PREFIX portable_microhaplotype_object:
PREFIX rdf:
PREFIX rdfs:
PREFIX xsd:
portable_microhaplotype_object:GenomeInfo a rdfs:Class ;
rdfs:comment "information on a genome" .
portable_microhaplotype_object:name a rdf:Property ;
rdfs:comment "name of the genome" ;
rdfs:range xsd:string .
portable_microhaplotype_object:gff_url a rdf:Property ;
rdfs:comment "a link to the where this genome's annotation file could be downloaded" ;
rdfs:range xsd:string .
portable_microhaplotype_object:url a rdf:Property ;
rdfs:comment "a link to the where this genome file could be downloaded" ;
rdfs:range xsd:string .
portable_microhaplotype_object:genome_version a rdf:Property ;
rdfs:comment "the genome version" ;
rdfs:range xsd:string .
portable_microhaplotype_object:chromosomes a rdf:Property ;
rdfs:comment "a list of the chromosomes/contigs found within this genome" ;
rdfs:range xsd:string .
portable_microhaplotype_object:taxon_id a rdf:Property ;
rdfs:comment "the NCBI taxonomy number, can be a list of values if it's a genome file that has been created by combining gnomes from different species" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:SpecimenInfo a rdfs:Class ;
rdfs:comment "Information on specimen info" .
portable_microhaplotype_object:env_broad_scale a rdf:Property ;
rdfs:comment "the broad environment from which the specimen was collected, e.g. highlands, lowlands, mountainous region" ;
rdfs:range xsd:string .
portable_microhaplotype_object:env_local_scale a rdf:Property ;
rdfs:comment "the local environment from which the specimen was collected, e.g. jungle, urban, rural" ;
rdfs:range xsd:string .
portable_microhaplotype_object:drug_usage a rdf:Property ;
rdfs:comment "Any drug used by subject and the frequency of usage; can include multiple drugs used" ;
rdfs:range xsd:string .
portable_microhaplotype_object:blood_meal a rdf:Property ;
rdfs:comment "whether host specimen has had a recent blood meal" ;
rdfs:range xsd:boolean .
portable_microhaplotype_object:geo_admin_3 a rdf:Property ;
rdfs:comment "geographical admin level 3, the third large demarcation of a nation (nation = admin level 0)" ;
rdfs:range xsd:string .
portable_microhaplotype_object:specimen_type a rdf:Property ;
rdfs:comment "what type of specimen this is, e.g. negative_control, positive_control, field_sample" ;
rdfs:range xsd:string .
portable_microhaplotype_object:alternate_identifiers a rdf:Property ;
rdfs:comment "a list of alternative names" ;
rdfs:range xsd:string .
portable_microhaplotype_object:specimen_taxon_id a rdf:Property ;
rdfs:comment "the NCBI taxonomy number of the organism(s) in the specimen, can list multiple if a mixed sample" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:storage_plate_info a rdf:Property ;
rdfs:comment "plate location of where specimen is stored if stored in a plate" ;
rdfs:range portable_microhaplotype_object:PlateInfo .
portable_microhaplotype_object:travel_out_six_month a rdf:Property ;
rdfs:comment "Specification of the countries travelled in the last six months; can include multiple travels" ;
rdfs:range portable_microhaplotype_object:TravelInfo .
portable_microhaplotype_object:project_id a rdf:Property ;
rdfs:comment "the index into the project_info list" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:specimen_store_loc a rdf:Property ;
rdfs:comment "the specimen store site, address or facility name" ;
rdfs:range xsd:string .
portable_microhaplotype_object:env_medium a rdf:Property ;
rdfs:comment "the environment medium from which the specimen was collected from" ;
rdfs:range xsd:string .
portable_microhaplotype_object:parasite_density_info a rdf:Property ;
rdfs:comment "one or more parasite densities in microliters for this specimen" ;
rdfs:range portable_microhaplotype_object:ParasiteDensity .
portable_microhaplotype_object:specimen_accession a rdf:Property ;
rdfs:comment "if specimen is deposited in a database, what accession is it associated with" ;
rdfs:range xsd:string .
portable_microhaplotype_object:host_age a rdf:Property ;
rdfs:comment "if specimen is from a person, the age in years of the person, can be float value so for 3 month old put 0.25" ;
rdfs:range xsd:double .
