Exported source
AVOGADRO = 6.02214076e23Configs
Several dictionaries used to generate
.toml configuration files copied under /home/.marisco folder and associated utilities function. These .toml files can be then adapted to your specific needs if required.
Exported source
NC_DIM = 'id'
Tip
FEEDBACK FOR NEXT VERSION: PH was included in NC_VARS but not in field-definition.ipynb.
Exported source
# Lookup variables names to MARIS NetCDF4 template variable names
NC_VARS = {
'ID': 'id',
'LON': 'lon',
'LAT': 'lat',
'SMP_DEPTH': 'smp_depth',
'TOT_DEPTH': 'tot_depth',
'TIME': 'time',
'AREA': 'area',
'SMP_ID': 'smp_id',
'NUCLIDE': 'nuclide',
'VALUE': 'value',
'UNIT': 'unit',
'UNC': 'unc',
'DL': 'dl',
'FILT': 'filt',
'COUNT_MET': 'count_met',
'SAMP_MET': 'samp_met',
'PREP_MET': 'prep_met',
#'DRY_MET': 'dry_met', # NOT IN USE, no LUT for this.
'VOL': 'vol',
'SAL': 'sal',
'TEMP': 'temp',
'PH': 'ph',
'BIO_GROUP': 'bio_group',
'SPECIES': 'species',
'BODY_PART': 'body_part',
'SED_TYPE': 'sed_type',
'TOP': 'top',
'BOTTOM': 'bottom',
'DRYWT': 'drywt',
'WETWT': 'wetwt',
'PERCENTWT': 'percentwt',
'LAB': 'lab',
'PROFILE_ID': 'profile_id', # NEED TO INCLUDE.
}CSV_VARS includes variables as defined in the OpenRefine MARIS CSV format.
base_path
base_path ()
Return the path to the .marisco folder under your home directory.
Exported source
CSV_VARS = {
'LON': 'longitude',
'LAT': 'latitude',
'SMP_DEPTH': 'sampdepth',
'TOT_DEPTH': 'totdepth',
'TIME': 'begperiod',
'AREA': 'area',
'NUCLIDE': 'nuclide_id',
'VALUE': 'activity',
'UNIT': 'unit_id',
'UNC': 'uncertaint',
'DL': 'detection',
'FILT': 'filtered',
'COUNT_MET': 'counmet_id',
#'DRY_MET': 'drymet_id', # NOT IN USE, no LUT for this.
'SAMP_MET': 'sampmet_id',
'PREP_MET': 'prepmet_id',
'VOL': 'volume',
'SAL': 'salinity',
'TEMP': 'temperatur',
'SPECIES': 'species_id',
'BODY_PART': 'bodypar_id',
'SED_TYPE': 'sedtype_id',
'TOP': 'sliceup',
'BOTTOM': 'slicedown',
'DRYWT': 'drywt',
'WETWT': 'wetwt',
'PERCENTWT': 'percentwt',
'LAB': 'lab_id',
'PROFILE_ID': 'profile_id', # NEED TO INCLUDE.
'SAMPLE_TYPE': 'samptype_id', # NEED TO INCLUDE.
'TAXONNAME': 'taxonname',
'TAXONREPNAME': 'taxonrepname',
'TAXONRANK': 'taxonrank',
'TAXONDB': 'taxondb',
'TAXONDBID': 'taxondb_id',
'TAXONDBURL': 'taxondb_url',
'REF_ID': 'ref_id',
'SMP_ID': 'samplelabcode'
# CSV_VARS not included in current workflow.
# 'STATION': 'station',
# 'SAMPLE_LAB_CODE': 'samplelabcode',
# 'SED_REPNAME': 'sedrepname',
# 'MEASURE_NOTE': 'measurenote',
# 'REFERENCE_NOTE': 'referencenote',
# 'SAMPLE_NOTE': 'samplenote',
}Exported source
NC_GROUPS = {'BIOTA': 'biota',
'SEAWATER': 'seawater',
'SEDIMENT': 'sediment',
'SUSPENDED_MATTER': 'suspended_matter'}Exported source
SMP_TYPE_LUT = {
'SEAWATER': 1,
'BIOTA': 2,
'SEDIMENT': 3,
'SUSPENDED_MATTER': 4
}Exported source
NC_DTYPES = {
'AREA': {
'name': 'area_t',
'fname': 'dbo_area.xlsx',
'key': 'displayName',
'value':'areaId'
},
'BIO_GROUP': {
'name': 'bio_group_t',
'fname': 'dbo_biogroup.xlsx',
'key': 'biogroup',
'value':'biogroup_id'
},
'BODY_PART': {
'name': 'body_part_t',
'fname': 'dbo_bodypar.xlsx',
'key': 'bodypar',
'value':'bodypar_id'
},
'COUNT_MET': {
'name': 'count_met_t',
'fname': 'dbo_counmet.xlsx',
'key': 'counmet',
'value':'counmet_id'
},
'DL': {
'name': 'dl_t',
'fname': 'dbo_detectlimit.xlsx',
'key': 'name_sanitized',
'value':'id'
},
'FILT': {
'name': 'filt_t',
'fname': 'dbo_filtered.xlsx',
'key': 'name',
'value':'id'
},
'NUCLIDE': {
'name': 'nuclide_t',
'fname': 'dbo_nuclide.xlsx',
'key': 'nc_name',
'value':'nuclide_id'
},
'PREP_MET': {
'name': 'prep_met_t',
'fname': 'dbo_prepmet.xlsx',
'key': 'prepmet',
'value':'prepmet_id'
},
'SAMP_MET': {
'name': 'samp_met_t',
'fname': 'dbo_sampmet.xlsx',
'key': 'sampmet',
'value':'sampmet_id'
},
'SED_TYPE': {
'name': 'sed_type_t',
'fname': 'dbo_sedtype.xlsx',
'key': 'sedtype',
'value':'sedtype_id'
},
'SPECIES': {
'name': 'species_t',
# 'fname': 'dbo_species_cleaned.xlsx',
'fname': 'dbo_species_2024_11_19.xlsx',
'key': 'species',
'value':'species_id'
},
'UNIT': {
'name': 'unit_t',
'fname': 'dbo_unit.xlsx',
'key': 'unit_sanitized',
'value':'unit_id'
},
'LAB': {
'name': 'lab_t',
#'fname': 'dbo_lab.xlsx',
'fname': 'dbo_lab_cleaned.xlsx',
'key': 'lab',
'value':'lab_id'
}
}Exported source
CSV_DTYPES = {
'AREA': {'state': 'decoded'},
'NUCLIDE': {'state': 'encoded'}, # encoded nuclide_id
'UNIT': {'state': 'encoded'}, # encoded unit_id
'DL': {'state': 'decoded'},
'FILT': {'state': 'decoded'},
'COUNT_MET': {'state': 'encoded'}, # encoded counmet_id
'SAMP_MET': {'state': 'encoded'}, # encoded sampmet_id
'PREP_MET': {'state': 'encoded'}, # encoded prepmet_id
'SPECIES': {'state': 'encoded'}, # encoded species_id
'BODY_PART': {'state': 'encoded'}, # encoded bodypar_id
'SED_TYPE': {'state': 'encoded'}, # encoded sedtype_id
'LAB': {'state': 'encoded'}, # encoded lab_id
}Exported source
CFG_FNAME = 'configs.toml'
#CDL_FNAME = 'cdl.toml'
NUCLIDE_LOOKUP_FNAME = 'dbo_nuclide.xlsx'
MARISCO_CFG_DIRNAME = '.marisco'Exported source
def base_path():
"Return the path to the `.marisco` folder under your home directory."
return Path.home() / MARISCO_CFG_DIRNAMEBy default, we create a folder named .marisco under your home directory that will receive all configuration files as defined in BASE_PATH:
base_path()Path('/home/niallmurphy93/.marisco')Exported source
CONFIGS = {
'gh': {
'owner': 'franckalbinet',
'repo': 'marisco'
},
'names': {
'nc_template': 'maris-template.nc'
},
'dirs': {
'lut': str(base_path() / 'lut'), # Look-up tables
'cache': str(base_path() / 'cache'), # Cache (e.f WoRMS species)
'tmp': str(base_path() / 'tmp')
},
'paths': {
'nc_template': 'nbs/files/nc',
'luts': 'nbs/files/lut'
},
# TO BE REMOVED:Now read directly from `maris.cdl` file
# 'units': {
# 'time': 'seconds since 1970-01-01 00:00:00.0'
# },
'zotero': {
'api_key': os.getenv('ZOTERO_API_KEY'),
'lib_id': '2432820'
}
}The CONFIGS dictionary defines general settings:
| key | Value | Description |
|---|---|---|
dirs/lut |
/Users/franckalbinet/.marisco/lut |
Location & name of the directory receiving lookup tables. |
dirs/cache |
/Users/franckalbinet/.marisco/cache |
Location & name of the directory receiving cache files such as WoRMS species retrieved. |
dirs/tmp |
/Users/franckalbinet/.marisco/tmp |
Location & name of temporary files. |
gh/owner |
franckalbinet |
GitHub account owner. |
gh/repo |
marisco |
GitHub user used to download specific files (e.g lookup tables) during installation. |
names/nc_template |
maris-template.nc |
Name of the MARIS NetCDF4 template. |
paths/nc |
nbs/files/nc |
GitHub repository directory name containing the MARIS NetCDF4 template. |
paths/luts |
nbs/files/lut |
GitHub repository directory name containing lookup tables. |
zotero/api_key |
your-zotero-api-key |
Zotero API key (“ZOTERO_API_KEY” environment variable). |
zotero/lib_id |
2432820 |
Zotero library ID. |
The main CONFIGS_CDL dictionary, used to generate a NetCDF CDL (Common Data Language) .toml file. This file is then used to generate a template MARIS netcdf file. For further details refers to the configs.ipynb file.
Below, the vars/defaults section printed:
cfg
cfg ()
Return the configuration as a dictionary.
Exported source
def cfg():
"Return the configuration as a dictionary."
return read_toml(base_path() / CFG_FNAME)lut_path
lut_path ()
Return the path to the lookup tables directory.
Exported source
def lut_path():
"Return the path to the lookup tables directory."
return Path(cfg()['dirs']['lut'])cache_path
cache_path ()
Return the path to the cache directory.
Exported source
def cache_path():
"Return the path to the cache directory."
return Path(cfg()['dirs']['cache'])Exported source
# TO BE REMOVED: Now read directly from `maris.cdl` file
CONFIGS_CDL = {
'placeholder': '_to_be_filled_in_',
'grps': {
'sea': {
'name': 'seawater',
'id': 1
},
'bio': {
'name': 'biota',
'id': 2
},
'sed': {
'name': 'sediment',
'id': 3
},
'sus': {
'name': 'suspended-matter',
'id': 4
}
},
'global_attrs': {
# Do not update keys. Only values if required
'id': '', # zotero?
