Registering
How do I register?
To register on Fishpathogens.eu, click on "create new account" at the top right corner. Fill in you details
and click "create new account".
I want to upload information in several databases. Do I need to register separately for all of them?
No. You only need to register once to gain access to all the databases on Fishpathogens. eu.
Why do I need to register?
To be able to upload information into any of the databases on Fishpathogens.eu and to be able to
download and use any information from Fishpathogens.eu, you need to be registered as user. This is to
prevent uploading of spam as well as to ensure that all users are aware of any restrictions within the site.
When you register you also agree to our Terms and Conditions which also contains information about our
cookie policy.
What is My Page?
My Page is where you will be able to change your account details, as well as view all your uploaded isolate
and sequence reports. You will also be able to edit your uploaded reports from here.
How do I configure my account?
Go to My page and click on Account Profile. From here you will be able to change your account details,
including your database preferences.
I've forgotten my password. What do I do?
Click on the link "Forgotten password?". Enter the email that you use for your Fishpathogens.eu account
and you will be emailed a link to reset your password.
How do I cancel my account?
To cancel your account, go to My Page and click "Cancel account". Sequence and isolate information that
you have uploaded to the Fishpathogens database will still be available even after deleting your account.
Uploading an Isolate report
How do I uploade an isolate report?
You need to be logged in to upload a report. Once you are logged in, go to the database pertaining to the
virus you want to upload. To upload an isolate report go to "add a report" on the top bar and choose add
an isolate report. Some fields will be text fields where you can write relevant commentaries while others
will contain a dropdown menu where you can select the right value. Fields marked with *** are required
fields that needs to be filled in. If you do not have the data it is often possible to answer "unknown" or
similar. When adding an isolate report to the database for an isolate which has already had a sequence
report added, it is very important to make sure that the isolate name is identical to the isolate name on the
sequence report. Otherwise the two reports will not be able to link together. When done, click the submit
form button.
The report will now show in your list of added reports. To view this click "my page" in the upper right
corner (only available if logged in) and under "View My Reports" click "Browse Reports". After a report has
been added an email will be sent to a pathogen expert who will have to approve the isolate report before it
is made publicly available.
I submitted an isolate report. Why did it not show up in the database?
All isolate and sequence reports are queued after being submitted. Before they are released to the public
part of the database, the information will be checked by a Fishpathogens.eu pathogen expert. These will
determine whether or not the information seems correct and is filled in correctly.
Can I restrict access to my report data?
Yes. While you fill in your report you get a chance to restrict who will be able to view your report. This
option can be used if you e.g. want to upload your data to the database before your article is published.
In this way you can then release all the data straight after publication. We encourage users to only restrict
information when absolutely necessary as one of the main goals of Fishpathogens.eu is to encourage
sharing of data.
Uploading a Sequence report
How do I uploade a sequence report?
You need to be logged in to upload a report. Once you are logged in, go to the database pertaining to the
virus you want to upload. To upload a sequence report go to "add a report" on the top bar and choose add
a sequence report. Some fields will be text fields where you can write relevant commentaries while others
while contain a dropdown menu where you can select the right value. Fields marked with *** are required
fields that needs to be filled in. If you do not have the data it is often possible to answer "unknown" or
similar. When adding a sequence report to the database for an isolate which has already had a sequence
report added, e.g. for another gene or had an isolate report added, it is very important to make sure that
the isolate name is identical to the isolate name on the other reports. Otherwise the reports will not be
able to link together. When done, click the submit form button.
The report will now show in your list of added reports. To view this click "my page" in the upper right
corner (only available if logged in) and under "View My Reports" click "Browse Reports". After a report has
been added a mail will be sent to a pathogen expert who will have to approve the sequence report before it
is made publicly available.
I submitted a sequence report. Why did it not show up in the database?
All isolate and sequence reports are queued after being submitted. Before they are released to the public
part of the database, the information will be checked by a Fishpathogens.eu pathogen expert. These will
determine whether or not the information seems correct.
Can I restrict access to my report data?
Yes. While you fill in your report you get a chance to restrict who will be able to view your report. This
option can be used if you e.g. want to upload your data to the database before your article is published.
In this way you can then release all the data straight after publication. We encourage users to only restrict
information when absolutely necessary as one of the main goals of Fishpathogens.eu is to encourage
sharing of data.
Search
How do I browse reports?
It is possible to browse all the reports in the database by clicking isolates on the bar at the top of the page
and choosing either isolate reports or sequence reports. You will now get a long list of all the isolates or
sequences in the database together with a sample of the information in the report. It is possible to change
what information to see for the list by going to My Page and changing your options there. It is also possible
to sort the list according to the different variables like country or genotype by clicking the small arrows at
the top of the browse list. From the browse list you can click into each individual report.
How do I use the search function?
In the search field it is possible to make a free text search if you chose the entire isolate report in the
dropdown menu. To make the search more specific it can also be chosen to search on a specific field in the
isolate report (click on left drop-down menu to get the options available). Click on the + sign to the right to
add another search criterion. It is also possible to search by gene region, date or geographical region using
the search fields further down the site. When searching for a geographical region it is possible to pick a
region on the Google map and then define an area around it by specifying how many kilometers from the
chosen point the search should include. You can also BLAST you sequence against other sequences in the
database using the BLAST page under Search reports.
What kind of output files do I get?
When using Fishpathogens.eu you get a choice of different output files. This includes Excel- (.csv), KML -and
fasta-files which can all be opened up in third-party programs.
Sequence matcher
Where do I find the sequence matcher?
The sequence matcher is located under the Search Reports tab.
What can I do with the sequence matcher?
The sequence matcher is meant as a fast way of getting an answer to what genotype/genogroup your
unknown sequence belong to. By picking neighbor-joining as the analysis you can input your unknown
sequence and pick what gene has been sequence. This will lead you to a page where you will be able to
pick which reference sequences you want in your tree. Once you have chosen those, as well as an outgroup
sequence, a tree will be created containing your query sequence. The tree will be color-coded pertaining to
genotypes/genogroups.
