FAQ - EMBL WWW submission system

Benny Shomer bshomer at ebi.ac.uk
Wed Nov 8 00:39:29 EST 1995


             EMBL nucleotide sequences database
               WWW sequence submission system
                        The FAQ list
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This is the second version of the  WWW based sequence data submission
tool Frequently Asked Questions (FAQ) list.

The FAQ list was written taking into consideration various queries
and problems that scientists from the users community have experienced.
It is probably far from being complete. We welcome any suggestions,
questions highlights...   Just send us mail at:     datalib at ebi.ac.uk

An HTML version of the FAQ file can be found on:

http://www.ebi.ac.uk/subs/subs_faq.html

or linked to, from the submission system page in the EMBL area of EBI
home page at:

http://www.ebi.ac.uk/

1.  What are the advantages of using EBI's WWW based sequence
    submission tool?

2.  Will my sequence be processed faster than normal when I use
    the WWW based system?  How soon will I get my accession 
    number?

3.  I need my accession number as soon as possible. 
    Any guidelines?

4.  Can I submit protein sequences with this tool?


5.  Which platforms / browsers are compatible with the system?


6.  Why is the submission system divided into so many parts?


7.  I have a few sequences - do I need to type all the
    information time and time again?

8.  I have previously submitted a sequence to EMBL. Can some of
    my data be used again for this submission?


9.  I specified my previous accession number but the system could
    not locate my entry. What's going on here?...

10. What's this thing with freezing a submission? How do I do it?

11. Is there a length limit for the sequence? why?

12. Must I specify features for the sequence?

13. Can I copy & paste my sequence with numbers etc.?

14. My system / browser has crashed. What do I do?...

15. I forgot to write my unique Id. How do I get it?

16. Why is it so important not to step back? When is it needed?

17. How can I add a feature from the final validation form?

18. How can I remove a feature from the final validation form?

19. During submission of the features I went into an endless loop,
    why did this happend?  How do I get out of it?

20. How do I request further help?

21. I have finished all my submissions, how do I stop the program?


==================================================================

1.  What are the advantages of using EBI's WWW based sequence
    submission tool?

a. In contrast to a stand-alone program, EBI constantly maintains 
and updates the program. This makes debugging and keeping up-to-date a
lot easier.
   
b. If you already have the WWW client installed, you don't have to
waste time, effort and disk space on installation of a program on your
computer.
   
c. The program uses the EBI database resources (like the list of
previous submitters, or journals), to enable a more user-friendly
interface.
   
d. You may freeze your session for a very long time.  

e. You can tell your friends that you have submitted a sequence using
EBI's new system...

                                 +++

2.  Will my sequence be processed faster than normal when I use
    the WWW based system?  How soon will I get my accession 
    number?

Generally, the process of submission is made somewhat shorter, since
the submission system itself, prevents the user from many common
mistakes during submission (like leaving out mandatory items, detecting
minor errors etc).  The system also enables EBI's data annotation staff
to automate the processes of loading the submitter's personal details
and the sequence data into the database system. Since your data comes
in already formated in the most optimal way for us to process, it
saves some manual editing steps.

We will process data submissions within 24-48 hours of receipt and send
authors notification of either what accession number(s) their data have
been assigned or what additional information is needed.

                                 +++

3.  I need my accession number as soon as possible. 
    Any guidelines?

There are several things authors can do to minimize the time it takes
to get an accession number:

a. Be sure that submissions include all the necessary information and
that all relevant questions have been fully answered. A very common
trap for many users is not providing the sequence features. This
introduced a delay, since our data annotators must communicate with
the submitter, asking for that information.

b. Check the data to be sure that they do not contain inconsistencies
/ errors (e.g., a stop codon in the middle of a coding region).

c. Take extra care and check that the provided Email address is
accurate. The submission system checks some syntax rules and the
country domain provided, but can't do more than that. If a wrong Email
address is provided, any attempt for further communication will 
slowed down the process. Your precise phone and fax number will also
help.

