cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11046401
title: Flow cytometry data from: "Computational measurable residual disease assessment in acute myeloid leukemia using mixture models"

description: This repository contains two large annotated flow cytometry datasets (BLAST110, LAIP29) for AML and healthy control patients used in Mocking et al.

The BLAST110 cohort was gated to identify immature myeloid blasts. 

The LAIP29 cohort comprises different patients and was gated to also identify leukemic (LAIP+) populations. 

Scripts for reproducing our analyses are available at: https://github.com/AUMC-HEMA/cMRD-manuscript

 

Datasets

Each dataset is structured contains the following two folders





/FCS/ contains raw .fcs files




/labels/ contains .csv files containing cell-specific annotations



The .csv files and .fcs files share a common parameter ("event_ID") which can be used to link the cell labels to each FCS file.

The LAIP29 contains an additional file folders /annotations/. This shows the characterization and abundance of each leukemic populations.

 

BLAST110

/BLAST110 contains FCS files from 110 different AML and healthy control samples:





20 normal bone marrow (NBM) samples




30 AML diagnosis ("Dx") samples




90 AML follow up ("FU") samples





Collected at different timepoints after induction chemotherapy




Different levels of measurable residual disease (MRD)





The breakdown of this available in sample_info.csv

 

LAIP29

/LAIP29 contains FCS files from 29 different AML samples measured at diagnosis and follow up.

Each sample can have matching diagnosis and follow up timepoints. This information is available in sample_info.csv

 

Manual gating

BLAST110

In the BLAST110 cohort, was manually gated according to the following gating hierarchy:





WBC based on FSC-A, SSC-A




WBC/Singlets based on FSC-A, FSC-H




WBC/Singlets/CD45pos based on SSC-A, CD45




WBC/Singlets/CD45pos/Lymphocytes based on SSC-A, CD45




WBC/Singlets/CD45pos/CD45dim based on SSC-A, CD45




WBC/Singlets/CD45pos/CD45dim/CD34pos based on SSC-A, CD34




WBC/Singlets/CD45pos/CD45dim/CD117pos based on SSC-A, CD117



The "Blast" label combines the ouptut of CD34pos and CD117pos

 

LAIP29

The LAIP29 cohort was gated according conventional MRD analysis by experts and was annotated similarly to the BLAST110 cohort, with added detail for leukemic cells.

The LAIP column indicates whether a cell was gated as LAIP+.

Each unique leukemic population was given a unique identifier LAIP_ID. Because overlap between LAIPs is not taken into account during gating, each leukemic cell can belong to multiple LAIPs, resulting in a string (e.g., "1" for only LAIP 1, "1_2_3" for a cell positive for 3 LAIPs).
DOI: 10.5281/zenodo.11046402
title: Flow cytometry data from: "Computational measurable residual disease assessment in acute myeloid leukemia using mixture models"

description: This repository contains two large annotated flow cytometry datasets (BLAST110, LAIP29) for AML and healthy control patients used in Mocking et al.

The BLAST110 cohort was gated to identify immature myeloid blasts. 

The LAIP29 cohort comprises different patients and was gated to also identify leukemic (LAIP+) populations. 

Scripts for reproducing our analyses are available at: https://github.com/AUMC-HEMA/cMRD-manuscript

 

Datasets

Each dataset is structured contains the following two folders





/FCS/ contains raw .fcs files




/labels/ contains .csv files containing cell-specific annotations



The .csv files and .fcs files share a common parameter ("event_ID") which can be used to link the cell labels to each FCS file.

The LAIP29 contains an additional file folders /annotations/. This shows the characterization and abundance of each leukemic populations.

 

BLAST110

/BLAST110 contains FCS files from 110 different AML and healthy control samples:





20 normal bone marrow (NBM) samples




30 AML diagnosis ("Dx") samples




90 AML follow up ("FU") samples





Collected at different timepoints after induction chemotherapy




Different levels of measurable residual disease (MRD)





The breakdown of this available in sample_info.csv

 

LAIP29

/LAIP29 contains FCS files from 29 different AML samples measured at diagnosis and follow up.

