cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31224112
title: data

description: Shift work has been recognized as a significant factor affecting depression in workers.
DOI: 10.6084/m9.figshare.31224112.v1
title: data

description: Shift work has been recognized as a significant factor affecting depression in workers.
DOI: 10.6084/m9.figshare.31224097
title: 16S microbial data

description: 16S rRNA sequencing for mice cecum microbiota/
DOI: 10.6084/m9.figshare.31224097.v1
title: 16S microbial data

description: 16S rRNA sequencing for mice cecum microbiota/
DOI: 10.15468/dl.c5bp52
title: Occurrence Download

description: A dataset containing 150 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leptonychia pallida",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 150 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005315-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18449986
title: PHI-base: the Pathogen-Host Interactions Database, version 5.3

description: Download the dataset here: phi-base_v5.3.zip

The Pathogen–Host Interactions Database (PHI-base) is an online database that catalogues experimentally-verified pathogenicity, virulence and effector genes from fungal, oomycete, and bacterial pathogens, which infect animal, plant, fungal, and insect hosts. PHI-base is a valuable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention.

Information in PHI-base is manually curated by domain experts and is supported by strong experimental evidence (for example, gene disruption and gene complementation experiments), as well as references to the literature in which the original experiments are described. Annotations are made using terms from ontologies and controlled vocabularies, including the Gene Ontology (GO), Brenda Tissue Ontology (BTO), and the Pathogen–Host Interaction Phenotype Ontology (PHIPO).

PHI-base 5 includes data that was curated using a new curation process described in Cuzick et. al (2023). Data releases for PHI-base 5 do not use the same schema as data releases from PHI-base 4, but all data records from PHI-base 4 that can be made compatible with the new schema are included with this release. Data releases from PHI-base 4 and PHI-base 5 will occur in parallel until such time that all data from PHI-base 4 can be migrated to PHI-base 5. The PHI-base 4 data releases are available on Zenodo at https://zenodo.org/doi/10.5281/zenodo.5356870.

For more information about the planned transition from PHI-base 4 to PHI-base 5, see the Help and Announcements page on the PHI-base 5 website.

Release statistics

This version of the PHI-base 5 dataset contains the following types of information:




Data type
Count




Genes
10353


Interactions
33498


Pathogen species
303


Host species
237


Diseases
343


References (publications)
5222


Annotations
 


Pathogen-host interaction phenotype
19419


Gene-for-gene phenotype
569


Pathogen phenotype
12130


Host phenotype
15


GO biological process
1476


GO cellular component
109


GO molecular function
157


Post-translational modification
7


Physical interaction
73


WT RNA expression
48


WT protein expression
2




File contents





phi-base_v5.3.xlsx: the PHI-base dataset as an Excel spreadsheet. This format follows the layout of the PHI-base 5 website, with sheets corresponding to the sections of gene pages on the website. This format is designed for use by non-technical users.




phi-base_v5.3.json: the PHI-base dataset in JSON format. This is modelled on the export format used by PHI-Canto, the curation tool used by PHI-base. This format is primarily intended for programmatic usage and has additional information (e.g. metadata for curation sessions) that is not included in the spreadsheet format.




phi-base.schema.json: a JSON Schema file for the JSON format of the dataset. This is included as documentation for the fields in the JSON file, but can also be used to validate the dataset.
DOI: 10.15468/dl.umnfs9
title: Occurrence Download

description: A dataset containing 1002 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Luehea grandiflora",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1002 records from 109 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005319-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14892195
title: RareFold

description: All compressions are made with zstd here. You can get it here (and it's amazing - thank me later): https://github.com/facebook/zstd

 

params50000.npy - parameters for RareFold single-chain protein structure prediction and design

finetuned_params25000.npy - parameters for RareFold peptide binder design (less tuned)

1ssc.tar.zst - design results for PDB ID 1ssc

val.tar.zst - validation results

test.tar.zst - RareFold test set predictions using the baseline model (The same data AF3 is/can be evaluated on)

test_LC.tar.zst - RareFold test set predictions using the large-crop fine-tuned weights

af3.tar.zst - AF3 predictions

native_valid_structures.tar.zst - native validation structures from the PDB

train_meta_20.csv - meta for train/val/test splits and 20% sequence identity cluster annotations

aa_count_per_chain.csv - Number of AAs of each type per chain id

aa_hist.csv - total occurrence of AA types in the dataset

immunogenicity_analysis.xlsx - results from the immunogenicity analysis of the peptide binders compared to the wild-type binder
DOI: 10.5281/zenodo.18420884
title: RareFold

description: All compressions are made with zstd here. You can get it here (and it's amazing - thank me later): https://github.com/facebook/zstd

