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portable-microhaplotype-object

A schema to define the minimum amount of data needed to export a microhaplotype calling pipeline analysis with associated metadata

URI: https://plasmogenepi.github.io/portable-microhaplotype-object

Name: portable-microhaplotype-object

Classes

Class Description
BioinformaticsMethodInfo the targeted amplicon bioinformatics pipeline
BioinformaticsRunInfo Information about the pipeline run that generated some of the microhaplotype ...
BioMethod methodology description of a portion of a bioinformatics pipeline
ExperimentInfo Information about a specific amplification and sequencing of a specimen
GenomeInfo information on a genome
GenomicLocation information on the genomic location of specific sequence
MarkerOfInterest A specific genomic location of interest, e
MaskingInfo information about a subsegment of the sequence that should be masked
MicrohaplotypeForTarget Microhaplotype detected for a specific target
MicrohaplotypesDetected the microhaplotypes detected in a targeted amplicon analysis
MicrohaplotypesForSample Microhaplotypes detected for a sample for all targets
MicrohaplotypesForTarget Microhaplotypes detected for a specific target
PanelInfo information on a panel of targeted amplicon primer pairs
ParasiteDensity method and value of determined parasite density
PlateInfo Information about a plate location in a standard 96 well plate
PmoGenerationMethod Information about how a PMO was generated
PmoHeader Information on the PMO file
PortableMicrohaplotypeObject Information on final results from a targeted amplicon analysis
PrimerInfo information on a primer sequence
ProjectInfo Information on project info
ReactionInfo information on a panel of targeted amplicon primer pairs
ReadCountsByStage Information on the reads counts at several stages of a pipeline
ReadCountsByStageForExperimentalSample Information on the reads counts at several stages of a pipeline for a experim...
ReadCountsByStageForTarget Information on the reads counts at several stages of a pipeline for a target
RepresentativeMicrohaplotype the representative sequence for a microhaplotype, similar to a fast(a/q) form...
RepresentativeMicrohaplotypes a collection of representative sequences for microhaplotypes for all targets
RepresentativeMicrohaplotypesForTarget a list of the representative sequence for a microhaplotypes, similar to a fas...
SequencingInfo Information on sequencing info
SpecimenInfo Information on specimen info
StageReadCounts Information on the reads counts at several stages
TargetInfo Information about a specific target within a genome

