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antimicrobial_resistance_genomic_analysis_result.schema.yml
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antimicrobial_resistance_genomic_analysis_result.schema.yml
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$namespaces:
obo: http://purl.obolibrary.org/obo/
edam_data: http://edamontology.org/data_
iao: http://purl.obolibrary.org/obo/IAO_
ncit: http://purl.obolibrary.org/obo/NCIT_
genepio: http://purl.obolibrary.org/obo/GENEPIO_
chebi: http://purl.obolibrary.org/obo/CHEBI_
aro: http://purl.obolibrary.org/obo/ARO_
$graph:
- name: AntimicrobialResistanceGenomicAnalysisResult
documentRoot: true
doc: |
Result of applying a computational analysis to genomic data for the purpose
of predicting or explaining resistance to antimicrobial agents based on
genomic features.
type: record
fields:
sample_id:
type: string?
doc: An identifier for the sample that is the subject of the analysis.
jsonldPredicate:
_id: edam_data:3273
input_file_name:
type: string
doc: The filename containing sequence data used as input for the analysis.
jsonldPredicate:
_id: edam_data:1050
contig_id:
type: string?
doc: The identifier specifying a particular contig in a collection.
start:
type: int?
doc: The identifier specifying a particular contig in a collection.
stop:
type: int?
doc: The last nucleotide of the termination codon in the user submitted sequence.
strand_orientation:
type: string?
doc: The orientation of a genomic element on the double stranded molecule.
jsonldPredicate:
_id: ncit:C48673
gene_symbol:
type: string
doc: |
The short name of a gene; a single word that does not contain white space characters.
It is typically derived from the gene name.
jsonldPredicate:
_id: edam_data:1026
gene_name:
type: string
doc: |
The name of a gene, (typically) assigned by a person and/or according to a naming scheme.
It may contain white space characters and is typically more intuitive and readable than a gene symbol.
It (typically) may be used to identify similar genes in different species and to derive a gene symbol.
jsonldPredicate:
_id: edam_data:2299
coverage_depth:
type: int?
doc: |
Coverage (read depth or depth) is the average number of reads representing
a given nucleotide in the reconstructed sequence, described as fold coverage.
jsonldPredicate:
_id: genepio:0000092
coverage_breadth:
type: float
doc: |
The percentage of the positions in the reference molecular sequence that
can be aligned with the target molecular sequence.
sequence_identity:
type: float
doc: |
Sequence identity is the number (%) of matches (identical characters)
in positions from an alignment of two molecular sequences.
jsonldPredicate:
_id: edam_data:1412
reference_database_id:
type: string
doc: |
Identifier for the database containing references genomes for
genome annotation, gene identification, characterization etc.
jsonldPredicate:
_id: edam_data:1048
reference_database_version:
type: string
doc: Version of a particular reference database.
reference_accession:
type: string
doc: A persistent, unique identifier of a molecular sequence database entry.
jsonldPredicate:
_id: edam_data:2091
reference_length:
type: int
doc: The length (number of positions) of the molecular sequence retrieved from the reference database.
jsonldPredicate:
_id: edam_data:1249
target_length:
type: int
doc: The length (number of positions) of the molecular sequence being analyzed.
jsonldPredicate:
_id: edam_data:1249
drug_class:
type: string?
doc: |
A set of medications and other compounds that have similar chemical structures,
the same mechanism of action (i.e., bind to the same biological target),
a related mode of action, and/or are used to treat the same disease.
antimicrobial_agent:
type: string?
doc: |
A substance that kills or slows the growth of microorganisms, including
bacteria, viruses, fungi and protozoans.
jsonldPredicate:
_id: chebi:33281
resistance_mechanism:
type: string?
doc: |
Cellular processes in a pathogen that result in antimicrobial drug resistance.
jsonldPredicate:
_id: aro:1000002
analysis_software_name:
type: string
doc: The name of a computer package, application, method or function.
jsonldPredicate:
_id: edam_data:1190
analysis_software_version:
type: string
doc: |
A version number is a unique number or set of numbers assigned to a specific
release of a software program, file, firmware, device driver, or even hardware.
Typically, as updates and entirely new editions of a program or driver are released,
the version number will increase.
jsonldPredicate:
_id: ncit:C111093