cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.wkhff7
title: Occurrence Download

description: A dataset containing 6640 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Anaxyrus debilis (Girard, 1854))"
 ]
}

 The dataset includes 6640 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039496-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/pbm-dr8-xlh
title: Dispharynx nasuta (Rudolphi, 1819)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/14j-j39-fzj
title: Dugesia bengalensis Kawakatsu, 1983

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/24k-094-zhz
title: Alitta succinea (Leuckart, 1847)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.c.3881383_d7
title: Additional file 7: Table S2. of Tartrate-resistant acid phosphatase (TRAP/ACP5) promotes metastasis-related properties via TGFβ2/TβR and CD44 in MDA-MB-231 breast cancer cells

description: Proteins significantly regulated upon TRAP perturbation in any of the phosphoproteomics or proteomics analyses (TRAP3high vs ctrl, phospho and standard proteomics analyses; TRAP sh2 or sh3 + 4 vs scrambled shRNA, standard proteomics analysis). The column “Enriched GO term” specifies whether the protein belong to any of the GO terms that were found to be enriched in the list of regulated proteins. The column “Protein class” describes to which of the examined protein class a protein belongs to. Examined proteins classes include protein kinases, protein phosphatases, ubiquitin and UBL system enzymes and transcription factors. (XLSX 79 kb)
DOI: 10.3535/3es-daq-lxh
title: Alitta succinea (Leuckart, 1847)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6xs-8j0-vqa
title: Platynereis dumerilii (Audouin & Milne Edwards, 1833)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.34etrg
title: Occurrence Download

description: A dataset containing 148674 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Zea mays L."
 ]
}

 The dataset includes 148674 records from 720 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039489-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/30x-pvv-pef
title: Alitta succinea (Leuckart, 1847)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jv9-gvy-5ez
title: Theromyzon

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d1v-dz4-42x
title: Gyrocotyle urna (Grube & Wagener in Wagener, 1852) Wagener, 1858

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/p4s-cgp-3v0
title: Serpulidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vbl-hc4-r7v
title: Cotylurus cornutus (Rudolphi, 1809) Szidat, 1928

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hg1-y0t-fg6
title: Nephtys cirrosa Ehlers, 1868

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6j1-a99-69s
title: Magelona papillicornis F. Müller, 1858

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/m83-gmx-hyz
title: Nephtys cirrosa Ehlers, 1868

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/812-j3w-w55
title: Hymenolepis Weinland, 1858

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/20f-q9y-w7s
title: Cylicocyclus nassatus (Looss, 1900) Chaves, 1930

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/80h-lqp-333
title: Synhimantus (Synhimantus) laticeps (Rudolphi, 1819) Railliet, Henry & Sisoff, 1912

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tn7-q4a-ga7
title: Nephtys cirrosa Ehlers, 1868

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tqw-fjc-lsb
title: Erpobdella

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5281/zenodo.14515811
title: Pretrained Transformer Encoder for SMILES Strings

description: Pretrained Transformer Encoder Parameters

This component provides the pretrained parameters for a transformer encoder designed to extract feature representations from SMILES strings. The model was trained using masked token prediction to capture intricate patterns and long-range dependencies within molecular sequences.

The transformer architecture includes:



10 sequential transformer blocks,

Multi-head self-attention for contextualized token embeddings,

Position-wise feed-forward layers with Gaussian Error Linear Unit (GELU) activation, residual connections, and layer normalization.


The global molecular representation is derived from the start token embedding, which aggregates sequence-wide information during self-attention computations.

Pretraining Dataset

This component provides the dataset used to pretrain the transformer encoder. It integrates SMILES strings from the following sources:



ChEMBL 33: ~2.4 million bioactive molecules with drug-like properties,

GuacaMol v1: ~1.6 million molecules derived from ChEMBL 24,

MOSES: ~1.8 million molecules selected from ZINC 15 for diversity and medicinal chemistry suitability,

BindingDB: ~1.2 million unique small molecules bound to proteins,

PDBbind v2020: ~15,710 unique small molecules bound to proteins.


