cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ysvrag
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:ACQ0291"
 ]
}

 The dataset includes 13 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004420-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.82wwua
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arabis nuristanica"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004421-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kbtuem
title: Occurrence Download

description: A dataset containing 1289 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cervus elaphus",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1289 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004423-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xp25yr
title: Occurrence Download

description: A dataset containing 4716602 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "HasCoordinate is true",
 "Modified is 2025-06-12,2025-07-12",
 {
 "or" : [
 "License is CC0 1.0",
 "License is CC-BY 4.0"
 ]
 },
 {
 "not" : {
 "Issue" : [
 "is Zero coordinate"
 ]
 }
 },
 {
 "not" : {
 "Issue" : [
 "is Coordinate out of range"
 ]
 }
 },
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 },
 {
 "not" : {
 "Issue" : [
 "is Coordinate invalid"
 ]
 }
 },
 {
 "not" : {
 "Issue" : [
 "is Geodetic datum invalid"
 ]
 }
 },
 {
 "not" : {
 "Issue" : [
 "is Country mismatch"
 ]
 }
 },
 {
 "not" : {
 "Issue" : [
 "is Country invalid"
 ]
 }
 },
 {
 "not" : {
 "Issue" : [
 "is Continent coordinate mismatch"
 ]
 }
 },
 {
 "not" : {
 "Issue" : [
 "is Continent invalid"
 ]
 }
 },
 {
 "not" : {
 "Issue" : [
 "is Coordinate reprojection suspicious"
 ]
 }
 },
 {
 "not" : {
 "Issue" : [
 "is Coordinate reprojection failed"
 ]
 }
 },
 {
 "not" : {
 "Issue" : [
 "is Coordinate uncertainty meters invalid"
 ]
 }
 },
 {
 "not" : {
 "Issue" : [
 "is Taxon match none"
 ]
 }
 },
 {
 "not" : {
 "Issue" : [
 "is Taxon match aggregate"
 ]
 }
 }
 ]
}

 The dataset includes 4716602 records from 151 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004412-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29550809
title: Tratamiento de Ansiedad e Insomnio con Medicina Biorreguladora de Sistemas- Otra opción terapéutica. Reporte de caso clínico.pdf

description: Mental illnesses represent a priority for countries' health systems, given the increasing prevalence of these pathologies, the economic burden, and the impact they entail on quality of life. In Colombia, the 2015 mental health survey shows that, as in the Americas, the most common mental disorders are anxiety disorders and mood disorders. In the case of anxiety disorders, social phobia and generalized anxiety disorder are the main presentations. Conventional treatment for anxiety disorders is based on pharmacotherapy, generally with selective serotonin reuptake inhibitors (SSRIs) and serotonin and norepinephrine reuptake inhibitors (SNRIs), and cognitive behavioral therapy. In this article, we report the case of a 35-year-old patient with an anxiety disorder associated with sleep and mood disorders, who had previously received allopathic pharmacological treatment and psychotherapy without significant improvement. The patient was treated with systems bioregulatory medicine (Nervoheel®, Neurexan®, and Centreel®) as the primary therapeutic strategy due to therapeutic failure with previous treatment.The Hospital Anxiety and Depression Scale (HADS) and the Pittsburg Sleep Quality Index (PSQI) were used to evaluate the intervention with systems bioregulatory medicine, obtaining pre-intervention scores of 38/42 and PSQI of 19/21. The patient was monitored monthly on two additional occasions after the initial evaluation. At the first follow-up, the HADS score was 29/42, with a moderate reduction in symptom quantification. Therefore, Centreel® was added as an intensification of the initial treatment with Nervoheel® and Neurexan®. At the second follow-up, a significant improvement in symptoms was recorded, with a HADS score of 8/42 and PSQI of 5/21. The case shows that bioregulatory medicine intervention in this patient was a favorable alternative for the treatment of symptoms.
DOI: 10.6084/m9.figshare.29550809.v1
title: Tratamiento de Ansiedad e Insomnio con Medicina Biorreguladora de Sistemas- Otra opción terapéutica. Reporte de caso clínico.pdf

