Awk.Info

"Cause a little auk awk
goes a long way."

About awk.info
 »  table of contents
 »  featured topics
 »  page tags


About Awk
 »  advocacy
 »  learning
 »  history
 »  Wikipedia entry
 »  mascot
Implementations
 »  Awk (rarely used)
 »  Nawk (the-one-true, old)
 »  Gawk (widely used)
 »  Mawk
 »  Xgawk (gawk + xml + ...)
 »  Spawk (SQL + awk)
 »  Jawk (Awk in Java JVM)
 »  QTawk (extensions to gawk)
 »  Runawk (a runtime tool)
 »  platform support
Coding
 »  one-liners
 »  ten-liners
 »  tips
 »  the Awk 100
Community
 »  read our blog
 »  read/write the awk wiki
 »  discussion news group

Libraries
 »  Gawk
 »  Xgawk
 »  the Lawker library
Online doc
 »  reference card
 »  cheat sheet
 »  manual pages
 »  FAQ

Reading
 »  articles
 »  books:

WHAT'S NEW?

Mar 01: Michael Sanders demos an X-windows GUI for AWK.

Mar 01: Awk100#24: A. Lahm and E. de Rinaldis' patent search, in AWK

Feb 28: Tim Menzies asks this community to write an AWK cookbook.

Feb 28: Arnold Robbins announces a new debugger for GAWK.

Feb 28: Awk100#23: Premysl Janouch offers a IRC bot, In AWK

Feb 28: Updated: the AWK FAQ

Feb 28: Tim Menzies offers a tiny content management system, in Awk.

Jan 31: Comment system added to awk.info. For example, see discussion bottom of ?keys2awk

Jan 31: Martin Cohen shows that Gawk can handle massively long strings (300 million characters).

Jan 31: The AWK FAQ is being updated. For comments/ corrections/ extensions, please mail tim@menzies.us

Jan 31: Martin Cohen finds Awk on the Android platform.

Jan 31: Aleksey Cheusov released a new version of runawk.

Jan 31: Hirofumi Saito contributes a candidate Awk mascot.

Jan 31: Michael Sanders shows how to quickly build an AWK GUI for windows.

Jan 31: Hyung-Hwan Chung offers QSE, an embeddable Awk Interpreter.

[More ...]

Bookmark and Share

categories: Awk100,Feb,2010,ALahm

PatentMatrix: survey gene/protien patents

(From Source Code Biol Med. 2007 Sep 6;2:4. by A. Lahm, E. de Rinaldis)

BACKGROUND: The number of patents associated with genes and proteins and the amount of information contained in each patent often present a real obstacle to the rapid evaluation of the novelty of findings associated to genes from an intellectual property (IP) perspective. This assessment, normally carried out by expert patent professionals, can therefore become cumbersome and time consuming. Here we present PatentMatrix, a novel software tool for the automated analysis of patent sequence text entries.

METHODS AND RESULTS: PatentMatrix is written in the Awk language and requires installation of the Derwent GENESEQtrade mark patent sequence database under the sequence retrieval system SRS.The software works by taking as input two files: i) a list of genes or proteins with the associated GENESEQtrade mark patent sequence accession numbers ii) a list of keywords describing the research context of interest (e.g. 'lung', 'cancer', 'therapeutics', 'diagnostics'). The GENESEQtrade mark database is interrogated through the SRS system and each patent entry of interest is screened for the occurrence of user-defined keywords. Moreover, the software extracts the basic information useful for a preliminary assessment of the IP coverage of each patent from the GENESEQtrade mark database. As output, two tab-delimited files are generated which provide the user with a detailed and an aggregated view of the results.An example is given where the IP position of five genes is evaluated in the context of 'development of antibodies for cancer treatment'.

CONCLUSION: PatentMatrix allows a rapid survey of patents associated with genes or proteins in a particular area of interest as defined by keywords. It can be efficiently used to evaluate the IP-related novelty of scientific findings and to rank genes or proteins according to their IP position.

blog comments powered by Disqus