cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10866875
title: GeneRAIN Human-Mouse

description: This repository presents our study on gene expression in humans and mice, utilizing deep learning on 410K human and 366K mouse bulk RNA-seq samples to investigate gene function and disease associations across species. Our research leverages our Transformer-based models [GeneRAIN] (https://www.biorxiv.org/content/10.1101/2024.03.07.583777v1) and cross-species gene embedding alignment to analyze RNA-level similarities between human and mouse genes, offering new insights into their evolutionary and functional relationships. This project enhances our understanding of mouse genes in biomedical research, providing a novel methodology for cross-species omics analysis.

This dataset comprises the following files:



Supervised Aligned Gene Embeddings (Protein-Coding Genes-Only GPT Model): Human_mouse_coding_gene_embeddings_supervised_aligned.txt. This file contains embeddings for genes derived using the protein-coding genes only model.

Supervised Aligned Gene Embeddings (Coding Genes, lncRNAs + Pseudogenes Model): Human_mouse_gene_embeddings_from_coding_lncRNA_pseudogene_model.txt. Embeddings in this file are derived from the model that includes coding genes, long non-coding RNAs (lncRNAs), and pseudogenes.

Pairwise Similarity Matrix: similarity_matrix_chunk*.npy and similarity_matrix.npy_ids.txt (containing gene IDs). This 37,926 x 37,926 matrix averages the similarities from the supervised alignment approach and the shared embeddings + supervised alignment approach. The matrix can be loaded using script load_similarity_matrix.py.

Top Ten Closest Mouse Genes for Each Human Gene: closest_10.*.txt. These files list the ten nearest mouse genes for each human gene, as determined by embedding similarity, for each gene class.

Data for Reproducing Study Results: data.tar.gz. This compressed file provides the necessary data for replicating the study's results using the GeneRAIN_HM (https://github.com/suzheng/GeneRAIN_HM).
DOI: 10.5281/zenodo.10866876
title: GeneRAIN Human-Mouse

description: This repository presents our study on gene expression in humans and mice, utilizing deep learning on 410K human and 366K mouse bulk RNA-seq samples to investigate gene function and disease associations across species. Our research leverages our Transformer-based models [GeneRAIN] (https://www.biorxiv.org/content/10.1101/2024.03.07.583777v1) and cross-species gene embedding alignment to analyze RNA-level similarities between human and mouse genes, offering new insights into their evolutionary and functional relationships. This project enhances our understanding of mouse genes in biomedical research, providing a novel methodology for cross-species omics analysis.

This dataset comprises the following files:



Supervised Aligned Gene Embeddings (Protein-Coding Genes-Only GPT Model): Human_mouse_coding_gene_embeddings_supervised_aligned.txt. This file contains embeddings for genes derived using the protein-coding genes only model.

Supervised Aligned Gene Embeddings (Coding Genes, lncRNAs + Pseudogenes Model): Human_mouse_gene_embeddings_from_coding_lncRNA_pseudogene_model.txt. Embeddings in this file are derived from the model that includes coding genes, long non-coding RNAs (lncRNAs), and pseudogenes.

Pairwise Similarity Matrix: similarity_matrix_chunk*.npy and similarity_matrix.npy_ids.txt (containing gene IDs). This 37,926 x 37,926 matrix averages the similarities from the supervised alignment approach and the shared embeddings + supervised alignment approach. The matrix can be loaded using script load_similarity_matrix.py.

Top Ten Closest Mouse Genes for Each Human Gene: closest_10.*.txt. These files list the ten nearest mouse genes for each human gene, as determined by embedding similarity, for each gene class.

Data for Reproducing Study Results: data.tar.gz. This compressed file provides the necessary data for replicating the study's results using the GeneRAIN_HM (https://github.com/suzheng/GeneRAIN_HM).
DOI: 10.15468/dl.kjuxjr
title: Occurrence Download

description: A dataset containing 84 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pilea insolens Wedd."
 ]
}

 The dataset includes 84 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072266-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.22rkfs
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phanera saigonensis (Pierre ex Gagnep.) Mackinder & R.Clark"
 ]
}

 The dataset includes 68 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072267-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w5qkpd
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllanthus angolensis Müll.Arg."
 ]
}

 The dataset includes 25 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072265-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kybp4b
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-100.00866425559983 19.775190838984148,-97.77078784920721 19.775190838984148,-97.77078784920721 22.013067245376764,-100.00866425559983 22.013067245376764,-100.00866425559983 19.775190838984148))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Agastache mexicana (Kunth) Lint & Epling",
 "Year 1947-2004"
 ]
}

