cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18332760
title: Blood memory CD8 T cell phenotypes in lung cancer patients predict immune checkpoint treatment responses

description: Rscript for figure generation and data analysis:

GenerateFigures_RevisedManuscript.R - A collection of R code used to generate the Figures and perform analyses.

Seurat objects containing processed data after quality control and other relevant files

NCCS_For_Zenodo.RDS - NCCS discovery cohort.

NCCS-Figure1.png  - Required for Figure generation

Sample_Info_For_Zenodo.txt - Simplified version of the metadat

 

RDS files containing DEGs or differentially abundant surface markers:

TestResults2GroupsLungOnly.rds - Cell type specific LTR vs Non Responder DEG on lung samples only

TestResults2GroupsLungOnlyADT.rds - Cell type specific LTR vs Non Responder differential surface markers on lung samples only

TestResults2GroupsLungOnlyGeneralRNA.rds - Across cell type LTR vs Non Responder DEG on lung samples only

TestResults2GroupsLungOnlyGeneralADT.rds - Across cell type LTR vs Non Responder differential surface markers on lung samples only

 

Logistic regression models trained on the NCCS discovery cohort:

PerCellPredictions_2Groups_LungOnly <CellType> * - Celltype specific models predicting either LTR or NonResponder group, trained on lung samples only.

 

Output of third party tools:

AUCcellOutput.csv  - SCENIC

ALL_ligand_target_heatmap_AGN.tsv - NICHENET
DOI: 10.5281/zenodo.10867208
title: Blood memory CD8 T cell phenotypes in lung cancer patients predict immune checkpoint treatment responses

description: Rscript for figure generation and data analysis:

GenerateFigures_RevisedManuscript.R - A collection of R code used to generate the Figures and perform analyses.

Seurat objects containing processed data after quality control and other relevant files

NCCS_For_Zenodo.RDS - NCCS discovery cohort.

NCCS-Figure1.png  - Required for Figure generation

Sample_Info_For_Zenodo.txt - Simplified version of the metadat

 

RDS files containing DEGs or differentially abundant surface markers:

TestResults2GroupsLungOnly.rds - Cell type specific LTR vs Non Responder DEG on lung samples only

TestResults2GroupsLungOnlyADT.rds - Cell type specific LTR vs Non Responder differential surface markers on lung samples only

TestResults2GroupsLungOnlyGeneralRNA.rds - Across cell type LTR vs Non Responder DEG on lung samples only

TestResults2GroupsLungOnlyGeneralADT.rds - Across cell type LTR vs Non Responder differential surface markers on lung samples only

 

Logistic regression models trained on the NCCS discovery cohort:

PerCellPredictions_2Groups_LungOnly <CellType> * - Celltype specific models predicting either LTR or NonResponder group, trained on lung samples only.

 

Output of third party tools:

AUCcellOutput.csv  - SCENIC

ALL_ligand_target_heatmap_AGN.tsv - NICHENET
DOI: 10.15468/dl.qshp8r
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((88.856774 24.252831, 88.77975600000001 24.247254, 88.704655 24.230662, 88.633336 24.203467, 88.56757 24.166346, 88.508985 24.12022, 88.45902700000001 24.066234, 88.418921 24.005726, 88.38964799999999 23.940194, 88.37191199999999 23.871258, 88.366134 23.800619, 88.37243599999999 23.730017, 88.39064399999999 23.66119, 88.420293 23.595828, 88.460639 23.535534, 88.51068100000001 23.481785, 88.569183 23.435896, 88.634708 23.398988, 88.705651 23.371963, 88.78028 23.35548, 88.856774 23.34994, 88.933268 23.35548, 89.007897 23.371963, 89.07884 23.398988, 89.14436499999999 23.435896, 89.202867 23.481785, 89.252909 23.535534, 89.293255 23.595828, 89.32290399999999 23.66119, 89.341112 23.730017, 89.347414 23.800619, 89.34163599999999 23.871258, 89.32389999999999 23.940194, 89.29462700000001 24.005726, 89.254521 24.066234, 89.20456299999999 24.12022, 89.145978 24.166346, 89.080212 24.203467, 89.008893 24.230662, 88.933792 24.247254, 88.856774 24.252831))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004297-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hns4ne
title: Occurrence Download

description: A dataset containing 226 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Agrostis gigantea",
 "Year 1970-2000"
 ]
}

