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1 {\rtf1\ansi\ansicpg1252\cocoartf1344\cocoasubrtf720
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2 {\fonttbl\f0\fnil\fcharset0 Monaco;}
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3 {\colortbl;\red255\green255\blue255;\red255\green0\blue0;\red85\green127\blue95;\red0\green0\blue192;
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4 \red127\green0\blue85;}
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5 \margl1440\margr1440\vieww21520\viewh8280\viewkind0
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6 \deftab720
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7 \pard\pardeftab720
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8
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9 \f0\fs22 \cf2 <?php\cf0 \
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10 \pard\pardeftab720
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11 \cf3 //$client = new SoapClient("http://biodbnet.abcc.ncifcrf.gov/webServices/bioDBnet.wsdl");\cf0 \
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12 \cf3 /*\cf0 \
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13 \cf3 $input = 'Ensembl Gene ID';\cf0 \
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14 \cf3 $inputValues = 'ENSG00000121410, ENSG00000171428';\cf0 \
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15 \cf3 $outputs = 'Gene Symbol, Ensembl Protein ID';\cf0 \
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16 \cf3 $taxonId = '9606';\cf0 \
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17 \cf3 $methods = array(\cf0 \
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18 \cf3 'getInputs',\cf0 \
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19 \cf3 'getOutputsForInput',XML: http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getoutputsforinput&input=genesymbol\cf0 \
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20 \cf3 'getDirectOutputsForInput',http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getdirectoutputsforinput&input=genesymbol&directOutput=1\cf0 \
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21 \cf3 'getPathways', http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getpathways&pathways=ncipid,kegg&taxonId=9606\cf0 \
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22 \cf3 'db2db',http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=db2db&input=geneid&inputValues=1,3&outputs=genesymbol,affyid&taxonId=9606&format=row\cf0 \
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23 \cf3 'dbReport',http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbreport&input=geneid&inputValues=1,3&taxonId=9606&format=row\cf0 \
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24 \cf3 'dbWalk',http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbwalk&inputValues=A1BG,MYC&dbPath=genesymbol-%3Egeneid-%3Eaffyid&taxonId=9606&format=row\cf0 \
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25 \cf3 'dbFind',http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbfind&inputValues=A1BG,MYC,1,3&output=geneid&taxonId=9606&format=row\cf0 \
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26 \cf3 'dbOrtho',http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbortho&input=geneid&inputValues=1,3&inputTaxon=9606&outputTaxon=10090&output=genesymbol&format=row\cf0 \
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27 \cf3 'dbAnnot'http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbannot&inputValues=1,MYC,MTOR_HUMAN&taxonId=9606&annotations=Genes,Pathways&format=row\cf0 \
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28 \cf3 )\cf0 \
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29 \cf3 */\cf0 \
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30 \
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31 $taxonId = \cf4 ""\cf0 ;\
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32 \
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33 \
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34 \cf3 //format='row' input='ensemblgeneid' inputValues='ENSG00000121410' outputs='genesymbol' taxonId='9606'\cf0 \
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35 \cf3 //&format=row&input=genesymbol&inputValues=MYC,MTOR&outputs=geneid,affyid&taxonId=9606";\cf0 \
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36 \cf3 //$biodbnetRestApiCall = "http://biodbnet.abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=getinputs";\cf0 \
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37 \
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38 \
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39 \cf3 //print_r($argv);\cf0 \
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40 \
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41 $biodbnetRestApiCall = \cf4 ''\cf0 ;\
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42 \pard\pardeftab720
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43 \cf5 foreach \cf0 ($argv \cf5 as \cf0 $val)\
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44 \{\
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45 $arr = preg_split(\cf4 "/=/"\cf0 , $val);\
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46 \cf5 if \cf0 (strcmp(\cf4 'input'\cf0 , $arr[0]) == 0)\
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47 \{\
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48 $input = $arr[1];\
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49 $biodbnetRestApiCall = $biodbnetRestApiCall . \cf4 "&input=" \cf0 . $input;\
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50 \}\
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51 \cf5 else if \cf0 (strcmp(\cf4 'taxonId'\cf0 , $arr[0]) == 0)\
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52 \{\