'title': '',
'summary': '',
'keywords': '',
'keywords_vocabulary': 'GCMD Science Keywords',
'keywords_vocabulary_url': 'https://gcmd.earthdata.nasa.gov/static/kms/',
'record': '',
'featureType': '',
'cdm_data_type': '',
# Conventions
'Conventions': 'CF-1.10 ACDD-1.3',
# Publisher [ACDD1.3]
'publisher_name': 'Paul MCGINNITY, Iolanda OSVATH, Florence DESCROIX-COMANDUCCI',
'publisher_email': 'p.mc-ginnity@iaea.org, i.osvath@iaea.org, F.Descroix-Comanducci@iaea.org',
'publisher_url': 'https://maris.iaea.org',
'publisher_institution': 'International Atomic Energy Agency - IAEA',
# Creator info [ACDD1.3]
'creator_name': '',
'institution': '',
'metadata_link': '',
'creator_email': '',
'creator_url': '',
'references': '',
'license': ' '.join(['Without prejudice to the applicable Terms and Conditions',
'(https://nucleus.iaea.org/Pages/Others/Disclaimer.aspx),',
'I hereby agree that any use of the data will contain appropriate',
'acknowledgement of the data source(s) and the IAEA Marine',
'Radioactivity Information System (MARIS).']),
'comment': '',
# Dataset info & coordinates [ACDD1.3]
#'project': '', # Network long name
#'platform': '', # Should be a long / full name
'geospatial_lat_min': '',
'geospatial_lon_min': '',
'geospatial_lat_max': '',
'geospatial_lon_max': '',
'geospatial_vertical_min': '',
'geospatial_vertical_max': '',
'geospatial_bounds': '', # wkt representation
'geospatial_bounds_crs': 'EPSG:4326',
# Time information
'time_coverage_start': '',
'time_coverage_end': '',
#'time_coverage_resolution': '',
'local_time_zone': '',
'date_created': '',
'date_modified': '',
#
# -- Additional metadata (custom to MARIS)
#
'publisher_postprocess_logs': ''
},
'dim': {
'name': 'sample',
'attrs': {
'long_name': 'Sample ID of measurement'
},
'dtype': 'u8'
},
'vars': {
'defaults': {
'lon': {
'name': 'lon',
'attrs': {
'long_name': 'Measurement longitude',
'standard_name': 'longitude',
'units': 'degrees_north',
'axis': 'Y',
'_CoordinateAxisType': 'Lon'
},
'dtype': 'f4'
},
'lat': {
'name': 'lat',
'attrs': {
'long_name': 'Measurement latitude',
'standard_name': 'latitude',
'units': 'degrees_east',
'axis': 'X',
'_CoordinateAxisType': 'Lat'
},
'dtype': 'f4'
},
'smp_depth': {
'name': 'smp_depth',
'attrs': {
'long_name': 'Sample depth below seal level',
'standard_name': 'sample_depth_below_sea_floor',
'units': 'm',
'axis': 'Z'
},
'dtype': 'f4'
},
'tot_depth': {
'name': 'tot_depth',
'attrs': {
'long_name': 'Total depth below seal level',
'standard_name': 'total_depth_below_sea_floor',
'units': 'm',
'axis': 'Z'
},
'dtype': 'f4'
},
'time': {
'name': 'time',
'attrs': {
'long_name': 'Time of measurement',
'standard_name': 'time',
'units': 'seconds since 1970-01-01 00:00:00.0',
'time_origin': '1970-01-01 00:00:00',
'time_zone': 'UTC',
'abbreviation': 'Date/Time',
'axis': 'T',
'calendar': 'gregorian'
},
'dtype': 'u8',
},
'area': {
'name': 'area',
'attrs': {
'long_name': 'Marine area/region id',
'standard_name': 'area_id'
},
'dtype': 'area_t'
},
},
'bio': {
'bio_group': {
'name': 'bio_group',
'attrs': {
'long_name': 'Biota group',
'standard_name': 'biota_group_tbd'
},
'dtype': 'bio_group_t'
},
'species': {
'name': 'species',
'attrs': {
'long_name': 'Species',
'standard_name': 'species'
},
'dtype': 'species_t'
},
'body_part': {
'name': 'body_part',
'attrs': {
'long_name': 'Body part',
'standard_name': 'body_part_tbd'
},
'dtype': 'body_part_t'
}
},
'sed': {
'sed_type': {
'name': 'sed_type',
'attrs': {
'long_name': 'Sediment type',
'standard_name': 'sediment_type_tbd'
},
'dtype': 'sed_type_t'
},
'top': {
'name': 'top',
'attrs': {
'long_name': 'Top depth of sediment layer',
'standard_name': 'top_depth_of_sediment_layer_tbd'
},
'dtype': 'f4'
},
'bottom': {
'name': 'bottom',
'attrs': {
'long_name': 'Bottom depth of sediment layer',
'standard_name': 'bottom_depth_of_sediment_layer_tbd'
},
'dtype': 'f4'
},
},
'suffixes': {
'uncertainty': {
'name': '_unc',
'attrs': {
'long_name': ' uncertainty',
'standard_name': '_uncertainty'
},
'dtype': 'f4'
},
'detection_limit': {
'name': '_dl',
'attrs': {
'long_name': ' detection limit',
'standard_name': '_detection_limit'
},
'dtype': 'dl_t'
},
'volume': {
'name': '_vol',
'attrs': {
'long_name': ' volume',
'standard_name': '_volume'
},
'dtype': 'f4'
},
'salinity': {
'name': '_sal',
'attrs': {
'long_name': ' salinity',
'standard_name': '_sal'
},
'dtype': 'f4'
},
'temperature': {
'name': '_temp',
'attrs': {
'long_name': ' temperature',
'standard_name': '_temp'
},
'dtype': 'f4'
},
'filtered': {
'name': '_filt',
'attrs': {
'long_name': ' filtered',
'standard_name': '_filtered'
},
'dtype': 'filt_t'
},
'counting_method': {
'name': '_counmet',
'attrs': {
'long_name': ' counting method',
'standard_name': '_counting_method'
},
'dtype': 'counmet_t'
},
'sampling_method': {
'name': '_sampmet',
'attrs': {
'long_name': ' sampling method',
'standard_name': '_sampling_method'
},
'dtype': 'sampmet_t'
},
'preparation_method': {
'name': '_prepmet',
'attrs': {
'long_name': ' preparation method',
'standard_name': '_preparation_method'
},
'dtype': 'prepmet_t'
},
'unit': {
'name': '_unit',
'attrs': {
'long_name': ' unit',
'standard_name': '_unit'
},
'dtype': 'unit_t'
}
}
},
'enums': [
{
'name': 'area_t',
'fname': 'dbo_area.xlsx',
'key': 'displayName',
'value':'areaId'
},
{
'name': 'bio_group_t',
'fname': 'dbo_biogroup.xlsx',
'key': 'biogroup',
'value':'biogroup_id'
},
{
'name': 'body_part_t',
'fname': 'dbo_bodypar.xlsx',
'key': 'bodypar',
'value':'bodypar_id'
},
{
'name': 'species_t',
'fname': 'dbo_species_cleaned.xlsx',
'key': 'species',
'value':'species_id'
},
{
'name': 'sed_type_t',
'fname': 'dbo_sedtype.xlsx',
'key': 'sedtype',
'value':'sedtype_id'
},
{
'name': 'unit_t',
'fname': 'dbo_unit.xlsx',
'key': 'unit_sanitized',
'value':'unit_id'
},
{
'name': 'dl_t',
'fname': 'dbo_detectlimit.xlsx',
'key': 'name_sanitized',
'value':'id'
},
{
'name': 'filt_t',
'fname': 'dbo_filtered.xlsx',
'key': 'name',
'value':'id'
},
{
'name': 'counmet_t',
'fname': 'dbo_counmet.xlsx',
'key': 'counmet',
'value':'counmet_id'
},
{
'name': 'sampmet_t',
'fname': 'dbo_sampmet.xlsx',
'key': 'sampmet',
'value':'sampmet_id'
},
{
'name': 'prepmet_t',
'fname': 'dbo_prepmet.xlsx',
'key': 'prepmet',
'value':'prepmet_id'
}
]
}# fc.AttrDict(CONFIGS_CDL['vars']['defaults'])# write_toml(Path('./files') / CDL_FNAME, CONFIGS_CDL)Exported source
# def cdl_cfg():
# "Return the CDL (Common Data Language) configuration as a dictionary."
# try:
# return read_toml(base_path() / CDL_FNAME)
# except FileNotFoundError:
# return CONFIGS_CDLExported source
# def grp_names():
# "Return the group names as defined in `cdl.toml`."
# return [v['name'] for v in cdl_cfg()['grps'].values()]Lookup tables paths
nuc_lut_path
nuc_lut_path ()
Return the path to the nuclide lookup table.
Exported source
def nuc_lut_path():
"Return the path to the nuclide lookup table."
return Path(cfg()['dirs']['lut']) / NUCLIDE_LOOKUP_FNAMEspecies_lut_path
species_lut_path ()
Return the path to the species lookup table.
Exported source
def species_lut_path():
"Return the path to the species lookup table."
src_dir = lut_path()
fname = NC_DTYPES['SPECIES']['fname']
return src_dir / fnamespecies_lut_path()Path('/home/niallmurphy93/.marisco/lut/dbo_species_2024_11_19.xlsx')bodyparts_lut_path
bodyparts_lut_path ()
Return the path to the body parts lookup table.
Exported source
def bodyparts_lut_path():
"Return the path to the body parts lookup table."
src_dir = lut_path()
fname = NC_DTYPES['BODY_PART']['fname']
return src_dir / fnamelab_lut_path
lab_lut_path ()
Return the path to the laboratory lookup table.
Exported source
def lab_lut_path():
"Return the path to the laboratory lookup table."
src_dir = lut_path()
fname = NC_DTYPES['LAB']['fname']
return src_dir / fnamelab_lut_path()Path('/home/niallmurphy93/.marisco/lut/dbo_lab_cleaned.xlsx')biogroup_lut_path
biogroup_lut_path ()
Return the path to the biota group lookup table.
Exported source
def biogroup_lut_path():
"Return the path to the biota group lookup table."
src_dir = lut_path()
fname = NC_DTYPES['BIO_GROUP']['fname']
return src_dir / fnamebiogroup_lut_path()Path('/home/niallmurphy93/.marisco/lut/dbo_biogroup.xlsx')sediments_lut_path
sediments_lut_path ()
Return the path to the sediment type lookup table.
Exported source
def sediments_lut_path():
"Return the path to the sediment type lookup table."
src_dir = lut_path()
fname = NC_DTYPES['SED_TYPE']['fname']
return src_dir / fnamesediments_lut_path()Path('/home/niallmurphy93/.marisco/lut/dbo_sedtype.xlsx')unit_lut_path
unit_lut_path ()
Return the path to the unit lookup table.
Exported source
def unit_lut_path():
"Return the path to the unit lookup table."
src_dir = lut_path()
fname = NC_DTYPES['UNIT']['fname']
return src_dir / fnameunit_lut_path()Path('/home/niallmurphy93/.marisco/lut/dbo_unit.xlsx')detection_limit_lut_path
detection_limit_lut_path ()
Return the path to the detection limit lookup table.
Exported source
def detection_limit_lut_path():
"Return the path to the detection limit lookup table."
src_dir = lut_path()
fname = NC_DTYPES['DL']['fname']
return src_dir / fnamedetection_limit_lut_path()Path('/home/niallmurphy93/.marisco/lut/dbo_detectlimit.xlsx')filtered_lut_path
filtered_lut_path ()
Return the path to the filtered lookup table.
