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llbase.cellbase-lib.6.2.1.source-code.mongodb-indexes.json Maven / Gradle / Ivy

{"collection": "clinical_variants", "fields": {"id": 1}, "options": {"background": true}}
{"collection": "clinical_variants", "fields": {"type": 1}, "options": {"background": true}}
{"collection": "clinical_variants", "fields": {"chromosome": 1, "start": 1, "end": 1}, "options": {"background": true}}
{"collection": "clinical_variants", "fields": {"annotation.id": 1}, "options": {"background": true}}
{"collection": "clinical_variants", "fields": {"annotation.hgvs": 1}, "options": {"background": true}}
{"collection": "clinical_variants", "fields": {"annotation.consequenceTypes.sequenceOntologyTerms.name": 1}, "options": {"background": true}}
{"collection": "clinical_variants", "fields": {"annotation.traitAssociation.id": 1}, "options": {"background": true}}
{"collection": "clinical_variants", "fields": {"annotation.traitAssociation.source.name": 1}, "options": {"background": true}}
{"collection": "clinical_variants", "fields": {"annotation.traitAssociation.consistencyStatus": 1}, "options": {"sparse": true}}
{"collection": "clinical_variants", "fields": {"annotation.traitAssociation.variantClassification.clinicalSignificance": 1}, "options": {"sparse": true}}
{"collection": "clinical_variants", "fields": {"annotation.traitAssociation.heritableTraits.inheritanceMode": 1}, "options": {"sparse": true}}
{"collection": "clinical_variants", "fields": {"annotation.traitAssociation.alleleOrigin": 1}, "options": {"sparse": true}}
{"collection": "clinical_variants", "fields": {"_traits": 1}, "options": {"background": true}}
{"collection": "clinical_variants", "fields": {"_featureXrefs": 1}, "options": {"background": true}}

{"collection": "conservation", "fields": {"_chunkIds": 1}, "options": {"background": true}}
{"collection": "conservation", "fields": {"chromosome": 1, "start": 1, "end": 1}, "options": {"background": true}}

{"collection": "genome_sequence", "fields": {"_chunkIds": 1}, "options": {"background": true}}
{"collection": "genome_sequence", "fields": {"chromosome": 1, "start": 1, "end": 1}, "options": {"background": true}}
{"collection": "genome_sequence", "fields": {"sequenceType": 1}, "options": {"background": true}}

{"collection": "gene", "fields": {"id": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"name": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"biotype": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"_chunkIds": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"chromosome": 1, "start": 1, "end": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"transcripts.id": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"transcripts.name": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"transcripts.biotype": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"transcripts.flags": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"transcripts.chromosome": 1, "transcripts.start": 1, "transcripts.end": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"transcripts.xrefs.id": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"transcripts.exons.id": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"transcripts.exons.chromosome": 1, "transcripts.exons.start": 1, "transcripts.exons.end": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"transcripts.tfbs.id": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"transcripts.tfbs.pfmId": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"transcripts.tfbs.transcriptionFactors": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"transcripts.annotation.ontologies.id": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"transcripts.annotation.ontologies.name": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"mirna.id": 1}, "options": {"background": true, "sparse": true}}
{"collection": "gene", "fields": {"mirna.accession": 1}, "options": {"background": true}, "sparse": true}
{"collection": "gene", "fields": {"mirna.matures.id": 1}, "options": {"background": true, "sparse": true}}
{"collection": "gene", "fields": {"annotation.diseases.id": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"annotation.diseases.name": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"annotation.expression.expression": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"annotation.expression.factorValue": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"annotation.drugs.drugName": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"annotation.constraints.name": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"annotation.constraints.value": 1}, "options": {"background": true}}
{"collection": "gene", "fields": {"annotation.mirnaTargets.id": 1}, "options": {"background": true, "sparse": true}}
{"collection": "gene", "fields": {"annotation.mirnaTargets.sourceId": 1}, "options": {"background": true, "sparse": true}}
{"collection": "gene", "fields": {"annotation.cancerAssociations.roleInCancer": 1}, "options": {"background": true, "sparse": true}}

{"collection": "missense_variation_functional_score", "fields": {"chromosome": 1, "position": 1, "reference": 1}, "options": {"background": true}}

