cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17197184
title: HP1β and densely packed chromatin form separate microdomains in mouse ES cells, which are reconfigured upon exit from naïve pluripotency - Figure 4 raw data Immob control

description: The dataset is linked to Ochirova et al, "HP1β and densely packed chromatin form separate microdomains in mouse ES cells, which are reconfigured upon exit from naïve pluripotency", BioRxiv 2025.

The repository contains the raw microscopy data used in the study. The data is uploaded as ZIP files, corresponding to each figure in the publication, which can be found in the main repository 10.5281/zenodo.17129884. Due to the large size of the raw datasets, the data related to Figure 4 has been split into multiple archives: Figure4_Analysis, Figure4_Rep1_Raw (main repository), Figure4_Rep2_Raw (separate repository: 10.5281/zenodo.17176857) and Figure4_Rep3_Raw (this repository). Please refer to the main repository to find the rest of the data, README file for detailed descriptions of the files, and to the publication for more details regarding data acquisition and analysis.
DOI: 10.15468/dl.rkbnyf
title: Occurrence Download

description: A dataset containing 557 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dengue virus"
 ]
}

 The dataset includes 557 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033541-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jyttec
title: Occurrence Download

description: A dataset containing 12397 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Andropogon virginicus)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 12397 records from 251 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033540-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xj8s8a
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pternistis ochropectus",
 "Country is one of (Brunei Darussalam, Indonesia, Philippines, Timor-Leste, Singapore)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033542-250920141307145/datasets/export for details.
DOI: 10.15468/dl.bv89df
title: Occurrence Download

description: A dataset containing 977121 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chinese Taipei",
 "GadmGid is TWN.3_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year 2020-2025"
 ]
}

 The dataset includes 977121 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033482-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e237626v1-188774
title: Zambia USAID Education Data

description: Zambia: Three USAID-funded projects’ data are included in this folder covering 2012–2021: 1) Early Childhood Education (ECE) Study, 2) Read to Succeed (RTS), and 3) Time to Learn (TTL). Across these projects, the folder contains the following files and numbers of each: codebooks (10), consent (4), data files (13), instruments (1), and reports (2).
DOI: 10.5281/zenodo.17224193
title: A complementary EsMeCaTa precomputed database for phyla with fewer sequenced genomes

description: Presentation

This is a secondary precomputed database of EsMeCaTa for phyla with fewer sequenced genomes. It complements the EsMeCaTa precomputed database. EsMeCaTa's default parameters ignored these phyla. This database has been generated using lower threshold values for esmecata proteomes in order to include these phyla:  busco_percentage_keep/--busco to 55 and minimal_number_proteomes/--minimal-nb-proteomes to 3.

This repository contains two files:



esmecata_database_phyla.zip: zip file containing the files of the precomputed database for the different phyla. It is the file to use with esmecata precomputed command.

database_phyla_proteomes_folder.zip: zip file containing several files/folders:



scripts to generate input files for esmecata (0_find_phyla_proteomes.py and 1_extract_phyla_poorly_characterised.py). They require the first precomputed database for esmecata (esmecata_database.zip) and generate two files (esmecata_input_phyla.tsv and phylum_uniprot_proteomes.tsv).

proteomes_phyla: a folder containing results from esmecata proteomes command with the following parameters: input file esmecata_input_phyla.tsv and with option "--busco 55 --minimal-nb-proteomes 3".




Usage

Since EsMeCaTa version 0.6.6, it can be used in conjunction of the first precomputed database:



esmecata precomputed -i input_file.tsv -o output_folder -d "esmecata_database.zip esmecata_database_phyla.zip"


Dendencies used to create the database




Dependencies
Version


UniProt
2025_02


Date
May 2025


NCBI Taxonomy database
2025-05-01


esmecata
0.6.5


mmseqs2
15.6f452


eggnog database
5.0.2


eggnog-mapper
2.1.12


ete4
4.3.0


pandas
2.2.2


biopython
1.83


requests
2.32.3


SPARQLWrapper
2.0.0




Acknowledgements

Most of the computations presented in this work were performed using the GRICAD infrastructure (https://gricad.univ-grenoble-alpes.fr), which is supported by the Grenoble research community.