portable_microhaplotype_object:gravidity a rdf:Property ;
rdfs:comment "the gravidity of the specimen host (number of previous pregnancies)" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:geo_admin_2 a rdf:Property ;
rdfs:comment "geographical admin level 2, the third large demarcation of a nation (nation = admin level 0)" ;
rdfs:range xsd:string .
portable_microhaplotype_object:gravid a rdf:Property ;
rdfs:comment "whether host specimen is currently pregnant" ;
rdfs:range xsd:boolean .
portable_microhaplotype_object:host_subject_name a rdf:Property ;
rdfs:comment "an identifier for the individual/person/patient a specimen was collected from" ;
rdfs:range xsd:string .
portable_microhaplotype_object:host_sex a rdf:Property ;
rdfs:comment "if specimen is collected from a host with a sex, the sex listed for that host" ;
rdfs:range xsd:string .
portable_microhaplotype_object:lat_lon a rdf:Property ;
rdfs:comment "the latitude and longitude of a specific site" ;
rdfs:range xsd:string .
portable_microhaplotype_object:geo_admin_1 a rdf:Property ;
rdfs:comment "geographical admin level 1, the secondary large demarcation of a nation (nation = admin level 0)" ;
rdfs:range xsd:string .
portable_microhaplotype_object:treatment_status a rdf:Property ;
rdfs:comment "If person has been treated with drugs, what was the treatment outcome" ;
rdfs:range xsd:string .
portable_microhaplotype_object:specimen_comments a rdf:Property ;
rdfs:comment "any additional comments about the specimen" ;
rdfs:range xsd:string .
portable_microhaplotype_object:has_travel_out_six_month a rdf:Property ;
rdfs:comment "has travelled out from local region in the last six months" ;
rdfs:range xsd:boolean .
portable_microhaplotype_object:specimen_collect_device a rdf:Property ;
rdfs:comment "the way the specimen was collected, e.g. whole blood, dried blood spot" ;
rdfs:range xsd:string .
portable_microhaplotype_object:collection_date a rdf:Property ;
rdfs:comment "the date of the specimen collection, can be YYYY, YYYY-MM, or YYYY-MM-DD" ;
rdfs:range xsd:string .
portable_microhaplotype_object:collection_country a rdf:Property ;
rdfs:comment "the name of country collected in, would be the same as admin level 0" ;
rdfs:range xsd:string .
portable_microhaplotype_object:host_taxon_id a rdf:Property ;
rdfs:comment "the NCBI taxonomy number of the host that the specimen was collected from" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:BioinformaticsRunInfo a rdfs:Class ;
rdfs:comment "Information about the pipeline run that generated microhaplotype_detected and reads_by_stage" .
portable_microhaplotype_object:run_date a rdf:Property ;
rdfs:comment "the date when the run was done, should be YYYY-MM-DD" ;
rdfs:range xsd:string .
portable_microhaplotype_object:bioinformatics_run_name a rdf:Property ;
rdfs:comment "a name to for this run, needs to be unique to each run " ;
rdfs:range xsd:string .
portable_microhaplotype_object:bioinformatics_methods_id a rdf:Property ;
rdfs:comment "the index into the bioinformatics_methods_info list" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:ProteinVariant a rdfs:Class ;
rdfs:comment "information on a variant in protein sequence" .
portable_microhaplotype_object:protein_location a rdf:Property ;
rdfs:comment "the position within the protein, the chromosome in this case would be the transcript name" ;
rdfs:range portable_microhaplotype_object:GenomicLocation .
portable_microhaplotype_object:codon_genomic_location a rdf:Property ;
rdfs:comment "the position within the genomic sequence of the codon" ;
rdfs:range portable_microhaplotype_object:GenomicLocation .
portable_microhaplotype_object:alternative_gene_name a rdf:Property ;
rdfs:comment "an alternative gene name" ;
rdfs:range xsd:string .
portable_microhaplotype_object:gene_name a rdf:Property ;
rdfs:comment "an identifier of the gene, if any, is being covered with this targeted" ;
rdfs:range xsd:string .
portable_microhaplotype_object:ReadCountsByStage a rdfs:Class ;
rdfs:comment "Information on the reads counts at several stages of a pipeline" .
portable_microhaplotype_object:read_counts_by_library_sample_by_stage a rdf:Property ;
rdfs:comment "a list by library_sample for the counts at each stage" ;
rdfs:range portable_microhaplotype_object:ReadCountsByStageForLibrarySample .
