251 Works

Supporting data and code for the African Rice Panreference produced by the frangiPANe software

Christine Tranchant, Clothilde Chenal, Mathieu Blaison, Laurence Albar, Valentin Klein, Cédric Mariac, Rod Wing, Yves Vigouroux & Francois Sabot
We present here FrangiPANe (https://github.com/tranchant/frangiPANe), a pipeline developed to build panreference using short reads through a map-then-assemble strategy and a dataset corresponding to 515 Mb of new sequences (484,394 non redundant sequences) in addition to the CG14 genome (iOMAP consortium). Applying this approach to 248 African rice genomes, we identified an average of 8 Mb of new sequences and 5,290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1,306,676 contigs,...

Impact of soil biodiversity in Southern Tunisia in 2019

P. Jouquet, H. Aroui, T. Henry-Des-Tureaux, P. Podwojewski, F. Garcia Ibarra & M. Labiadh
Measure of the impact of soil biodiversity (termites, ants, rodents) on soil properties (soil bulk density, water hydraulic conductivity, particle size distribution, C content, spectral signature in the infrared region by FTIR) in a semi-arid area in the south of Tunisia (region of Médenine, protected area).

Soil macrofauna diversity and activity in Dong Cao catchment, Northern Vietnam, 2005

P. Jouquet, N. Bottinelli, P. Podwojewski, T. Tran Minh & T. Tran Duc
This dataset has been collected thanks to the long-term partnership with Soils and Fertilizers Research Institute (SFRI), Vietnam. The dataset holds soil macrofauna diversity and activity in Dong Cao. Sites are: (i) a fallow + Eucalyptus trees, (ii) a fallow, (iii) a cassava plantation, (iv) forests (2 sites) and (v) plantation of bracharia sp. Two soil depths are considered: 0-15 and 15-30 cm. Variables are (i) soil diversity (number of earthworms, termites, ants...), (ii) earthworm...

Soil macrofauna in Chiang Rai province, Northern Thailand, 2015, 2016

P Jouquet, J-L Janeau, N Suvannang, K Trisophon, N Krisdatarn, P Thaller & H Robain
Soil macrofauna diversity (nb ind. TSBF-1) in 4 sites (maize, rice + young rubber trees, rubber tree plantation close to the trees or in the interrow) in Huai Lang, Chiang Rai province, Northern Thailand. This study was realized during a research project of Sorbonne University and Institut de Recheche pour le Développement and was supported by the ANR HévéAdapt project, grant ANR-14-CE03-0012-04, of the French Agence Nationale de la Recherche. Fieldwork was realized with the...

Analysis of earthworm casts and soils collected over Dong Cao catchment in Northern Vietnam in 2017

N. Bottinelli, P. Jouquet, H. Aroui, M. Mendez & T. Tran Minh
Earthworm casts and their surrounding topsoil were taken in collaboration with the Soils and Fertilizers Research Institute (SFRI) under different vegetation cover at the long term observatory catchment of Dong Cao in Northern Vietnam in 2017. This dataset holds general chemical parameters of soil samples. Dry combustion analysis (CHN) was used to assess organic Carbon (TOC) and Nitrogen (N) concentrations. Potassium dichromate oxidation titration was as well used to quantify organic Carbon (TOC). Natural isotopes...

User centric metadata model

Valentina BERETTA
The user centric metadata model aims to foster multi-disciplinary research, describing dataset of different disciplines in the same manner. It is able to favour the user viewpoint using the observation paradigm, adopted by the Observation data model, for specifying the dataset content. The advantages of the proposed metadata model are that the model specifies the semantics of the involved entities and links the technical description, usually provided by existing metadata models, with the thematic description....

Analysis of soil samples collected over Huay Ma Nai catchment in Northern Thailand in 2017

J-L. Janeau, P. Podwojewski & A. Boonsaner
This dataset has been collected thanks to the long-term partnership with National Park, Wildlife and Plant Conservation Department (DNP), Thailand, which granted the permission for field access, and to the financial, scientific, technical, and/or logistical support of the Multiscale TROPIcal CatchmentS (SNO M-TROPICS; https://mtropics.obs-mip.fr/) critical zone observatory (previously MSEC). The soil samples were taken under different vegetation covers at the long-term observatory catchment Huay Ma Nai in northern Thailand in 2017. This dataset holds some...