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53 $taxonId = $arr[1];\
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54 $biodbnetRestApiCall = $biodbnetRestApiCall . \cf4 "&taxonId=" \cf0 . $taxonId;\
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55 \}\
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56 \cf5 else if \cf0 (strcmp(\cf4 'inputValues'\cf0 , $arr[0]) == 0)\
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57 \{\
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58 $inputValues = $arr[1];\
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59 $biodbnetRestApiCall = $biodbnetRestApiCall . \cf4 "&inputValues=" \cf0 . $inputValues;\
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60 \}\
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61 \cf5 else if \cf0 (strcmp(\cf4 'outputs'\cf0 , $arr[0]) == 0)\
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62 \{\
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63 $outputs = $arr[1];\
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64 $biodbnetRestApiCall = $biodbnetRestApiCall . \cf4 "&outputs=" \cf0 . $outputs;\
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65 \}\
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66 \cf5 else if \cf0 (strcmp(\cf4 'fileType'\cf0 , $arr[0]) == 0)\
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67 \{\
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68 $fileType = strtolower($arr[1]);\
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69 \cf5 if \cf0 ($fileType == \cf4 'xml'\cf0 )\{\
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70 $biodbnetRestApiCallCore = \cf4 "http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.xml?method=db2db"\cf0 ;\
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71 \}\
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72 \cf5 else\cf0 \{\
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73 $biodbnetRestApiCallCore = \cf4 "http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db"\cf0 ;\
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74 \}\
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75 \cf5 if \cf0 ($fileType == \cf4 'table'\cf0 )\{\
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76 $biodbnetRestApiCall = $biodbnetRestApiCall . \cf4 "&format=row"\cf0 ;\
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77 \}\
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78 \}\
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79 \}\
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80 $restApiCall = $biodbnetRestApiCallCore . $biodbnetRestApiCall;\
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81 $response = file_get_contents($restApiCall);\
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82 \cf5 if \cf0 ($fileType == \cf4 'xml' \cf0 || $fileType == \cf4 'json'\cf0 )\{\
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83 print_r($response);\
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84 \}\cf5 elseif \cf0 ($fileType == \cf4 'table'\cf0 )\{\
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85 \
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86 $formattedResponse = json_decode($response, \cf5 true\cf0 );\
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87 \cf3 //print_r($formattedResponse);\cf0 \
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88 \
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89 \cf5 echo \cf4 "<html>\\n"\cf0 ;\
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90 \cf5 echo \cf4 "<br/><br/><b>bioDBnet: db2db results</b><br/>"\cf0 ;\
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91 \cf5 echo \cf4 "<table border=1>\\n"\cf0 ;\
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92 $colNames = array_keys($formattedResponse[0]);\
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93 \cf5 echo \cf4 "<tr>"\cf0 ;\
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94 \cf5 foreach \cf0 ($colNames \cf5 as \cf0 $col)\
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95 \{\
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96 \cf5 if \cf0 ($col == \cf4 'InputValue'\cf0 )\
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97 $col = $input;\
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98 \cf5 echo \cf4 "<th>\cf0 $col\cf4 </th>"\cf0 ;\
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99 \}\
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100 \cf5 echo \cf4 "</tr>\\n"\cf0 ;\
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101 \cf5 foreach \cf0 ($formattedResponse \cf5 as \cf0 $row)\
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102 \{\
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103 \cf5 echo \cf4 "<tr>"\cf0 ;\
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104 \cf5 foreach \cf0 ($row \cf5 as \cf0 $key => $col)\
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105 \{\
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106 \cf5 echo \cf4 "<td>\cf0 $col\cf4 </td>"\cf0 ;\
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107 \}\
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108 \cf5 echo \cf4 "</tr>\\n"\cf0 ;\
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109 \}\
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110 \
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111 \cf5 echo \cf4 "</table>\\n"\cf0 ;\
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112 \cf5 echo \cf4 "</html>\\n"\cf0 ;\
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113 \}\
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114 \
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115 \
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116 \pard\pardeftab720
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117 \cf2 ?>} |
