CIRAD Dataverse
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TropGene Coffee
No full textThe data come from the TropGeneDB CIRAD information system (https://tropgenedb.cirad.fr/tropgene/JSP/index.jsp).
TropGeneDB contains data from studies on tropical and mediterranean plants for various kinds of topics such as marker, QTL, genotype, genetic, phenotype, cartography (genetic, physical and linkage disequilibrium maps), linkage disequilibrium, association and germplasm.
The plants concerned are banana, breadfruit, citrus, cocoa, coconut palm, cotton, oil palm, rice, rubber, sorghum and sugarcane.
The IS has a database per plant. The data were produced by CIRAD researchers or by CIRAD researchers and colleagues associated in research projects.
All The data have been published.
The COFFEE data in this dataset produced between 2003 and 2021 were extracted from the TROPGENE_COFFEE database in tabulated text format files. There is a file for each type of data which name includes the data type. Each line of a file has several columns describing the study (title, description, year, country, place, contact) it belongs to.
The tropgene_coffee_references‧txt file contains the references of the scientific publications on these data
Replication Data for: sRNA dataset of PKWxPKW banana plant (GWT-16)
No full textDeep sequencing of sRNA from PKW self-pollinated plant
GWT-16 is heterozygous for the endogenous Banana streak Obino l'Ewai virus with the infective (eBSOLV-1) and the non-infective (eBSOLV-2) alleles, homozygous for the infective allele of endogenous Banana streak Goldfinger virus (eBSGFV-7) and homozygous for the endogenous Banana streak Imové virus (eBSIMV)
Scripts for sRNA and RNAseq analyses
No full textScripts used for sRNA and RNAseq analyses in Duroy et al., 2024 (New Phytologist
Data and Rscripts for: "Hierarchizing multiscale environmental effects on agricultural pest population dynamics: a case study on the annual onset of Bactrocera dorsalis population growth in Senegalese orchards"
No full textThese data and scripts are provided as supplementary material, in order to illustrate the main analyses presented in the following article: "Caumette, Cécile; Diatta, Paterne; Piry, Sylvain; Chapuis, Marie-Pierre; Faye, Emile; Sigrist, Fabio; Martin, Olivier; Papaïx, Julien; Brévault, Thierry; Berthier, Karine. Hierarchizing multi-scale environmental effects on agricultural pest population dynamics: a case study on the annual onset of Bactrocera dorsalis population growth in Senegalese orchards. Peer Community Journal, Volume 4 (2024), article no. e65. doi : 10.24072/pcjournal.438. https://peercommunityjournal.org/articles/10.24072/pcjournal.438/</a
Impact of experimental design on the vector competence of Ornithodoros ticks for African swine fever virus: a meta-analysis
No full textThis dataset describes the vector competence of the soft ticks Ornithodoros for African Swine Fever Virus. It gathers all available informations published in the litterature. By reviewing the original research studies dating back to the 1960s on the vector competence of Ornithodoros for ASFV, we estimated the vector competence of 10 tick species in association with 38 viral strains resulting in 51 tick-virus associations
sRNA dataset of Cavendish BSIMV infected plant (BPO-66)
No full textDeep sequencing of sRNA from Cavendish BSIMV infected plant (BPO-66
LCI for traditional firewood, burned in a three-stone fire
No full textLife Cycle Inventory dataset for traditional firewood burned in a three-stone fire.
It includes emissions from firewood combustion, considering whether greenhouse gas emissions actually contribute to climate change depending on the renewability of firewood supply, and the underlying contributions to deforestation and its consequences. Firewood extraction and transport processes are not included, and should be added, especially if they are not done manually.
The current version is representative of the local conditions of southern Burkina Faso, but a set of calibration parameters allows the inventory to be adapted to specific conditions. For each parameter, a description and recommendations for adapting values are given.
The file can be read independently, or imported to the SimaPro LCA software through the ELDAM software (https://doi.org/10.21105/joss.02765)
Source Data to study Genome assemblies of Musa wild banana ancestors and draw figures.
No full textSource data associated with the paper "Unravelling genomic drivers of speciation in Musa through genome assemblies of wild banana ancestors" (includes sequence data and data and configuration files for figures and artworks generation).
multiple types of data are present :
raw Image files from cytological studies.
Image files generated for chromosome scale assembly studies.
Sequence file of genome assemblies.
Multifasta gene alignments that allows plylogenetic analysis within the Musaceae family.
Multifasta files of non redundant repeat sequences identified in genome assemblies that allows for repeated fraction genome analysis.
tabulated, text and conf files for artwork and figures generation.
Sequence file of genome assemblies.
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Genotyping and phenotyping data of 250 individuals of the Fleur11 x IpaCor AB-QTL population phenotyped during three consecutive years (2020, 2021 and 2022) at Nioro research Station, Senegal
No full textThis dataset relates to the paper "Mapping QTLs for early leafspot resistance and yield component traits using an interspecific AB-QTL population in peanut" published in 2024 in Frontiers in Plant Science. It gathers three years of phenotyping data collected during the rainy season (July-October) 2020, 2021, and 2022, including traits such as leafspot and yield components-related traits, as well as genotyping data for 2329 SNPs. The data is in a .csv file, with a format that fits the r/qtl packag
Dataset for Evaluating location strategies in Padiweb
No full textThis dataset has been built in the framework of the optimization of the MUlti-Source surveillance Tool for the detection of Avian Influenza outbreaks in mammalian species (MUST-AI). The MUST-AI tool collects health events reported from 3 sources: two official sources, WAHIS from the World Animal Health Organization and mails from Program for Monitoring Emerging Diseases (ProMED); and one unofficial source, PADI-web, which collects online media articles. PADI-web uses 5 various strategies to locate health events mentioned in the text articles. The aim of our study was to assess the various strategies.
The dataset consists 7 case studies (outbreak events from official sources WAHIS or the scientific literature) associated to 222 validated media articles collected by PADI-web through the 5 strategies. The matching criteria to associate a case study to a PADI-web article are based on the country of the outbreak and the time period.
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The five evaluated strategies are:.
(A) SpaCy locations in Outbreak articles: extraction with SpaCy of locations in articles classified as an epidemiological outbreak. .
(B) SpaCy locations in Outbreak articles and Current event sentences: extraction with SpaCy of locations in articles classified as an epidemiological outbreak and in a sentence that has been classified as relating to a current event..
(C) SpaCy locations in beginning of Outbreak articles: extraction with SpaCy of locations found in the first 300 characters of the text of an article classified as an epidemiological outbreak. .
(D) PADI-web-specific locations: extraction of locations by the location extraction model trained on PADI-web data..
(E) SpaCy locations in beginning of articles: extraction with SpaCy of locations found in the first 300 characters of the text of an article...
Each case study is associated with an identification number. For each case study, the set of Padiweb articles is given with a unique identification number. The dataset contains the values as follows: .
- Source: source of the case study, as WAHIS or published article in the scientific literature.
- Id_gold_standard: case study identification number as the outbreak id reported in WAHIS or ranked literature case study number.
- Id_article: identification number of media articles as generated in PADI-web
- URL: url to the source article.
- Strategy X: binary value that stipulates whether the article has been returned by the strategy X.<br