function OBO2TTL($indir, $outdir, $file)
{
global $gns, $gns_backup, $options;
$gns = $gns_backup;
$infile = $indir . $file;
$outfile = $outdir . $file . '.ttl';
$in = gzopen($infile, "r");
if (FALSE === $in) {
trigger_error("unable to open " . $infile);
exit;
}
$out = fopen($outfile, "w");
if (FALSE === $out) {
trigger_error("unable to open " . $outfile);
exit;
}
echo "Converting {$infile} to {$outfile}" . PHP_EOL;
if (FALSE !== ($pos = strrpos($infile, '\\'))) {
$file = substr($infile, $pos + 1);
} else {
if (FALSE !== ($pos = strrpos($infile, '/'))) {
$file = substr($infile, $pos + 1);
} else {
$file = $infile;
}
}
$file .= ".ttl";
$pos = strpos($file, ".");
$ontology = substr($file, 0, $pos);
$furi = "bio2rdf_resource:file/{$file}";
$ouri = "registry:{$ontology}";
$header = N3NSHeader();
$buf = QQuad($furi, "rdf:type", "sio:Document");
$buf .= QQuadL($furi, "rdfs:label", "Turtle converted OBO file for {$ontology} ontology (obtained through NCBO Bioportal) [bio2rdf_resource:{$file}]");
$buf .= QQuadL($furi, "dc:creator", "Michel Dumontier");
$buf .= QQuadL($furi, "sio:encodes", $ouri);
$buf .= QQuad($ouri, "rdf:type", "owl:Ontology");
$buf .= QQuadL($ouri, "rdfs:label", "{$ontology} ontology");
$buf .= QQuad($ouri, "sio:is-encoded-by", $furi);
$tid = '';
$first = true;
$is_a = false;
$is_deprecated = false;
$min = $buf;
while ($l = gzgets($in)) {
$lt = trim($l);
if (strlen($lt) == 0) {
continue;
}
if ($lt[0] == '!') {
continue;
}
if (strstr($l, "[Term]")) {
// top level node?
if ($first == true) {
// ignore the first case
$first = false;
} else {
if ($tid != '' && $is_a == false && $is_deprecated == false) {
$t = QQuad($tid, "rdfs:subClassOf", "bio2rdf_vocabulary:Entity");
$buf .= $t;
$min .= $t;
}
}
$is_a = false;
$is_deprecated = false;
unset($typedef);
$term = '';
$tid = '';
continue;
} else {
if (strstr($l, "[Typedef]")) {
$is_a = false;
$is_deprecated = false;
unset($term);
$tid = '';
$typedef = '';
continue;
}
}
// to fix error in obo generator
$lt = str_replace("synonym ", "synonym: ", $lt);
$lt = preg_replace("/\\{.*\\} !/", " !", $lt);
$a = explode(" !", $lt);
if (isset($a[1])) {
$exc = trim($a[1]);
}
$a = explode(": ", trim($a[0]), 2);
// let's go
if (isset($intersection_of)) {
if ($a[0] != "intersection_of") {
$intersection_of .= ")]." . PHP_EOL;
$buf .= $intersection_of;
if ($options['minimal+']['value'] == 'true') {
$min .= $intersection_of;
}
unset($intersection_of);
}
}
if (isset($typedef)) {
if ($a[0] == "id") {
$c = explode(":", $a[1]);
if (count($c) == 1) {
$ns = "obo";
$id = $c[0];
} else {
$ns = strtolower($c[0]);
$id = $c[1];
}
$id = str_replace(array("(", ")"), array("_", ""), $id);
$tid = $ns . ":" . $id;
$header .= AddToGlobalNS($ns);
$buf .= QQuadL($tid, "dc:identifier", $tid);
} else {
if ($a[0] == "name") {
$buf .= QQuadL($tid, "rdfs:label", addslashes(stripslashes($a[1])) . " [{$tid}]");
} else {
if ($a[0] == "is_a") {
if (FALSE !== ($pos = strpos($a[1], "!"))) {
$a[1] = substr($a[1], 0, $pos - 1);
}
$buf .= QQuad($tid, "rdfs:subPropertyOf", "obo:" . strtolower($a[1]));
} else {
if ($a[0] == "is_obsolete") {