portable_microhaplotype_object:bioinformatics_run_id a rdf:Property ;
rdfs:comment "the index into bioinformatics_run_info list" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:MicrohaplotypeForTarget a rdfs:Class ;
rdfs:comment "Microhaplotype detected for a specific target" .
portable_microhaplotype_object:umis a rdf:Property ;
rdfs:comment "the unique molecular identifier (umi) count for this microhaplotype" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:mhap_id a rdf:Property ;
rdfs:comment "the index for a microhaplotype for a target in the representative_microhaplotypes list, e.g. representative_microhaplotypes[mhaps_target_id][mhap_id]" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:reads a rdf:Property ;
rdfs:comment "the read count for this microhaplotype" , "the read counts for this stage" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:ParasiteDensity a rdfs:Class ;
rdfs:comment "method and value of determined parasite density" .
portable_microhaplotype_object:parasite_density_method a rdf:Property ;
rdfs:comment "the method of how this density was obtained" ;
rdfs:range xsd:string .
portable_microhaplotype_object:parasite_density a rdf:Property ;
rdfs:comment "the density in microliters" ;
rdfs:range xsd:double .
portable_microhaplotype_object:date_measured a rdf:Property ;
rdfs:comment "the date the qpcr was performed, can be YYYY, YYYY-MM, or YYYY-MM-DD" ;
rdfs:range xsd:string .
portable_microhaplotype_object:density_method_comments a rdf:Property ;
rdfs:comment "additional comments about how the density was performed" ;
rdfs:range xsd:string .
portable_microhaplotype_object:MarkerOfInterest a rdfs:Class ;
rdfs:comment "A specific genomic location of interest, e.g. drug resistance, or other phenotypical marker" .
portable_microhaplotype_object:marker_location a rdf:Property ;
rdfs:comment "the genomic location" ;
rdfs:range portable_microhaplotype_object:GenomicLocation .
portable_microhaplotype_object:associations a rdf:Property ;
rdfs:comment "a list of associations with this marker, e.g. SP resistance, etc" ;
rdfs:range xsd:string .
portable_microhaplotype_object:DetectedMicrohaplotypesForTarget a rdfs:Class ;
rdfs:comment "Microhaplotypes detected for a specific target" .
portable_microhaplotype_object:mhaps a rdf:Property ;
rdfs:comment "a list of the microhaplotypes detected for this target" ;
rdfs:range portable_microhaplotype_object:MicrohaplotypeForTarget .
portable_microhaplotype_object:mhaps_target_id a rdf:Property ;
rdfs:comment "the index for a target in the representative_microhaplotypes list" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:RepresentativeMicrohaplotypesForTarget a rdfs:Class ;
rdfs:comment "a list of the representative sequence for the microhaplotypes for a target" .
portable_microhaplotype_object:microhaplotypes a rdf:Property ;
rdfs:comment "a list of all the microhaplotypes for a target" ;
rdfs:range portable_microhaplotype_object:RepresentativeMicrohaplotype .
portable_microhaplotype_object:mhap_location a rdf:Property ;
rdfs:comment "a genomic location that was analyzed for this target info, this allows listing location that may be different from the full target location (e.g 1 trimmed off the full length) " ;
rdfs:range portable_microhaplotype_object:GenomicLocation .
portable_microhaplotype_object:PanelInfo a rdfs:Class ;
rdfs:comment "information on a panel of targeted amplicon primer pairs" .
portable_microhaplotype_object:reactions a rdf:Property ;
rdfs:comment "a list of 1 or more reactions that this panel contains, each reactions list the targets that were amplified in that reaction, e.g. pool1, pool2" ;
rdfs:range portable_microhaplotype_object:ReactionInfo .
portable_microhaplotype_object:panel_name a rdf:Property ;
rdfs:comment "a name for the panel" ;
rdfs:range xsd:string .
portable_microhaplotype_object:RepresentativeMicrohaplotype a rdfs:Class ;
rdfs:comment "the representative sequence for a microhaplotype" .
portable_microhaplotype_object:quality a rdf:Property ;
rdfs:comment "the ASCII fastq per base quality score for this sequence, this is optional, must be same length as the sequence" ;
rdfs:range xsd:string .
