cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.m4zgpn
title: Occurrence Download

description: A dataset containing 3997 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Rhynchophorus ferrugineus (A.G.Olivier, 1791)"
 ]
}

 The dataset includes 3997 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064373-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.auoqv3
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Erwinia amylovora (Burrill, 1882) Winslow et al., 1920",
 "OccurrenceId is CFBP_179",
 "DatasetKey is Collection Francaise de Bacteries Phytopathogenes"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025263-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rnildz
title: Occurrence Download

description: A dataset containing 38820 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gyps fulvus (Hablizl, 1783)"
 ]
}

 The dataset includes 38820 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0077921-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cgszt3
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((10.77201 48.48052,12.09766 48.48052,12.09766 48.98106,10.77201 48.98106,10.77201 48.48052))",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "TaxonKey is Bromus tectorum L.",
 "TaxonKey is Erucastrum gallicum (Willd.) O.E.Schulz",
 "TaxonKey is Lepidium campestre (L.) R.Br.",
 "TaxonKey is Centaurea stoebe subsp. australis (Pancic ex A.Kern.) Greuter"
 ]
 },
 "Year 2000-2020"
 ]
}

 The dataset includes 68 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025265-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wqsn46
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((69.37031999999999 65.07073733333334, 69.37031999999999 82.15736799999999, 35.32496433333334 82.15736799999999, 35.32496433333334 65.07073733333334, 69.37031999999999 65.07073733333334))",
 "EventDate is 2023-04-01,2023-04-30"
 ]
}

 The dataset includes 39 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064391-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b67e5s
title: Occurrence Download

description: A dataset containing 38820 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gyps fulvus (Hablizl, 1783)"
 ]
}

 The dataset includes 38820 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0077922-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a9kntk
title: Occurrence Download

description: A dataset containing 36515 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Taxon occurrence data for the FungalRoot database"
 ]
}

 The dataset includes 36515 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010974-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j3yavs
title: Occurrence Download

description: A dataset containing 144 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((10.77201 48.48052,12.09766 48.48052,12.09766 48.98106,10.77201 48.98106,10.77201 48.48052))",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "TaxonKey is Bromus tectorum L.",
 "TaxonKey is Erucastrum gallicum (Willd.) O.E.Schulz",
 "TaxonKey is Lepidium campestre (L.) R.Br.",
 "TaxonKey is Centaurea stoebe subsp. australis (Pancic ex A.Kern.) Greuter"
 ]
 },
 "Year 1990-2020"
 ]
}

 The dataset includes 144 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025268-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tlopnn
title: Occurrence Download

description: A dataset containing 219 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Melanocoryphus Stal, 1872"
 ]
}

 The dataset includes 219 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0077929-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.twdxvg
title: Occurrence Download

description: A dataset containing 109 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Micrurus tschudii Jan, 1858"
 ]
}

 The dataset includes 109 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025275-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hhpg37
title: Occurrence Download

description: A dataset containing 89 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Acropyga guianensis Weber, 1944"
 ]
}

 The dataset includes 89 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010969-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4ammpi
title: Occurrence Download

description: A dataset containing 117 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lygaeus Fabricius, 1794",
 {
 "or" : [
 "Country is Andorra",
 "Country is Belgium",
 "Country is Portugal",
 "Country is Switzerland",
 "Country is Italy",
 "Country is France",
 "Country is Spain"
 ]
 }
 ]
}

 The dataset includes 117 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0077931-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.l2ogaa
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 2008-2018",
 "Geometry POLYGON((-160.51025390625 18.74267578125,-154.676513671875 18.74267578125,-154.676513671875 22.56591796875,-160.51025390625 22.56591796875,-160.51025390625 18.74267578125))",
 "HasCoordinate is true",
 "TaxonKey is Sophora chrysophylla (Salisb.) Seem."
 ]
}

 The dataset includes 36 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025281-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rpuvyk
title: Occurrence Download

description: A dataset containing 125 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "CoordinateUncertaintyInMeters 0.0-1.0",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Polistes fuscatus (Fabricius, 1793)"
 ]
}

 The dataset includes 125 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040199-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b5sik4
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Melanocoryphus Stal, 1872",
 {
 "or" : [
 "Country is Andorra",
 "Country is Belgium",
 "Country is Portugal",
 "Country is Switzerland",
 "Country is Italy",
 "Country is France",
 "Country is Spain"
 ]
 }
 ]
}

 The dataset includes 38 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0077935-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ksf98r
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Metastelma broadwayi (Schltr.) R.A.Howard"
 ]
}