                                 +++

4.  Can I submit protein sequences with this tool?

The submission system is currently intended, and is specifically
designed for submission of nucleotide sequences only.  If you need to
submit protein sequences to SWISS-PROT, please send a request for a
data submission form to: datalib at ebi.ac.uk

                                 +++

5.  Which platforms / browsers are compatible with the system?

The submission system has been thoroughly tested and is known to be
compatible with all the common platforms (i.e. PC's Mac's Xclients and
workstations). Most of the common browsers have been tested: mosaic,
Netscape, MacWeb, lynx, Magimix.

Users of Netscape for Mac & PC's should be aware of a Netscape
acossiated limitations. Some Netscape browsers are incapable of
saving the html source code generated by scripts (in fact they simply
do it in the wrong way, asking the server to reload the source,
something a CGI script can not provide). Users of Netscape should not
attempt to 'freeze' their submission (see section 9), by saving the
HTML source code of the form. They should resume their session by
using the rescue mechanism provided by the system (see section 12).

                                 +++

6.  Why is the submission system divided into so many parts?

The task of submitting a sequence to the databank(s) is a very
complicated and demanding one. Breaking the process to many smaller
forms enables some major advantages:

a. It enables a high level of interactivity with the user. The system
responds on the users input, checking validity on many data fields.

b. It enables data hiding. Data items which are of no concern to all
the users will be hidden and will appear only when the need arises.
For example, if you submit a human cDNA, you don't need to see
questions related to viral sequences. 

c. It enables managing the complicated task even when the network load
is heavy. The forms are broken into a single network packet (or two),
so traffic is cut down to a minimum.

                                 +++

7.  I have a few sequences - do I need to type all the
    information time and time again?

Having X different sequences, calls for cycling through the submission
system X times. Yet, the system will keep most of the submission
details (according to your specifications) for re-usage. This means
that on each of the remaining X-1 submissions, the selected forms will
appear pre-filled with the appropriate details. The chance to specify
which details should be recycled by the system is given following the
completion of each submission.  If you intend to submit several
sequences that are related to each other, please mention this in the
first page of the submission system, so that our sequence annotation
group will know to process them together.

                                 +++

8.  I have previously submitted a sequence to EMBL. Can some of
    my data be used again for this submission?

Yes. If your submission has been made directly to EMBL / EBI you may
type your previous accession number. That will get you the first form
of your personal details pre-filled with your details as they appear
in the database. You have an option to modify any details if needed.
Please review your data and check for any errors.

                                 +++

9.  I specified my previous accession number but the system could
    not locate my entry. What's going on here?...

Well, normally - either your entry is still tagged as confidential, so
it's not available to the public, or it is new and is not yet updated
in the local names database of the submission system (it is not an
automatic process yet).  If neither is true, please let us know about
it. It will be checked.

                                 +++

10. What's this thing with freezing a submission? How do I do it?

Before your submission is complete your data items are stored in a
temporary storage area and are identified by your unique Id. Each one of
the submission forms is carrying the unique Id in the HTML source code. 
When you submit the form, the system picks up the unique Id and acts
accordingly. Theoretically, this means that if you will save the HTML
source code to your disk, and open it later on as a local file, you will
be able to press continue and go on with the submission. This is true for
the amount of time specified by EBI (currently unlimited).

>From the practical point of view - just forget it. Many people (typically
users of Netscape) had problems doing this and the rescue mechanism is so
much simpler to use that it is the preferred method of resuming a session.

See the explanations in section 14.

Using the rescu mechanism enables you to gather pieces of information you
have forgotten, go get coffee from the coffee machine, fall asleep
leaning on your monitor or take a plane to Hawaii (unless your'e lucky
enough to be there already), leaving us in anticipation :-)


                                 +++

11. Is there a length limit for the sequence? why?

Due to a current limitation of the WWW system, there is no possibility
to transfer documents larger than 22500 characters. This means you can
not submit directly, sequences larger than 22500 base pair.

What to do if your sequence is longer than that?   Instead of a real
sequence, type in 4 bases, and send (only) the sequence itself to
datasubs at ebi.ac.uk  mentioning your unique Id.  If you know in advance
about this (you obviously do if you are reading this FAQ list...),
please mention this fact in the comments box at the begining (or end)
of the submission process.

                                 +++

12. Must I specify features for the sequence?

Indeed so. If you fail to provide the appropriate features, it will
cause delays in the processing of your entry (See section 6). This is,
since the data annotators will have to communicate with you further,
to obtain the features from you.


