Gene Information Search Tool

Richard Finney · 02-26-2013, 10:17 AM

This is a little tool I made and use frequently :

Trawler : https://cgwb.nci.nih.gov/cgi-bin/trawler

It is primarily for looking around for any information about a gene when Entrez RIFs and google aren't enough. Often there's extra information available through the various publisher's websites and via other search sites.

It was inspired by the old "Bioinformatics Harvester" from Heidelburg(?) which was quite cool before many sites put javascript breakout code in the HTML to prevent frames.

The solution is just call the websites in separate tabs, all from one place without having to type in a bunch of stuff to get at various resources.

I'd appreciate any comments. Any missing resources? Any usability issues?

GenoMax · 02-26-2013, 11:06 AM

That is neat.

Additional candidates? GeneCards (http://genecards.org/), Human Protein reference database (http://www.hprd.org/) or Mouse protein reference database(http://www.mprd.in/)

Richard Finney · 02-26-2013, 11:34 AM

I"ll take at look at them. "Gene Cards" 'most always shows up at top of Google/Yandex/DuckDuck so it's always easily gettable. iHOP is great, you just have to click on the "!" Information icon on top right. I haven't figured out how to point straight to the real iHOP page that you want.

If someone wanted to port this or customize it to their needs, I imagine it would be easy to make it a fully javascript driven engine that would require no client/host back and forth to get going.

The journal publishers probably prohibit google bot and other robots from looking too deep; but they do provide their own search pages. This just cuts out all the work of checking them all.

ArXiv is there but more bio type folks need to pre-publish there so that it will return results more often.

gene_x · 02-26-2013, 02:06 PM

Neat tool +1 !

Richard Finney · 02-27-2013, 05:58 AM

Note that TRAWLER takes parameters , for example : https://cgwb.nci.nih.gov/cgi-bin/trawler?q=DLX2 where DLX2 is the gene (or term) to search.

You can create links in a (EXCEL) spreadsheet by putting something like this in a cell :

=HYPERLINK("https://cgwb.nci.nih.gov/cgi-bin/trawler?q="&A1,"Trawl "&A1)

where the search term (i.e. the gene to get more infomation about) is in cell A1.

This makes it easy to review what's known about your gene list.

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02-26-2013, 10:17 AM	#1
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	Gene Information Search Tool This is a little tool I made and use frequently : Trawler : https://cgwb.nci.nih.gov/cgi-bin/trawler It is primarily for looking around for any information about a gene when Entrez RIFs and google aren't enough. Often there's extra information available through the various publisher's websites and via other search sites. It was inspired by the old "Bioinformatics Harvester" from Heidelburg(?) which was quite cool before many sites put javascript breakout code in the HTML to prevent frames. The solution is just call the websites in separate tabs, all from one place without having to type in a bunch of stuff to get at various resources. I'd appreciate any comments. Any missing resources? Any usability issues?

02-26-2013, 11:34 AM	#3
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	I"ll take at look at them. "Gene Cards" 'most always shows up at top of Google/Yandex/DuckDuck so it's always easily gettable. iHOP is great, you just have to click on the "!" Information icon on top right. I haven't figured out how to point straight to the real iHOP page that you want. If someone wanted to port this or customize it to their needs, I imagine it would be easy to make it a fully javascript driven engine that would require no client/host back and forth to get going. The journal publishers probably prohibit google bot and other robots from looking too deep; but they do provide their own search pages. This just cuts out all the work of checking them all. ArXiv is there but more bio type folks need to pre-publish there so that it will return results more often. Last edited by Richard Finney; 02-26-2013 at 11:52 AM.

02-27-2013, 05:58 AM	#5
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	Note that TRAWLER takes parameters , for example : https://cgwb.nci.nih.gov/cgi-bin/trawler?q=DLX2 where DLX2 is the gene (or term) to search. You can create links in a (EXCEL) spreadsheet by putting something like this in a cell : =HYPERLINK("https://cgwb.nci.nih.gov/cgi-bin/trawler?q="&A1,"Trawl "&A1) where the search term (i.e. the gene to get more infomation about) is in cell A1. This makes it easy to review what's known about your gene list. Last edited by Richard Finney; 02-27-2013 at 06:21 AM.

02-26-2013, 11:06 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	That is neat. Additional candidates? GeneCards (http://genecards.org/), Human Protein reference database (http://www.hprd.org/) or Mouse protein reference database(http://www.mprd.in/)

02-26-2013, 02:06 PM	#4
gene_x Senior Member Location: MO Join Date: May 2010 Posts: 108	Neat tool +1 !