Exported source
def filtered_lut_path():
"Return the path to the filtered lookup table."
src_dir = lut_path()
fname = NC_DTYPES['FILT']['fname']
return src_dir / fnamefiltered_lut_path()Path('/home/niallmurphy93/.marisco/lut/dbo_filtered.xlsx')area_lut_path
area_lut_path ()
Return the path to the area lookup table.
Exported source
def area_lut_path():
"Return the path to the area lookup table."
src_dir = lut_path()
fname = NC_DTYPES['AREA']['fname']
return src_dir / fname
# area_lut_path()area_lut_path()Path('/home/niallmurphy93/.marisco/lut/dbo_area.xlsx')prepmet_lut_path
prepmet_lut_path ()
Return the path to the prepmet lookup table.
Exported source
def prepmet_lut_path():
"Return the path to the prepmet lookup table."
src_dir = lut_path()
fname = NC_DTYPES['PREP_MET']['fname']
return src_dir / fname
# prepmet_lut_path()prepmet_lut_path()Path('/home/niallmurphy93/.marisco/lut/dbo_prepmet.xlsx')sampmet_lut_path
sampmet_lut_path ()
Return the path to the sampmet lookup table.
Exported source
def sampmet_lut_path():
"Return the path to the sampmet lookup table."
src_dir = lut_path()
fname = NC_DTYPES['SAMP_MET']['fname']
return src_dir / fname
# sampmet_lut_path()sampmet_lut_path()Path('/home/niallmurphy93/.marisco/lut/dbo_sampmet.xlsx')counmet_lut_path
counmet_lut_path ()
Return the path to the counmet lookup table.
Exported source
def counmet_lut_path():
"Return the path to the counmet lookup table."
src_dir = lut_path()
fname = NC_DTYPES['COUNT_MET']['fname']
return src_dir / fname
# counmet_lut_path()counmet_lut_path()Path('/home/niallmurphy93/.marisco/lut/dbo_counmet.xlsx')Utilities function
Exported source
NETCDF_TO_PYTHON_TYPE = {
'u8': int,
'f4': float
}Exported source
# def name2grp(
# name: str, # Group name
# cdl: dict, # CDL configuration
# ):
# # Reverse `cdl.toml` config group dict so that group config key can be retrieve based on its name
# return {v['name']:k for k, v in cdl['grps'].items()}[name]Example:
# TO BE REMOVED: Now read directly from `maris.cdl` file
# name2grp('seawater', cdl=CONFIGS_CDL)nc_tpl_name
nc_tpl_name ()
Return the name of the MARIS NetCDF template as defined in configs.toml
Exported source
def nc_tpl_name():
"Return the name of the MARIS NetCDF template as defined in `configs.toml`"
p = base_path()
return read_toml(p / 'configs.toml')['names']['nc_template']nc_tpl_path
nc_tpl_path ()
Return the path of the MARIS NetCDF template as defined in configs.toml
Exported source
def nc_tpl_path():
"Return the path of the MARIS NetCDF template as defined in `configs.toml`"
p = base_path()
return p / read_toml(p / 'configs.toml')['names']['nc_template']get_time_units
get_time_units (nc_path:Callable=<function nc_tpl_path>)
Get the units attribute of the time variable from a NetCDF file.
| Type | Default | Details | |
|---|---|---|---|
| nc_path | Callable | nc_tpl_path | Function returning Path to NetCDF template file |
| Returns | str | Time units string (e.g. ‘seconds since 1970-01-01 00:00:00.0’) |
Exported source
def get_time_units(
nc_path: Callable=nc_tpl_path # Function returning Path to NetCDF template file
) -> str: # Time units string (e.g. 'seconds since 1970-01-01 00:00:00.0')
"Get the units attribute of the time variable from a NetCDF file."
with Dataset(nc_tpl_path(), 'r') as nc:
for group in nc.groups.values():
if 'time' in group.variables:
return group.variables['time'].units
raise ValueError("Time variable not found in NetCDF file")Usage example:
time_units = get_time_units(); time_units'seconds since 1970-01-01 00:00:00.0'Enumeration types
Enumeration types are used to avoid using strings as NetCDF4 variable values. Instead, enumeration types (lookup tables) such as {'Crustaceans': 2, 'Echinoderms': 3, ...} are prepended to the NetCDF file template and associated ids (integers) are used as values.
sanitize
sanitize (s:str|float)
*Sanitize dictionary key to comply with NetCDF enumeration type:
- Remove
(,),.,/,- - Strip the string
- Return original value if it’s not a string (e.g., NaN)*
| Type | Details | |
|---|---|---|
| s | str | float | String or float to sanitize |
| Returns | str | float | Sanitized string or original float |
Exported source
def sanitize(
s: str|float # String or float to sanitize
) -> str|float: # Sanitized string or original float
"""
Sanitize dictionary key to comply with NetCDF enumeration type:
- Remove `(`, `)`, `.`, `/`, `-`
- Strip the string
- Return original value if it's not a string (e.g., NaN)
"""
if isinstance(s, str):
s = re.sub(r'[().]', '', s)
return re.sub(r'[/-]', ' ', s).strip()
elif pd.isna(s): # This covers np.nan, None, and pandas NaT
return s
else:
return str(s).strip()For example:
fc.test_eq(sanitize('key (sanitized)'), 'key sanitized')
fc.test_eq(sanitize('key san.itized'), 'key sanitized')
fc.test_eq(sanitize('key-sanitized'), 'key sanitized')
fc.test_eq(sanitize('key/sanitized'), 'key sanitized')NetCDF4 enumeration type seems to not accept keys containing non alphanumeric characters like parentheses, dots, slash, … As a result, MARIS lookup table needs to be sanitized.
get_lut
get_lut (src_dir:str, fname:str, key:str, value:str, do_sanitize:bool=True, reverse:bool=False, check_duplicates:bool=False)
Convert MARIS db lookup table excel file to dictionary {'name': id, ...} or {id: name, ...} if reverse is True.
| Type | Default | Details | |
|---|---|---|---|
| src_dir | str | Directory containing lookup tables | |
| fname | str | Excel file lookup table name | |
| key | str | Excel file column name to be used as dict keys | |
| value | str | Excel file column name to be used as dict values | |
| do_sanitize | bool | True | Sanitization required? |
| reverse | bool | False | Reverse lookup table (value, key) |
| check_duplicates | bool | False | Check for duplicates in lookup table |
| Returns | Dict | MARIS lookup table (key, value) |
Exported source
def get_lut(
src_dir: str, # Directory containing lookup tables
fname: str, # Excel file lookup table name
key: str, # Excel file column name to be used as dict keys
value: str, # Excel file column name to be used as dict values
do_sanitize: bool=True, # Sanitization required?
reverse: bool=False, # Reverse lookup table (value, key)
check_duplicates: bool=False # Check for duplicates in lookup table
) -> Dict[str, int]: # MARIS lookup table (key, value)
"Convert MARIS db lookup table excel file to dictionary `{'name': id, ...}` or `{id: name, ...}` if `reverse` is True."
fname = Path(src_dir) / fname
df = pd.read_excel(fname, usecols=[key, value]).dropna(subset=value)
if check_duplicates:
duplicates = df[key][df[key].duplicated()].tolist()
if duplicates: print(f"Warning: {fname.name}: found duplicate keys: {duplicates}")
df[value] = df[value].astype('int')
df = df.set_index(key)
lut = df[value].to_dict()
if do_sanitize: lut = {sanitize(k): v for k, v in lut.items()}
lut = {try_int(k): try_int(v) for k, v in lut.items()}
return {v: k for k, v in lut.items()} if reverse else lutFor example:
lut_src_dir = './files/lut'
get_lut(lut_src_dir, 'dbo_biogroup.xlsx', key='biogroup', value='biogroup_id', reverse=False){'Not applicable': -1,
'Not available': 0,
'Birds': 1,
'Crustaceans': 2,
'Echinoderms': 3,
'Fish': 4,
'Mammals': 5,
'Molluscs': 6,
'Others': 7,
'Plankton': 8,
'Polychaete worms': 9,
'Reptile': 10,
'Seaweeds and plants': 11,
'Cephalopods': 12,
'Gastropods': 13,
'Bivalves': 14}Enums
Enums (lut_src_dir:str, dtypes:Dict[str,Dict[str,str]]={'AREA': {'name': 'area_t', 'fname': 'dbo_area.xlsx', 'key': 'displayName', 'value': 'areaId'}, 'BIO_GROUP': {'name': 'bio_group_t', 'fname': 'dbo_biogroup.xlsx', 'key': 'biogroup', 'value': 'biogroup_id'}, 'BODY_PART': {'name': 'body_part_t', 'fname': 'dbo_bodypar.xlsx', 'key': 'bodypar', 'value': 'bodypar_id'}, 'COUNT_MET': {'name': 'count_met_t', 'fname': 'dbo_counmet.xlsx', 'key': 'counmet', 'value': 'counmet_id'}, 'DL': {'name': 'dl_t', 'fname': 'dbo_detectlimit.xlsx', 'key': 'name_sanitized', 'value': 'id'}, 'FILT': {'name': 'filt_t', 'fname': 'dbo_filtered.xlsx', 'key': 'name', 'value': 'id'}, 'NUCLIDE': {'name': 'nuclide_t', 'fname': 'dbo_nuclide.xlsx', 'key': 'nc_name', 'value': 'nuclide_id'}, 'PREP_MET': {'name': 'prep_met_t', 'fname': 'dbo_prepmet.xlsx', 'key': 'prepmet', 'value': 'prepmet_id'}, 'SAMP_MET': {'name': 'samp_met_t', 'fname': 'dbo_sampmet.xlsx', 'key': 'sampmet', 'value': 'sampmet_id'}, 'SED_TYPE': {'name': 'sed_type_t', 'fname': 'dbo_sedtype.xlsx', 'key': 'sedtype', 'value': 'sedtype_id'}, 'SPECIES': {'name': 'species_t', 'fname': 'dbo_species_2024_11_19.xlsx', 'key': 'species', 'value': 'species_id'}, 'UNIT': {'name': 'unit_t', 'fname': 'dbo_unit.xlsx', 'key': 'unit_sanitized', 'value': 'unit_id'}, 'LAB': {'name': 'lab_t', 'fname': 'dbo_lab_cleaned.xlsx', 'key': 'lab', 'value': 'lab_id'}})
Return dictionaries of MARIS NetCDF’s enumeration types.
