Full descriptions of objects found in an example NEON HDF5 file are provided in the objDesc data table. This readme covers the file layout.

The NEON HDF5 file structure was developed following the NEON data product (DP) naming convention provided in NEON.DOC.002651, where portions of the naming convention as described below were selected to develop the hierarchical structure of the HDF5 file:

NEON.DOM.SITE.DPL.PRNUM.REV.TERMS.HOR.VER.TMI

Where (* indicates used in HDF5 structure): 
NEON = NEON
DOM = DOMAIN, e.g. D10
*SITE = SITE, e.g. STER
*DPL = DATA PRODUCT LEVEL, e.g. DP1. Showed as dp01 in HDF5 file
*PRNUM = PRODUCT NUMBER =>5-digit number. Set in data products catalog. We use the data product names instead of the associated unique identifying (UID) numbers to increase readability of the file.
    Example = irgaCo2 for turbulent CO2 concentration measured by LI-7200 IRGA (00034); co2Stor for storage (or profile) CO2 concentration measured by LI-840 IRGA (00099).
*REV = REVISION, e.g. 001.
*TERMS = TERMS, from a controlled list of NEON terms.  We use the terms instead of the associated unique identifying (UID) numbers to increase readability of the file. Examples: rtioMoleDryCo2 = dry molar fraction of CO2 in the air; dlta13CCo2 = ?13C of CO2 in the air.
*HOR = HORIZONTAL INDEX.  
    Examples: Tower=000, Hut =700, soil plot 1 to soil plot 5 = 001 to 005.
*VER = VERTICAL INDEX. 
    Examples: Ground level=000, second tower level=020. The soil sensor depth level closest to ground surface = 501, second soil sensor depth from ground surface = 502. 
*TMI = TEMPORAL INDEX. Averaging interval, in minutes, is directly represented in the temporal index: 001 = 1 minute, 005 = 5 minutes, 030 = 30 minutes, etc. We use 01m, 05m or 30 m, etc. in HDF5 file to increase readability of the file. Examples: 01m = 1 minute, 30m = 30 minute, 999=irregular intervals.

One additional level that is not included in the NEON (DP) naming convention is the TYPE field, which describes the type of data provided such as data statistics (data), quality information (qfqm), or uncertainty quantification (ucrt).

The hierarchical structure of the NEON HDF5 in its generic form is as follows (indentation used to show hierarchy):
 /SITE: measurement site four-letter site code
    /SITE/DPL: Data product level, i.e., dp01 for Level 1 data products
       /SITE/DPL/TYPE: The type of information provided, i.e. data (data), quality flags or quality metrics (qfqm), or uncertainty (ucrt) estimates
          /SITE/DPL/TYPE/PRNUM : Data product identification code (irgaCo2 = NEON.DP1.00034) matching a data product number
             /SITE/DPL/TYPE/PRNUM/HOR_VER_TMI: horizontal position, vertical position and time resolution index of data products during sampling periods. During field calibration/validation periods, the format will be calibration/validation standard_TMI, i.e., co2High_02m = 2 min average data during field calibration/validation using a known High CO2 concentration standard
                /SITE/DPL/TYPE/PRNUM/HOR_VER_TMI/TERMS: term name of the data provided


Practical realization for Eddy-covariance turbulent exchange level 1 data products (example for CO2 concentration at the Smithsonian Ecological Research Center (SERC) site):
 /SERC: measurement site four-letter site code
    /SERC/dp01: Level 1 data products
       /SERC/dp01/data: Data information
          /SERC/dp01/data/irgaCo2: Data product identification code (co2Turb = NEON.DP1.00034)
             /SERC/dp01/data/irgaCo2/000_060_30m: LI-7200 CO2 data product at the tower (HOR = 000), top level (VER = 060) and 30 minute time resolution (TMI = 30m)
                /SERC/dp01/data/irgaCo2/000_060_30m/densMoleCo2: molar density of carbon dioxide
                  ::::
             /SERC/dp01/data/irgaCo2/000_060_01m, with sub-folders analogous to /SERC/dp01/data/irgaCo2/000_060_30m
          /SERC/dp01/data/irgaH2o (NEON.DP1.00035), with sub-folders analogous to /SERC/dp01/data/irgaCo2
          /SERC/dp01/data/soni (NEON.DP1.00007), with sub-folders analogous to /SERC/dp01/data/irgaCo2
          /SERC/dp01/data/soniAmrs (NEON.DP1.00010), with sub-folders analogous to /SERC/dp01/data/irgaCo2
       /SERC/dp01/qfqm: Quality information, with sub-folders analogous to /SERC/dp01/data
                  ::::
       /SERC/dp01/ucrt: Uncertainty information, with sub-folders analogous to /SERC/dp01/data
                  ::::
    /SERC/dp02: Level 2 data products
    /SERC/dp03: Level 3 data products
    /SERC/dp04: Level 4 data products
    /SERC/dp0p: Level 0 prime data products

Metadata are packaged with the data as attributes  either at the site group level,  a data product group level, or directly to the data tables for the L1-L4 processed products.