oih/oih-wis2 huggingface dataset:
KUBI Ichthyology Collection

Keywords: ichthyology, Kansas, Occurrence, USA, Specimen, Specify Software, fish
Temporal coverage: 1882/2019

The University of Kansas Ichthyology collection contains more than 680,000 specimens of fishes from around the world and is the basis of the research and educational activities of the Division of Ichthyology. The collection has an emphasis on freshwater fishes of the central United States and also has significant marine and estuarine collections. The fish collection has representation from 3171 taxa (297 families and 1262 genera) and 79 countries including Ecuador, Fiji, Mexico, Nepal, Nicaragua and various marine localities. The collections and the scope of research activities in the division continue to grow due to the ongoing activities of ichthyology staff and students.

The collection is used by national and international researchers as well as by state and federal agencies. The Division of Ichthyology is designated as a Regional Center in the Midwest and Great Plains Regions (Collette &amp; Lachner 1976, Copeia 1976: 625-642; Poss and Collette 1995, Copeia 1995: 48-70) and is among the top twenty ichthyological collections in the country. Almost 60% of the specimens in the collection are from the Great Plains Region. The collection is an important resource for anyone interested in the region's fishes. The data concerning these faunas are not extensively duplicated by other ichthyological collections.

The Ichthyology collection comprises whole, wet, voucher specimens in 70% ethanol (98%), specimens maintained as dry skeletons (0.3%) and cleared and stained preparations in glycerine (1.7%). Other ancillary collections include a large slide and digital image collection of specimens and locations (some of which are linked to specimen records through the database), a large field note collection and a map collection.

The wet specimens are housed in a state-of-the-art fluid collection facility, opened in 1996. The facility has 2,400 square feet of collection storage space on four floors and is shared with Herpetology, Mammalogy, Ornithology, Entomology and Invertebrate Zoology. The collection storage environment is maintained at 65°F year-round by an HVAC system. Specimens are housed in state of the art glassware and stainless steel tanks and protected by a sprinkler fire suppression system and UV-shielded lighting. The division has both morphological research facilities and a shared molecular systematic laboratory.
CRED Rapid Ecological Assessment of Benthic Habitat Cover in the Pacific Ocean 2005-2010

Keywords: Occurrence, Observation
Temporal coverage: 2005/2010

When the Pacific Islands Fisheries Science Center established the Coral Reef Ecosystems Division (CRED) in 2001, the Center initiated a program to extend habitat mapping in the U.S. Pacific Islands into deeper water that cannot be readily mapped using satellite and aerial techniques. Since that time NOAA Fisheries has led the effort to map these deeper reefs using ship-based acoustic mapping systems, coupled with video and still-camera observations. These sonar and optical data are combined with the IKONOS-based data products and oceanographic information to provide integrated products that describe the benthic habitats of the Pacific Islands.
Coral Reef Evaluation and Monitoring Project Florida Keys 1996

Keywords: biogeographic, biology, dry tortugas, fwc-fwri, institute, occurrenceID, project, record, siteid, station, status, system, taxon_rank, taxonomic, time, authorship_information, accepted_authorship_information, percent_coverage, absence, area, coral, habitatid, keys, latitude, longitude, monitoring, name, recorded, species, data_set_identification, authorship, basis of record, class, comprehensive, conservation, coverage, data, date, fish, hierarchy, large, obis, reef, sample, scientific_name, statement, worms, taxonomic_status, array-data, database, eventID, eventdate, family, fwri, gulf of mexico, occurrence, register, revisited, scientific, scientificname, taxon, taxon_status, unaccepted, v2.3, aphia_database_identification_number, scientificnameid, about, basisOfRecord, data_set_name, dataset, florida, identification, marine, organism, rank, recordedBy, samples, subregionid, usage, vernacular, vernacularName, wildlife, acceptedNameUsageID, organism_per_sample_area, acceptedNameAuthorship, acceptedNameUsage, accepted, aphia, array, common, datasetName, florida keys, identifier, ocean, order, percent, sitecode, stewardship, taxonomy, scientificNameAuthorship, occurrence_identification, coral monitoring, cremp, evaluation, fwc, genus, information, meters, number, per, presence, species_name, specificEpithet, taxonRank, vernacular_name, world, year, organismQuantity, accepted_name_usage, organismQuantityType, Samplingevent, basis, commission, event, kingdom, phylum, research, set, square, taxonomicStatus, value, associatedreferences, accepted_aphia_database_identification_number, occurrenceStatus
Temporal coverage: 1996/1996