| Type | Default | Details | |
|---|---|---|---|
| lut_src_dir | str | Directory containing lookup tables | |
| dtypes | Dict | {‘AREA’: {‘name’: ‘area_t’, ‘fname’: ‘dbo_area.xlsx’, ‘key’: ‘displayName’, ‘value’: ‘areaId’}, ‘BIO_GROUP’: {‘name’: ‘bio_group_t’, ‘fname’: ‘dbo_biogroup.xlsx’, ‘key’: ‘biogroup’, ‘value’: ‘biogroup_id’}, ‘BODY_PART’: {‘name’: ‘body_part_t’, ‘fname’: ‘dbo_bodypar.xlsx’, ‘key’: ‘bodypar’, ‘value’: ‘bodypar_id’}, ‘COUNT_MET’: {‘name’: ‘count_met_t’, ‘fname’: ‘dbo_counmet.xlsx’, ‘key’: ‘counmet’, ‘value’: ‘counmet_id’}, ‘DL’: {‘name’: ‘dl_t’, ‘fname’: ‘dbo_detectlimit.xlsx’, ‘key’: ‘name_sanitized’, ‘value’: ‘id’}, ‘FILT’: {‘name’: ‘filt_t’, ‘fname’: ‘dbo_filtered.xlsx’, ‘key’: ‘name’, ‘value’: ‘id’}, ‘NUCLIDE’: {‘name’: ‘nuclide_t’, ‘fname’: ‘dbo_nuclide.xlsx’, ‘key’: ‘nc_name’, ‘value’: ‘nuclide_id’}, ‘PREP_MET’: {‘name’: ‘prep_met_t’, ‘fname’: ‘dbo_prepmet.xlsx’, ‘key’: ‘prepmet’, ‘value’: ‘prepmet_id’}, ‘SAMP_MET’: {‘name’: ‘samp_met_t’, ‘fname’: ‘dbo_sampmet.xlsx’, ‘key’: ‘sampmet’, ‘value’: ‘sampmet_id’}, ‘SED_TYPE’: {‘name’: ‘sed_type_t’, ‘fname’: ‘dbo_sedtype.xlsx’, ‘key’: ‘sedtype’, ‘value’: ‘sedtype_id’}, ‘SPECIES’: {‘name’: ‘species_t’, ‘fname’: ‘dbo_species_2024_11_19.xlsx’, ‘key’: ‘species’, ‘value’: ‘species_id’}, ‘UNIT’: {‘name’: ‘unit_t’, ‘fname’: ‘dbo_unit.xlsx’, ‘key’: ‘unit_sanitized’, ‘value’: ‘unit_id’}, ‘LAB’: {‘name’: ‘lab_t’, ‘fname’: ‘dbo_lab_cleaned.xlsx’, ‘key’: ‘lab’, ‘value’: ‘lab_id’}} | Custom NetCDF types |
Exported source
class Enums():
"Return dictionaries of MARIS NetCDF's enumeration types."
def __init__(self,
lut_src_dir: str, # Directory containing lookup tables
dtypes: Dict[str, Dict[str, str]]=NC_DTYPES, # Custom NetCDF types
):
fc.store_attr()
self.types = self.lookup()
def filter(self, var_name, values):
return {name: id for name, id in self.types[var_name].items() if id in values}
def lookup(self):
types = {}
for var_name, dtype in self.dtypes.items():
name, fname, key, value = dtype.values()
lut = get_lut(self.lut_src_dir, fname, key=key, value=value)
types[var_name] = lut
return typeslut_src_dir_test = './files/lut'
enums = Enums(lut_src_dir=lut_src_dir_test)enums.types['DL']{'Not applicable': -1,
'Not available': 0,
'Detected value': 1,
'Detection limit': 2,
'Not detected': 3,
'Derived': 4}for k,v in enums.types['SPECIES'].items():
print(k, v)NOT AVAILABLE 0
Aristeus antennatus 1
Apostichopus 2
Saccharina japonica var religiosa 3
Siganus fuscescens 4
Alpheus dentipes 5
Hexagrammos agrammus 6
Ditrema temminckii 7
Parapristipoma trilineatum 8
Scombrops boops 9
Pseudopleuronectes schrenki 10
Desmarestia ligulata 11
Saccharina japonica 12
Neodilsea yendoana 13
Costaria costata 14
Sargassum yezoense 15
Acanthephyra pelagica 16
Sargassum ringgoldianum 17
Acanthephyra quadrispinosa 18
Sargassum thunbergii 19
Sargassum patens 20
Asterias rubens 21
Sargassum miyabei 22
Homarus gammarus 23
Acanthephyra stylorostratis 24
Acanthocybium solandri 25
Acanthopagrus bifasciatus 26
Acanthophora muscoides 27
Acanthophora spicifera 28
Acanthurus triostegus 29
Actinopterygii 30
Adamussium colbecki 31
Ahnfeltiopsis densa 32
Alepes melanoptera 33
Ampharetidae 34
Anchoviella lepidentostole 35
Anguillidae 36
Aphroditidae 37
Arnoglossus 38
Aurigequula fasciata 39
Balaenoptera musculus 40
Balaenoptera physalus 41
Balistes 42
Beryciformes 43
Bryopsis maxima 44
Callinectes sp 45
Callorhinus ursinus 46
Carassius auratus auratus 47
Carcharhinus sorrah 48
Caridae 49
Clupea harengus 50
Cathorops spixii 51
Caulerpa racemosa 52
Caulerpa scalpelliformis 53
Caulerpa sertularioides 54
Cellana radiata 55
Coscinasterias tenuispina 56
Centroceras clavulatum 57
Centropomus parallelus 58
Crangon crangon 59
Ceramium diaphanum 60
Ceramium rubrum 61
Chaenocephalus aceratus 62
Chaetodipterus faber 63
Chaetomorpha antennina 64
Chaetomorpha linoides 65
Chelidonichthys kumu 66
Chelon ramada 67
Chiloscyllium 68
Chionodraco hamatus 69
Chlamys islandica 70
Chlorophyta 71
Chondrichthyes 72
Chrysaora 73
Cladophora nitellopsis 74
Cladophora vagabunda 75
Cladophoropsis membranacea 76
Clupea 77
Coccotylus truncatus 78
Codium fragile 79
Crassostrea 80
Cynoscion acoupa 81
Cynoscion jamaicensis 82
Cynoscion leiarchus 83
Engraulis encrasicolus 84
Cypselurus agoo agoo 85
Cystophora cristata 86
Cystoseira barbata 87
Cystoseira crinita 88
Decapodiformes 89
Decapterus russelli 90
Decapterus scombrinus 91
Delphinapterus leucas 92
Delphinus capensis 93
Diapterus rhombeus 94
Dicentrarchus punctatus 95
Fucus vesiculosus 96
Funchalia woodwardi 97
Ecklonia bicyclis 98
Gadus morhua 99
Ecklonia kurome 100
Gennadas elegans 101
Eisenia arborea 102
Encrasicholina devisi 103
Enteromorpha 104
Enteromorpha flexuosa 105
Enteromorpha intestinalis 106
Epinephelinae 107
Epinephelus diacanthus 108
Exocoetidae 109
Saccharina latissima 110
Gracilaria corticata 111
Ligur ensiferus 112
Gracilaria debilis 113
Gracilaria edulis 114
Gracilariales 115
Grateloupia elliptica 116
Grateloupia filicina 117
Lysmata seticaudata 118
Gymnogongrus griffithsiae 119
Mya arenaria 120
Halichoerus grypus 121
Macoma balthica 122
Marthasterias glacialis 123
Halimeda macroloba 124
Harengula clupeola 125
Harpagifer antarcticus 126
Hemifusus ternatanus 127
Hemiramphus brasiliensis 128
Mytilus edulis 129
Metapenaeus affinis 130
Heteroscleromorpha 131
Heterosigma akashiwo 132
Hilsa ilisha 133
Metapenaeus monoceros 134
Metapenaeus stebbingi 135
Holothuria 136
Hoplobrotula armata 137
Hypnea musciformis 138
Merlangius merlangus 139
Iridaea cordata 140
Jania rubens 141
Meganyctiphanes norvegica 142
Johnius glaucus 143
Kappaphycus 144
Kappaphycus alvarezii 145
Laevistrombus canarium 146
Lagenodelphis hosei 147
Lambia 148
Laminaria japonica 149
Laminaria longissima 150
Larimus breviceps 151
Laurencia papillosa 152
Leiognathidae 153
Leiognathus dussumieri 154
Lepidochelys olivacea 155
Leptonychotes weddellii 156
Limanda yokohamae 157
Nephrops norvegicus 158
Neuston 159
Littoraria undulata 160
Loligo vulgaris 161
Lumbrineridae 162
Lutjanus fulviflamma 163
Marginisporum aberrans 164
Megalaspis cordyla 165
Octopus vulgaris 166
Menticirrhus americanus 167
Mesoplodon densirostris 168
Palaemon longirostris 169
Metapenaeus brevicornis 170
Pasiphaea multidentata 171
Pasiphaea sivado 172
Parapenaeopsis stylifera 173
Miichthys miiuy 174
Mirounga leonina 175
Brachidontes striatulus 176
Monodon monoceros 177
Mugil platanus 178
Penaeus semisulcatus 179
Mullus barbatus 180
Mycteroperca rubra 181
Philocheras echinulatus 182
Myelophycus simplex 183
Mytilus coruscus 184
Penaeus indicus 185
Natator depressus 186
Pandalus jordani 187
Melicertus kerathurus 188
Parapenaeus longirostris 189
Plesionika 190
Platichthys flesus 191
Pleuronectes platessa 192
Nematopalaemon tenuipes 193
Nematoscelis difficilis 194
Nemipterus 195
Aegaeon lacazei 196
Nephtyidae 197
Nereididae 198
Netuma bilineata 199
Nibea maculata 200
Oceana serrulata 201
Palaemon serratus 202
Ocypode 203
Odobenus rosmarus 204
Ogcocephalus vespertilio 205
Oligoplites saurus 206
Onuphidae 207
Opheliidae 208
Opisthonema oglinum 209
Opisthopterus tardoore 210
Orientomysis mitsukurii 211
Otolithes cuvieri 212
Padina pavonica 213
Padina tetrastromatica 214
Padina vickersiae 215
Pagellus affinis 216
Pagophilus groenlandicus 217
Paguroidea 218
Pagurus 219
Systellaspis debilis 220
Sergestes 221
Sergestes arcticus 222
Pampus argenteus 223
Sergestes arachnipodus 224
Sergestes henseni 225
Sergestes prehensilis 226
Sergestes robustus 227
Pangasius pangasius 228
Panulirus homarus 229
Paracentrotus lividus 230
Pasiphaea sp 231
Pectinariidae 232
Penaeus 233
Phoca vitulina 234
Photopectoralis bindus 235
Phyllospadix iwatensis 236
Plectorhinchus mediterraneus 237
Pleuronectes mochigarei 238
Pleuronectes obscurus 239
Plocamium brasiliense 240
Polynemus paradiseus 241
Polysiphonia 242
Sprattus sprattus 243
Scomber scombrus 244
Polysiphonia fucoides 245
Gonostomatidae 246
Perca fluviatilis 247
Pomadasys crocro 248
Porphyra tenera 249
Potamogeton pectinatus 250
Priacanthus hamrur 251
Pseudorhombus malayanus 252
Pterocladiella capillacea 253
Pusa caspica 254
Pusa sibirica 255
Pylaiella littoralis 256
Sabellidae 257
Salangichthys ishikawae 258
Sarconema filiforme 259
Sardinella albella 260
Sardinella brasiliensis 261
Sardinops melanostictus 262
Sargassum cymosum 263
Sargassum linearifolium 264
Sargassum micracanthum 265
Xiphias gladius 266
Sargassum novae hollandiae 267
Sargassum oligocystum 268
Esox lucius 269