The work was funded by the ANR project HyLife (ANR-23-CETP-0002) associated with the CETP project HyLife.
DOI: 10.5281/zenodo.17224194
title: A complementary EsMeCaTa precomputed database for phyla with fewer sequenced genomes

description: Presentation

This is a secondary precomputed database of EsMeCaTa for phyla with fewer sequenced genomes. It complements the EsMeCaTa precomputed database. EsMeCaTa's default parameters ignored these phyla. This database has been generated using lower threshold values for esmecata proteomes in order to include these phyla:  busco_percentage_keep/--busco to 55 and minimal_number_proteomes/--minimal-nb-proteomes to 3.

This repository contains two files:



esmecata_database_phyla.zip: zip file containing the files of the precomputed database for the different phyla. It is the file to use with esmecata precomputed command.

database_phyla_proteomes_folder.zip: zip file containing several files/folders:



scripts to generate input files for esmecata (0_find_phyla_proteomes.py and 1_extract_phyla_poorly_characterised.py). They require the first precomputed database for esmecata (esmecata_database.zip) and generate two files (esmecata_input_phyla.tsv and phylum_uniprot_proteomes.tsv).

proteomes_phyla: a folder containing results from esmecata proteomes command with the following parameters: input file esmecata_input_phyla.tsv and with option "--busco 55 --minimal-nb-proteomes 3".




Usage

Since EsMeCaTa version 0.6.6, it can be used in conjunction of the first precomputed database:



esmecata precomputed -i input_file.tsv -o output_folder -d "esmecata_database.zip esmecata_database_phyla.zip"


Dendencies used to create the database




Dependencies
Version


UniProt
2025_02


Date
May 2025


NCBI Taxonomy database
2025-05-01


esmecata
0.6.5


mmseqs2
15.6f452


eggnog database
5.0.2


eggnog-mapper
2.1.12


ete4
4.3.0


pandas
2.2.2


biopython
1.83


requests
2.32.3


SPARQLWrapper
2.0.0




Acknowledgements

Most of the computations presented in this work were performed using the GRICAD infrastructure (https://gricad.univ-grenoble-alpes.fr), which is supported by the Grenoble research community.

The work was funded by the ANR project HyLife (ANR-23-CETP-0002) associated with the CETP project HyLife.
DOI: 10.15468/dl.w469cf
title: Occurrence Download

description: A dataset containing 4344 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Registros de los dípteros causantes de la transmisión del agente etiológico del dengue en el departamento del Cauca, Colombia"
 ]
}

 The dataset includes 4344 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033545-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jutv4c
title: Occurrence Download

description: A dataset containing 78235 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "OccurrenceStatus is Present",
 "TaxonKey is Aralia",
 "Year 1000-2025"
 ]
}

 The dataset includes 78235 records from 127 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033477-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tow9hn
title: Occurrence Download

description: A dataset containing 1757 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Puma yagouaroundi (É.Geoffroy Saint-Hilaire, 1803)"
 ]
}

 The dataset includes 1757 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009128-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.taycdk
title: Occurrence Download

description: A dataset containing 75 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Vitis retordii Rom.Caill. ex Planch."
 ]
}

 The dataset includes 75 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058499-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m2c5w9
title: Occurrence Download

description: A dataset containing 74730 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is African Plants - a photo guide"
 ]
}

 The dataset includes 74730 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0151499-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yimrdk
title: Occurrence Download

description: A dataset containing 729 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Zygophyllum fabago L.",
 "TaxonKey is Zygophyllum fabago L.",
 "TaxonKey is Zygophyllum fabago L.",
 "TaxonKey is Zygophyllum fabago L.",
 "TaxonKey is Zygophyllum fabago L."
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 729 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010343-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ljtsfd
title: Occurrence Download

description: A dataset containing 25941 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Porcellio scaber Latreille, 1804",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 25941 records from 316 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009128-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cc9pnu
title: Occurrence Download

description: A dataset containing 153 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is false",
 "TaxonKey is Hypostomus plecostomus (Linnaeus, 1758)",
 "Year 1955-2021"
 ]
}

 The dataset includes 153 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072290-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tjq3hy
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coregonus maxillaris Günther, 1866"
 ]
}

 The dataset includes 18 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010343-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gt6ypd
title: Occurrence Download

description: A dataset containing 413 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hydrops martii (Wagler, 1824)"
 ]
}

