cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26188/22338016.v2
title: Supplementary Material S1 - Eucalypt bait kit - full methods for designing the bait kit and FASTA file of genes in kit to use as targets for recovery.

description: To combine the A353, OzBaits, and Myrtaceae target capture bait kits and design a eucalypt specific kit, the target sequence files for each kit were used as inputs to recover the genes from the <em>E. grandis</em> and <em>C. citriodora</em> genomes using the tool BYO_transcriptomes.py (https://github.com/chrisjackson-pellicle/NewTargets/blob/master/BYO_transcriptome.py; McLay et al. 2021). This pipeline performs a hidden Markov model (HMM) search against a set of genes (in this case nucleotide sequences for each bait kit), and extracts matching sequences from input transcriptomes or proteomes. An HMM e-value of 1e-10 was used to identify the target genes from the reference proteomes. For the Angiosperms353 kit, we first expanded the file of target genes to include all 1000 Plants (1KP) Myrtaceae transcriptomes with the NewTargets pipeline (https://github.com/chrisjackson-pellicle/NewTargets; McLay et al 2021); all non-Myrtaceae transcriptomes were then removed from the target file. <br> The following steps were performed in Geneious Prime v2022.2.2 (Kearse et al. 2012). Local BLAST searches (Altschul et al. 1990) were used to identify overlapping genes between the three kits. Genes that were represented two or more times were visually confirmed to be the same gene, and then one version was kept (preferably the longest if there was a length difference). To compare the target loci between the Eucalyptus and Corymbia genomes, we aligned the two sequences for each locus, calculated pairwise identity for each alignment, and then manually inspected the most divergent loci; as we would expect the Eucalyptus and Corymbia sequence to be similar, this search was performed to check whether there were misassignment or misassemblies from the reference proteomes. Very divergent locus alignments were manually fixed by removing poorly matched regions (e.g. where introns were not removed from the proteome) or, in some cases, by removing the entire sequence for either the Eucalyptus or Corymbia sequence if it appeared to be a poor match both to the other reference genome and to the original target sequence. Some genes were flagged by BYO_transcriptomes.py as being out of frame, and these were also manually checked. In most cases, these included regions that appeared to be introns or untranslated/non-coding regions, and these sections were removed. <br> The FASTA file contains all 568 gene target sequences for the eucalypt bait kit.
DOI: 10.26188/22338016
title: Supplementary Material S1 - Eucalypt bait kit - full methods for designing the bait kit and FASTA file of genes in kit to use as targets for recovery.

