cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8124854
title: BOCK: Biological networks and Oligogenic Combinations as a Knowledge graph

description: BOCK is a new knowledge graph integrating oligogenic disease information (originally from the Oligogenic Disease Database (Nachtegael et al. 2022) together with multiple biological networks and ontologies.

Compared to more generic knowledge graphs, we selected specifically networks relevant to understand the molecular mechanisms of epistasis, placing genes as the central entities, and focused on trusted resources describing a large set of human genes and their interactions.

All entities in the KG are linked to their source database entry via an URI (Uniform Resource Identifier) to facilitate integrations within larger bioinformatics linked data repositories.

We provide BOCK in three formats:



RDF (Resource Description Framework): W3C standard for linked data exchange. Triplets are encoded in the Turtle syntax. Additionally, the KG model is provided in OWL.

GraphML (Graph Markup Language): a network format enabling the fast import of the KG by multiple libraries (e.g networkx) and tools (e.g Cytoscape).

Neo4J import files: tab-separated files that can be easily imported into Neo4J using the neo4j-admin utils.


 
description: This work was supported by the European Regional Development Fund (ERDF) and the Brussels-Capital Region-Innoviris within the framework of the Operational Programme 2014-2020 through the ERDF-2020 project ICITY-RDI.BRU [27.002.53.01.4524], an F.N.R.S-F.R.S CDR  [35276964], an Innoviris Joint R\&D project Genome4Brussels [2020 RDIR 55b], a Research Foundation-Flanders (F.W.O.) Infrastructure project associated with ELIXIR Belgium [I002819N], the Imagica2 IRP project by the Vrije Universiteit Brussel  [IRP8b] and by TAILOR, a project funded by the EU Horizon 2020 research and innovation program [952215].
The authors also thank Foundation 101 Genomes (f101g.org) for fruitful collaboration, creative exchange and scientific support.
DOI: 10.5281/zenodo.14980070
title: bulk RNAseq to control and RIF Patient

description: bulk RNAseq to human endometrial epithelial cell and stromal cell from control and RIF patient and bulk RNAseq to RIF patient with or without drug treatment in rds, h5seurat and h5ad format file, respectively
DOI: 10.15468/dl.2yy4sp
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salicornia alpini Lag.",
 "Geometry POLYGON((-4.57907617500001 39.884719509, -4.57907617500001 41.165844755, -3.05298331400002 41.165844755, -3.05298331400002 39.884719509, -4.57907617500001 39.884719509))"
 ]
}

 The dataset includes 4 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006901-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.77qkwd
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "OccurrenceStatus is Present",
 "TaxonKey is Sphyrna lewini (Griffith & Smith, 1834)",
 "Year is 2024"
 ]
}

 The dataset includes 50 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006902-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zxygvg
title: Occurrence Download

description: A dataset containing 1967 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Chinese Taipei, Hong Kong)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Pinus massoniana Lamb."
 ]
}

 The dataset includes 1967 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006903-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17864/1947.001407
title: Dataset supporting the article 'd10s2 Post-Transition Metal Anions: Identifying and Analyzing Their Dual-Mode Lewis Basicity'

description: This compressed file is supplementary to the article cited in the 'Related publication' section below. Its contents are two-fold: (1) Experimental X-ray photoelectron spectroscopy data of a select few ionic liquids studied in the article, in .vms - which can be accessed using CasaXPS - and .txt (2) The output files of three of the ionic liquids studied computationally using Gaussian 16.
DOI: 10.15468/dl.5cnxr4
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Satureja intricata Lange",
 "Geometry POLYGON((-4.57907617500001 39.884719509, -4.57907617500001 41.165844755, -3.05298331400002 41.165844755, -3.05298331400002 39.884719509, -4.57907617500001 39.884719509))"
 ]
}

