cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.3bnnh4
title: Occurrence Download

description: A dataset containing 708854 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "HasCoordinate is true",
 "Year is 2007",
 "Month is July"
 ]
}

 The dataset includes 708854 records from 592 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000172-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sktkh2
title: Occurrence Download

description: A dataset containing 21217 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Adelotus brevis (Günther, 1863)"
 ]
}

 The dataset includes 21217 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000182-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13929907
title: Training dataset for the TRENDY method

description: This dataset is used for training the TRENDY method for gene regulatory network inference. It also contains the SINC test data set.

For a brief description of the code for TRENDY method, see https://github.com/YueWangMathbio/TRENDY. 

See https://github.com/YueWangMathbio/TRENDY/blob/main/GRN_transformer.pdf for the manuscript of TRENDY method.

 

To use the data:

1 download all files from https://github.com/YueWangMathbio/TRENDY

2 download all files from this database (both https://zenodo.org/records/14927741 and https://zenodo.org/records/13929908)

3 in the folder with all files from GitHub, creat a folder named "total_data_10", and unzip all files with name "dataset....zip" in this folder

4 unzip "rev_wendy_all_10.zip" in the folder with all files from GitHub

5 unzip "SINC_data.zip", and the files into the folder "SINC"

 

The "total_data_10" folder will contain 102 groups of data, where each group has eight files with different name endings:

xxx_A: 1000 ground truth gene regulatory networks, each of size 10*10

xxx_cov: 11000 covariance matrices for 1000 samples at 11 time points, each of size 10*10

xxx_data: 1000 gene expression samples, each of size 100*10*11 (100 cells, 10 genes, 11 time points)

xxx_genie: 10000 inferred gene regulatory networks by GENIE3 method for 1000 samples at 10 time points, each of size 10*10

xxx_nlode: 1000 inferred gene regulatory networks by NonlinearODEs method for 1000 samples, each of size 10*10

xxx_revcov: 10000 constructed pseudo covariance matrices for 1000 samples at 10 time points, each of size 10*10

xxx_sinc:1000 inferred gene regulatory networks by SINCERITIES method for 1000 samples, each of size 10*10

xxx_wendy: 10000 inferred gene regulatory networks by WENDY method for 1000 samples at 10 time points, each of size 10*10

 

The "rev_wendy_all_10" folder will contain two groups of data, where each group has eight files with different name endings:

xxx_ktstar: 10000 inferred covariance matrices by the first half of TRENDY for 1000 samples at 10 time points, each of size 10*10

xxx_revwendy: 10000 inferred gene regulatory networks by the first half of TRENDY for 1000 samples at 10 time points, each of size 10*10

 

The first 100 group with numbering are for training. The one group with "val" is for validation. The one group with "test" is for testing.

 

If you want to train or test new GRN inference methods, then just use the xxx_A files and xxx_data files.
DOI: 10.5281/zenodo.13929908
title: Training dataset for the TRENDY method

description: This dataset is used for training the TRENDY method for gene regulatory network inference. It also contains the SINC test data set.

For a brief description of the code for TRENDY method, see https://github.com/YueWangMathbio/TRENDY. 

See https://github.com/YueWangMathbio/TRENDY/blob/main/GRN_transformer.pdf for the manuscript of TRENDY method.

 

To use the data:

1 download all files from https://github.com/YueWangMathbio/TRENDY

2 download all files from this database (both https://zenodo.org/records/14927741 and https://zenodo.org/records/13929908)

3 in the folder with all files from GitHub, creat a folder named "total_data_10", and unzip all files with name "dataset....zip" in this folder

4 unzip "rev_wendy_all_10.zip" in the folder with all files from GitHub

5 unzip "SINC_data.zip", and the files into the folder "SINC"

 

The "total_data_10" folder will contain 102 groups of data, where each group has eight files with different name endings:

xxx_A: 1000 ground truth gene regulatory networks, each of size 10*10

xxx_cov: 11000 covariance matrices for 1000 samples at 11 time points, each of size 10*10

xxx_data: 1000 gene expression samples, each of size 100*10*11 (100 cells, 10 genes, 11 time points)

xxx_genie: 10000 inferred gene regulatory networks by GENIE3 method for 1000 samples at 10 time points, each of size 10*10

xxx_nlode: 1000 inferred gene regulatory networks by NonlinearODEs method for 1000 samples, each of size 10*10

xxx_revcov: 10000 constructed pseudo covariance matrices for 1000 samples at 10 time points, each of size 10*10

xxx_sinc:1000 inferred gene regulatory networks by SINCERITIES method for 1000 samples, each of size 10*10

xxx_wendy: 10000 inferred gene regulatory networks by WENDY method for 1000 samples at 10 time points, each of size 10*10

 

The "rev_wendy_all_10" folder will contain two groups of data, where each group has eight files with different name endings:

xxx_ktstar: 10000 inferred covariance matrices by the first half of TRENDY for 1000 samples at 10 time points, each of size 10*10

xxx_revwendy: 10000 inferred gene regulatory networks by the first half of TRENDY for 1000 samples at 10 time points, each of size 10*10

 

The first 100 group with numbering are for training. The one group with "val" is for validation. The one group with "test" is for testing.