 The dataset includes 413 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070457-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vfsk8j
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Guettarda hypoglauca Standl."
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000621-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h1sypa
title: Occurrence Download

description: A dataset containing 297 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Melanophryniscus moreirae (Miranda-Ribeiro, 1920)"
 ]
}

 The dataset includes 297 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010343-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25318/4510010201-fra
title: Confiance à l'égard des médias et principale source de nouvelles selon le genre et la province

description: Pourcentage de personnes âgées de 15 ans et plus selon la confiance à l'égard des médias et la principale source de nouvelles, selon le genre, à l’échelle du Canada, des régions et des provinces.
DOI: 10.15468/dl.u283r4
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-108.68112 8.93066,-73.31888 8.93066,-73.31888 23.06934,-108.68112 23.06934,-108.68112 8.93066))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Myrtillocactus eichlamii Britton & Rose"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063287-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rockye
title: Occurrence Download

description: A dataset containing 4920 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Florida Fish and Wildlife Conservation Commission - Freshwater Fishes of Florida - 1956-2000",
 "HasCoordinate is true",
 "TaxonKey is Lepomis macrochirus Rafinesque, 1819",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4920 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018403-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.adq8h7
title: Occurrence Download

description: A dataset containing 64 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-109.68112 8.93066,-74.31888 8.93066,-74.31888 23.06934,-109.68112 23.06934,-109.68112 8.93066))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Peromyscus mayensis Carleton & Huckaby, 1975"
 ]
}

 The dataset includes 64 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063278-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rzjpgw
title: Occurrence Download

description: A dataset listing the 31 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Prosopis argentina Burkart"
 ]
}

 The dataset's 31 records were derived from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010343-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zxzdee
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Opuntia molesta Brandegee"
 ]
}

 The dataset includes 80 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0115038-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.swbwqt
title: Occurrence Download

description: A dataset containing 1444 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tremarctos ornatus (F.G.Cuvier, 1825)"
 ]
}

 The dataset includes 1444 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010343-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e68sxz
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polypterus teugelsi Britz, 2004"
 ]
}

 The dataset includes 13 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009129-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pfr5nm
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Opuntia rosarica G.E.Linds."
 ]
}

 The dataset includes 17 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0115040-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.1cfi4o
title: Occurrence Download

description: A dataset containing 73517 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Literature Occurrence",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Living Specimen"
 ]
 },
 "Geometry POLYGON((-111.26268 29.65461,-104.08799 24.27517,-96.93791 32.59718,-98.6291 50.14435,-104.75402 53.0243,-115.87148 53.32426,-116.1791 39.69772,-111.26268 29.65461))",
 "HasCoordinate is true",
 "TaxonKey is Acrididae",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 73517 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010344-180412121330197/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p7t6oo
title: Occurrence Download

description: A dataset containing 343063 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Annual Census on Waterfowl (Anatidae) Population"
 ]
}

 The dataset includes 343063 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009129-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.494dpu
title: Occurrence Download

description: A dataset containing 5401 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Caracara cheriway (Jacquin, 1784)"
 ]
}

 The dataset includes 5401 records from 235 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0424534-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tg37qe
title: Occurrence Download

description: A dataset containing 1166 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "TaxonKey is Crotalus scutulatus Kennicott, 1861",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1166 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010344-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d3xf0z
title: Occurrence Download

description: A dataset containing 13367 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-100.59631 27.03956,-100.6073 26.25401,-99.73938 26.24416,-99.71741 27.04934,-100.59631 27.03956))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 13367 records from 144 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009129-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3cxbkm
title: Occurrence Download

description: A dataset containing 1222 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arctocephalus pusillus pusillus"
 ]
}

 The dataset includes 1222 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0186520-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ifuya3
title: Occurrence Download

description: A dataset containing 629 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Colombia",
 "Issue is Geodetic datum assumed WGS84",
 "HasCoordinate is true",
 "TaxonKey is Podilymbus podiceps (Linnaeus, 1758)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 629 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010344-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pb2632
title: Occurrence Download

description: A dataset containing 4422 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Quercus castanea Née"
 ]
}

 The dataset includes 4422 records from 126 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0179729-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.