 

params50000.npy - parameters for RareFold single-chain protein structure prediction and design

finetuned_params25000.npy - parameters for RareFold peptide binder design (less tuned)

1ssc.tar.zst - design results for PDB ID 1ssc

val.tar.zst - validation results

test.tar.zst - RareFold test set predictions using the baseline model (The same data AF3 is/can be evaluated on)

test_LC.tar.zst - RareFold test set predictions using the large-crop fine-tuned weights

af3.tar.zst - AF3 predictions

native_valid_structures.tar.zst - native validation structures from the PDB

train_meta_20.csv - meta for train/val/test splits and 20% sequence identity cluster annotations

aa_count_per_chain.csv - Number of AAs of each type per chain id

aa_hist.csv - total occurrence of AA types in the dataset

immunogenicity_analysis.xlsx - results from the immunogenicity analysis of the peptide binders compared to the wild-type binder
DOI: 10.5281/zenodo.10722192
title: PHI-base: the Pathogen-Host Interactions Database, version 5.3

description: Download the dataset here: phi-base_v5.3.zip

The Pathogen–Host Interactions Database (PHI-base) is an online database that catalogues experimentally-verified pathogenicity, virulence and effector genes from fungal, oomycete, and bacterial pathogens, which infect animal, plant, fungal, and insect hosts. PHI-base is a valuable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention.

Information in PHI-base is manually curated by domain experts and is supported by strong experimental evidence (for example, gene disruption and gene complementation experiments), as well as references to the literature in which the original experiments are described. Annotations are made using terms from ontologies and controlled vocabularies, including the Gene Ontology (GO), Brenda Tissue Ontology (BTO), and the Pathogen–Host Interaction Phenotype Ontology (PHIPO).

PHI-base 5 includes data that was curated using a new curation process described in Cuzick et. al (2023). Data releases for PHI-base 5 do not use the same schema as data releases from PHI-base 4, but all data records from PHI-base 4 that can be made compatible with the new schema are included with this release. Data releases from PHI-base 4 and PHI-base 5 will occur in parallel until such time that all data from PHI-base 4 can be migrated to PHI-base 5. The PHI-base 4 data releases are available on Zenodo at https://zenodo.org/doi/10.5281/zenodo.5356870.

For more information about the planned transition from PHI-base 4 to PHI-base 5, see the Help and Announcements page on the PHI-base 5 website.

Release statistics

This version of the PHI-base 5 dataset contains the following types of information:




Data type
Count




Genes
10353


Interactions
33498


Pathogen species
303


Host species
237


Diseases
343


References (publications)
5222


Annotations
 


Pathogen-host interaction phenotype
19419


Gene-for-gene phenotype
569


Pathogen phenotype
12130


Host phenotype
15


GO biological process
1476


GO cellular component
109


GO molecular function
157


Post-translational modification
7


Physical interaction
73


WT RNA expression
48


WT protein expression
2




File contents





phi-base_v5.3.xlsx: the PHI-base dataset as an Excel spreadsheet. This format follows the layout of the PHI-base 5 website, with sheets corresponding to the sections of gene pages on the website. This format is designed for use by non-technical users.




phi-base_v5.3.json: the PHI-base dataset in JSON format. This is modelled on the export format used by PHI-Canto, the curation tool used by PHI-base. This format is primarily intended for programmatic usage and has additional information (e.g. metadata for curation sessions) that is not included in the spreadsheet format.




phi-base.schema.json: a JSON Schema file for the JSON format of the dataset. This is included as documentation for the fields in the JSON file, but can also be used to validate the dataset.
DOI: 10.5281/zenodo.17506404
title: PHI-base: the Pathogen-Host Interactions Database, version 5.2

description: ⚠️ This release is outdated. The latest release is available at: doi:10.5281/zenodo.10722192

The Pathogen–Host Interactions Database (PHI-base) is an online database that catalogues experimentally-verified pathogenicity, virulence and effector genes from fungal, oomycete, and bacterial pathogens, which infect animal, plant, fungal, and insect hosts. PHI-base is a valuable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention.