 The dataset includes 12 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0175474-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dxktqt
title: Occurrence Download

description: A dataset containing 233176 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Salix alba L.)",
 "HasCoordinate is true",
 "Geometry POLYGON ((25.280527 74.385866, 34 74.516506, 34 35.773364, 32.861584 35.588421, 26.375071 34.609982, 22.816449 34.504241, 13.627633 36.690862, 10.001544 38.719154, -0.356862 36.404548, -9.323257 35.627079, -12.292937 57.408982, 25.280527 74.385866))"
 ]
}

 The dataset includes 233176 records from 1444 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010963-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11288249
title: How can we biochemically validate protein function predictions with the deoxycytidine kinase family? - Associated data

description: This is the data that accompanies the pub "How can we biochemically validate ProteinCartography with the deoxycytydine kinase family?" It's part of a group of pubs focused on validating ProtienCartography that begins with "A strategy to validate protein functions in vitro." 

For this repository, we ran ProteinCartography v0.5.0 on the deoxycytidine kinase (dCK) using human dCK as our input (UniProt ID: P27707). We asked for 3,000 Foldseek hits and 7,000 BLAST hits for a total of 10,000 structures. The updated configuration file is in the zipped folder in this repository. Also included in the zipped folder are the inputs, structures of all hits, and all ProteinCartography results. 

Finally, we created a custom overlay for the protein map using this notebook and the manually annotated TSV file in this repository, where we denoted which group of substrates a protein is predicted to act on based on its annotation from UniProt.
DOI: 10.5281/zenodo.11288250
title: How can we biochemically validate protein function predictions with the deoxycytidine kinase family? - Associated data

description: This is the data that accompanies the pub "How can we biochemically validate ProteinCartography with the deoxycytydine kinase family?" It's part of a group of pubs focused on validating ProtienCartography that begins with "A strategy to validate protein functions in vitro." 

For this repository, we ran ProteinCartography v0.5.0 on the deoxycytidine kinase (dCK) using human dCK as our input (UniProt ID: P27707). We asked for 3,000 Foldseek hits and 7,000 BLAST hits for a total of 10,000 structures. The updated configuration file is in the zipped folder in this repository. Also included in the zipped folder are the inputs, structures of all hits, and all ProteinCartography results. 

Finally, we created a custom overlay for the protein map using this notebook and the manually annotated TSV file in this repository, where we denoted which group of substrates a protein is predicted to act on based on its annotation from UniProt.
DOI: 10.5281/zenodo.11264122
title: A strategy to validate protein function predictions in vitro - accompanying data

description: This repository contains the ProteinCartography analyses that accompany the pub "A strategy to validate protein function predictions in vitro." These proteins were selected from a list of the 200 most studied human proteins in the Protein Data Bank (PDB) which was published in Liu and Buck, 2021. 

Each analysis was done using v0.5.0 of ProteinCartography using the standard configuration parameters. Each analysis is in its own zipped file corresponding to the protein name. The zipped files contain inputs, configuration files, all the structures, and all ProteinCartography results. Additionally, for a handful of the proteins, we ran a scaled-up version of ProteinCartography asking for 10,000 hit proteins instead of the standard. These are also included with the file prefix "Scaled-up_". 

Finally, we've decided to move forward with 2 protein families for validation of our tool, ProteinCartography. These protein families are deoxycytidine kinase and Ras GTPase. For more about these two protein families, visit the mentioned pubs!
DOI: 10.5281/zenodo.11264123
title: A strategy to validate protein function predictions in vitro - accompanying data

description: This repository contains the ProteinCartography analyses that accompany the pub "A strategy to validate protein function predictions in vitro." These proteins were selected from a list of the 200 most studied human proteins in the Protein Data Bank (PDB) which was published in Liu and Buck, 2021. 

Each analysis was done using v0.5.0 of ProteinCartography using the standard configuration parameters. Each analysis is in its own zipped file corresponding to the protein name. The zipped files contain inputs, configuration files, all the structures, and all ProteinCartography results. Additionally, for a handful of the proteins, we ran a scaled-up version of ProteinCartography asking for 10,000 hit proteins instead of the standard. These are also included with the file prefix "Scaled-up_". 

Finally, we've decided to move forward with 2 protein families for validation of our tool, ProteinCartography. These protein families are deoxycytidine kinase and Ras GTPase. For more about these two protein families, visit the mentioned pubs!
DOI: 10.15468/dl.spgcdn
title: Occurrence Download

description: A dataset containing 352 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Canavalia gladiata (Jacq.) DC."
 ]
}

 The dataset includes 352 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000012-150827100048397/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11288429
title: How can we biochemically validate protein function predictions with the Ras GTPase family? - Associated data

description: This is the data that accompanies the pub "How can we biochemically validate ProteinCartography with the Ras GTPase family?" It's part of a group of pubs focused on validating ProtienCartography that begins with "A strategy to validate protein functions in vitro." 

