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

description: A dataset containing 27927 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Alchemilla plicatula Gand., Alchemilla subsericea Reut., Alchemilla xanthochlora Rothm.)",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 27927 records from 178 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0309723-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ekwuzh
title: Occurrence Download

description: A dataset containing 178 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-99.18813 38.0416,-99.08987 37.41282,-98.80648 38.82395,-99.76996 39.6399,-99.18813 38.0416))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sigmodon hispidus Say & Ord, 1825"
 ]
}

 The dataset includes 178 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107072-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dcnkgz
title: Occurrence Download

description: A dataset containing 83 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "OccurrenceStatus is Present",
 "TaxonKey is Anolis vittigerus Cope, 1862",
 "Year 2010-2022"
 ]
}

 The dataset includes 83 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0308862-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11088252
title: Datasets for Integration into UAB UBRITE/PHARMALCHEMY Resource

description: This represents a semester project completed for INFO603 at the University of Alabama at Birmingham. This is a collection of datasets which were curated, either directly from the original source or from staged UAB-Cheaha copies, for integration into the UAB PharmAlchemy system.

Some data were also used to complete a personal semester project to test the viability of using cell painting data to determine compound toxicities.

All data can be found within the UAB-Cheaha-UBRITE system at the following location: /data/project/ubrite/PharmAlchemy24/RomanFinalDeliverables/ .

Coversheets explaining each delivered dataset in more detail are attached here. They specify the file directory within Cheaha where each delivered dataset can be found, and also the github repo location where the code used to perform the transformations can be found.

 

Data were analyzed directly or indirectly from the following sources:



https://clinicaltrials.gov/

Drugbank: Knox C, Wilson M, Klinger CM, et al. DrugBank 6.0: the DrugBank Knowledgebase for 2024. Nucleic Acids Res. 2024 Jan 5;52(D1):D1265-D1275. doi: 10.1093/nar/gkad976.

Drug Repurposing Hub: Corsello, S., Bittker, J., Liu, Z. et al. The Drug Repurposing Hub: a next-generation drug library and information resource. Nat Med 23, 405–408 (2017). https://doi.org/10.1038/nm.4306

Disease Ontology: Schriml, L. M., Mitraka, E., Munro, J., Tauber, B., Schor, M., Nickle, L., … Greene, C. (2018). Human Disease Ontology 2018 update: classification, content and workflow expansion. Nucleic acids research, 47(D1), D955–D962. doi:10.1093/nar/gky1032

Mitotoxicity Data: Predicting the Mitochondrial Toxicity of Small Molecules: Insights from Mechanistic Assays and Cell Painting Data, Marina Garcia de Lomana, Paula Andrea Marin Zapata, and Floriane Montanari Chemical Research in Toxicology 2023 36 (7), 1107-1120 DOI: 10.1021/acs.chemrestox.3c00086

Cell Painting Data: Haghighi, M., Caicedo, J.C., Cimini, B.A. et al. High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations. Nat Methods 19, 1550–1557 (2022). https://doi.org/10.1038/s41592-022-01667-0

Online Mendelian Inheritance in Man: Online Mendelian Inheritance in Man, OMIM®. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD), 2024. World Wide Web URL: https://omim.org/

Therapeutic Target Database: Chen X, Ji ZL, Chen YZ. TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. doi: 10.1093/nar/30.1.412. PMID: 11752352; PMCID: PMC99057.
DOI: 10.5281/zenodo.11088253
title: Datasets for Integration into UAB UBRITE/PHARMALCHEMY Resource

description: This represents a semester project completed for INFO603 at the University of Alabama at Birmingham. This is a collection of datasets which were curated, either directly from the original source or from staged UAB-Cheaha copies, for integration into the UAB PharmAlchemy system.

Some data were also used to complete a personal semester project to test the viability of using cell painting data to determine compound toxicities.

All data can be found within the UAB-Cheaha-UBRITE system at the following location: /data/project/ubrite/PharmAlchemy24/RomanFinalDeliverables/ .

Coversheets explaining each delivered dataset in more detail are attached here. They specify the file directory within Cheaha where each delivered dataset can be found, and also the github repo location where the code used to perform the transformations can be found.

 

Data were analyzed directly or indirectly from the following sources:



https://clinicaltrials.gov/

Drugbank: Knox C, Wilson M, Klinger CM, et al. DrugBank 6.0: the DrugBank Knowledgebase for 2024. Nucleic Acids Res. 2024 Jan 5;52(D1):D1265-D1275. doi: 10.1093/nar/gkad976.

