Occurrence record: MGYA00166832_Bacteria::Proteobacteria:Gammaproteobacteria:Thiotrichales:Piscirickettsiaceae:Piscirickettsia:Piscirickettsia_salmonis

MaterialSample of Piscirickettsia salmonis

API

Dataset

Data partner	GBIF
Data resource	Amplicon sequencing of Tara Oceans DNA samples corresponding to size fractions for protists.
Occurrence ID	MGYA00166832_Bacteria::Proteobacteria:Gammaproteobacteria:Thiotrichales:Piscirickettsiaceae:Piscirickettsia:Piscirickettsia_salmonis
Basis of record	MaterialSample Supplied basis "MATERIAL_SAMPLE"
License	CC-BY 4.0 (Int) Supplied as CC_BY_4_0
Organism quantity type	DNA sequence reads
Dynamic properties	"{""temperature"":""17.32198"",""project name"":""Tara Oceans"",""geographic location (longitude)"":""17.715"",""environment (biome)"":""marine biome (ENVO:00000447)"",""environment (feature)"":""surface water (ENVO:00002042) layer"",""environment (material)"":""particulate matter, including plankton (ENVO:xxxxxxxx)"",""environmental package"":""water"",""sample collection device or method"":""PUMP (High Volume Peristaltic Pump)"",""salinity"":""38.201397"",""geographic location (latitude)"":""42.2038"",""instrument model"":""Illumina Genome Analyzer IIx"",""ENA checklist"":""ERC000030""}"
Occurrence status	present Supplied as PRESENT
Organism quantity	1.0
Identification references	https://www.ebi.ac.uk/metagenomics/pipelines/4.1
Abcd identification qualifier	Not provided
Identification remarks	SSU rRNA annotated using the taxonomic reference database described here: https://www.ebi.ac.uk/metagenomics/pipelines/4.1. This occurrence appeared in following analyses: SSU taxonomy from analyses https://www.ebi.ac.uk/metagenomics/analyses/MGYA00166832#taxonomic.

Event

Event ID	MGYA00166832
Identification remarks	SSU rRNA annotated using the taxonomic reference database described here: https://www.ebi.ac.uk/metagenomics/pipelines/4.1. This occurrence appeared in following analyses: SSU taxonomy from analyses https://www.ebi.ac.uk/metagenomics/analyses/MGYA00166832#taxonomic.
Date precision	Not Supplied
Event remarks	This sample (TARA_A100000553) was collected in the marine biome (ENVO:00000447) during Tara Oceans expedition on date/time=2009-11-18T08:41Z at station TARA_023 (latitudeN=42.2038, longitudeE=17.715) from a surface water (ENVO:00002042) layer at a depth of 3-7 m, using a PUMP (High Volume Peristaltic Pump). The sample material (particulate matter, including plankton (ENVO:xxxxxxxx)) was size-fractionated (5-20 micrometres) and preserved on board in liquid nitrogen for later phylogenetic analysis of protist (unicellular eukaryote) nucleotide sequences identification by pyrosequencing methods.

Taxonomy

Scientific name	Piscirickettsia salmonis Supplied scientific name "Piscirickettsia salmonis Fryer et al., 1992"
Taxon rank	species
Kingdom	Bacteria
Phylum	Proteobacteria
Class	Gammaproteobacteria
Order	Piscirickettsiales
Family	Piscirickettsiaceae
Genus	Piscirickettsia
Species	Piscirickettsia salmonis
Taxonomic issue	No issues
Name match metric	Exact match The supplied name matched the name exactly.
Name parse type	SCIENTIFIC
Taxonomic status	ACCEPTED

Geospatial

Country	Croatia
latitude	42.2038
longitude	17.715
Geodetic datum	EPSG:4326
Coordinate precision	Unknown
Verbatim depth	5.0
Country code	HR

Additional properties

Accepted scientific name	Piscirickettsia salmonis Fryer et al., 1992
Accepted taxon key	3222967
Class key	362
Dataset key	d596fccb-2319-42eb-b13b-986c932780ad
depth accuracy	0.0
Family key	5608
Gbif id	2017306597
Gbif region	EUROPE
Generic name	Piscirickettsia
Genus key	3222966
Has coordinate	true
Has geospatial issues	false
Is sequenced	false
Iucn red list category	NE
Kingdom key	3
Last crawled	2025-02-15T14:53:27.275Z
Last interpreted	2025-02-15T15:07:00.784Z
Last parsed	2025-02-15T15:07:00.784Z
Material sample ID	https://www.ebi.ac.uk/metagenomics/samples/ERS477989
Order key	10700392
Phylum key	111
Protocol	DWC_ARCHIVE
Published by gbif region	EUROPE
Publishing country	GB
relative organism quantity	6.214507394642349E-7
Repatriated	true
Sample size unit	DNA sequence reads
Sample size value	1609138.0
Species key	3222967
Taxon key	3222967
Verbatim scientific name	Piscirickettsia salmonis

