cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.60712/si-id169246.2
title: StrainInfo SI-ID 169246.2

description: StrainInfo dataset 169246 about a strain of Aspergillus melleus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169249.2
title: StrainInfo SI-ID 169249.2

description: StrainInfo dataset 169249 about a strain of Aspergillus sclerotiorum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169252.2
title: StrainInfo SI-ID 169252.2

description: StrainInfo dataset 169252 about a strain of Trichurus spiralis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169253.2
title: StrainInfo SI-ID 169253.2

description: StrainInfo dataset 169253 about a strain of Skvortzovia furfuracea. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169254.2
title: StrainInfo SI-ID 169254.2

description: StrainInfo dataset 169254 about a strain of Aspergillus auricomus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169257.2
title: StrainInfo SI-ID 169257.2

description: StrainInfo dataset 169257 about a strain of a not identified species. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169260.2
title: StrainInfo SI-ID 169260.2

description: StrainInfo dataset 169260 about a strain of Xenomyrothecium tongaense. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169265.2
title: StrainInfo SI-ID 169265.2

description: StrainInfo dataset 169265 about a strain of Beauveria amorpha. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169274.2
title: StrainInfo SI-ID 169274.2

description: StrainInfo dataset 169274 about a strain of Pleurotus cystidiosus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169277.2
title: StrainInfo SI-ID 169277.2

description: StrainInfo dataset 169277 about a strain of Athelia arachnoidea. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169280.2
title: StrainInfo SI-ID 169280.2

description: StrainInfo dataset 169280 about a strain of Chaetomium arcuatum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169282.2
title: StrainInfo SI-ID 169282.2

description: StrainInfo dataset 169282 about a strain of Mucor amphibiorum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169283.2
title: StrainInfo SI-ID 169283.2

description: StrainInfo dataset 169283 about a strain of Mucor amphibiorum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169284.2
title: StrainInfo SI-ID 169284.2

description: StrainInfo dataset 169284 about a strain of Mucor amphibiorum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169285.2
title: StrainInfo SI-ID 169285.2

description: StrainInfo dataset 169285 about a strain of Lactarius sanguifluus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169293.2
title: StrainInfo SI-ID 169293.2

description: StrainInfo dataset 169293 about a strain of Lichtheimia corymbifera. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169295.2
title: StrainInfo SI-ID 169295.2

description: StrainInfo dataset 169295 about a strain of Curvularia senegalensis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169298.2
title: StrainInfo SI-ID 169298.2

description: StrainInfo dataset 169298 about a strain of Petriella setifera. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169300.2
title: StrainInfo SI-ID 169300.2

description: StrainInfo dataset 169300 about a strain of Penicillium simplicissimum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169302.2
title: StrainInfo SI-ID 169302.2

description: StrainInfo dataset 169302 about a strain of Aspergillus acanthosporus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169303.2
title: StrainInfo SI-ID 169303.2

description: StrainInfo dataset 169303 about a strain of Aspergillus lucknowensis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169309.2
title: StrainInfo SI-ID 169309.2

description: StrainInfo dataset 169309 about a strain of Thamnostylum nigricans. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169314.2
title: StrainInfo SI-ID 169314.2

description: StrainInfo dataset 169314 about a strain of Dichotomocladium elegans. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169315.2
title: StrainInfo SI-ID 169315.2

description: StrainInfo dataset 169315 about a strain of Mucor ctenidius. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169325.2
title: StrainInfo SI-ID 169325.2

description: StrainInfo dataset 169325 about a strain of Diaporthe sclerotioides. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169327.2
title: StrainInfo SI-ID 169327.2

description: StrainInfo dataset 169327 about a strain of Myrmecridium schulzeri. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169330.2
title: StrainInfo SI-ID 169330.2

description: StrainInfo dataset 169330 about a strain of Exophiala heteromorpha. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169334.2
title: StrainInfo SI-ID 169334.2

description: StrainInfo dataset 169334 about a strain of Sclerotinia pseudotuberosa. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.5281/zenodo.14366156
title: Innate antiviral systems are major defensome components that influence prophage distribution in Acinetobacter baumannii

description: In this project, we have analysed the defensome of Acinetobacter baumannii with the aim of profiling different defense systems associated with particular prophage profiles, as well as to predict which systems are more effective and against which specific phages, associating both positively and negatively prophages to defense systems using machine learning techniques.

DOI (Biorxiv): https://doi.org/10.1101/2024.10.26.620419

Python scripts

Package versions: numpy 1.26.4 pandas 2.2.2

binary_matrix.py 

Generate a binary matrix of defense systems using genomes without prophages, as input of the Upset plot.

coocurr_matrix.py

Generate a matrix of defense systems coappearance, as input in the fig 2A.

defsys_pres_ann.py

Create a presence-absence matrix of defense systems.

freq_phages_bymlst.py

Get the most frequent prophages (10% of genomes) per MLST (provided in a list).

matrix_mlst_phages_freq.py

Generate two matrix of absolute and relative frequency, respectively, of prophages by frequent MLST group.

pres_aus_matrix_cl.py

Create a presence-absence matrix of prophages.

matrix_preaus_ml.py

Add to the presence-absence matrix of prophages two columns: one with the defense systems of each genome and another with the MLST group to which they belong.

 

Phylogeny

Use assembly_seq.pl and uniq_sl.pl to build the initial multifasta with only the core genes, as input of MAFFT software. The generated MSA is processed using Clipkit, to eliminate gaps and keep the most informative regions. The processed MSA is used as input to iqTREE to generate the tree.

Circos

Circos were plotted using files generated by prepareForCircos2.pl. This script uses "defsys_presaus_ann.tsv", "logical_viruses.tsv" and a list of genomes of each MLST group to create the input file for the figure. These files are also provided.
DOI: 10.5281/zenodo.14963303
title: Innate antiviral systems are major defensome components that influence prophage distribution in Acinetobacter baumannii

description: In this project, we have analysed the defensome of Acinetobacter baumannii with the aim of profiling different defense systems associated with particular prophage profiles, as well as to predict which systems are more effective and against which specific phages, associating both positively and negatively prophages to defense systems using machine learning techniques.

DOI (Biorxiv): https://doi.org/10.1101/2024.10.26.620419

Python scripts

Package versions: numpy 1.26.4 pandas 2.2.2

binary_matrix.py 

Generate a binary matrix of defense systems using genomes without prophages, as input of the Upset plot.

coocurr_matrix.py

Generate a matrix of defense systems coappearance, as input in the fig 2A.

defsys_pres_ann.py

Create a presence-absence matrix of defense systems.

freq_phages_bymlst.py

Get the most frequent prophages (10% of genomes) per MLST (provided in a list).

matrix_mlst_phages_freq.py

Generate two matrix of absolute and relative frequency, respectively, of prophages by frequent MLST group.

pres_aus_matrix_cl.py

Create a presence-absence matrix of prophages.

matrix_preaus_ml.py

Add to the presence-absence matrix of prophages two columns: one with the defense systems of each genome and another with the MLST group to which they belong.

 

Phylogeny

Use assembly_seq.pl and uniq_sl.pl to build the initial multifasta with only the core genes, as input of MAFFT software. The generated MSA is processed using Clipkit, to eliminate gaps and keep the most informative regions. The processed MSA is used as input to iqTREE to generate the tree.

Circos

Circos were plotted using files generated by prepareForCircos2.pl. This script uses "defsys_presaus_ann.tsv", "logical_viruses.tsv" and a list of genomes of each MLST group to create the input file for the figure. These files are also provided.

README.txt

A more detailed version of the protocol used to generate the results and figures used in the paper.
DOI: 10.5281/zenodo.8080173
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Ernst Georg Pritzel, http://www.wikidata.org/entity/Q3057340. 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/Q3057340
DOI: 10.60712/si-id169338.2
title: StrainInfo SI-ID 169338.2

description: StrainInfo dataset 169338 about a strain of Diaporthe sojae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.5281/zenodo.14963319
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Ernst Georg Pritzel, http://www.wikidata.org/entity/Q3057340. 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/Q3057340
DOI: 10.5281/zenodo.8080172
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Ernst Georg Pritzel, http://www.wikidata.org/entity/Q3057340. 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/Q3057340
DOI: 10.60712/si-id169340.2
title: StrainInfo SI-ID 169340.2

description: StrainInfo dataset 169340 about a strain of Chrysosporium queenslandicum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169343.2
title: StrainInfo SI-ID 169343.2