Limanda limanda 270
Abramis brama 271
Anguilla anguilla 272
Arctica islandica 273
Cerastoderma edule 274
Cyprinus carpio 275
Echinodermata 276
Fish larvae 277
Myoxocephalus scorpius 278
Osmerus eperlanus 279
Plankton 280
Scophthalmus maximus 281
Rhodophyta 282
Rutilus rutilus 283
Saduria entomon 284
Sander lucioperca 285
Gasterosteus aculeatus 286
Zoarces viviparus 287
Gymnocephalus cernua 288
Furcellaria lumbricalis 289
Cladophora glomerata 290
Lateolabrax japonicus 291
Okamejei kenojei 292
Sebastes pachycephalus 293
Squalus acanthias 294
Gadus macrocephalus 295
Paralichthys olivaceus 296
Ovalipes punctatus 297
Pseudopleuronectes yokohamae 298
Hemitripterus villosus 299
Clidoderma asperrimum 300
Microstomus achne 301
Lepidotrigla microptera 302
Hexagrammos otakii 303
Kareius bicoloratus 304
Pleuronichthys cornutus 305
Enteroctopus dofleini 306
Ammodytes personatus 307
Lophius litulon 308
Eopsetta grigorjewi 309
Takifugu porphyreus 310
Loliolus japonica 311
Sepia andreana 312
Sebastes cheni 313
Portunus trituberculatus 314
Sebastes schlegelii 315
Pennahia argentata 316
Platichthys stellatus 317
Gadus chalcogrammus 318
Chelidonichthys spinosus 319
Conger myriaster 320
Heterololigo bleekeri 321
Stichaeus grigorjewi 322
Pseudopleuronectes herzensteini 323
Octopus conispadiceus 324
Hippoglossoides dubius 325
Cleisthenes pinetorum 326
Glyptocephalus stelleri 327
Tanakius kitaharae 328
Nibea mitsukurii 329
Dasyatis matsubarai 330
Verasper moseri 331
Hemitrygon akajei 332
Triakis scyllium 333
Trachurus japonicus 334
Zeus faber 335
Pagrus major 336
Acanthopagrus schlegelii 337
Dentex tumifrons 338
Mustelus manazo 339
Seriola quinqueradiata 340
Hyperoglyphe japonica 341
Carcharhinus 342
Platycephalus 343
Scomber japonicus 344
Squatina japonica 345
Alopias pelagicus 346
Zenopsis nebulosa 347
Cynoglossus joyneri 348
Verasper variegatus 349
Oncorhynchus keta 350
Physiculus japonicus 351
Oplegnathus punctatus 352
Arothron hispidus 353
Stereolepis doederleini 354
Takifugu snyderi 355
Scomber australasicus 356
Liparis tanakae 357
Thamnaconus modestus 358
Gnathophis nystromi 359
Sebastes oblongus 360
Sebastiscus marmoratus 361
Takifugu pardalis 362
Mugil cephalus 363
Ditrema temminckii temminckii 364
Konosirus punctatus 365
Tribolodon brandtii 366
Oncorhynchus masou 367
Aluterus monoceros 368
Todarodes pacificus 369
Myoxocephalus stelleri 370
Myliobatis tobijei 371
Scyliorhinus torazame 372
Lophiomus setigerus 373
Heterodontus japonicus 374
Sebastes vulpes 375
Paraplagusia japonica 376
Ostrea edulis 377
Melanogrammus aeglefinus 378
Pollachius virens 379
Pollachius pollachius 380
Sebastes marinus 381
Anarhichas minor 382
Anarhichas denticulatus 383
Reinhardtius hippoglossoides 384
Trisopterus esmarkii 385
Micromesistius poutassou 386
Coryphaenoides rupestris 387
Argentina silus 388
Salmo salar 389
Sebastes viviparus 390
Buccinum undatum 391
Fucus serratus 392
Merluccius merluccius 393
Littorina littorea 394
Fucus 395
Rhodymenia 396
Solea solea 397
Trachurus trachurus 398
Eutrigla gurnardus 399
Pelvetia canaliculata 400
Ascophyllum nodosum 401
Mallotus villosus 402
Pecten maximus 403
Hippoglossoides platessoides 404
Sebastes mentella 405
Modiolus modiolus 406
Boreogadus saida 407
Sepia 408
Gadus 409
Sardina pilchardus 410
Pleuronectiformes 411
Molva molva 412
Patella 413
Crassostrea gigas 414
Dasyatis pastinaca 415
Lophius piscatorius 416
Porphyra umbilicalis 417
Patella vulgata 418
Brosme brosme 419
Glyptocephalus cynoglossus 420
Galeus melastomus 421
Chimaera monstrosa 422
Etmopterus spinax 423
Dicentrarchus labrax 424
Osilinus lineatus 425
Hippoglossus hippoglossus 426
Cyclopterus lumpus 427
Molva dypterygia 428
Microstomus kitt 429
Fucus distichus 430
Tapes 431
Sebastes norvegicus 432
Phycis blennoides 433
Fucus spiralis 434
Laminaria digitata 435
Dipturus batis 436
Anarhichas lupus 437
Lumpenus lampretaeformis 438
Lycodes vahlii 439
Argentina sphyraena 440
Trisopterus minutus 441
Thunnus 442
Hyperoplus lanceolatus 443
Gaidropsarus argentatus 444
Engraulis japonicus 445
Mytilus galloprovincialis 446
Undaria pinnatifida 447
Chlorophthalmus albatrossis 448
Sargassum fusiforme 449
Eisenia bicyclis 450
Spisula sachalinensis 451
Strongylocentrotus nudus 452
Haliotis discus hannai 453
Dexistes rikuzenius 454
Ruditapes philippinarum 455
Apostichopus japonicus 456
Pterothrissus gissu 457
Helicolenus hilgendorfii 458
Buccinum isaotakii 459
Neptunea intersculpta 460
Apostichopus nigripunctatus 461
Sebastes thompsoni 462
Oratosquilla oratoria 463
Oncorhynchus kisutch 464
Erimacrus isenbeckii 465
Sillago japonica 466
Trachysalambria curvirostris 467
Mytilus unguiculatus 468
Crassostrea nippona 469
Laminariales 470
Uroteuthis edulis 471
Takifugu poecilonotus 472
Neptunea arthritica 473
Katsuwonus pelamis 474
Doederleinia berycoides 475
Metapenaeopsis dalei 476
Seriola dumerili 477
Pseudorhombus pentophthalmus 478
Stephanolepis cirrhifer 479
Cookeolus japonicus 480
Panulirus japonicus 481
Thunnus orientalis 482
Halocynthia roretzi 483
Etrumeus sadina 484
Cololabis saira 485
Coryphaena hippurus 486
Sarda orientalis 487
Octopus ocellatus 488
Sardinops sagax 489
Sphyraena pinguis 490
Sebastes ventricosus 491
Occella iburia 492
Glossanodon semifasciatus 493
Mizuhopecten yessoensis 494
Neosalangichthys ishikawae 495
Bothrocara tanakae 496
Malacocottus zonurus 497
Coelorinchus macrochir 498
Neptunea constricta 499
Beringius polynematicus 500
Sebastes nivosus 501
Pandalus eous 502
Synaphobranchus kaupii 503
Sebastolobus macrochir 504
Marsupenaeus japonicus 505
Japelion hirasei 506
Pleurogrammus azonus 507
Monostroma nitidum 508
Atheresthes evermanni 509
Takifugu rubripes 510
Chionoecetes opilio 511
Pandalopsis coccinata 512
Chionoecetes japonicus 513
Sebastes matsubarae 514
Scombrops gilberti 515
Hyporhamphus sajori 516
Trichiurus lepturus 517
Alcichthys elongatus 518
Volutharpa perryi 519
Mercenaria stimpsoni 520
Berryteuthis magister 521
Aptocyclus ventricosus 522
Euphausia pacifica 523
Salangichthys microdon 524
Telmessus acutidens 525
Ceratophyllum demersum 526
Pandalus nipponensis 527
Sebastes owstoni 528
Cociella crocodilus 529
Conger japonicus 530
Sardinella zunasi 531
Cheilopogon pinnatibarbatus japonicus 532
Oplegnathus fasciatus 533
Macridiscus aequilatera 534
Repomucenus ornatipinnis 535
Clupea pallasii 536
Scorpaena neglecta 537
Scomberomorus niphonius 538
Leucopsarion petersii 539
Sebastes scythropus 540
Strongylura anastomella 541
Laemonema longipes 542
Fusitriton oregonensis 543
Japelion pericochlion 544
Sebastes steindachneri 545
Auxis rochei 546
Lobotes surinamensis 547
Auxis thazard 548
Chlorophthalmus borealis 549
Etelis coruscans 550
Sebastes inermis 551
Cynoglossus interruptus 552
Erilepis zonifer 553
Tridentiger obscurus 554
Caranx sexfasciatus 555
Thunnus thynnus 556
Takifugu stictonotus 557
Euthynnus affinis 558
Synagrops japonicus 559
Okamejei schmidti 560
Suggrundus meerdervoortii 561
Sebastes baramenuke 562
Pleurogrammus monopterygius 563
Decapterus maruadsi 564
Girella punctata 565
Sphyraena japonica 566
Ommastrephes bartramii 567
Sepiella japonica 568
Sepioteuthis lessoniana 569
Eucleoteuthis luminosa 570
Gloiopeltis furcata 571
Macrobrachium nipponense 572
Sepia kobiensis 573
Eriocheir japonica 574
Magallana nippona 575
Meretrix lusoria 576
Chondrus ocellatus 577
Chondrus elatus 578
Gloiopeltis 579
Holothuroidea 580
Corbicula japonica 581
Sunetta menstrualis 582
Pseudorhombus cinnamoneus 583
Takifugu niphobles 584
Lagocephalus gloveri 585
Beryx splendens 586
Parastichopus nigripunctatus 587
Venerupis philippinarum 588
Haliotis 589
Liparis agassizii 590
Seriola lalandi 591
Niphon spinosus 592
Pleuronichthys japonicus 593
Sergia lucens 594
Sphoeroides pachygaster 595
Coryphaenoides acrolepis 596
Pseudopleuronectes obscurus 597
Pyropia yezoensis 598
Isurus oxyrinchus 599
Sargassum fulvellum 600
Prionace glauca 601
Kajikia audax 602
Thunnus albacares 603
Thunnus alalunga 604
Thunnus obesus 605
Lamna ditropis 606
Glyptocidaris crenularis 607
Asterias amurensis 608
Sepiida 609
Congridae 610
Takifugu 611
Sargassum horneri 612
Haliotis discus 613
Pleuronectidae 614
Acanthogobius flavimanus 615
Acanthogobius lactipes 616
Pholis nebulosa 617
Hemigrapsus penicillatus 618
Palaemon paucidens 619
Mysidae 620
Zostera marina 621
Ulva pertusa 622
Gobiidae 623
Atherinidae 624
Tribolodon 625
Alpheus 626
Polychaeta 627
Sebastes 628
Charybdis japonica 629
Hemigrapsus 630
Favonigobius gymnauchen 631