description: Mental illnesses represent a priority for countries' health systems, given the increasing prevalence of these pathologies, the economic burden, and the impact they entail on quality of life. In Colombia, the 2015 mental health survey shows that, as in the Americas, the most common mental disorders are anxiety disorders and mood disorders. In the case of anxiety disorders, social phobia and generalized anxiety disorder are the main presentations. Conventional treatment for anxiety disorders is based on pharmacotherapy, generally with selective serotonin reuptake inhibitors (SSRIs) and serotonin and norepinephrine reuptake inhibitors (SNRIs), and cognitive behavioral therapy. In this article, we report the case of a 35-year-old patient with an anxiety disorder associated with sleep and mood disorders, who had previously received allopathic pharmacological treatment and psychotherapy without significant improvement. The patient was treated with systems bioregulatory medicine (Nervoheel®, Neurexan®, and Centreel®) as the primary therapeutic strategy due to therapeutic failure with previous treatment.The Hospital Anxiety and Depression Scale (HADS) and the Pittsburg Sleep Quality Index (PSQI) were used to evaluate the intervention with systems bioregulatory medicine, obtaining pre-intervention scores of 38/42 and PSQI of 19/21. The patient was monitored monthly on two additional occasions after the initial evaluation. At the first follow-up, the HADS score was 29/42, with a moderate reduction in symptom quantification. Therefore, Centreel® was added as an intensification of the initial treatment with Nervoheel® and Neurexan®. At the second follow-up, a significant improvement in symptoms was recorded, with a HADS score of 8/42 and PSQI of 5/21. The case shows that bioregulatory medicine intervention in this patient was a favorable alternative for the treatment of symptoms.
DOI: 10.15468/dl.p76rbg
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:ACQ3952"
 ]
}

 The dataset includes 17 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004424-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.82vv4v
title: Occurrence Download

description: A dataset containing 1246 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arabis nuttallii"
 ]
}

 The dataset includes 1246 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004425-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.595fg5
title: Occurrence Download

description: A dataset containing 4045230 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-74.6826 8.01889,-72.99401 8.01889,-72.99401 11.69086,-74.6826 11.69086,-74.6826 8.01889))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 4045230 records from 825 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004406-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/12452108
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.v546vg
title: Occurrence Download

description: A dataset containing 16936 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dama dama",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 16936 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004426-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nae8ee
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:ACS3403"
 ]
}

 The dataset includes 22 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004427-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ygrz4x
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arabis olympica"
 ]
}

 The dataset includes 20 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004428-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rjx4r2
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:ACQ6939"
 ]
}

 The dataset includes 10 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004429-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zxgfuu
title: Occurrence Download

description: A dataset containing 867 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rusa timorensis",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 867 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004431-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14366155
title: The evolutionary replacement of restriction-modification by Ssp antiviral systems is associated with the distribution of prophages in the major clonal group of 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.

cdhit_heamtap.py

Read CD-HIT output files and builds a variant matrix with the most prevalent clusters.

triangle_to_square.py

Read an upper triangular matrix (emboss format) format and converts it into a square matrix.

merge_dist.py

Merge both distance values (phylogenetic distance from the tree built in IQ-TREE and Kimura distance from the sequence alignment) from the same genome.and determine the MLST relationship between those genomes.

 

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.15871372
title: The evolutionary replacement of restriction-modification by Ssp antiviral systems is associated with the distribution of prophages in the major clonal group of 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.

cdhit_heamtap.py

Read CD-HIT output files and builds a variant matrix with the most prevalent clusters.

triangle_to_square.py

Read an upper triangular matrix (emboss format) format and converts it into a square matrix.

merge_dist.py

Merge both distance values (phylogenetic distance from the tree built in IQ-TREE and Kimura distance from the sequence alignment) from the same genome.and determine the MLST relationship between those genomes.

 

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: 10.15468/dl.sxpxht
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:ACQ6940"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004432-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3kjpdr
title: Occurrence Download

description: A dataset containing 262 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arabis oregana"
 ]
}

 The dataset includes 262 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004433-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rwx2wy
title: Occurrence Download

description: A dataset containing 366 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Myanmar",
 "Year is 2010",
 "InstitutionCode is iNaturalist"
 ]
}

 The dataset includes 366 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013375-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17515945
title: Data Associated with Gerson et al., in prep, NAR
DOI: 10.7910/dvn/s65rqi
title: Dabirian et al. Supplementary Lipidomic Data - Aging Lipids

description: Semiquantitative analysis of distal colon digesta in young and aged mice treated with antibiotics.
DOI: 10.5281/zenodo.17515484
title: Measuring Photocatalytic Degradation and Quantum Efficiency: an Automated All-In-One Setup
DOI: 10.5281/zenodo.17515946
title: Measuring Photocatalytic Degradation and Quantum Efficiency: an Automated All-In-One Setup
DOI: 10.15468/dl.8ey6z3
title: Occurrence Download

description: A dataset containing 31691642 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia",
 "InstitutionCode is iNaturalist",
 "Country is United States of America",
 "Year is greater than or equal to 2010"
 ]
}