 The dataset includes 226 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004298-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p8s7dd
title: Occurrence Download

description: A dataset containing 9980 records in GBIF matching the query:
SELECT
 '90' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= -16.25916876999866
 AND decimalLatitude &lt;= -12.166598047573723
 AND decimalLongitude &gt;= -76.74356973936868
 AND decimalLongitude &lt;= -70.83067653341342
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 9980 records were derived from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004292-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b3st64
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((88.856774 24.252831, 88.77975600000001 24.247254, 88.704655 24.230662, 88.633336 24.203467, 88.56757 24.166346, 88.508985 24.12022, 88.45902700000001 24.066234, 88.418921 24.005726, 88.38964799999999 23.940194, 88.37191199999999 23.871258, 88.366134 23.800619, 88.37243599999999 23.730017, 88.39064399999999 23.66119, 88.420293 23.595828, 88.460639 23.535534, 88.51068100000001 23.481785, 88.569183 23.435896, 88.634708 23.398988, 88.705651 23.371963, 88.78028 23.35548, 88.856774 23.34994, 88.933268 23.35548, 89.007897 23.371963, 89.07884 23.398988, 89.14436499999999 23.435896, 89.202867 23.481785, 89.252909 23.535534, 89.293255 23.595828, 89.32290399999999 23.66119, 89.341112 23.730017, 89.347414 23.800619, 89.34163599999999 23.871258, 89.32389999999999 23.940194, 89.29462700000001 24.005726, 89.254521 24.066234, 89.20456299999999 24.12022, 89.145978 24.166346, 89.080212 24.203467, 89.008893 24.230662, 88.933792 24.247254, 88.856774 24.252831))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004300-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bwwbkr
title: Occurrence Download

description: A dataset containing 210 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Agrostis micrantha",
 "Year 1970-2000"
 ]
}

 The dataset includes 210 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004301-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fkf98a
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((88.856774 24.252831, 88.77975600000001 24.247254, 88.704655 24.230662, 88.633336 24.203467, 88.56757 24.166346, 88.508985 24.12022, 88.45902700000001 24.066234, 88.418921 24.005726, 88.38964799999999 23.940194, 88.37191199999999 23.871258, 88.366134 23.800619, 88.37243599999999 23.730017, 88.39064399999999 23.66119, 88.420293 23.595828, 88.460639 23.535534, 88.51068100000001 23.481785, 88.569183 23.435896, 88.634708 23.398988, 88.705651 23.371963, 88.78028 23.35548, 88.856774 23.34994, 88.933268 23.35548, 89.007897 23.371963, 89.07884 23.398988, 89.14436499999999 23.435896, 89.202867 23.481785, 89.252909 23.535534, 89.293255 23.595828, 89.32290399999999 23.66119, 89.341112 23.730017, 89.347414 23.800619, 89.34163599999999 23.871258, 89.32389999999999 23.940194, 89.29462700000001 24.005726, 89.254521 24.066234, 89.20456299999999 24.12022, 89.145978 24.166346, 89.080212 24.203467, 89.008893 24.230662, 88.933792 24.247254, 88.856774 24.252831))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004303-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.54mpt8
title: Occurrence Download

description: A dataset containing 223533 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Taxus baccata",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 223533 records from 985 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004282-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c5xd0r99h
title: MassIVE MSV000098882 - Validation proteomics of Jurkat T cells stimulated with and without PMA
title: Proteomics validation of Jurkat T cells carrying an asthma risk allele at chromosome 17q21 (ORMDL3 SNP). STING knock down was performed in the edited and unedited Jurkat cells stimulated with and without PMA to validate role of STING in mediating ORMDL3 SNP-associated changes. Data was searched with FragPipe using PNNL's DMS processing pipeline.
DOI: 10.6084/m9.figshare.29108438
title: Results of AI segmentations and cell files research Part.1

description: These figures are the graphical results of my Master 2 internship on automatic segmentation using SAM2(Segment Anything Model 2)an artificial intelligence. The red line represents the best cell line from which anatomical measurements were made.
DOI: 10.5281/zenodo.15473123
title: myosotis_latifolia_zanfona_1.fasta.gz
DOI: 10.5281/zenodo.15473124
title: myosotis_latifolia_zanfona_1.fasta.gz
DOI: 10.15468/dl.ah5fbh
title: Occurrence Download

