Introducing JBEI XML formats

[Timothy Ham]

In addition to existing web service mechanisms to exchange data, the
JBEI-ICE group is pleased to announce the availability of an XML
format for exchanging data with JBEI-ICE.

The xml format is divided into two parts: ice-xml and seq-xml. Each
have schemas as defined here:
ice-xml: http://code.google.com/p/gd-ice/source/browse/docs/ice.xsd
seq-xml: http://code.google.com/p/gd-ice/source/browse/docs/seq.xsd

Ice-xml contains complete information about a record, and seq-xml
contains annotated sequences. An Ice-xml record can have a seq-xml to
hold annotated sequence information.

Currently there are generators and parser in these files:
http://code.google.com/p/gd-ice/source/browse/src/main/java/org/jbei/ice/lib/utils/IceXmlSerializer.java
http://code.google.com/p/gd-ice/source/browse/src/main/java/org/jbei/ice/lib/utils/SeqXmlSerializer.java

The seq-xml is able to capture almost all the intricacies of a Genbank
file. Be warned, however, the current *implementation* of ICE does not
(yet) understand all of these intricacies expressible by seq-xml or
Genbank.

Ice-xml has features that facilitate exchange of information between
different instances of ICE that are not connected to each other.
- Each entry is identified by a UUID.
- Even though user account information are not included, user's email
can be used as a distinct identifier for the owner and creator of an
entry.
- File attachments can be included in ice-xml.
- Instance specific information, such as user and group permissions
are omitted.
- Part numbers are included, but they do not suffer from collision
between instances.

Entries can be exported as XML via a link available on every page for
an entry, and also from group of entries, such as from search results
or collections. Currently only administrators are able to import these
data files in bulk, but user importation of files will be available in
the future.

Best,
Tim