Hi Chuck, Here is some additional information about the location of the source code you need:
Our main search code is in src/hg/lib/hgFind.c -- the code is not easy to just jump into, but a good start is to look at this call stack: hgFindUsingSpec -> searchSpecial -> findKnownGeneFullText findKnownGeneFullText calls trix*() functions that are defined in src/inc/trix.h and src/lib/trix.c, and those read the /gbdb/$db/knownGene.ix and .ixx files. Those files are generated by the ixIxx program (src/index/ixIxx/ixIxx.c). I hope this information is helpful. Katrina Learned UCSC Genome Bioinformatics Group Katrina Learned wrote, On 01/07/11 14:12: > Hi Chuck, > > One of our developers provided this information: > > We don't search with SQL statements. Our only interaction with SQL is > which column to search. Our search mechansim is constructed in C code in > the browser library code. > > Please don't hesitate to contact the mail list again if you have any > further questions. > > Katrina Learned > UCSC Genome Bioinformatics Group > > Borromeo, Charles wrote, On 01/07/11 05:55: > >> Hi Mary, >> Thanks for the information. Restricting the search definitely makes >> sense. Is it possible for someone to direct me to the source code >> containing the SQL statements that search the database for a search term >> like 'hedgehog', 'cleft', etc? >> Thanks, >> Chuck >> >> From: Mary Goldman <[email protected]<mailto:[email protected]>> >> Date: Thu, 6 Jan 2011 18:01:43 -0500 >> To: Charles Borromeo <[email protected]<mailto:[email protected]>> >> Cc: "[email protected]<mailto:[email protected]>" >> <[email protected]<mailto:[email protected]>> >> Subject: Re: [Genome] CGI Search >> >> >> Hi Chuck, >> >> While you can eliminate the "clade", "org", "hgt.suggest" and "pix" parts of >> the URL, you will always need to specify the "db" since our CGIs require >> this term to know which database to search. Otherwise, our CGIs would need >> to search almost 100 databases and countless tracks for a particular search >> term, which would take a very long time. >> >> I hope this information is helpful. Please feel free to contact the mail >> list again if you require further assistance. >> >> Best, >> Mary >> ------------------ >> Mary Goldman >> UCSC Bioinformatics Group >> >> On 1/6/11 1:50 PM, Borromeo, Charles wrote: >> >> Hello, >> We are attempting to augment our search tool within our website to map to >> concepts found within our mirror of the Genome Browser. The search tool >> will allow our users to execute queries containing gene names (IRF6) or >> concepts (cleft palate). The following cgi URL allows me to execute this >> query against the browser: >> >> http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=Human&db=hg19&position=cleft&hgt.suggest=&pix=800&Submit=submit >> >> Where the search term in this case is 'cleft'. I noticed that I needed to >> specify the organism and assembly as part of the cgi parameters. Is there >> some way to leave these blank? In most cases our users will be looking for >> human data, in other cases they may be starting with mouse, zebrafish, etc. >> >> Thanks, >> Chuck Borromeo >> _______________________________________________ >> Genome maillist - >> [email protected]<mailto:[email protected]>https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
