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ORDB Frequently Asked Questions
What is the Olfactory Receptor Database?
The Olfactory Receptor Database is hosted in senselab.med.yale.edu, in one of the Windows NT servers of the Yale Center for Medical Informatics, communicating using active server page technology with the main Oracle database of Yale University School of Medicine, which stores the actual ORDB data. The database aims to house all of the known olfactory receptor and chemoreceptor sequences in both nucleotide and amino acid form and serves four main purposes:
- It is a repository of olfactory receptor sequences.
- It provides tools for sequence analysis.
- It supports similarity searches (screens) which reduces duplicate work.
- It provides links to other types of receptor information, e.g. 3D models.
Who can use the database?
The database is accessible to two classes of users:
- General public www users have full access to all the public sequences, models and resources in the database.
- Source laboratories are the laboratories that clone olfactory receptors and submit sequences in the private or public database. They can search any sequence they deposited to the database against any private or public sequence in the database. This user level is suited for laboratories that are actively cloning olfactory receptors. [Apply]
What tools are available?
We have recently added a new feature to enable users to manipulate
visually the molecular models of olfactory receptors. This program
needs a chime plugin which is available for Windows and MacIntosh
systems and Netscape and Internet Explorer (not all versions).
The chime plug-in can be obtained from
http://www.mdlchime.com
The database houses records of olfactory receptors that include both amino
acid and nucleotide sequences as well as links to bibliographic and clonning
laboratory information. It is updated weekly to insure accurate and up to date
information. The public records can be searched
using keywords. Sequence similarity searches of the public records can be
performed by all members of the ORDB user group using a locally available BLAST
search engine. Sourse laboratories may additionally screen both the private and
the public database using BLAST for similar sequences to their private
sequences. BLAST screens all sequences in ORDB and returns a list of the closest
matches. Sequences are listed along with the source lab, source organism, and
various ways to get in contact with the source lab. If the receptors identified
by BLAST are public, there are direct links to their sequences that can be
accessed for comparison. If they are private only the names and addresses of the
source lab and the species is revealed, ensuring the security of each lab's
unpublished data.
What are the responsibilities of the Source Laboratories?
This resource belongs to the field of receptor research and source laboratories are encouraged to submit as many sequences as possible as the more sequences in the private database the greater the utility of the database. In addition, source laboratories are encouraged to change the status of a sequence to public once it is published in Genbank.
What about the security of my unpublished data?
All unpublished sequences are kept completely confidential and cannot be viewed by other users. The data files are maintained on a secure UNIX file system which is protected by encrypted passwords. Only the database administrator, a computer scientist with no involvement in olfactory receptor research, has access to the files.
Who administers the database?
The Olfactory Receptor Database is a component of SenseLab, a pilot project of the Human Brain Project. It is administered jointly by the laboratories of Gordon M. Shepherd, Section of Neurobiology, Yale School of Medicine, and Perry L. Miller, Center for Medical Informatics, Yale School of Medicine. The ORDB is currently managed by Dr. Chiquito Crasto who should be contacted with any queries and comments.
Who supports the database?
The database is supported by grants from the National Aeronautics and Space Administration, the National Institute for Mental Health, and the National Institute for Deafness and other Communicative Disorders, through the Human Brain Project, and by the National Library of Medicine's IAIMS program.
How do I get more information?
For general database and olfactory receptor questions
email the ORDB administrator