Skip to content

Commit d34050b

Browse files
micheldumontiermicheldumontier
committed
initial import
1 parent 1fd302d commit d34050b

File tree

1 file changed

+232
-0
lines changed

1 file changed

+232
-0
lines changed

‎miriam/miriam.php‎

Lines changed: 232 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,232 @@
1+
<?php
2+
/**
3+
Copyright (C) 2012 Michel Dumontier
4+
5+
Permission is hereby granted, free of charge, to any person obtaining a copy of
6+
this software and associated documentation files (the "Software"), to deal in
7+
the Software without restriction, including without limitation the rights to
8+
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
9+
of the Software, and to permit persons to whom the Software is furnished to do
10+
so, subject to the following conditions:
11+
12+
The above copyright notice and this permission notice shall be included in all
13+
copies or substantial portions of the Software.
14+
15+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16+
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18+
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19+
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20+
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21+
SOFTWARE.
22+
*/
23+
24+
require_once(__DIR__.'/../../php-lib/bio2rdfapi.php');
25+
require_once(__DIR__.'/../../php-lib/xmlapi.php');
26+
27+
/**
28+
* MIRIAM DB RDFizer
29+
* @version 1.0
30+
* @author Michel Dumontier
31+
* @description http://www.ebi.ac.uk/miriam/
32+
*/
33+
class MIRIAMParser extends Bio2RDFizer
34+
{
35+
private $version = null;
36+
37+
function __construct($argv) {
38+
parent::__construct($argv,"miriam");
39+
parent::addParameter('files',true,'all','all','files to process');
40+
parent::addParameter('download_url',false,null,'http://www.ebi.ac.uk/miriam/main/export/xml/');
41+
parent::addParameter('overwrite',false,'true|false','false','overwrite existing files with download option');
42+
parent::initialize();
43+
}
44+
45+
function Run()
46+
{
47+
echo "processing miriam database";
48+
49+
// directory shortcuts
50+
$ldir = $this->getParameterValue('indir');
51+
$odir = $this->getParameterValue('outdir');
52+
53+
// download and set the read file
54+
$file = 'miriam.xml';
55+
$rfile = $this->getParameterValue("download_url");
56+
$lfile = $ldir.$file;
57+
if(!file_exists($lfile) || $this->getParameterValue("download") == "true") {
58+
utils::downloadSingle($rfile,$lfile);
59+
}
60+
61+
parent::setReadFile($lfile);
62+
63+
// set the write file
64+
$outfile = "miriam.".parent::getParameterValue('output_format');
65+
$gz = (strstr(parent::getParameterValue('output_format'),".gz") === FALSE)?false:true;
66+
parent::setWriteFile(parent::getParameterValue("outdir").$outfile,$gz);
67+
$this->parse();
68+
parent::WriteRDFBufferToWriteFile();
69+
$this->getWriteFile()->Close();
70+
71+
return true;
72+
}
73+
74+
function parse()
75+
{
76+
// convert into json
77+
$lfile = parent::getReadFile()->getFileName();
78+
$xml = simplexml_load_file($lfile);
79+
$json = json_encode($xml);
80+
$db = json_decode($json,TRUE);
81+
82+
// miriam metadata
83+
// $attributes = $db['@attributes'];
84+
foreach($db['datatype'] AS $item) {
85+
$this->parseItem($item);
86+
}
87+
}
88+
89+
function parseItem($item)
90+
{
91+
$id = $item['@attributes']['id'];
92+
$label = $item['name'];
93+
94+
parent::addRDF(
95+
parent::describeIndividual($id, $item['name'], parent::getVoc()."Entry").
96+
parent::describeClass(parent::getVoc()."Entry","MIRIAM database entry").
97+
parent::triplifyString($id, parent::getVoc()."namespace", $item['namespace'])
98+
);
99+
100+
if(isset($item['@attributes'])) {
101+
foreach($item['@attributes'] AS $k => $v) {
102+
parent::addRDF(
103+
parent::triplifyString($id, parent::getVoc().$k, $v)
104+
);
105+
}
106+
}
107+
if(isset($item['comment'])) parent::addRDF(parent::triplifyString($id, parent::getVoc()."comment", $item['comment']));
108+
if(isset($item['definition'])) parent::addRDF(parent::triplifyString($id, parent::getVoc()."definition", $item['definition']));
109+
if(isset($item['synonyms'])) {
110+
$mylist = null;
111+
if(is_array($item['synonyms']['synonym'])) $mylist = $item['synonyms']['synonym'];
112+
else $mylist[] = $item['synonyms']['synonym'];
113+
foreach($mylist AS $myitem) {
114+
parent::addRDF(
115+
parent::triplifyString($id, "skos:altLabel", $myitem)