description: A dataset containing 1100 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (VectorNet data Luxembourg 2023-2024, Tick collection_OH ALLIES project_Ireland, OH_SURVector_Hungary_Mosquitoes, VectorNet, Investigating the Role of Stable Flies (Stomoxys calcitrans) and Biting Midges (Culicoides spp.) of the genus Culicoides as Potential Mechanical Vectors of African Swine Fever Virus in Lithuania, Poland and Romania, Vector collection_OH surveillance project_Sweden, Monitoring competent vectors of Crimea Congo Haemorragic Fever (ticks) , West Nile and Rift Valley Fever in Spain (mosquitos), OH4Surveillance vector collection in Latvia, OH4Surveillance vector collection in Latvia)",
 "DatasetId is one of (eu4health_cp-g-22-04.01)"
 ]
}

 The dataset includes 1100 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009684-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.6146865
title: Miscellanies [IO Bijapur 420A]

description: Miscellanies.

This manuscript is now IO Bijapur 420A in the India Office collections.

[metadata: Otto Loth, A Catalogue of the Arabic Manuscripts in the Library of the India Office, (volume 1), no. 1032 here with further notations and hyperlinks].


1032.

B420A. Size 101/2 in. by 6 in.; foll. 58. About thirty lines in a page.

A collection of treatises copied by Zain b. ‘Abdallah Muḳaibil for his own use (compare the preceding no.).

I.Foll. 1-35v. JALÂL AL-DÎN DAWWÂNÎ’S (d. A.H. 907) Commentary on Suhrawardî’s (d. A.H. 587) هیاکل النور. See no. 485.

A considerable defect after fol. 8, corresponding to foll. 23-43 of no. 485. The rest complete.

The epilogue of the author begins as follows:

اقول و انا الفقیر الی عفو ربه الغنی محمد بن اسعد بن محمد المدعو بجلال الدین الصدیقی الدوانی هذا ما تیسر لی فی شرح هذه اللمعة فی اثنی (اثناء .r) عوائق شتی و علائق فوضی مع ما عم الزمان من اختلاف الامن و الامان و ما تخصصتُ به [من] مهاجرة الاوطان و مفارقة الخلان و ملازمة بیت الاحزان الخ.

He also speaks of his intention to write a commentary on Suhrawardî’s (حکمة) الاشراق.

Corrections and some notes.

II.Foll. 35v.-46v. هذا کتاب النصوص فی بحر التحقیق و جواهر الفصوص (!) للفرد الاکمل صدر الدین القونوی رحمه الله الخ.

Theosophic Statutes, by ṢADR AL-DÎN Muḥammad b. Isḥâḳ b. Yûsuf Rûmî ḲÛNAWÎ1 (d. A.H. 673). See Ḥ. Kh. vi. 349, who, however, gives the title differently, and Cat. Lugd. iii. 365 sq., where the work is merely styled کتاب النصوص, as it is also in the colophon of this copy.

Each of the statutes begins: نص شریف.

Notes by the author and by “Molla As’ad” on the margin.

Dated 2nd Dhû-alḳa’dah, 1084.

III.Fol. 46v. کتاب مراة العالم تصنیف الامام الهمام خاتمة المحققین السید السند الجرجانی...و تعریبها للشیخ الکبیر قطب دائرة الوجود تاج الدین بن زکریاء الذی ینتهی نسبه الی سیدنا و مولانا ذی النورین عثمان بن عفان الاموی القرشی الخ.

Only the first page of this work. It begins:

حمدا بلا عدٍّ و شکرا بلا حدّ لذات صارت وحدتها منشأ الاحدیة الخ.

IV.Foll. 47r. The end of a mystic treatise, the title and author of which are not mentioned. The first words are: العلم الحقیقی, and the conclusion begins: فهذا قدر ما امکن فی هذه الاوراق الخ.

V.Foll. 47v.-51. هذه الرسالة للامام المحقق مرتضی الفریقین محمد شیرین قدس الله سره آمین.

A mystic interpretation of the first Sûrah, فاتحة الکتاب, by MUḤAMMAD SHÎRÎN (probably the writer mentioned by Ḥ. Kh. iii. 315, who died A.H. 809). The author entitles it مرآة العارفین فی ملتمس زین العابدین, without explaining what he means by the latter words.

