/10.3897/neobiota.63.55260[5] Diagne, C., Leroy, B., Gozlan, R.E. et al. InvaCost, a public database of the economic costs of biological invasions worldwide. Sci Data 7, 277 (2020). https://doi.org/10.1038/s41597-020-00586-z
DOI: 10.15468/ktx5ev
title: New or rare Madagascar tiger beetles- 18. Pogonostoma (Pogonostoma) ondravybirali sp. nov., elaborated redescriptions of P. (P.) atrorotundatum, P. (P.) densisculptum and P. (Microstenocera) fabiocassolai (Coleoptera: Cicindelidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Moravec, Jiří, Vybíral, Jan (2020): New or rare Madagascar tiger beetles- 18. Pogonostoma (Pogonostoma) ondravybirali sp. nov., elaborated redescriptions of P. (P.) atrorotundatum, P. (P.) densisculptum and P. (Microstenocera) fabiocassolai (Coleoptera: Cicindelidae). Zootaxa 4881 (2): 201-230, DOI: https://doi.org/10.11646/zootaxa.4881.2.1
DOI: 10.6084/m9.figshare.12928145.v1
title: Complementary search database for Invacost

description: This database is complementary to the original version of Invacost<sup>[1]</sup>. An updated version of this database is now incorporated within this core database.<b>CONTENT</b>: This page contains (a) the original version of the 'Complementary Search’ database' ('InvaCost_SC database') and (b) full definition and details about the descriptive columns used in this database (‘Descriptors’ file). <b>METHODOLOGY</b>: The construction of this complementary database results from a collective work made by members of the <i>InvaCost</i> consortium<sup>[2]</sup> following the InvaCost workshop<sup>[3,4].</sup> We have screened a total of 304 new references (collected but not processed in the building process of original InvaCost) from which we extracted 2,374 cost entries. Most of the screened references belong to plants; however, they also contain costs for other invasive organisms (animals and pathogens). All cost entries have been standardized for both costs and text, however not all have been yet double-checked (i.e. process to ensure quality of the integrated information, usually made by one or two independent researchers) as the other parts of the Invacost database (i.e. original InvaCost_1.0 and Non-English).<b>UPDATES, RECOMMENDATIONS & CAUTION: </b>Please consider information already described elsewhere<sup>[5]</sup> for the original InvaCost database. <b> </b><b>RELATED LINKS AND PUBLICATIONS</b>: [1]Database: https://figshare.com/articles/dataset/InvaCost_References_and_description_of_economic_cost_estimates_associated_with_biological_invasions_worldwide_/12668570 [2] Researchgate page: https://www.researchgate.net/project/InvaCost-assessing-the-economic-costs-of-biological-invasions[3] InvaCost workshop: https://www.biodiversitydynamics.fr/invacost-workshop/ [4] Diagne C, Catford JA, Essl F, Nuñez MA, Courchamp F (2020) What are the economic costs of biological invasions? A complex topic requiring international and interdisciplinary expertise. NeoBiota 63: 25–37.https://doi.org/10.3897/neobiota.63.55260[5] Diagne, C., Leroy, B., Gozlan, R.E. et al. InvaCost, a public database of the economic costs of biological invasions worldwide. Sci Data 7, 277 (2020). https://doi.org/10.1038/s41597-020-00586-z
DOI: 10.25934/00005116.0
title: Available IPD datapackage for study 'Efficacy and Safety of CDP870 400 mg in Combination With Methotrexate Compared to Methotrexate Alone in the Treatment of the Signs and Symptoms of Patients With Rheumatoid Arthritis Who Are Partial Responders to Methotrexate'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/00005116.1
title: IPD datapackage for study 'Efficacy and Safety of CDP870 400 mg in Combination With Methotrexate Compared to Methotrexate Alone in the Treatment of the Signs and Symptoms of Patients With Rheumatoid Arthritis Who Are Partial Responders to Methotrexate' and research request: 'Individualized Prediction of Treatment Response to Methotrexate in Patients with Rheumatoid Arthritis: A Machine Learning Approach - Myasoedova'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.5281/zenodo.4080904
title: OBSOLETE FILES DO NOT USE: G2G-EBV GWAS summary statistics

