http://lod.bco-dmo.org/id/dataset/991175
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2026-01-08
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Cleaned species occurrence data from 2005 to 2025 from GBIF as part of a workflow to assemble species and community temperature indices for Port Fourchon, LA in 2006, 2016, 2022 and 2023
2026-01-08
publication
2026-01-08
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2026-04-14
publication
https://doi.org/10.26008/1912/bco-dmo.991175.1
James Nelson
University of Georgia
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Nelson, J. (2026) Cleaned species occurrence data from 2005 to 2025 from GBIF as part of a workflow to assemble species and community temperature indices for Port Fourchon, LA in 2006, 2016, 2022 and 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-01-08 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.991175.1 [access date]
Dataset Description: <p>This is one of four datasets that were produced with the "Fourchon Nekton Turnover Workflow"&nbsp; (v1.0.0, doi: https://doi.org/10.5281/ZENODO.18165331). The datasets and supplemental data produced by this workflow have had minor modifications to enhance the interoperability of the data (See more in section "BCO-DMO Processing"). The workflow contains the exact formats of the data files produced and used by the workflow scripts. It also contains scripts, configurations, readme files, and input/output files for four stages listed below. Each workflow stage corresponds to a dataset in the "Related Datasets" section.<br />
<br />
"Fourchon Nekton Turnover Workflow" steps with corresponding dataset IDs:</p>
<ul>
<li>"1_raw_data" = includes raw drop-sampling data corresponding to BCO-DMO dataset 991168&nbsp;(doi: 10.26008/1912/bco-dmo.991168.1)</li>
<li>"2_gbif_workflow" = includes&nbsp;GBIF species observation data&nbsp;corresponding to metadata in BCO-DMO dataset 991175&nbsp;(doi:&nbsp;10.26008/1912/bco-dmo.991175.1)</li>
<li>"3_CTI_calculations" = includes community temperature index (CTI) data corresponding to BCO-DMO dataset 941250&nbsp;(doi: 10.26008/1912/bco-dmo.941250.1)</li>
<li>"4_species_of_interest" = includes&nbsp;the results of a species pool analysis identifying species of interest&nbsp;corresponding to BCO-DMO dataset 991182 (doi:&nbsp;10.26008/1912/bco-dmo.991182.1)</li>
</ul>
<p>The workflow release (v1.0.0) contains data and scripts used to run analyses and produce figures for publication Leavitt, H; Thomas, A; Doerr, J; Johnson, D; Nelson, J. (In press) Resilient Nekton Composition in the Face of Climate-Driven Foundation Species Shifts. Ecology. Accepted 2025-11-14<br />
<br />
This dataset maintains the original source data licenses and rightsHolders specified at GBIF within the main dataset table 991175_v1_port-fourchon_cleaned-occurrence.csv. See the data user agreement and citation guidelines at GBIF:<br />
GBIF Data User Agreement: https://www.gbif.org/terms/data-user&nbsp;&nbsp;<br />
GBIF data usage and citation guidelines: https://www.gbif.org/citation-guidelines</p> Methods and Sampling: <p>We downloaded all human observations and preserved specimens for each of the species observed from 2005 to the access date in 2025 from the Global Biodiversity Information Facility (GBIF)(Accessed on 6/6/2025).&nbsp; &nbsp;See query parameters in supplemental file "gbif_source_metadata.csv."<br />
<br />
Species occurrence records were downloaded from GBIF using the&nbsp;<span style="font-size:13px">Interface to the Global Biodiversity Information&nbsp;Facility API (rgbif API, https://github.com/ropensci/rgbif; doi: 10.5281/zenodo.1045299)</span>&nbsp;and subjected to a multi-stage quality-control workflow prior to analysis.&nbsp; See Supplemental File "gbif_source_metadata.csv" for citations for each derived data query. Only post-2005 human observation records with valid geographic coordinates and no flagged geospatial issues were retained. Records lacking coordinates or returned as empty downloads were excluded.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2418012 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2418012
completed
James Nelson
University of Georgia
jimmy.nelson@uga.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
GBIF_query_doi
gbifID
datasetKey
occurrenceID
kingdom
phylum
class
order
family
genus
species
infraspecificEpithet
taxonRank
scientificName
verbatimScientificName
verbatimScientificNameAuthorship
countryCode
locality
stateProvince
occurrenceStatus
individualCount
publishingOrgKey
decimalLatitude
decimalLongitude
coordinateUncertaintyInMeters