The purpose of the Coral Reef Evaluation and Monitoring Project (CREMP) is to monitor the status and trends of selected reefs in the Florida Keys National Marine Sanctuary(FKNMS). CREMP assessments have been conducted annually at fixed sites since 1996 and data collected provides information on the temporal changes in benthic cover and diversity of stony corals and associated marine flora and fauna. The core field methods continue to be underwater videography and timed coral species inventories. Findings presented in this report include data from 109 stations at 37 sites sampled from 1996 through 2008 in the Florida Keys and 1999 through 2008 in the Dry Tortugas. The report describes the annual differences (between 2007 and 2008) in the percent cover of major benthic taxa (stony corals, octocorals, sponges, and macroalgae), mean coral species richness and the incidence of stony coral conditions. Additionally, it examines the long-term trends of the major benthic taxa, five coral complex, Montastraea cavernosa, Colpophyllia natans, Siderastrea siderea, and Porites astreoides) and the clionaid sponge, Cliona delitrix.
AMAPPS Southeast Aerial Cruise Winter 2015

Keywords: Occurrence,Marine Animal Survey,Marine Biology,Marine mammals,Sea turtles,Visual Sighting,Aircraft, Occurrence, Observation
Temporal coverage: 2015/2015

Original provider:
NOAA Southeast Fisheries Science Center (SEFSC)

Dataset credits:
NOAA Southeast Fisheries Science Center (SEFSC)

Abstract:
As part of the AMAPPS program, the Southeast Fisheries 
Science Center conducts aerial surveys of continental 
shelf waters along the US east coast from Cape Canaveral, 
Florida to Cape May, New Jersey. The survey was conducted 
during 2015 between 23 January and 3 March. It was 
conducted along tracklines oriented perpendicular to the 
shoreline that were latitudinally spaced 20 km apart 
aboard a NOAA Twin Otter aircraft at an altitude of 600 
feet (183 m) and a speed of 110 knots. The survey was 
designed for analysis using Distance sampling and a two-
team (independent observer) approach to correct for 
visibility bias in resulting abundance estimates.
The survey covered waters from Cape May, NJ to Cape 
Canaveral, FL including “fine-scale” tracklines in waters 
offshore of New Jersey. The majority of survey effort 
occurred in waters from Cape Hatteras, NC and south. Due 
to weather conditions during the survey, a few areas of 
the study area were not surveyed.

Purpose:
The goal of the survey was to conduct line-transect surveys 
using the Distance sampling approach to estimate the 
abundance and spatial distribution of marine mammals and 
turtles in waters over the continental shelf (shoreline to 
200m isobaths) from Florida to New Jersey.

Supplemental information:
Perpendicular distance to the animal is not publicly 
available.
The dataset is accompanied by transect (effort) data 
which is provided as a separate file. 
Data were further audited in 2018 since publication of 
Annual Report in 2015.

Sightings included were detected on-effort by the forward 
team only; you may request the full dataset and sightings 
including opportunistic ones directly to the provider.

Environmental Attribute Codes
Beaufort Sea state
0 Calm, mirror like seas
1 Waves &lt;1ft, rippled surface
2 Small wavelets (&lt;2 ft), no white caps
3 Large wavelets (&lt;3ft), scattered white caps
4 Swell 3-4 ft, numerous white caps
5 Swell &gt;5 ft, many white caps, some spray
6 Swell &gt;10 ft, white caps everywhere, spray
CloudCover
0 Clear
1 0-25% Cloudy
2 26-50% Cloudy
3 51-75% Cloudy
4 76-100% Cloudy
5 Overcast
Glare
0 No Glare
1 &lt;10% of visual field
2 10-25% of visual field
3 25-50% of visual field
4 50-75% of visual field
5 &gt;75% of visual field
Weather
0 Clear
1 Mist
2 Light Rain
3 Heavy Rain
Visibility
0 Clear
1 Good
2 Fair
3 Poor
Haze
0 No
1 Yes
Fog
0 No
1 Yes
Sun penetration (Sun pen)
0 Poor
1 Fair
2 Good
3 Excellent
Turbidity
0 Poor
1 Fair
2 Good
3 Excellent
LBBG_ZEEBRUGGE - Lesser black-backed gulls (Larus fuscus, Laridae) breeding at the southern North Sea coast (Belgium and the Netherlands) [subsampled representation]

Keywords: Observation, altitude, Occurrence, temperature, accelerometer, birds, gps tracking, UvA-BiTS, biologging, LifeWatch, frictionlessdata, animal movement, Movebank, animal tracking
Temporal coverage: 2013/2021