description: To combine the A353, OzBaits, and Myrtaceae target capture bait kits and design a eucalypt specific kit, the target sequence files for each kit were used as inputs to recover the genes from the <em>E. grandis</em> and <em>C. citriodora</em> genomes using the tool BYO_transcriptomes.py (https://github.com/chrisjackson-pellicle/NewTargets/blob/master/BYO_transcriptome.py; McLay et al. 2021). This pipeline performs a hidden Markov model (HMM) search against a set of genes (in this case nucleotide sequences for each bait kit), and extracts matching sequences from input transcriptomes or proteomes. An HMM e-value of 1e-10 was used to identify the target genes from the reference proteomes. For the Angiosperms353 kit, we first expanded the file of target genes to include all 1000 Plants (1KP) Myrtaceae transcriptomes with the NewTargets pipeline (https://github.com/chrisjackson-pellicle/NewTargets; McLay et al 2021); all non-Myrtaceae transcriptomes were then removed from the target file. <br> The following steps were performed in Geneious Prime v2022.2.2 (Kearse et al. 2012). Local BLAST searches (Altschul et al. 1990) were used to identify overlapping genes between the three kits. Genes that were represented two or more times were visually confirmed to be the same gene, and then one version was kept (preferably the longest if there was a length difference). To compare the target loci between the Eucalyptus and Corymbia genomes, we aligned the two sequences for each locus, calculated pairwise identity for each alignment, and then manually inspected the most divergent loci; as we would expect the Eucalyptus and Corymbia sequence to be similar, this search was performed to check whether there were misassignment or misassemblies from the reference proteomes. Very divergent locus alignments were manually fixed by removing poorly matched regions (e.g. where introns were not removed from the proteome) or, in some cases, by removing the entire sequence for either the Eucalyptus or Corymbia sequence if it appeared to be a poor match both to the other reference genome and to the original target sequence. Some genes were flagged by BYO_transcriptomes.py as being out of frame, and these were also manually checked. In most cases, these included regions that appeared to be introns or untranslated/non-coding regions, and these sections were removed. <br> The FASTA file contains all 568 gene target sequences for the eucalypt bait kit.
DOI: 10.5281/zenodo.8041240
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by José Demetrio Rodríguez, http://www.wikidata.org/entity/Q4396045. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q4396045
DOI: 10.5281/zenodo.8041243
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Georges Roffavier, http://www.wikidata.org/entity/Q2886286. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q2886286
DOI: 10.5281/zenodo.8041242
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Georges Roffavier, http://www.wikidata.org/entity/Q2886286. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q2886286
DOI: 10.5281/zenodo.8041247
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Knut Rognes, http://www.wikidata.org/entity/Q21338109. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21338109
DOI: 10.5281/zenodo.8041246
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Knut Rognes, http://www.wikidata.org/entity/Q21338109. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21338109
DOI: 10.5281/zenodo.8041249
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Kathryn Wachtelhausen Rollins, http://www.wikidata.org/entity/Q108729780. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q108729780
DOI: 10.5281/zenodo.8041248
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Kathryn Wachtelhausen Rollins, http://www.wikidata.org/entity/Q108729780. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q108729780
DOI: 10.5281/zenodo.8041251
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Lars Romell, http://www.wikidata.org/entity/Q4397557. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q4397557
DOI: 10.5281/zenodo.8041250
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Lars Romell, http://www.wikidata.org/entity/Q4397557. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q4397557
DOI: 10.57967/hf/0775
title: houses_test
DOI: 10.5281/zenodo.8041255
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Theodore Roosevelt, http://www.wikidata.org/entity/Q33866. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q33866
DOI: 10.5281/zenodo.8041257
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Kermit Roosevelt, http://www.wikidata.org/entity/Q330431. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q330431
DOI: 10.5281/zenodo.8041256
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Kermit Roosevelt, http://www.wikidata.org/entity/Q330431. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q330431
DOI: 10.5281/zenodo.8041254
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Theodore Roosevelt, http://www.wikidata.org/entity/Q33866. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q33866
DOI: 10.5281/zenodo.8041259
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Muriel Victoria Roscoe, http://www.wikidata.org/entity/Q67188310. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q67188310
DOI: 10.5281/zenodo.8041258
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Muriel Victoria Roscoe, http://www.wikidata.org/entity/Q67188310. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q67188310
DOI: 10.5281/zenodo.8041261
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Richard Heinrich Rosenblatt, http://www.wikidata.org/entity/Q16091613. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q16091613
DOI: 10.5281/zenodo.8041260
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Richard Heinrich Rosenblatt, http://www.wikidata.org/entity/Q16091613. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q16091613
DOI: 10.5281/zenodo.8041265
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by George Bowyer Rossbach, http://www.wikidata.org/entity/Q21607430. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21607430
DOI: 10.5281/zenodo.8041264
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by George Bowyer Rossbach, http://www.wikidata.org/entity/Q21607430. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21607430
DOI: 10.5281/zenodo.8041267
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Vigleik Rosseland, http://www.wikidata.org/entity/Q106872773. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q106872773
DOI: 10.5281/zenodo.8041266
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Vigleik Rosseland, http://www.wikidata.org/entity/Q106872773. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q106872773
DOI: 10.5281/zenodo.8041273
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Werner Rothmaler, http://www.wikidata.org/entity/Q68942. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q68942
DOI: 10.5281/zenodo.8041272
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Werner Rothmaler, http://www.wikidata.org/entity/Q68942. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q68942
DOI: 10.5281/zenodo.8041292
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Robert Runyon, http://www.wikidata.org/entity/Q7349427. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q7349427
DOI: 10.5281/zenodo.8041291
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Robert Runyon, http://www.wikidata.org/entity/Q7349427. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q7349427
DOI: 10.5281/zenodo.8041294
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Johan Tidemand Ruud, http://www.wikidata.org/entity/Q105940546. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q105940546
DOI: 10.5281/zenodo.8041293
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Johan Tidemand Ruud, http://www.wikidata.org/entity/Q105940546. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q105940546
DOI: 10.5281/zenodo.8041312
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Anne Elizabeth Howden, http://www.wikidata.org/entity/Q61857482. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q61857482
DOI: 10.5281/zenodo.8041314
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Miguel Ángel Morón, http://www.wikidata.org/entity/Q22105830. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q22105830
DOI: 10.5281/zenodo.8041311
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Anne Elizabeth Howden, http://www.wikidata.org/entity/Q61857482. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q61857482
DOI: 10.5281/zenodo.8041313
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Miguel Ángel Morón, http://www.wikidata.org/entity/Q22105830. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q22105830
DOI: 10.6084/m9.figshare.23520291
title: ES_AT_BSA