coordinatePrecision
elevation
elevationAccuracy
depth
depthAccuracy
eventDate
day
month
year
taxonKey
speciesKey
AphiaID
LSID
basisOfRecord
institutionCode
collectionCode
catalogNumber
recordNumber
identifiedBy
dateIdentified
license
rightsHolder
recordedBy
typeStatus
establishmentMeans
lastInterpreted
mediaType
issue
theme
None, User defined
external_link
accession number
occurrence identifier
kingdom
phylum
taxonomic class
order
family
genus
species_epithet
sample description
The taxonomic rank of the most specific name in scientific name
taxon
site description
occurrence status (presence or absence)
count
latitude
longitude
coordinate uncertainty radius
No BCO-DMO term
sea surface elevation
depth
date
day of month
month of year
year
taxon_code
Life Science Identifier (LSID)
person name
brief description
sample type
quality flag
featureType
BCO-DMO Standard Parameters
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
CAREER: Integrating Seascapes and Energy Flow: learning and teaching about energy, biodiversity, and ecosystem function on the frontlines of climate change
http://www.nelsonecolab.net/career
CAREER: Integrating Seascapes and Energy Flow: learning and teaching about energy, biodiversity, and ecosystem function on the frontlines of climate change
<p><em>NSF Award Abstract:</em><br />
Coastal marshes provide a suite of vital functions that support natural and human communities. Humans frequently take for granted and exploit these ecosystem services without fully understanding the ecological feedbacks, linkages, and interdependencies of these processes to the wider ecosystem. As demands on coastal ecosystem services have risen, marshes have experienced substantial loss due to direct and indirect impacts from human activity. The rapidly changing coastal ecosystems of Louisiana provide a natural experiment for understanding how coastal change alters ecosystem function. This project is developing new metrics and tools to assess food web variability and test hypotheses on biodiversity and ecosystem function in coastal Louisiana. The research is determining how changing habitat configuration alters the distribution of energy across the seascape in a multitrophic system. This work is engaging students from the University of Louisiana Lafayette and Dillard University in placed-based learning by immersing them in the research and local restoration efforts to address land loss and preserve critical ecosystem services. Students are developing a deeper understanding of the complex issues facing coastal regions through formal course work, directed field work, and outreach. Students are interacting with stakeholders and managers who are currently battling coastal change. Their directed research projects are documenting changes in coastal habitat and coupling this knowledge with the consequences to ecosystems and the people who depend on them. By participating in the project students are emerging with knowledge and training that is making them into informed citizens and capable stewards of the future of our coastal ecosystems, while also preparing them for careers in STEM. The project is supporting two graduate students and a post-doc.</p>
<p>The transformation and movement of energy through a food web are key links between biodiversity and ecosystem function. A major hurdle to testing biodiversity ecosystem function theory is a limited ability to assess food web variability in space and time. This research is quantifying changing seascape structure, species diversity, and food web structure to better understand the relationship between biodiversity and energy flow through ecosystems. The project uses cutting edge tools and metrics to test hypotheses on how the distribution, abundance, and diversity of key species are altered by ecosystem change and how this affects function. The hypotheses driving the research are: 1) habitat is a more important indirect driver of trophic structure than a direct change to primary trophic pathways; and 2) horizontal and vertical diversity increases with habitat resource index. Stable isotope analysis is characterizing energy flow through the food web. Changes in horizontal and vertical diversity in a multitrophic system are being quantified using aerial surveys and field sampling. To assess the spatial and temporal change in food web resources, the project is combining results from stable isotope analysis and drone-based remote sensing technology to generate consumer specific energetic seascape maps (E-scapes) and trophic niche metrics. In combination these new metrics are providing insight into species’ responses to changing food web function across the seascape and through time.</p>