description: StrainInfo dataset 169343 about a strain of Chrysosporium lobatum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169344.2
title: StrainInfo SI-ID 169344.2

description: StrainInfo dataset 169344 about a strain of Chrysosporium keratinophilum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169362.2
title: StrainInfo SI-ID 169362.2

description: StrainInfo dataset 169362 about a strain of Gymnopus fuscopurpureus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169363.2
title: StrainInfo SI-ID 169363.2

description: StrainInfo dataset 169363 about a strain of Gymnopus fuscopurpureus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169364.2
title: StrainInfo SI-ID 169364.2

description: StrainInfo dataset 169364 about a strain of Gymnopus fuscopurpureus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169370.2
title: StrainInfo SI-ID 169370.2

description: StrainInfo dataset 169370 about a strain of Spinellus fusiger. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169376.2
title: StrainInfo SI-ID 169376.2

description: StrainInfo dataset 169376 about a strain of Arthrobotrys entomopaga. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169378.2
title: StrainInfo SI-ID 169378.2

description: StrainInfo dataset 169378 about a strain of Clonostachys rosea. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169382.2
title: StrainInfo SI-ID 169382.2

description: StrainInfo dataset 169382 about a strain of Engyodontium rectidentatum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169384.2
title: StrainInfo SI-ID 169384.2

description: StrainInfo dataset 169384 about a strain of Arthroderma melis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169385.2
title: StrainInfo SI-ID 169385.2

description: StrainInfo dataset 169385 about a strain of Amesia gelasinospora. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169386.2
title: StrainInfo SI-ID 169386.2

description: StrainInfo dataset 169386 about a strain of Aspergillus striatus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.15468/dl.xpyfws
title: Occurrence Download

description: A dataset containing 568 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Scytalopus urubambae Zimmer, 1939"
 ]
}

 The dataset includes 568 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004354-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id169393.2
title: StrainInfo SI-ID 169393.2

description: StrainInfo dataset 169393 about a strain of Mortierella indohii. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169395.2
title: StrainInfo SI-ID 169395.2

description: StrainInfo dataset 169395 about a strain of Pseudocercospora cruenta. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169397.2
title: StrainInfo SI-ID 169397.2

description: StrainInfo dataset 169397 about a strain of Exserohilum rostratum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169403.2
title: StrainInfo SI-ID 169403.2

description: StrainInfo dataset 169403 about a strain of Microthecium fallax. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169405.2
title: StrainInfo SI-ID 169405.2

description: StrainInfo dataset 169405 about a strain of Rhamphoriopsis glauca. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169406.2
title: StrainInfo SI-ID 169406.2

description: StrainInfo dataset 169406 about a strain of Rhamphoriopsis glauca. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169419.2
title: StrainInfo SI-ID 169419.2

description: StrainInfo dataset 169419 about a strain of Graphilbum sparsum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.60712/si-id169426.2
title: StrainInfo SI-ID 169426.2

description: StrainInfo dataset 169426 about a strain of Hyphomucor assamensis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data.
DOI: 10.15468/dl.runj5h
title: Occurrence Download

description: A dataset containing 1088924 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Elevation 1000.0-5000.0m",
 "Geometry POLYGON((-151.31418 -48.90696,181.72705 -48.90696,181.72705 44.37147,-151.31418 44.37147,-151.31418 -48.90696))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0)",
 "TaxonKey is one of (Mammalia, Aves, Amphibia, Reptilia)",
 "Year 2000-2025"
 ]
}

 The dataset includes 1088924 records from 706 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004325-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jvjvj6
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Portugal",
 "TaxonKey is Spergularia tangerina P.Monnier",
 "Year 1975-2025"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006755-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jjsktk
title: Occurrence Download

description: A dataset containing 6667 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "TaxonKey is Lycalopex griseus (Gray, 1837)",
 "Year 2000-2025"
 ]
}

 The dataset includes 6667 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006758-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x7rgg2
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((121.26541 25.51484,120.62843 24.82556,119.92186 23.47616,120.40242 21.83911,120.87281 21.71239,121.08479 22.30073,121.61073 23.21981,122.34387 25.19608,121.26541 25.51484))",
 "TaxonKey is Prunus taiwaniana Hayata",
 "Year 1993-2022"
 ]
}

 The dataset includes 71 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006756-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.