 The dataset includes 31691642 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013338-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17515965
title: NeRF-LLFF Datasets

description: Original data were produced by Mildenhall et al. (2019) as part of the NeRF-LLFF dataset. This upload reproduces and archives the dataset for research reproducibility and open access
DOI: 10.5281/zenodo.17515966
title: NeRF-LLFF Datasets

description: Original data were produced by Mildenhall et al. (2019) as part of the NeRF-LLFF dataset. This upload reproduces and archives the dataset for research reproducibility and open access
DOI: 10.5281/zenodo.17515949
title: S74 | REFTPS | Transformation Products and Reactions from Literature

description: This is the collection associated with list S74 REFTPS Transformation Products and Reactions from Literature on the NORMAN Suspect List Exchange.

https://www.norman-network.com/nds/SLE/

This dataset is designed to provide an entry point for users to contribute transformation products and reactions documented in the literature for addition to the NORMAN SLE, SusDat and the PubChem Transformations section.

Change logs and version tracking at the ECI GitLab site.

Change log: v0.0.2 added InChIKey file. v0.1.0 added new reactions from Anca Baesu and DTXSIDs. v0.2.0 added PFAS TPs from Parviel Chirsir. v0.2.1 more PFAS TPs from Parviel. v0.3.0 Emma added HMMM TPs; v0.3.1 updated references and added new CIDs; added new MS/MS file. v0.4.0 new PFAS TPs plus MS/MS and NMR. v0.4.1 new CID added, plus CID 67543 updated to 14571268. v0.5.0 new 8:2 FT TPs plus annotation data; new structures. v0.5.1 added new CIDs. v0.5.2 added 2:2 to 6:2 FT TPs, updated ref for Bugsel. v0.5.3: added new CIDs. v0.6.0 added new structures. v0.7.0 added more new structures. v 0.7.1: updated CIDs in substances, fixed PFHpA mapping in transformations (some were mismapped to CID 67819). v 0.7.2: updated Biosystem description for many records. v0.8.0: updated CID 163201609 => 166001338, adjusted last 4 MS/MS, added Barisci AOP transformations. v0.9.0 added new structures. v0.9.1 updated CIDs and added radical structures from deposition. v0.10.0 added new irgarol reaction; v0.10.1 added new CID. v0.11.0 added Avendano and Mabury transformations from Parviel. v0.12.0 added Washington MS/MS and Marjanovic MS/MS and reactions. v0.13.0 added Galaxolide transformation. v0.14.0 added Zweigle PFAS TPs with MSMS. v0.14.1 added new CIDs. v0.15.0 added antibiotic TPs from Paul Löffler, SLU, incl. entries with no CID. v0.15.1 added new CIDs. v0.16.0 added benzothiazole reactions. v0.17.0 added TooCOLD TPs from Rick. v0.18.0 added new TFA reactions. v0.19.0 added pak choi reactions, several with no CID. v0.19.1 added new CIDs. v0.20.0 added dimers from Li Ji. v0.20.1 added new CIDs. v0.21.0 added the EJ Weber PFAS libraries "EnvLib" and "MetaLib", curation by Parviel and Emma. Some new CIDs to come. v0.21.1: fixed char issues in substance & transformation files. v0.21.2 added new CIDs. v0.22.0 added "Class_parent" column to the substance deposition file to aid annotation. v0.23.0: added Parviel's zebrafish entries. v0.24.0: added Lingmin Jin, Shiyang Chen & Li Ji's atrazine data.
description: NOTE: This deposition is continually updating as new data is added!
DOI: 10.15468/dl.mcpu3v
title: Occurrence Download

description: A dataset containing 481 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Myanmar",
 "Year is 2011",
 "InstitutionCode is iNaturalist"
 ]
}

 The dataset includes 481 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013380-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.66s52c
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ruellia harveyana",
 "Year 1000-2025"
 ]
}

 The dataset includes 54 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013378-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17515989
title: THE INFLUENCE OF FAMILY CRISES ON ADOLESCENT SELF-ESTEEM: A MIXED-METHODS STUDY
DOI: 10.5281/zenodo.17515988
title: THE INFLUENCE OF FAMILY CRISES ON ADOLESCENT SELF-ESTEEM: A MIXED-METHODS STUDY
DOI: 10.15468/dl.9seghv
title: Occurrence Download

description: A dataset containing 5019 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (Marine Turtle Nesting Locations, Queensland and Northern Territory coastlines, Australia 1915-2012, Fauna Atlas N.T., Team Turtle CQ, NSW BioNet Atlas, iNaturalist Research-grade Observations, Northern Territory WildWatch)",
 "TaxonKey is Natator depressus"
 ]
}

 The dataset includes 5019 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013379-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.