Information in PHI-base is manually curated by domain experts and is supported by strong experimental evidence (for example, gene disruption and gene complementation experiments), as well as references to the literature in which the original experiments are described. Annotations are made using terms from ontologies and controlled vocabularies, including the Gene Ontology (GO), Brenda Tissue Ontology (BTO), and the Pathogen–Host Interaction Phenotype Ontology (PHIPO).

PHI-base 5 includes data that was curated using a new curation process described in Cuzick et. al (2023). Data releases for PHI-base 5 do not use the same schema as data releases from PHI-base 4, but all data records from PHI-base 4 that can be made compatible with the new schema are included with this release. Data releases from PHI-base 4 and PHI-base 5 will occur in parallel until such time that all data from PHI-base 4 can be migrated to PHI-base 5. The PHI-base 4 data releases are available on Zenodo at https://zenodo.org/doi/10.5281/zenodo.5356870.

For more information about the planned transition from PHI-base 4 to PHI-base 5, see the Help and Announcements page on the PHI-base 5 website.

Release statistics

This version of the PHI-base 5 dataset contains the following types of information:




Data type
Count




Genes
10353


Interactions
33498


Pathogen species
303


Host species
237


Diseases
343


References (publications)
5222


Annotations
 


Pathogen-host interaction phenotype
19419


Gene-for-gene phenotype
569


Pathogen phenotype
12130


Host phenotype
15


GO biological process
1476


GO cellular component
109


GO molecular function
157


Post-translational modification
7


Physical interaction
73


WT RNA expression
48


WT protein expression
2




File contents





phi-base_v5.2.xlsx: the PHI-base dataset as an Excel spreadsheet. This format follows the layout of the PHI-base 5 website, with sheets corresponding to the sections of gene pages on the website. This format is designed for use by non-technical users.




phi-base_v5.2.json: the PHI-base dataset in JSON format. This is modelled on the export format used by PHI-Canto, the curation tool used by PHI-base. This format is primarily intended for programmatic usage and has additional information (e.g. metadata for curation sessions) that is not included in the spreadsheet format.




phi-base.schema.json: a JSON Schema file for the JSON format of the dataset. This is included as documentation for the fields in the JSON file, but can also be used to validate the dataset.
DOI: 10.15468/dl.ujknn7
title: Occurrence Download

description: A dataset containing 4207321 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Solidago canadensis, Euphorbia prostrata, Lepidium virginicum, Plantago virginica, Sphagneticola trilobata, Paspalum distichum, Amaranthus retroflexus, Ipomoea indica, Solanum aculeatissimum, Bidens bipinnata, Erigeron canadensis, Chenopodium ficifolium, Chamaecrista mimosoides, Mimosa diplotricha, Bromus catharticus, Datura stramonium, Senna occidentalis, Chenopodiastrum hybridum, Senecio vulgaris, Lolium temulentum, Datura innoxia, Paspalum dilatatum, Portulaca pilosa, Solanum torvum, Veronica persica, Galinsoga parviflora, Stachys arvensis, Euphorbia heterophylla, Sieruela rutidosperma, Sorghum halepense, Ageratina adenophora, Oenothera rosea, Tridax procumbens, Cenchrus echinatus, Mikania micrantha, Ambrosia artemisiifolia, Chromolaena odorata, Dysphania ambrosioides, Amaranthus palmeri, Anredera cordifolia, Ipomoea purpurea, Conyza sumatrensis, Symphyotrichum subulatum, Bidens frondosa, Bidens pilosa, Ambrosia trifida, Tithonia diversifolia, Ageratum conyzoides, Liriomyza trifolii, Paratrechina longicornis, Bactrocera correcta, Liriomyza huidobrensis, Heterobostrychus aequalis, Icerya purchasi, Callosobruchus maculatus, Pheidole megacephala, Blattella germanica, Corythucha ciliata, Phenacoccus solenopsis, Dysmicoccus neobrevipes, Matsucoccus matsumurae, Bemisia tabaci, Bactrocera dorsalis, Lissorhoptrus oryzophilus, Rhynchophorus ferrugineus, Solenopsis invicta, Eriosoma lanigerum, Spodoptera frugiperda, Daktulosphaira vitifoliae, Opogona sacchari, Bruchus rufimanus, Lissachatina fulica, Frankliniella occidentalis, Bruchus pisorum, Phthorimaea operculella, Pomacea canaliculata, Pterygoplichthys pardalis, Avena fatua, Cenchrus longispinus, Lantana camara, Liriomyza sativae, Phthorimaea absoluta, Mimosa bimucronata, Praxelis clematidea, Cyclachaena xanthiifolia, Lactuca serriola)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4207321 records from 6770 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005279-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3929/ethz-b-000733129
title: Dataset for the article "Quantification of stretch-induced stimuli altering the mechanome of dermal fibroblasts"
DOI: 10.5281/zenodo.15536018
title: Test Code Review in the Era of GitHub Actions: A Replication Study(RQ2 Codebook)

