Genome Annotation Markup Elements (GAME)
Here's an HTML
version of the GAME dtd.
Please contact Suzanna Lewis
for more information
The motivation for GAME is a desire to provide a syntax, together with
some simple tools, that will facilitate the exchange of genomic annotations.
It will enable genome centres, model organism databases, an individual
researchers to clearly specify the conclusions they have drawn from their
analyses of primary sequence data and share these XML descriptions with
one another. The development of GAME was necessary to allow the Drosophila
Genome Project to coordinate their efforts with Celera, which required
a stable and expressive interchange format.
GAME and GFF
GAME complements the existing work that has been done with GFF
(Gene-Finding Features). GFF is largely targeted at standardizing the
output of gene prediction software. GAME is inclusive of these types of
sequence descriptions, but extend beyond this to include curated results
as well. Tools will be added to convert between these two syntaxes (although
it is likely that there is information loss when going from GAME to GFF).
GAME does not aim to be a replacement for the established flat file formats
from GenBank or EMBL, or the ASN.1 model of the GenBank database. GAME
aims to be an interchange format for annotations which can make the necessary
distinctions to allow a full interchange of data between genome centres.
The flat file formats are focused on archival storage of the DNA sequence
as submitted, and the ASN.1 model provides a rich object model for manipulation
of these sequences with the NCBI toolkit. Of course, conversion tools between
the formats for the common information that they share are in development,
but there is not a one to one mapping between a GAME document and GenBank/EMBL/DDBJ
Ewan Birney has started a FAQ about GAME. Please
read it if you are unfamiliar with the Project. The CORBA Life Science
Research (LSR) is considering a standard for biosequence analysis. This
has considerable overlap with the GAME document in terms of the information
which both standards define, but as CORBA is focused on an interface and
therefore methods definition and XML is focused on a data
definition, the two standards are largely speaking orthogonal. We believe
that GAME is a sensible data orientated view of a number of interfaces
defined in the LSR standard, and hope to define a sensible mapping between
the two standards soon.
Since this effort has just begun there is a consider
These basics entities and their relationships are described below
Annotations are quite broadly defined in GAME as a collection of
features found on an associated set of sequences.
Features in turn are conclusions describing intervals on different
sequences. Features are supported by analytical evidence.
Analyses are either computational assessments or biological experiments
carried out on a sequence. They are comprised of results that describe
some characteristic of an interval on a sequence.
Sequences of course are the molecules that are the subject of study.