htmlLinker.h File Reference

Go to the source code of this file.

Functions

char * htmlLinker_generateLinkToAmiGO (char *goId)

Generates a link to AmiGO.

char * htmlLinker_generateLinkToEntrezGene (char *term)

Generates a link to EntrezGene.

char * htmlLinker_generateLinkToFlyBaseGeneDescriptionPage (char *flyBaseId)

Generates a link to FlyBase gene description page.

char * htmlLinker_generateLinkToGeneDescriptionPageAtUCSC (char *database, char *geneName, char *chromosome, int start, int end)

Generates a link to KnownGene description page.

char * htmlLinker_generateLinkToGenomeBrowserAtUCSC (char *database, char *clade, char *organism, char *chromosome, int start, int end)

Generates a link to the UCSC genome browser.

char * htmlLinker_generateLinkToHumanPseudogenePageAtYale (char *pseudogeneId)

Generates a link to the Yale human pseudogene site.

char * htmlLinker_generateLinkToInterPro (char *interProId)

Generates a link to InterPro.

char * htmlLinker_generateLinkToMouseGeneDescriptionPage (char *mgiId)

Generates a link to Mouse Genome Informatics (MGI) gene description page.

char * htmlLinker_generateLinkToPfam (char *pfamId)

Generates a link to Pfam.

char * htmlLinker_generateLinkToPubmed (char *pmid)

Generates a link to PubMed.

char * htmlLinker_generateLinkToRatGeneDescriptionPage (char *rgdId)

Generates a link to Rat Genome Database (RGD) gene description page.

char * htmlLinker_generateLinkToTrackElementDescriptionPageAtUCSC (char *database, char *trackName, char *elementName, char *chromosome, int start, int end)

Generates a link to the UCSC track element description page.

char * htmlLinker_generateLinkToUniProt (char *uniProtId)

Generates a link to Uniprot.

char * htmlLinker_generateLinkToWormBaseGeneDescriptionPage (char *wormBaseGeneId)

Generates a link to WormBase gene description page.

char * htmlLinker_generateLinkToYeastGeneDescriptionPage (char *sgdId)

Generates a link to Saccharomyces Genome Database (SGD) gene description page.

Detailed Description

Author:: Lukas Habegger (lukas.habegger@yale.edu)

Definition in file htmlLinker.h.

Function Documentation

char* htmlLinker_generateLinkToAmiGO ( char * goId )

Generates a link to AmiGO.

Example: http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0051240

Definition at line 261 of file htmlLinker.c.

char* htmlLinker_generateLinkToEntrezGene ( char * term )

Generates a link to EntrezGene.

Example: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=NP_001069323 or http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=1812

Definition at line 216 of file htmlLinker.c.

char* htmlLinker_generateLinkToFlyBaseGeneDescriptionPage ( char * flyBaseId )

Generates a link to FlyBase gene description page.

Example: http://flybase.bio.indiana.edu/reports/FBgn0033837.html

Definition at line 86 of file htmlLinker.c.

char* htmlLinker_generateLinkToGeneDescriptionPageAtUCSC	(	char *	database,
		char *	geneName,
		char *	chromosome,
		int	start,
		int	end
	)

Generates a link to KnownGene description page.

Example: http://genome.ucsc.edu/cgi-bin/hgGene?db=rn4&hgg_gene=NM_012824&hgg_chrom=chr1&hgg_start=78996678&hgg_end=78999875

Definition at line 20 of file htmlLinker.c.

char* htmlLinker_generateLinkToGenomeBrowserAtUCSC	(	char *	database,
		char *	clade,
		char *	organism,
		char *	chromosome,
		int	start,
		int	end
	)

Generates a link to the UCSC genome browser.

Example: http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&clade=vertebrate&org=Mouse&position=chr12:10000-20000

Definition at line 54 of file htmlLinker.c.

char* htmlLinker_generateLinkToHumanPseudogenePageAtYale ( char * pseudogeneId )

Generates a link to the Yale human pseudogene site.

Example: http://tables.pseudogene.org/human/200550

Definition at line 71 of file htmlLinker.c.

char* htmlLinker_generateLinkToInterPro ( char * interProId )

Generates a link to InterPro.

Example: http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR001922

Definition at line 200 of file htmlLinker.c.

char* htmlLinker_generateLinkToMouseGeneDescriptionPage ( char * mgiId )

Generates a link to Mouse Genome Informatics (MGI) gene description page.

Example: http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:1351646

Note:: Instructions for linking to MGI can be found at http://www.informatics.jax.org/mgihome/other/link_instructions.shtml

Definition at line 137 of file htmlLinker.c.

char* htmlLinker_generateLinkToPfam ( char * pfamId )

Generates a link to Pfam.