Wood density data of central African rainforest trees

Pierre PLOTON, Stéphane MOMO TAKOUDJOU, Bonaventure SONKE, Faustin BOYEMBA, Joel LOUMETO, Vincent MEDJIBE, Alfred NGOMANDA, Diosdado OBIANG & Olga YONGO
The dataset contains wood density measures (n=3820) from 822 trees (55 species, 16 families) destructively sampled in six countries of central Africa. Wood density estimations are reported for six tree compartments along tree vertical profile, from the stump to the smallest branches. Field and laboratory protocols are described in publications associated to these data, notably Fayolle et al. (2018, Forest ecology and management) and Momo Ploton et al. (2020, Scientific Reports).

Replication Data for: Complex evolutionary history of coffees including Coffea canephora (Robusta coffee) revealed by full plastid genomes and 28,800 nuclear SNPs analyses

Romain Guyot, Jean-Claude Charr, Andrea Garavito, Christophe Guyeux, Dominique Crouzillat, Patrick Descombes, Serigne Ly, Eva Raharimalala, Jean-Jacques Rakotomalala, Piet Stoffelen, Steven Janssen & Perla Hamon
The dataset concerns all chloroplast complete sequences for Coffea genus. Sequences were annotated with the Genbank format (*.gb).

Data of non-volcanic, polygenic, andic soils in the southern central Ecuadorian highlands as the result of long-lasting pedogenesis and geodynamic processes

P. Podwojewski, J. Poulenard & T. Toulkeridis
In the high altitude (>3000 m asl) grasslands of Ecuador, the Páramo ecosystem, soils generally formed on recent volcanic ashes being 10 000 years old in the northern and central part of the cordilleras. With time these soils evolved in to non-allophanic Andisols with hydric properties such as evidenced in profiles from the CAJAS massif located in the western central Cordillera. However soils at the Fierro Urcu massif and at the Oña plateau at the...

Microplastic concentrations in riverine and lake environments of Da Nang province and Quang Nam provinces, Central Vietnam, under COMPOSE (2019-2021) and CounterMEASUREII (2021-2022) projects

Tran Nguyen Quynh Anh, Trinh Dang Mau, & Emilie Strady
Microplastic (300-5000µm) concentrations were measured in the Central Park Lake, Hoa Phu Lake and Han River environments of Da Nang city, and in the Thu Bon River and Cu De River of Quang Nam province Central Vietnam, under the COMPOSE project (2019-2021)and the CounterMEASUREII project (2021-2022). Microplastic were sampled using a 80µm mesh size net from a local boat. The samples were extracted in the laboratory using enzymatic digestion, NaCl density separation and were filtrated...

A systematic review meta-analysis of dietary behaviours in two African countries: data synthesis

Emily Rousham, Rebecca Pradeilles, Robert Akparibo, Richmond Aryeetey, Kristin Bash, Andrew Booth, Stella Muthuri, Hibbah Osei-Kwasi, Colette Marr, Tom Norris & Michelle Holdsworth
We undertook a systematic review and meta-analyses to synthesise evidence of urban dietary behaviours (macronutrients, types of foods consumed, dietary diversity and dietary practices) in two African countries (Ghana and Kenya) in relation to postulated changes in the context of nutrition transition. The study protocol is registered at PROSPERO CRD42017067718. We include data on dietary behaviours extracted from the 47 included studies that encompass 20,726 individuals and 6,526 households.

Geographical mapping of food outlets and foods and beverages advertised in Kenya

Mark Green, Rebecca Pradeilles, Milka Wanjohi, Elizabeth Kimani-Murage, Stella Muthuri, Paula Griffiths & Michelle Holdsworth
The aim of this study was to characterise the local foods and beverages sold and advertised in a deprived urban neighbourhood in Nairobi, Kenya. In 2017, a cross-sectional observational study design was used to audit all food outlets (outlet type and food type sold) and food advertisements. Data available on: types of foods and beverages sold and/or advertised in food outlets. A total of 499 food outlets or adverts were identified and assessed in Nairobi.

Dataset from an in-field experimental rainfall simulation – Thailand, Nan Province, 2019

J.-L. Janeau, R. Chanisara, S. Grellier, C. Hammecker, S. Intanon, A. Khwanrawee & W. Pansak
In North Thailand land use/-cover change quickly especially in steep agrosystem land. Under rainfall simulation, we are looking at the effect of the topographic situation along the slope and catena using 24 microplots of 1m2 each located down, middle, up and top of the slope. We quantified seed dispersion, soil detachment, soil losses and runoff processes for two soil treatment: tradition cropping and with biochar amendments.

Dataset from an in-field experimental rainfall simulation - Influence of macrofauna on runoff and erosion - Vietnam, Hanoi Province, Dong Cao, March 2011

J.-L. Janeau, P. Jouquet, A. Pisano, Tran Si Hai, D. Orange, Luu Thi Nguyet Minh & C. Valentin
We assessed the effect of the micro-relief generated by earthworms and termites on soil hydrodynamic properties, and soil and nutrient losses. Eighteen 1 m×1 m plots were established for rainfall simulation experiments (2 runs of 40 min rain, intensity 90 mm h−1) in a steep slope fallow in Northern Vietnam. The soil surface of the micro-plots differed in the proportions of earthworm casts and termite sheetings. The results confirmed the importance of soil biostructures in...

Informal waste collectors and aggregators space and activities in Ho Chi Minh City, Vietnam, COMPOSE project (2019-2021)

Thai Huyen Nguyen, Thi Thao Trang Le, Thai Hoa Nguyen, Thi Hai Yen Nguyen, Thien An Dinh, Ngoc Anh Dinh, Viet Anh Le, Van Chien Hoang, Ngoc Tan Pham, Tuan Minh Le, Cong Hung Phan, Tien Quoc Anh Nguyen, Khac Hoai Son Do, Duc Loc Nguyen & Tien Tam Nguyen
The system of informal waste collectors and aggregators in Ho Chi Minh city (Vietnam) was surveyed in the framework of the COMPOSE project (2019-2021). The social survey based on questionnaire was carried out in the entire area of Ho Chi Minh city to identify the location of the aggregator warehouse participating to the informal waste collection and recycling in the city. Then, the collectors and aggregators were interviewed individually to collect information on the space,...

Dataset describing soil sheeting properties produced by termites sampled in 21 countries from 2015 to 2020

P. Jouquet, A. Harit, C. Tiago, D. Donoso, H.F. Da Cunha, D. Eldridge, C. Choosai, J-L. Janeau, J. Van Thuyne, A. Maingan, O. P. Pinzon Florian, O. Malam Issa, M. Labiadh, R. Muon, V. Ann, S. Cheik, S. Fall, S. Traoré, T. Chouvenc, T. Tran Minh, A. Auclerc, H. Huot, D. Sillam-Dussès & S. Dupont
Dataset describing sheeting properties made by termites (names, and feeding and building categories are given) sampled in 34 study sites, including M-Tropics observatories, from 19 countries. Data coming from 15 published studies are also given, for a total of 49 sites and 21 countries. The dataset include the locations (site names, countries, GPS coordinates, mean annual precipitations ‚MAP‘) and soil properties (electrical conductivity in µS cm-1, pH, C content in %, soil aggregate stability (in...

Results of a survey describing the utilization of termite mounds by the population in Cambodia in 2021

R. Muon, V. Ann, E. Bureau-Point, K. Sok, A. Savouré, F. Wieringa, J. Berger, B. Diene, F. Chassagne, M. Audibert, R. Zaiss, T. Azomahou, P. Ket & P. Jouquet
This dataset comes from a survey carried out in Chrey Back long term observatory (Cambodia). 61 persons from 13 villages located in Chrey Back watershed were interviewed in order to understand the local perception of the utilization of termite mounds. The dataset describes the questions and responses of villagers in differentiating the soil type (Arenosol vs. Acrisol) and position within the watershed (lower land (LL) vs. upper land (UL)). Survey_detail.csv describes the number of responses...

