"Proteinpedia" catalogues detailed info for biologists

By: Jeffrey Siegel

Posted: 11/6/08

Scientists have recently set up the Human Proteinpedia, an online clearinghouse for sharing data about human proteins, allowing researchers to more easily access and use this information to develop new medications and further their own research.

The Proteinpedia will be a centralized repository for proteomics data, which emerges from studies of proteins.

Akhilesh Pandey, a Hopkins scientist who led the team that developed the Proteinpedia, calls it the "protein Wikipedia envisioned to make scientific information, including both published and unpublished studies, accessible to the biomedical community.

Free access to scientific information would enable systems biology-type research and thus accelerate new discoveries."

According to Pandey, the Proteinpedia offers significant advantages over previous repositories.

"Human Proteinpedia accepts data derived from seven different experimental platforms, unlike other proteomics resources which are limited to one or two experimental conditions. Also, the existing proteomics repositories are limited in the type of protein features, whereas Human Proteinpedia provides multiple annotation features of proteins."

"Other researchers will get the comprehensive information about a particular protein at the Proteinpedia, so that it will save time by avoiding replication of experiments. More importantly, all the information and links to the information pertaining to each protein is available in one place," Raghothama Chaerkady, a member of the team that developed Proteinpedia, said.

Proteins are a key subject of medical research. Knowledge of protein functions "is vital for understanding the cellular mechanisms especially in diseased states including cancers," Pandesh said.

"As most of the biomarkers and/or drug targets are also proteins, this offers a great advantage and makes proteomics an indispensable method in the field of biomedical research."

The Proteinpedia will include detailed information on every human protein. It will include basic information on the amino acid sequence and chemistry of each molecule, as well as data on its interactions with other proteins as obtained through a wide range of experimental techniques.

By centralizing the breadth of information available on each protein, the Hopkins group and its collaborators, the Institute of Bioinformatics in Bangalore, India, hope to help translate basic discoveries into the clinic.

"Proteomics data is a great repository for bionformatics, genomics, vaccine development, antibody development and drug design. Very recently, proteomics applications have begun to include bedside diagnostic tests, such as multiple reaction monitoring of hundreds of biomarkers (markers of diseases)," Chaerkady said.

The need for central repositories for proteomics data emerged due to increasing amounts of data available to researchers. "Since mass spectrometry based proteomics has evolved recently, the Proteinpedia dream came true with this large chunk of experimental data for each human protein," Chaerkady said.

Pandey hopes the new database will help scientists cope with the recent explosion of proteomics data. "With the advancements in proteomics technologies, the amount of proteomics data being generated is enormous. Through a centralized repository like Human Proteinpedia, researchers across the globe can get access to both published and unpublished data."