Each sample can have matching diagnosis and follow up timepoints. This information is available in sample_info.csv

 

Manual gating

BLAST110

In the BLAST110 cohort, was manually gated according to the following gating hierarchy:





WBC based on FSC-A, SSC-A




WBC/Singlets based on FSC-A, FSC-H




WBC/Singlets/CD45pos based on SSC-A, CD45




WBC/Singlets/CD45pos/Lymphocytes based on SSC-A, CD45




WBC/Singlets/CD45pos/CD45dim based on SSC-A, CD45




WBC/Singlets/CD45pos/CD45dim/CD34pos based on SSC-A, CD34




WBC/Singlets/CD45pos/CD45dim/CD117pos based on SSC-A, CD117



The "Blast" label combines the ouptut of CD34pos and CD117pos

 

LAIP29

The LAIP29 cohort was gated according conventional MRD analysis by experts and was annotated similarly to the BLAST110 cohort, with added detail for leukemic cells.

The LAIP column indicates whether a cell was gated as LAIP+.

Each unique leukemic population was given a unique identifier LAIP_ID. Because overlap between LAIPs is not taken into account during gating, each leukemic cell can belong to multiple LAIPs, resulting in a string (e.g., "1" for only LAIP 1, "1_2_3" for a cell positive for 3 LAIPs).
DOI: 10.15468/dl.j94v8k
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Calotes ceylonensis Müller, 1887)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 34 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042710-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gyjusc
title: Occurrence Download

description: A dataset containing 841 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is North America",
 "TaxonKey is Thuja plicata Donn ex D.Don"
 ]
}

 The dataset includes 841 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0077339-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8vv5pf
title: Occurrence Download

description: A dataset containing 1490 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Plum pox virus"
 ]
}

 The dataset includes 1490 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008641-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wwqm44
title: Occurrence Download

description: A dataset containing 149 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cansjera rheedei J.F.Gmel."
 ]
}

 The dataset includes 149 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073041-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3bz57h
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-93.2995630000000062 37.1923150000000007, -93.2995630000000062 37.1928858599999970, -93.2995630000000062 37.1934186499999981, -93.2995630000000062 37.1942559100000025, -93.2995630000000062 37.1948267599999980, -93.2995630000000062 37.1955878999999996, -93.2995630000000062 37.1961207000000016, -93.2989534099999958 37.1961207000000016, -93.2983437700000025 37.1961207000000016, -93.2975055299999951 37.1961207000000016, -93.2965148699999958 37.1961207000000016, -93.2954861099999988 37.1961207000000016, -93.2945717000000059 37.1961207000000016, -93.2945717000000059 37.1953595600000000, -93.2945717000000059 37.1946745300000003, -93.2945717000000059 37.1937992200000025, -93.2945717000000059 37.1929239099999975, -93.2945717000000059 37.1923150000000007, -93.2953717999999981 37.1923150000000007, -93.2959433300000001 37.1923150000000007, -93.2966291700000028 37.1923150000000007, -93.2972007099999985 37.1923150000000007, -93.2978103399999981 37.1923150000000007, -93.2985723900000039 37.1923150000000007, -93.2995630000000062 37.1923150000000007))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1932",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Observation, Specimen, Machine Observation)"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0077378-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.femyrk
title: Occurrence Download

description: A dataset containing 52 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Calotes nigrilabris Peters, 1860)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 52 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042748-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wytu8m
title: Occurrence Download

description: A dataset containing 7980 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Adansonia digitata L."
 ]
}

 The dataset includes 7980 records from 210 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0100826-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fhsgxg
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phaseolus sonorensis Standl."
 ]
}

 The dataset includes 54 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073043-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4hse64
title: Occurrence Download

description: A dataset containing 8044 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Erigeron alpinus L.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 8044 records from 123 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0100816-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ce22tx
title: Occurrence Download

description: A dataset containing 1651 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Limaria hians (Gmelin, 1791)"
 ]
}

 The dataset includes 1651 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042787-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hvqw46
title: Occurrence Download

description: A dataset containing 7980 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Adansonia digitata L."
 ]
}

 The dataset includes 7980 records from 210 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0100811-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4ej4n5
title: Occurrence Download

description: A dataset containing 3336 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leptospron adenanthum (G.Mey.) A.Delgado"
 ]
}

 The dataset includes 3336 records from 245 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073044-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9c7rcv
title: Occurrence Download

description: A dataset containing 7980 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Adansonia digitata L."
 ]
}

 The dataset includes 7980 records from 210 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0100790-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gmzzsp
title: Occurrence Download

description: A dataset containing 175760 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Marine data from Natural Resources Wales (NRW) Technical Support (Research & Monitoring) Contracts, Wales"
 ]
}

 The dataset includes 175760 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020200-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5fwxu5
title: Occurrence Download

description: A dataset containing 175805 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is River Macrophytes Database"
 ]
}

 The dataset includes 175805 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020199-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yxqz5n
title: Occurrence Download

description: A dataset containing 329173 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Corydalis DC."
 ]
}

 The dataset includes 329173 records from 1314 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020197-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tcnlql
title: Occurrence Download

description: A dataset containing 66188 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Literature Occurrence"
 ]
 },
 "Year 1950-2018",
 "TaxonKey is Viperidae"
 ]
}

 The dataset includes 66188 records from 205 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001105-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wgqfqz
title: Occurrence Download

description: A dataset containing 1624 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Human Observation"
 ]
 },
 "Geometry POLYGON((-139.7461 57.5332,-135.66797 42.06445,-109.65234 15.48633,-93.33985 27.7207,-95.16796 35.31445,-102.90234 52.18945,-116.54297 61.89258,-139.7461 57.5332))",
 "HasCoordinate is true",
 "TaxonKey is Berberis aquifolium Pursh",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1624 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001105-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kfgreu
title: Occurrence Download

description: A dataset listing the 291 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Formicivora erythronotos Hartlaub, 1852"
 ]
}

 The dataset's 291 records were derived from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001105-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lfiomd
title: Occurrence Download

description: A dataset containing 2428 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 {
 "or" : [
 "Month is July",
 "Month is August",
 "Month is June"
 ]
 },
 "Year 2015-2019",
 "Geometry POLYGON((-80.39795 43.67582,-74.20166 43.67582,-74.20166 46.22545,-80.39795 46.22545,-80.39795 43.67582))",
 "TaxonKey is Haliaeetus leucocephalus (Linnaeus, 1766)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2428 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001105-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zzlxqo
title: Occurrence Download

description: A dataset containing 720 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arytera divaricata F.Muell.",
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 720 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039220-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gpvwea
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Banksia dryandroides Baxter",
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 80 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039272-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qtda3b
title: Occurrence Download

description: A dataset containing 102 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alloxylon pinnatum (Maiden & Betche) P.H.Weston & Crisp",
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 102 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039182-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.srz58y
title: Occurrence Download

description: A dataset containing 139 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Archontophoenix alexandrae (F.Muell.) H.Wendl. & Drude",
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 139 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039213-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jzwnqp
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Banksia hookeriana Meisn.",
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 49 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039280-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gvyh8x
title: Occurrence Download

description: A dataset containing 203750 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Psittacula cyanocephala (Linnaeus, 1766))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 203750 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059433-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6yildz
title: Occurrence Download

description: A dataset containing 2142 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Castilleja miniata Douglas",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2142 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005057-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dyd6u2
title: Occurrence Download

description: A dataset containing 8740 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Parapholis incurva (L.) C.E.Hubb."
 ]
}

 The dataset includes 8740 records from 210 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013765-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.slbg9r
title: Occurrence Download

description: A dataset containing 1359 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anopterus glandulosus Labill.",
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1359 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039194-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.czdxv2
title: Occurrence Download

description: A dataset containing 1029 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aphananthe philippinensis Planch.",
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1029 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039201-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hzbtwp
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anthocercis littorea Labill.",
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 49 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039197-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.