description: OBSOLETE FILES DO NOT USE!!!<br> GWAS results from manuscript titled: <strong>The influence of human genetic variation on Epstein-Barr virus sequence diversity</strong>
DOI: 10.5281/zenodo.4080903
title: OBSOLETE FILES DO NOT USE: G2G-EBV GWAS summary statistics

description: OBSOLETE FILES DO NOT USE!!!<br> GWAS results from manuscript titled: <strong>The influence of human genetic variation on Epstein-Barr virus sequence diversity</strong>
DOI: 10.6084/m9.figshare.13283141.v1
title: HCW Data v3.xlsx

description: This data is in reference to a paper published in PLOS One on the association of healthcare worker status on outcomes in patients with COVID-19
DOI: 10.6084/m9.figshare.13283141
title: HCW Data v3.xlsx

description: This data is in reference to a paper published in PLOS One on the association of healthcare worker status on outcomes in patients with COVID-19
DOI: 10.15468/63c4cj
title: Some lesser known silent crickets (Orthoptera: Gryllidae: Euscyrtinae) from the hilly tracts of India

description: This dataset contains the digitized treatments in Plazi based on the original journal article Meena, Ashok Kumar, Swaminathan, Rajamani, Swaminathan, Tatiana (2020): Some lesser known silent crickets (Orthoptera: Gryllidae: Euscyrtinae) from the hilly tracts of India. Zootaxa 4881 (3): 559-572, DOI: https://doi.org/10.11646/zootaxa.4881.3.8
DOI: 10.15468/k9rxe3
title: A new species of Pseudovaigamus Amado, Ho & Rocha, 1984 (Cyclopoida Ergasilidae) from the teleost Pimelodus maculatus Lacepède, 1803

description: This dataset contains the digitized treatments in Plazi based on the original journal article Narciso, Rodrigo B., Perbiche-Neves, Gilmar, Silva, Reinaldo José Da (2020): A new species of Pseudovaigamus Amado, Ho & Rocha, 1984 (Cyclopoida Ergasilidae) from the teleost Pimelodus maculatus Lacepède, 1803. Zootaxa 4881 (2): 349-360, DOI: https://doi.org/10.11646/zootaxa.4881.2.8
DOI: 10.15468/cafdsy
title: A new species of Boethella Bennett, 2003 (Hymenoptera: Ichneumonidae Tryphoninae) from Brazil, redescription of the genus and a key to world species

description: This dataset contains the digitized treatments in Plazi based on the original journal article Ferreira, João Pascoal Da Silva, Onody, Helena Carolina, Bennett, Andrew Michael Reeve, Timóteo, Ferreira Manuel, Penteado-Dias, Angélica Maria (2020): A new species of Boethella Bennett, 2003 (Hymenoptera: Ichneumonidae Tryphoninae) from Brazil, redescription of the genus and a key to world species. Zootaxa 4881 (2): 337-348, DOI: https://doi.org/10.11646/zootaxa.4881.2.7
DOI: 10.5517/ccdc.csd.cc21sh1d
title: CCDC 1900363: Experimental Crystal Structure Determination

description: Related Article: Vadym Syngaevsky, Andrew Karkhut, Sviatoslav Polovkovych, Andrzej Gzella, Roman Lesyk, Volodymyr Novikov|2020|Synth.Commun.|50|3165|doi:10.1080/00397911.2020.1795880
DOI: 10.5517/ccdc.csd.cc21sh2f
title: CCDC 1900364: Experimental Crystal Structure Determination

description: Related Article: Vadym Syngaevsky, Andrew Karkhut, Sviatoslav Polovkovych, Andrzej Gzella, Roman Lesyk, Volodymyr Novikov|2020|Synth.Commun.|50|3165|doi:10.1080/00397911.2020.1795880
DOI: 10.5517/ccdc.csd.cc21sh3g
title: CCDC 1900365: Experimental Crystal Structure Determination

description: Related Article: Vadym Syngaevsky, Andrew Karkhut, Sviatoslav Polovkovych, Andrzej Gzella, Roman Lesyk, Volodymyr Novikov|2020|Synth.Commun.|50|3165|doi:10.1080/00397911.2020.1795880
DOI: 10.17632/68n8sfcggh.1
title: Data for: Detailed tephrochronology and composition of major Holocene eruptions from Avachinsky, Kozelsky, and Koryaksky volcanoes in Kamchatka