Drug Repurposing Hub: Corsello, S., Bittker, J., Liu, Z. et al. The Drug Repurposing Hub: a next-generation drug library and information resource. Nat Med 23, 405–408 (2017). https://doi.org/10.1038/nm.4306

Disease Ontology: Schriml, L. M., Mitraka, E., Munro, J., Tauber, B., Schor, M., Nickle, L., … Greene, C. (2018). Human Disease Ontology 2018 update: classification, content and workflow expansion. Nucleic acids research, 47(D1), D955–D962. doi:10.1093/nar/gky1032

Mitotoxicity Data: Predicting the Mitochondrial Toxicity of Small Molecules: Insights from Mechanistic Assays and Cell Painting Data, Marina Garcia de Lomana, Paula Andrea Marin Zapata, and Floriane Montanari Chemical Research in Toxicology 2023 36 (7), 1107-1120 DOI: 10.1021/acs.chemrestox.3c00086

Cell Painting Data: Haghighi, M., Caicedo, J.C., Cimini, B.A. et al. High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations. Nat Methods 19, 1550–1557 (2022). https://doi.org/10.1038/s41592-022-01667-0

Online Mendelian Inheritance in Man: Online Mendelian Inheritance in Man, OMIM®. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD), 2024. World Wide Web URL: https://omim.org/

Therapeutic Target Database: Chen X, Ji ZL, Chen YZ. TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. doi: 10.1093/nar/30.1.412. PMID: 11752352; PMCID: PMC99057.
DOI: 10.15468/dl.p8d52c
title: Occurrence Download

description: A dataset containing 40037 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mephitidae"
 ]
}

 The dataset includes 40037 records from 281 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107070-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7mvev9
title: Occurrence Download

description: A dataset containing 24277633 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Insecta)",
 "BasisOfRecord is one of (Human Observation, Literature Occurrence, Living Specimen, Observation, Specimen, Occurrence evidence)",
 "Year is greater than or equal to 2014",
 "Year is less than or equal to 2018",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 24277633 records from 2742 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0356038-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/examiner-ouc11697747
title: Victorville layout, 1952

description: 40 images. Victorville layout, 8 June 1952. Frank E. Chambers (Victorville -ostmaster); Attorney William Johnstone; Main intersection in Victorville; Bridge over Mojave River leading to Victorville from Apple Valley; C.J. Bowan (Fish Hatchery Superintendent); Bill Caran (Employee of Jess Ranch -- Apple Valley); Lieutenant Colonel Martin H. Johnson -- 34 years (Commanding Officer, 190th Fighter-Bomber Squadron); George Air Force Base at Victorville; Fighter planes in formation; Southwest Portland Cement Company plant; Mrs. Isabel Bywater; Mrs. Violet Gradwohl (Proprietor of doll factory); Apple Valley Inn. ; Supplementary material reads: "Photo captions for Victorville story -- 69-70: Frank E. Chambers, Victorville postmaster (in sweater) chats outside post office with Attorney William Johnstone. 85-86: Pix shows intersection of Seventh and D streets in Victorville -- Main intersection. 51-52-1: Pix shows traffic on D street, Victorville. Street leads to Barstow. 9-10-2: Pix shows bridge over Mojave River leading into Victorville from Apple Valley and Big Bear Lake via State Highway 16. -- C.J. Bowan, fish hatchery suptd. at Jess Ranch, Apple Valley, with fish net. 79-80: Bill Caran, employee of Jess Ranch, Apple Valley, dumping trout in a 'live' box. -- Gale Houston, in shorts, dumps trout in 'live' box at Jess Ranch, Apple Valley. 17, L to R: Lt. Col. Martin H. Johnson, 34, Commanding Officer, 190th Fighter-Bomber Sqd., George Air Force Base, Victorville, conducts pre-flight briefing. Others, l to r: are 1st Lt. Orlando Dalke, 28; Capt. Wm. R. Sproat, 30; and 1st Lt. Albert P. Winkleman, 30. All are National Guard flyers from Boise, Idaho. 63-64: Formation of F-51 fighter planes of 190th Fighter-Bomber Sqd., George AFB, take off on practice mission. 73-74, L to R: Airman 2/C Jack Corathers; Airman 2/C Douglas Howard; T/Sgt. Marvin Bertram and Capt. Eusebio Arriaga, 32, ex-Sun Valley ski instructor, at plane that is being equipped with .50 cal. bullets. 57, L to R: Airman 2/C Jack Corathersl T/Sgt. Marvin Bertram and Airman 2/C Douglas Howard fit 100-pound bomb to F-51 racks. 58-93-94: Exterior of Southwestern Portland Cement Co. plant at Victorville. 71-72, L to R: Mrs. Isabel Bywater; Mrs. Violet Gradwohl, proprietor of a doll factory in Apple Valley; and Mrs. Maxine De Mark. 13: Mrs. Violet Gradwohl, owner of toy doll factory at Apple Valley, inspects some dolls. 65-66-14: Connie Fall, of San Francisco, relaxes in sun on diving board of Apple Valley Inn pool. She is on vacation. -- L to R: Carol Dahl, 15; Bud Lanyon, 19; Bob Potter, 20; and Dorothy Surratt, 17, all Victor Valley High School students, return from ride on desert in Apple Valley. Chef in pix at steak fry is Charles Hostettler of the Apple Valley Inn culinary staff. Other pixes of steak fry may be identified as nameless entertainers, playing banjo and singing by open fire to throng of visitors to Apple Valley Inn in Apple Valley."
DOI: 10.15468/dl.du62as
title: Occurrence Download