This animal tracking dataset is derived from Stienen et al. (2022, <a href="https://doi.org/10.5281/zenodo.6579497">https://doi.org/10.5281/zenodo.6579497</a>) a deposit of Movebank study <a href="https://www.movebank.org/cms/webapp?gwt_fragment=page=studies,path=study985143423">985143423</a>. Data have been standardized to Darwin Core using the <a href="https://inbo.github.io/movepub/">movepub</a> R package and are downsampled to the first GPS position per hour. The original dataset description follows.
<em>LBBG_ZEEBRUGGE - Lesser black-backed gulls (Larus fuscus, Laridae) breeding at the southern North Sea coast (Belgium and the Netherlands)</em> is a bird tracking dataset published by the <a href="https://www.inbo.be/en">Research Institute for Nature and Forest (INBO)</a>. It contains animal tracking data collected by the LifeWatch GPS tracking network for large birds (<a href="http://lifewatch.be/en/gps-tracking-network-large-birds">http://lifewatch.be/en/gps-tracking-network-large-birds</a>) for the project/study <strong>LBBG_ZEEBRUGGE</strong>, using trackers developed by the University of Amsterdam Bird Tracking System (UvA-BiTS, <a href="http://www.uva-bits.nl">http://www.uva-bits.nl</a>). The study has been operational since 2013. In total 162 individuals of Lesser black-backed gull (<em>Larus fuscus</em>) have been tagged in or near their breeding area at the southern North Sea coast (Zeebrugge and Ostend in Belgium and Vlissingen in the Netherlands), mainly to study their habitat use and migration behaviour. Data are periodically uploaded from the UvA-BiTS database to Movebank and from there archived on Zenodo (see <a href="https://github.com/inbo/bird-tracking">https://github.com/inbo/bird-tracking</a>).
This dataset was collected using infrastructure provided by VLIZ and INBO funded by Research Foundation - Flanders (FWO) as part of the Belgian contribution to LifeWatch.
Fish monitoring of the shelf region of the Huon Australian Marine Park, Tasmania, Australia (2021)

Keywords: Samplingevent
Temporal coverage: 2021/2021

Fish monitoring of the shelf region of the Huon Australian Marine Park, Tasmania, Australia in June-July 2021 using  stereo-BRUVs funded by Parks Australia. Data sourced from GlobalArchive Project 319 (https://globalarchive.org/) on 2023-07-01.
Benthic Epifauna Biomass and Abundance Data, Arctic Marine Biodiversity Observing Network (AMBON) research cruise on the Norseman II, 9 August 2015 - 3 September 2015

Keywords: Samplingevent
Temporal coverage: 2015/2015

This dataset contains benthic epifauna biomass and abundance data collected in the Chukchi Sea, U.S. Arctic during the 9 August - 3 September 2015 Arctic Marine Biodiversity Observing Network (AMBON) research cruise aboard the vessel Norseman II. The dataset contains two comma separated values (csv) files exported from Microsoft Excel. These data were generated from epifauna samples conducted using beam trawls during the research cruise.
The genus Cycloscala Dall, 1889 (Gastropoda: Epitoniidae) in the Indo-Pacific

Keywords: Observation, Occurrence
Temporal coverage: 1982/2000

This dataset is from a paper by Emilio Garcia (2004) which is the third part of a study of Indo-Pacific Epitoniidae in which extensions of known geographical ranges of a number of species and the description of new species is reported (Garcia, 2003, Garcia, 2004). The present article deals with epitoniid species placed in the genus Cycloscala Dali, 1889. The material used in these reports was obtained as a result of expeditions by the Institut de Recherche pour le Développement (IRD, Nouméa) and the Muséum National d'Histoire Naturelle (MNHN, Paris).
All described Indo-Pacific taxa referable to the epitoniid genus Cycloscala Dali, 1889 are listed and evaluated. The type species, Cycloscala echinaticosta (d'Orbigny, 1842) is discussed. Four described Indo-Pacific Cycloscala species, considered valid herewith, are treated: Cycloscala crenulata Pease, 1867; C. gazae Kilbum, 1985; C. hyalina Sowerby II, 1844; and C. revoluta Hedley, 1899.
DFO Pacific IOS zooplankton database - Zooplankton samples collected during cruises to the Canadian Arctic, 2006-2009

Keywords: biological classification, Observation, oceans, zooplankton, Occurrence, arctic, sub-arctic, biota
Temporal coverage: null/null

Zooplankton are an essential component of marine ecosystems.  Understanding the distribution, abundance and community composition of marine zooplankton is essential for understanding overall ecosystem function. Monitoring of the status and trends of marine zooplankton informs decision making around issues of sustainable resource use, environmental protection, and adaptation to changing conditions. To this end we report zooplankton presence data based on samples collected from Canadian Coast Guard ice breakers traveling to and within arctic waters.  This data will be useful for understanding marine zooplankton ecology and hence provide insight into overall ecosystem status and function. 

This resource contains zooplankton species presence information obtained between 2006 and 2009 inclusive.
Data on cetacean strandings (1999 - 2014) on the Ukrainian coast of the Black Sea and the Sea of Azov and adjoining areas

Keywords: Delphinus, Tursiops, strandings, Observation, Black Sea, cetaceans, Occurrence, The Sea of Azov, Phocoena
Temporal coverage: 2009/2012

This dataset contains data on cetacean strandings collected from 1999 to 2014 on the coastal areas of the Black sea and the Sea of Azov. Observations were conducted by  Pavel Gol'din and Karina Vishnyakova, with the help provided by D. Markov, E. Gladilina, E. Gol'din, V. Sokhin, E. Kushnir, V. Serbin, Yu. Lyashenko, L. Godlevska, A. Nadolny, M. Kovalyova, O. Savenko, N. Kukharev and other colleagues and volunteers who took part in the field excursions and provided information on strandings.
Zooplankton abundance in the Kerguelen Axis region 2016

Keywords: Specimen, Occurrence
Temporal coverage: null/null

Zooplankton were collected with a Rectangular Midwater Trawl (RMT 8+1 net) from 37 sampling sites on and near the Southern Kerguelen Plateau. The contents of each net were preserved in 5% buffered formaldehyde. This dataset covers the counts of the contents of the RMT1 net. The contents were split in the laboratory using a Motoda Box and then identified and counted under a Leica M165C stereo-microscope. A flow meter attached to the mouth of the RMT 8 was used to record the volume of seawater passing through the net, and this volume was  converted to water passing through the RMT 1 by applying the conversion factor of 2.027357. The organisms in the samples were identified to the lowest taxonomic level possible. For copepods and euphausiids this level was to species, and generally to sex and/or development stage. For other groups, the identifications were to high levels such as Family or Order.
Quality: No problems with the data collection or the analysis.

2018-08-29 - The original datasheet was reformatted to fit IPT Biodiversity.AQ standard. The new datasheet "ZooplanktonKerguelenPlateau.csv" provides the datasetID, eventID (Cruiser and sampling site), eventDate, decimalLatitude, decimalLongitude, locationID, continent, occurrenceStatus, and basisOfRecord, samplingProtocol, and preparation. The individuals abundance in 1000 m-3. The taxonomical organization is provided to the lowest taxonomical rank that could be determined, after matched in WoRMS (World Register of Marine Species). Some species showed sex and life stage classification.
Blue Whale Study aerial surveys, southern Australia, 2007-2012

Keywords: Observation, Occurrence, Occurrence,Marine Animal Survey,Marine Biology,Marine mammals,Visual Sighting,Aircraft
Temporal coverage: 2007/2012

Original provider:
Blue Whale Study Inc.

Dataset credits:
Blue Whale Study Inc.

Abstract:
Wind-forced cold water upwelling occurs seasonally along the continental shelf of south-east Australia, where pygmy blue whales aggregate to forage. Seasonality and variability are apparent for both blue whale encounter rates and upwelling, within and between seasons. Here we quantify upwelling variability over 11 seasons (2001/02 to 2011/12) and relate it to blue whale encounter rates. Two indices, cumulative wind stress (Intensity) quantifying physical forcing, and surface chlorophyll-a (chl-a) quantifying the ocean’s biological response, revealed variability in upwelling at a variety of temporal scales. Within seasons, upwelling Intensity peaked during February, and chl-a during February–March. Blue whale encounter rate from 52 aerial surveys was modelled against upwelling indices and the climate signal SAM (Southern Annular Mode), at individual survey- and aggregated season-levels, using General Additive Models (GAMs). Survey-level GAMs showed that encounter rate increased with increasing chl-a, and with increasing upwelling Intensity to a point beyond which further increases in Intensity resulted in declining encounter rates. This indicated the importance of productivity, as well as relaxation of upwelling, in producing optimal blue whale foraging conditions. In exploratory season-level models, a strong influence of SAM was apparent, with higher encounter rates associated with positive SAM during the preceding 12 months. Including chl-a improved the model, indicating that both broad-scale climatic signals inherently incorporating environmental variability and uncertainty, as well as more proximal regional factors may influence blue whale occurrence in the study area. Measuring the complex relationships between whale occurrence and upwelling is complicated by the fact that the population of blue whales using the Bonney Upwelling is open, and moves between alternate foraging areas. The findings were interpreted in the context of blue whale foraging ecology in this system.

