cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/0al-f6n-p4c
title: Amaranthus retroflexus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0al-fcr-p8p
title: Anemone nemorosa L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0al-lh5-f03
title: Salix pentandra L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15468/896xyy
title: Seal Observation Database (NRM)

description: This data set contains observations of dead seals made by the public, mostly around the Swedish coast. Each observation is verified at the Swedish Museum of Natural History before it is approved and published on the web. The verification consists of controlling the accuracy of coordinates and taxonomic determination. If the specimen is considered valuable to collect for autopsy, then observers may be contacted by the National Museum of Natural History or the Swedish Veterinary Agency (SVA) in Uppsala to obtain more information about the findings.
DOI: 10.3535/0al-pls-aq5
title: Montia fontana subsp. fontana

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0al-tk0-cfv
title: Salix caprea L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0al-xvz-9jf
title: Carex brunnescens subsp. brunnescens

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0al-yt3-t69
title: Lotus corniculatus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.5281/zenodo.17978009
title: Example input and output files for the virus variant caller pipeline

description: For a description of the pipeline, see the corresponding article in F1000Research (F1000Research 2025, 14:794).

example_config_files.zip: reference annotations for HSV-1 strain 17 and config files describing the input files.

example_bam_files.zip: alignment files (in BAM format) for two replicates each of the ICP0 and vhs knockout mutants.

example_fastq_files.zip: read sequences (in FASTQ format) for two replicates each of the ICP0 and vhs knockout mutants.

example_output.zip: output files for running the pipeline on this dataset, including used software versions and expected runtimes for each step. All steps of the pipeline can be run on a laptop with 16 GB RAM, except for the assembly of inserted sequences with rnaSPAdes, which can be omitted. rnaSPAdes can be run with 32 GB RAM.

files_for_docker_image.zip: files for creating a Docker image pre-configured to run the example. The Docker image is also availabe at the docker hub as carolinefriedel/virus-variant-caller (https://hub.docker.com/r/carolinefriedel/virus-variant-caller)

After downloading and unpacking the zip-archives, adjust the constants in the Watchdog workflow as follows:

<const name="REFERENCE">/path/to/chrHsv1_s17.fa</const><const name="REFERENCE_SNPS">/path/to/reference_snps.txt</const><const name="CONFIG">/path/to/config_strains_HSV1.txt</const><const name="GTF">/path/to/HSV1_Annotation_chrHsv1_s17.gtf</const><const name="samples">/path/to/example_samples.txt</const><const name="replicates">/path/to/example_replicates.txt</const>

where /path/to/ is the directory the content of the archive zip-archives is located in.

Furthermore, change /path/to/ in the example_replicates.txt  and example_samples.txt files to the directory the content of the archive zip-archives is located in.

To run the example with Docker, pull the Docker image from Docker hub with docker pull carolinefriedel/virus-variant-caller:latest (or create a (modified) Docker image using the files in files_for_docker_image.zip) and then run as described at https://hub.docker.com/r/carolinefriedel/virus-variant-caller.

The docker image already contains the files example_config_files.zip, but you need to download the large files in example_bam_files.zip and example_fastq_files.zip. The workflow included in the Docker image already has the constants preconfigured.
DOI: 10.3535/0am-2mw-w9d
title: Dactylorhiza maculata (L.) Soó

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.5281/zenodo.14266852
title: Example input and output files for the virus variant caller pipeline

description: For a description of the pipeline, see the corresponding article in F1000Research (F1000Research 2025, 14:794).

example_config_files.zip: reference annotations for HSV-1 strain 17 and config files describing the input files.

example_bam_files.zip: alignment files (in BAM format) for two replicates each of the ICP0 and vhs knockout mutants.

example_fastq_files.zip: read sequences (in FASTQ format) for two replicates each of the ICP0 and vhs knockout mutants.

example_output.zip: output files for running the pipeline on this dataset, including used software versions and expected runtimes for each step. All steps of the pipeline can be run on a laptop with 16 GB RAM, except for the assembly of inserted sequences with rnaSPAdes, which can be omitted. rnaSPAdes can be run with 32 GB RAM.

