mirna_base.py 文件源码

def create_graph(self):
        self.g.open(self.path +  mirbasegraph_name, create=True)
        data = self.parse_mirbase(self.path)
        #g = ConjunctiveGraph(store="SPARQLUpdateStore")
        # g.bind()
        mirna_class = URIRef("http://purl.obolibrary.org/obo/SO_0000276")
        for mid in data:
            mirna_instance = URIRef(MIRBASE + data[mid]["acc"])
            self.g.add((mirna_instance, RDF.type, mirna_class))
            label = Literal(data[mid]["name"])
            self.g.add((mirna_instance, RDFS.label, label))
            description = Literal(data[mid]["description"])
            self.g.add((mirna_instance, RDFS.comment, description))
            for p in data[mid]["previous_names"]:
                if p.strip():
                    previous_name = Literal(p)
                    self.g.add((mirna_instance, MIRBASE["previous_acc"], previous_name))
            for mature in data[mid]["mature"]:
                mature_instance = URIRef(MIRBASE + data[mid]["mature"][mature]["acc"])
                self.g.add((mature_instance, RDF.type, mirna_class))
                mature_label = Literal(data[mid]["mature"][mature]["name"])
                self.g.add((mature_instance, RDFS.label, mature_label))
                for mature_p in data[mid]["mature"][mature]["previous_names"]:
                    if mature_p.strip():
                        mature_previous_name = Literal(mature_p)
                        self.g.add((mature_instance, MIRBASE["previous_acc"], mature_previous_name))
                self.g.add((mirna_instance, MIRBASE["stemloopOf"], mature_instance))
        self.get_label_to_acc()
        self.choices = self.labels.keys()
        goa_data = self.parse_goa_gaf("data/goa_human_rna.gaf")
        for label in self.labels:
            if label in goa_data:
                for go_id in goa_data[label]:
                    mirna_instance = self.labels[label]
                    self.g.add((mirna_instance, MIRBASE["goa"], Literal(go_id)))