Palaemon 632
Planiliza haematocheila 633
Palaemonidae 634
Pholis crassispina 635
Laminaria 636
Distolasterias nipon 637
Lophiiformes 638
Alpheus brevicristatus 639
Undaria undariodes 640
Neomysis awatschensis 641
Alpheidae 642
Macrobrachium 643
Hediste 644
Gymnogobius breunigii 645
Luidia quinaria 646
Rhizoprionodon acutus 647
Carangoides equula 648
Carcinoplax longimana 649
Anomura 650
Spatangoida 651
Plesiobatis daviesi 652
Eusphyra blochii 653
Ruditapes variegata 654
Sinonovacula constricta 655
Penaeus monodon 656
Litopenaeus vannamei 657
Solenocera crassicornis 658
Stomatopoda 659
Teuthida 660
Octopus 661
Larimichthys polyactis 662
Scomberomorini 663
Channa argus 664
Ranina ranina 665
Lates calcarifer 666
Scomberomorus commerson 667
Lutjanus malabaricus 668
Thenus parindicus 669
Amusium pleuronectes 670
Loligo 671
Plectropomus leopardus 672
Sillago ciliata 673
Scylla serrata 674
Pinctada maxima 675
Lutjanus argentimaculatus 676
Protonibea diacanthus 677
Polydactylus macrochir 678
Rachycentron canadum 679
Ibacus peronii 680
Arripis trutta 681
Sarda australis 682
Seriola hippos 683
Choerodon schoenleinii 684
Panulirus ornatus 685
Neotrygon kuhlii 686
Lethrinus nebulosus 687
Parupeneus multifasciatus 688
Saccostrea cucullata 689
Lutjanus sebae 690
Thunnus maccoyii 691
Acanthopagrus butcheri 692
Lambis lambis 693
Gerres subfasciatus 694
Zooplankton 695
Phytoplankton 696
Rapana venosa 697
Scapharca inaequivalvis 698
Ulva intestinalis 699
Ulva linza 700
Ceramium virgatum 701
Gayralia oxysperma 702
Vertebrata fucoides 703
Stuckenia pectinata 704
Rochia nilotica 705
Ctenochaetus striatus 706
Serranidae 707
Turbo setosus 708
Pandalidae 709
Gymnosarda unicolor 710
Epinephelini 711
Pisces 712
Liza klunzingeri 713
Acanthopagrus latus 714
Liza subviridis 715
Sparidentex hasta 716
Otolithes ruber 717
Crenidens crenidens 718
Ensis 719
Gastropoda 720
Euheterodonta 721
Scomber 722
Theragra chalcogramma 723
Engraulidae 724
Ostreidae 725
Phaeophyceae 726
Porphyra 727
Ulva reticulata 728
Perna viridis 729
Fenneropenaeus indicus 730
Merluccius 731
Soleidae 732
Mugilidae 733
Marine algae 734
Scarus rivulatus 735
Scarus coeruleus 736
Sardinella fimbriata 737
Dussumieria acuta 738
Lutjanus kasmira 739
Lutjanus rivulatus 740
Lutjanus bohar 741
Priacanthus blochii 742
Pelates quadrilineatus 743
Epinephelus fasciatus 744
Upeneus vittatus 745
Lethrinus laticaudis 746
Lethrinus lentjan 747
Lethrinus microdon 748
Sphyraena barracuda 749
Alectis indica 750
Epinephelus latifasciatus 751
Nemipterus japonicus 752
Raconda russeliana 753
Lactarius lactarius 754
Aetomylaeus bovinus 755
Pennahia anea 756
Leiognathus fasciatus 757
Sardinella longiceps 758
Tenualosa ilisha 759
Pellona ditchela 760
Stolephorus indicus 761
Setipinna breviceps 762
Rastrelliger kanagurta 763
Chanos chanos 764
Lepturacanthus savala 765
Epinephelus niveatus 766
Lutjanus johnii 767
Carangoides malabaricus 768
Ablennes hians 769
Chirocentrus dorab 770
Scomberomorus cavalla 771
Scomberomorus semifasciatus 772
Scomberomorus guttatus 773
Etrumeus teres 774
Spondyliosoma cantharus 775
Brama brama 776
Dasyatis zugei 777
Harpadon nehereus 778
Carcharhinus melanopterus 779
Penaeus plebejus 780
Sepia officinalis 781
Johnius dussumieri 782
Lutjanus campechanus 783
Ruditapes decussatus 784
Carcinus aestuarii 785
Squilla mantis 786
Epinephelus polyphekadion 787
Lutjanus gibbus 788
Lethrinus mahsena 789
Epinephelus chlorostigma 790
Carangoides bajad 791
Aethaloperca rogaa 792
Atule mate 793
Macolor niger 794
Carangoides fulvoguttatus 795
Plectropomus areolatus 796
Cephalopholis argus 797
Cephalopholis 798
Scarus sordidus 799
Scomberomorus tritor 800
Triaenodon obesus 801
Pomadasys commersonnii 802
Monotaxis grandoculis 803
Plectropomus maculatus 804
Trachinotus blochii 805
Pristipomoides filamentosus 806
Acanthurus gahhm 807
Acanthurus sohal 808
Siganus argenteus 809
Naso unicornis 810
Chanos 811
Oedalechilus labiosus 812
Plectorhinchus gaterinus 813
Mercenaria mercenaria 814
Mytilus 815
Turbo cornutus 816
Decapoda 817
Sphyraena 818
Arius maculatus 819
Penaeus merguiensis 820
Tegillarca granosa 821
Mullus barbatus barbatus 822
Chamelea gallina 823
Metanephrops thomsoni 824
Magallana gigas 825
Branchiostegus japonicus 826
Cephalopoda 827
Lutjanidae 828
Lethrinidae 829
Sphyraena argentea 830
Chirocentrus nudus 831
Trachinotus 832
Mugil auratus 833
Euthynnus alletteratus 834
Sparus aurata 835
Pagrus caeruleostictus 836
Scorpaena scrofa 837
Pagellus erythrinus 838
Epinephelus aeneus 839
Dentex maroccanus 840
Caranx rhonchus 841
Sardinella 842
Siganus 843
Solea 844
Diplodus sargus 845
Lithognathus mormyrus 846
Oblada melanura 847
Siganus rivulatus 848
Chelon labrosus 849
Cynoscion microlepidotus 850
Genypterus brasiliensis 851
Myoxocephalus polyacanthocephalus 852
Hexagrammos lagocephalus 853
Hexagrammos decagrammus 854
Sebastes ciliatus 855
Lepidopsetta polyxystra 856
Clupeiformes 857
Gadidae 858
Brachyura 859
Dasyatis 860
Carcharias 861
Saurida 862
Upeneus 863
Cynoglossus 864
Scomberomorus 865
Terapon 866
Leiognathus 867
Terapontidae 868
Caranx 869
Diplodus 870
Plectorhinchus flavomaculatus 871
Salmonidae 872
Mollusca 873
Boops boops 874
Sarpa salpa 875
Pagellus acarne 876
Spicara smaris 877
Diplodus vulgaris 878
Chelidonichthys lucerna 879
Sarda sarda 880
Serranus cabrilla 881
Diplodus annularis 882
Pagrus pagrus 883
Alosa fallax 884
Belone belone 885
Dentex dentex 886
Sphyraena viridensis 887
Trisopterus capelanus 888
Arnoglossus laterna 889
Procambarus clarkii 890
Nemadactylus macropterus 891
Pagrus auratus 892
Jasus edwardsii 893
Perna canaliculus 894
Pseudophycis bachus 895
Haliotis iris 896
Hoplostethus atlanticus 897
Rhombosolea leporina 898
Zygochlamys delicatula 899
Galeorhinus galeus 900
Parapercis colias 901
Tiostrea chilensis 902
Genypterus blacodes 903
Evechinus chloroticus 904
Austrovenus stutchburyi 905
Micromesistius australis 906
Macruronus novaezelandiae 907
Nototodarus 908
Perna perna 909
Sepia pharaonis 910
Turbo bruneus 911
Portunus sanguinolentus 912
Charybdis natator 913
Charybdis lucifera 914
Panulirus argus 915
Ethmalosa fimbriata 916
Sardinella brachysoma 917
Thryssa mystax 918
Plicofollis dussumieri 919
Nibea soldado 920
Epinephelus melanostigma 921
Megalops cyprinoides 922
Decapterus macarellus 923
Drepane punctata 924
Sillago sihama 925
Tylosurus crocodilus crocodilus 926
Saurida tumbil 927
Cynoglossus macrostomus 928
Parupeneus indicus 929
Synechogobius hasta 930
Busycotypus canaliculatus 931
Pampus cinereus 932
Pomadasys kaakan 933
Epinephelus coioides 934
Sepiella inermis 935
Uroteuthis duvauceli 936
Stomatella auricula 937
Cerithium scabridum 938
Marcia recens 939
Circe intermedia 940
Marcia opima 941
Fulvia fragile 942
Charybdis feriatus 943
Charybdis annulata 944
Atergatis integerrimus 945
Matuta lunaris 946
Calappa lophos 947
Uca annulipes 948
Chlamys varia 949
Cololabis adocetus 950
Seriola lalandi dorsalis 951
Brunneifusus ternatanus 952
Metapenaeus joyneri 953
Epinephelus tauvina 954
Coilia dussumieri 955
Carcharhinus dussumieri 956
Upeneus tragula 957
Sartoriana spinigera 958
Lamellidens marginalis 959
Polydactylus sextarius 960
Johnius macrorhynus 961
Hexanematichthys sagor 962
Sargassum swartzii 963
Argyrops spinifer 964
Synodus intermedius 965
Muraenesox cinereus 966
Carangoides armatus 967
Eleutheronema tetradactylum 968
Mustelus mosis 969
Nemipterus bipunctatus 970
Lutjanus quinquelineatus 971
Platycephalus indicus 972
Rhabdosargus haffara 973
Argyrops filamentosus 974
Brachirus orientalis 975
Mene maculata 976
Hemiramphus marginatus 977
Encrasicholina heteroloba 978
Trachinotus africanus 979
Bramidae 980
Escualosa thoracata 981
Sepia arabica 982
Scatophagus argus 983
Parastromateus niger 984
Planiliza subviridis 985
Labeo rohita 986
Oreochromis niloticus 987
Cardiidae 988
Sargassum angustifolium 989
Pomacea bridgesii 990
Sebastes fasciatus 991
Batoidea 992
Urophycis chuss 993
Dalatias licha 994
Trisopterus luscus 995
Scyliorhinus canicula 996
Ruvettus pretiosus 997
Aphanopus carbo 998
Alepocephalus bairdii 999
Centroscymnus coelolepis 1000
Loligo forbesii 1001
Lutjanus cyanopterus 1002
Mugil liza 1003
Micropogonias furnieri 1004
Balistes capriscus 1005
Haemulidae 1006
Stenotomus caprinus 1007
Hemanthias leptus 1008
Micropogonias undulatus 1009
Cynoscion nebulosus 1010
Rhomboplites aurorubens 1011
Bothidae 1012
Pogonias cromis 1013
Lutjanus synagris 1014
Netuma thalassina 1015