$buf .= QQuad($tid, "rdf:type", "owl:DeprecatedClass");
$is_deprecated = true;
} else {
if ($a[0][0] == "!") {
$a[0] = substr($a[0], 1);
}
$buf .= QQuadL($tid, "obo:{$a['0']}", str_replace('"', '', stripslashes($a[1])));
}
}
}
}
} else {
if (isset($term)) {
if ($a[0] == "is_obsolete" && $a[1] == "true") {
$t = QQuad($tid, "rdf:type", "owl:DeprecatedClass");
$t .= QQuad($tid, "rdfs:subClassOf", "owl:DeprecatedClass");
$min .= $t;
$buf .= $t;
$is_deprecated = true;
} else {
if ($a[0] == "id") {
ParseQNAME($a[1], $ns, $id);
$header .= AddToGlobalNS($ns);
$tid = $ns . ":" . $id;
$buf .= QQuad($tid, "rdfs:isDefinedBy", $ouri);
$buf .= QQuadL($tid, "dc:identifier", $tid);
} else {
if ($a[0] == "name") {
$t = QQuadL($tid, "rdfs:label", str_replace(array("\"", "'"), array("", "\\\\'"), stripslashes($a[1])) . " [{$tid}]");
$min .= $t;
$buf .= $t;
} else {
if ($a[0] == "def") {
$t = str_replace(array("'", "\"", "\\", "\\\\'"), array("\\\\'", "", "", ""), $a[1]);
$min .= QQuadL($tid, "dc:description", $t);
$buf .= QQuadL($tid, "dc:description", $t);
} else {
if ($a[0] == "property_value") {
$b = explode(" ", $a[1]);
$buf .= QQuadL($tid, "obo_vocabulary:" . strtolower($b[0]), str_replace("\"", "", strtolower($b[1])));
} else {
if ($a[0] == "xref") {
// http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG
// Medical Dictionary:http\://www.medterms.com/
// KEGG COMPOUND:C02788 "KEGG COMPOUND"
// first get the comment
if (FALSE !== ($pos = strpos($a[1], '"'))) {
$comment = substr($a[1], $pos + 1, -1);
$identifier = substr($a[1], 0, $pos - 1);
} else {
$identifier = $a[1];
}
// next identify the namespace and identifier
if (FALSE !== ($pos = strpos($identifier, ":"))) {
$id = trim(substr($identifier, $pos + 1));
$raw_ns = strtolower(substr($identifier, 0, $pos));
// the raw ns is likely to be very dirty
// should map to the registry
// but for now, just add this namespace
$ns = str_replace(" ", "_", $raw_ns);
$header .= AddToGlobalNS($ns);
if (strstr($id, "http")) {
$buf .= Quad(GetFQURI($tid), GetFQURI("rdfs:seeAlso"), stripslashes($id));
} else {
$buf .= QQuad($tid, "rdfs:seeAlso", strtolower($ns) . ":" . str_replace(" ", " ", stripslashes($id)));
}
}
} else {
if ($a[0] == "synonym") {
// synonym: "entidades moleculares" RELATED [IUPAC:]
// synonym: "molecular entity" EXACT IUPAC_NAME [IUPAC:]
// synonym: "Chondrococcus macrosporus" RELATED synonym [NCBITaxonRef:Krzemieniewska_and_Krzemieniewski_1926]
//grab string inside double quotes
preg_match('/"(.*)"(.*)/', $a[1], $matches);
if (!empty($matches)) {
$a[1] = str_replace(array("\\", "\"", "'"), array("", "", "\\\\'"), $matches[1] . $matches[2]);
} else {
$a[1] = str_replace(array("\"", "'"), array("", "\\\\'"), $a[1]);
}
$rel = "SYNONYM";
$list = array("EXACT", "BROAD", "RELATED", "NARROW");
$found = false;
foreach ($list as $keyword) {
// get everything after the keyword up until the bracket [
if (FALSE !== ($k_pos = strpos($a[1], $keyword))) {
$str_len = strlen($a[1]);
$keyword_len = strlen($keyword);
$keyword_end_pos = $k_pos + $keyword_len;
$b1_pos = strrpos($a[1], "[");
$b2_pos = strrpos($a[1], "]");
$b_text = substr($a[1], $b1_pos + 1, $b2_pos - $b1_pos - 1);