description: A dataset containing 3729 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Asparagus prostratus Dumort."
 ]
}

 The dataset includes 3729 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032742-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.neksje
title: Occurrence Download

description: A dataset containing 25156 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tillandsia usneoides (L.) L."
 ]
}

 The dataset includes 25156 records from 449 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007002-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/examiner-c44-8230
title: Caltech electron synchrotron, 1951

description: 10 images. Caltech electron synchrotron, June 20, 1951. Bruce H. Rule (chief engineer); Robert V. Langmuir (prof); General shots of the "Thing"; Dr. Ralph E. Wilson.
DOI: 10.15468/dl.onduku
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ensis directus (Conrad, 1844)",
 "Country is United Kingdom of Great Britain and Northern Ireland"
 ]
}

 The dataset includes 17 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033679-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5n4kvu
title: Occurrence Download

description: A dataset containing 230 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carya cathayensis Sarg."
 ]
}

 The dataset includes 230 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032755-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/examiner-c44-6055
title: Graduation of servicemen, Hollywood Bowl, 1951

description: 2 images. Graduation of servicemen, Hollywood Bowl, June 14, 1951. Dick Spero (seaman apprentice) 18 years; Ernest D. Johnson (electronic seaman) 22 years; Paul Wiltsee -- 23 years (aviation mechanist mate); Louis F. Foley (principal).; More descriptive information with originals.
DOI: 10.15468/dl.w8ltek
title: Occurrence Download

description: A dataset containing 2611 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 {
 "or" : [
 "TaxonKey is Narcissus nevadensis subsp. enemeritoi Sánchez-Gómez, A.F.Carrillo, A.Hern., M.A.Carrión & Güemes",
 "SpeciesKey is Narcissus cyclamineus DC.",
 "SpeciesKey is Narcissus nevadensis Pugsley",
 "SpeciesKey is Narcissus alcaracensis S.Ríos, D.Rivera, Alcaraz & Obón",
 "SpeciesKey is Narcissus juressianus Fern.Casas",
 "SpeciesKey is Narcissus segurensis S.Ríos, D.Rivera, Alcaraz & Obón",
 "SpeciesKey is Narcissus longispathus Degen & Hervier ex Pugsley",
 "SpeciesKey is Narcissus yepesii S.Ríos, D.Rivera, Alcaraz & Obón",
 "SpeciesKey is Leucojum valentinum Pau",
 "SpeciesKey is Luronium natans (L.) Raf.",
 "SpeciesKey is Lemna trisulca L.",
 "SpeciesKey is Carpinus betulus L.",
 "SpeciesKey is Quercus pauciradiata Penas, Llamas, Pérez Morales & Acedo",
 "SpeciesKey is Empetrum nigrum",
 "SpeciesKey is Adoxa moschatellina L.",
 "SpeciesKey is Geranium dolomiticum Rothm.",
 "SpeciesKey is Geranium cazorlense Heywood",
 "TaxonKey is Rubia balearica subsp. caespitosa (Font Quer & Marcos) Rosselló, L.Sáez & Mus",
 "SpeciesKey is Galium erythrorrhizon Boiss. & Reut.",
 "SpeciesKey is Galium arenarium Loisel.",
 "SpeciesKey is Galium pulvinatum Boiss.",
 "SpeciesKey is Galium tunetanum Lam.",
 "SpeciesKey is Galium viridiflorum Boiss. & Reut.",
 "SpeciesKey is Galium belizianum Ortega Oliv., Devesa & Rodr.Riaño",
 "SpeciesKey is Galium geminiflorum Lowe",
 "SpeciesKey is Galium brunneum Munby",
 "SpeciesKey is Solanum lidii Sunding",
 "SpeciesKey is Solanum vespertilio Aiton",
 "TaxonKey is Solanum vespertilio subsp. doramae Marrero Rodr. & Gonz.-Mart.",
 "SpeciesKey is Cicer canariense A.Santos & G.P.Lewis",
 "SpeciesKey is Adenocarpus ombriosus Ceballos & Ortuño",
 "SpeciesKey is Medicago citrina (Font Quer) Greuter",
 "SpeciesKey is Onobrychis reuteri Leresche",
 "SpeciesKey is Vicia chaetocalyx Webb & Berthel.",
 "SpeciesKey is Vicia bifoliolata J.J.Rodr.",
 "SpeciesKey is Vicia altissima Desf.",
 "SpeciesKey is Ononis leucotricha Coss.",
 "SpeciesKey is Rubus cyclops Mon.-Huelin",
 "SpeciesKey is Rubus pauanus Mon.-Huelin",
 "SpeciesKey is Rubus palmensis A.Hansen"
 ]
 }
 ]
}