description: This repository includes supporting material for a paper draft of "Test Code Review in the Era of GitHub Actions: A Replication Study"
DOI: 10.5281/zenodo.15547926
title: Test Code Review in the Era of GitHub Actions: A Replication Study(RQ2 Codebook)

description: This repository includes supporting material for a paper draft of "Test Code Review in the Era of GitHub Actions: A Replication Study"
DOI: 10.5281/zenodo.15536017
title: Test Code Review in the Era of GitHub Actions: A Replication Study

description: This repository includes supporting material for a paper draft of "Test Code Review in the Era of GitHub Actions: A Replication Study". Due to the extended time required to fetch the raw data (2–8 days per project depending on PR volume) and the total size exceeding 10GB, we did not upload the raw datasets. Instead, we share the processed data and the original fetching scripts to support reproducibility.
DOI: 10.5281/zenodo.15580077
title: Test Code Review in the Era of GitHub Actions: A Replication Study

description: This repository includes supporting material for a paper draft of "Test Code Review in the Era of GitHub Actions: A Replication Study". Due to the extended time required to fetch the raw data (2–8 days per project depending on PR volume) and the total size exceeding 10GB, we did not upload the raw datasets. Instead, we share the processed data and the original fetching scripts to support reproducibility.
DOI: 10.15468/dl.9tgag2
title: Occurrence Download

description: A dataset containing 1103549 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Belgium, Germany, Netherlands)",
 "TaxonKey is one of (Ondatra zibethicus (Linnaeus, 1766), Myocastor coypus (Molina, 1782))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1103549 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016467-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sd23mx
title: Occurrence Download

description: A dataset containing 64760 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Knautia arvensis (L.) Coult.",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 64760 records from 241 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012554-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vspj76
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Argentina euchus Cohen, 1961",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((51.9067 10.3601,51.6539 10.8496,44.9648 10.8496,44.9648 1.8496,45.9851 1.8496,46.3652 2.0796,48.3314 4.1285,49.4027 5.7662,49.6642 6.5145,51.2543 9.1551,51.377 9.8685,51.7452 10.0272,51.9067 10.3601))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012561-250525065834625/datasets/export for details.
DOI: 10.15468/dl.799mha
title: Occurrence Download

description: A dataset containing 35828 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gaillardia pulchella Foug.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 35828 records from 239 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012562-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gf3k9q
title: Occurrence Download

description: A dataset containing 143 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Kobresia humilis (C.A.Mey. ex Trautv.) Serg.",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 143 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012563-250525065834625/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.29206184
title: crux

description: Executable file to run Crux toolkit for Q-ranker
DOI: 10.6084/m9.figshare.29206184.v1
title: crux

description: Executable file to run Crux toolkit for Q-ranker
DOI: 10.15468/dl.68aqa8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Argentina euchus Cohen, 1961",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-0.0352 19.8496,-9.0352 19.8496,-9.0352 10.8496,-0.0352 10.8496,-0.0352 19.8496))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012564-250525065834625/datasets/export for details.
DOI: 10.15468/dl.fvz64s
title: Occurrence Download

description: A dataset containing 5155 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Onopordum illyricum L.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 5155 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012565-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x7brwg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Argentina euchus Cohen, 1961",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-1.9734 4.2478,-0.0352 5.0957,-0.0352 10.8496,-9.0352 10.8496,-9.0352 4.4397,-8.4168 4.1049,-7.389 3.8664,-5.7288 4.5489,-4.0108 4.7359,-1.9734 4.2478))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012568-250525065834625/datasets/export for details.