cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48443/qtwt-ad46
title: Surface water microbe group abundances (DP1.20278.001)
title: RELEASE-2021

description: This data product contains the quality-controlled laboratory data and metadata for NEON's surface water bacterial, archaeal and fungal group abundances analysis, which are derived from surface water microbial sampling. For details, see the user guide, protocols, and science design listed in the Documentation section in this data product's details webpage. Queries for the basic data product package will return laboratory results of gene copy number data. Queries for the expanded package will include two additional tables: a batch-level data and QC results table, and a summary table of the lab methods used for processing and analysis.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

mga_swGroupAbundances:  240

mga_batchResults: 14

mga_labSummary: 14
description: Surface water samples for microbial molecular analyses are collected at the same time and location as surface water chemistry samples once per month in wadeable streams (12 times per year) and every-other month in lakes and rivers (6 times per year). In wadeable streams, microbe samples are collected near the downstream S2 sensor location. In lakes and rivers, samples are collected near the buoy sensor set at 1 sampling depth in unstratified systems and up to 3 depths in stratified lakes. Surface water grab samples are filtered on 0.22 um Sterivex capsule filters, capped and flash-frozen in the field. The filters are stored on dry ice in the field and shipped frozen to an analytical facility for DNA extraction, sample preparation and qPCR analysis using primer sets targeting the small subunit of the ribosomal RNA gene operon. Laboratory data are passed through the NEON automated ingest process for QC testing and acceptance, and are published on the NEON data portal.
DOI: 10.48443/ey0c-1v43
title: Ground beetle sequences DNA barcode (DP1.10020.001)
title: RELEASE-2021

description: This data product contains the quality-controlled laboratory metadata and QA results for NEON's cytochrome oxidase I (COI) barcoding of ground beetles sequences. The DNA barcoding procedure involves the removal of tissue, extracting and sequencing DNA from the tissue, and matching that sequence data to sequences from previously identified voucher specimens. DNA analysis serves a number of purposes, including verification of taxonomy of specimens that do not receive expert identification, clarification of the taxonomy of rare or cryptic species, and characterization of diversity using molecular markers. For additional details, see the user guide, protocols, and science design listed in the Documentation section in this data product's details webpage. Queries for this data product will return metadata tables formatted for submission to the Barcode of Life Database. These queries will also provide links to the actual sequence data, which are publicly available on the Barcode of Life Datasystems (BOLD, http://www.barcodinglife.com/). The sequence data can be obtained by following the links from the NEON data portal, or by directly querying NEON data sets on the BOLD server. From the NEON portal, the link "BOLD Project: Ground beetle sequences DNA barcode" redirects to a page on the BOLD public data portal for the queried data. This is a dynamic link and will automatically update based on the user query.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

bet_BOLDcollectionData:  614

bet_BOLDspecimenDetails:  614

bet_BOLDtaxonomy:  614

bet_BOLDvoucherInfo:  614
description: Ground beetle legs are subsampled from individual specimens collected as part of the Ground beetles sampled from pitfall traps (DP1.10022.001) data product. Up to 10 individuals per species per site for a total of up to 95 individuals per site per year are selected for barcoding. Beetles that are rare, particularly difficult to identify, or poorly represented in previous collection events are prioritized for DNA sequencing. Only beetle specimens that have been identified by an expert taxonomist are eligible for DNA barcoding.  Leg tissue is preserved in an appropriate tissue vial and shipped to an external lab, where DNA is extracted and target sequences amplified via PCR. Barcodes of cytochrome oxidase I are generated per specimen.
DOI: 10.48443/p2hp-j476
title: Surface water microbe community composition (DP1.20141.001)
title: RELEASE-2021

description: This data product contains the quality-controlled laboratory data and metadata for NEON's surface water bacterial, archaeal, and fungal community composition analysis derived from microbial sampling in lakes, rivers and streams. Taxon tables are derived from the 16S and ITS marker gene sequencing data product, NEON.DP1.20282. The DNA sequence data are processed using standard bioinformatics software to generate taxonomic data. For additional details, see the user guide, protocols, and science design listed in the Documentation section in this data product's details webpage.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

mcc\_swSeqVariantMetadata\_16S:  730

mcc\_swSeqVariantMetadata\_ITS:  730

mcc\_taxonTableLabSummary:  7
description: Surface water microbe samples are collected at the same time and location as surface water cell count samples and surface water chemistry samples, which occurs once per month in wadeable streams (12 times per year), and every other month in lakes and rivers (6 times per year). In wadeable streams, samples are collected near the downstream S2 sensor location. In lakes and rivers, samples are collected near the buoy sensor set at 1 sampling depth in unstratified systems and up to 3 depths in stratified lakes. Surface water grab samples are filtered on 0.22 um Sterivex capsule filters, capped and flash-frozen in the field. The filters are stored and shipped frozen to an analytical facility for DNA sequence analysis using primer sets targeting the small subunit of the ribosomal RNA gene. Sequence data undergo QAQC and are processed bioinformatically using an in-house pipeline to identify unique sequence variants in the data and to taxonomically identify each sequence variant.
DOI: 10.48443/17cz-g567
title: Fish electrofishing, gill netting, and fyke netting counts (DP1.20107.001)
title: RELEASE-2021

description: This data product contains the quality-controlled, native sampling resolution data from NEON's fish sampling. Fish are sampled using a combination of electrofishing, gill-nets and mini-fyke nets. Field technicians identify fish to the lowest practical taxonomic level and then weigh and measure a subset of captured individuals before releasing. Fish that cannot be identified  to species in the field are assigned a morphospecies name and comments on potential identification traits are noted in the comments. In addition at D04 decapod bycatch is collected, identified, tallied, and recorded.  For additional details, see the user guide, protocols, and science design listed in the Documentation section in this data product's details webpage.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

fsh_fieldData:  45

fsh_perPass:  45

fsh_perFish:  45

fsh_bulkCount:  45

fsh_invertBycatch: 45

fsh_morphospecies:  390
description: Fish are sampled twice per year at lakes and wadeable stream sites, during spring and fall. 10 fish sampling reaches or segments are established at each site; with 3 fixed reaches sampled during every sampling bout and a random subset of 3 additional reaches or segments selected for sampling each year.
DOI: 10.48443/855x-0n27
title: Macroinvertebrate collection (DP1.20120.001)
title: RELEASE-2021

description: This data product contains the quality-controlled, native sampling resolution data from NEON's aquatic macroinvertebrate collection and field metadata, as well as associated taxonomic, morphometric, and count analyses data provided by a contracted lab. Benthic field samples are collected in wadeable streams, rivers, and lakes three times per year during the growing season using the type of sampler most suitable to the habitat types present at the site. Samples are preserved in ethanol in the field and shipped to a contracting lab for analysis. For additional details, see the user guide, protocols, science design, and lab SOPs listed in the Documentation section in this data product's details webpage.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

inv_fieldData:  30

inv_persample:  210

inv_taxonomyProcessed:  210

inv_taxonomyRaw:  210

inv_pervial:  210
description: Benthic macroinvertebrate samples are collected three times per year at wadeable stream, river, and lake sites during aquatic biology bout windows, roughly in spring, summer, and fall. Samples are collected using the most appropriate sampler for the habitat type, including Surber, Hess, hand corer, modified kicknet, D-frame sweep, and petite ponar samplers. In wadeable streams, samples are collected in the two most dominant habitat types (e.g. riffles, runs, pools, step pools). In lakes, samples are collected near the buoy, and nearshore sensors using a petite ponar, and in littoral areas using a D-frame sweep. In rivers, samples are collected near the buoy and two other deep-water locations using a petite ponar sampler, and in littoral areas using a D-frame sweep or large-woody debris sampler. Samples are preserved in ethanol in the field, returned to the domain support facility for a preservative change where a small volume of glycerol is added to help keep invertebrates from getting brittle. Samples are shipped to a taxonomy lab for sorting and identification, including count of each taxon per size class (to nearest mm) and identification to lowest practical taxon (genus or species).
DOI: 10.48443/s9wy-t644
title: Relative humidity (DP1.00098.001)
title: RELEASE-2021

description: This data product contains the relative humidity, air temperature, and  dew point/frost point temperature measurements made at all NEON sites. It is reported as 1-minute mean measurements and 30-minute mean values.

Latency:
Data collected in any given month are published during the second full week of the following month.
description: The sensors are installed at the top level of the tower infrastructure, at the soil array and on the aquatic met station at a standard height above ground level. Instrumentation: Vaisala HUMICAP Humidity and Temperature Probe - HMP 155
DOI: 10.48443/fzzj-g053
title: Soil microbe metagenome sequences (DP1.10107.001)
title: RELEASE-2021