The preface begins: الحمدلله الذی اخرج من النون ما ادرج فی القلم الخ.

VI.Foll. 51v.-58. ‘ABD AL-KARÎM JÎLÎ’S (d. A.H. 811) مراتب الوجود. See no. 665.

The last page pf the MS. is wanting, although the treatise ends with fol. 58. Corrections and notes.

Cat. 232, xx.

 

1 So the name is given in the colophon. Cf. Nafaḥât al-uns, ed. Lees, p. ٦٤٥.
DOI: 10.5281/zenodo.6146866
title: Miscellanies [IO Bijapur 420A]

description: Miscellanies.

This manuscript is now IO Bijapur 420A in the India Office collections.

[metadata: Otto Loth, A Catalogue of the Arabic Manuscripts in the Library of the India Office, (volume 1), no. 1032 here with further notations and hyperlinks].


1032.

B420A. Size 101/2 in. by 6 in.; foll. 58. About thirty lines in a page.

A collection of treatises copied by Zain b. ‘Abdallah Muḳaibil for his own use (compare the preceding no.).

I.Foll. 1-35v. JALÂL AL-DÎN DAWWÂNÎ’S (d. A.H. 907) Commentary on Suhrawardî’s (d. A.H. 587) هیاکل النور. See no. 485.

A considerable defect after fol. 8, corresponding to foll. 23-43 of no. 485. The rest complete.

The epilogue of the author begins as follows:

اقول و انا الفقیر الی عفو ربه الغنی محمد بن اسعد بن محمد المدعو بجلال الدین الصدیقی الدوانی هذا ما تیسر لی فی شرح هذه اللمعة فی اثنی (اثناء .r) عوائق شتی و علائق فوضی مع ما عم الزمان من اختلاف الامن و الامان و ما تخصصتُ به [من] مهاجرة الاوطان و مفارقة الخلان و ملازمة بیت الاحزان الخ.

He also speaks of his intention to write a commentary on Suhrawardî’s (حکمة) الاشراق.

Corrections and some notes.

II.Foll. 35v.-46v. هذا کتاب النصوص فی بحر التحقیق و جواهر الفصوص (!) للفرد الاکمل صدر الدین القونوی رحمه الله الخ.

Theosophic Statutes, by ṢADR AL-DÎN Muḥammad b. Isḥâḳ b. Yûsuf Rûmî ḲÛNAWÎ1 (d. A.H. 673). See Ḥ. Kh. vi. 349, who, however, gives the title differently, and Cat. Lugd. iii. 365 sq., where the work is merely styled کتاب النصوص, as it is also in the colophon of this copy.

Each of the statutes begins: نص شریف.

Notes by the author and by “Molla As’ad” on the margin.

Dated 2nd Dhû-alḳa’dah, 1084.

III.Fol. 46v. کتاب مراة العالم تصنیف الامام الهمام خاتمة المحققین السید السند الجرجانی...و تعریبها للشیخ الکبیر قطب دائرة الوجود تاج الدین بن زکریاء الذی ینتهی نسبه الی سیدنا و مولانا ذی النورین عثمان بن عفان الاموی القرشی الخ.

Only the first page of this work. It begins:

حمدا بلا عدٍّ و شکرا بلا حدّ لذات صارت وحدتها منشأ الاحدیة الخ.

IV.Foll. 47r. The end of a mystic treatise, the title and author of which are not mentioned. The first words are: العلم الحقیقی, and the conclusion begins: فهذا قدر ما امکن فی هذه الاوراق الخ.

V.Foll. 47v.-51. هذه الرسالة للامام المحقق مرتضی الفریقین محمد شیرین قدس الله سره آمین.

A mystic interpretation of the first Sûrah, فاتحة الکتاب, by MUḤAMMAD SHÎRÎN (probably the writer mentioned by Ḥ. Kh. iii. 315, who died A.H. 809). The author entitles it مرآة العارفین فی ملتمس زین العابدین, without explaining what he means by the latter words.

The preface begins: الحمدلله الذی اخرج من النون ما ادرج فی القلم الخ.

VI.Foll. 51v.-58. ‘ABD AL-KARÎM JÎLÎ’S (d. A.H. 811) مراتب الوجود. See no. 665.