files_for_docker_image.zip: files for creating a Docker image pre-configured to run the example. The Docker image is also availabe at the docker hub as carolinefriedel/virus-variant-caller (https://hub.docker.com/r/carolinefriedel/virus-variant-caller)

After downloading and unpacking the zip-archives, adjust the constants in the Watchdog workflow as follows:

<const name="REFERENCE">/path/to/chrHsv1_s17.fa</const><const name="REFERENCE_SNPS">/path/to/reference_snps.txt</const><const name="CONFIG">/path/to/config_strains_HSV1.txt</const><const name="GTF">/path/to/HSV1_Annotation_chrHsv1_s17.gtf</const><const name="samples">/path/to/example_samples.txt</const><const name="replicates">/path/to/example_replicates.txt</const>

where /path/to/ is the directory the content of the archive zip-archives is located in.

Furthermore, change /path/to/ in the example_replicates.txt  and example_samples.txt files to the directory the content of the archive zip-archives is located in.

To run the example with Docker, pull the Docker image from Docker hub with docker pull carolinefriedel/virus-variant-caller:latest (or create a (modified) Docker image using the files in files_for_docker_image.zip) and then run as described at https://hub.docker.com/r/carolinefriedel/virus-variant-caller.

The docker image already contains the files example_config_files.zip, but you need to download the large files in example_bam_files.zip and example_fastq_files.zip. The workflow included in the Docker image already has the constants preconfigured.
DOI: 10.3535/0am-2yy-lqn
title: Rumex obtusifolius subsp. obtusifolius

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0am-31y-371
title: Potentilla crantzii (Crantz) Beck ex Fritsch

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0am-7dx-k5b
title: Butomus umbellatus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0am-ans-jpn
title: Salix myrtilloides L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0am-azd-n8p
title: Botrychium lunaria (L.) Sw.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0am-h04-gfv
title: Sparganium gramineum Georgi

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0am-kg6-wxe
title: Calamagrostis canescens (Weber) Roth

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0am-kqs-mlj
title: Salix myrtilloides L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0am-l7f-h8c
title: Luzula sudetica (Willd.) Schult.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0am-lks-996
title: Dianthus deltoides L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0am-mg7-fdj
title: Potamogeton gramineus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.5281/zenodo.17913105
title: Pre-processed inputs to support standardised calculation of Area of Habitat (AOH) for terrestrial species

description: This data accompanies the submission titled 'Global threat abatement potential for terrestrial vertebrates' for publication to the journal Global Ecology and Biogeography.

It contains pre-processed data layers that are useful for the standardised generation of Area of Habitat (AOH) maps as described in the submitted manuscript.

This description will be completed in-line with the description in the manuscript on acceptance.

 

STAR_template_1000m.tif Standardised template raster grid at roughly 1 km resolution created by dissagregating an output raster from Mair et al. (2021) Nature Ecology & Evolution.

FABDEM_1km_min_patched Preprocessed digital elevation model. Minimum per 1 km cell

FABDEM_1km_max_patched Preprocessed digital elevation model. Maximum per 1 km cell

CGLS100_Inland.tif Binary raster used to define terrestrial areas based on the fractional cover of Copernicus Global Land Surface Terrestrial Land-cover layers only - 1km resolution

MissingLandcover_1km_cover.tif Fractional cover of potentially missing terrestrial landcover based on the intersection between species entirely affected by missing terrestrial landcover and gadm administrative boundaries.

CGLS100Inland_withGADMIslands.tif Updated binary raster to define terrestrial (inland) areas corrected for erroneously missing terrestrial landcover over islands
DOI: 10.5281/zenodo.17913104
title: Pre-processed inputs to support standardised calculation of Area of Habitat (AOH) for terrestrial species

description: This data accompanies the submission titled 'Global threat abatement potential for terrestrial vertebrates' for publication to the journal Global Ecology and Biogeography.

It contains pre-processed data layers that are useful for the standardised generation of Area of Habitat (AOH) maps as described in the submitted manuscript.

This description will be completed in-line with the description in the manuscript on acceptance.

 

STAR_template_1000m.tif Standardised template raster grid at roughly 1 km resolution created by dissagregating an output raster from Mair et al. (2021) Nature Ecology & Evolution.