                                 +++

13. Can I copy & paste my sequence with numbers etc.?

If you copy and paste your sequence from any program or text editor,
the sequence may contain spaces, tabs and numbers. These will not be
regarded by the system and your sequence will be reformated.

                                 +++

14. My system / browser has crashed. What do I do?...

Ouch. It's time for a rescue...

>From the submission home page (the one with the logo), there's a link to
the rescue mechanism. Select this link, specify the unique Id that is
given to you at the begining of the submission and pray.  You will be
taken to the last step at which your submission has stopped. This
however, refers to a submission while it is at process. After the
submission has been completed, the rescue mechanism can not be in
operation.

Please note a recent change (since November 95). Since now the same
system serves several submission systems (currently EMBL and the PCR
primers databases  and soon to come the SWISS-PROT database), you are now
required to specify to which database you were submitting when your
session was stopped.

You may certainly use the rescue mechanism instead of "freezing" your
submission at any time (although molecular biologists DO tend to
freeze everything...).

                                 +++

15. I forgot to write my unique Id. How do I get it?

Just send a request by email to: datalib at ebi.ac.uk
We can detect your unique Id, provided your entry still exists in the
system.

                                 +++

16. Why is it so important not to step back? When is it needed?

On any step of the submission, if you go back to more than one
previous form and press "continue", it will result in loss of
the recent data items. Say that you have submitted 1, 2, 3, 4 and 5.
You now press 'back' and go to 3, then you press "continue", it will
erase 4 and 5. If, however, you step only one form back and press
"continue", your data is safe. This allows you to correct the last
form you entered. 

So what if I'm at step 5 and discovered an error in 2?

There is a special form at the end, allowing you to correct any data
item you wish. Please use it.

                                 +++

17. How can I add a feature from the final validation form?

If you need to add a feature during the final validation step (where
you are given the full list of all your data for approval), select the
last feature's checkbox (that is unless you need to correct a feature
entry anyway), and continue. Continue (unless a correction is needed)
without change. You will get back to the final validation step, but
two empty feature entries will be appended to the list. Check one of
their boxes and press "continue", to enter their data. Specific
help for each feature's options and qualifiers is given after
selecting a feature.  If you have initially chosen not to add any
feature, but made up your mind to add one in the final validation
step, check the box for correcting the sequence and press continue
after specifying that you need a feature. Again - you will have a
checkbox associated with an empty area. Check it and press continue.

                                 +++

18. How can I remove a feature from the final validation form?

Check the feature's checkbox and press continue. This will give you a
chance to correct the feature's entry.  Specify locations from 0 to 0,
leaving the qualifiers lists empty. This is a sign for us to cancel
this feature entry. DO NOT  leave both feature lists empty (i.e.
containing '------'). This will get you into an endless loop with
funny looking qualifier boxes.  If you have mistakenly went into such
a loop, simply step back, and re-submit the unwanted feature as
described above.

                                 +++

19. During submission of the features I went into an endless loop,
    why did this happend?  How do I get out of it?

The system currently enters an endless loop if both feature lists are
left empty (i.e. containing '------'). If you have mistakenly went
into such a loop, simply step back, and re-submit with a feature
selected. If it happend while trying to cancel a previously submitted
feature, see section 18.

                                 +++

20. How do I request further help?

Open the window and shout "HELLLLP", or...

In any of the submission's context sensitive help files, at the
bottom, there's a special area where you can type your help request.
Be sure to enter your correct Email address.

You can also send Email directly to: datalib at ebi.ac.uk. Please specify
your problem in clear words and try to be as descriptive as you can.

                                 +++

21. I have finished all my submissions, how do I stop the program?

There's actually nothing to stop. If you don't intend to submit any
more sequences, just use your Web browser as you would normally.
Either choose any other URL, go to EBI's home page, kill your
browser...



~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Benny Shomer
External Biological Liaison Officer,
EMBL outstation - The EBI,
Hinxton Hall, Hinxton,Cambridge CB10 1RQ, UK

Tel:   +44-223-494437
Fax:   +44-223-494468
Email: bshomer at EBI.ac.uk
http://www.ebi.ac.uk/ebi_docs/staff/benny.html

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~





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