navigating the patent maze

Free resources for searching nucleotide and amino acid sequences in patent documents are scarce. Two resources are PatentLens and Patome@Korea. PatentLens will be reviewed in a separate posting.

Patome@Korea is newly launched. The database contains biological sequences obtained from Korean Patent Intellectual Property Office (KIPO) and from KRIBB (Korea Research Institute of Bioscience & Biotechnology), a research institute and Center of Excellence for national biotechnology R&D. Data

The main search page allows queries for patent or publication no., keywords in title, and accession numbers. Results are presented as a list of patent documents that contain the sequence data. A second type of search if for patent information related to genes. A gene-related query, such as gene ID, gene name or RefSeq number will display sequence data associated with the query terms.

BLAST searches can be performed as well. Two different entry pages separate programs for searching protein and nucleotide data. In addition to searching the entire data set, data from Korean patents and applications can be specifically searched.

The site and information about the data isn’t terribly easy to navigate, so it might take some time browsing around to find what you want.

*see also: Lee et al., “Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications.” Nucleic Acids Res 35:D47-D50, 2007. (link)

IP Australia is undertaking to provide a patent data search facility that will eventually provide online access to all Australia patent data. (announcement)  Anyone who has tried to obtain Australian patents or search for patents becomes stone-walled by the paucity of data available.  Unfortunately, IP Australia has maintained patent data in a variety of systems and formats, including on microfiche for patent documents pre-1998.  The diagram illustrates the various systems.  View diagram

Looking forward in 2007, IP Australia plans to

• provide access to bulk patent bibliographic and status data with weekly updates;
• scan patent specification for ultimate production of searchable documents;
• set up a single access point for searching patent bibliographic and status data (currently access occurs through a web-based site for some data and a mainframe connection for other data).

Steve Nipper’s blog keeps a very up-to-date list of sites that allow downloads of patent documents in PDF or TIFF format.  I have put a permanent link to it in the sidebar "Patent data on-line". 

There is another place to go if you want PDFs of patents without paying.

• Download US, EP, PCT, Canadian, DE, UK and FR patents in PDF format at Intelprop.  The main functionality lies in its ability to download from a highlighted portion of text in a browser (IE, Opera and Firefox instructions are available.)

A reader of this site has alerted me to his website www.asitri.com where you can get text or PDFs of U.S. patent publications. When a patent number is typed into the search box, the abstract of the document is returned along with all the U.S. patent documents that are referenced on the front page. Links are provided to the text at the U.S. PTO site, PDFs of the document, as well as other U.S. patents that have referenced the one of interest.

The advantages of this site are the PDF documents, it is no charge, and ready linkage to other U.S. patents that are referenced by and reference to the one of interest.

What is lacking on this site is the ability to obtain U.S. patent applications that are published. My own very small whinge is that (like many other sites) asitri does not work properly in Firefox 1.0, which is my preferred web browser these days.

NOTE: to use this site, you first need to know the patent number of the document you want.

From the Economic Research Service arm of the USDA (U.S. Department of Agriculture):

The Economic Research Service has a newly available online-searchable database on agricultural biotechnology patents. The database is freely available for use by all. This database identifies and describes U.S. utility patents on inventions in biotechnology and other biological processes*with issue dates between 1976 and 2000*that are used in food and agriculture. The database also provides information about the ownership of these patents, whether patents are held in the public or private sector, and changes in patent ownership due to firm mergers, acquisitions, and spinoffs. The database can be accessed at www.ers.usda.gov/data/AgBiotechIP. The attached PDF file provides a brief summary of information contained in the data.

Unfortunately, one of my favorite sites (www.pat2pdf.com) has gone to a pay site. There are only two sites right now that I know of where U.S. patents can be downloaded as PDF files (without having to download a single page at a time). They are:

- www.pat2pdf.org (not related to the other pat2pdf site but based on the same scripts)
- Patent Fetcher.

A nice grid of many of the sites that have patent searching capabilities, some of which are free to use and others of which are pay sites, can be found here.