static void gadPrint(struct section *section,
struct sqlConnection *conn, char *geneId)
/* Print out GAD section. */
{
int refPrinted = 0;
boolean showCompleteGadList;
char condStr[256];
char query[256];
struct sqlResult *sr;
char **row;
struct dyString *currentCgiUrl;
char *upperDisease;
char *url =
cloneString("http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=gene=");
char *itemName;
if (url != NULL && url[0] != 0)
{
safef(condStr, sizeof(condStr),
"k.kgId='%s' and k.geneSymbol = g.geneSymbol", geneId);
itemName = sqlGetField(database, "kgXref k, gadAll g", "k.geneSymbol", condStr);
showCompleteGadList = FALSE;
if (cgiOptionalString("showAllRef") != NULL)
{
if (sameWord(cgiOptionalString("showAllRef"), "Y") ||
sameWord(cgiOptionalString("showAllRef"), "y") )
{
showCompleteGadList = TRUE;
}
}
currentCgiUrl = cgiUrlString();
printf("<B>Genetic Association Database: ");
printf("<A HREF=\"%s'%s'\" target=_blank>", url, itemName);
printf("%s</B></A>\n", itemName);
printf("<BR><B>CDC HuGE Published Literature: ");
printf("<A HREF=\"%s%s%s\" target=_blank>",
"http://hugenavigator.net/HuGENavigator/searchSummary.do?firstQuery=",
itemName,
"&publitSearchType=now&whichContinue=firststart&check=n&dbType=publit&Mysubmit=go");
printf("%s</B></A>\n", itemName);
/* List diseases associated with the gene */
safef(query, sizeof(query),
"select distinct broadPhen from gadAll where geneSymbol='%s' and association = 'Y' order by broadPhen",
itemName);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
{
upperDisease = replaceChars(row[0], "'", "''");
touppers(upperDisease);
printf("<BR><B>Positive Disease Associations: </B>");
printf("<A HREF=\"%s%s%s%s%s\" target=_blank>",
"http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=upper(DISEASE)%20like%20'%25",
cgiEncode(upperDisease), "%25'%20AND%20upper(GENE)%20%20like%20'%25", itemName, "%25'");
printf("%s</B></A>\n", row[0]);
row = sqlNextRow(sr);
}
while (row != NULL)
{
upperDisease = replaceChars(row[0], "'", "''");
touppers(upperDisease);
printf(", <A HREF=\"%s%s%s%s%s\" target=_blank>",
"http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=upper(DISEASE)%20like%20'%25",
cgiEncode(upperDisease), "%25'%20AND%20upper(GENE)%20%20like%20'%25", itemName, "%25'");
printf("%s</B></A>\n", row[0]);
row = sqlNextRow(sr);
}
sqlFreeResult(&sr);
refPrinted = 0;
safef(query, sizeof(query),
"select broadPhen,reference,title,journal, pubMed, conclusion from gadAll where geneSymbol='%s' and association = 'Y' order by broadPhen",
itemName);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL) printf("<BR><B>Related Studies: </B><OL>");
while (row != NULL)
{
printf("<LI><B>%s </B>", row[0]);
printf("<br>%s, %s, %s.\n", row[1], row[2], row[3]);
if (!sameWord(row[4], ""))
{
printf(" [PubMed ");
printf("<A HREF=\"%s%s%s'\" target=_blank>",
"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=",
row[4],"&query_hl=1&itool=genome.ucsc.edu");
printf("%s</B></A>]\n", row[4]);
}
printf("<br><i>%s</i>\n", row[5]);
printf("</LI>\n");
refPrinted++;
if ((!showCompleteGadList) && (refPrinted >= 3)) break;
row = sqlNextRow(sr);
}
sqlFreeResult(&sr);
printf("</OL>");
if ((!showCompleteGadList) && (row != NULL))
{
printf("<B>   more ... </B>");
printf(
"<A HREF=\"%s?showAllRef=Y&%s#gad\">click here to view the complete list</A> ",
"hgGene", currentCgiUrl->string);
}
}
}
static void ctdPrint(struct section *section,
struct sqlConnection *conn, char *geneId)
/* Print out CTD section. */
{
char query[256];
struct sqlResult *sr;
char **row;
char *chemId, *chemName;
int chemCnt;
int first = 1;
boolean showCompleteCtdList;
struct dyString *currentCgiUrl;
showCompleteCtdList = FALSE;
if (cgiOptionalString("showAllCtdRef") != NULL)
{
if (sameWord(cgiOptionalString("showAllCtdRef"), "Y") ||
sameWord(cgiOptionalString("showAllCtdRef"), "y") )
{
showCompleteCtdList = TRUE;
}
cartRemove(cart, "showAllCtdRef");
}
currentCgiUrl = cgiUrlString();
/* List chemicals related to this gene */
if (isRgdGene(conn))
{
sqlSafef(query, sizeof(query),
"select ChemicalId, ChemicalName from rgdGene2Xref x, hgFixed.ctdSorted c where x.info=c.GeneSymbol and rgdGeneId='%s' and infoType='Name'",
geneId);
}
else
{
sqlSafef(query, sizeof(query),
"select ChemicalId, ChemicalName from kgXref x, hgFixed.ctdSorted c where x.geneSymbol=c.GeneSymbol and kgId='%s'",
geneId);
}
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
chemCnt = 0;
while (row != NULL)
{
chemId = cloneString(row[0]);
chemName = cloneString(row[1]);
if (first)
{
printf("<B>The following chemicals interact with this gene</B>\n");
printf("<UL>");
first = 0;
}
printf("<LI><A HREF=\"http://ctd.mdibl.org/detail.go?type=chem&acc=%s\" target=_blank>",
chemId);
printf("%s</A>\n", chemId);
printf("%s\n", chemName);
printf("</LI>");
chemCnt++;
row = sqlNextRow(sr);
/* Initially, just show no more than 10 items */
if ((!showCompleteCtdList) && (chemCnt >= 10) && (row != NULL))
{
chemCnt++;
break;
}
}
sqlFreeResult(&sr);
if (!first) printf("</UL>");
/* Offer user the option to see the complete list */
if ((!showCompleteCtdList) && chemCnt > 10)
{
printf("<B> more ... </B>");
printf("<A HREF=\"%s?showAllCtdRef=Y&%s#ctd\">click here to view the complete list</A> "
,"hgGene", currentCgiUrl->string);
}
return;
}