description: Database on the Holocene tephra compositions of Avachinsky, Koryaksky and Kozelsky volcanoes (Kamchatka). Bulk tephra major and trace element contents, glass major and trace element compositions and results of the Bayesian framework age calibration procedure. OxCal CQL code of Bayesian age model.
DOI: 10.25934/00005135.1
title: IPD datapackage for study 'A Phase IIIB, Multi-center, Double-blind, Placebo-controlled, Parallel Group, 52-week Study to Evaluate the Safety and Efficacy of Certolizumab Pegol, Administered With DMARDs, in Patients With Low to Moderate Disease Activity Rheumatoid Arthritis' and research request: 'Predicting the Treatment Response of Certolizumab for Individual Patients with Rheumatoid Arthritis: An Individual Participant Data Meta-Analysis - Luo'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/00005136.0
title: Available IPD datapackage for study 'A Phase IIIb Open-label run-in Double-blind, Placebo Controlled, Randomized Study to Evaluate the Safety/Efficacy of Certolizumab Pegol Administered Concomitantly With Stable-dose Methotrexate in Patients With Active Rheumatoid Arthritis.'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/00005136.1
title: IPD datapackage for study 'A Phase IIIb Open-label run-in Double-blind, Placebo Controlled, Randomized Study to Evaluate the Safety/Efficacy of Certolizumab Pegol Administered Concomitantly With Stable-dose Methotrexate in Patients With Active Rheumatoid Arthritis.' and research request: 'MIDRA : influence of demographic and environmental factors on anti- tumor necrosis factor efficacy in rheumatoid arthritis: a systematic review and meta-analysis of randomized controlled trials'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.6084/m9.figshare.13283507
title: Morphological and phylogeographic evidence for budding speciation: an example in hominins

description: Input/output files, raw data, scripts, and commands used for analyses of speciation mode in fossil hominins.
DOI: 10.5281/zenodo.4289064
title: CellO Data Sets

description: <strong>Overview</strong> A permanent archive of the datasets used in the CellO manuscript (https://www.biorxiv.org/content/10.1101/634097v2). <strong>Expression data</strong> Quantified gene expression for all bulk RNA-seq samples used in this study are available as an HDF5 file (in log transcripts per million): <strong>bulk_log_tpm.h5</strong> Each bulk RNA-seq experiment accession is mapped to a set of cell type labels from the Cell Ontology: <strong>bulk_labels.json</strong> The single-cell data used in this study are also available as an HDF5 file (in log transcripts per million): <strong>single_cell_log_tpm.h5</strong> Each single-cell experiment accession is mapped to a set of cell type labels from the Cell Ontology: <strong>single_cell_labels.json</strong> <strong>Dataset partitions</strong> We partitioned the bulk RNA-seq data into several subsets that were used for various purposes in the study: The list of bulk RNA-seq samples used for training the classifier for evaluation on the bulk validation-set (i.e. the pre-taining set): <strong>pre_training_bulk_experiments.json</strong> The list of bulk RNA-seq samples in the validation-set:<strong> validation_bulk_experiments.json</strong> The list of single-cell experiments in the test set used for evaluting CellO. These are all samples with cell type terms that also appear in the bulk RNA-seq data (i.e. the training data): <strong>test_single_cell_experiments.json</strong> <strong>Technical variable annotations</strong> We annotated 27,097 RNA-seq samples in the Sequence Read Archive (SRA) with technical variables in order to derive a set of primary, healthy, untreated samples (i.e. the datasets above). Our annotations were based on a custom label-hierarchy of technical variables: <strong>tags.json</strong> The mapping from each SRA experiment accession to its set of technical variable labels: <strong>experiment_tags.json</strong> <strong>Trained model coefficients</strong> After training the binary classifiers for each cell type, the model coefficients can be used to investigate up and downregulated genes in each cell type. Below, we post the model coefficients for the one-versus-rest trained binary classifiers (used in the Isotonic Regression and True Path Rule algorithms) as well as the coefficients for the classifiers in the Cascaded Logistic Regression algorithm. Each model was trained on the full set of bulk RNA-seq samples used in the study. Each algorithm's cell type model coefficients are available in a tab-separated-value file: One-versus-rest classifier coefficients: <strong>one_vs_rest_coefficients.tsv.gz</strong> Cascaded logistic regression coefficients: <strong>cascaded_logistic_regression_coefficients.tsv.gz</strong>
DOI: 10.5281/zenodo.4281433
title: CellO Data Sets