FABDEM_1km_min_patched Preprocessed digital elevation model. Minimum per 1 km cell

FABDEM_1km_max_patched Preprocessed digital elevation model. Maximum per 1 km cell

CGLS100_Inland.tif Binary raster used to define terrestrial areas based on the fractional cover of Copernicus Global Land Surface Terrestrial Land-cover layers only - 1km resolution

MissingLandcover_1km_cover.tif Fractional cover of potentially missing terrestrial landcover based on the intersection between species entirely affected by missing terrestrial landcover and gadm administrative boundaries.

CGLS100Inland_withGADMIslands.tif Updated binary raster to define terrestrial (inland) areas corrected for erroneously missing terrestrial landcover over islands
DOI: 10.3535/0am-zrx-04t
title: Luzula sudetica (Willd.) Schult.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0an-07q-lcq
title: Allium scorodoprasum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0an-5xh-3le
title: Plantae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.17632/2k7m8fwp3p
title: Iceberg Segmentation Data

description: This repository contains image patches and masks used to train, validate, test UNet++ models for delineating icebergs in Greenland ice mélange. The image patches and masks were extracted from Sentinel-1, and Sentinel-2 data, to train two separate UNet++ models for each dataset. The train_validate_test folder contains pickle files that can be read as numpy arrays (images, masks that were split for train/validate/test). The relevant Python code is located here: https://github.com/hfisser/IcebergSegmentation.
DOI: 10.3535/0an-6rc-q41
title: Rumex crispus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0an-6rq-0zj
title: Rhynchospora fusca (L.) W.T.Aiton

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0an-c1j-yc4
title: Potentilla L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.17632/2k7m8fwp3p.1
title: Iceberg Segmentation Data

description: This repository contains image patches and masks used to train, validate, test UNet++ models for delineating icebergs in Greenland ice mélange. The image patches and masks were extracted from Sentinel-1, and Sentinel-2 data, to train two separate UNet++ models for each dataset. The train_validate_test folder contains pickle files that can be read as numpy arrays (images, masks that were split for train/validate/test). The relevant Python code is located here: https://github.com/hfisser/IcebergSegmentation.
DOI: 10.3535/0an-dnh-nn1
title: Persicaria lapathifolia subsp. pallida (With.) Á. Löve

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0an-pf1-f7n
title: Deschampsia cespitosa (L.) P.Beauv.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0an-x3g-c8b
title: Carex brunnescens subsp. brunnescens

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0an-xz3-xrx
title: Sparganium glomeratum (Laest. ex Beurl.) Beurl.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0ap-21g-g0t
title: Salix myrsinifolia subsp. borealis (Fr.) Hyl.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0ap-5bl-4w4
title: Trichophorum alpinum (L.) Pers.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0ap-cld-r20
title: Carex brunnescens subsp. brunnescens

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0ap-cs1-f3d
title: Potamogeton × nitens Weber

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.17632/n4xdw5zbxf.1
title: A double-blind, randomized, placebo-controlled study assessing polarity-analysis-guided individualized homeopathic therapy for chronic primary heel pain in adults.

description: This double-blind, randomized, placebo-controlled trial (n=74, 2:1 allocation) evaluated polarity analysis-guided individualized homeopathic medicines (IHMs) versus placebo over 3 months in adults with chronic primary heel pain, using Foot Function Index (FFI) total score as primary outcome and MYMOP-2 as secondary, revealing monotonic FFI improvement in IHMs versus flat placebo trajectories (FDA divergence by week 3; p&lt;0.001), placebo ending 29.9 points higher (GEE; p&lt;0.001), 100% Bayesian superiority probability (slope difference 16.06), 100% responder rates (MCID ≥7; OR=741, NNT=1.1; AUC difference -96.7; p&lt;0.001), robust across subgroups/sensitivity analyses via MLMM/GEE, confirming PA-guided IHMs as safe, rapidly effective therapy warranting larger confirmatory trials.
DOI: 10.3535/0ap-p6y-xm8
title: Fumaria officinalis L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.17026/ar/thvdax
title: PAN-00156131 - jug (Roman smooth ware pottery)

