[BiO BB] San Diegans :UniProt 2.0 Talks at UCSD - Tue, Wed, Thu this Week

[Iddo]

For Bioinformaticists in the San Diego Area:


******

You are cordially invited to a series of talks at the San Diego
Supercomputer Center Auditorium, September 28, 29, and 30th on

UniProt 2.0 and Protein Kinase annotation

to be presentd by Sandra Orchard and Samuel Kerrien (who will present 
instead of Ernst Kretschmann) from the EMBL - European Bioinformatics 
Institute.

Specific details of each days talk is given below. Refreshments will be
served.

Questions or if you would like to meet with the guest speakers please
contact Hannes Niedner (hannes at sdsc.edu)

--------

Title:UniProt 2.0 - General Overview

Date/Time/Place: September 28, 2004, SDSC Auditorium
1-2 pm seminar
2-3 pm technical discussion/walk through

Speaker: Sandra Orchard
EMBL - European Bioinformatics Institute

Abstract: The Swiss-Prot, TrEMBL and PIR protein databaseactivities have
united to form the Universal Protein Knowledgebase(UniProt) consortium, 
to
provide a comprehensive,fully classified, richly and accurately 
annotated
protein sequenceknowledgebase, with extensive cross-references and query
interfaces.The central database will has two sections, corresponding 
tothe
familiar Swiss-Prot (fully manually curated entries) andTrEMBL (enriched
with automated classification, annotation andextensive 
cross-references).
For convenient sequence searches, UniProt also provides several
non-redundant sequence databases.The UniProt NREF (UniRef) databases
provide representative subsetsof the knowledgebase suitable for 
efficient
searching. The comprehensiveUniProt Archive (UniParc) is updated daily
from many publicsource databases and includes many predicted and 
synthetic
sequences which are not appropriate for inclusion within UniProt.

-------

Title:UniProt 2.0 - Technical Overview & Discussion

Date/Time/Place: September 29, 2004, SDSC Auditorium
3-4 pm Seminar
4-5 pm Technical Discussion

Speaker: Samuel Kerrien
EMBL - European Bioinformatics Institute

Abstract: The annotation in gene and gene product is deeply rooted in a
flat file/free text tradition. Relational or object oriented models of 
the
data and their implementations are rare and usually have access
restrictions for end users. Users of the UniProt data set, which is
encompassing the former Swiss-Prot, TrEMBL and PIR content also has to
deal with these legacy problems. The flat file format that has been 
used,
extended and maintained over many years is readable for human eyes but
difficult to process algorithmically. With the exponential growth of
protein information, doubling the data amount approximately every two
years, downloading the whole sets and parsing out what is actually 
needed
on the end users side became cumbersome and CPU intensive. With UniProt,
we are trying to overcome this situation and give users query access to
our data sources. We are trying to make parsing procedures on the user
side redundant by providing a solid interface to the data set as a whole
and also to the individual protein entries.
This presentation will give an overview over the libraries that are used
at the EBI to present the UniProt data and to automatically process
protein entries. Those libraries will be made available shortly for 
users
and additional services are in the planning. The speaker will be going
into some detail in terms of how to make use of the read only copy of 
the
UniProt data base inside Java program code.

------

Title: UniProt 2.0 and the annotation of Protein Kinases

Date/Time/Place: September 30, 2004, 1-2 pm, SDSC Auditorium

Speaker: Sandra Orchard
EMBL - European Bioinformatics Institute

Abstract: A tour through the functionality of UniProt 2.0 will be 
provided
with particular reference to annotation of members of the Protein Kinase
family, one of the largest, and arguably best conserved protein 
families -
members of which can be found in species as diverse as man and bacteria.

The Swiss-Prot, TrEMBL and PIR protein databaseactivities have united to
form the Universal Protein Knowledgebase(UniProt) consortium, to 
provide a
comprehensive,fully classified, richly and accurately annotated protein
sequenceknowledgebase, with extensive cross-references and query
interfaces.The central database will has two sections, corresponding 
tothe
familiar Swiss-Prot (fully manually curated entries) andTrEMBL (enriched
with automated classification, annotation andextensive 
cross-references).
For convenient sequence searches, UniProt also provides several
non-redundant sequence databases.The UniProt NREF (UniRef) databases
provide representative subsetsof the knowledgebase suitable for 
efficient
searching. The comprehensiveUniProt Archive (UniParc) is updated daily
from many publicsource databases and includes many predicted and 
synthetic
sequences which are not appropriate for inclusion within UniProt. A tour
through the functionality of UniProt 2.0 will be provided with 
particular
reference to annotation of members of the Protein Kinase family, one of
the largest, and arguably best conserved protein families - members of
which can be found in species as diverse as man and bacteria.




-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo