cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11267982
title: SARS-CoV-2 RBD data along with ESM embeddings

description: This data is published along with the paper "Biophysical principles predict fitness of SARS-CoV-2 variants" and the code. 

Description:

rbd_df.csv : RBD sequences filtered from GISAID data, along with occurence time, up untill May 2023.

unique_mutant_sequence_emb_esm1v_650m.pkl : esm1v embeddings for unqiue RBDs in rbd_df.csv

df_Desai_15loci_complete.csv: esm1v embeddings for the Desai combinatoric dataset

If you use the code or predictions please consider citing:

@article{
doi:10.1073/pnas.2314518121,
author = {Dianzhuo Wang  and Marian Huot  and Vaibhav Mohanty  and Eugene I. Shakhnovich },
title = {Biophysical principles predict fitness of SARS-CoV-2 variants},
journal = {Proceedings of the National Academy of Sciences},
volume = {121},
number = {23},
pages = {e2314518121},
year = {2024},
doi = {10.1073/pnas.2314518121},
URL = {https://www.pnas.org/doi/abs/10.1073/pnas.2314518121},
eprint = {https://www.pnas.org/doi/pdf/10.1073/pnas.2314518121},
}
DOI: 10.5281/zenodo.11267983
title: SARS-CoV-2 RBD data along with ESM embeddings

description: This data is published along with the paper "Biophysical principles predict fitness of SARS-CoV-2 variants" and the code. 

Description:

rbd_df.csv : RBD sequences filtered from GISAID data, along with occurence time, up untill May 2023.

unique_mutant_sequence_emb_esm1v_650m.pkl : esm1v embeddings for unqiue RBDs in rbd_df.csv

df_Desai_15loci_complete.csv: esm1v embeddings for the Desai combinatoric dataset

If you use the code or predictions please consider citing:

@article{
doi:10.1073/pnas.2314518121,
author = {Dianzhuo Wang  and Marian Huot  and Vaibhav Mohanty  and Eugene I. Shakhnovich },
title = {Biophysical principles predict fitness of SARS-CoV-2 variants},
journal = {Proceedings of the National Academy of Sciences},
volume = {121},
number = {23},
pages = {e2314518121},
year = {2024},
doi = {10.1073/pnas.2314518121},
URL = {https://www.pnas.org/doi/abs/10.1073/pnas.2314518121},
eprint = {https://www.pnas.org/doi/pdf/10.1073/pnas.2314518121},
}
DOI: 10.15468/dl.8gxvbh
title: Occurrence Download

description: A dataset containing 7612 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Russian Federation",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "Country is Norway",
 "Country is Iceland",
 "Country is Finland",
 "Country is France",
 "Country is Sweden",
 "Country is Canada",
 "Country is Austria"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhodiola rosea L.",
 "Year 1960-2000"
 ]
}

 The dataset includes 7612 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058348-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gxhuou
title: Occurrence Download

description: A dataset containing 95550 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Apis mellifera Linnaeus, 1758"
 ]
}

 The dataset includes 95550 records from 484 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008806-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dlusj0
title: Occurrence Download

description: A dataset containing 1668 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Argolamprotes micella (Denis & Schiffermüller), 1775",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1668 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004142-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7d8nrz
title: Occurrence Download

description: A dataset containing 89 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Trachemys venusta cataspila (Günther, 1885)"
 ]
}

 The dataset includes 89 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0253018-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bmbvht
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((21.5625 -24.8111,114.68751 -24.8111,114.68751 39.54924,21.5625 39.54924,21.5625 -24.8111))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhopilema nomadica Galil, Spanier & Ferguson, 1990"
 ]
}

 The dataset includes 19 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083553-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sbxs92
title: Occurrence Download

description: A dataset containing 489 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "TaxonKey is Geotrigona acapulconis (Strand, 1919)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 489 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004143-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4udtcz
title: Occurrence Download

description: A dataset containing 98245 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Erinaceus europaeus Linnaeus, 1758",
 "Year 2017-2020"
 ]
}

 The dataset includes 98245 records from 151 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104302-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7xw8ea
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Croton kurzii Croizat"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009557-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.scs0mn
title: Occurrence Download

description: A dataset containing 71685 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Triticum aestivum L.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 71685 records from 328 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012755-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e6nh5t
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Chile",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Molothrus bonariensis (Gmelin, 1789)",
 "Year 2001-2020"
 ]
}

 The dataset includes 61 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095750-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cddwvr
title: Occurrence Download

description: A dataset containing 8762 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Echmepteryx madagascariensis (Kolbe, 1885)",
 "TaxonKey is Eclectus roratus (Statius Muller, 1776)",
 "TaxonKey is Eclipidrilus lacustris (Verrill, 1871)",
 "TaxonKey is Eclipta prostrata (L.) L."
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 8762 records from 261 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012756-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y8w5jd
title: Occurrence Download

description: A dataset containing 81 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Corydalis appendiculata Hand.-Mazz."
 ]
}

 The dataset includes 81 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009560-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d7j55g
title: Occurrence Download

description: A dataset containing 11467 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Parus xanthogenys Vigors, 1831"
 ]
}

