cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17015725
title: Dataset for manuscript "Self-supervised Domain Adaptation of Protein Language Model Based Solely on Positive Enzyme-reaction Pairs"

description: License Notice

Data in `dataset/processed/kcat` partly includes materials licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0). https://creativecommons.org/licenses/by/4.0/ > Kroll, A., Rousset, Y., Hu, X.-P., Liebrand, N., & Lercher, M. (2022). Dataset for manuscript "Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning" [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8367052

The file `dataset/raw//rxnaamapper_sequences_1024.txt` partly includes materials licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0). https://creativecommons.org/licenses/by/4.0/ > Yves Gaetan Nana Teukam, Loıc Kwate Dassi, Matteo Manica, Daniel Probst, Philippe Schwaller, & Teodoro Laino. (2023). Dataset of biocatalyzed reactions [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7530180

Data in the dir `dataset/processed/embeding` and the files `dataset/processed/enzsrp_full_*` partly include materials licensed under Creative Commons Attribution 4.0 International (CC BY 4.0). https://creativecommons.org/licenses/by/4.0/ > The UniProt Consortium. (2023). UniProt: The Universal Protein Knowledgebase in 2023. Nucleic Acids Research, 51(D1), D523–D531. https://doi.org/10.1093/nar/gkac1052 > Lombardot, T., Morgat, A., Bansal, P., Coudert, E., Axelsen, K. B., Aimo, L., Hyka-Nouspikel, N., Gasteiger, E., Kerhornou, A., Neto, T. B., Ignatchenko, A., Redaschi, N., Bridge, A., & Xenarios, I. (2022). Rhea, the reaction knowledgebase in 2022. Nucleic Acids Research, 50(D1), D693–D700. https://doi.org/10.1093/nar/gkab1016

Data Modification Notice

Due to licensing restrictions, reaction direction information was removed from the created EnzSRP dataset and the its processed files (“enzsrp_full_*”). Please refer to ‘make_public_version_enzsrp.py’ in https://github.com/motonuko/adaptplm for details of this deletion process. The execution log is in the zip file `make_public_version_enzsrp.log`. As a result, reaction directions originally from MetaCyc were unified to “left-to-right” direction and rows that became duplicates due to this normalization were deleted. For the purpose of reproducing the EnzSRP dataset, please refer to https://github.com/motonuko/enzsrp and rebuild the dataset from scratch, or refer to the 'reactions.dat' file provided in the MetaCyc distribution. In the latter case, you will need to map reactions with direction_source set to “MetaCyc” as left-to-right, right-to-left, or both.
DOI: 10.15468/dl.ywzuga
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Megacarpaea gigantea"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003944-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zmetzs
title: Occurrence Download

description: A dataset containing 2598 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Citrus reticulata"
 ]
}

 The dataset includes 2598 records from 275 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003945-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15203905
title: Modelized harvest dates (2005-2023) by crop and UTM 10x10 km grid in peninsular Spain

description: DEPRECATED DATA. DO NOT USE
DOI: 10.15468/dl.b8z82v
title: Occurrence Download

description: A dataset containing 309 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is China",
 "TaxonKey is Megacarpaea delavayi"
 ]
}

 The dataset includes 309 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003946-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15987483
title: Modelized harvest dates (2005-2023) by crop and UTM 10x10 km grid in peninsular Spain

description: DEPRECATED DATA. DO NOT USE
DOI: 10.5281/zenodo.15203926
title: Modelized harvest dates (2005-2023) by crop and UTM 10x10 km grid in peninsular Spain

description: DEPRECATED DATA. DO NOT USE
DOI: 10.34740/kaggle/dsv/13837421
title: Supermarket-Superstore-Dataset-Bundle
DOI: 10.15468/dl.qw4cgv
title: Occurrence Download

description: A dataset containing 5272 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-120.778 32.735,-113.606 32.735,-113.606 35.112,-120.778 35.112,-120.778 32.735))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lynx rufus",
 "Year 2000-2025"
 ]
}