$diff = $b1_pos - $keyword_end_pos - 1;
if ($diff != 0) {
// then there is more stuff here
$k = substr($a[1], $keyword_end_pos + 1, $diff);
$rel = trim($k);
} else {
// create the long predicate
$rel = $keyword . "_SYNONYM";
}
$found = true;
$str = substr($a[1], 0, $k_pos - 1);
break;
}
}
// check to see if we still haven't found anything
if ($found === false) {
// we didn't find one of the keywords
// so take from the start to the bracket
$b1_pos = strrpos($a[1], "[");
$str = substr($a[1], 0, $b1_pos - 1);
}
$rel = str_replace(" ", "_", $rel);
// $lit = addslashes($str.($b_text?" [".$b_text."]":""));
$l = QQuadL($tid, "obo_vocabulary:" . strtolower($rel), $str);
$buf .= $l;
} else {
if ($a[0] == "alt_id") {
ParseQNAME($a[1], $ns, $id);
if ($id != 'curators') {
$header .= AddToGlobalNS($ns);
$buf .= QQuad("{$ns}:{$id}", "rdfs:seeAlso", $tid);
}
} else {
if ($a[0] == "is_a") {
// do subclassing
ParseQNAME($a[1], $ns, $id);
$header .= AddToGlobalNS($ns);
$t = QQuad($tid, "rdfs:subClassOf", "{$ns}:{$id}");
$buf .= $t;
$min .= $t;
$is_a = true;
} else {
if ($a[0] == "intersection_of") {
if (!isset($intersection_of)) {
$intersection_of = GetFQURITTL($tid) . ' ' . GetFQURITTL('owl:equivalentClass') . ' [' . GetFQURITTL('rdf:type') . ' ' . GetFQURITTL('owl:Class') . '; ' . GetFQURITTL('owl:intersectionOf') . ' (';
}
/*
intersection_of: develops_from VAO:0000092 ! chondrogenic condensation
intersection_of: OBO_REL:has_part VAO:0000040 ! cartilage tissue
*/
$c = explode(" ", $a[1]);
if (count($c) == 1) {
// just a class
ParseQNAME($c[0], $ns, $id);
$header .= AddToGlobalNS($ns);
$intersection_of .= GetFQURITTL("{$ns}:{$id}");
} else {
if (count($c) == 2) {
// an expression
ParseQNAME($c[0], $pred_ns, $pred_id);
$header .= AddToGlobalNS($pred_ns);
ParseQNAME($c[1], $obj_ns, $obj_id);
$header .= AddToGlobalNS($obj_ns);
$intersection_of .= ' [' . GetFQURITTL('owl:onProperty') . ' ' . GetFQURITTL("obo:" . $pred_id) . '; ' . GetFQURITTL('owl:someValuesFrom') . ' ' . GetFQURITTL("{$obj_ns}:{$obj_id}") . '] ';
}
}
} else {
if ($a[0] == "relationship") {
if (!isset($relationship)) {
$relationship = GetFQURITTL($tid) . ' ' . GetFQURITTL('rdfs:subClassOf') . ' [' . GetFQURITTL('rdf:type') . ' ' . GetFQURITTL('owl:Class') . '; ' . GetFQURITTL('owl:intersectionOf') . ' (';
}
/*
relationship: develops_from VAO:0000092 ! chondrogenic condensation
relationship: OBO_REL:has_part VAO:0000040 ! cartilage tissue
*/
$c = explode(" ", $a[1]);
if (count($c) == 1) {
// just a class
ParseQNAME($c[0], $ns, $id);
$header .= AddToGlobalNS($ns);
$relationship .= GetFQURITTL("{$ns}:{$id}");
} else {
if (count($c) == 2) {
// an expression
ParseQNAME($c[0], $pred_ns, $pred_id);
$header .= AddToGlobalNS($pred_ns);
ParseQNAME($c[1], $obj_ns, $obj_id);
$header .= AddToGlobalNS($obj_ns);
$relationship .= ' [' . GetFQURITTL('owl:onProperty') . ' ' . GetFQURITTL("obo:" . $pred_id) . '; ' . GetFQURITTL('owl:someValuesFrom') . ' ' . GetFQURITTL("{$obj_ns}:{$obj_id}") . '] ';
$relationship .= ")]." . PHP_EOL;
$buf .= $relationship;
if ($options['minimal+']['value'] == 'true') {
$min .= $relationship;