 The dataset includes 17 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006905-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13981203
title: CS#1B Monitoring Data of Subsurface Passage in Managed Aquifer Recharge: Raw flow cytometry data (fcs)

description: This dataset contains data on microbial cell counts from flow cytometry (FCM). Data were collected over a four month monitoring period at three sampling locations along a transect: recharge basin (Basin), observation well (ObsWell) and abstraction well (Well).
DOI: 10.5281/zenodo.13981204
title: CS#1B Monitoring Data of Subsurface Passage in Managed Aquifer Recharge: Raw flow cytometry data (fcs)

description: This dataset contains data on microbial cell counts from flow cytometry (FCM). Data were collected over a four month monitoring period at three sampling locations along a transect: recharge basin (Basin), observation well (ObsWell) and abstraction well (Well).
DOI: 10.5281/zenodo.14980196
title: QOL
DOI: 10.5281/zenodo.14980197
title: QOL
DOI: 10.13135/ela-452
title: Decree
DOI: 10.15468/dl.casfmg
title: Occurrence Download

description: A dataset containing 262 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oxytropis ochrocephala Bunge"
 ]
}

 The dataset includes 262 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006906-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28082687
title: Metadata from - Impact of metformin on HBV replication: no evidence of suppression in vitro

description: These are the metadata associated with the article 'Impact of metformin on HBV replication: no evidence of suppression in vitro' from Hawkins et al,<br><b>Background</b>: Chronic Hepatitis B (CHB) infection has been increasingly associated with various metabolic syndromes, with a potential for exacerbation of liver disease progression. There is some evidence that metformin, a widely used anti-diabetic drug, may reduce HCC incidence in both people living with Hepatitis B Virus (HBV), with little to no evidence of impact on the virus itself <i>in vivo</i>. In contrast, previous <i>in vitro</i> studies suggest metformin may have a direct impact on HBV replication, although the mechanism remains unclear.<b>Objectives</b>: We aimed to investigate the impact of metformin on HBV replication <i>in vitro</i>.<b>Study</b> <b>design</b>: Hepatocyte cell lines constitutively expressing HBV (HepAD38) were treated once or thrice with escalating doses of metformin, using lamivudine and water as controls. We monitored cellular cytotoxicity as well as HBV biomarkers (HBeAg, HBsAg, HBV DNA and RNA) throughout the assay.<b>Results</b>: We did not observe any impact of metformin on HBV replication after a single dose or repeat treatments.<b>Conclusions</b>: In HepAD38 cells, HBV is not susceptible to metformin treatment. This contrasts with prior <i>in vitro</i> data but is in line with clinical evidence that suggests metformin acts through an influence on liver disease progression rather than a direct antiviral impact on HBV itself.<br>
DOI: 10.6084/m9.figshare.28082687.v1
title: Metadata from - Impact of metformin on HBV replication: no evidence of suppression in vitro

description: These are the metadata associated with the article 'Impact of metformin on HBV replication: no evidence of suppression in vitro' from Hawkins et al,<br><b>Background</b>: Chronic Hepatitis B (CHB) infection has been increasingly associated with various metabolic syndromes, with a potential for exacerbation of liver disease progression. There is some evidence that metformin, a widely used anti-diabetic drug, may reduce HCC incidence in both people living with Hepatitis B Virus (HBV), with little to no evidence of impact on the virus itself <i>in vivo</i>. In contrast, previous <i>in vitro</i> studies suggest metformin may have a direct impact on HBV replication, although the mechanism remains unclear.<b>Objectives</b>: We aimed to investigate the impact of metformin on HBV replication <i>in vitro</i>.<b>Study</b> <b>design</b>: Hepatocyte cell lines constitutively expressing HBV (HepAD38) were treated once or thrice with escalating doses of metformin, using lamivudine and water as controls. We monitored cellular cytotoxicity as well as HBV biomarkers (HBeAg, HBsAg, HBV DNA and RNA) throughout the assay.<b>Results</b>: We did not observe any impact of metformin on HBV replication after a single dose or repeat treatments.<b>Conclusions</b>: In HepAD38 cells, HBV is not susceptible to metformin treatment. This contrasts with prior <i>in vitro</i> data but is in line with clinical evidence that suggests metformin acts through an influence on liver disease progression rather than a direct antiviral impact on HBV itself.<br>
DOI: 10.5281/zenodo.14980217
title: plantago_coronopus_spades_01.fasta.gz
DOI: 10.5281/zenodo.14980218
title: plantago_coronopus_spades_01.fasta.gz
DOI: 10.15468/dl.jamjqg
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Specimen, Human Observation, Living Specimen, Occurrence evidence)",
 "Country is Ethiopia",
 "TaxonKey is Podocarpus falcatus (Thunb.) R.Br. ex Mirb."
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006893-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7tf2n3
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sedum aetnense Tineo",
 "Geometry POLYGON((-4.57907617500001 39.884719509, -4.57907617500001 41.165844755, -3.05298331400002 41.165844755, -3.05298331400002 39.884719509, -4.57907617500001 39.884719509))"
 ]
}