{"collection": "ontology", "fields": {"id": 1}, "options": {"background": true}}
{"collection": "ontology", "fields": {"name": 1}, "options": {"background": true}}
{"collection": "ontology", "fields": {"source": 1}, "options": {"background": true}}
{"collection": "ontology", "fields": {"namespace": 1}, "options": {"background": true}}
{"collection": "ontology", "fields": {"synonyms": 1}, "options": {"background": true}}
{"collection": "ontology", "fields": {"xrefs": 1}, "options": {"background": true}}
{"collection": "ontology", "fields": {"parents": 1}, "options": {"background": true}}
{"collection": "ontology", "fields": {"children": 1}, "options": {"background": true}}

{"collection": "protein", "fields": {"accession": 1}, "options": {"background": true}}
{"collection": "protein", "fields": {"name": 1}, "options": {"background": true}}
{"collection": "protein", "fields": {"protein.recommendedName.fullName.value": 1}, "options": {"background": true}}
{"collection": "protein", "fields": {"gene.name.value": 1}, "options": {"background": true}}
{"collection": "protein", "fields": {"dbReference.id": 1}, "options": {"background": true}}
{"collection": "protein", "fields": {"dbReference.type": 1}, "options": {"background": true}}
{"collection": "protein", "fields": {"keyword.value": 1}, "options": {"background": true}}
{"collection": "protein", "fields": {"feature.id": 1}, "options": {"background": true}}
{"collection": "protein", "fields": {"feature.type": 1}, "options": {"background": true}}
{"collection": "protein", "fields": {"feature.location.position.position": 1}, "options": {"background": true}}
{"collection": "protein", "fields": {"feature.location.begin.position": 1,"feature.location.end.position": 1}, "options": {"background": true}}
{"collection": "protein", "fields": {"sequence.checksum": 1}, "options": {"background": true}}

{"collection": "protein_functional_prediction", "fields": {"checksum": 1}, "options": {"background": true}}
{"collection": "protein_functional_prediction", "fields": {"uniprotId": 1}, "options": {"background": true}}
{"collection": "protein_functional_prediction", "fields": {"transcriptId": 1}, "options": {"background": true}}

{"collection": "refseq", "fields": {"id": 1}, "options": {"background": true}}
{"collection": "refseq", "fields": {"name": 1}, "options": {"background": true}}
{"collection": "refseq", "fields": {"biotype": 1}, "options": {"background": true}}
{"collection": "refseq", "fields": {"_chunkIds": 1}, "options": {"background": true}}
{"collection": "refseq", "fields": {"chromosome": 1, "start": 1, "end": 1}, "options": {"background": true}}
{"collection": "refseq", "fields": {"transcripts.id": 1}, "options": {"background": true}}
{"collection": "refseq", "fields": {"transcripts.name": 1}, "options": {"background": true}}
{"collection": "refseq", "fields": {"transcripts.biotype": 1}, "options": {"background": true}}
{"collection": "refseq", "fields": {"transcripts.chromosome": 1, "transcripts.start": 1, "transcripts.end": 1}, "options": {"background": true}}
{"collection": "refseq", "fields": {"transcripts.xrefs.id": 1}, "options": {"background": true}}
{"collection": "refseq", "fields": {"transcripts.exons.id": 1}, "options": {"background": true}}
{"collection": "refseq", "fields": {"transcripts.exons.chromosome": 1, "transcripts.exons.start": 1, "transcripts.exons.end": 1}, "options": {"background": true}}
{"collection": "refseq", "fields": {"annotation.diseases.id": 1}, "options": {"background": true}}
{"collection": "refseq", "fields": {"annotation.diseases.name": 1}, "options": {"background": true}}
{"collection": "refseq", "fields": {"annotation.drugs.drugName": 1}, "options": {"background": true}}
{"collection": "refseq", "fields": {"annotation.mirnaTargets.id": 1}, "options": {"background": true, "sparse": true}}
{"collection": "refseq", "fields": {"annotation.mirnaTargets.sourceId": 1}, "options": {"background": true, "sparse": true}}

{"collection": "regulatory_pfm", "fields": {"id": 1}, "options": {"background": true}}
{"collection": "regulatory_pfm", "fields": {"name": 1}, "options": {"background": true}}
{"collection": "regulatory_pfm", "fields": {"transcriptionFactors": 1}, "options": {"background": true}}
{"collection": "regulatory_pfm", "fields": {"threshold": 1}, "options": {"background": true}}
{"collection": "regulatory_pfm", "fields": {"source": 1}, "options": {"background": true}}
{"collection": "regulatory_pfm", "fields": {"maxPositionSum": 1}, "options": {"background": true}}
{"collection": "regulatory_pfm", "fields": {"length": 1}, "options": {"background": true}}

