A new genome-based protein database called the Oxford Genome Anatomy Project was launched last week in London by Oxford Genome Sciences, a spin-off of Oxford GlycoSciences, which was acquired by Celltech last December.
OGAP is modified from the Protein Atlas database developed by members of Confirmant, a joint venture formed between Oxford GlycoSciences and Marconi in 2001. The database uses the genome as a backbone to summarize information about a given protein and disease.
The old Protein Atlas database was licensed from Celltech along with all of Oxford GlycoSciences’ bioinformatics infrastructure last December, said Christian Rohlff, the CEO of Oxford Genome Sciences.
“Celltech recognized that by supporting us, they would further the value of the work,” said Rohlff. “We have retained here with Oxford Genome Sciences a lot of expertise in taking the project forward.”
The OGAP database uses a human genome database called Golden Path to build a virtual transcription database. The transcriptome is then used to build a tryptic digest, and all the users’ proteins are then mapped on top of this virtual digest.
So far, the OGAP database contains about a million MALDI peptides and 300,000 tandem sequences, which combined map to about 15,000 genes. A demo version of the free-to-use database is available at www.oxfordgenomesciences.com.
“OGAP was built largely based on feedback and demand that we received from our pharma customers. They really helped us to shape this product,” said Rohlff. “It’s built purely as a proteomics database, rather than trying to remodel a genomics database.”
Rohlff said the main users of the database will be pharmaceutical companies that already have a major proteomics effort, academic institutions with proteomic centers, and biologists who are focused on developing therapeutic antibodies for inflammation and cancer.
“In terms of a timeline, we want to get this into customers’ hands as quickly as possible and to get some good stories of successes coming out,” said Rohlff. “Everybody [at the launch] thought that this was a very powerful approach.”
At its pea,k Confirmant’s old team included about 50 people in proteomics, including 10 bioinformatisticians and three biomathematicists, said Martin Gouldstone, the former executive business developer for Confirmant.
“It was quite an intensive undertaking,” said Gouldstone. “It included quite an extensive pipeline from Oxford GlycoSciences that supplied us with the basic proteomics data.”
Once Confirmant was closed, all rights of the database went to Celltech, and the rights were then licensed by Rohlff when he started his new company.
Compared to the old Protein Atlas database, which was more of a rigid database model, OGAP is more flexible and has expanded functionality, said Rohlff.
“We want to be very flexible because different pharmas are in different stages of incorporating the database,” said Rohlff. “Oxford GlycoSciences talked to all the big pharmas and found that no two companies have the same approach. The conclusion was that we have to be very dynamic and flexible.”
OGAP will adhere to guidelines proposed by the Human Proteome Organization’s Proteomic Standards Inititative, which was created in 2002 to standardize data formats within the field of proteomics. Currently, the database adheres to the PSI’s Minimium Information About a Proteomics Experiment guidelines.
“The long-term idea is that we will be freely exchanging information between public databases,” said Rohlff.
Though OGAP is presently not linked to any other protein databases, it gives protein reference numbers for Swiss-Prot and NCBI Protein databases. In the future, Oxford Genome Sciences may work to establish more connectivity between OGAP and other databases.
OGAP is the only protein database that maps back to the genome, said Rohlff. It can be most useful for helping researchers to verify gene structures, helping them to verify antibody structures that they’re developing and helping to determine the selectivity and specificity of biomarkers. In addition, it can help verify SNP variants, in antigen targets.
Oxford Genome Sciences began developing the OGAP database this summer as part of the bioinformatic infrastructure of the company. It will try to maintain the database so that it is free-of-charge, but may consider some sort of subscription or fee model in order to cover the costs of updating the database more frequently, said Rohlff.
Currently, there are about 25 employees at Oxford Genome Sciences. Martin Barnes, who oversaw about 40 information technology staff during his three and a half years at Oxford GlycoSciences, was recently appointed as the head of bioinformatics.
Aside from Barnes and Rohlff, other key players of Oxford Genome Sciences include Jim Bruce, the chief technology officer and Albert Platt, the director of engineering.
In addition, the company is in the process of forming a scientific advisory board. So far members of the board include Rolf Apweiler of the European Bioinformatics Institute, who will be helping to ensure that OGAP meets Minimum Information About a Proteomics Experiment standards, and Athula Herath, the former director of biometrics and bioinformatics at Oxford GlycoSciences.
— TSL