Sillaginopsis panijus 1016
Leptomelanosoma indicum 1017
Therapon 1018
Pterotolithus maculatus 1019
Ilisha filigera 1020
Hilsa kelee 1021
Pampus chinensis 1022
Palaemon styliferus 1023
Argyrosomus regius 1024
Lutjanus 1025
Sciades 1026
Mullus 1027
Albula vulpes 1028
Selar crumenophthalmus 1029
Centropomus 1030
Sardinella aurita 1031
Harengula humeralis 1032
Diapterus auratus 1033
Gerres cinereus 1034
Haemulon parra 1035
Ocyurus chrysurus 1036
Sphyraena guachancho 1037
Anoplopoma fimbria 1038
Nerita versicolor 1039
Bulla striata 1040
Melongena melongena 1041
Trachycardium muricatum 1042
Isognomon alatus 1043
Brachidontes exustus 1044
Crassostrea virginica 1045
Protothaca granulata 1046
Cittarium pica 1047
Penaeus schmitti 1048
Penaeus notialis 1049
Callinectes sapidus 1050
Callinectes danae 1051
Dasyatidae 1052
Caridea 1053
Nephropidae 1054
Sparus 1055
Sargassum boveanum 1056
Haliotis tuberculata 1057
Littorinidae 1058
Seaweed 1059
Echinoidea 1060
Ostreida 1061
Donax trunculus 1062
Scrobicularia plana 1063
Venus verrucosa 1064
Solen marginatus 1065
Testudines 1066
Mullidae 1067
Amphipoda 1068
Cystosphaera jacquinotii 1069
Daption capense 1070
Desmarestia anceps 1071
Himantothallus grandifolius 1072
Mirounga 1073
Nacella concinna 1074
Notothenia coriiceps 1075
Pygoscelis antarcticus 1076
Pygoscelis papua 1077
Oncorhynchus gorbuscha 1078
Oncorhynchus mykiss 1079
Oncorhynchus nerka 1080
Oncorhynchus tshawytscha 1081
Erignathus barbatus 1082
Pusa hispida 1083
Hippoglossus stenolepis 1084
Squalus suckleyi 1085
Sargassum 1086
Codium 1087
Membranoptera alata 1088
Dictyota dichotoma 1089
Plocamium cartilagineum 1090
Galatea paradoxa 1091
Crassostrea tulipa 1092
Macrobrachium sp 1093
Portunus 1094
Tympanotonos fuscatus 1095
Thais 1096
Bivalvia 1097
Cynoglossus senegalensis 1098
Carlarius heudelotii 1099
Fontitrygon margarita 1100
Chrysichthys nigrodigitatus 1101
Acanthephyra purpurea 1102
Actinauge abyssorum 1103
Alaria marginata 1104
Anadara transversa 1105
Anthomedusae 1106
Archosargus probatocephalus 1107
Argyropelecus aculeatus 1108
Ariopsis felis 1109
Astrometis sertulifera 1110
Astropecten 1111
Atherina breviceps 1112
Atolla 1113
Aulacomya atra 1114
Auxis rochei rochei 1115
Auxis thazard thazard 1116
Avicennia marina 1117
Balaena mysticetus 1118
Balaenoptera acutorostrata 1119
Balanus 1120
Berardius bairdii 1121
Beroe 1122
Boopsoidea inornata 1123
Calanoida 1124
Calanus finmarchicus finmarchicus 1125
Callorhinchus milii 1126
Cepphus columba 1127
Cladonia rangiferina 1128
Clinus superciliosus 1129
Codium tomentosum 1130
Copepoda 1131
Coregonus autumnalis 1132
Coregonus nasus 1133
Coregonus sardinella 1134
Coryphaenoides armatus 1135
Coryphoblennius galerita 1136
Creseis sp 1137
Crinoidea 1138
Crossota 1139
Cryptochiton stelleri 1140
Delphinus delphis 1141
Diacria 1142
Dichistius capensis 1143
Dosinia alta 1144
Dugong dugon 1145
Electrona risso 1146
Engraulis capensis 1147
Ensis siliqua 1148
Eryonidae 1149
Eualaria fistulosa 1150
Eupasiphae gilesii 1151
Euphausiacea 1152
Euphausiidae 1153
Eurypharynx pelecanoides 1154
Eurythenes gryllus 1155
Euthynnus lineatus 1156
Fratercula cirrhata 1157
Galeichthys feliceps 1158
Gelidium corneum 1159
Gibbula umbilicalis 1160
Gnathophausia ingens 1161
Gonatus fabricii 1162
Haliaeetus leucocephalus 1163
Haliclona 1164
Halodule uninervis 1165
Hemilepidotus 1166
Hemilepidotus jordani 1167
Heterocarpus ensifer 1168
Heterodontus portusjacksoni 1169
Hippasteria phrygiana 1170
Homola barbata 1171
Hyperoodon planifrons 1172
Hypleurochilus geminatus 1173
Invertebrata 1174
Isognomon bicolor 1175
Isopoda 1176
Kogia breviceps 1177
Labrus bergylta 1178
Lagenorhynchus obliquidens 1179
Lampris guttatus 1180
Larus glaucescens 1181
Leander serratus 1182
Libinia emarginata 1183
Lichia amia 1184
Lipophrys pholis 1185
Lipophrys trigloides 1186
Lithognathus lithognathus 1187
Lithophaga aristata 1188
Lobianchia gemellarii 1189
Loliginidae 1190
Loligo reynaudii 1191
Lophius budegassa 1192
Magallana angulata 1193
Majoidea 1194
Megachasma pelagios 1195
Megaptera novaeangliae 1196
Menippe mercenaria 1197
Mesoplodon carlhubbsi 1198
Mesoplodon stejnegeri 1199
Microstomus pacificus 1200
Morone saxatilis 1201
Mullus surmuletus 1202
Mycteroperca xenarcha 1203
Myliobatis australis 1204
Mysida 1205
Mytilus californianus 1206
Mytilus trossulus 1207
Nephasoma Nephasoma flagriferum 1208
Nudibranchia 1209
Odobenus rosmarus divergens 1210
Ommastrephidae 1211
Ophiomusa lymani 1212
Ophiothrix lineata 1213
Orcinus orca 1214
Ostracoda 1215
Pagellus bogaraveo 1216
Pandalus borealis 1217
Paphies subtriangulata 1218
Parabrotula 1219
Paracalanus 1220
Patella aspera 1221
Periphylla 1222
Phocoena phocoena 1223
Phocoenoides dalli 1224
Phronima 1225
Physeter macrocephalus 1226
Pinctada radiata 1227
Plesionika edwardsii 1228
Pododesmus macrochisma 1229
Pomatomus saltatrix 1230
Portunus pelagicus 1231
Praunus 1232
Pyrosoma 1233
Rangifer tarandus 1234
Rhabdosargus globiceps 1235
Saccorhiza polyschides 1236
Sagitta 1237
Salpa 1238
Salvelinus alpinus 1239
Salvelinus malma 1240
Sarda chiliensis 1241
Sargassum aquifolium 1242
Scalibregmatidae 1243
Sebastes alutus 1244
Sebastes melanops 1245
Seriola dorsalis 1246
Serranus scriba 1247
Sigmops bathyphilus 1248
Silicula fragilis 1249
Sipunculidae 1250
Somateria mollissima 1251
Somateria spectabilis 1252
Sparodon durbanensis 1253
Spicara maena 1254
Squatina australis 1255
Striostrea margaritacea 1256
Stromateus fiatola 1257
Strongylocentrotus polyacanthus 1258
Taractichthys steindachneri 1259
Tectura scutum 1260
Tegula viridula 1261
Thais haemastoma 1262
Thegrefg 1263
Themisto 1264
Thunnus tonggol 1265
Trachurus picturatus 1266
Trachurus symmetricus 1267
Trygonorrhina fasciata 1268
Ulva lactuca 1269
Ursus maritimus 1270
Vampyroteuthis infernalis 1271
Ziphius cavirostris 1272
Alepes kleinii 1273
Alepes vari 1274
Decapterus macrosoma 1275
Lutjanus madras 1276
Lutjanus russellii 1277
Rastrelliger brachysoma 1278
Rastrelliger faughni 1279
Selar boops 1280
Selaroides leptolepis 1281
Sphyraena obtusata 1282
Geloina expansa 1283
Caesio erythrogaster 1284
Euristhmus microceps 1285
Pomacanthus annularis 1286
Scylla 1287
Plotosus lineatus 1288
Prionotus stephanophrys 1289
Trachurus murphyi 1290
Dosidicus gigas 1291
Sarda chiliensis chiliensis 1292
Cynoscion analis 1293
Merluccius gayi peruanus 1294
Brotula ordwayi 1295
Loligo gahi 1296
Merluccius gayi 1297
Ophichthus remiger 1298
Penaeus sp 1299
Trachinotus paitensis 1300
Cheilopogon heterurus 1301
Engraulis ringens 1302
Sciaena deliciosa 1303
Isacia conceptionis 1304
Odontesthes regia 1305
Bodianus diplotaenia 1306
Concholepas concholepas 1307
Diplectrum conceptione 1308
Genypterus maculatus 1309
Labrisomus philippii 1310
Paralabrax humeralis 1311
Prionotus horrens 1312
Dasyatis akajei 1313
Arctoscopus japonicus 1314
Sepia esculenta 1315
Bothrocara hollandi 1316
Cynoglossidae 1317
Lepidotrigla 1318
Lepidotrigla alata 1319
Octopus sinensis 1320
Rhabdosargus sarba 1321
Lophiidae 1322
Muraenesox 1323
Physiculus maximowiczi 1324
Pleuronectoidei 1325
Sciaenidae 1326
Triglidae 1327
Atherina presbyter 1328
Bentheogennema intermedia 1329
Benthesicymidae 1330
Benthesicymus 1331
Buccinum striatissimum 1332
Callinectes 1333
Cancer pagurus 1334
Chaetognatha 1335
Chama macerophylla 1336
Cirripedia 1337
Cyclosalpa 1338
Cymopolia barbata 1339
Cynoscion 1340
Cystoseira amentacea 1341
Ectocarpus siliculosus 1342
Ellisolandia elongata 1343
Enteromorpha linza 1344
Euphausia superba 1345
Gaidropsarus mediterraneus 1346
Gennadas valens 1347
Globicephala 1348
Haliptilon virgatum 1349
Halocynthia aurantium 1350
Heliocidaris crassispina 1351
Hymenodora gracilis 1352
Lagodon rhomboides 1353
Lepas Anatifa anatifera 1354
Lobophora variegata 1355
Macrocystis pyrifera 1356
Maculabatis gerrardi 1357
Nemacystus decipiens 1358
Neptunea polycostata 1359
Padina pavonia 1360
Penaeidae 1361
Petricolinae 1362
Polynemidae 1363
Pristipomoides aquilonaris 1364
Pyropia fallax 1365
Radiolaria 1366
Salpidae 1367
Sardinops melanosticta 1368
Sargassum vulgare 1369
Sciaena umbra 1370
Scorpaena porcus 1371
Sergestidae 1372
Sicyonia brevirostris 1373
Sphaerococcus coronopifolius 1374
Stenella coeruleoalba 1375
Stichopus japonicus 1376
Thalia democratica 1377
Themisto gaudichaudii 1378
Undaria 1379
Analipus japonicus 1380
Sargassum yamadae 1381
Ahnfeltiopsis paradoxa 1382
Scytosiphon lomentaria 1383
Chondria crassicaulis 1384
Grateloupia lanceolata 1385
Colpomenia sinuosa 1386