{"collection": "regulatory_region", "fields": {"_chunkIds": 1}, "options": {"background": true}}
{"collection": "regulatory_region", "fields": {"chromosome": 1, "start": 1, "end": 1}, "options": {"background": true}}
{"collection": "regulatory_region", "fields": {"featureType": 1}, "options": {"background": true}}

{"collection": "repeats", "fields": {"_chunkIds": 1}, "options": {"background": true}}
{"collection": "repeats", "fields": {"chromosome": 1, "start": 1, "end": 1}, "options": {"background": true}}

{"collection": "variation", "fields": {"id": 1}, "options": {"background": true}}
{"collection": "variation", "fields": {"chromosome": 1, "start": 1, "end": 1}, "options": {"background": true}}
{"collection": "variation", "fields": {"_chunkIds": 1}, "options": {"background": true}}
{"collection": "variation", "fields": {"chromosome": 1, "sv.ciStartLeft": 1, "sv.ciStartRight": 1, "sv.ciEndLeft": 1, "sv.ciEndRight": 1, "type": 1, "sv.type": 1}, "options": {"background": true, "sparse": true, "index_name": "chrom_type_sv"}}
{"collection": "variation", "fields": {"annotation.consequenceTypes.geneName": 1}, "options": {"background": true, "sparse": true}}
{"collection": "variation", "fields": {"annotation.consequenceTypes.geneId": 1}, "options": {"background": true, "sparse": true}}
{"collection": "variation", "fields": {"annotation.consequenceTypes.transcriptId": 1}, "options": {"background": true, "sparse": true}}
{"collection": "variation", "fields": {"annotation.consequenceTypes.sequenceOntologyTerms.name": 1}, "options": {"background": true}}

{"collection": "variation_functional_score", "fields": {"_chunkIds": 1}, "options": {"background": true}}
{"collection": "variation_functional_score", "fields": {"chromosome": 1, "start": 1, "end": 1}, "options": {"background": true}}
{"collection": "variation_functional_score", "fields": {"source": 1}, "options": {"background": true}}

{"collection": "splice_score", "fields": {"_chunkIds": 1}, "options": {"background": true}}
{"collection": "splice_score", "fields": {"chromosome": 1, "position": 1}, "options": {"background": true}}

{"collection": "pubmed", "fields": {"medlineCitation.pmid.content": 1}, "options": {"background": true}}

{"collection": "pharmacogenomics", "fields": {"_chunkIds": 1}, "options": {"background": true}}
{"collection": "pharmacogenomics", "fields": {"id": 1}, "options": {"background": true}}
{"collection": "pharmacogenomics", "fields": {"name": 1}, "options": {"background": true}}
{"collection": "pharmacogenomics", "fields": {"source": 1}, "options": {"background": true}}
{"collection": "pharmacogenomics", "fields": {"types": 1}, "options": {"background": true}}
{"collection": "pharmacogenomics", "fields": {"variants.variantId": 1}, "options": {"background": true}}
{"collection": "pharmacogenomics", "fields": {"variants.location": 1}, "options": {"background": true}}
{"collection": "pharmacogenomics", "fields": {"variants.chromosome": 1, "variants.position": 1}, "options": {"background": true}}
{"collection": "pharmacogenomics", "fields": {"variants.haplotypes": 1}, "options": {"background": true}}
{"collection": "pharmacogenomics", "fields": {"variants.geneNames": 1}, "options": {"background": true}}
{"collection": "pharmacogenomics", "fields": {"variants.phenotypes": 1}, "options": {"background": true}}
{"collection": "pharmacogenomics", "fields": {"variants.phenotypeType": 1}, "options": {"background": true}}
{"collection": "pharmacogenomics", "fields": {"variants.confidence": 1}, "options": {"background": true}}
{"collection": "pharmacogenomics", "fields": {"variants.evidences.pubmed": 1}, "options": {"background": true}}

{"collection": "snp", "fields": {"id": 1}, "options": {"background": true}}
{"collection": "snp", "fields": {"chromosome": 1, "position": 1, "reference": 1}, "options": {"background": true}}