 The dataset includes 35 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072268-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.asn2dr
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllanthus angustatus Hutch."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072269-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c55unz
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pilea intumescens C.B.Rob."
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072271-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.93592v
title: Occurrence Download

description: A dataset containing 239 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phanera scandens (L.) Lour. ex Raf."
 ]
}

 The dataset includes 239 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072270-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mwp7bf
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Cacajao calvus ucayalii (Thomas, 1928)"
 ]
}

 The dataset includes 28 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072272-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jsx4fw
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllanthus anisophyllioides Merr."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072273-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.97e67b
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pilea ivohibeensis Leandri"
 ]
}

 The dataset includes 23 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072274-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nrz8tm
title: Occurrence Download

description: A dataset containing 461 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phanera semibifida (Roxb.) Benth."
 ]
}

 The dataset includes 461 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072275-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.adfmza
title: Occurrence Download

description: A dataset containing 94 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllanthus ankarana Leandri"
 ]
}

 The dataset includes 94 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072276-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kwyd2g
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pilea jayaensis A.K.Monro"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072277-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.833wcm
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phanera similis (Craib) de Wit"
 ]
}

 The dataset includes 33 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072278-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.42hqcg
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllanthus ankaratrae (Leandri) Petra Hoffm. & McPherson"
 ]
}

 The dataset includes 8 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072279-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7tunjk
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pilea johniana Stapf"
 ]
}

 The dataset includes 70 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072280-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.smn8db
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phanera steenisii (K.Larsen & S.S.Larsen) Bandyop., Ghoshal & M.K.Pathak"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072281-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9haauh
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllanthus ankazobensis Ralim. & Petra Hoffm."
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072282-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.awx2xa
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pilea johnsii A.K.Monro"
 ]
}

 The dataset includes 15 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072283-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j3w4mx
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phanera stipularis (Korth.) Benth."
 ]
}

 The dataset includes 71 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072284-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.phfc8w
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllanthus ankirindrensis Ralim. & Cable"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072285-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.he7s7a
title: Occurrence Download

description: A dataset containing 210 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pilea johnstonii Oliv."
 ]
}

 The dataset includes 210 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072286-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h9sf5v
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phanera strychnoidea (Prain) Bandyop. & Ghoshal"
 ]
}

 The dataset includes 10 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072287-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4mcmwd
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllanthus aoraiensis Nadeaud"
 ]
}

 The dataset includes 8 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072288-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tnfxsr
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pilea kanaii H.Hara"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072289-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mu3m5u
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phanera sulphurea (C.E.C.Fisch.) Thoth."
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072290-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k2epd5
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pentameris pungens (H.P.Linder) Galley & H.P.Linder"
 ]
}

 The dataset includes 38 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072291-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7esmfu
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pipturus micronesicus Kaneh."
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072292-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/jhp-rgp-cke
title: Funa jeffreysii (E. A. Smith, 1875)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vfx-7r2-mrp
title: Tenellia adspersa (von Nordmann, 1845)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/63c-ad0-de7
title: Patellidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/eqs-y93-gsj
title: Fissurellidae J. Fleming, 1822

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ndj-q3y-rbr
title: Patellidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wee-xtq-xpg
title: Fissurellidae J. Fleming, 1822

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c02-yht-q9d
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s79-11d-t73
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/m5b-sdl-04j
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kye-lhr-mly
title: Conidae J. Fleming, 1822

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/v58-3z7-lmm
title: Conidae J. Fleming, 1822

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9zz-0yb-9mw
title: Conidae J. Fleming, 1822

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.3znbvs
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Zephyranthes montana"
 ]
}

 The dataset includes 37 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008685-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/7bw-g0v-acv
title: Patellidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6l9-ppm-bcd
title: Conidae J. Fleming, 1822

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tp8-ths-amh
title: Fissurellidae J. Fleming, 1822

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dc8-jfd-5qr
title: Patellidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.ru4tpx
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Clupisoma naziri)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008686-250827131500795/datasets/export for details.
DOI: 10.3535/5zl-gz4-b4t
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7te-7zp-mn0
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/m5t-bxm-kr5
title: Fissurellidae J. Fleming, 1822

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0e3-dx9-lne
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9ds-8cr-91r
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/n4f-74d-zpf
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4kt-pyg-pse
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/f5z-yq8-h7r
title: Fissurellidae J. Fleming, 1822

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nqh-mxa-4hh
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5jf-3z7-p9z
title: Patellidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/aab-5k5-8yn
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c3d-qq6-ph6
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/axf-9ej-tqe
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mh3-dcm-vr2
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nea-by4-pem
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/493-k16-z9a
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/g7f-n7p-3fe
title: Muricidae Rafinesque, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kr9-lkk-d6y
title: Cerithiopsidae H. Adams & A. Adams, 1853

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