description: aaaaa
DOI: 10.6084/m9.figshare.23520291.v1
title: ES_AT_BSA

description: aaaaa
DOI: 10.5281/zenodo.8041285
title: LEPset

description: LEPset is a large-scale EUS-based pancreas image dataset from the Department of Goenterology, Changhai Hospital, Second Military Medical University/Naval Medical University. This dataset consists of 420 patients and 3,500 images, and it has been divided into two categories (PC and NPC). We have invited experienced clinicians to annotate the category labels for all 3500 EUS images. Moreover, our LEPset also has 8,000 EUS images without any classification annotation. 1. After downloading the data set LEPset.zip, select the appropriate unzip file to extract it<br> 2. After unzipping, there will be two folders: unlabeled and labeled<br> 3. There are 8000 EUS images in the unlabeled folder and two folders in the labeled folder, NPC and PC, representing non-pancreatic cancer and pancreatic cancer respectively. 140 patients (1820 images) in NPC and 280 patients (1680 images) in PC<br> 4. Unlabelled images can be used for pre-training of the model, and labelled images can be used for training and validation of the supervised model
description: To respect the contribution of the contributors to this dataset, this dataset cannot be used commercially, but only for scientific research, so please cite it if it has been used
DOI: 10.5281/zenodo.8041092
title: iPscDB single-cell data for download

description: iPscDB has already integrated 1,118,601 cells from 182 samples of 9 plants, covering 12 tissues and 6 sequencing platforms. The scRNA-seq data from different studies were analyzed and integrated on study, tissue, and species levels with a standardized pipeline. iPscDB provides three different levels of atlas for the collected six plant species: whole plant level, tissue level and study level.
DOI: 10.25913/wjec-8n57
title: Combination Antibiotic Therapy for Methicillin Resistant Staphylococcus Aureus infection (CAMERA2)

description: HeSANDA 1.0.0
description: The dataset contains baseline participant characteristics, details of treatments received, and primary and secondary outcome data. This includes data on mortality, antibiotic treatment, markers for acute kidney injury, microbiologic and serum pathology data and current dialysis, relating to study timepoints at days 5, day 14, 42 and 90.
DOI: 10.5281/zenodo.8041284
title: LEPset

description: LEPset is a large-scale EUS-based pancreas image dataset from the Department of Goenterology, Changhai Hospital, Second Military Medical University/Naval Medical University. This dataset consists of 420 patients and 3,500 images, and it has been divided into two categories (PC and NPC). We have invited experienced clinicians to annotate the category labels for all 3500 EUS images. Moreover, our LEPset also has 8,000 EUS images without any classification annotation. 1. After downloading the data set LEPset.zip, select the appropriate unzip file to extract it<br> 2. After unzipping, there will be two folders: unlabeled and labeled<br> 3. There are 8000 EUS images in the unlabeled folder and two folders in the labeled folder, NPC and PC, representing non-pancreatic cancer and pancreatic cancer respectively. 140 patients (1820 images) in NPC and 280 patients (1680 images) in PC<br> 4. Unlabelled images can be used for pre-training of the model, and labelled images can be used for training and validation of the supervised model
description: To respect the contribution of the contributors to this dataset, this dataset cannot be used commercially, but only for scientific research, so please cite it if it has been used
DOI: 10.5281/zenodo.8041091
title: iPscDB single-cell data for download

description: iPscDB has already integrated 1,118,601 cells from 182 samples of 9 plants, covering 12 tissues and 6 sequencing platforms. The scRNA-seq data from different studies were analyzed and integrated on study, tissue, and species levels with a standardized pipeline. iPscDB provides three different levels of atlas for the collected six plant species: whole plant level, tissue level and study level.
DOI: 10.5281/zenodo.7352276
title: Evaluating the role of the nuclear microenvironment in gene function by population-based modeling

description: This repository accompanies the manuscript "<strong>Evaluating the role of the nuclear microenvironment in gene function by population-based modeling</strong>", available in <em>Nature Structural & Molecular Biology</em>. It contains the files for the population of 3D structures for GM12878 in 200-kb resolution generated using IGM (https://github.com/alberlab/igm) and the derived structural features. Please see README.txt for more information. For any inquiries please reach out to Dr. Frank Alber (falber@g.ucla.edu).