description: <strong>Overview</strong> A permanent archive of the datasets used in the CellO manuscript (https://www.biorxiv.org/content/10.1101/634097v2). <strong>Expression data</strong> Quantified gene expression for all bulk RNA-seq samples used in this study are available as an HDF5 file (in log transcripts per million): <strong>bulk_log_tpm.h5</strong> Each bulk RNA-seq experiment accession is mapped to a set of cell type labels from the Cell Ontology: <strong>bulk_labels.json</strong> The single-cell data used in this study are also available as an HDF5 file (in log transcripts per million): <strong>single_cell_log_tpm.h5</strong> Each single-cell experiment accession is mapped to a set of cell type labels from the Cell Ontology: <strong>single_cell_labels.json</strong> <strong>Dataset partitions</strong> We partitioned the bulk RNA-seq data into several subsets that were used for various purposes in the study: The list of bulk RNA-seq samples used for training the classifier for evaluation on the bulk validation-set (i.e. the pre-taining set): <strong>pre_training_bulk_experiments.json</strong> The list of bulk RNA-seq samples in the validation-set:<strong> validation_bulk_experiments.json</strong> The list of single-cell experiments in the test set used for evaluting CellO. These are all samples with cell type terms that also appear in the bulk RNA-seq data (i.e. the training data): <strong>test_single_cell_experiments.json</strong> <strong>Technical variable annotations</strong> We annotated 27,097 RNA-seq samples in the Sequence Read Archive (SRA) with technical variables in order to derive a set of primary, healthy, untreated samples (i.e. the datasets above). Our annotations were based on a custom label-hierarchy of technical variables: <strong>tags.json</strong> The mapping from each SRA experiment accession to its set of technical variable labels: <strong>experiment_tags.json</strong> <strong>Trained model coefficients</strong> After training the binary classifiers for each cell type, the model coefficients can be used to investigate up and downregulated genes in each cell type. Below, we post the model coefficients for the one-versus-rest trained binary classifiers (used in the Isotonic Regression and True Path Rule algorithms) as well as the coefficients for the classifiers in the Cascaded Logistic Regression algorithm. Each model was trained on the full set of bulk RNA-seq samples used in the study. Each algorithm's cell type model coefficients are available in a tab-separated-value file: One-versus-rest classifier coefficients: <strong>one_vs_rest_coefficients.tsv.gz</strong> Cascaded logistic regression coefficients: <strong>cascaded_logistic_regression_coefficients.tsv.gz</strong>
DOI: 10.5281/zenodo.4289076
title: Radiocarbon Data from Middle Horizon Sites in the Upper Majes Valley, Arequipa Peru

description: In 2019, fifteen AMS radiocarbon dates were obtained across four Middle Horizon (AD 600-1000) sites located in the upper Majes Valley in Arequipa, Peru. These include Wari contexts from the sites Pakaytambo and El Tambo, and local road waystations of Santa Rosa II and La Angostura. Dating of both construction and abandonment contexts indicate these sites correspond to the late Middle Horizon, a time of intense connectivity in the prehistoric Andes and Wari state expansionism. This data is a component of the PhD dissertation entitled <em>Networks of Empire: The Role of Infrastructure in Wari State Expansion in Arequipa, Peru (AD 600-1000)</em> by David A. Reid (University of Illinois at Chicago). Funding was provided by the National Science Foundation’s Doctoral Dissertation Research Improvement Award (#1854651).
DOI: 10.5281/zenodo.4289075
title: Radiocarbon Data from Middle Horizon Sites in the Upper Majes Valley, Arequipa Peru

description: In 2019, fifteen AMS radiocarbon dates were obtained across four Middle Horizon (AD 600-1000) sites located in the upper Majes Valley in Arequipa, Peru. These include Wari contexts from the sites Pakaytambo and El Tambo, and local road waystations of Santa Rosa II and La Angostura. Dating of both construction and abandonment contexts indicate these sites correspond to the late Middle Horizon, a time of intense connectivity in the prehistoric Andes and Wari state expansionism. This data is a component of the PhD dissertation entitled <em>Networks of Empire: The Role of Infrastructure in Wari State Expansion in Arequipa, Peru (AD 600-1000)</em> by David A. Reid (University of Illinois at Chicago). Funding was provided by the National Science Foundation’s Doctoral Dissertation Research Improvement Award (#1854651).