portable_microhaplotype_object:alt_annotations a rdf:Property ;
rdfs:comment "a list of additional annotations associated with this microhaplotype, e.g. wildtype" ;
rdfs:range xsd:string .
portable_microhaplotype_object:associated_seq_variants a rdf:Property ;
rdfs:comment "a list of sequence variants for this haplotype, e.g. SNPS, indels" ;
rdfs:range portable_microhaplotype_object:GenomicLocation .
portable_microhaplotype_object:microhaplotype_name a rdf:Property ;
rdfs:comment "an optional name for this microhaplotype" ;
rdfs:range xsd:string .
portable_microhaplotype_object:masking a rdf:Property ;
rdfs:comment "masking info for the sequence" ;
rdfs:range portable_microhaplotype_object:MaskingInfo .
portable_microhaplotype_object:associated_protein_variants a rdf:Property ;
rdfs:comment "a list of protein variants for this haplotype, e.g. amino acid changes/INDELS" ;
rdfs:range portable_microhaplotype_object:ProteinVariant .
portable_microhaplotype_object:pseudocigar a rdf:Property ;
rdfs:comment "the pseudocigar of the haplotype" ;
rdfs:range portable_microhaplotype_object:Pseudocigar .
portable_microhaplotype_object:seq a rdf:Property ;
rdfs:comment "the sequence" ;
rdfs:range xsd:string .
portable_microhaplotype_object:StageReadCounts a rdfs:Class ;
rdfs:comment "Information on the reads counts at several stages" .
portable_microhaplotype_object:stage a rdf:Property ;
rdfs:comment "the stage of the pipeline, e.g. demultiplexed, denoised, etc" ;
rdfs:range xsd:string .
portable_microhaplotype_object:ReadCountsByStageForTarget a rdfs:Class ;
rdfs:comment "Information on the reads counts at several stages of a pipeline for a target" .
portable_microhaplotype_object:stages a rdf:Property ;
rdfs:comment "the read counts by each stage" ;
rdfs:range portable_microhaplotype_object:StageReadCounts .
portable_microhaplotype_object:target_id a rdf:Property ;
rdfs:comment "the index into the target_info list" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:BioMethod a rdfs:Class ;
rdfs:comment "bioinformatics methodology description with info on program, version, and arguments different from the default" .
portable_microhaplotype_object:program a rdf:Property ;
rdfs:comment "name of the program used for this portion of the pipeline" ;
rdfs:range xsd:string .
portable_microhaplotype_object:program_version a rdf:Property ;
rdfs:comment "the version of program, should be in the format of v[MAJOR].[MINOR].[PATCH]" ;
rdfs:range xsd:string .
portable_microhaplotype_object:additional_argument a rdf:Property ;
rdfs:comment "any additional arguments that differ from the default arguments" ;
rdfs:range xsd:string .
portable_microhaplotype_object:program_url a rdf:Property ;
rdfs:comment "a url pointing to code base of a program, e.g. a github link" ;
rdfs:range xsd:string .
portable_microhaplotype_object:program_description a rdf:Property ;
rdfs:comment "a short description of what this method does" ;
rdfs:range xsd:string .
portable_microhaplotype_object:SequencingInfo a rdfs:Class ;
rdfs:comment "Information on sequencing info" .
portable_microhaplotype_object:seq_center a rdf:Property ;
rdfs:comment "Name of facility where sequencing was performed (lab, core facility, or company)" ;
rdfs:range xsd:string .
portable_microhaplotype_object:nucl_acid_ext a rdf:Property ;
rdfs:comment "Link to a reference or kit that describes the recovery of nucleic acids from the sample" ;
rdfs:range xsd:string .
portable_microhaplotype_object:library_layout a rdf:Property ;
rdfs:comment "Specify the configuration of reads, e.g. paired-end, single" ;
rdfs:range xsd:string .
portable_microhaplotype_object:library_selection a rdf:Property ;
rdfs:comment "how amplification was done (common are PCR=Source material was selected by designed primers, RANDOM =Random selection by shearing or other method)" ;
rdfs:range xsd:string .
portable_microhaplotype_object:library_kit a rdf:Property ;
rdfs:comment "Name, version, and applicable cell or cycle numbers for the kit used to prepare libraries and load cells or chips for sequencing. If possible, include a part number, e.g. MiSeq Reagent Kit v3 (150-cycle), MS-102-3001" ;
rdfs:range xsd:string .
