The future of annotation/biocuration

Talk given at 3rd International Biocuration Conference. Berlin 200

The ENZYME data bank in 1999

The ENZYME data bank is a repository of information related to the nomenclature of enzymes. In recent years it has become an indispensable resource for the development of metabolic databases. The current version contains information on 3704 enzymes. It is available through the ExPASy WWW server (http://www.expasy.ch/

Bioinformatics for Human Proteomics: Current State and Future Status

We are entering a new era in the exploration of the human proteome.
Advances in technologies are allowing researchers to map with a much
better resolution and improved accuracy this very complex universe. Such
an exploration also requires a compendium of adequate bioinformatics
tools, data repositories and knowledge resources. We are going to describe
what are the state of the art in term of data and knowledge resources for
human proteins: from repositories of proteomics data such as PRIDE,
PeptideAtlas or Peptidome, databases such as SRMAtlas and HPA and
knowledgebase such as UniProtKB/Swiss-Prot. 

In September 2008, the UniProt/Swiss-Prot group achieved a major
milestone: the first complete manual annotation of what is believed to be
the full set of human proteins (derived from about 20'000 genes). This
corpus of data is already quite rich in information pertinent to modern
biomolecular medical research, but made us realize how large is the gap in
our knowledge of human proteins in terms of functional information as well
as protein characterization (PTMs, protein/protein interactions,
subcellular locations, etc). 

This gap resides not only in the available experimental information, but
also in the way this information has been stored, which is far from being
sufficient to help researchers making sense of what all these human
proteins do in our bodies! Therefore, in the framework of CALIPHO, a new
interdisciplinary group created jointly by the University of Geneva and
the Swiss Institute of Bioinformatics (SIB), we are developing neXtProt, a
new human-centric protein knowledge resource. 

neXtProt is developed with the aim to help researchers answer pertinent
questions relevant to human proteins. This requires answering 3 different
challenges: 

1) Add to the corpus of data on human proteins that is already in Swiss-
Prot, a lot of additional information. We will import in neXtProt data
originating from a variety of high-throughput approaches such as
microarray, antibodies, proteomics, siRNAs, interactomics, etc. All of
these data sets must be carefully selected so as to only provide high-
quality data as we want to avoid creating a noisy and dirty compendium. 

2) Organize the data in such a way that it is possible to make powerful
queries in the most user-friendly environment. Here also, it is necessary
to be able to capture the complexity and the heterogeneity of the data
that will be available in neXtProt, yet make it easy for the user to
forget this complexity! 

3) Build a software platform that will allows tools ranging from sequence
analysis to text and data mining to be integrated in various research
environments so as to answer specific needs of academic and industrial
users. 

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The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999

SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include: cross-references to additional databases; a variety of new documentation files and improvements to TrEMBL, a computer annotated supplement to SWISS-PROT. TrEMBL consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except the CDS already included in SWISS-PROT. The URLs for SWISS-PROT on the WWW are: http://www.expasy.ch/sprot and http://www.ebi.ac.uk/spro

The PROSITE database, its status in 1999

The PROSITE database (http://www.expasy.ch/sprot/prosite.html) consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of protein (if any) a new sequence belongs, or which known domain(s) it contain

Design and Implementation of the UniProt Website

The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community. The "www.uniprot.org":http://www.uniprot.org website is the primary access point to this data and to documentation and basic tools for the data. This paper discusses the design and implementation of the new website, which was released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines for programmatic access

ExPASy: the proteomics server for in-depth protein knowledge and analysis

The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics (SIB). It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment. These databases and tools are tightly interlinked: a special emphasis is placed on integration of database entries with related resources developed at the SIB and elsewhere, and the proteomics tools have been designed to read the annotations in SWISS-PROT in order to enhance their predictions. ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user communit

The SWISS-2DPAGE database: what has changed during the last year

Swiss-2DPAGE (http://www.expasy.ch/ch2d/) is an annotated two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) database established in 1993. The current release contains 21 reference maps from human and mouse biological samples, as well as from Saccharomyces cerevisiae, Escherichia coli and Dictyostelium discoideum origin. These reference maps now have 2480 identified spots, corresponding to 528 separate protein entries in the database, in addition to virtual entries for each SWISS-PROT sequence. During the last year, the SWISS-2DPAGE has undergone major changes. Six new maps have been added, and new functions to access the data have been provided through the ExPASy server. Finally, an important change concerns the database funding sourc