 

If you want to train or test new GRN inference methods, then just use the xxx_A files and xxx_data files.
DOI: 10.15468/dl.kh8hdu
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-128.37087 59.23933,-128.45514 60.86154,-140.6533 70.0681,-141.53814 67.16077,-139.72632 60.18738,-132.85827 58.88118,-128.37087 59.23933))",
 "TaxonKey is Limnophyes brachytomus (Kieffer, 1922)"
 ]
}

 The dataset includes 36 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000183-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t8fg4t
title: Occurrence Download

description: A dataset containing 245425 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lacerta horvathi Méhely, 1904, Lacerta agilis Linnaeus, 1758, Bombina variegata (Linnaeus, 1758))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 245425 records from 980 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000176-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ka7yvz
title: Occurrence Download

description: A dataset containing 267 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ambystoma mexicanum (Shaw & Nodder, 1798)"
 ]
}

 The dataset includes 267 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070090-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-194999
title: A letter to senior presbyters concerning a meeting with Pentecostal believers, 1970

description: [description english/roman)] Notice of a meeting of the Presidium of the AUECB (All-Union Council of Evangelical Christian-Baptists), 12-13 May 1970, in which the AUECB plans a project on the 25th anniversary of the unification of AUECB with the CEF (Christians of Evangelical Faith) and CFE (Christians of Faith Evangelical), to visit workers in some areas on the unity of CFE. Included is the 1970 schedule of interviews of regional the Presbyterian Council on the issue of unity with the CFE.
DOI: 10.15468/dl.rfvdea
title: Occurrence Download

description: A dataset containing 14348 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tyto javanica (J.F.Gmelin, 1788)"
 ]
}

 The dataset includes 14348 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018332-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-194766
title: 1945 - A copy of the August agreement
DOI: 10.15468/dl.vaf39n
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.90849 51.57888,17.97764 51.57888,17.97764 57.20388,3.90849 57.20388,3.90849 51.57888))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Conger conger (Linnaeus, 1758)"
 ]
}

 The dataset includes 17 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0163771-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-194869
title: 1956 - Meeting with Undreeva on HEV in 1956
DOI: 10.15468/dl.ys6a9g
title: Occurrence Download

description: A dataset containing 171 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sporophila beltoni Repenning & Fontana, 2013"
 ]
}

 The dataset includes 171 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018340-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f3rt9s
title: Occurrence Download

description: A dataset containing 258 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sirobasidium Lagerh. & Pat."
 ]
}

 The dataset includes 258 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0435893-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-195435
title: 1963 union congress
DOI: 10.15468/dl.xmc3w4
title: Occurrence Download

description: A dataset containing 172 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Spiridens reinwardtii Nees"
 ]
}

 The dataset includes 172 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004424-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dtdc82
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lupinus digitatus Forssk.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 11 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070078-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-195049
title: 1970 - Meetings with the Pentecostal 9.7 April 1970
DOI: 10.25549/pcra-c14-3445
title: Primiritel' = [Reconciler], vol. 9, no. 1-2 (January-February 1937)

description: [description english/roman)] 12 issues per year; For a history of Reconciler, see https://cdm15799.contentdm.oclc.org/cdm/compoundobject/collection/p15799coll14/id/2561/rec/12
DOI: 10.15468/dl.e84fnd
title: Occurrence Download

description: A dataset containing 602 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Turdus maximus (Seebohm, 1881)"
 ]
}

 The dataset includes 602 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018333-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sarpnc
title: Occurrence Download

description: A dataset containing 8151 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((-79.5966 -4.89726,-65.06393 -4.89726,-65.06393 12.39208,-79.5966 12.39208,-79.5966 -4.89726))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Anolis auratus Daudin, 1802"
 ]
}

 The dataset includes 8151 records from 101 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070214-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-3265
title: Primiritel' = [Reconciler], vol. 7, no. 5-6 (May-June 1935)

description: [description english/roman)] 12 issues per year; For a history of Reconciler, see https://cdm15799.contentdm.oclc.org/cdm/compoundobject/collection/p15799coll14/id/2561/rec/12
DOI: 10.15468/dl.2sx5va
title: Occurrence Download

description: A dataset containing 284 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Côte d’Ivoire",
 "OccurrenceStatus is Present",
 "TaxonKey is Striga"
 ]
}