portable_microhaplotype_object:nucl_acid_amp a rdf:Property ;
rdfs:comment "Link to a reference or kit that describes the enzymatic amplification of nucleic acids" ;
rdfs:range xsd:string .
portable_microhaplotype_object:seq_date a rdf:Property ;
rdfs:comment "the date of sequencing, should be YYYY-MM or YYYY-MM-DD" ;
rdfs:range xsd:string .
portable_microhaplotype_object:library_source a rdf:Property ;
rdfs:comment "Source of amplification material e.g. was it DNA (GENOMIC) or RNA (TRANSCRIPTOMIC) (common names GENOMIC, TRANSCRIPTOMIC)" ;
rdfs:range xsd:string .
portable_microhaplotype_object:pcr_cond a rdf:Property ;
rdfs:comment "the method/conditions for PCR, List PCR cycles used to amplify the target" ;
rdfs:range xsd:string .
portable_microhaplotype_object:seq_instrument_model a rdf:Property ;
rdfs:comment "the sequencing instrument model used to sequence the run, e.g. NextSeq 2000, MinION, Revio" ;
rdfs:range xsd:string .
portable_microhaplotype_object:nucl_acid_amp_date a rdf:Property ;
rdfs:comment "the date of the nucleoacid amplification" ;
rdfs:range xsd:string .
portable_microhaplotype_object:library_screen a rdf:Property ;
rdfs:comment "Describe enrichment, screening, or normalization methods applied during amplification or library preparation, e.g. size selection 390bp, diluted to 1 ng DNA/sample" ;
rdfs:range xsd:string .
portable_microhaplotype_object:sequencing_info_name a rdf:Property ;
rdfs:comment "a name for a specific sequencing run, e.g. batch1" ;
rdfs:range xsd:string .
portable_microhaplotype_object:library_strategy a rdf:Property ;
rdfs:comment "what the nuceloacid sequencing/amplification strategy was (common names are AMPLICON, WGS)" ;
rdfs:range xsd:string .
portable_microhaplotype_object:seq_platform a rdf:Property ;
rdfs:comment "the sequencing technology used to sequence the run, e.g. ILLUMINA, NANOPORE, PACBIO" ;
rdfs:range xsd:string .
portable_microhaplotype_object:nucl_acid_ext_date a rdf:Property ;
rdfs:comment "the date of the nucleoacid extraction" ;
rdfs:range xsd:string .
portable_microhaplotype_object:BioinformaticsMethodInfo a rdfs:Class ;
rdfs:comment "the targeted amplicon bioinformatics methods used to generate the microhaplotype data in this PMO" .
portable_microhaplotype_object:methods a rdf:Property ;
rdfs:comment "methodology used to generate the microhaplotype data stored in this PMO, e.g. demultiplexing method, denosing method, or a pipeline method that ties all th steps together" ;
rdfs:range portable_microhaplotype_object:BioMethod .
portable_microhaplotype_object:TargetInfo a rdfs:Class ;
rdfs:comment "Information about a specific targeted microhaplotype" .
portable_microhaplotype_object:insert_location a rdf:Property ;
rdfs:comment "the intended genomic location of the insert of the amplicon (the location between the end of the forward primer and the beginning of the reverse primer)" ;
rdfs:range portable_microhaplotype_object:GenomicLocation .
portable_microhaplotype_object:markers_of_interest a rdf:Property ;
rdfs:comment "a list of markers of interest that are covered by this target" ;
rdfs:range portable_microhaplotype_object:MarkerOfInterest .
portable_microhaplotype_object:target_attributes a rdf:Property ;
rdfs:comment "a list of classification types for this target" ;
rdfs:range xsd:string .
portable_microhaplotype_object:forward_primer a rdf:Property ;
rdfs:comment "the forward primer for this target" ;
rdfs:range portable_microhaplotype_object:PrimerInfo .
portable_microhaplotype_object:reverse_primer a rdf:Property ;
rdfs:comment "the reverse primer for this target" ;
rdfs:range portable_microhaplotype_object:PrimerInfo .
portable_microhaplotype_object:target_name a rdf:Property ;
rdfs:comment "a name for this target" ;
rdfs:range xsd:string .
portable_microhaplotype_object:TravelInfo a rdfs:Class ;
rdfs:comment "Information on travel info" .
