Unique name for isolate. Ensure that the value is unique, and that no other report contains the isolate name.
yes
text
30
yes
yes
Synonyms
isolate_synonyms
Pipe-separated list (|) of isolate synonyms. Values should only be added for an isolate that has been published under different names. This is relevant for older isolates; newer isolates should only have one name. The isolate name is defined by person who isolated the pathogen.
textarea
255
yes
Other Isolates in Same Outbreak
other_isolates_same_outbreak
Pipe-separated list (|) of other isolate name for other isolates in same outbreak
textarea
255
yes
Relevant References for Isolate
isolate_reference
Pipe-separated list (|) of Pubmed Id's of relevant references. References not in Pubmed can be added as text in the field 'General Notes' under 'Notes'
textarea
255
yes
title
Genomics
Gene Used For Genotyping
genotype_subtype_generegion
Gene used for genotyping according to specified publication. Full-length G-gene is preferred.
yes
select
50
yes
yes
Genotype Gene Region Publication Reference
genotype_subtype_generegion_pubref
Gene region used for genotyping - publication reference (Pubmed Id)
G-gene
N-gene
Nv-gene
not genotyped
http://www.ncbi.nlm.nih.gov/pubmed/
genotype_subtype_generegion
read-only
200
yes
Genotype
genotype
If not genotyped select 'unknown'. If genotyped start by selecting gene used for genotyping above
G-gene
N-gene
Nv-gene
not genotyped
genotype_subtype_generegion
yes
select
255
yes
yes
yes
Genotype Subtype
genotype_subtype
If it is not possible to assign a subtype please choose the same value as chosen under 'Genotype' above
unknown|not genotyped
I|G-gene
II|G-gene
III|G-gene
IV|G-gene
unknown|G-gene
I|N-gene
II|N-gene
III|N-gene
IV|N-gene
unknown|N-gene
I|Nv-gene
II|Nv-gene
III|Nv-gene
IV|Nv-gene
unknown|Nv-gene
genotype
yes
select
255
yes
yes
yes
title
Geographical Location
Country
country
yes
select
100
yes
yes
yes
Comments on Exact Location
exact_location
no
textarea
yes
Select type of geographical co-ordinates
geo_type
The database records both UTM and latitude/longitude. When necessary, please ensure that you convert your values using the tool provided.
select
no
Latitude
latitude
text
30
Longitude
longitude
text
30
Datum / Geodetic System
datum
Datum used for longitude and latitude values
Latitude Longitude
geo_type
select
50
Global UTM Northing
global_utm_northing
text
30
Global UTM Easting
global_utm_easting
text
30
Global UTM Zone Number
global_utm_zone_number
select
2
Global UTM hemisphere
global_utm_hemisphere
select
title
Sample
Sample Tissue
sample_tissue
textarea
200
yes
yes
Number of Fish in Sample
sample_number_fish
yes
select
yes
yes
Date of Sampling
sampling_date
Format YYYY-MM-DD according to ISO 8601. In case date and/or month are unknown add 00. For example, an isolate only known to be from year 2000 will be 2000-00-00.
If the host is not present on the list please contact us.