Example: http://pfam.sanger.ac.uk/family?acc=PF09582

Definition at line 185 of file htmlLinker.c.

char* htmlLinker_generateLinkToPubmed ( char * pmid )

Generates a link to PubMed.

Example: http://www.ncbi.nlm.nih.gov/pubmed/18276894

Definition at line 231 of file htmlLinker.c.

char* htmlLinker_generateLinkToRatGeneDescriptionPage ( char * rgdId )

Generates a link to Rat Genome Database (RGD) gene description page.

Example: http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=727972

Note:: The rgdId must be numeric.

Definition at line 153 of file htmlLinker.c.

char* htmlLinker_generateLinkToTrackElementDescriptionPageAtUCSC	(	char *	database,
		char *	trackName,
		char *	elementName,
		char *	chromosome,
		int	start,
		int	end
	)

Generates a link to the UCSC track element description page.

Example: http://genome.ucsc.edu/cgi-bin/hgc?db=hg18&g=intronEst&i=BI755927&c=chrX&l=149673899&r=152783129

Definition at line 37 of file htmlLinker.c.

char* htmlLinker_generateLinkToUniProt ( char * uniProtId )

Generates a link to Uniprot.

Example: http://www.pir.uniprot.org/cgi-bin/upEntry?id=Q91V24 or http://www.pir.uniprot.org/cgi-bin/upEntry?id=ADA1A_BOVIN

Definition at line 119 of file htmlLinker.c.

char* htmlLinker_generateLinkToWormBaseGeneDescriptionPage ( char * wormBaseGeneId )

Generates a link to WormBase gene description page.

Both the WormBase gene ID or the gene symbol can be used. Example: http://www.wormbase.org/db/gene/gene?name=WBGene00002239 or http://www.wormbase.org/db/gene/gene?name=ksr-1

Definition at line 103 of file htmlLinker.c.

char* htmlLinker_generateLinkToYeastGeneDescriptionPage ( char * sgdId )

Generates a link to Saccharomyces Genome Database (SGD) gene description page.

Both the SGD gene ID or the gene symbol can be used. Example: http://db.yeastgenome.org/cgi-bin/locus.pl?locus=AAC3 or http://db.yeastgenome.org/cgi-bin/locus.pl?locus=S000000289

Definition at line 170 of file htmlLinker.c.


Functions
char *	htmlLinker_generateLinkToAmiGO (char *goId)
	Generates a link to AmiGO.
char *	htmlLinker_generateLinkToEntrezGene (char *term)
	Generates a link to EntrezGene.
char *	htmlLinker_generateLinkToFlyBaseGeneDescriptionPage (char *flyBaseId)
	Generates a link to FlyBase gene description page.
char *	htmlLinker_generateLinkToGeneDescriptionPageAtUCSC (char database, char geneName, char *chromosome, int start, int end)
	Generates a link to KnownGene description page.
char *	htmlLinker_generateLinkToGenomeBrowserAtUCSC (char database, char clade, char organism, char chromosome, int start, int end)
	Generates a link to the UCSC genome browser.
char *	htmlLinker_generateLinkToHumanPseudogenePageAtYale (char *pseudogeneId)
	Generates a link to the Yale human pseudogene site.
char *	htmlLinker_generateLinkToInterPro (char *interProId)
	Generates a link to InterPro.
char *	htmlLinker_generateLinkToMouseGeneDescriptionPage (char *mgiId)
	Generates a link to Mouse Genome Informatics (MGI) gene description page.
char *	htmlLinker_generateLinkToPfam (char *pfamId)
	Generates a link to Pfam.
char *	htmlLinker_generateLinkToPubmed (char *pmid)
	Generates a link to PubMed.
char *	htmlLinker_generateLinkToRatGeneDescriptionPage (char *rgdId)
	Generates a link to Rat Genome Database (RGD) gene description page.
char *	htmlLinker_generateLinkToTrackElementDescriptionPageAtUCSC (char database, char trackName, char elementName, char chromosome, int start, int end)
	Generates a link to the UCSC track element description page.
char *	htmlLinker_generateLinkToUniProt (char *uniProtId)
	Generates a link to Uniprot.
char *	htmlLinker_generateLinkToWormBaseGeneDescriptionPage (char *wormBaseGeneId)
	Generates a link to WormBase gene description page.
char *	htmlLinker_generateLinkToYeastGeneDescriptionPage (char *sgdId)
	Generates a link to Saccharomyces Genome Database (SGD) gene description page.