This model has been optimized for drug discovery applications, including protein-ligand binding affinity prediction, and can serve as a foundational tool for researchers working on cheminformatics, computational biology, and medicinal chemistry.
DOI: 10.5281/zenodo.14515812
title: Pretrained Transformer Encoder for SMILES Strings

description: This dataset provides the pretrained parameters for a transformer encoder designed for extracting feature representations from SMILES strings. The model was pretrained on masked token prediction using a comprehensive dataset combining SMILES from various sources: ChEMBL 33 (~2.4M molecules), GuacaMol v1 (~1.6M molecules), MOSES (~1.8M molecules), BindingDB (~1.2M molecules), and PDBbind v2020 (~15,710 molecules).

The architecture consists of 10 sequential transformer blocks, each implementing multi-head self-attention followed by position-wise feed-forward layers with Gaussian Error Linear Unit (GELU) activation, residual connections, and layer normalization for stable training. The model produces contextualized embeddings for each token, and the global molecular representation is derived from the start token embedding, which aggregates sequence-wide information.

This model has been optimized for drug discovery applications, including protein-ligand binding affinity prediction, and can serve as a foundational tool for researchers working on cheminformatics, computational biology, and medicinal chemistry.
DOI: 10.5281/zenodo.14516013
title: Pretrained Transformer Encoder for SMILES Strings

description: Pretrained Transformer Encoder Parameters

This component provides the pretrained parameters for a transformer encoder designed to extract feature representations from SMILES strings. The model was trained using masked token prediction to capture intricate patterns and long-range dependencies within molecular sequences.

The transformer architecture includes:



10 sequential transformer blocks,

Multi-head self-attention for contextualized token embeddings,

Position-wise feed-forward layers with Gaussian Error Linear Unit (GELU) activation, residual connections, and layer normalization.


The global molecular representation is derived from the start token embedding, which aggregates sequence-wide information during self-attention computations.

Pretraining Dataset

This component provides the dataset used to pretrain the transformer encoder. It integrates SMILES strings from the following sources:



ChEMBL 33: ~2.4 million bioactive molecules with drug-like properties,

GuacaMol v1: ~1.6 million molecules derived from ChEMBL 24,

MOSES: ~1.8 million molecules selected from ZINC 15 for diversity and medicinal chemistry suitability,

BindingDB: ~1.2 million unique small molecules bound to proteins,

PDBbind v2020: ~15,710 unique small molecules bound to proteins.


This model has been optimized for drug discovery applications, including protein-ligand binding affinity prediction, and can serve as a foundational tool for researchers working on cheminformatics, computational biology, and medicinal chemistry.
DOI: 10.3535/7v4-ep4-f75
title: Rhabdias bufonis (Schrank, 1788) Stiles & Hassall, 1905

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/v8a-0d5-4j6
title: Hediste diversicolor (O.F. Müller, 1776)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3x8-71s-xte
title: Ascaridia Dujardin, 1844

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/a3b-ryz-vz6
title: Leucochloridium paradoxum Carus, 1835

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/aq7-hjk-e86
title: Camallanus Railliet & Henry, 1915

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pnm-07h-ydg
title: Paramphistomum cervi (Zeder, 1790) Fischoeder, 1901

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pdh-n1c-1vw
title: Microphthalmus sczelkowii Mecznikow, 1865

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/t05-tq0-m92
title: Harmothoe imbricata (Linnaeus, 1767)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zl9-sk5-tr2
title: Syllis gracilis Grube, 1840

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.c.3881365_d21.v1
title: Additional file 6: Table S2. of Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes

description: Model results for all microbial taxa identified through 16S rRNA sequencing, metabolites, and metadata. Each tab corresponds to a different set of analyses: (A) phylum, (B) class, (C), order, (D) family, (E) genus, (F) OTU, (G) metabolome, (H) metadata. For the microbiome (A-F), the columns indicate the taxa; full taxonomy (p for phylum, c for class, o for order, f for family, g for genus); mean and standard deviation for rural and urban in timepoint 1, timepoint 2 and both timepoints; linear model P-values (unadjusted and Benjamini and Hochberg-adjusted); linear model R2; and Wilcoxon rank sum test P-values for timepoint 1 and 2 (unadjusted and Benjamini and Hochberg-adjusted). (G-H) The columns indicate the metabolite or metadata name; the super and sub pathway for the metabolite (G only); the mean and standard deviation for rural and urban; the linear model P-values (unadjusted and Benjamini and Hochberg-adjusted); and the linear model R2. (G) The last two columns are the unadjusted and Benjamini and Hochberg-adjusted P-values from a Wilcoxon rank sum test. (H) The last three columns indicate the nonparametric test used (Wilcox: Wilcoxon rank sum test, used for continuous data; Fisher: Fisherâ  s exact test for categorical data), followed by the unadjusted and Benjamini and Hochberg-adjusted nonparametric test P-values for urban vs. rural status. For antibiotic or probiotic use, a 0 indicated no use and a 1 indicated use. For gender, a 1 indicated male and a 2 indicated female. All sections are sorted by P-value for urban vs. rural status. (XLSX 392Â kb)
DOI: 10.3535/2y7-283-jwc
title: Dugesia gonocephala (Duges, 1830)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hc3-z8y-md1
title: Girardia dorotocephala (Woodworth, 1897)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c32-kle-frk
title: Girardia dorotocephala (Woodworth, 1897)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/j6g-bxj-np2
title: Spirobranchus latiscapus (Marenzeller, 1884)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lkt-wge-h92
title: Dugesia ryukyuensis Kawakatsu, 1976

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/sfs-0hl-shq
title: Romankenkius libidinosus Sluys & Rohdes, 1991

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.c.3881365_d21
title: Additional file 6: Table S2. of Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes

description: Model results for all microbial taxa identified through 16S rRNA sequencing, metabolites, and metadata. Each tab corresponds to a different set of analyses: (A) phylum, (B) class, (C), order, (D) family, (E) genus, (F) OTU, (G) metabolome, (H) metadata. For the microbiome (A-F), the columns indicate the taxa; full taxonomy (p for phylum, c for class, o for order, f for family, g for genus); mean and standard deviation for rural and urban in timepoint 1, timepoint 2 and both timepoints; linear model P-values (unadjusted and Benjamini and Hochberg-adjusted); linear model R2; and Wilcoxon rank sum test P-values for timepoint 1 and 2 (unadjusted and Benjamini and Hochberg-adjusted). (G-H) The columns indicate the metabolite or metadata name; the super and sub pathway for the metabolite (G only); the mean and standard deviation for rural and urban; the linear model P-values (unadjusted and Benjamini and Hochberg-adjusted); and the linear model R2. (G) The last two columns are the unadjusted and Benjamini and Hochberg-adjusted P-values from a Wilcoxon rank sum test. (H) The last three columns indicate the nonparametric test used (Wilcox: Wilcoxon rank sum test, used for continuous data; Fisher: Fisherâ  s exact test for categorical data), followed by the unadjusted and Benjamini and Hochberg-adjusted nonparametric test P-values for urban vs. rural status. For antibiotic or probiotic use, a 0 indicated no use and a 1 indicated use. For gender, a 1 indicated male and a 2 indicated female. All sections are sorted by P-value for urban vs. rural status. (XLSX 392Â kb)
DOI: 10.3535/bpg-wak-vx5
title: Pentacoelum kazukolinda (Kawakatsu & Mitchell, 1984)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ger-gdv-4c5
title: Dugesia gonocephala (Duges, 1830)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pas-378-jy1
title: Hyalopomatus Marenzeller, 1878

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lmq-lld-2tt
title: Nephtys cirrosa Ehlers, 1868

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pkh-brb-595
title: Phagocata vivida (Ijima & Kaburaki, 1916)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/06x-sw9-mek
title: Hediste diversicolor (O.F. Müller, 1776)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w0w-e2p-ndp
title: Nephtys cirrosa Ehlers, 1868

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3sh-g62-a36
title: Pseudosagitta lyra (Krohn, 1853)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jt6-9tt-090
title: Phagocata vivida (Ijima & Kaburaki, 1916)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/k1l-rbl-fey
title: Cylicostephanus longibursatus (Yorke & Macfie, 1918) Cram, 1924