Ostali atributi

User flagged issues

Data quality tests

Test name	Result
Invalid collection date	Failed
Incomplete collection date	Warning
Geodetic datum assumed WGS84	Warning
Country inferred from coordinates	Warning
Show/Hide 23 passed properties
Basis of record not supplied	Passed
Basis of record badly formed	Passed
Missing identification references	Passed
Data are generalised	Passed
Missing taxonomic rank	Passed
Name not supplied	Passed
Kingdom not recognised	Passed
Name not recognised	Passed
Invalid scientific name	Passed
Name not in national checklists	Passed
Decimal coordinates not supplied	Passed
Depth out of range	Passed
Depth value non-numeric	Passed
Depth value supplied in feet	Passed
Coordinates are transposed	Passed
Coordinates are out of range for species	Passed
Supplied coordinates are zero	Passed
Zero latitude	Passed
Zero longitude	Passed
Location not supplied	Passed
Supplied coordinates centre of state	Passed
Coordinates centre of country	Passed
Missing geodetic datum	Passed
Show/Hide 12 missing properties
No collection date supplied	Missing
Missing an identification qualifier	Missing
Missing name of person who identified the specimen/observation	Missing
Missing identification date	Missing
Missing catalogue number	Missing
Missing coordinate precision	Missing
Coordinate uncertainty not specified	Missing
Missing name of person who georeferenced the occurrence	Missing
Missing georeferenced protocol	Missing
Missing georeferenced sources	Missing
Missing georeferenced verification status	Missing
Missing georeference date	Missing
Show/Hide 47 tests that have not been run
Coordinates dont match supplied state	Unchecked (lack of data)
Habitat incorrect for species	Unchecked (lack of data)
Min and max depth reversed	Unchecked (lack of data)
Coordinate uncertainty not valid	Unchecked (lack of data)
Image URL invalid	Unchecked (lack of data)
Longitude is negated	Unchecked (lack of data)
Precision / range mismatch	Unchecked (lack of data)
Altitude value non-numeric	Unchecked (lack of data)
Decimal latitude/longitude conversion failed	Unchecked (lack of data)
Higher taxonomy missing	Unchecked (lack of data)
Coordinate precision and uncertainty transposed	Unchecked (lack of data)
Media unrepresentative	Unchecked (lack of data)
Latitude Longitude calculated from grid reference	Unchecked (lack of data)
Homonym issues with supplied name	Unchecked (lack of data)
Resource taxonomic scope mismatch	Unchecked (lack of data)
Coordinates converted from UTM	Unchecked (lack of data)
Date precision invalid	Unchecked (lack of data)
Cultivated / escapee	Unchecked (lack of data)
Latitude is negated	Unchecked (lack of data)
First of the month	Unchecked (lack of data)
unrecognisedOccurrenceStatus	Unchecked (lack of data)
Invalid geodetic datum	Unchecked (lack of data)
Min and max altitude reversed	Unchecked (lack of data)
Possible duplicate record	Unchecked (lack of data)
Coordinates dont match supplied country	Unchecked (lack of data)
Collector name unparseable	Unchecked (lack of data)
Supplied country not recognised	Unchecked (lack of data)
First of the century	Unchecked (lack of data)
Institution code not recognised	Unchecked (lack of data)
Georeferenced after occurrence date	Unchecked (lack of data)
Identification date before occurrence date	Unchecked (lack of data)
Coordinates derived from verbatim coordinates	Unchecked (lack of data)
Badly formed altitude	Unchecked (lack of data)
Outside expert range for species	Unchecked (lack of data)
Unrecognized geodetic datum	Unchecked (lack of data)
Collection code not recognised	Unchecked (lack of data)
Unparseable verbatim coordinates	Unchecked (lack of data)
Coordinates converted to WGS84	Unchecked (lack of data)
Altitude out of range	Unchecked (lack of data)
Altitude value supplied in feet	Unchecked (lack of data)
Occurrence status assumed to be present	Unchecked (lack of data)
Unable to convert UTM coordinates	Unchecked (lack of data)
Type status not recognised	Unchecked (lack of data)
Coordinate precision not valid	Unchecked (lack of data)
Media unrepresentative for taxon	Unchecked (lack of data)
Day and month transposed	Unchecked (lack of data)
First of the year	Unchecked (lack of data)