yes
select
yes
yes
Host NCBI Taxid
host_taxid
Acanthopagrus schlegelii schlegelii
Ambloplites rupestris
Ameiurus nebulosus
Ammodytes hexapterus
Ammodytes personatus
Anguilla anguilla
Anoplopoma fimbria
Aplodinotus grunniens
Argentina sphyraena
Aulorhynchus flavidus
Barbus graellsii
Chondrostoma polylepis
Clupea harengus
Clupea pallasii
Coregonus clupeaformis
Coregonus lavaretus
Cymatogaster aggregata
Danio rerio
Dicentrarchus labrax
Dorosoma cepedianum
Enchelyopus cimbrius
Epinephelus akaara
Esox lucius
Esox masquinongy
Fundulus heteroclitus heteroclitus
Gadus macrocephalus
Gadus morhua
Gasterosteus aculeatus
Hippoglossus hippoglossus
Hypomesus pretiosus
Ictalurus punctatus
Lampetra fluviatilis
Lepomis gibbosus
Lepomis macrochirus
Limanda limanda
Lota lota
Mallotus villosus
Melanogrammus aeglefinus
Merlangius merlangus
Merluccius productus
Microgadus proximus
Micromesistius poutassou
Micropterus dolomieu
Micropterus salmoides
Morone Americana
Morone chrysops
Morone saxatilis
Moxostoma anisurum
Moxostoma macrolepidotum
Notropis atherinoides
Notropis hudsonius
Oncorhynchus aguabonita
Oncorhynchus gorbuscha
Oncorhynchus keta
Oncorhynchus kisutch
Oncorhynchus mykiss
Oncorhynchus tshawytscha
Pagrus major
Paralichthys olivaceus
Parophrys vetulus
Perca flavescens
Percopsis omiscomaycus
Pimephales notatus
Platichthys flesus
Pleuronectes platessa
Pomatoschistus minutus
Pomoxis nigromaculatus
Psetta maxima
Reinhardtius hippoglossoides
Salmo salar
Salmo trutta trutta
Salmo trutta fario
Salvelinus alpinus alpinus
Salvelinus fontinalis
Salvelinus namaycush
Sander vitreus
Sardinops sagax
Scomber japonicus
Sebastes schlegelii
Seriola quinqueradiata
Sparus aurata
Sprattus sprattus sprattus
Thaleichthys pacificus
Theragra chalcogramma
Thymallus thymallus
Trisopterus esmarkii
Trisopterus minutus
host_species_latin_name
read-only
Host Species Common Name
host_species_common_name
Acanthopagrus schlegelii schlegelii
Ameiurus nebulosus
Ambloplites rupestris
Ammodytes hexapterus
Ammodytes personatus
Anguilla anguilla
Anoplopoma fimbria
Aplodinotus grunniens
Argentina sphyraena
Aulorhynchus flavidus
Chondrostoma polylepis
Clupea harengus
Clupea pallasii
Coregonus clupeaformis
Coregonus lavaretus
Cymatogaster aggregata
Danio rerio
Dicentrarchus labrax
Dorosoma cepedianum
Enchelyopus cimbrius
Epinephelus akaara
Esox lucius
Esox masquinongy
Fundulus heteroclitus heteroclitus
Gadus morhua
Gadus macrocephalus
Gasterosteus aculeatus
Hippoglossus hippoglossus
Hypomesus pretiosus
Ictalurus punctatus
Lampetra fluviatilis
Lepomis gibbosus
Lepomis macrochirus
Limanda limanda
Lota lota
Mallotus villosus
Melanogrammus aeglefinus
Merlangius merlangus
Merluccius productus
Microgadus proximus
Micromesistius poutassou
Micropterus dolomieu
Micropterus salmoides
Morone Americana
Morone chrysops
Morone saxatilis
Moxostoma anisurum
Moxostoma macrolepidotum
Notropis atherinoides
Notropis hudsonius
Oncorhynchus aguabonita
Oncorhynchus gorbuscha
Oncorhynchus keta
Oncorhynchus kisutch
Oncorhynchus mykiss
Oncorhynchus tshawytscha
Pagrus major
Paralichthys olivaceus
Parophrys vetulus
Perca flavescens
Percopsis omiscomaycus
Pimephales notatus
Platichthys flesus
Pleuronectes platessa
Pomatoschistus minutus
Pomoxis nigromaculatus
Psetta maxima
Reinhardtius hippoglossoides
Salmo salar
Salmo trutta fario
Salmo trutta trutta
Salvelinus alpinus alpinus
Salvelinus fontinalis
Salvelinus namaycush
Sander vitreus
Sardinops sagax
Scomber japonicus
Sebastes schlegelii
Seriola quinqueradiata
Sparus aurata
Sprattus sprattus sprattus
Thaleichthys pacificus
Theragra chalcogramma
Thymallus thymallus
Trisopterus esmarkii
Trisopterus minutus
host_species_latin_name
read-only
yes
Comments on Host Species
host_comments
textarea
yes
Host Origin
host_origin
Note: feral = having escaped from domestication and become wild
yes
select
20
yes
yes
Disease Status of Host
host_disease_status
yes
select
yes
yes
title
Epidemiology
Epizootic
epizootic
Answer yes if mortality rate substantially exceeds background mortality. Further information can be added in text box below.
