hAMRonization_specification_details.csv

Interface Label,Required/Optional,Definition,Value Type,Example,Guidance,Comments,
Input File Name,Mandatory,Name or other identifier of an entry from a sample database.,String,ERR3581801,Tools can have multiple input files (genomic/amino acid). Multiple input files will be accomodated by their corresponding parser. ,,
Input Sequence ID,Optional,The identifier of a molecular sequence being analyzed.,String,DAAGAT010000041.1,Can be left blank if not provided.,,
Input Protein Start ,Optional,The position of the first amino acid in a protein sequence being analyzed (input protein sequence). Also known as the query protein start site in a BLAST search. ,Int,6,"The value should be biologically relevant, and should not start with 0. This field only applies to tools providing gene sequence outputs. Can be left blank if output not provided/applicable.","can start at 1 or 0, fmin/fmax (start at 0), NCBI starts at 1 but CARD database starts at 0",
Input Protein Stop ,Optional,The position of the last amino acid in a protein sequence being analyzed (input protein sequence). Also known as the query protein stop site in a BLAST search. ,Int,307,This field only applies to tools providing gene sequence outputs. Can be left blank if output not provided/applicable.,,
Input Gene Start ,Optional,The position of the first nucleotide in a gene sequence being analyzed (input gene sequence). Also known as the query gene start site in a BLAST search. ,Int,18,,,
Input Gene Stop,Optional,The position of the last nucelotide in a gene sequence being analyzed (input gene sequence). Also known as the query gene stop site in a BLAST search. ,Int,921,,,
Reference Protein Start ,Optional,The position of the first amino acid in a reference protein sequence (sequence being used for comparison). Also known as the subject protein start site in a BLAST search. ,Int,1,This field only applies to tools providing amino acid sequence outputs. Can be left blank if output not provided/applicable.,,
Reference Protein Stop ,Optional,The position of the last amino acid in a reference protein sequence (sequence being used for comparison). Also known as the subject protein stop site in a BLAST search.,Int,300,This field only applies to tools providing gene sequence outputs. Can be left blank if output not provided/applicable.,,
Reference Gene Start ,Optional,The position of the first nucleotide in a reference gene sequence (sequence being used for comparison). Also known as the subject gene start site in a BLAST search.,Int,1,,,
Reference Gene Stop ,Optional,The position of the last nucelotide in a reference sequence (sequence being used for comparison). Also known as the subject gene stop site in a BLAST search.,Int,900,,,
Strand Orientation,Optional,The orientation of a gene in a double stranded DNA replicon. ,String,"(+), sense","Values should be sense or antisense, or the corresponding short form ""+"" or ""-"". The terms ""positive"" and ""negative"" should be avoided. Can be left blank if not provided.","sense or antisense, or use short hand +/-",
Gene Symbol,Mandatory,The short name of a gene or gene product; a single word that does not contain white space characters. It is typically derived from the gene/gene product name.,String,"catA1, blaOXA-101","Acceptable values may represent gene symbols or gene product symbols. ""Gene symbol"" and ""allele"" (based on amino acid variations) may be used interchangeably due to nuances in resistance gene family nomenclature. Parsers should include values from ""gene symbol"" and ""allele"" fields in this category. Either the ""gene symbol"" or the ""gene name"" must be provided.","every aa diff for beta lactamases is a new allele, not the case for all amr gene families; novel allele, leave it blank","Comment: I don't think if it's a novel allele, this should be blank (hence why it's mandatory); it should instead say 'blaOXA', just without a number afterwards designating a specific allele (or it will alternatively list the allele with closest homology)"
Gene Name,Mandatory,"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.",String,type A-1 chloramphenicol O-acetyltransferase ,"The long name for the gene/protein. Gene names or gene product names are acceptable.  Either the ""gene symbol"" or the ""gene name"" must be provided.",stress long form (describes protein); gene name or protein name?,
Coverage (depth),Optional,Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.,Float,56,The value is expressed as a fold value e.g. 56x.,,