portable_microhaplotype_object:travel_country a rdf:Property ;
rdfs:comment "the name of country, would be the same as admin level 0" ;
rdfs:range xsd:string .
portable_microhaplotype_object:bed_net_usage a rdf:Property ;
rdfs:comment "approximate usage of bed net while traveling, 1 = 100% nights with bed net, 0 = 0% no bed net usage" ;
rdfs:range xsd:double .
portable_microhaplotype_object:travel_end_date a rdf:Property ;
rdfs:comment "the date of the end of travel, can be approximate, should be YYYY-MM or YYYY-MM-DD (preferred)" ;
rdfs:range xsd:string .
portable_microhaplotype_object:travel_start_date a rdf:Property ;
rdfs:comment "the date of the start of travel, can be approximate, should be YYYY-MM or YYYY-MM-DD (preferred)" ;
rdfs:range xsd:string .
portable_microhaplotype_object:PrimerInfo a rdfs:Class ;
rdfs:comment "information on a primer sequence" .
portable_microhaplotype_object:location a rdf:Property ;
rdfs:comment "what the intended genomic location of the primer is" ;
rdfs:range portable_microhaplotype_object:GenomicLocation .
portable_microhaplotype_object:PmoGenerationMethod a rdfs:Class ;
rdfs:comment "Information about how a PMO was generated" .
portable_microhaplotype_object:program_name a rdf:Property ;
rdfs:comment "the name of the program" ;
rdfs:range xsd:string .
portable_microhaplotype_object:MaskingInfo a rdfs:Class ;
rdfs:comment "information about a subsegment of the sequence that should be masked" .
portable_microhaplotype_object:seq_start a rdf:Property ;
rdfs:comment "the start of the masking" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:seq_segment_size a rdf:Property ;
rdfs:comment "the size of the masking" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:replacement_size a rdf:Property ;
rdfs:comment "the size of replacement mask" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:masking_generation_description a rdf:Property ;
rdfs:comment "a description of how the masking information was generated " ;
rdfs:range xsd:string .
portable_microhaplotype_object:RepresentativeMicrohaplotypes a rdfs:Class ;
rdfs:comment "a collection of representative sequences for microhaplotypes for all targets" .
portable_microhaplotype_object:targets a rdf:Property ;
rdfs:comment "a list of the microhaplotypes for each targets " ;
rdfs:range portable_microhaplotype_object:RepresentativeMicrohaplotypesForTarget .
portable_microhaplotype_object:DetectedMicrohaplotypesForSample a rdfs:Class ;
rdfs:comment "Microhaplotypes detected for a sample for all targets" .
portable_microhaplotype_object:target_results a rdf:Property ;
rdfs:comment "a list of the microhaplotypes detected for a list of targets" ;
rdfs:range portable_microhaplotype_object:DetectedMicrohaplotypesForTarget .
portable_microhaplotype_object:library_sample_id a rdf:Property ;
rdfs:comment "the index into the library_sample_info list" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:PmoHeader a rdfs:Class ;
rdfs:comment "Information on the PMO file itself" .
portable_microhaplotype_object:pmo_version a rdf:Property ;
rdfs:comment "the version of the PMO file, should be in the format of v[MAJOR].[MINOR].[PATCH]" ;
rdfs:range xsd:string .
portable_microhaplotype_object:creation_date a rdf:Property ;
rdfs:comment "the date of when the PMO file was created or modified, should be YYYY-MM-DD" ;
rdfs:range xsd:string .
portable_microhaplotype_object:generation_method a rdf:Property ;
rdfs:comment "the generation method to create this PMO " ;
rdfs:range portable_microhaplotype_object:PmoGenerationMethod .
portable_microhaplotype_object:LibrarySampleInfo a rdfs:Class ;
rdfs:comment "Information about a specific amplification and sequencing of a specimen" .
portable_microhaplotype_object:run_accession a rdf:Property ;
rdfs:comment "ERA/SRA run accession number for the sample if it was submitted" ;
rdfs:range xsd:string .
portable_microhaplotype_object:panel_id a rdf:Property ;
rdfs:comment "the index into the panel_info list" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:qpcr_parasite_density_info a rdf:Property ;
rdfs:comment "qpcr parasite density measurement for this extracted sample" ;
rdfs:range portable_microhaplotype_object:ParasiteDensity .