 The dataset includes 284 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058363-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8jsr5v
title: Occurrence Download

description: A dataset containing 4120 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is one of (Brazil, Argentina, Paraguay)",
 "TaxonKey is Chrysolampis mosquitus (Linnaeus, 1758)",
 "Year 1000-2024"
 ]
}

 The dataset includes 4120 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007232-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rhkn9u
title: Occurrence Download

description: A dataset listing the 2601 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Mammalia"
 ]
}

 The dataset's 2601 records were derived from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007284-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7u8yby
title: Occurrence Download

description: A dataset containing 11582998 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 11582998 records from 1306 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007262-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kgv6kq
title: Occurrence Download

description: A dataset containing 3932 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Brazil",
 "TaxonKey is Lophornis magnificus (Vieillot, 1817)",
 "Year 1000-2024"
 ]
}

 The dataset includes 3932 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007288-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g4kswu
title: Occurrence Download

description: A dataset containing 4079 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is one of (Brazil, Paraguay, Argentina)",
 "TaxonKey is Stephanoxis lalandi (Vieillot, 1818)",
 "Year 1000-2024"
 ]
}

 The dataset includes 4079 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007233-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.etqc9m
title: Occurrence Download

description: A dataset containing 4091 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Hamamelis virginiana L."
 ]
}

 The dataset includes 4091 records from 173 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007234-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2dz4mb
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "StateProvince is Puebla",
 "TaxonKey is Carnivora"
 ]
}

 The dataset includes 28 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0091266-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zssydd
title: Occurrence Download

description: A dataset containing 60566 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Herbario COFC de la Universidad de Córdoba: colección general de plantas vasculares"
 ]
}

 The dataset includes 60566 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014679-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mten3e
title: Occurrence Download

description: A dataset containing 420 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Camelina rumelica Velen., Camelina rumelica subsp. transcaspica (Fritsch) Hegi, Camelina rumelica subsp. transcaspica (Fritsch) Hedge, Camelina rumelica subsp. rumelica, Camelina sativa subsp. rumelica (Velen.) O.Bolòs & Vigo, Camelina hispida Boiss., Camelina hispida var. lasiocarpa (Boiss. & Balansa) Post, Camelina laxa C.A.Mey.)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1943",
 "Year is less than or equal to 2023",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 }
 ]
}

 The dataset includes 420 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066032-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8exfyh
title: Occurrence Download

description: A dataset containing 6039 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "Geometry POLYGON((-98.74177 20.18633,-98.93703 20.0727,-99.00948 19.9656,-99.09737 19.88039,-99.10732 19.76929,-98.88004 19.74926,-98.71559 19.77575,-98.65105 19.68138,-98.61088 19.69367,-98.56144 19.7053,-98.49621 19.7499,-98.42411 19.77769,-98.46874 19.87458,-98.4684 19.93591,-98.39424 19.92559,-98.37811 20.01465,-98.44334 20.01336,-98.45295 19.95915,-98.55251 20.02368,-98.55114 20.10688,-98.62186 20.12171,-98.61774 20.24996,-98.73808 20.38615,-98.85721 20.62572,-98.89034 20.68483,-98.76932 20.6845,-98.71267 20.78244,-98.68898 20.8694,-98.65328 21.00664,-98.68778 21.19914,-98.77138 21.25706,-98.84245 21.23818,-99.00021 21.11973,-99.13273 21.03388,-99.20757 20.99414,-99.23006 20.89249,-99.23092 20.86202,-99.22062 20.82673,-99.30714 20.80041,-99.32636 20.77024,-99.28791 20.63664,-99.16912 20.6784,-99.11968 20.58587,-99.05788 20.45404,-98.86425 20.22097,-98.82648 20.16361,-98.74177 20.18633))",
 "TaxonKey is Amphibia",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6039 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014680-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.htctuf
title: Occurrence Download

description: A dataset containing 1452 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leopardus wiedii (Schinz, 1821)"
 ]
}

 The dataset includes 1452 records from 136 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0118284-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.76z58n
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amorphophallus fuscus Hett."
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006924-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hcr5q2
title: Occurrence Download

description: A dataset containing 2169 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Oceania",
 "TaxonKey is Sesbania cannabina (Retz.) Poir."
 ]
}

 The dataset includes 2169 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0283432-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.53zs8y
title: Occurrence Download

description: A dataset containing 337752 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ilex aquifolium L."
 ]
}

 The dataset includes 337752 records from 624 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0118272-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yqeg4p
title: Occurrence Download

description: A dataset containing 133 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Limnias ceratophylli Schrank, 1803)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 133 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042029-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.