yes
select
Clinical and Epidemiological Observation in Stock
clinical_epidemiological_observation
textarea
1000
yes
title
Notes
General Notes
notes
textarea
10000
yes
Private Notes
private_notes
Information written in this field will only be visible to the user adding the report.
textarea
10000
author-only
title
Laboratory Source
Isolate Source
isolate_source
Name of Laboratory that isolated the virus
yes
text
200
yes
yes
Isolate Contact
isolate_contact
Contact details for isolate e.g. name, address, email address
textarea
1000
yes
title
Metadata
Report Author Name
author
text
20
yes
yes
yes
Last Modified Date
modified_date
text
20
Approved by
approved
text
20
no
yes
Report Permissions
public
Who is able to view the report?.
yes
select
no
User Accounts with permission to view report
user_permissions
Only relevant if restricted permission is chosen. Press 'control' to select multiple users.
multi-select-db
no
Sequence Report
Section heading?
title
field name in database
description
values
URL prefix
link
required?
pattern to match
type
max length
public?
display statistics?
in summary tables?
search filter?
title
Sequence Report
Database Identifier
id
yes
yes
Fishpathogens.eu Database Isolate Identifier
fpdbid
20
yes
yes
Isolate Name
isolate_name
Make sure that the isolate name written is identical to the isolate name in the isolate report that you want the sequence report to link to.
yes
text
200
yes
yes
yes
Has this specific sequence been added to Genbank?
added2genbank
yes
select
no
yes
Genbank Accession Number
accession_number
If not submitted to Genbank then leave this blank
no
text
yes
yes
Has isolate been through cell culture before sequencing?
cell_culture
yes
select
yes
Passage Number for the Virus
passage_number_virus
If not known, select unknown
no
select
yes
title
Sequence
Nucleotide Sequence
nucleotide_sequence
Enter sequence and press 'Identify Gene Regions and Protein Sequences' located just above. Make sure that added sequence is of high quality otherwise the identification of gene regions and protein sequences will introduce mistakes.
yes
textarea
65530
Gene Region(s)
gene_region
Gene regions identified by alignment to reference sequence. This box is filled out automatically after identification of gene regions and protein sequences.
no
textarea
yes
yes
Protein Name(s)
protein_name
This box is filled out automatically after identification of gene regions and protein sequences.
textarea
yes
yes
Sequencing General Comments
sequencing_general_comments
textarea
yes
yes
title
Sequencing Project
Sequencing Project Contact
sequencing_project_contact
Contact details for sequence e.g. name, address, email address.
textarea
1000
yes
Sequencing Method
sequencing_method
Comments to sequencing method can be added below.
yes
select
yes
yes
Primer Publication (Pubmed Id)
primer_reference
Publication reference for sequence or if not published then publication reference for sequencing primers used. Add reference as PubMed ID (PMID) or if not possible then write relevant information under Sequencing Method Comments below.
text
yes
Sequencing Method Comments
sequencing_method_comments
textarea
yes
title
Metadata
Report Author Name
author
text
20
yes
Last Modified Date
modified_date
text
20
Approved by
approved
text
20
no
Report Permissions
public
Who is able to view the report?
yes
select
no
User Accounts with permission to view report
user_permissions
Only relevant if restricted permission is chosen. Press 'control' to select multiple users.