portable_microhaplotype_object:fastqs_loc a rdf:Property ;
rdfs:comment "the location (url or filename path) of the fastqs for a library run" ;
rdfs:range xsd:string .
portable_microhaplotype_object:library_prep_plate_info a rdf:Property ;
rdfs:comment "plate location of where library was prepared for sequencing" ;
rdfs:range portable_microhaplotype_object:PlateInfo .
portable_microhaplotype_object:specimen_id a rdf:Property ;
rdfs:comment "the index into the specimen_info list" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:sequencing_info_id a rdf:Property ;
rdfs:comment "the index into the sequencing_info list" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:experiment_accession a rdf:Property ;
rdfs:comment "ERA/SRA experiment accession number for the sample if it was submitted" ;
rdfs:range xsd:string .
portable_microhaplotype_object:PortableMicrohaplotypeObject a rdfs:Class ;
rdfs:comment "Information on final microhaplotype results from a targeted amplicon analysis with associated meta data" .
portable_microhaplotype_object:targeted_genomes a rdf:Property ;
rdfs:comment "a list of genomes that any genomic location information refers to" ;
rdfs:range portable_microhaplotype_object:GenomeInfo .
portable_microhaplotype_object:project_info a rdf:Property ;
rdfs:comment "the information about the projects stored in this PMO" ;
rdfs:range portable_microhaplotype_object:ProjectInfo .
portable_microhaplotype_object:library_sample_info a rdf:Property ;
rdfs:comment "a list of libraries of all the seq/amp of the specimens within this PMO file" ;
rdfs:range portable_microhaplotype_object:LibrarySampleInfo .
portable_microhaplotype_object:bioinformatics_methods_info a rdf:Property ;
rdfs:comment "the bioinformatics pipeline/methods used to generated the microhaplotype analysis for this project" ;
rdfs:range portable_microhaplotype_object:BioinformaticsMethodInfo .
portable_microhaplotype_object:pmo_header a rdf:Property ;
rdfs:comment "the PMO information for this file including version etc" ;
rdfs:range portable_microhaplotype_object:PmoHeader .
portable_microhaplotype_object:bioinformatics_run_info a rdf:Property ;
rdfs:comment "the runtime info for the bioinformatics pipeline used to generated the microhaplotypes analysis for this project" ;
rdfs:range portable_microhaplotype_object:BioinformaticsRunInfo .
portable_microhaplotype_object:target_info a rdf:Property ;
rdfs:comment "a list of info on the targets" ;
rdfs:range portable_microhaplotype_object:TargetInfo .
portable_microhaplotype_object:sequencing_info a rdf:Property ;
rdfs:comment "a list of sequencing infos for this PMO file" ;
rdfs:range portable_microhaplotype_object:SequencingInfo .
portable_microhaplotype_object:representative_microhaplotypes a rdf:Property ;
rdfs:comment "a list of the information on the representative microhaplotypes" ;
rdfs:range portable_microhaplotype_object:RepresentativeMicrohaplotypes .
portable_microhaplotype_object:panel_info a rdf:Property ;
rdfs:comment "a list of info on the panels" ;
rdfs:range portable_microhaplotype_object:PanelInfo .
portable_microhaplotype_object:detected_microhaplotypes a rdf:Property ;
rdfs:comment "the microhaplotypes detected in this projects" ;
rdfs:range portable_microhaplotype_object:DetectedMicrohaplotypes .
portable_microhaplotype_object:specimen_info a rdf:Property ;
rdfs:comment "a list of all the specimens within this PMO file" ;
rdfs:range portable_microhaplotype_object:SpecimenInfo .
portable_microhaplotype_object:read_counts_by_stage a rdf:Property ;
rdfs:comment "the read counts for library_samples for different stages of the pipeline" ;
rdfs:range portable_microhaplotype_object:ReadCountsByStage .
portable_microhaplotype_object:ProjectInfo a rdfs:Class ;
rdfs:comment "Information on a project underwhich a collection of specimens belong to" .
portable_microhaplotype_object:project_contributors a rdf:Property ;
rdfs:comment "a list of collaborators who contributed to this project" ;
rdfs:range xsd:string .
portable_microhaplotype_object:bio_project_accession a rdf:Property ;
rdfs:comment "an SRA bioproject accession e.g. PRJNA33823" ;
rdfs:range xsd:string .