 The dataset includes 2611 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033681-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/examiner-ouc11697723
title: Victorville layout, 1952

description: 40 images. Victorville layout, 8 June 1952. Frank E. Chambers (Victorville -ostmaster); Attorney William Johnstone; Main intersection in Victorville; Bridge over Mojave River leading to Victorville from Apple Valley; C.J. Bowan (Fish Hatchery Superintendent); Bill Caran (Employee of Jess Ranch -- Apple Valley); Lieutenant Colonel Martin H. Johnson -- 34 years (Commanding Officer, 190th Fighter-Bomber Squadron); George Air Force Base at Victorville; Fighter planes in formation; Southwest Portland Cement Company plant; Mrs. Isabel Bywater; Mrs. Violet Gradwohl (Proprietor of doll factory); Apple Valley Inn. ; Supplementary material reads: "Photo captions for Victorville story -- 69-70: Frank E. Chambers, Victorville postmaster (in sweater) chats outside post office with Attorney William Johnstone. 85-86: Pix shows intersection of Seventh and D streets in Victorville -- Main intersection. 51-52-1: Pix shows traffic on D street, Victorville. Street leads to Barstow. 9-10-2: Pix shows bridge over Mojave River leading into Victorville from Apple Valley and Big Bear Lake via State Highway 16. -- C.J. Bowan, fish hatchery suptd. at Jess Ranch, Apple Valley, with fish net. 79-80: Bill Caran, employee of Jess Ranch, Apple Valley, dumping trout in a 'live' box. -- Gale Houston, in shorts, dumps trout in 'live' box at Jess Ranch, Apple Valley. 17, L to R: Lt. Col. Martin H. Johnson, 34, Commanding Officer, 190th Fighter-Bomber Sqd., George Air Force Base, Victorville, conducts pre-flight briefing. Others, l to r: are 1st Lt. Orlando Dalke, 28; Capt. Wm. R. Sproat, 30; and 1st Lt. Albert P. Winkleman, 30. All are National Guard flyers from Boise, Idaho. 63-64: Formation of F-51 fighter planes of 190th Fighter-Bomber Sqd., George AFB, take off on practice mission. 73-74, L to R: Airman 2/C Jack Corathers; Airman 2/C Douglas Howard; T/Sgt. Marvin Bertram and Capt. Eusebio Arriaga, 32, ex-Sun Valley ski instructor, at plane that is being equipped with .50 cal. bullets. 57, L to R: Airman 2/C Jack Corathersl T/Sgt. Marvin Bertram and Airman 2/C Douglas Howard fit 100-pound bomb to F-51 racks. 58-93-94: Exterior of Southwestern Portland Cement Co. plant at Victorville. 71-72, L to R: Mrs. Isabel Bywater; Mrs. Violet Gradwohl, proprietor of a doll factory in Apple Valley; and Mrs. Maxine De Mark. 13: Mrs. Violet Gradwohl, owner of toy doll factory at Apple Valley, inspects some dolls. 65-66-14: Connie Fall, of San Francisco, relaxes in sun on diving board of Apple Valley Inn pool. She is on vacation. -- L to R: Carol Dahl, 15; Bud Lanyon, 19; Bob Potter, 20; and Dorothy Surratt, 17, all Victor Valley High School students, return from ride on desert in Apple Valley. Chef in pix at steak fry is Charles Hostettler of the Apple Valley Inn culinary staff. Other pixes of steak fry may be identified as nameless entertainers, playing banjo and singing by open fire to throng of visitors to Apple Valley Inn in Apple Valley."
DOI: 10.15468/dl.z8hz2e
title: Occurrence Download

description: A dataset containing 1923 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Frankliniella schultzei (Trybom, 1910)"
 ]
}

 The dataset includes 1923 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0062825-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4nbsbs
title: Occurrence Download

description: A dataset containing 474 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "GadmGid is DEU.10_1",
 "TaxonKey is one of (Carabus nemoralis O.F.Müller, 1764, Rosalia alpina (Linnaeus, 1758))"
 ]
}

 The dataset includes 474 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032748-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.