[3dem] Updated header format for the EMDB archive

[outreach at emdatabank.org]

Dear all,

 

We are announcing that on 16 January 2013, the EMDB archive will adopt an
updated format, 1.9.0, for the entry header file (XML file associated with
each map). This means that EMDB header files distributed from wwPDB partner
sites will conform to the 1.9.0 format, and our deposition/annotation/search
services will start using this format. The schema is available for download
at
ftp://ftp.ebi.ac.uk/pub/databases/emdb/doc/XML-schemas/Header-schema/candida
te/emdb.xsd. Example header files using this format can be found here:
ftp://ftp.ebi.ac.uk/pub/databases/emdb/examples1.9.0. We announce this
change now to allow time for developers to make any necessary modifications
to software/services that make use of EMDB header files. If there are any
questions please feel free to contact us at help at emdatabank.org.

 

v. 1.9.0 EMDB xml schema highlights:

 

1.      Two new descriptors allow a map to be separately described by both
specimen state and the methodology. These replace the aggregation state
descriptor of v.1.8 and earlier schema versions, which mixed this
information and did not allow depositors to indicate, e.g., that a deposited
map resulted from tomography on 2D crystals or subtomogram averaging on
helical samples. 

2.      The methodology descriptor now explicitly includes tomography and
subtomogram averaging as enumeration values.

3.      Obsolete/supersede entry information is now provided.

 

Major changes:

 

* 'status': a new code has been added for obsolete entries ('OBS'). These
entries will be available in FTP under the 'obsoleted' directory.

* 'aggregationState': has been removed. This item was used to describe both
the type of EM methodology and the state of the sample. Two new terms have
been created to describe these two different meanings:

1.      'method': this new item describe the EM methodology been used. A new
method, 'subtomogramAveraging', has been added. We now distinguish between
'subtomogramAveraging' and 'tomography'.

2.      'specimenState': is used to describe the state of the sample in the
grid.

* 'refUniProt': UniProt identifiers for protein components are now
supported.

* 'appliedSymmetry': describes the point group symmetry imposed on the
deposited map.

 

The actual schema file  includes a complete list of changes at the top.

 

 

Best Wishes

 

Ardan and Cathy 

 

EMDataBank

 

 

Ardan Patwardhan, 

EMBL-EBI

Hinxton, Cambridge CB10 1SD, UK
Tel: +44 1223 492649

 

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