portable_microhaplotype_object:project_type a rdf:Property ;
rdfs:comment "the type of project conducted, e.g. TES vs surveillance vs transmission" ;
rdfs:range xsd:string .
portable_microhaplotype_object:project_description a rdf:Property ;
rdfs:comment "a short description of the project" ;
rdfs:range xsd:string .
portable_microhaplotype_object:project_collector_chief_scientist a rdf:Property ;
rdfs:comment "can be collection of names separated by a semicolon if multiple people involved or can just be the name of the primary person managing the specimen" ;
rdfs:range xsd:string .
portable_microhaplotype_object:PlateInfo a rdfs:Class ;
rdfs:comment "Information about a plate location, e.g. a standard 96 well plate with row having a letter and column having a number" .
portable_microhaplotype_object:plate_name a rdf:Property ;
rdfs:comment "a name for the plate" ;
rdfs:range xsd:string .
portable_microhaplotype_object:plate_row a rdf:Property ;
rdfs:comment "the row position" ;
rdfs:range xsd:string .
portable_microhaplotype_object:plate_col a rdf:Property ;
rdfs:comment "the column position" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:DetectedMicrohaplotypes a rdfs:Class ;
rdfs:comment "the microhaplotypes detected in a targeted amplicon analysis" .
portable_microhaplotype_object:library_samples a rdf:Property ;
rdfs:comment "a list of the microhaplotypes detected for all samples with a list for each target " ;
rdfs:range portable_microhaplotype_object:DetectedMicrohaplotypesForSample .
portable_microhaplotype_object:ReactionInfo a rdfs:Class ;
rdfs:comment "information on a panel of targeted amplicon primer pairs" .
portable_microhaplotype_object:panel_targets a rdf:Property ;
rdfs:comment "a list of the target indexes in the target_info list" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:reaction_name a rdf:Property ;
rdfs:comment "a name for this reaction" ;
rdfs:range xsd:string .
portable_microhaplotype_object:Pseudocigar a rdfs:Class ;
rdfs:comment "information on pseudocigar for a sequence" .
portable_microhaplotype_object:pseudocigar_seq a rdf:Property ;
rdfs:comment "the pseudocigar itself" ;
rdfs:range xsd:string .
portable_microhaplotype_object:ref_loc a rdf:Property ;
rdfs:comment "the genomic location the pseudocigar is in reference to" ;
rdfs:range portable_microhaplotype_object:GenomicLocation .
portable_microhaplotype_object:pseudocigar_generation_description a rdf:Property ;
rdfs:comment "a description of how the pseudocigar information was generated " ;
rdfs:range xsd:string .
portable_microhaplotype_object:ReadCountsByStageForLibrarySample a rdfs:Class ;
rdfs:comment "Information on the reads counts at several stages of a pipeline for a library_sample" .
portable_microhaplotype_object:total_raw_count a rdf:Property ;
rdfs:comment "the raw counts off the sequencing machine that a sample began with" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:read_counts_for_targets a rdf:Property ;
rdfs:comment "a list of counts by stage for a target" ;
rdfs:range portable_microhaplotype_object:ReadCountsByStageForTarget .
portable_microhaplotype_object:GenomicLocation a rdfs:Class ;
rdfs:comment "information on the genomic location of specific sequence" .
portable_microhaplotype_object:alt_seq a rdf:Property ;
rdfs:comment "a possible alternative sequence of this genomic location" ;
rdfs:range xsd:string .
portable_microhaplotype_object:chrom a rdf:Property ;
rdfs:comment "the chromosome name" ;
rdfs:range xsd:string .
portable_microhaplotype_object:ref_seq a rdf:Property ;
rdfs:comment "the reference sequence of this genomic location" ;
rdfs:range xsd:string .
portable_microhaplotype_object:genome_id a rdf:Property ;
rdfs:comment "the index to the genome in the targeted_genomes list that this location refers to" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:end a rdf:Property ;
rdfs:comment "the end of the location, 0-based positioning" ;
rdfs:range xsd:integer .
portable_microhaplotype_object:strand a rdf:Property ;
rdfs:comment "which strand the location is, either + for plus strand or - for negative strand" ;
rdfs:range xsd:string .
portable_microhaplotype_object:start a rdf:Property ;
rdfs:comment "the start of the location, 0-based positioning" ;
rdfs:range xsd:integer .