For this repository, we ran ProteinCartography v0.5.0 using human HRas and KRas as our inputs for a single run (UniProt ID: P01112 and P01116). We asked for 3,000 Foldseek hits and 7,000 BLAST hits for a total of 10,000 structures. The updated configuration file is in the zipped folder in this repository. Also included in the zipped folder are the inputs, structures of all hits, and all ProteinCartography results. 

Finally, we created a custom overlay for the protein map using this notebook and the manually annotated TSV file in this repository, where we denoted which group of substrates a protein is predicted to act on based on its annotation from UniProt.
DOI: 10.5281/zenodo.11288430
title: How can we biochemically validate protein function predictions with the Ras GTPase family? - Associated data

description: This is the data that accompanies the pub "How can we biochemically validate ProteinCartography with the Ras GTPase family?" It's part of a group of pubs focused on validating ProtienCartography that begins with "A strategy to validate protein functions in vitro." 

For this repository, we ran ProteinCartography v0.5.0 using human HRas and KRas as our inputs for a single run (UniProt ID: P01112 and P01116). We asked for 3,000 Foldseek hits and 7,000 BLAST hits for a total of 10,000 structures. The updated configuration file is in the zipped folder in this repository. Also included in the zipped folder are the inputs, structures of all hits, and all ProteinCartography results. 

Finally, we created a custom overlay for the protein map using this notebook and the manually annotated TSV file in this repository, where we denoted which group of substrates a protein is predicted to act on based on its annotation from UniProt.
DOI: 10.15468/dl.u9fruu
title: Occurrence Download

description: A dataset containing 156675 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mus musculus Linnaeus, 1758"
 ]
}

 The dataset includes 156675 records from 562 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0191666-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.spwb5p
title: Occurrence Download

description: A dataset containing 3531 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Perisoreus Bonaparte, 1831"
 ]
}

 The dataset includes 3531 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0241434-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9tb35m
title: Occurrence Download

description: A dataset containing 4278 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Antigone canadensis (Linnaeus, 1758)",
 "Year 2011-2018"
 ]
}

 The dataset includes 4278 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0241439-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rp2llb
title: Occurrence Download

description: A dataset containing 371 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Saltator fuliginosus (Daudin, 1800)"
 ]
}

 The dataset includes 371 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001643-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5apzjr
title: Occurrence Download

description: A dataset containing 401 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepidobatrachus laevis Budgett, 1899"
 ]
}

 The dataset includes 401 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0145961-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kgpp9k
title: Occurrence Download

description: A dataset containing 1003329 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "TaxonKey is Apidae"
 ]
}

 The dataset includes 1003329 records from 189 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0191556-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v3xcue
title: Occurrence Download

description: A dataset containing 1589 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Clangula hyemalis (Linnaeus, 1758)",
 "Year 2011-2018"
 ]
}

 The dataset includes 1589 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0241447-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6nfv49
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-156.2377 72.46886,-171.45169 69.30596,-168.22448 66.04251,-168.68551 65.0243,-175.13993 63.48955,-176.36374 59.14698,-189.73361 53.35499,-189.57994 50.51369,-181.8961 49.62598,-158.84459 45.48036,-151.92914 55.67365,-137.32985 57.61651,-133.79529 53.7203,-129.49234 53.99222,-126.72616 55.41281,-131.02911 59.3826,-138.86662 61.5043,-139.32765 71.9653,-156.2377 72.46886))",
 "HasGeospatialIssue is false",
 "TaxonKey is Festuca rubra subsp. pruinosa (Hack.) Piper"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0418442-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.auuczv
title: Occurrence Download

description: A dataset containing 1594 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Themeda triandra Forssk.)",
 "HasCoordinate is true",
 "Country is South Africa"
 ]
}

 The dataset includes 1594 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0145734-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d7usuv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Glaucidium brasilianum cactorum van Rossem, 1937",
 "HasCoordinate is True",
 "Country is United States of America",
 "Year is greater than or equal to 1999",
 "Year is less than or equal to 2001",
 "Month is greater than or equal to January",
 "Month is less than or equal to December",
 "HasGeospatialIssue is False",
 "DecimalLatitude is greater than or equal to 24.5",
 "DecimalLatitude is less than or equal to 49.5",
 "DecimalLongitude is greater than or equal to -125.0",
 "DecimalLongitude is less than or equal to -66.5"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0229432-210914110416597/datasets/export for details.