Diagnostic and Prognostic Biomarker Database

Accessory Database

Questions and Answers about biomarker database

1. You have listed more than 29,000 biomarkers in your database. We did not come across similar database with these many numbers of biomarkers. Does the database just contains random list of all biomarker names that are mentioned anywhere in patent publications?
   
   The biomarkers listed in our database are the only ones that were claimed as true biomarkers; hypothetical biomarkers are excluded. Another important consideration is the type of biomarkers listed in our database. For example, a protein with phosphorylated serine at position 236 will be a biomarker for a particular type of cancer. The same protein with tyrosine phosphorylation at a different position may be biomarker for similar or another type of cancer. The same protein with different phosphorylation states are listed as distinct biomarkers in our database. This is also true with gene mutations, methylation etc.



2. Why should I buy the subscription without knowing the quality or the content of this database?
   
   We have kept the Protein/peptide/antibody biomarkers for Breast cancer as open access (in each section the first disease category). Please access this open access data to evaluate the contents of our database.



3. Your database contains just a list of biomarkers with link to the citation, Uniprot database, GenBank and Google scholar search. Are you going to offer additional information or services?
   
   Yes, we will provide several new additions to our database in coming months. This includes a protein biomarker sequence database (for proteomics applications), protein-protein interaction information with regard to each biomarker, clinical validation of the biomarkers in our database, drug target information related to each biomarkers and an innovative interactive tool for integrative information on all the biomarkers listed in our database. Note: Depending upon the new additions, we may change our subscription charges.
   
   Note: Protein and gene biomarkers listed in our database are linked to Uniprot and GenBank database (generic search) respectively. For our database subscribers, we will extract Uniprot/Genbank accession numbers and sequences for up to 100 protein/gene biomarkers listed in our database at free of cost . In addition to this service, we also offer a free custom search to identify whether a protein or gene of your interest (not listed in our database) is reported as a biomarker in patent database or PubMed abstracts (limited to one protein or gene per customer). We will send you the custom search reports by e-mail as PDF files. Please contact us at contact@sciclips.com with names of protein/gene of your interest. The above-mentioned free services are available only to customers who have subscribed to our database and this offer is valid only through the subscription period. Disease specific custom biomarker search is not available through this free offer.



4. What is the clinical relevance of biomarkers listed in your database?
   
   More than 95% of the biomarkers listed in our databases are extracted from patent publications, mainly patent applications. We extract the data exactly as reported in each patent publication. We do data mining to confirm the protein/gene names and other details from protein/gene databases. Most of these data from patent publications are based on clinical data/samples (as evidenced from the claims), especially the drug efficacy and diseases predictive biomarkers. Interestingly, most of these patent publications are from pharmaceutical and biotech companies. We will not be able to confirm whether these biomarkers are validated or not. We will follow these biomarkers in clinical journals, if it is available. Some of the biomarkers extracted from PubMed articles can be considered as "potential biomarkers".



5. What is the importance or relevance of extracting biomarkers from patent publications?
   
   More than 80% of the information in patents and patent applications are not published in journals or elsewhere (a,b). Patent publications are neither cited nor utilized for knowledge gathering because the scientific information in patent applications is represented in complex legal language and need specialized skills to read and understand contents of patent publications. Most of the biomarkers in our database are extracted from patent applications (as oppose to patents issued/granted). The reason is all patent applications (or all the claims in a particular patent application) may not granted the patent. The rejected patent applications/claims will not appear in patent database (issued/granted). However, these patent applications may contain valuable scientific information that can be useful for biomarker research or applications.
   Citiations a. Bregonje, M. (2005) Patents: A unique source for scientific technical information in chemistry related industry? World Patent Information. 27: 09-315. b. WIPO/GRTKF/IC/6/INF/4: Patents as a source of technological information in technology transfer process (2004).


6. I heard that people just file patents with broader claims, which may not be scientifically true or experimentally confirmed. If this is true, how reliable are the biomarkers (from patent publications listed in your database?
   
   Though patents applications are not peer-reviewed, the claims should be scientifically true and should be repeatable by a person with scientific skills. Majority of the patent claims are supported by experimental validations. Hypothetical patent claims are exceptions. However, in this case a prophetic example or experimental conditions have been described in patent applications. If a patent is filed or granted with false claims, that patent can become invalid. Considering the huge cost associated with each patent filing and future commercial success, the question would be how many inventors or companies are willing to file patents with false claims?



7. Why should I subscribe to your database if it is freely available from patent documents?
   
   Of course, one can search patent publications and extract the information. However, extraction of data form patent publications is not easy as journal articles, as we mentioned earlier. Sciclips has been a pioneer in developing databases in the field of drug targets and combination therapy from patent publications. Please follow this link to see these open access databases. The biomarkers listed in our database are are extracted from patent publications and PubMed abstracts manually by our scientific team who are highly skilled scientists from diverse scientific background.



8. How often you will udpate your database?
   
   Our current schedule is to update the database once in a month depending on the number of biomarkers reported. The updates will be informed by e-mail to database subscribers.



9. Most of your database is open access and we have considered you as an "open access provider". Why did you start charging for accessing this database?
   
   It is true; our goal is to keep most of our databases open access. At the same time we need to cover the cost associated with data collection and web site maintenance. Extraction of data, especially biomarkers, from patent publications took enormous amount of our time. We need to read and analyze thousands of patent publications for creating this database. It can take 1-2 hours to extract data from a single patent publication. The fee we are currently charging is only a fraction of our actual cost and the fees charged by other commercially available database or by a customs service provider. We kept the fee low so that it is affordable by the scientific community.

Custom service