 The dataset includes 5272 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006453-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60723/11294
title: Molecular diagnosis due to a hemizygous TAF1 Variant

description: This case report describes an 8-year-old male with a complex clinical presentation characterized by global developmental delay and refractory epilepsy. His medical history is significant for a term birth complicated by umbilical cord avulsion during a water delivery. His birth measurements were a weight of 2600g, a body length of 49cm, and a head circumference of 34.5cm, with APGAR scores of 6, 8, and 8 at one, five, and ten minutes, respectively. A postaxial hexadactyly was noted at birth and subsequently underwent surgical correction. The patient exhibited profound developmental delays, achieving independent ambulation at 6 years of age and remaining nonverbal. He developed epilepsy at one year of age with seizures that have been refractory to treatment with cannabidiol (CBD) and clobazam. His co-morbidities include gastrointestinal dysfunction and exocrine pancreatic insufficiency. There was no known family history of similar disorders.

Given the constellation of symptoms, whole-genome sequencing was performed. This revealed a hemizygous missense variant in the TAF1 gene (NM_004606.5:c.1726C>T;p.(P576S)). The patient's mother was identified as a heterozygous carrier of this variant. No other family members had similar known disorders. Pathogenic variants in TAF1 are known to cause an X-linked intellectual disability syndrome. This specific variant had been previously reported in a family with developmental delay, as described by O'Rawe et al. in 2015. Subsequent studies have expanded the phenotypic spectrum associated with TAF1 mutations to include seizures and polydactyly, consistent with this patient's presentation.
DOI: 10.15468/dl.jrvtpt
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "Geometry POLYGON((-88.24825 49.00988,-88.22925 49.00988,-88.22925 49.02215,-88.24825 49.02215,-88.24825 49.00988))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Insecta"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006455-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fnhjrc
title: Occurrence Download

description: A dataset containing 605 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bison bison athabascae"
 ]
}

 The dataset includes 605 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006456-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60723/14511
title: Novel PAX3 splice-site variant in a woman with Waardenburg syndrome

description: We report a case 36-year-women who presented with unilateral congenital sensorineural hearing loss, dystopia canthorum (W index of 2,11), complete hair hypopigmentation which started as a white forelock during puberty, complete heterochromia iridium and patchy Skin hypopigmentation on her abdomen and right forearm. No skeletal malformations of the limbs were present. Together, the symptoms allowed establishing the clinical diagnosis of Waardenburg syndrome type 1 according to the Waardenburg Consortium criteria. Gene panel sequencing revealed a novel heterozygous splice-site variant (NM_181458.4:c.85+1G>T) in PAX3 predicted to affect the PAI subdomain, which we consequently classified as likely pathogenic (ACMG criteria PVS1_S, PP4), confirming the clinical diagnosis. The Patient reported premature gray hair without additional symptoms in both her mother and maternal grandmother, raising a possibility of an inherited variant with variable expressivity and a significantly milder phenotype without dystopia canthorum in the family. Testing of further family members was pending at time of reporting.
DOI: 10.15468/dl.qjb3gd
title: Occurrence Download

description: A dataset listing the 4346 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((0.90247 41.08499,0.93629 41.06237,1.02712 41.06426,1.13544 41.07692,1.26679 41.11745,1.25003 41.17578,1.204 41.19952,1.05576 41.17369,0.90895 41.15344,0.89489 41.11729,0.90247 41.08499))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset's 4346 records were derived from 136 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006452-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25346/s6collfi/lth51c
title: msXL_240v_MMSIoverhead.tif
DOI: 10.25346/s6collfi/xlkqme
title: msXL_240r_MMSIoverhead.tif
DOI: 10.25346/s6collfi/yjcllb
title: Color_center.tif
DOI: 10.25346/s6collfi/bpmlib
title: msXL_335v_MMSIoverhead.tif
DOI: 10.25346/s6collfi/chq5jl
title: msXL_335r_MMSIoverhead.tif
DOI: 10.25346/s6collfi/d6nxxz
title: msXL_334v_MMSIoverhead.tif
DOI: 10.25346/s6collfi/elmstw
title: msXL_334r_MMSIoverhead.tif
DOI: 10.25346/s6collfi/vrfesf
title: msXL_331v_MMSI.tif
DOI: 10.25346/s6collfi/0hiqfl
title: msXL_331r_MMSI.tif
DOI: 10.25346/s6collfi/dhrbbk
title: msXL_323v_MMSIoverhead.tif
DOI: 10.3886/e240579
title: Longitudinally Measuring Personal and Health Outcomes for People with Intellectual and Developmental Disabilities who Use Home and Community-Based Services