<p>This project is jointly funded by Biological Oceanography and the Established Program to Stimulate Competitive Research (EPSCoR).</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Louisiana E-scapes
largerWorkCitation
project
eng; USA
oceans
-90.244
-90.16
29.095
29.168
2005-01-01
2025-01-01
Saltmarsh ecosystem near Port Fourchon, LA
0
BCO-DMO catalogue of parameters from Cleaned species occurrence data from 2005 to 2025 from GBIF as part of a workflow to assemble species and community temperature indices for Port Fourchon, LA in 2006, 2016, 2022 and 2023
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/996593.rdf
Name: GBIF_query_doi
Units: unitless
Description: <p>DOI representing each GBIF database query. Each species was queried indevidually. DOI was generated by the rgbif API</p>
http://lod.bco-dmo.org/id/dataset-parameter/996594.rdf
Name: gbifID
Units: unitless
Description: <p>Unique GBIF key for the occurrence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996595.rdf
Name: datasetKey
Units: unitless
Description: <p>The UUID of the GBIF dataset containing this occurrence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996596.rdf
Name: occurrenceID
Units: unitless
Description: <p>An identifier for the dwc:Occurrence (as opposed to a particular digital record of the dwc:Occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the dwc:occurrenceID globally unique.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996597.rdf
Name: kingdom
Units: unitless
Description: <p>The kingdom name (excluding authorship) for the kingdom from the GBIF backbone matched to this occurrence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996598.rdf
Name: phylum
Units: unitless
Description: <p>The phylum name (excluding authorship) for the phylum from the GBIF backbone matched to this occurrence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996599.rdf
Name: class
Units: unitless
Description: <p>The class name (excluding authorship) for the class from the GBIF backbone matched to this occurrence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996600.rdf
Name: order
Units: unitless
Description: <p>The order name (excluding authorship) for the order from the GBIF backbone matched to this occurrence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996601.rdf
Name: family
Units: unitless
Description: <p>The family name (excluding authorship) for the family from the GBIF backbone matched to this occurrence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996602.rdf
Name: genus
Units: unitless
Description: <p>The genus name (excluding authorship) for the genus from the GBIF backbone matched to this occurrence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996603.rdf
Name: species
Units: unitless
Description: <p>The species name (excluding authorship) for the species from the GBIF backbone matched to this occurrence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996604.rdf
Name: infraspecificEpithet
Units: unitless
Description: <p>The infraspecific name part of the species name from the GBIF backbone matched to this occurrence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996605.rdf
Name: taxonRank
Units: unitless
Description: <p>The taxonomic rank of the most specific name in the scientificName.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996606.rdf
Name: scientificName
Units: unitless
Description: <p>The scientific name (including authorship) for the taxon from the GBIF backbone matched to this occurrence. This could be a synonym, see also acceptedScientificName.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996607.rdf
Name: verbatimScientificName
Units: unitless
Description: <p>Scientific name as provided by the source.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996608.rdf
Name: verbatimScientificNameAuthorship
Units: unitless
Description: <p>The authorship information for the dwc:scientificName formatted according to the conventions of the applicable dwc:nomenclaturalCode.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996609.rdf
Name: countryCode
Units: unitless
Description: <p>The 2-letter country code (as per ISO-3166-1) of the country, territory or area in which the occurrence was recorded.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996610.rdf
Name: locality
Units: unitless
Description: <p>The specific description of the place.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996611.rdf
Name: stateProvince
Units: unitless