Chondrus giganteus 1387
Sargassum muticum 1388
Ulva prolifera 1389
Petalonia fascia 1390
Balanus roseus 1391
Chaetomorpha moniligera 1392
Lomentaria hakodatensis 1393
Neodilsea longissima 1394
Polyopes affinis 1395
Schizymenia dubyi 1396
Dictyopteris pacifica 1397
Ahnfeltiopsis flabelliformis 1398
Bangia fuscopurpurea 1399
Calliarthron 1400
Cladophora 1401
Cladophora albida 1402
Dasya sessilis 1403
Delesseria serrulata 1404
Ecklonia cava 1405
Gelidium elegans 1406
Grateloupia turuturu 1407
Hypnea asiatica 1408
Mazzaella japonica 1409
Pachydictyon coriaceum 1410
Padina arborescens 1411
Pterosiphonia pinnulata 1412
Alatocladia yessoensis 1413
Bryopsis plumosa 1414
Ceramium kondoi 1415
Chondracanthus intermedius 1416
Codium contractum 1417
Codium lucasii 1418
Corallina pilulifera 1419
Dictyopteris undulata 1420
Gastroclonium pacificum 1421
Gelidium amansii 1422
Grateloupia sparsa 1423
Laurencia okamurae 1424
Leathesia marina 1425
Lomentaria catenata 1426
Meristotheca papulosa 1427
Sargassum confusum 1428
Sargassum siliquastrum 1429
Tinocladia crassa 1430
Saccharina yendoana 1431
Thalassiophyllum clathrus 1432
Mytilida 1433
Pteriomorphia 1434
Conger 1435
Scyliorhinidae 1436
Labrus 1437
Algae 1438
Necora puber 1439
Anguilla 1440
Rajidae 1441
Buccinidae 1442
Crustacea 1443
Green algae 1444
Ammodytes japonicus 1445
Evynnis tumifrons 1446
Gnathophis nystromi nystromi 1447
Loligo bleekeri 1448
Platichthys bicoloratus 1449
Limanda punctatissima 1450
Loliolus Nipponololigo japonica 1451
Acanthopagrus schlegelii schlegelii 1452
Sepiolina 1453
Gelidium 1454
Atrina pectinata 1455
Echinocardium cordatum 1456
Lamnidae 1457
Meretrix lamarckii 1458
Noctiluca scintillans 1459
Philine argentata 1460
Sergestes lucens 1461
Corbicula sandai 1462
Ulva 1463
Actiniaria 1464
Ctenopharyngodon idella 1465
Ophiuroidea 1466
Scomberoides lysan 1467
Scomberoides tol 1468
Sebastolobus 1469
Selachimorpha 1470
Selene setapinnis 1471
Selene vomer 1472
Sepia elliptica 1473
Sergestes sp 1474
Setipinna taty 1475
Siganus canaliculatus 1476
Sigmops gracile 1477
Solenocera sp 1478
Sparidae 1479
Spermatophytina 1480
Sphoeroides testudineus 1481
Sphyraena jello 1482
Spyridia hypnoides 1483
Squaliformes 1484
Squillidae 1485
Stegophiura sladeni 1486
Stenella longirostris 1487
Stenobrachius leucopsarus 1488
Sternaspidae 1489
Stoechospermum polypodioides 1490
Stolephorus commersonnii 1491
Stromateus cinereus 1492
Stromateus niger 1493
Stromateus sinensis 1494
Synidotea 1495
Takifugu vermicularis 1496
Telatrygon zugei 1497
Terapon jarbua 1498
Terebellidae 1499
Thryssa dussumieri 1500
Thunnini 1501
Tibia curta 1502
Tonna dolium 1503
Trachinus draco 1504
Trematomus bernacchii 1505
Tridacna 1506
Trinectes paulistanus 1507
Trochus radiatus 1508
Turbinaria 1509
Tursiops truncatus 1510
Ucides 1511
Ulva compressa 1512
Ulva fasciata 1513
Ulva flexuosa 1514
Ulva rigida 1515
Upeneus taeniopterus 1516
Upogebiidae 1517
Uroteuthis Photololigo edulis 1518
Valoniopsis pachynema 1519
Veneridae 1520
Venus foveolata 1521
Vertebrata 1522
Volutharpa ampullacea perryi 1523
Zannichellia palustris 1524
Zeus japonicus 1525
Favites 1526
Gadiformes 1527
Gafrarium dispar 1528
Galaxaura frutescens 1529
Gelidium crinale 1530
Genidens genidens 1531
Girella elevata 1532
Girella tricuspidata 1533
Dentex hypselosomus 1534
Saurida elongata 1535
Pseudolabrus eoethinus 1536
Atrobucca nibe 1537
Diagramma pictum 1538
Sepia lycidas 1539
Plectorhinchus cinctus 1540
Metapenaeopsis acclivis 1541
Metapenaeopsis barbata 1542
Nibea albiflora 1543
Girella leonina 1544
Sphyraenidae 1545
Parapercis pulchella 1546
Parapercis sexfasciata 1547
Thysanoteuthis rhombus 1548
Lepidotrigla kishinouyi 1549
Cystoseira 1550
Padina 1551
Halimeda 1552
Pacifastacus leniusculus 1553
Salmo trutta 1554
Chondrus crispus 1555
Ictalurus punctatus 1556
Acanthurus 1557
Scombridae 1558
Leukoma staminea 1559
Trochidae 1560
Protonibea 1562
Anchoa compressa 1563
Ensis magnus 1564
Bolinus brandaris 1565
Lutjanus notatus 1566
Lethrinus olivaceus 1567
Carassius auratus 1569
Mugil 1570
Gobius 1571
Lajonkairia lajonkairii 1572
Chrysophrys auratus 1573
Galeorhinus australis 1574
Nototodarus sloanii gouldi 1575
Tylosurus crocodilus 1576
Acanthogobius hasta 1577
Penaeus chinensis 1578
Ruditapes variegatus 1579
Marcia marmorata 1580
Rachycentron 1581
Scomber kanagurta 1582
Arius 1583
Panulirus versicolor 1584
Tilapia zillii 1585
Schizoporella errata 1586
Phallusia nigra 1587
Physeter catodon 1588
Salmo trutta trutta 1589
Tachysurus thalassinus 1590
Sillago domina 1591
Otolithus argenteus 1592
Trichiurus haumela 1593
Otolithes maculata 1594
Hilsa kanagurta 1595
Oreochromis mossambicus 1596
Siluriformes 1597
Theodoxus euxinus 1598
Formio niger 1599
Rastrelliger 1600
Nephasoma flagriferum 1601
Ophiomusium lymani 1602
Nematonurus armatus 1603
Thalamitoides spinigera 1604
Capros aper 1605
Gadiculus argenteus thori 1606
Phorcus lineatus 1607
Penaeus vannamei 1608
Raja montagui 1609
Scophthalmus rhombus 1610
Crambe maritima 1611
Fucus ceranoides 1612
Maja squinado 1613
Salicornia europaea 1614
Aequipecten opercularis 1615
Galathea squamifera 1616
Cynoglossus semilaevis 1617
Loliolus beka 1619
Octopus variabilis 1620
Abudefduf sexfasciatus 1621
Acanthurus blochii 1622
Achillea millefolium 1623
Alaria crassifolia 1624
Albulidae 1625
Ammodytes 1626
Anadara satowi 1627
Argyrosomus japonicus 1628
Ascidiacea 1629
Aulopiformes 1630
Babylonia japonica 1631
Babylonia kirana 1632
Bathylagidae 1633
Beryx decadactylus 1634
Branchiostegus 1635
Buccinum 1636
Caesio lunaris 1637
Callionymus curvicornis 1638
Campylaephora hypnaeoides 1639
Cetoscarus ocellatus 1640
Charonia tritonis 1641
Chelon haematocheilus 1642
Chlorurus sordidus 1643
Choerodon azurio 1644
Chromis notata 1645
Cladosiphon okamuranus 1646
Cociella punctata 1647
Coryphaena 1648
Cyclina sinensis 1649
Cymbacephalus beauforti 1650
Dendrobranchiata 1651
Digenea simplex 1652
Ditrema viride 1653
Enteromorpha prolifera 1654
Epinephelus 1655
Epinephelus akaara 1656
Epinephelus awoara 1657
Etelis carbunculus 1658
Fistularia commersonii 1659
Fulvia mutica 1660
Fusinus colus 1661
Gafrarium tumidum 1662
Gelidiaceae 1663
Girella cyanea 1664
Girella mezina 1665
Goniistius zonatus 1666
Gracilaria 1667
Gymnocranius euanus 1668
Heikeopsis japonica 1669
Hemitrygon 1670
Hippoglossoides pinetorum 1671
Holothuria atra 1672
Holothuria leucospilota 1673
Idiosepiidae 1674
Inegocia japonica 1675
Inimicus didactylus 1676
Ishige 1677
Lagocephalus spadiceus 1678
Lambis truncata 1679
Leiognathus equula 1680
Lethrinus xanthochilus 1681
Lutjanus erythropterus 1682
Lutjanus semicinctus 1683
Monodonta labio 1684
Monostroma kuroshiense 1685
Mulloidichthys flavolineatus 1686
Mulloidichthys vanicolensis 1687
Muraenesocidae 1688
Myagropsis myagroides 1689
Mytilisepta virgata 1690
Naso brevirostris 1691
Nematalosa japonica 1692
Nemipterus virgatus 1693
Nipponacmea 1694
Nuchequula nuchalis 1695
Octopus cyanea 1696
Panopea generosa 1697
Paralichthys 1698
Paralithodes camtschaticus 1699
Parascolopsis inermis 1700
Pectinidae 1701
Pentapodus aureofasciatus 1702
Pinctada fucata 1703
Pitar citrinus 1704
Platycephalidae 1705
Plecoglossus altivelis 1706
Pleuronectes herzensteini 1707
Priacanthus macracanthus 1708
Pristipomoides 1709
Psenopsis anomala 1710
Pseudobalistes fuscus 1711
Pseudocaranx dentex 1712
Pseudolabrus sieboldi 1713
Pseudorhombus arsius 1714
Pterocaesio chrysozona 1715
Rhynchopelates oxyrhynchus 1716
Ryukyupercis gushikeni 1717
Saccostrea echinata 1718
Sargassum hemiphyllum 1719
Sargassum piluliferum 1720
Saurida micropectoralis 1721
Saurida undosquamis 1722
Saurida wanieso 1723
Scarus forsteni 1724
Scarus ghobban 1725
Scarus ovifrons 1726
Scarus rubroviolaceus 1727
Scyphozoa 1728
Sebastes iracundus 1729
Semicossyphus reticulatus 1730
Sepia latimanus 1731
Siganus guttatus 1732
Siganus luridus 1733
Sphaerotrichia divaricata 1734
Sphyrnidae 1735
Spondylus regius 1736
Spratelloides gracilis 1737
Sthenoteuthis oualaniensis 1738
Tetraodontidae 1739
Trichiurus lepturus japonicus 1740
Tridacna crocea 1741
Turbo argyrostomus 1742
Tylosurus pacificus 1743
Ulvophyceae 1744
Upeneus japonicus 1745
Upeneus moluccensis 1746
Uranoscopus japonicus 1747
Anguilliformes 1748
Crithmum maritimum 1749
Littorina 1750
Nucella lapillus 1752
Scyliorhinus stellaris 1753
Annelida 1754
Aphrodita aculeata 1755
Callionymus lyra 1756
Urticina felina 1757
Gebiidea 1758
Bonellia viridis 1759
Alcyonium glomeratum 1760