description: <br>People with intellectual and developmental disabilities (IDD), like all
Americans, are living in a rapidly changing world. The COVID-19 pandemic and
significant policy shifts are causing major transformations in how people with
IDD live in their communities, the supports that are available to them, and the
personal outcomes they experience as a result. In the context of such dramatic
societal and policy changes, it is essential for states to be able to use the
best available data In order to design their systems of service and supports,
and for advocates to have access to rigorous yet understandable information to
inform their work to demand supports for inclusive life in the community. This project aimed to help state policymakers and advocates get the
information they needed to make data-informed decisions for developing services and supports that respond to the needs of people
with IDD in these changing times. <br><br>This research was based on the merger of four major datasets, each of
which provides unique and important insight into the relationship between
Medicaid utilization, a person’s support needs, and personal and system-level
outcomes for people with IDD. Medicaid is the single largest funder for
services and supports for people with IDD and the first two data sources we
will work with represent Virginia’s Medicaid system: (a) Medicaid Home and
Community Based Services expenditure data, which includes services that help
people with IDD live in their communities and (b) Medicaid Managed Care acute
medical encounter data, which shows the medical services a person with IDD has
used, including those related to COVID-19. The third data set is the National
Core Indicators In Person Survey (NCI-IPS), which is used in the majority of
states to assess IDD system performance as well as personal outcomes for people
with IDD. Finally, the fourth data source is the Supports Intensity Scale,
which is a standardized instrument for assessing the support needs of people
with IDD across several distinct domains.<br>The ultimate aim of this project was to not only inform state IDD system
administrators and advocates in Virginia, but to provide a blueprint for other
states to follow to gain better insight into how their own Medicaid services
translate to outcomes.
description: Stratified random sampling.
description: Medicaid HCBS users age 18 or older with intellectual and developmental disabilities living in Virginia, United States.
description: computer-assisted personal interview (CAPI); face-to-face interview;
DOI: 10.25346/s6collfi/okpqbw
title: msXL_323r_MMSIoverhead.tif
DOI: 10.3886/e240579v1
title: Longitudinally Measuring Personal and Health Outcomes for People with Intellectual and Developmental Disabilities who Use Home and Community-Based Services

description: <br>People with intellectual and developmental disabilities (IDD), like all
Americans, are living in a rapidly changing world. The COVID-19 pandemic and
significant policy shifts are causing major transformations in how people with
IDD live in their communities, the supports that are available to them, and the
personal outcomes they experience as a result. In the context of such dramatic
societal and policy changes, it is essential for states to be able to use the
best available data In order to design their systems of service and supports,
and for advocates to have access to rigorous yet understandable information to
inform their work to demand supports for inclusive life in the community. This project aimed to help state policymakers and advocates get the
information they needed to make data-informed decisions for developing services and supports that respond to the needs of people
with IDD in these changing times. <br><br>This research was based on the merger of four major datasets, each of
which provides unique and important insight into the relationship between
Medicaid utilization, a person’s support needs, and personal and system-level
outcomes for people with IDD. Medicaid is the single largest funder for
services and supports for people with IDD and the first two data sources we
will work with represent Virginia’s Medicaid system: (a) Medicaid Home and
Community Based Services expenditure data, which includes services that help
people with IDD live in their communities and (b) Medicaid Managed Care acute
medical encounter data, which shows the medical services a person with IDD has
used, including those related to COVID-19. The third data set is the National
Core Indicators In Person Survey (NCI-IPS), which is used in the majority of
states to assess IDD system performance as well as personal outcomes for people
with IDD. Finally, the fourth data source is the Supports Intensity Scale,
which is a standardized instrument for assessing the support needs of people
with IDD across several distinct domains.<br>The ultimate aim of this project was to not only inform state IDD system
administrators and advocates in Virginia, but to provide a blueprint for other
states to follow to gain better insight into how their own Medicaid services
translate to outcomes.
description: Stratified random sampling.
description: Medicaid HCBS users age 18 or older with intellectual and developmental disabilities living in Virginia, United States.
description: computer-assisted personal interview (CAPI); face-to-face interview;
DOI: 10.25346/s6collfi/ywonfm
title: msXL_323r_MMSI.tif
DOI: 10.25346/s6collfi/cwna0o
title: msXL_322v_MMSI.tif
DOI: 10.25346/s6collfi/hyhbzu
title: msXL_322r_MMSI.tif
DOI: 10.15468/dl.pezemb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Buteo augur",
 "Country is Italy",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006457-251120083545085/datasets/export for details.
DOI: 10.25346/s6collfi/mfldzf
title: msXL_319v_MMSI.tif
DOI: 10.5281/zenodo.17605121
title: BeadBuddy Demo Project