Slots

Slot Description
accession ERA/SRA accession number for the sample if it was submitted
additional_argument any additional arguments that differ from the default
additional_methods any additional methods used to analyze the data
alt_annotations a list of additional annotations associated with this microhaplotype, e
alternate_identifiers a list of optional alternative names for the specimens
associations a list of associations with this marker, e
bioinformatics_method_name name of the collection of methods is called, e
bioinformatics_methods_id the index into the bioinformatics_methods_info list
bioinformatics_methods_info the bioinformatics pipeline/methods used to generated the amplicon analysis f...
bioinformatics_run_id the index into bioinformatics_run_info list
bioinformatics_run_info the runtime info for the bioinformatics pipeline used to generated the amplic...
bioinformatics_run_name a name to for this run
BioProject_accession an SRA bioproject accession e
chrom the chromosome name
chromosomes a list of chromosomes found within this genome
collection_country the name of country collected in, would be the same as admin level 0
collection_date the date of the specimen collection, can be YYYY, YYYY-MM, or YYYY-MM-DD
creation_date the date of when the PMO file was created or modified, should be YYYY-MM-DD
date_measured the date the qpcr was performed, can be YYYY, YYYY-MM, or YYYY-MM-DD
demultiplexing_method the demultiplexing method used to separate raw reads from barcodes and primer...
denoising_method the method used to de-noise and/or cluster the raw reads
density_method the method of how this density was obtained
density_method_comments additional comments about how the density was performed
drug_usage Any drug used by subject and the frequency of usage; can include multiple dru...
end the end of the location, 0-based positioning
env_broad_scale the broad environment from which the specimen was collected, e
env_local_scale the local environment from which the specimen was collected, e
env_medium the environment medium from which the specimen was collected from
experiment_info a list of experiments of all the seq/amp of the specimens within this project
experiment_sample_id the index into the experiment_info list
experiment_sample_name a unique identifier for this sequence/amplification run on a specimen_name
experiment_samples a list of the microhaplotypes detected for a sample by targets
forward_primer the forward primer associated with this target
gene_name an identifier of the gene, if any, is being covered with this targeted
generation_method the generation method to create this PMO
genome_id the index to the genome in the targeted_genomes list that this location refer...
genome_version the genome version
geo_admin1 geographical admin level 1, the secondary large demarcation of a nation (nati...
geo_admin2 geographical admin level 2, the third large demarcation of a nation (nation =...
geo_admin3 geographical admin level 3, the third large demarcation of a nation (nation =...
gff_url a link to the where this genome's annotation file could be downloaded
haps a list of the microhaplotypes detected for this target
host_age if specimen is from a person, the age in years of the person, can be float va...
host_sex if specimen is from a person, the sex listed for that person
host_subject_id an identifier for the individual a specimen was collected from
host_taxon_id the NCBI taxonomy number of the host that the specimen was collected from
insert_location the intended genomic location of the insert of the amplicon (the location bet...
lat_lon the latitude and longitude of the collection site of the specimen
library_kit Name, version, and applicable cell or cycle numbers for the kit used to prepa...
library_layout Specify the configuration of reads, e
library_prep_plate_info plate location of where experiment was prepared for sequencing
library_screen Describe enrichment, screening, or normalization methods applied during ampli...
library_selection how amplification was done (common are PCR=Source material was selected by de...
library_source Source of amplification material (common names GENOMIC, TRANSCRIPTOMIC)
library_strategy what the nuceloacid sequencing/amplification strategy was (common names are A...
location what the intended genomic location of the primer is
marker_location the genomic location
markers_of_interest a list of covered markers of interest
masking masking info for the sequence
mhap_id the index for a microhaplotype for a target in the microhaplotypes_info list,...
mhap_location a genomic location that was analyzed for this target info, this allows listin...
mhaps_target_id the index for a target in the microhaplotypes_info list
microhaplotype_name an optional name for this microhaplotype
microhaplotypes a list of the microhaplotypes detected for a target
microhaplotypes_detected the microhaplotypes detected in this projects
microhaplotypes_info a list of the information on the representative microhaplotypes
microscopy_parasite_density_info one or more parasite densities in microliters for this specimen
name name of the genome
nucl_acid_amp Link to a reference or kit that describes the enzymatic amplification of nucl...
nucl_acid_amp_date the date of the nucleoacid amplification
nucl_acid_ext Link to a reference or kit that describes the recovery of nucleic acids from ...
nucl_acid_ext_date the date of the nucleoacid extraction
panel_id the index into the panel_info list
panel_info a list of info on the panels
panel_name a name for the panel
panel_targets a list of the target indexes in the target_info list
parasite_density the density in microliters
pcr_cond the method/conditions for PCR, List PCR cycles used to amplify the target
plate_col the column the specimen was in
plate_name a name of plate the specimen was in
plate_row the row the specimen was in
pmo_header the PMO information for this file including version etc
pmo_version the version of the PMO file, should be in the format of v[MAJOR]
program name of the program used for this portion of the pipeline
program_description a short description of what this method does
program_name the name of the program
program_version the version of generation method, should be in the format of v[MAJOR]
project_collector_chief_scientist can be collection of names separated by a semicolon if multiple people involv...
project_contributors a list of collaborators who contributed to this project
project_description a short description of the project
project_id the index into the project_info list
project_info the information about the projects stored in this PMO
project_name a name for the project, should be unique if multiple projects listed
project_type the type of project conducted, e
pseudocigar the pseudocigar of the haplotype
qpcr_parasite_density_info qpcr parasite density measurement
quality the ansi fastq per base quality score for this sequence, this is optional
reaction_name a name for this reaction
reactions a list of 1 or more reactions that this panel contains, each reactions list t...
read_count the read counts
read_counts_by_experimental_sample_by_stage a list by experiment_sample for the counts at each stage
read_counts_by_stage the read counts for different stages of the pipeline
read_counts_for_targets a list of counts by stage for a target
reads the read count associated with this microhaplotype
ref_seq the reference sequence of this genomic location
replacement_size the size of replacement mask
reverse_primer the reverse primer associated with this target
run_date the date when the run was done, should be YYYY-MM-DD
seq the DNA sequence
seq_center Name of facility where sequencing was performed (lab, core facility, or compa...
seq_date the date of sequencing, should be YYYY-MM or YYYY-MM-DD
seq_instrument_model the sequencing instrument model used to sequence the run, e
seq_platform the sequencing technology used to sequence the run, e
seq_segment_size the size of the masking
seq_start the start of the masking
sequencing_info a list of sequencing info for this project
sequencing_info_id the index into the sequencing_info list
sequencing_info_name a name of for the sequencing done, e
specimen_collect_device the way the specimen was collected, e
specimen_comments any additional comments about the specimen
specimen_id the index into the specimen_info list
specimen_info a list of all the specimens within this project
specimen_name an identifier for the specimen, should be unique within this sample set
specimen_store_loc the specimen store site, address or facility name
specimen_taxon_id the NCBI taxonomy number of the organism in specimen, can list multiple if a ...
specimen_type what type of specimen this is, e
stage the stage of the pipeline, e
stages the read counts by each stage
start the start of the location, 0-based positioning
storage_plate_info plate location of where specimen is stored if stored in a plate
strand which strand the location is, either + for plus strand or - for negative stra...
target_attributes a list of classification type for the primer target
target_id the index into the target_info list
target_info a list of info on the targets
target_name an identifier for this target
target_results a list of the microhaplotypes detected for a list of targets
targeted_genomes a list of genomes that the targets in TargetInfo refer to
targets a list of the microhaplotype for each targets
taxon_id the NCBI taxonomy number
total_raw_count the raw counts off the sequencing machine that a sample began with
travel_out_six_month Specification of the countries travelled in the last six months; can include ...
umis the unique molecular identifier (umi) count associated with this microhaploty...
url a link to the where this genome file could be downloaded

Enumerations

Enumeration Description

Types

Type Description
Boolean A binary (true or false) value
Curie a compact URI
Date a date (year, month and day) in an idealized calendar
DateOrDatetime Either a date or a datetime
Datetime The combination of a date and time
Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double A real number that conforms to the xsd:double specification
Float A real number that conforms to the xsd:float specification
Integer An integer
Jsonpath A string encoding a JSON Path
Jsonpointer A string encoding a JSON Pointer
Ncname Prefix part of CURIE
Nodeidentifier A URI, CURIE or BNODE that represents a node in a model
Objectidentifier A URI or CURIE that represents an object in the model
Sparqlpath A string encoding a SPARQL Property Path
String A character string
Time A time object represents a (local) time of day, independent of any particular...
Uri a complete URI
Uriorcurie a URI or a CURIE

Subsets

Subset Description