116+
);
117+
}
118+
}
119+
120+
if(isset($item['uris'])) {
121+
foreach($item['uris']['uri'] AS $uri) {
122+
parent::addRDF(
123+
parent::triplifyString($id, parent::getVoc()."uri", $uri)
124+
);
125+
}
126+
}
127+
if(isset($item['resources'])) {
128+
$mylist = null;
129+
if(!isset($item['resources']['resource']['dataEntry'])) $mylist = $item['resources']['resource'];
130+
else $mylist[] = $item['resources']['resource'];
131+
foreach($mylist AS $myitem) {
132+
$rid = $myitem['@attributes']['id'];
133+
parent::addRDF(
134+
parent::describeIndividual($rid, $myitem['dataInfo'], parent::getVoc()."Resource").
135+
parent::describeClass(parent::getVoc()."Resource", "MIRIAM Resource").
136+
parent::triplify($rid, parent::getVoc()."url", $myitem['dataResource']).
137+
parent::triplifyString($rid, parent::getVoc()."urlTemplate", $myitem['dataEntry']).
138+
parent::triplifyString($rid, parent::getVoc()."organization", is_array($myitem['dataInstitution'])?"":$myitem['dataInstitution']).
139+
parent::triplifyString($rid, parent::getVoc()."location", is_array($myitem['dataLocation'])?"":$myitem['dataLocation']).
140+
parent::triplify($id, parent::getVoc()."resource", $rid)
141+
);
142+
}
143+
}
144+
if(isset($item['tags'])) {
145+
$i = $item['tags']['tag'];
146+
$mylist = null;
147+
if(!is_array($i)) $mylist[] = $i;
148+
else $mylist = $i;
149+
foreach($mylist AS $myitem) {
150+
parent::addRDF(
151+
parent::triplifyString($id, parent::getvoc()."tag", $myitem)
152+
);
153+
}}
154+
155+
if(isset($item['documentations'])) {
156+
$i = $item['documentations']['documentation'];
157+
$mylist = null;
158+
if(!is_array($i)) $mylist[] = $i;
159+
else $mylist = $i;
160+
foreach($mylist AS $myitem) {
161+
if(strstr($myitem, "pubmed")) $uri = "pubmed:".substr($myitem, strrpos($myitem, ":")+1);
162+
else if(strstr($myitem, "doi")) $uri = "http://dx.doi.org/".substr($myitem, strpos($myitem, "doi:"));
163+
else $uri = $myitem;
164+
165+
parent::addRDF(
166+
parent::triplify($id, parent::getvoc()."documentation", $uri)
167+
);
168+
}}
169+
170+
if(isset($item['restrictions'])) {
171+
$mylist = null;
172+
if(!isset($item['restrictions']['restriction']['statement'])) $mylist = $item['restrictions']['restriction'];
173+
else $mylist[] = $item['restrictions']['restriction'];
174+
foreach($mylist AS $i => $myitem) {
175+
$rid = parent::getRes().str_replace(":","",$id)."_".($i+1);
176+
$a = $myitem['@attributes'];
177+
$rid_type = parent::getVoc().'restriction_type_'.$a['type'];
178+
179+
parent::addRDF(
180+
parent::describeIndividual($rid, $a['desc'], parent::getVoc()."Restriction").
181+
parent::describeClass(parent::getVoc()."Restriction", "Resource Restriction").
182+
parent::triplify($rid, "rdf:type", $rid_type).
183+
parent::describeClass($rid_type, $a['desc'], parent::getVoc()."Restriction").
184+
parent::triplifyString($rid, "dct:description", $myitem['statement']).
185+
parent::triplify($rid, "foaf:page", isset($myitem['link'])?$myitem['link']:"").
186+
parent::triplify($id, parent::getVoc()."restriction", $rid)
187+
);
188+
}}
189+
190+
/*
191+
<annotation>
192+
<format name="SBML">
193+
<elements>
194+
<element>reaction</element>
195+
<element>event</element>
196+
<element>rule</element>
197+
<element>species</element>
198+
</elements>
199+
</format>
200+
*/
201+
if(isset($item['annotation'])) {
202+
$mylist = null;
203+
if(!isset($item['annotation']['format']['elements'])) $mylist = $item['annotation']['format'];
204+
else $mylist[] = $item['annotation']['format'];
205+
foreach($mylist AS $i => $myitem) {
206+
$name = $myitem['@attributes']['name'];
207+
$myid = str_replace("MIR:",parent::getRes(), $id)."_annotation_".($i+1)."_".urlencode($name);
208+
parent::addRDF(
209+
parent::describeIndividual($myid, "$label used by $name", parent::getVoc()."ValueSet").
210+
parent::describeClass(parent::getVoc()."ValueSet", "MIRIAM Value Set").
211+
parent::triplifyString($myid, parent::getVoc()."used-in", $name).
212+
parent::triplify($myid, parent::getVoc()."uses", $id)
213+
);
214+
215+
$b = $myitem['elements']['element'];
216+
$mylist2 = null;
217+
if(!is_array($b)) $mylist2[] = $b;
218+
else $mylist2 = $b;
219+
foreach($mylist2 AS $i => $e) {
220+
parent::addRDF(
221+
parent::triplifyString($myid, parent::getVoc()."used-for", $e)
222+
);
223+
}
224+
}
225+
226+
}
227+
228+
}
229+
230+
}
231+
232+
?>

0 commit comments

Comments
 (0)