Investigation of leptospirosis in rodents, Mahé, Seychelles, 2013-2014

Leon Biscornet, Christophe Révillion, Sylvaine Jégo, Erwan Lagadec, Yann Gomard, Gildas Le Minter, Gérard Rocamora, Vanina Guernier-Cambert, Julien Mélade, Koussay Dellagi, Pablo Tortosa & Vincent Herbreteau
This dataset is related to the description of rodents (morphology, status of leptospirosis infection and environment around the capture sites) collected in Mahé, the main island of Seychelles, and analyzed in the framework of the LEPTOI 32913 Project (FEDER INTERREG V program). It includes two small rodent species (Rattus norvegicus and Rattus rattus), their leptospirosis infection status (determined through RT-qPCR or culture on their kidney samples), their GPS location, rainfall information (interpolated from weather stations),...

Géographie de l'économie de plantation durable en Côte d'Ivoire : introduction et soutenabilité de l'agriculture biologique du Cacao dans les terroirs paysans de la zone forestière ivoirienne (2019-2022)

Kouadio Apolinaire Kouassi
Cette opération de recherche correspond à la réalisation d'une thèse sous le thème « Géographie de l'économie de plantation durable en Côte d'Ivoire : introduction et soutenabilité de l'agriculture biologique du Cacao dans les terroirs paysans de la zone forestière ivoirienne » par Kouassi Kouadio Apolinaire à l'Institut de Géographie Tropicale de l'Université Félix Houphouët Boigny (IGT-UFHB), Abidjan Côte d’Ivoire, sous la direction de madame Koffi-Didia Adjoba Marthe, Maître de conférences. La zone de l'étude...

Rainfall dataset of the May 16 2019 flood event in Bamako, Mali

Matias Alcoba Kait, Nogmana Noumaguel & Frederic Cazenave
On May 16 2019, an intense rainfall event led to devastating floods in Bamako, Mali. The Early Flood Warning System (EWS) Rain Cell app Bamako was partially operational. 6 rain gauges, spread over the city, recorded and sent rainfall intensities in real time. This text file contains the rainfall data (millimeters) at 15-minutes times steps collected by the 6 rain gauges (Tab-separated values). Le 16 mai 2019, des précipitations intenses ont provoqué des inondations dévastatrices...

La filière des farines infantiles produites localement dans six pays sahéliens : Burkina Faso, Mali, Mauritanie, Niger, Sénégal, Tchad : rapport de l'étude \"La filière des farines infantiles produites localement dans 6 pays sahéliens\" réalisée de juillet 2019 à janvier 2020

Fanny Olive, Claire Mouquet Rivier , N. Fioroni , A. Bichard, N. Boulle-Martinaud, C. Kaboré, M. Denizeau, N.M. Zagré, A.S Le Dain , N.F. Ndiaye , E.H.K.P Tou & A. Aho

15 minutes flow in the rivers linked to the Aghien lagoon (2015-)

Bamory Kamagate, Luc Seguis, Jean-Louis Perrin, Maurice Guilliod & Serge Ehouman Koffi
To face the difficulties involved in supplying freshwater to Abidjan (Côte d’Ivoire), the Aghien Lagoon is a potential resource for production of drinking water. A hydro-meteorological network was installed with the objective of assessing the sustainability of the lagoon in terms of both quantity and quality. The automatic measurement of the water level is converted into a flow rate by means of a flow height rating curve established by gauging.

Water Quality - Aghien Lagoon and its catchment (Ivory Coast) (2015-2016)

Jean-Louis Perrin, , Séguis Luc, , , Seidel Jean-Luc &
Measurement campaigns of the water quality of the Aghien Lagoon and its main tributaries between 2015 and 2016, carried out under the program "The Aghien lagoon: a sustainable source of drinking water for the city of Abidjan? (2015-2018)" Nine Excel data files corresponding to the 9 sampling sites, containing the results of the 10 measurement campaigns. The list of measured parameters can be viewed in the "ORIESA_MeasuredParameters_ParametresMesures" file associated with the data files.

Simulated peak flow for the May 16 2019 flood event in Bamako, Mali

Christophe Bouvier, Nanée Chahinian, Matias Alcoba Kait, N'dji Dit Jacques Dembélé & Frédéric Cazenave
On May 16 2019, an intense rainfall event led to devastating floods in Bamako (Mali). The Rain Cell app Bamako was partially operational, with 6 rain gauges recording and sending in real time rainfall over the city of Bamako. This raster file in ASCII ESRI format contains peakflow values simulated by the Raincell Bamako App. Maximum peakflow is expressed in liters per seconds. Missing data are coded as -9999. The projection system is EPSG:32629- WGS...

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