Coverage (%),Optional,The percentage of the reference sequence covered by the sequence of interest.,Float,90,"The sequences can refer to reads and genome, nucelotides and genes, or amino acids and proteins. This value should be normalized and expressed as percentage. Do not include the ""%"" sign in the value. Either ""% Coverage (breadth)"" of ""Coverage (breadth) is required.","Comment: I think this should be mandatory; if you have a hit for a gene, the first question you have is the % identity and % length. This is necessary context to determine whether it's likely a functional protein.",
Coverage (ratio),Optional,The ratio of the reference sequence covered by the sequence of interest.,,450/500,"The sequences can refer to reads and genome, nucelotides and genes, or amino acids and proteins. This value should not be normalized and expressed as the ratio of actual positions being compared e.g. 450/500. Either ""% Coverage (breadth)"" of ""Coverage (breadth) is required.",,
Sequence Identity,Optional,Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences.,Float,1,"The sequences can refer to reads and genome, nucelotides and genes, or amino acids and proteins. The value should be expressed as a percentage. Do not include the ""%"" sign in the value.",,
Reference Database ID,Mandatory,"Database containing references genomes for genome annotation, gene identification, characterization etc.",String,"ncbi, ResFinder",,,
Reference Database Version,Mandatory,Version of a particular database.,String,,,ISSUE: No standards available for database versioning,
Reference Accession,Mandatory,"A persistent, unique identifier of a molecular sequence database entry.",String,NF000491.1 ,,,
Reference Gene Length,Optional,The length (number of positions) of a gene sequence being used as a reference for comparison.,Int,657,,"more specific term under ""Genetic Sequence Length (NCIT:C135487)""",
Reference Protein Length,Optional,The length (number of positions) of a protein sequence being used as a reference for comparison.,Int,219,,,
Input Gene Length,Optional,The length (number of positions) of a gene sequence being analyzed (input gene sequence).,Int,657,,"more specific term under ""Genetic Sequence Length (NCIT:C135487)""",
Input Protein Length,Optional,The length (number of positions) of a protein sequence being analyzed (input protein sequence).,Int,219,,,
Drug Class,Optional,"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.",String,Phenicol,Standardized terms from the ChEBI ontology should be used. Find terms using https://www.ebi.ac.uk/ols/ontologies/chebi. Can be left blank if not provided.,,
Antimicrobial Agent ,Optional,"A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.",String,CHLORAMPHENICOL,This should describe a specific agent. Standardized terms from the ChEBI ontology should be used. Find terms using https://www.ebi.ac.uk/ols/ontologies/chebi. Can be left blank if not provided.,,
Resistance mechanism,Optional,Cellular processes in a pathogen that result in antimicrobial drug resistance.,String,target alteration,Standardized terms from the ChEBI ontology should be used. Find terms using https://www.ebi.ac.uk/ols/ontologies/aro. Can be left blank if not provided. ,,
Analysis Software Name,Mandatory,"The name of a computer package, application, method or function.",String,amrfinder,Not typically included in an AMR prediction output. The user may have to provide the value.,,
Analysis Software Version,Mandatory,"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.",String,1.2.5,Not typically included in an AMR prediction output. The user may have to provide the value. Semantic versioning is strongly recommended.,https://semver.org/,"Comment: the version of the gene database is more typical than the software, so this should perhaps not be required"
Genetic Variation Type,Mandatory,"The type of genetic variant (e.g. gene presence, gene absence, protein variant, nucleotide variant).",String,protein_mutation,,,
Variant Frequency,Optional,The frequency of the variant in the data.,Float,0.5,,,
Nucleotide Mutation,Optional,The nucleotide sequence change(s) detected in the sequence being analyzed compared to a reference in HGVS format.,String,c.1349C>T,,,
Nucleotide Mutation Interpretation,Optional,The description of the HGVS encoded nucelotide mutation(s) for clinical interpretation. ,String,This is a subst found in rpoB at position 1349 where the reference has a C and the sample has a T,,,
Protein Mutation,Optional,The protein sequence change(s) detected in the sequence being analyzed compared to a reference in HGVS format.,String,p.Ser450Leu,,,
Protein Mutation Interpretation,Optional,The description of the HGVS encoded protein mutation(s) for clinical interpretation. ,String,This is a amino acid subst found in rpoB at position 450 where the reference has a Serine and the sample has a Leucine,,,