}
unset($relationship);
}
}
} else {
// default handler
$buf .= QQuadL($tid, "obo:{$a['0']}", str_replace(array("\"", "'"), array("", "\\\\'"), stripslashes($a[1])));
}
}
}
}
}
}
}
}
}
}
}
} else {
//header
//format-version: 1.0
$a = explode(": ", trim($l));
$buf .= QQuadL($ouri, "obo:{$a['0']}", str_replace(array('"', '\\:'), array('\\"', ':'), isset($a[1]) ? $a[1] : ""));
}
}
fwrite($out, $header);
if ($options['minimal']['value'] == 'true' || $options['minimal+']['value'] == 'true') {
fwrite($out, $min);
} else {
fwrite($out, $buf);
}
$min = '';
$buf = '';
$header = '';
}
if (isset($intersection_of)) {
$buf .= $intersection_of . ")]." . PHP_EOL;
}
if (isset($relationship)) {
$buf .= $relationship . ")]." . PHP_EOL;
}
gzclose($in);
if ($options['minimal']['value'] == 'true' || $options['minimal+']['value'] == 'true') {
fwrite($out, $min);
} else {
fwrite($out, $buf);
}
fclose($out);
}
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
*/
define('BIO2RDF_URI', 'http://bio2rdf.org/');
// namespace declarations
$gns = array('xsd' => 'http://www.w3.org/2001/XMLSchema#', 'rdf' => 'http://www.w3.org/1999/02/22-rdf-syntax-ns#', 'rdfs' => 'http://www.w3.org/2000/01/rdf-schema#', 'owl' => 'http://www.w3.org/2002/07/owl#', 'dc' => 'http://purl.org/dc/terms/', 'skos' => 'http://www.w3.org/2004/02/skos/core#', 'foaf' => 'http://xmlns.com/foaf/0.1/', 'sio' => 'http://semanticscience.org/resource/', 'bio2rdf' => BIO2RDF_URI, 'bio2rdf_resource' => BIO2RDF_URI . 'bio2rdf_resource:', 'bio2rdf_vocabulary' => BIO2RDF_URI . 'bio2rdf_vocabulary:');
// valid dataset namespaces
$gdataset_ns = array('afcs', 'apo', 'atc', 'bind', 'bindingdb', 'biogrid', 'blastprodom', 'candida', 'cas', 'chebi', 'chemspider', 'coil', 'corum', 'ctd', 'cygd', 'dbsnp', 'dip', 'ddbj', 'dpd', 'drugbank', 'ec', 'embl', 'ensembl', 'eco', 'euroscarf', 'flybase', 'fprintscan', 'kegg', 'gene3d', 'genbank', 'geneid', 'germonline', 'go', 'gp', 'grid', 'het', 'hprd', 'innatedb', 'intact', 'ipi', 'irefindex', 'iubmb', "rogid", "irogid", "rigid", "irigid", "crigid", "crogid", "icrogid", "icrigid", 'iupharligand', 'matrixdb', 'mesh', 'metacyc', 'mi', 'mint', 'mips', 'mpact', 'mpi', 'ncbi', 'ndc', 'refseq', 'obo', 'omim', 'ophid', 'patternscan', 'pato', 'panther', 'pfam', 'pharmgkb', 'pir', 'prf', 'prodom', 'profilescan', 'pdb', 'pubmed', 'pubchem', 'pubchemcompound', 'pubchemsubstance', 'reactome', 'registry', 'registry_dataset', 'seg', 'sgd', 'smart', 'snomed', 'so', 'superfamily', 'swissprot', 'symbol', 'taxon', 'tcdb', 'tigr', 'tpg', 'trembl', 'ttd', 'offsides', 'twosides', 'umls', 'uniparc', 'uniprot', 'uo');
// add the valid namespaces to the global namespace array
foreach ($gdataset_ns as $ns) {
AddToGlobalNS($ns, true);
}
$gns_backup = $gns;
function AddToGlobalNS($ns, $add_voc_and_resource = false)
{
global $gns;
if (!isset($gns[$ns])) {
$gns[$ns] = BIO2RDF_URI . $ns . ':';
if ($add_voc_and_resource) {
$gns[$ns . '_vocabulary'] = BIO2RDF_URI . $ns . '_vocabulary:';
$gns[$ns . '_resource'] = BIO2RDF_URI . $ns . '_resource:';
}
return "@prefix {$ns}: <http://bio2rdf.org/{$ns}:> ." . PHP_EOL;
}
return '';
}