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00156131&lt;/p&gt;
description: Modified: 2025-11-19T10:27:24+01:00
DOI: 10.3535/0ap-wx2-6wy
title: Dryopteris filix-mas (L.) Schott

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0aq-68g-66f
title: Potamogeton perfoliatus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0aq-71f-pf8
title: Saxifraga cespitosa L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0aq-75g-9yq
title: Ranunculus acris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0aq-dkv-32h
title: Comarum palustre L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0aq-v9c-l3l
title: Saxifraga cespitosa L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0ar-018-l3k
title: Carex digitata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0ar-0b8-sr8
title: Betula pubescens Ehrh.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0ar-477-p9t
title: Dryopteris expansa (C. Presl) Fraser-Jenk. & Jermy

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0ar-agh-40e
title: Spinulum annotinum (L.) A. Haines

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0ar-f5l-3aw
title: Plantae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0ar-fg5-vlr
title: Triglochin palustris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0ar-kkw-2r2
title: Alchemilla micans Buser

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0ar-mwr-jyq
title: Dactylorhiza viridis (L.) R.M.Bateman, Pridgeon & M.W.Chase

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.25502/waxp-3t50/d
title: Bundled innovation for sustainable intensification of smallholder maize-livestock production
DOI: 10.3535/0ar-vh2-t9d
title: Spergula morisonii Boreau

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0as-aws-k69
title: Carex dioica L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0as-dg9-ah3
title: Alnus glutinosa (L.) Gaertn.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0as-ekq-4pp
title: Geum rivale L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0as-g5n-80h
title: Woodsia alpina (Bolton) Gray

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0as-kzz-39w
title: Juncus compressus Jacq.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0as-qvj-5g5
title: Sparganium natans L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0at-7np-bq4
title: Juncus articulatus subsp. articulatus

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0at-7vy-aty
title: Micranthes nivalis (L.) Small

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0at-7yj-avd
title: Plantae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0at-g63-w9v
title: Salix glauca × myrsinifolia x glauca ssp. glauca × myrsinifolia ssp. myrsinifolia

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0at-p4m-c7e
title: Lepidium campestre (L.) W. T. Aiton

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0at-rem-3wf
title: Betula pubescens Ehrh.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0at-v2r-kl8
title: Carex saxatilis L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0av-6p0-hv0
title: Salix myrsinifolia subsp. myrsinifolia

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0av-mre-3ky
title: Diphasiastrum complanatum subsp. montellii (Kukkonen) Kukkonen

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0av-rcx-v8f
title: Carex vaginata Tausch

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0at-alq-jrm
title: Salix myrsinifolia × phylicifolia x myrsinifolia ssp. myrsinifolia × phylicifolia

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0at-yqh-mb5
title: Luzula spicata (L.) DC.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0av-vd2-8y1
title: Fragaria moschata Duchesne

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.17632/sn49zt6jpw
title: Pig pose estimation

description: This dataset was used in Brunner et al. "Skeleton integrity: A method for the efficient fine-tuning of pose estimation models for pigs". Biosystems Engineering, 2026. It contains 200 images of pigs and associated keypoint labels in the COCO format. The keypoint skeleton consists of 22 keypoints.
DOI: 10.17632/sn49zt6jpw.1
title: Pig pose estimation

description: This dataset was used in Brunner et al. "Skeleton integrity: A method for the efficient fine-tuning of pose estimation models for pigs". Biosystems Engineering, 2026. It contains 200 images of pigs and associated keypoint labels in the COCO format. The keypoint skeleton consists of 22 keypoints.
DOI: 10.3535/0av-xpw-0zr
title: Sparganium natans L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0av-ylk-gzn
title: Carex elongata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0av-z9c-jes
title: Euphorbia peplus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0aw-1sl-w79
title: Epipogium aphyllum Sw.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0aw-8a9-kdm
title: Lolium multiflorum Lam.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0aw-bsx-xzc
title: Elymus caninus (L.) L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0aw-r70-7k0
title: Fragaria moschata Duchesne

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0aw-s58-pal
title: Carex magellanica subsp. irrigua (Wahlenb.) Hiitonen

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0aw-zxw-sm9
title: Carex echinata Murray

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.