The last page pf the MS. is wanting, although the treatise ends with fol. 58. Corrections and notes.

Cat. 232, xx.

 

1 So the name is given in the colophon. Cf. Nafaḥât al-uns, ed. Lees, p. ٦٤٥.
DOI: 10.17044/scilifelab.19411403
title: SH information from UNITE databases

description: The data in this repository is the result of querying the PlutoF API (https://plutof.docs.apiary.io, Abarenkov et al 2010) with all sequence names in the UNITE general FASTA release (https://doi.org/10.15156/BIO/2959332; Abarenkov et al. 2024), in order to find the sequence hypothesis (SH) at level 1.5, version 10, for each sequence, resulting in a sequence-to-SH matching file (*.seq2SH.tsv). For each SH, the complete taxonomy is extracted from PlutoF by querying the PlutoF API, and stored in the *.SH.tax files.Files are available for UNITE version 10.0; sh_general_release_dynamic_04.04.2024.seq2sh.tsv.bz2 containing sequence to SH matchings, and sh_general_release_dynamic_04.04.2024.SHs.tax.bz2 containing SH taxonomies. Corresponding files are also available for the all eukaryotes version of the UNITE database (https://doi.org/10.15156/BIO/2959334; Abarenkov et al 2024b). All files are tab separated text files compressed with bzip2.Assignment of species hypothesis to ITS amplicons using this data and the UNITE general FASTA release is available as an optional argument to the nf-core/ampliseq Nextflow workflow from version 2.3.2: `--addsh` together with `--dada_ref_taxonomy unite-fungi` or `--dada_ref_taxonomy unite-alleuk` (https://nf-co.re/ampliseq; Straub et al. 2020).<br><b>Generation of files</b><br>After download and file extraction of the UNITE general FASTA release, each sequence name in the fasta file was used as query to PlutoF to find which SH at level 1.5 in release 10 the sequence belongs to, in order to generate the *.seq2sh.tsv files with sequence to SH matchings. Each SH was subsequently used as query to PlutoF to extract the complete taxonomy for the SH, stored in the *.SHs.tax files.<br>Two python scripts for automatic querying and generation of the files can be found in the `scripts` folder in the GitHub repo: https://github.com/biodiversitydata-se/unite-shinfo. See the accompanying README file for usage information.<br>
DOI: 10.17044/scilifelab.19411403.v4
title: SH information from UNITE databases

description: The data in this repository is the result of querying the PlutoF API (https://plutof.docs.apiary.io, Abarenkov et al 2010) with all sequence names in the UNITE general FASTA release (https://doi.org/10.15156/BIO/2959332; Abarenkov et al. 2024), in order to find the sequence hypothesis (SH) at level 1.5, version 10, for each sequence, resulting in a sequence-to-SH matching file (*.seq2SH.tsv). For each SH, the complete taxonomy is extracted from PlutoF by querying the PlutoF API, and stored in the *.SH.tax files.Files are available for UNITE version 10.0; sh_general_release_dynamic_04.04.2024.seq2sh.tsv.bz2 containing sequence to SH matchings, and sh_general_release_dynamic_04.04.2024.SHs.tax.bz2 containing SH taxonomies. Corresponding files are also available for the all eukaryotes version of the UNITE database (https://doi.org/10.15156/BIO/2959334; Abarenkov et al 2024b). All files are tab separated text files compressed with bzip2.Assignment of species hypothesis to ITS amplicons using this data and the UNITE general FASTA release is available as an optional argument to the nf-core/ampliseq Nextflow workflow from version 2.3.2: `--addsh` together with `--dada_ref_taxonomy unite-fungi` or `--dada_ref_taxonomy unite-alleuk` (https://nf-co.re/ampliseq; Straub et al. 2020).<br><b>Generation of files</b><br>After download and file extraction of the UNITE general FASTA release, each sequence name in the fasta file was used as query to PlutoF to find which SH at level 1.5 in release 10 the sequence belongs to, in order to generate the *.seq2sh.tsv files with sequence to SH matchings. Each SH was subsequently used as query to PlutoF to extract the complete taxonomy for the SH, stored in the *.SHs.tax files.<br>Two python scripts for automatic querying and generation of the files can be found in the `scripts` folder in the GitHub repo: https://github.com/biodiversitydata-se/unite-shinfo. See the accompanying README file for usage information.<br>