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lindenblindenb
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so2java
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‎stylesheets/bio/so/so2java.md‎

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# motivation
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converts 'Sequence ontology in OWL' to a C/java/... code to recreate the ontology tree in memory
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# Usage
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```
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curl -L "https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-simple.owl?raw=true" | xsltproc so2java.xsl -|
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``
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# Output
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function:
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```c
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newTerm(term_accession, term_label, term_parent1, term_parent2, .... term_parentN);
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```
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```c
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newTerm("SO:0000001","region","SO:0000110");
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newTerm("SO:0000002","sequence_secondary_structure","SO:0001411");
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newTerm("SO:0000003","G_quartet","SO:0000002");
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newTerm("SO:0000004","interior_coding_exon","SO:0000195");
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newTerm("SO:0000005","satellite_DNA","SO:0000705");
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newTerm("SO:0000006","PCR_product","SO:0000695");
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newTerm("SO:0000007","read_pair","SO:0000150");
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newTerm("SO:0000010","protein_coding","SO:0000401");
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newTerm("SO:0000011","non_protein_coding","SO:0000401");
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newTerm("SO:0000012","scRNA_primary_transcript","SO:0000483");
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newTerm("SO:0000013","scRNA","SO:0000655");
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newTerm("SO:0000014","INR_motif","SO:0001660");
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newTerm("SO:0000015","DPE_motif","SO:0001660");
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newTerm("SO:0000016","BREu_motif","SO:0001660");
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newTerm("SO:0000017","PSE_motif","SO:0000713");
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newTerm("SO:0000018","linkage_group","SO:0001411");
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newTerm("SO:0000020","RNA_internal_loop","SO:0000715");
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newTerm("SO:0000021","asymmetric_RNA_internal_loop","SO:0000020");
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newTerm("SO:0000022","A_minor_RNA_motif","SO:0000715");
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newTerm("SO:0000023","K_turn_RNA_motif","SO:0000021");
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newTerm("SO:0000024","sarcin_like_RNA_motif","SO:0000021");
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newTerm("","symmetric_RNA_internal_loop","SO:0000020");
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newTerm("SO:0000026","RNA_junction_loop","SO:0000715");
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newTerm("SO:0000027","RNA_hook_turn","SO:0000026");
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newTerm("SO:0000028","base_pair","SO:0000002");
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newTerm("SO:0000029","WC_base_pair","SO:0000028");
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newTerm("SO:0000030","sugar_edge_base_pair","SO:0000028");
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newTerm("SO:0000031","aptamer","SO:0000696");
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newTerm("SO:0000032","DNA_aptamer","SO:0000031");
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newTerm("SO:0000033","RNA_aptamer","SO:0000031");
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(...)
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newTerm("SO:1001281","flanking_three_prime_quadruplet_recoding_signal","SO:1001277");
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newTerm("SO:1001282","UAG_stop_codon_signal","SO:1001288");
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newTerm("SO:1001283","UAA_stop_codon_signal","SO:1001288");
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newTerm("SO:1001284","regulon","SO:0005855");
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newTerm("SO:1001285","UGA_stop_codon_signal","SO:1001288");
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newTerm("SO:1001286","three_prime_repeat_recoding_signal","SO:1001277");
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newTerm("SO:1001287","distant_three_prime_recoding_signal","SO:1001277");
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newTerm("SO:1001288","stop_codon_signal","SO:1001268");
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newTerm("SO:2000061","databank_entry","SO:0000695");
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newTerm("SO:3000000","gene_segment","SO:0000842");
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```
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‎stylesheets/bio/so/so2java.xsl‎

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<?xml version="1.0" encoding="ASCII"?>
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<xsl:stylesheet
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version="1.0"
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xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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xmlns:owl="http://www.w3.org/2002/07/owl#"
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xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
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xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
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xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
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xmlns:so="http://purl.obolibrary.org/obo/so#"
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xmlns:obo="http://purl.obolibrary.org/obo/">
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<xsl:output method='text'/>
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<xsl:template match="/">
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<xsl:apply-templates select="rdf:RDF"/>
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</xsl:template>
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<xsl:template match="rdf:RDF">
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<xsl:apply-templates select="owl:Class" mode="nodes"/>
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</xsl:template>
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<xsl:template match="owl:Class[owl:deprecated/text() = 'true']" mode="nodes">
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<!-- ignore deprecated -->
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</xsl:template>
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<xsl:template match="owl:Class" mode="nodes">
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<xsl:text>newTerm("</xsl:text>
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<xsl:value-of select="oboInOwl:id/text()"/>
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<xsl:text>","</xsl:text>
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<xsl:value-of select="rdfs:label/text()"/>
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<xsl:text>"</xsl:text>
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<xsl:for-each select="rdfs:subClassOf[@rdf:resource]">
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<xsl:variable name="rsrc" select="@rdf:resource"/>
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<xsl:text>,"</xsl:text>
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<xsl:value-of select="/rdf:RDF/owl:Class[@rdf:about = $rsrc]/oboInOwl:id/text()"/>
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<xsl:text>"</xsl:text>
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</xsl:for-each>
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<xsl:text>);
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</xsl:text>
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</xsl:template>
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<xsl:template match="owl:Class[owl:deprecated/text() = 'true']" mode="bind">
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<!-- ignore deprecated -->
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</xsl:template>
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</xsl:stylesheet>
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