 The dataset includes 11467 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0393276-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ydzr7k
title: Occurrence Download

description: A dataset containing 86 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Humbertacalia leucopappa (DC.) Pruski"
 ]
}

 The dataset includes 86 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026943-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qiw2up
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((15.57904 58.42684,15.51244 58.40933,15.51278 58.36521,15.58351 58.35491,15.65166 58.36693,15.65217 58.41208,15.57904 58.42684))",
 "TaxonKey is Glechoma hederacea L."
 ]
}

 The dataset includes 22 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012756-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.scq7fm
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Subantarctic Fur sealsat Heard Island, 1987/88"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140022-200613084148143/datasets/export for details.
DOI: 10.15468/dl.jvwoqv
title: Occurrence Download

description: A dataset containing 1405044 species occurrences available in GBIF matching the query:
{
 "or" : [
 "TaxonKey is Serinus serinus (Linnaeus, 1766)",
 "TaxonKey is Oriolus oriolus (Linnaeus, 1758)",
 "TaxonKey is Upupa epops Linnaeus, 1758",
 "TaxonKey is Regulus ignicapilla (Temminck, 1820)",
 "TaxonKey is Ficedula albicollis (Temminck, 1815)",
 "TaxonKey is Pluvialis apricaria (Linnaeus, 1758)"
 ]
}

 The dataset includes 1405044 records from 716 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012757-180412121330197/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c52kju
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Vellozia nanuzae L.B.Sm. & Ayensu"
 ]
}

 The dataset includes 45 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095761-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jfcah7
title: Occurrence Download

description: A dataset containing 109 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Impatiens meruensis Gilg"
 ]
}

 The dataset includes 109 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026954-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ndqdg3
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Simpsonichthys nigromaculatus Costa, 2007"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012760-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.622n9y
title: Occurrence Download

description: A dataset containing 215 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Syngnathus tenuirostris Rathke, 1837"
 ]
}

 The dataset includes 215 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0345647-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xs47ey
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Humbertacalia amplexifolia (Humb.) C.Jeffrey"
 ]
}

 The dataset includes 12 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026931-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c4sccr
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vitex oxycuspis Baker"
 ]
}

 The dataset includes 82 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0135270-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.go4dnm
title: Occurrence Download

description: A dataset containing 147 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sulfolobus solfataricus Zillig et al., 1980"
 ]
}

 The dataset includes 147 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012760-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hwxisw
title: Occurrence Download

description: A dataset containing 2524 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rubus L.",
 "Country is Brazil"
 ]
}

 The dataset includes 2524 records from 89 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000352-150827100048397/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hus4bc
title: Occurrence Download

description: A dataset containing 270 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tauraco ruspolii (Salvadori, 1896)"
 ]
}

 The dataset includes 270 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0172913-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uz2aur
title: Occurrence Download

description: A dataset containing 579 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "TaxonKey is Oubanguia africana Baill."
 ]
}

 The dataset includes 579 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000522-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ccjq2q
title: Occurrence Download

description: A dataset containing 7527 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cervus canadensis Erxleben, 1777"
 ]
}

 The dataset includes 7527 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0172937-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h9u50z
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhyssota Pfeiffer, 1856",
 "HasGeospatialIssue is false",
 "Geometry POLYGON((110.59 3.79,110.59 20.85,138.14 20.85,138.14 3.79,110.59 3.79))"
 ]
}

 The dataset includes 21 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000352-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bghuj5
title: Occurrence Download

description: A dataset containing 115601 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "TaxonKey is Berberis vulgaris L."
 ]
}

 The dataset includes 115601 records from 744 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000531-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jeaej7
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cetrelia pseudolivetorum (Asahina) W.L.Culb. & C.F.Culb.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000352-160430102343922/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6ufxb6
title: Occurrence Download

description: A dataset containing 15278 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Elevation is greater than or equal to 9000m"
 ]
}

 The dataset includes 15278 records from 224 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0173001-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ubn4z2
title: Occurrence Download

description: A dataset containing 597 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Draba bruniifolia Steven"
 ]
}

 The dataset includes 597 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0183184-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x9stop
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-71.3562 -24.70825,-72.63062 -29.43237,-68.5437 -29.73999,-67.8186 -25.19165,-71.3562 -24.70825))",
 "HasCoordinate is true",
 "TaxonKey is Lontra felina (Molina, 1782)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 18 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024123-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gz3zn1
title: Occurrence Download

description: A dataset containing 1564 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Solanum lycocarpum A.St.-Hil."
 ]
}

 The dataset includes 1564 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000352-160509122628363/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.93ngpz
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Draba burkei (C.L.Hitchc.) Windham & Beilstein"
 ]
}

 The dataset includes 45 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0183196-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rvtand
title: Occurrence Download

description: A dataset containing 1341 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Draba borealis DC."
 ]
}

 The dataset includes 1341 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0183159-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zmbpoe
title: Occurrence Download

description: A dataset containing 2605 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Athyrium filix-femina (L.) Roth",
 {
 "or" : [
 "Country is Canada",
 "Country is United States of America"
 ]
 }
 ]
}

 The dataset includes 2605 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000352-160526112335914/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.