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Metadatabase view - dataset: AMAZON FISH database

General information

dataset entry ID:
AF_1
name of the dataset:
full name of the dataset:
AMAZON FISH database
dataset short name:
AMAZON FISH database
type of dataset (more information):
species distribution data
data type:
point data/observation data
short description of the dataset/summary:
The title "AMAZON FISH database" is a working title for the Amazonian Freshwater Fish Biodiversity database that was constructed in the framework of the AMAZON FISH (ERANetLAC/DCC-0210) project.

In order to construct the AMAZON FISH database, which aims to become a high quality freshwater fish biodiversity database covering the entire Amazon drainage basin, data from a wide range of sources were compiled in a central database. The content of this database can be considered as a collection of curated datasets or dataset exports (as the database only covers the Amazon basin, while source datasets may cover larger areas).

These datasets are of different nature and include:
A. Information extracted from the literature (published articles, books, gray literature).
B. Data available from museums/collections and universities.
C. Data held or compiled by project partners (e.g. at country level). Some of these have previously been published through the Global Biodiversity Information Facility (GBIF) network, while others will be released in the framework of AMAZON FISH.
D. Data extracted from online databases such as GBIF, FishNet, SpeciesLink and IABIN.
E. New data obtained during (a) sampling campaign(s) in the framework of the project.

At this stage (December 2018), the database already provides a comprehensive overview of the fish diversity and distribution in the Amazon basin, with over 305.000 occurrence records from 123 sources (mostly covering B, C & D). After the project formally ends, it will still be updated by including new data from the project partners (C), from literature references (A) and potentially by including data from new sampling campaigns (E) to areas for which we identified a gap in the available data.

Through the integration of these different data sources, the AMAZON FISH database constitutes a unique resource on the Amazon basin, which concentrates the highest freshwater biodiversity on earth. By compiling the knowledge on the spatial distribution of freshwater fishes and addressing the taxonomic and sampling gaps, this database should enable comprehensive analysis and modeling. As such it will answer the essential need for understanding this unique ecosystem that has produced such high freshwater fish diversity.
keywords according to GCMD:
topic:
Biosphere, Biological Classification
ISO topic category according to ISO 19115:
Biota, Environment, Inland Waters
INSPIRE keywords according to GEMET:
Species distribution
own science keywords:
freshwater fish, Amazon river drainage, Amazon basin, occurrence database, species distribution
related project:
AMAZON FISH (ERANet-LAC/DCC-0210)
funding:
ERANet-LAC: Network of the European Union, Latin America and the Caribbean Countries on Joint Innovation and Research Activities

Technical and administrative specifications

data format:
others/specify
others/details:
PostgreSQL
operating system:
all operating systems
English
current access level:
restricted access
currently available through GBIF:
no
exchange planned:
no
data in data repository:
no
Do you plan to publish the data on the Freshwater Biodiversity Data Portal:
yes
update level:
update planned
type:
others/specify
others/details:
Data Management Plan (https://doi.org/10.6084/m9.figshare.5150716.v1)
language:
English
contact details:
metadata contact person:
first, last name:
Céline
 
Jézéquel
email:
celine.jezequel@ird.fr
institution:
Institut de Recherche pour le Développement (IRD)
address:
UMR EDB, 118 route de Narbonne
postal code, city:
31000
 
Toulouse
country
France
technical contact person:
Céline
 
Jézéquel
celine.jezequel@ird.fr
institution:
Institut de Recherche pour le Développement (IRD)
address:
UMR EDB, 118 route de Narbonne
postal code, city:
31000 Toulouse
country:
France
scientific contact person:
first, last name:
Thierry
 
Oberdorff
email:
thierry.oberdorff@ird.fr

Intellectual property rights and citation

dataset creator (data compiler):
contact name:
Thierry Oberdorff
contact email:
thierry.oberdorff@ird.fr
contact institution:
Institut de Recherche pour le Développement (IRD), UMR EDB 5174
data contributors to/owners of this dataset:
multiple
number:
20
data contributor/owner 1
contact name:
Thierry Oberdorff
contact email:
thierry.oberdorff@ird.fr
contact institute:
Institut de Recherche pour le Développement (IRD), UMR
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 2
contact name:
Javier A. Maldonado-Ocampo
contact email:
maldonadoj@javeriana.edu.co
contact institute:
Pontificia Universidad Javeriana, Unidad de Ecología y Sistemática (UNESIS)
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 3
contact name:
Hernán Ortega
contact email:
hortega@gmail.com
contact institute:
Museo de Historia Natural, Universidad Nacional Mayor de San Marcos
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 4
contact name:
Aaike De Wever
contact email:
aaike.dewever@naturalsciences.be
contact institute:
Royal Belgian Institute of Natural Sciences (RBINS)
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

comments:
No direct data contributions included. Contribution mainly consisted of technical advise during database construction.
data contributor/owner 5
contact name:
Jansen Zuanon
contact email:
jzuanon3@gmail.com
contact institute:
Instituto Nacional de Pesquisas da Amazônia (INPA)
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 6
contact name:
Gislene Torrente-Vilara
contact email:
gtvilara@gmail.com
contact institute:
Universidade Federal de São Paulo (UNIFESP)
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 7
contact name:
Leandro M. Sousa
contact email:
m.sousa@gmail.com
contact institute:
Universidade Federal do Pará (UFPA)
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 8
contact name:
Jonathan Valdiviezo
contact email:
jonathan.valdiviezo@biodiversidad.gob.ec
contact institute:
Instituto Nacional De Biodiversidad (INABIO) - Ecuador
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 9
contact name:
Jaime Sarmiento
contact email:
jsarmientotavel@gmail.com
contact institute:
Museo Nacional de Historia Natural, Instituto de Ecología
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 10
contact name:
Mabel Maldonado
contact email:
mabelmaldonado.m@fcyt.umss.edu.bo
contact institute:
Universidad Mayor de San Simón, Unidad de Limnología y Recursos Acuáticos (ULRA)
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 11
contact name:
Takayuki Yunoki
contact email:
takayukiyunoki@yahoo.com
contact institute:
Universidad Autónoma del Beni, Centro de Investigación de Recursos Acuáticos
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 12
contact name:
Carlos Donascimiento
contact email:
cdonascimiento@humboldt.org.co
contact institute:
Instituto Alexander von Humboldt (IAvHP)
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 13
contact name:
Edwin Agudelo
contact email:
eagudelo@sinchi.org.co
contact institute:
Instituto Amazónico de Investigaciones Científicas SINCHI (CIACOL)
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 14
contact name:
José Iván Mojica
contact email:
jimojicac@unal.edu.co
contact institute:
Instituto de Ciencias Naturales, Universidad Nacional de Colombia (ICNMHN)
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 15
contact name:
Raúl Ríos Herrera
contact email:
raulriosh@gmail.com
contact institute:
Instituto para la Investigación y la Preservación del Patrimonio Cultural y Natu
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 16
contact name:
Francisco A. Villa-Navarro
contact email:
favilla@ut.edu.co
contact institute:
Universidad del Tolima (CZUT-IC)
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 17
contact name:
Max Hidalgo
contact email:
mhidalgod@unmsm.edu.pe
contact institute:
UNMSM, Peru
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 18
contact name:
Fernando M. Carvajal-Vallejos
contact email:
fernando.carvajal@faunagua.org
contact institute:
FAUNAGUA
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 19
contact name:
Céline Jézéquel
contact email:
celine.jezequel@ird.fr
contact institute:
IRD
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

data contributor/owner 20
contact name:
Pablo A. Tedesco
contact email:
pablo.tedesco@ird.fr
contact institute:
IRD
criteria for using this part of the dataset:
The dataset needs to be requested from dataset creator with specific conditions of use.

citation of this dataset:
author(s):
Jézéquel, C., Tedesco, P. A., Maldonado-Ocampo, J. A., Prada-Pedreros, S., Ortega, H., Hildalgo, M., Martens, K., De Wever, A., Zuanon, J., Torrente-Vilara, G., Sousa, L. M., Guiarrizzo, T., Valdiviezo, J., Sarmiento, J., Maldonado, M., Carvajal-Vallejos, F. M., Yunoki, T., Donascimiento, C., Agudelo, E., Mojica, J. I., Herrera, R. R., Villa, F. & Oberdorff, T.
title and journal (name, number, pages):
The Amazon Fish database: freshwater fish distribution for the entire Amazon drainage
year:
2019
citation of the metadata:
author(s):
Jézéquel C., Tedesco P. A., Maldonado-Ocampo J. A., Prada-Pedreros S., Ortega H., Hildalgo M., Martens K., De Wever A., Zuanon J., Torrente-Vilara G., Sousa L. M., Guiarrizzo T., Valdiviezo J., Sarmiento J., Maldonado M., Carvajal-Vallejos F. M., Yunoki T., Donascimiento C., Agudelo E., Mojica J. I., Herrera R. R., Villa F. & Oberdorff T.
title and journal (name, number, pages):
Metadata description of the AMAZON FISH database. Freshwater Metadata Journal 43: 1-9
year:
2019
doi (if applicable):
https://doi.org/10.15504/fmj.2019.43
comments:
The AMAZON FISH database integrates a wide range of datasets from different public and project partners sources, and results from a three years international team effort.

The entire, curated database at the sub-basins scale (modified HydroBASINS dataset) will be documented and released in a data paper that should be submitted during the year 2019. All occurrence records (point scale data) for which we obtained permission for public release will be made available through the AMAZON FISH data online repository or through the Freshwater Biodiversity Portal (http://data.freshwaterbiodiversity.eu/; which is a member of the Freshwater Information Platform). The release of the occurrence records will be effective three years after the official publication of the data paper, a timeframe considered sufficient to publish the analyses suggested in the initial AMAZON FISH projet. During this embargo period, site scale data may be available on request pending agreement of all partners and with authorship negotiation possible.

The sub-basins scale data paper will include an extensive database description along with a discussion on the database content, gap analysis and database statistics, in parallel with the on-line release of the database at the sub-basins scale.

In addition to the publication of the datasets and database itself, key maps produced during the AMAZON FISH project will be disseminated through the Global Freshwater Biodiversity Atlas (http://atlas.freshwaterbiodiversity.eu/) following the publication of scientific paper(s) describing those results.

General data specifications

regional coverage of the dataset:
spatial extent of the dataset:
catchment
continents:
South America
spatial extent (bounding coordinates):
southernmost latitude [°]:
-25
northernmost latitude [°]:
5
westernmost longitude [°]:
-85
easternmost longitude [°]:
-45
        
minimum altitude:
0
 
metres
maximum altitude:
6200
 
metres
countries:
South America: Bolivia, Brazil, Colombia, Ecuador, Peru, Venezuela
world climatic regions according to Köppen:
Group A: tropical/megathermal climates
freshwater ecoregions of the world (FEOW) according to WWF:
 
South America:
Amazonas Estuary & Coastal Drainages, Amazonas Guiana Shield, Amazonas High Andes, Amazonas Lowlands, Guapore - Itenez, Madeira Brazilian Shield, Mamore - Madre de Dios Piedmont, Rio Negro, Tapajos - Juruena, Ucayali - Urubamba Piedmont, Western Amazon Piedmont, Xingu
ecosystem type:
rivers, wetlands
covered timeframe:
year from
1865
 
year to:
2017

Site specifications

coordinate system/grid data:
latitude/longitude
projected
datum (e.g. WGS84):
WGS84
grid data available:
no
 
number of sites:
>1000
exact number of sites:
22000

Biological data

biological data origin:
from sampling
specify project:
AMAZON FISH project ERANetLAC/DCC-0210
specify method:
comments:
Timeframe of the sampled sites: 1865 to 2017.
organism group addressed:
fish

Sample resolution

fish

taxonomic resolution:
species
percentage of species level data:
100
taxonomic coding:
taxalist according to:
FishBase & California Academy of Sciences-Catalogue of Fishes
reference(s):
Fricke, R., Eschmeyer, W. & Van der Laan, R. (2018). Catalog of Fishes: Genera, Species, References. http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp Froese, R. & Pauly, D. (2018). FishBase. World Wide Web electronic publication. www.fishbase.org
sample specifications:

Other specifications

GIS layers, shape files related to the dataset:
catchments, river-sub-basins
others/details:
Modified version of HydroBASINS.
availability of photos:
no
availability of maps:
no
quality control procedures:
Were any quality control procedures applied to your dataset?
yes
quality control protocols and comments:
To avoid any duplication when integrating data from different sources, all duplicates are identified and excluded during import by either verifying unique identifiers for occurrences (or fields that should constitute unique identifiers when considered together; e.g. institute + collection + collection number) or based on sampling details in combination with the geographical coordinates of the data.

Where available, details on provenance, citation, along with a modification/"last updated" timestamp (e.g. only available for GBIF and SpeciesLink) are systematically documented for the retained records.

In addition, during import, each record is systematically checked for reliability and consistency, using the FishBase Consortium database, and the California Academy of Science's Catalog of Fishes, as nomenclature authority files. During the process of building the database, a taxonomic checklist work is achieved to validate all species actually present in the Amazon drainage basin. This important work is done in collaboration with taxonomic experts covering all groups and will be made publicly available through a checklist publication.
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