Over the past six months SGD staff have worked to significantly
enhance the way data are stored at SGD. During this time,
much of the data has been checked and updated as needed. These changes
will allow SGD to incorporate new data and datatypes, such as additional
chromosomal features, with greater ease.
Highlights of changes to the SGD schema
include:
- Adopting aspects of the CHADO
database schema
- Increased flexibility in relating features to other
features
- Increased flexibility in expanding the types of data that
can be added
- Defining explicit relationships between the SGDIDs of
features at SGD to unique identifiers at other databases
In addition, the following new options have been added to existing tools:
- Additional GO Slim sets have been added to the GO Slim
Mapper
- A customized set of GOIDs can be entered to the
Chromosomal Features Search in order to retrieve the desired
features
- Genomic DNA, coding and intron sequences can
be retrieved from the "Sequence Information" section of the
Locus page
- A Phenotype Resources pull-down menu has been added as an
option on the right hand side of the Locus page
As a consequence of the changes to the way data are stored at SGD, the
following changes and additions have been made to the available
data at SGD:
- Expansion of SGDIDs from 8 digits to 10 digits.
Two additional padding zeros were added to the numerical
portion of the SGDID (for example, S0000981 is now S000000981). The shorter 8 digit SGDID will still
be supported via web interfaces, but only the longer 10
digit SGDID will be used in files available on the ftp
site
- SGDIDs now associated with references. These
SGDIDs are now the official database identifier for
references within the database and will be used
on SGD reference pages and within any file in which we
provide reference information, such as the gene_associations.sgd
file available from the GO Consortium and SGD ftp sites
- Implementation of Sequence Ontology
terms. The majority of feature types and subfeature types
have remained the same. However, one significant change is the use
of CDS
instead of exon. SGD has chosen to implement the use of CDS in order
to reserve the word exon for
instances when we have data that provide the entire exon, including any
5'-UTR or 3'-UTR sequences
- Embedded features displayed on Locus page.
Chromosomal features that are fully contained within the given
feature are listed in the "Sequence Information"
section of the Locus page.
- Dates associated with chromosomal features.
These dates are displayed in the "Sequence Information"
section of the Locus page. The dates are in the following
format: year-month-date. There are two types of dates:
- Coordinate dates indicate the date the coordinates
of the feature were last changed. In most cases this
is likely due to an insertion or deletion to the left
of the feature, resulting in a shift of all chromosomal
coordinates for features located to the right of the
insertion or deletion.
- Sequence dates indicate the date that the sequence of
the feature was last changed. This can be due to a
sequence change within the feature, a change in the intron/CDS structure
of the feature, or an change in the the start or stop
coordinate of the feature which extends or shortens the
feature. At the present time, the
oldest date displayed is 2000-05-19.
- Reorganized pull-down menus. The order and
location of items
on the pull-down menus on the right hand side of the Locus
page have changed. The majority of options are now
alphabetical within each pull-down menu. Please see the help page for more details on the
location of pull-down menu items.
- References associated with standard gene names and
aliases. Citations referring to the standard gene name
or to an alias name are available on the Locus History page for
that gene.
- Categorization of notes. In order to clarify the
types of notes displayed on the Locus History page, they
have been divided into sections, such as Nomenclature
History, Mapping Notes, and Sequence Annotation Notes.
Please see the help page for more information.
- Reorganized GO Term page. Please see the help page for more information.
- Modified Clone pages. Tools and resources that
were previously available on the Clone page, such as the Physical map,
are currently still under development.
- Creation of Chromosome pages.
Additional tools and resources for Chromosome
pages are currently under development.