Group	Field Name	Original Value	Processed Value
Classification	Name parse type		SCIENTIFIC
	Species	Piscirickettsia salmonis	Piscirickettsia salmonis
	Name match metric		exactMatch
	Scientific name	Piscirickettsia salmonis Fryer et al., 1992	Piscirickettsia salmonis
	Class	Gammaproteobacteria	Gammaproteobacteria
	Genus id		3222966
	Taxon concept ID		3222967
	Kingdom id		3
	Left		6383721
	Phylum	Proteobacteria	Proteobacteria
	Kingdom	Bacteria	Bacteria
	Class id		362
	Genus	Piscirickettsia	Piscirickettsia
	Phylum id		111
	Order	Piscirickettsiales	Piscirickettsiales
	Taxon rank	SPECIES	species
	Specific epithet	salmonis
	Order id		10700392
	Taxonomic issue		["noIssue"]
	Species id		3222967
	Family id		5608
	Taxonomic status	ACCEPTED
	Family	Piscirickettsiaceae	Piscirickettsiaceae
	Taxon rank id		7000
	Right		6383721
Event	Date precision		Not Supplied
	Event remarks	This sample (TARA_A100000553) was collected in the marine biome (ENVO:00000447) during Tara Oceans expedition on date/time=2009-11-18T08:41Z at station TARA_023 (latitudeN=42.2038, longitudeE=17.715) from a surface water (ENVO:00002042) layer at a depth of 3-7 m, using a PUMP (High Volume Peristaltic Pump). The sample material (particulate matter, including plankton (ENVO:xxxxxxxx)) was size-fractionated (5-20 micrometres) and preserved on board in liquid nitrogen for later phylogenetic analysis of protist (unicellular eukaryote) nucleotide sequences identification by pyrosequencing methods.
	Event ID	MGYA00166832
Identification	Identification references	https://www.ebi.ac.uk/metagenomics/pipelines/4.1
	Determinacijski kvalifikator Abcd		Not provided
	Identification qualifier		Not provided
	Identification remarks	SSU rRNA annotated using the taxonomic reference database described here: https://www.ebi.ac.uk/metagenomics/pipelines/4.1. This occurrence appeared in following analyses: SSU taxonomy from analyses https://www.ebi.ac.uk/metagenomics/analyses/MGYA00166832#taxonomic.
Occurrence	Occurrence ID	MGYA00166832_Bacteria::Proteobacteria:Gammaproteobacteria:Thiotrichales:Piscirickettsiaceae:Piscirickettsia:Piscirickettsia_salmonis
	Basis of record	MATERIAL_SAMPLE	MaterialSample
	Organism quantity type	DNA sequence reads
	Dynamic properties	"{""temperature"":""17.32198"",""project name"":""Tara Oceans"",""geographic location (longitude)"":""17.715"",""environment (biome)"":""marine biome (ENVO:00000447)"",""environment (feature)"":""surface water (ENVO:00002042) layer"",""environment (material)"":""particulate matter, including plankton (ENVO:xxxxxxxx)"",""environmental package"":""water"",""sample collection device or method"":""PUMP (High Volume Peristaltic Pump)"",""salinity"":""38.201397"",""geographic location (latitude)"":""42.2038"",""instrument model"":""Illumina Genome Analyzer IIx"",""ENA checklist"":""ERC000030""}"
	Occurrence status	PRESENT	present
	Organism quantity	1.0
Attribution	Data resource		Amplicon sequencing of Tara Oceans DNA samples corresponding to size fractions for protists.
	Data provider uid		dp8
	License	CC_BY_4_0	CC-BY 4.0 (Int)
	Data resource uid	dr81
	Data partner		GBIF
Location	Decimal latitude	42.2038	42.2038
	Country		Croatia
	Decimal longitude	17.715	17.715
	Verbatim depth	5.0	5.0
	Geodetic datum		EPSG:4326
	Country code	HR

Occurrence record: MGYA00166832_Bacteria::Proteobacteria:Gammaproteobacteria:Thiotrichales:Piscirickettsiaceae:Piscirickettsia:Piscirickettsia_salmonis

Dataset

Event

Taxonomy

Geospatial

Additional properties

Ostali atributi

User flagged issues

Data quality tests

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