description: This is a demo dataset that accompanies the BeadBuddy MATLAB tool developed by the Lionnet Lab at NYU Langone. 

Code deposited at: https://github.com/timotheelionnet/BeadBuddy.git
DOI: 10.5281/zenodo.17605122
title: BeadBuddy Demo Project

description: This is a demo dataset that accompanies the BeadBuddy MATLAB tool developed by the Lionnet Lab at NYU Langone. 

Code deposited at: https://github.com/timotheelionnet/BeadBuddy.git
DOI: 10.5281/zenodo.17703878
title: Wood Use Scenarios in Sweden through Integrated Monetary-Physical Input-Output Framework, Supplementary Information

description: This file contain supporting information (SI) for the scientific article "Wood Use Scenarios in Sweden through Integrated Monetary-Physical Input-Output Framework" submitted to the Journal of Industrial Ecology. The SI provides data from figures 2 to 5, as well as the following: (1) CLT bill of materials; (2) Half-lives of wood-based products and corresponding flows used in the model; (3) Top ten industry contributors to the net results in each scenarios compared to baseline ; (4) the economy-only yearly stocks and stock changes as a result of the dynamic carbon stock model (the stocks in the forest are not modelled); and (5) the forest carbon stock assumption check using information from the Heureka system standard model run (SKA22).
DOI: 10.25346/s6collfi/h5ommk
title: msXL_319r_MMSI.tif
DOI: 10.5281/zenodo.17703877
title: Wood Use Scenarios in Sweden through Integrated Monetary-Physical Input-Output Framework, Supplementary Information