description: Abstract: This data product contains the quality-controlled laboratory metadata and minimally processed sequence data from NEON's soil microbial shotgun metagenomics sequencing. Typically, measurements are done on plot-level composite samples and represent up to three randomly selected sampling locations within a plot. For additional details, see the user guide, protocols, and science design listed in the Documentation section in this data product's details webpage. Queries for the basic data product package will return metadata tables that include laboratory methods and results from DNA extraction, sample preparation, and DNA sequencing for samples from the specified sites and within the specified date range. Queries for the expanded package will also include a table containing links to the raw sequence data files. Some of the sequence data are also publicly available and may be queried on the [Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST)](http://metagenomics.anl.gov/) server. Note that there may be lags between publication of data on the NEON data portal and availability of sequence data on the public sequence repository.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

mms_metagenomeDnaExtraction:  240

mms_metagenomeSequencing:  240

mms_rawDataFiles: 240
description: Three pre-determined, randomly assigned locations are selected for each sampling event within each of 10 plots distributed throughout a site; sampling locations within a plot are not re-sampled. Soil metagenomics sampling occurs annually during the historic peak in vegetation greenness. Soil samples are collected to a maximum depth of 30 cm, with organic and mineral soils sampled separately. Subsamples of homogenized soil (rocks, roots and organic debris removed) from each of the 3 sampling locations are combined to form a plot-level composite sample that is used for metagenomics analysis. Samples are frozen on dry ice and shipped to an analytical facility for DNA extraction, sample preparation and shotgun metagenomic sequencing. Laboratory metadata are then delivered to NEON for QC testing and acceptance, and then are formatted for upload to public sequence repositories.
DOI: 10.48443/55wa-5032
title: Bathymetric and morphological maps (DP4.00132.001)
title: RELEASE-2021

description: Bathymetric maps are obtained using hydroacoustic (sonar) instrumentation and interfaced with differential global positioning system (DGPS) mounted on a boat. Hydroacoustics are utilized to detect the depth of a water body, sediment characteristics as well as the presence or absence, approximate abundance, distribution, size, and behavior of underwater biota. For additional details, see the user guide, protocols, and science design listed in the Documentation section in this data product's details webpage.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.
 
bat_fieldData:  60

bat_pointcollection:  60

bat_resultsFile:  180

bat_sonarRecord:  60
description: A dual beam echosounder with side scan sonar and WAAS GPS are used to collect bathymetric (depth) and backscatter (signal strength) data. These data are collected using a boat-mounted system applied during surveys of NEON lakes and river sites. Bathymetric surveys are completed every 5 years; if an extreme event results in substantial changes to the physical environment then an out-of-cycle survey may be conducted. Depth data are used to produce bathymetric maps and side scan sonar data are used to classify subaquatic features to produce a habitat map. Instrumentation: Humminbird 1198c Si Combo
DOI: 10.48443/2wt7-e375
title: Small mammal sequences DNA barcode (DP1.10076.001)
title: RELEASE-2021

description: This data product contains the quality-controlled laboratory metadata and QA results for NEON's cytochrome oxidase I (COI) barcoding of small mammal sequences. The DNA barcoding procedure involves the non-distructive collection of tissue from live specimens in the field, extracting and sequencing DNA from the tissue, and matching that sequence data to sequences from previously identified voucher specimens. DNA analysis serves a number of purposes, including verification of taxonomy of specimens that do not receive expert identification, clarification of the taxonomy of rare or cryptic species, and characterization of diversity using molecular markers. For additional details, see the user guide, protocols, and science design listed in the Documentation section in this data product's details webpage. These queries will also provide links to the actual sequence data, which are publicly available on the Barcode of Life Datasystem (BOLD, http://www.barcodinglife.com/). The sequence data can be obtained by following the links from the NEON data portal, or by directly querying NEON data sets on the BOLD server. From the NEON portal, the link "BOLD Project: Small Mammal sequences DNA barcode" redirects to a page on the BOLD public data portal for the queried data. This is a dynamic link and will automatically update based on the user query.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

mam_BOLDcollectionData:  375

mam_BOLDspecimenDetails:  375

mam_BOLDtaxonomy:  375

mam_BOLDvoucherInfo:  375
description: Up to 240 ear punches will be collected from each target and opportunistic species per site per year. These tissues will be preserved in an appropriate tissue vial and up to 95 tissue samples per domain will be shipped to an external lab. DNA will be extracted and target sequences amplified via PCR. Barcodes of cytochrome oxidase I will be generated per specimen.
DOI: 10.48443/rfmw-p030
title: Soil physical and chemical properties, Megapit (DP1.00096.001)
title: RELEASE-2021

description: Soil properties affect the movement of water, heat and gases into and out of the soil. They also influence the availability of nutrients to plants and soil organisms and the production and stabilization of soil organic matter. Soil physical and chemical properties are measured by horizon from a single temporary soil "Megapit" at each terrestrial site at depths of up to 200 cm at non-permafrost sites (up to 300 cm at Alaskan sites). The Megapit sampling location is expected to be representative of the NEON sensor-based soil plots and this sampling activity is expected to occur once at each NEON terrestrial site.