 The dataset includes 14 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006894-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14728687
title: Data and scripts for "Noise-shaped hysteresis cycles of the AMOC under increasing CO2 forcing"

description: This dataset contains supplementary material for the paper Noise-shaped hysteresis cycles of the AMOC under increasing CO2 forcing (M.Cini, G. Zappa, F. Ragone, S. Corti, 2023) submitted to Chaos, APJ publishing.  Here we uploaded most relevant data and scripts concerning this study. Feel free to contact us for other resources.This datasets contains:

1) The diagnostic output of one 6000-years simulation composed by a ramp up 3000-year simulation with concentration increasing from 354 ppm to 954ppm, and a ramp down 3000-simulation with concentration decreasing from 954 ppm to 354ppm2) All scripts that have been used to plot the figures in the paper.

Simulation Architecture and model setup

The simulations have been performed with an intermediate complexity coupled climate model, composed by the Planet Simulator (PlaSim) and the Large Scale Geostrophic Ocean (LSG). All simulations are perfomed with increasing/dereasing co2 concentrations (0.2 ppm/year) starting from 354 ppm to 954ppm and vice versa for the ramp down.   More information about model setup and scope of the simulations can be found in the paper.We performed 3 single member  simulations. Each simulation is composed of a 3000 years ramp up and 3000 years ramp down fo the co2. Here we upload only the diagnostic output of one of the three simulationAMOC_LD_amoc_pos_changeco2_0.2y1_ntraj1_k0_LBlock360_p1_startIDl207-y2490_r2.tar.gz    &    AMOC_LD_amoc_pos_changeco2_-0.2y1_ntraj1_k0_LBlock360_p1_startIDl207-y2490_r2.tar.gz

These are the ramp up and ramp down part of one simulation. Folders contain the diag files where Amoc index can be extracted. They contain also executbale files and namelists of the model.

time teries_Co2

Script for plotting time series. It has been used to plot fig.1, fig.2, fig.S1, fig.S2, fig.S3 of the paper

EWS_Co2

Scripts for the Early-Warning-Signal analysis. It has been used to plot fig.3, fig.S4, fig.S5, fig.S6 of the paperNB: In the second cell, the first plot (fig 3a of the paper) is perfromed as :

run_fit_a_ar1(stemp[i], ws)

while the others (Fig 3b and 3c) are performed as 

run_fit_a_ar1(stemp[i] - funcfit4(time,*popt31), ws)

But the results are the same with both approaches. This means that the use of funcfit4, in our case didn't change the results, since a linear detrending is already applied inside the window.
DOI: 10.5281/zenodo.14728688
title: Data and scripts for "Noise-shaped hysteresis cycles of the AMOC under increasing CO2 forcing"

description: This dataset contains supplementary material for the paper Noise-shaped hysteresis cycles of the AMOC under increasing CO2 forcing (M.Cini, G. Zappa, F. Ragone, S. Corti, 2023) submitted to Chaos, APJ publishing.  Here we uploaded most relevant data and scripts concerning this study. Feel free to contact us for other resources.This datasets contains:

1) The diagnostic output of one 6000-years simulation composed by a ramp up 3000-year simulation with concentration increasing from 354 ppm to 954ppm, and a ramp down 3000-simulation with concentration decreasing from 954 ppm to 354ppm2) All scripts that have been used to plot the figures in the paper.

Simulation Architecture and model setup

The simulations have been performed with an intermediate complexity coupled climate model, composed by the Planet Simulator (PlaSim) and the Large Scale Geostrophic Ocean (LSG). All simulations are perfomed with increasing/dereasing co2 concentrations (0.2 ppm/year) starting from 354 ppm to 954ppm and vice versa for the ramp down.   More information about model setup and scope of the simulations can be found in the paper.We performed 3 single member  simulations. Each simulation is composed of a 3000 years ramp up and 3000 years ramp down fo the co2. Here we upload only the diagnostic output of one of the three simulationAMOC_LD_amoc_pos_changeco2_0.2y1_ntraj1_k0_LBlock360_p1_startIDl207-y2490_r2.tar.gz    &    AMOC_LD_amoc_pos_changeco2_-0.2y1_ntraj1_k0_LBlock360_p1_startIDl207-y2490_r2.tar.gz

These are the ramp up and ramp down part of one simulation. Folders contain the diag files where Amoc index can be extracted. They contain also executbale files and namelists of the model.

time teries_Co2

Script for plotting time series. It has been used to plot fig.1, fig.2, fig.S1, fig.S2, fig.S3 of the paper

EWS_Co2

Scripts for the Early-Warning-Signal analysis. It has been used to plot fig.3, fig.S4, fig.S5, fig.S6 of the paperNB: In the second cell, the first plot (fig 3a of the paper) is perfromed as :

run_fit_a_ar1(stemp[i], ws)

while the others (Fig 3b and 3c) are performed as 

run_fit_a_ar1(stemp[i] - funcfit4(time,*popt31), ws)

But the results are the same with both approaches. This means that the use of funcfit4, in our case didn't change the results, since a linear detrending is already applied inside the window.
DOI: 10.15468/dl.8f82e4
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Dendrobium perpaulum Seidenf."
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006907-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wnzpad
title: Occurrence Download

description: A dataset listing the 24 species recorded in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Butterfly distribution records for the UK from Butterfly Conservation, up to 2019",
 "Geometry POLYGON((-1.4 50.9,-1.3 50.9,-1.3 51,-1.4 51,-1.4 50.9))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 2015-2015"
 ]
}

 The dataset's 24 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006904-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d9bgfx
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sedum rubens L.",
 "Geometry POLYGON((-4.57907617500001 39.884719509, -4.57907617500001 41.165844755, -3.05298331400002 41.165844755, -3.05298331400002 39.884719509, -4.57907617500001 39.884719509))"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006908-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.njthbv
title: Occurrence Download

description: A dataset containing 129 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coffea humblotiana Baill."
 ]
}

 The dataset includes 129 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006909-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.555rx7
title: Occurrence Download

description: A dataset containing 68539 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Catapodium rigidum (L.) C.E.Hubb.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 68539 records from 1084 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006885-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/cc12q071
title: CCDC 1004252: Experimental Crystal Structure Determination

description: Related Article: J.L. Wallick, C.G. Riordan, G.P.A. Yap|2014|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|70|640|doi:10.1107/S2053229614011620
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc12q082
title: CCDC 1004253: Experimental Crystal Structure Determination

description: Related Article: J.L. Wallick, C.G. Riordan, G.P.A. Yap|2014|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|70|640|doi:10.1107/S2053229614011620
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc12q0jb
title: CCDC 1004261: Experimental Crystal Structure Determination

description: Related Article: T. Assoumatine, H. Stoeckli-Evans|2014|Acta Crystallogr.,Sect.E:Struct.Rep.Online|70|o887|doi:10.1107/S1600536814011246
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc12q0mf
title: CCDC 1004264: Experimental Crystal Structure Determination

description: Related Article: D.S. Cati, H. Stoeckli-Evans|2014|Acta Crystallogr.,Sect.E:Struct.Rep.Online|70|23|doi:10.1107/S1600536814011520
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc12q0ng
title: CSD 1004265: Experimental Crystal Structure Determination

description: Related Article: M. Weil|2014|Acta Crystallogr.,Sect.E:Struct.Rep.Online|70|14|doi:10.1107/S1600536814009520
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc12q0ld
title: CCDC 1004263: Experimental Crystal Structure Determination

description: Related Article: T. Assoumatine, H. Stoeckli-Evans|2014|Acta Crystallogr.,Sect.E:Struct.Rep.Online|70|51|doi:10.1107/S1600536814011337
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc12q0wp
title: CCDC 1004272: Experimental Crystal Structure Determination

description: Related Article: D.S. Cati, H. Stoeckli-Evans|2014|Acta Crystallogr.,Sect.E:Struct.Rep.Online|70|18|doi:10.1107/S1600536814009519
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.