description: This file contain supporting information (SI) for the scientific article "Wood Use Scenarios in Sweden through Integrated Monetary-Physical Input-Output Framework" submitted to the Journal of Industrial Ecology. The SI provides data from figures 2 to 5, as well as the following: (1) CLT bill of materials; (2) Half-lives of wood-based products and corresponding flows used in the model; (3) Top ten industry contributors to the net results in each scenarios compared to baseline ; (4) the economy-only yearly stocks and stock changes as a result of the dynamic carbon stock model (the stocks in the forest are not modelled); and (5) the forest carbon stock assumption check using information from the Heureka system standard model run (SKA22).
DOI: 10.25346/s6collfi/zez0sl
title: msXL_318v_MMSI.tif
DOI: 10.25346/s6collfi/qpyiok
title: msXL_318r_MMSI.tif
DOI: 10.25346/s6collfi/l9zzad
title: msXL_315v_MMSI.tif
DOI: 10.25346/s6collfi/kwjbo8
title: msXL_315r_MMSI.tif
DOI: 10.25346/s6collfi/fq0k9t
title: msXL_307v_MMSIoverhead.tif
DOI: 10.25346/s6collfi/pgzm4o
title: msXL_307r_MMSIoverhead.tif
DOI: 10.25346/s6collfi/y81efl
title: msXL_027r_MMSI+overhead+W385B47_38_F.tif
DOI: 10.25346/s6collfi/twlzbg
title: msXL_027r_MMSI+overhead+W365R25_29_F.tif
DOI: 10.25346/s6collfi/cywysa
title: msXL_027r_MMSI+overhead+W365G58_33_F.tif
DOI: 10.25346/s6collfi/tne6dj
title: msXL_027r_MMSI+overhead+W365B47_37_F.tif
DOI: 10.25346/s6collfi/wq7fkl
title: msXL_027r_MMSI+overhead+TX940IR_26_F.tif
DOI: 10.25346/s6collfi/xlzdey
title: msXL_027r_MMSI+overhead+TX735IR_25_F.tif
DOI: 10.25346/s6collfi/unjnyc
title: msXL_027r_MMSI+overhead+TX630RD_24_F.tif
DOI: 10.25346/s6collfi/lbvp33
title: msXL_027r_MMSI+overhead+TX1050R_28_F.tif
DOI: 10.25346/s6collfi/pbn5rc
title: msXL_027r_MMSI+overhead+TX1050R_27_F.tif
DOI: 10.25346/s6collfi/5ait6q
title: msXL_027r_MMSI+overhead+RR940IR_23_F.tif
DOI: 10.25346/s6collfi/3mbl3j
title: msXL_027r_MMSI+overhead+RR450RB_22_F.tif
DOI: 10.25346/s6collfi/p4zoed
title: msXL_027r_MMSI+overhead+RL940IR_21_F.tif
DOI: 10.25346/s6collfi/13cent
title: msXL_027r_MMSI+overhead+RL450RB_20_F.tif
DOI: 10.25346/s6collfi/ehrq8u
title: msXL_027r_MMSI+overhead+M1050IR_19_F.tif
DOI: 10.25346/s6collfi/smpidn
title: msXL_027r_MMSI+overhead+M0940IR_67_F.tif
DOI: 10.25346/s6collfi/b8wchi
title: msXL_027r_MMSI+overhead+M0940IR_18_F.tif
DOI: 10.25346/s6collfi/acbqnn
title: msXL_027r_MMSI+overhead+M0850IR_66_F.tif
DOI: 10.25346/s6collfi/dele2y
title: msXL_027r_MMSI+overhead+M0850IR_17_F.tif
DOI: 10.25346/s6collfi/jisso0
title: msXL_027r_MMSI+overhead+M0780IR_16_F.tif
DOI: 10.25346/s6collfi/z8zcxp
title: msXL_027r_MMSI+overhead+M0735IR_65_F.tif
DOI: 10.25346/s6collfi/zy7x56
title: msXL_027r_MMSI+overhead+M0735IR_15_F.tif
DOI: 10.25346/s6collfi/esu3e1
title: msXL_027r_MMSI+overhead+M0700IR_14_F.tif
DOI: 10.25346/s6collfi/pz95ic
title: msXL_027r_MMSI+overhead+M0655DR_64_F.tif
DOI: 10.25346/s6collfi/8ayxvn
title: msXL_027r_MMSI+overhead+M0655DR_13_F.tif
DOI: 10.15468/dl.x678vx
title: Occurrence Download

description: A dataset containing 4589603 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Archilochus colubris",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4589603 records from 145 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006380-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25346/s6collfi/gyojt4
title: msXL_027r_MMSI+overhead+M0630RD_63_F.tif
DOI: 10.25346/s6collfi/y0pj0a
title: msXL_027r_MMSI+overhead+M0630RD_12_F.tif
DOI: 10.25346/s6collfi/v6781v
title: msXL_027r_MMSI+overhead+M0615RO_62_F.tif
DOI: 10.7910/dvn/30kqie
title: Curated Dataset of High-Yield Organic Reactions for Chemistry Education and Research

description: The Curated Dataset of High-Yield Organic Reactions for Chemistry Education and Research is a structured collection of essential organic transformations compiled from authoritative textbooks, peer-reviewed publications, and standard curricula. This dataset emphasizes reaction conditions, reagents, mechanisms, and representative examples, making it a valuable resource for both academic learning and computational chemistry applications.

Designed for educators, students, and researchers, the dataset provides:
 🔹 Reaction Pathways – Detailed descriptions of transformations including substitution, elimination, addition, oxidation–reduction, rearrangements, name reactions, and multi-step syntheses.
 🔹 Mechanistic Insights – Stepwise representation of bond-breaking and bond-forming events where applicable.
 🔹 Standardized Metadata – Includes reaction type, functional group transformations, conditions, and notes on selectivity or limitations.
 🔹 Educational Alignment – Mapped to commonly taught high-yield reactions in chemistry education, ensuring classroom and examination relevance.
 🔹 Research Utility – Structured format suitable for integration into machine learning models, reaction prediction systems, and digital chemistry platforms.