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1gb-c5n-63z
title: Diphyllobothriidae Lühe, 1910

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/j7l-lp5-yq2
title: Nephtys Cuvier, 1817

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nwd-2qx-5ln
title: Paramphistomum Fischoeder, 1901

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pv0-ydt-9a1
title: Otostrongylus circumlitus (Railliet, 1899) de Bruyn, 1933

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bp1-dbg-dl2
title: Nephtys Cuvier, 1817

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d48-z5h-vq1
title: Serratosagitta serratodentata (Krohn, 1853)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d23-pv6-x7h
title: Dugesia uenorum Kawakatsu & Mitchel, 1995

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6bb-klp-vk2
title: Cerebratulus bedfordii Punnett, 1900

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gbp-x9r-yha
title: Phagocata teshirogi Ichikawa & Kawakatsu, 1962

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1ez-qe4-0t4
title: Dendrocoelopsis ezensis Ichikawa & Okugawa, 1958

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/80c-1l2-bmj
title: Phocanema decipiens (Krabbe, 1878) Myers, 1959

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mle-4s0-wwg
title: Phyllodoce maculata (Linnaeus, 1767)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/x8x-frm-3b5
title: Toxocara canis (Werner, 1782) Stiles in Stiles & Hassall, 1905

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/r9j-b9d-shy
title: Manayunkia aestuarina (Bourne, 1883)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rp5-573-xmp
title: Manayunkia aestuarina (Bourne, 1883)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.c.3881524_d9
title: Additional file 9: of Rapid transcriptional and metabolic regulation of the deacclimation process in cold acclimated Arabidopsis thaliana

description: Metabolites transiently up- or down-regulated upon transfer of cold acclimated plants to deacclimating conditions for 24Â h (compare Fig. 4). Transiently regulated metabolites were identified using manual inspection and pair-wise t-tests. FDR corrected P-values are shown. (XLSX 17 kb)
DOI: 10.3535/qj5-7dm-1j2
title: Coronocyclus labiatus (Looss, 1902) Hartwich, 1986

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/57m-xvx-d04
title: Davaineidae Braun, 1900

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/v5e-e27-d7y
title: Echinocotyle Blanchard, 1891

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qxf-58z-eef
title: Serratosagitta serratodentata (Krohn, 1853)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tgw-xb7-z97
title: Paramphistomum Fischoeder, 1901

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2zz-h33-5jv
title: Schizocephala Serville, 1831

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z1p-y19-zp3
title: Eiseniella tetraedra (Savigny in Cuvier, 1826)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/f2c-6w6-v6l
title: Enantiodrilus Cognetti, 1902

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ffw-fzl-vjk
title: Stylaria lacustris (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.c.3882709_d1.v1
title: Additional file 1: Table S1. of Regulatory networks underlying mycorrhizal development delineated by genome-wide expression profiling and functional analysis of the transcription factor repertoire of the plant symbiotic fungus Laccaria bicolor

description: List of L. bicolor TFs identified in silico displaying similarities with characterized TFs (183 proteins); sharing similarities with predicted or hypothetical proteins with no proved role as transcriptional regulators (94 proteins); sharing similarities with proteins identified as transcriptional regulators without DBD (8 proteins). General information of protein is given (e.g., protein ID from both L. bicolor genome version 1 and version 2, length of the polypeptide, TF name, EST support). Accession number, Description, Species, % identity, E-value and Score are related to BLAST results using L. bicolor protein as query against fungal NCBI database. m.c. = manually curated. Best Blast reciprocal hit = “YES” indicates that the TF was positive to the Best reciprocal hit analysis. BLAST masked DBD = “YES” indicates that L. bicolor TF was still similar to the characterized protein after masking its DBD in a BLAST search. See Methods section for a detailed description. TFs retrieved from and functionally validated by the TAT screen are in bold. (XLSX 48 kb)
DOI: 10.3535/bzn-5p0-g5x
title: Erpobdella

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hhm-vhg-1ps
title: Dugesia batuensis Ball, 1970

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.