Description: <p>The name of the next-smaller administrative region than country (state, province, canton, department, region, etc.) in which the occurrence occurs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996612.rdf
Name: occurrenceStatus
Units: unitless
Description: <p>A statement about the presence or absence of a Taxon at a Location. For definitions, see the GBIF occurrence status vocabulary.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996613.rdf
Name: individualCount
Units: unitless
Description: <p>The number of individuals present at the time of the Occurrence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996614.rdf
Name: publishingOrgKey
Units: unitless
Description: <p>The UUID of the organization which publishes the dataset containing this occurrence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996615.rdf
Name: decimalLatitude
Units: unitless
Description: <p>The geographic latitude (in decimal degrees, using the WGS84 datum) of the geographic centre of the location of the occurrence</p>
http://lod.bco-dmo.org/id/dataset-parameter/996616.rdf
Name: decimalLongitude
Units: decimal degrees
Description: <p>The geographic longitude (in decimal degrees, using the WGS84 datum) of the geographic centre of the location of the occurrence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996617.rdf
Name: coordinateUncertaintyInMeters
Units: meters
Description: <p>The horizontal distance (in metres) from the given decimalLatitude and decimalLongitude describing the smallest circle containing the whole of the Location.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996618.rdf
Name: coordinatePrecision
Units: decimal degrees
Description: <p>A decimal representation of the precision of the coordinates given in the decimalLatitude and decimalLongitude.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996619.rdf
Name: elevation
Units: meters
Description: <p>Elevation (altitude) in metres above sea level. This is not a current Darwin Core term.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996620.rdf
Name: elevationAccuracy
Units: meters
Description: <p>The value of the potential error associated with the elevation. This is not a current Darwin Core term.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996621.rdf
Name: depth
Units: meters
Description: <p>Depth in metres below sea level. This is not a current Darwin Core term.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996622.rdf
Name: depthAccuracy
Units: meters
Description: <p>The value of the potential error associated with the depth. This is not a current Darwin Core term.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996623.rdf
Name: eventDate
Units: unitless
Description: <p>The date-time during which an Event occurred. For occurrences, this is the date-time when the event was recorded. Not suitable for a time in a geological context.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996624.rdf
Name: day
Units: day
Description: <p>The integer day of the month on which the Event occurred.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996625.rdf
Name: month
Units: month
Description: <p>The integer month in which the Event occurred.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996626.rdf
Name: year
Units: year
Description: <p>The four-digit year in which the event occurred, according to the Common Era calendar.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996627.rdf
Name: taxonKey
Units: unitless
Description: <p>A taxon key from the GBIF backbone for the most specific (lowest rank) taxon for this occurrence. This could be a synonym, see acceptedTaxonKey.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996628.rdf
Name: speciesKey
Units: unitless
Description: <p>A taxon key from the GBIF backbone for the species of thisoccurrence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996629.rdf
Name: AphiaID
Units: unitless
Description: <p>AphiaID of the species matched to this occurance. Used by WorMS as a unique species identifier to query and link data</p>
http://lod.bco-dmo.org/id/dataset-parameter/996630.rdf
Name: LSID
Units: unitless
Description: <p>Life Science Identifyer (LSID) of the species matched to this occurrence. This is used by the ZooBank registry as a unique digital signature for a taxa</p>
http://lod.bco-dmo.org/id/dataset-parameter/996631.rdf
Name: basisOfRecord
Units: unitless
Description: <p>The values of the Darwin Core term Basis of Record which can apply to occurrences.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996632.rdf
Name: institutionCode
Units: unitless
Description: <p>The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996633.rdf
