- Why did you decide to develop yet another database instead of integrating other existing databases?
We believe that biological databases are still in their early stages and no protein database can be considered as an established standard. We feel that a variety of databases trying to solve problems in diverse ways provide the biologists the possibility of choosing their favorite. Our approach is radically different from existing databases and we want to offer biologists the possibility of choosing instead of imposing one database by default. Besides, most of the databases are automated and ours is manually curated to avoid errors. We are also trying to provide information that few other databases provide.
- Is the Human Protein Reference Database interoperable?
Yes, all the information contained in this database will be available for downloading as XML and FLAT files. The schema is very simple,making it possible for anyone to manipulate the data.
- Is the information contained in this database available for free? Can I download all the information in HPRD?
Everything in HPRD is free as long as it is not used for commercial purposes. Commercial entitites will have to pay a fee under a licensing arrangement which will be used to make this database even better. Commercial users should send an e-mail for details. This model of HPRD is similar to the SWISS-PROT licensing arrangement.
- What is the background of the scientists involved in establishing HPRD?
HPRD has been established by a team of biologists, bioinformaticists and software engineers led by Dr. Akhilesh Pandey at Johns Hopkins University.
- Do you intend to commercialize the database?
We do not have any intentions to profit from HPRD. Our goal is to promote science by creating the infrastructure of HPRD. We hope to keep it updated with the assistance of the entire biomedical community. Any licensing fee, if generated, will be used to annotate HPRD better and to add more entries and features.
- Is HPRD a Gene Ontology (GO) compliant database ?
Our ontology is fully GO compliant.
- Are you using any literature mining algorithm?
We are not using any literature mining program. Our trained biologists read and interpret each and every paper related to the molecule of interest.
- Why did you decide against automation?
We simply realized that our method of manual extraction is far more efficient and accurate than any literature mining algorithm.
- Doesn't your manual curation create and propagate more errors in databases?
We have taken into account the most reliable sources of protein data and then curated them manually. The information provided by these sources is considered including the information available from the literature and then the biologists make the final decision as to how it should be reported. In this sense, we are trying to eliminate a majority of the errors that creep into databases because of automation. However, no database could possibly be completely error-free. We have made it easy for you to submit comments and would like to hear from you. If you would like to review a molecule or even an entire protein family, we will be happy to credit you as a 'Reviewer' for that molecule.