Queries for this data product will return field collection metadata, soil taxonomy, bulk density, coarse fragment content, and particle size distribution, and a host of geochemical measurements on a per horizon basis. For additional details, see the user guide, protocols, and ATBDs listed in the Documentation section below. Associated with these data are soil pedon descriptions and photos. These documents can be found on the NEON Data Portal under the Resources section, or here: https://data.neonscience.org/megapit-info Additional soil samples collected from the same soil pit are archived in the [NEON Megapit Soil Archive](http://www.neonscience.org/request-megapit-soil-samples) and are available upon request.

Latency:
Data were collected once, at the establishment of each site. Data were published within one year of collection, and future collections at existing sites are not expected
description: The Soil physical and chemical properties, Megapit data product is available at each terrestrial site. The soil pit location was chosen to be representative of the sensor-based Soil Plots based on soil type, vegetation and topography, as well as being accessible by a backhoe and outside the main measurement zone of other sensors. The soil pit is usually within a few hundred meters of the sensor-based Soil Plots and NEON tower. Soil samples were collected by soil horizon up to 200 cm at non-permafrost sites (up to 300 cm at Alaskan sites). Laboratory analyses were conducted at the Kellogg Soil Survey Laboratory in Lincoln, Nebraska following the standard operating procedures outlined in the Soil Survey Laboratory Methods Manual, Report No. 42, Version 5, 2014.
DOI: 10.48443/bakr-aj85
title: Soil water content and water salinity (DP1.00094.001)
title: RELEASE-2021

description: Soil volumetric water content and an index of soil water ion content (salinity) are measured at various depths below the soil surface from approximately 2 cm up to 200 cm at non-permafrost sites (up to 300 cm at Alaskan sites). Soil moisture is an important component of the hydrologic cycle and is the dominant source of water for most plants and soil organisms making it a key indicator of drought. In addition, soil moisture status influences the severity of flooding and temperature extremes, as well as physical, chemical and biological processes in the soil. Measurements are made in vertical profiles consisting of up to eight depths in all five instrumented soil plots at each terrestrial site, and presented as 1-minute and 30-minute averages.

Latency:
Data collected in any given month are published during the second full week of the following month.
description: When possible the soil plots were arranged in a transect with the first plot approximately 15-40 m from the tower in the expected dominant airshed. The middle of airshed was used as the transect vector and plot spacing was based on the distance required for surface soil temperature and moisture measurements to be spatially independent at the 1 hectare scale during site characterization (capped at approximately 40 m due to logistical constraints). Soil plots were microsited as necessary to avoid obstacles (e.g., boulders, streams, and paths) and more compact plot layouts were used at small sites. Soil moisture and salinity index are measured at up to eight depths within each plot, with the mid-point of the shallowest sensors at approximately 6, 16, and 26 cm. Depths for deeper sensors vary among sites and are based on megapit soil horizon data (NEON.DP1.00097) and depth to restrictive feature (see NEON.DOC.003146). Instrumentation: Sentek - EnviroSCAN TriSCAN
DOI: 10.48443/qzr1-jr79
title: Zooplankton collection (DP1.20219.001)
title: RELEASE-2021

description: This data product contains the quality-controlled, native sampling resolution data and metadata from NEON's aquatic zooplankton collection protocol, as well as associated taxonomic, morphometric, and count analyses data provided by a contracted lab. Field samples are collected in the water column of lakes using the most appropriate sampler (vertical tow net or Schindler trap) for the depth of water, preserved in ethanol in the field, and shipped to a contracting lab for analysis. For additional details, see the user guide, protocols, science design, and lab SOPs listed in the Documentation section in this data product's details webpage.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

zoo_fieldData:  30

zoo_taxonomyProcessed:  210

zoo_taxonomyRaw:  210

zoo_perVial:  210
description: Zooplankton samples are collected three times per year at lake sites during aquatic biology bout windows, roughly in spring, summer, and fall. Samples are collected using either a tow net (water deeper than 4 m) or a Schindler-Patalas trap (water shallower than 4 m) depending on the depth at the sampling location. Samples are collected near the NEON profiling buoy as well as two littoral sensor sets. Samples are preserved in ethanol in the field and shipped to a taxonomy lab for sorting and identification, including count of each taxon, summary length and width measurements for each taxon per sample (to nearest mm) and identification to lowest practical taxon (genus or species).