Purpose:
Relate variability in blue whale relative abundance to variability in upwelling off southern Australia
Marine Microbes from RV Southern Surveyor voyage SS2012_T06, Australia (2012)

Keywords: occurrence, 16S rRNA
Temporal coverage: 2012/2012

This dataset was acquired on the RV Southern Surveyor voyage SS2012_T06. The aim was to characterize the bacterial community structure in surface waters along a 2500 km transect in the eastern Indian Ocean Full details of data, reports and publications of the voyage is at http://www.marine.csiro.au/data/trawler/survey_details.cfm?survey=SS2012_T06
Note on data download/processing:
Data downloaded from Australian Microbiome Initiative via Bioplatforms Australia Data Portal on 17 June 2022. The search filter applied to download data from Bioplatforms Australia Data portal are stored in the Darwin Core property (identificationRemarks). Taxonomy is assigned according to the taxonomic database (SILVA 138) and method (Sklearn) which is stored in the Darwin Core Extension
DNA derived data property (otu_db). Prefix were removed from the taxonomic names as shown in the example (e.g. d__Bacteria to Bacteria). Scientific name is assigned to the valid name available from the highest taxonomic rank.
This collection is published as Darwin Core Occurrence, so the event level measurements need to be replicated for every occurrence. Instead of data replication, the event level eMoF data are made available separately at https://www.marine.csiro.au/data/services/obisau/emof_export.cfm?ipt_resource=bioplatforms_mm_ss2012_t06
IMOS National Reference Stations (NRS) Phytoplankton Abundance and Biovolume

Keywords: Observation, Occurrence
Temporal coverage: 2009/2021

This dataset comprises the phytoplankton abundance and biovolume estimates of a broader sampling program carried out by the Plankton National Reference Station within the Integrated Marine Observing system. Regular monthly phytoplankton samples are undertaken at the stations as part of a larger water sampling program by the Australian National Reference Stations. In total nine stations are sampled regularly around the Australian coastline. Sampling is conducted monthly (Esperance and Ningaloo 3 monthly) off small vessels at each of the nine reference stations. The sampling is an integrated water sample collected with niskin bottles at 10m depth intervals and preserved in lugols solution. The depth of the sample varies at each station. The plankton ecology lab (based in Queensland) will analyse the samples collected for: 1. Community composition / abundance (cells/l) 2. Biovolume (um3/L). Data storage and access is planned to be interoperable with other national and international programs through the IMOS Infrastructure. Station metadata can be found through this resource. Data is available freely via the AODN portal: https://portal.aodn.org.au. As the taxonomic resolution of the data has changed over time, due to continual training, it is important that users refer to the change log tables included in your data download. These will provide information on the validity of the taxa, from what date we have been identifying certain taxa etc. Classification fields may be blank depending on the level to which that taxa has been identified, i.e. if only identified to family, genus and species will be blank.
Data downloaded from IMOS 14-March-2017 from https://catalogue-imos.aodn.org.au/geonetwork/srv/eng/metadata.show?uuid=c13451a9-7cfc-091c-e044-00144f7bc0f4 and taxonomy matched to WoRMS. Added additional records on 2022-03-01
MEL: Benthic samples collected by divers with a suction dredge from Bedeque Bay, an estuary in Prince Edward Island, Canada in 1967.

Keywords: biota, Occurrence, biological classification, Observation, oceans
Temporal coverage: 1967/1967

Bedeque Bay, an estuary in Prince Edward Island, yields a consistently large crop of oysters. In 1967, oyster production throughout Prince Edward Island in general was declining and a benthic survey of the main fishing area in the bay was conducted in order to identify the ecological factors or gradients causing the observed spatial composition of the benthos.

The benthic survey was carried out between July 12th and August 14th, 1967, just following the oyster fishing season. Samples were collected underwater by SCUBA divers using a modified suction dredge. The area enclosed by a 1 m2 quadrat was sampled with the dredge (which was equipped with a 4 mm mesh collecting bag) to a depth of 50 era. Forty four stations, covering most of the estuary, were each sampled by a single quadrat.

Animals were counted and plants recorded by dry weight. Only subjective classifications of sediment type based on field observations were made. These measurements are not part of this version of the dataset.

Species distribution information associated with this study were digitized, standardized and republished as part of the Atlantic Coastal Zone Information Steering Committee (ACZISC) Atlantic Ecosystem Initiative (AEI) funded project “Atlantic Canada’s Biological Data for Ecosystem Planning and Decision-making” and OBIS Canada.