Name: collectionCode
Units: unitless
Description: <p>The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996634.rdf
Name: catalogNumber
Units: unitless
Description: <p>An identifier (preferably unique) for the record within the data set or collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996635.rdf
Name: recordNumber
Units: unitless
Description: <p>An identifier given to the dwc:Occurrence at the time it was recorded. Often serves as a link between field notes and a dwc:Occurrence record, such as a specimen collector's number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996636.rdf
Name: identifiedBy
Units: unitless
Description: <p>A list (concatenated and separated) of names of people, groups, or organizations who assigned the Taxon to the occurrence. Note (may contain non-standard characters, emojis, etc. as some are usernames from identification platforms like iNaturalist).</p>
http://lod.bco-dmo.org/id/dataset-parameter/996637.rdf
Name: dateIdentified
Units: unitless
Description: <p>The date on which the subject was determined as representing the Taxon. ISO 8601 Date.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996638.rdf
Name: license
Units: unitless
Description: <p>License for the original source data at GBIF for the occurrence record. See GBIF data usage and citation guidelines: <a href="https://www.gbif.org/citation-guidelines">https://www.gbif.org/citation-guidelines</a></p>
http://lod.bco-dmo.org/id/dataset-parameter/996639.rdf
Name: rightsHolder
Units: unitless
Description: <p>Rights holder for the original source data at GBIF for the occurrence record. Note (may contain non-standard characters, emojis, etc. as some are usernames from identification platforms like iNaturalist).</p>
http://lod.bco-dmo.org/id/dataset-parameter/996640.rdf
Name: recordedBy
Units: unitless
Description: <p>A person, group, or organization responsible for recording the original occurrence. Note (may contain non-standard characters, emojis, etc. as some are usernames from identification platforms like iNaturalist).</p>
http://lod.bco-dmo.org/id/dataset-parameter/996641.rdf
Name: typeStatus
Units: unitless
Description: <p>A list (concatenated and separated) of nomenclatural types (type status, typified scientific name, publication) applied to the occurrence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996642.rdf
Name: establishmentMeans
Units: unitless
Description: <p>Statement about whether an organism or organisms have been introduced to a given place and time through the direct or indirect activity of modern humans.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996643.rdf
Name: lastInterpreted
Units: unitless
Description: <p>The time this occurrence was last processed by GBIF's interpretation system Pipelines.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996644.rdf
Name: mediaType
Units: unitless
Description: <p>The media type given as Dublin Core type values, in particular StillImage, MovingImage or Sound.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996645.rdf
Name: issue
Units: unitless
Description: <p>A specific interpretation issue found during processing and interpretation of the record.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
https://doi.org/10.26008/1912/bco-dmo.991175.1
download
onLine
dataset
<p>We downloaded all human observations and preserved specimens for each of the species observed from 2005 to the access date in 2025 from the Global Biodiversity Information Facility (GBIF)(Accessed on 6/6/2025).&nbsp; &nbsp;See query parameters in supplemental file "gbif_source_metadata.csv."<br />
<br />
Species occurrence records were downloaded from GBIF using the&nbsp;<span style="font-size:13px">Interface to the Global Biodiversity Information&nbsp;Facility API (rgbif API, https://github.com/ropensci/rgbif; doi: 10.5281/zenodo.1045299)</span>&nbsp;and subjected to a multi-stage quality-control workflow prior to analysis.&nbsp; See Supplemental File "gbif_source_metadata.csv" for citations for each derived data query. Only post-2005 human observation records with valid geographic coordinates and no flagged geospatial issues were retained. Records lacking coordinates or returned as empty downloads were excluded.</p>
Specified by the Principal Investigator(s)
<p>We further filtered occurrences to retain only records with an occurrence status of “present” and removed fossil and captive/living specimen records. Spatial accuracy was enforced by removing records with coarse coordinate precision (&gt;0.01 degrees) or large coordinate uncertainty, using a threshold of 1,000 m for most taxa and a relaxed threshold of 30,000 m for threatened taxa to avoid disproportionate data loss. Records with known placeholder or erroneous uncertainty values (e.g., 301, 999, 9999, 3036 m) and records with zero latitude or longitude were also removed.</p>
