cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/axd-j2v-tq1
title: †Skenidioides Schuchert & Cooper, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/bfk-ntn-dqa
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/dj3-94f-5sp
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/nyt-nae-n4h
title: Nucleurus abyssalis (Männil, 1977)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/v74-3rk-g5e
title: carbonate rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/azm-0jl-r29
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/gly-vfn-595
title: Dayia J. M. Porter

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/cq9-20e-dwj
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/l49-cnj-byg
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/fh1-q8w-6ny
title: †Hammariella Martinsson, 1962

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/wja-y16-q5q
title: †Clavofabella maxima Sarv, 1968

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/34w-b9j-qxk
title: †Atraktoprion Kielan-Jaworowska, 1962

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/kkn-958-1k6
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/j3e-xp3-2mx
title: †Dicoelosia King, 1850

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/s35-svm-gdb
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/66g-b94-dcz
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vph-bl5-ha8
title: †Proetidae

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xec-2sy-nr9
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/8sm-v7c-z9q
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/spw-cw8-rkm
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/at5-2ex-8b9
title: †Nothorthis Ulrich & Cooper, 1938

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/d0a-kcw-r05
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5281/zenodo.10452633
title: Human Microbiome Compendium dataset

description: The Human Microbiome Compendium is an ongoing project to build a large collection of human microbiome sequencing data processed with a uniform pipeline. Currently, the compendium contains 16S rRNA amplicon sequencing data for human gut microbiome samples retrieved from the Sequence Read Archive. Our website at microbiomap.org has more information about the project and links to related resources. This data is freely available under a CC-BY license; if you use it in your work, please cite our preprint, "Integration of 168,000 samples reveals global patterns of the human gut microbiome" (doi: 10.1101/2023.10.11.560955).

If you are using this dataset in conjunction with your own results, it's important to note that starting in version 1.0.1, the nomenclature used in this taxonomic table diverges from the output generated by DADA2 and the SILVA database. See the v1.0.1 release notes directly below for details.

Version history

1.0.1: The "asv_assignments" table was corrected to fix entries in which the taxonomic levels were incorrectly inferred from the reference database by DADA2 (e.g. genus "Brassicibacter" was listed as a family, genus "Gelria" was listed as an order). The problem is documented in issues attached to repositories for DADA2, DADA2 reference databases, and our MicroBioMap library. In short, problems were noted in v138 of the SILVA database in which taxonomic names were not recorded properly if they were missing levels (e.g. a taxon has been assigned a proposed genus, but not a family). This was addressed in v138.1, which we originally used for generating this dataset. However, several dozen entries remain incorrectly annotated in v138.1—our 1.0.1 release corrects these by filling in the nomenclature gaps with "(unclassified)" and moving the existing data to the correct level. 2881 ASV assignments were affected out of about 4.3 million. The new file "taxa_corrections.tsv" is a copy of the "bad-taxa.csv" list generated by Michael McLaren, with notes added to reflect what we changed.

1.0.0: Added README.md file to the repository, and added a link to the preprint and title/author metadata for the Zenodo entry

0.2.1: "sample_metadata.tsv" was missing (Note: This was accidentally tagged "0.2.0" in the version history.)

0.2.0: Replacing "country" column in sample_metadata.tsv with an "iso" column using the country code rather than name.

0.1.0: Prepping for public release
DOI: 10.5281/zenodo.13733642
title: Human Microbiome Compendium dataset

description: The Human Microbiome Compendium is an ongoing project to build a large collection of human microbiome sequencing data processed with a uniform pipeline. Currently, the compendium contains 16S rRNA amplicon sequencing data for human gut microbiome samples retrieved from the Sequence Read Archive. Our website at microbiomap.org has more information about the project and links to related resources.

This data is freely available under the Creative Commons Attribution 4.0 International license (CC BY 4.0). If you use it in your work, please cite our preprint:

Abdill, Richard J., Samantha P. Graham, Vincent Rubinetti, Frank W. Albert, Casey S. Greene, Sean Davis, and Ran Blekhman. “Integration of 168,000 Samples Reveals Global Patterns of the Human Gut Microbiome.” bioRxiv, October 11, 2023. https://doi.org/10.1101/2023.10.11.560955.

If you are using this dataset in combination with your own results, it's important to note that the taxonomic classifications may differ between releases, as documented in CHANGELOG.md. The most recent release (1.1.0) includes assignments made using SILVA 138.2 (SSU Ref NR 99) and Greengenes2 (2022.10 backbone).
DOI: 10.5281/zenodo.15122187
title: Human Microbiome Compendium dataset

description: The Human Microbiome Compendium is an ongoing project to build a large collection of human microbiome sequencing data processed with a uniform pipeline. Currently, the compendium contains 16S rRNA amplicon sequencing data for human gut microbiome samples retrieved from the Sequence Read Archive. Our website at microbiomap.org has more information about the project and links to related resources.

This data is freely available under the Creative Commons Attribution 4.0 International license (CC BY 4.0). If you use it in your work, please cite our publication:

Abdill, Richard J., Samantha P. Graham, Vincent Rubinetti, et al. “Integration of 168,000 Samples Reveals Global Patterns of the Human Gut Microbiome.” Cell 188, no. 4 (2025): 1100–18. https://doi.org/10.1016/j.cell.2024.12.017

If you are using this dataset in combination with your own results, it's important to note that the taxonomic classifications may differ between releases, as documented in CHANGELOG.md. The most recent release (1.1.1) includes assignments made using SILVA 138.2 (SSU Ref NR 99) and Greengenes2 (2022.10 backbone).
DOI: 10.5281/zenodo.8186993
title: Human Microbiome Compendium dataset

description: The Human Microbiome Compendium is an ongoing project to build a large collection of human microbiome sequencing data processed with a uniform pipeline. Currently, the compendium contains 16S rRNA amplicon sequencing data for human gut microbiome samples retrieved from the Sequence Read Archive. Our website at microbiomap.org has more information about the project and links to related resources.

This data is freely available under the Creative Commons Attribution 4.0 International license (CC BY 4.0). If you use it in your work, please cite our publication:

Abdill, Richard J., Samantha P. Graham, Vincent Rubinetti, et al. “Integration of 168,000 Samples Reveals Global Patterns of the Human Gut Microbiome.” Cell 188, no. 4 (2025): 1100–18. https://doi.org/10.1016/j.cell.2024.12.017

If you are using this dataset in combination with your own results, it's important to note that the taxonomic classifications may differ between releases, as documented in CHANGELOG.md. The most recent release (1.1.1) includes assignments made using SILVA 138.2 (SSU Ref NR 99) and Greengenes2 (2022.10 backbone).
DOI: 10.5281/zenodo.8186994
title: hmc preliminary dataset

description: Prepping for public release
DOI: 10.5281/zenodo.8226547
title: hmc preliminary dataset

description: 0.2.0: Replacing "country" column in sample_metadata.tsv with an "iso" column using the country code rather than name. 0.1.0: Prepping for public release
DOI: 10.5281/zenodo.8226567
title: hmc preliminary dataset

description: 0.2.1: "sample_metadata.tsv" was missing 0.2.0: Replacing "country" column in sample_metadata.tsv with an "iso" column using the country code rather than name. 0.1.0: Prepping for public release
DOI: 10.5281/zenodo.8431937
title: Human Microbiome Compendium dataset

description: The Human Microbiome Compendium is an ongoing project to build a large collection of human microbiome sequencing data processed with a uniform pipeline. Currently, the compendium contains 16S rRNA amplicon sequencing data for human gut microbiome samples retrieved from the Sequence Read Archive. Our website at microbiomap.org has more information about the project and links to related resources. This data is freely available under a CC-BY license; if you use it in your work, please cite our preprint, "Integration of 168,000 samples reveals global patterns of the human gut microbiome" (doi: 10.1101/2023.10.11.560955). <strong>Version history</strong> <strong>1.0.0:</strong> Added README.md file to the repository, and added a link to the preprint and title/author metadata for the Zenodo entry <strong>0.2.1:</strong> "sample_metadata.tsv" was missing (Note: This was accidentally tagged "0.2.0" in the version history.) <strong>0.2.0:</strong> Replacing "country" column in sample_metadata.tsv with an "iso" column using the country code rather than name. <strong>0.1.0:</strong> Prepping for public release
DOI: 10.3535/e98-zlk-69y
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zae-25w-8s4
title: †Vogdesella Baker, 1924

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/7ws-khd-s2y
title: Platycladus Spach

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/yaa-8tw-0lh
title: †Opsiconidion Ludvigsen, 1974

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/5eg-hc0-v8t
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/dc3-bgk-bhp
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/51c-e4h-tfm
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/l3t-gz8-28w
title: limestone

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/4fc-f4d-ze1
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/4tz-1rn-yb7
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/t1w-zec-jn5
title: limy marl

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ayk-sq5-cbm
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/lvq-e8g-rly
title: †Lingulella Salter, 1866

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/72n-1tt-sve
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/z6t-9zr-dhl
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/jgx-dz4-g3v
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/w6h-nhf-cad
title: †Schizambon Walcott, 1884

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/e39-34y-lnm
title: carbonate rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/x7y-b04-q5a
title: †Anolotichiina laciniata (Eichwald, 1860)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/3lf-tt2-dkk
title: †Clavofabella vicina Sarv, 1968

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/acn-n42-4l0
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/0nd-yfq-l74
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/1l7-kks-73y
title: †Schizambon Walcott, 1884

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/s45-h4w-ljr
title: †Plicibeyrichia calcarispinosa Sarv, 1968

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/rg9-edy-ean
title: †Tvaerenella longa Sarv, 1959

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/3p6-elz-eyt
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/wst-a1w-0de
title: †Clavofabella juvenca Sarv, 1968

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/078-tqc-sh4
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/2pg-ewx-0cf
title: †Cavellinidae Egorov, 1950

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/bs5-wpv-47l
title: †Opsiconidion Ludvigsen, 1974

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/fwt-z1x-0fh
title: †Proetidae

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/v3f-5bx-vtl
title: Echinodermata

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/y3m-7jy-624
title: †Opsiconidion Ludvigsen, 1974

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/600-p7b-gl7
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/x21-xrd-n6m
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/bd8-3xr-dwp
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/mn9-sj4-e02
title: †Rectella Neckaja, 1958

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/mbr-z3j-wvn
title: †Cavellinidae Egorov, 1950

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/01s-83k-w9h
title: †Rectella Neckaja, 1958

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/4ps-tt6-vpk
title: Semiacontiodus cornuformis (Sergeeva, 1963)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/3yv-80a-64k
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/v2m-1p4-6g4
title: †Dalmanella Hall & Clarke, 1892

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/b1n-kk3-0ha
title: Dayia J. M. Porter

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xra-yr5-pnc
title: †Ungula ingrica (Eichwald, 1829)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/41a-vg7-qvd
title: †Ungula inornata (Mickwitz, 1896)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/8w2-q31-lz6
title: †Orbithele Sdzuy, 1955

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/61j-7r1-qpf
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/lnm-ker-1fr
title: †Ungula convexa Pander, 1830

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/2fr-avc-wjj
title: †Encrinurus punctatus (Wahlenberg, 1821)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/rts-n2w-9ks
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/7e5-x69-gpl
title: Dolomite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/nax-3ql-w2b
title: Ostracoda Latreille, 1802

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/x0a-jzb-npg
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/826-hkg-5z9
title: Sophora L.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ljm-hht-q66
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/1hc-5vf-76l
title: Ostracoda Latreille, 1802

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/9c8-9xe-fv7
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/d8r-2jm-03h
title: †Chonetes Fischer de Waldheim, 1830

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/tha-hab-ml3
title: Sophora L.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/3e4-ryz-pbt
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/91s-lm5-s3h
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/e08-x0j-yvh
title: Minerals

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/k1r-ahk-qfq
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/g13-4hj-1bs
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/gbc-49p-hhm
title: Exallaspis

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/h3g-0rz-39a
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/hg5-a97-k1a
title: Dolomite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/0r6-sb1-hmj
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/5qe-k7z-2zs
title: Platycladus Spach

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/brg-xmr-2ys
title: †Idiospira Cooper, 1956

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/bnv-v6r-7g1
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ykr-hym-d0e
title: Platycladus Spach

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/a4y-g3g-nn6
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/k24-99b-dsp
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/r74-4a0-hxb
title: †Amygdalella Martinsson, 1957

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/y5z-jjn-b1n
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/hqr-qkq-j4p
title: †Scipionis Gailite, 1966

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/k6e-0ra-41h
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/8yb-kcr-rkt
title: †Distobolbina Sarv, 1959

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/bjb-460-bvv
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/1kv-kpa-cdp
title: †Eukloedenella Ulrich & Bassler, 1923

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/5f1-zp8-efe
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/flk-keg-kqf
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.