<p>To reduce common spatial artifacts, we applied automated coordinate cleaning using the <em>CoordinateCleaner</em> framework (Zizka et. al, 2023), excluding records falling within 2 km buffers of country centroids, capital cities, and known biodiversity institutions. Finally, duplicate records were removed based on identical longitude, latitude, species key, and dataset key combinations. The resulting cleaned datasets were saved for downstream analyses, and all GBIF download DOIs or citations were archived to ensure reproducibility and data provenance.</p>
<hr />
<p><br />
This dataset corresponds to Step&nbsp;"2_gbif_workflow"&nbsp;of the study's processing workflow&nbsp;'Fourchon Nekton Turnover Workflow',&nbsp;doi: 10.5281/zenodo.18165331).&nbsp; See "Description" and "BCO-DMO Processing" sections for context about the relationship between the workflow files and the data as published at BCO-DMO.</p>
<h1 dir="auto">Workflow README for Step "2_gbif_workflow" :<br />
Step 2: GBIF Downloads and Cleaning</h1>
<h2 dir="auto">Abstract</h2>
<p dir="auto">This step assembles GBIF occurrence records for all taxa detected in the Port Fourchon nekton surveys, cleans spatial artifacts, and delivers per-taxon CSVs ready for thermal niche extraction. The workflow expands harmonized taxon names into GBIF queries, submits authenticated bulk downloads, filters out problematic coordinates and land points, and documents all DOI citations needed for downstream analyses and reporting.</p>
<p dir="auto">Purpose: fetch occurrence data for target taxa, apply coordinate/data-quality filters, and save cleaned per-taxon CSVs with citation logs.</p>
<p dir="auto">Primary script</p>
<ul dir="auto">
<li dir="auto">gbif_download_BCODMO.R: annotated script that expands pooled taxa, submits GBIF downloads, cleans coordinates (CoordinateCleaner), and logs citations/DOIs.</li>
</ul>
<p dir="auto">Inputs</p>
<ul dir="auto">
<li dir="auto">../1_raw_data/outputs/presence_pivot_merged_sp.csv: taxon list used to build download targets.</li>
<li dir="auto">Environment variables:&nbsp;GBIF_USER,&nbsp;GBIF_EMAIL,&nbsp;GBIF_PWD&nbsp;for GBIF API access.</li>
</ul>
<p dir="auto">Outputs</p>
<ul dir="auto">
<li dir="auto">gbif_downloads/clean_csvs/&lt;taxon&gt;_clean.csv: cleaned occurrences per taxon.&nbsp;&nbsp;</li>
<li dir="auto">gbif_citations.txt: citations/DOIs for all downloads.</li>
</ul>
<p dir="auto">Software</p>
<ul dir="auto">
<li dir="auto">R &gt;= 4.3 with rgbif, tidyverse, terra, sp, sdmpredictors, CoordinateCleaner.</li>
</ul>
<p dir="auto">Run order</p>
<ol dir="auto">
<li dir="auto">Ensure Step 1 outputs are present.</li>
<li dir="auto">Set GBIF credentials in the environment.</li>
<li dir="auto">Run&nbsp;gbif_download_BCODMO.R; verify cleaned CSVs and&nbsp;gbif_citations.txt.</li>
</ol>
Specified by the Principal Investigator(s)
Version 1 (2026-01-08):
Data from the processing workflow were prepared and published at BCO-DMO after reorganization into datasets with minor changes performed to meet the required conventions implemented by BCO-DMO designed for interoperability, standardization, and a variety of data access methods.
Main data table "991175_v1_port-fourchon_cleaned-occurrence.csv" was created by merging submitted files.
Submitted folder "Fourchon Nekton Turnover Workflow/clean_csvs/" contained 75 csv files named with <sciname>_clean.csv (one per species, a file per GBIF query, see gbif_source_metadata.csv). These were imported into the BCO-DMO data system, concatenated and additional columns added (GBIF_query_doi, AphiaID, LSID). Empty columns removed, columns subselected. The original format of the "Fourchon Nekton Turnover Workflow/clean_csvs/" is available in the Workflow package (doi: 10.5281/zenodo.18165331).
Submitted data files for this dataset correspond to the study's outputs in workflow (doi: 10.5281/zenodo.18165331) step 2:
The supplemental file "gbif_source_metadata.csv" contains additional information about the source GBIF data that was obtained by using the GBIF DOIs contained within workflow file "Fourchon Nekton Turnover Workflow/2_gbif_workflow/gbif_citations.txt" and adding additional information provided by the following APIs on 2026-01-09:
GBIF_API = "https://api.gbif.org/v1"
WORMS_API = "https://www.marinespecies.org/rest"
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact