diff --git a/templates/arrayexpress/library construction_v1.1.0.json b/templates/arrayexpress/library construction_v1.1.0.json new file mode 100644 index 0000000..7734df3 --- /dev/null +++ b/templates/arrayexpress/library construction_v1.1.0.json @@ -0,0 +1,145 @@ +{ + "metadata": { + "name": "library construction", + "group": "arrayexpress", + "group_order": 3, + "temporary_name": "3_arrayexpress_library_construction", + "template_version": "1.1.0", + "isa_config": "genome_seq_default_v2015-07-02", + "isa_measurement_type": "genome sequencing", + "isa_technology_type": "nucleotide sequencing", + "isa_protocol_type": "library construction", + "repo_schema_id": "ENA General experiment information 2021", + "organism": "any", + "level": "assay" + }, + "data": [ + { + "name": "protocol type", + "description": "type of assay or experimental step performed.", + "required": true, + "ontology": null, + "CVList": ["library construction"] + }, + { + "name": "library source", + "description": "The LIBRARY_SOURCE specifies the type of source material that is being sequenced. (SRA 1.2 documentation)", + "required": true, + "ontology": null, + "CVList": [ + "GENOMIC", + "GENOMIC SINGLE CELL", + "TRANSCRIPTOMIC", + "TRANSCRIPTOMIC SINGLE CELL", + "METAGENOMIC", + "METATRANSCRIPTOMIC", + "SYNTHETIC", + "VIRAL RNA", + "OTHER" + ] + }, + { + "name": "library strategy", + "description": "Sequencing technique intended for this library (SRA 1.2 documentation)", + "required": true, + "ontology": null, + "CVList": [ + "WGS", + "WGA", + "WXS", + "RNA-Seq", + "ssRNA-seq", + "miRNA-Seq", + "ncRNA-Seq", + "FL-cDNA", + "EST", + "Hi-C", + "ATAC-seq", + "WCS", + "RAD-Seq", + "CLONE", + "POOLCLONE", + "AMPLICON", + "CLONEEND", + "FINISHING", + "ChIP-Seq", + "MNase-Seq", + "DNase-Hypersensitivity", + "Bisulfite-Seq", + "CTS", + "MRE-Seq", + "MeDIP-Seq", + "MBD-Seq", + "Tn-Seq", + "VALIDATION", + "FAIRE-seq", + "SELEX", + "RIP-Seq", + "ChIA-PET", + "Synthetic-Long-Read", + "Targeted-Capture", + "OTHER" + ] + }, + { + "name": "library selection", + "description": "Whether any method was used to select for or against, enrich, or screen the material being sequenced. (SRA 1.2 documentation)", + "required": true, + "ontology": null, + "CVList": [ + "RANDOM", + "PCR", + "RANDOM PCR", + "RT-PCR", + "HMPR", + "MF", + "repeat fractionation", + "size fractionation", + "MSLL", + "cDNA", + "cDNA_randomPriming", + "cDNA_oligo_dT", + "PolyA", + "Oligo-dT", + "Inverse rRNA", + "Inverse rRNA selection", + "ChIP", + "ChIP-Seq", + "MNase", + "DNase", + "Hybrid Selection", + "Reduced Representation", + "Restriction Digest", + "5-methylcytidine antibody", + "MBD2 protein methyl-CpG binding domain", + "CAGE", + "RACE", + "MDA", + "padlock probes capture method", + "other", + "unspecified" + ] + }, + { + "name": "library layout", + "description": "specifies whether to expect single, paired, or other configuration of reads.", + "required": true, + "ontology": null, + "CVList": ["SINGLE", "PAIRED"] + }, + { + "name": "library strand", + "description": "", + "required": false, + "ontology": null, + "CVList": ["first strand", "second strand", "not applicable"] + }, + { + "name": "orientation", + "description": "", + "required": false, + "ontology": null, + "CVList": ["5'-3'-3'-5'", "5'-3'-5'-3'"] + } + ] + } \ No newline at end of file diff --git a/templates/arrayexpress/nucleic acid extraction_v1.1.0.json b/templates/arrayexpress/nucleic acid extraction_v1.1.0.json new file mode 100644 index 0000000..443031c --- /dev/null +++ b/templates/arrayexpress/nucleic acid extraction_v1.1.0.json @@ -0,0 +1,52 @@ +{ + "metadata": { + "name": "nucleic acid extraction", + "group": "arrayexpress", + "group_order": 2, + "temporary_name": "2_arrayexpress_nucleic_acid_extraction", + "template_version": "1.1.0", + "isa_config": "genome_seq_default_v2015-07-02", + "isa_measurement_type": "genome sequencing", + "isa_technology_type": "nucleotide sequencing", + "isa_protocol_type": "nucleic acid extraction", + "repo_schema_id": "NA", + "organism": "any", + "level": "assay" + }, + "data": [ + { + "name": "protocol type", + "description": "type of assay or experimental step performed.", + "required": true, + "ontology": null, + "CVList": ["nucleic acid extraction"] + }, + { + "name": "sample volume or weight for DNA extraction", + "description": "Volume (mL) or weight (g) of sample processed for DNA extraction", + "required": "false", + "ontology": null, + "unit": null + }, + { + "name": "Extract Name", + "description": "User-defined names for each portion of extracted material.", + "required": true, + "ontology": null, + "CVList": null + }, + { + "name": "Material type", + "description": "This column contains terms describing the type of each material, for examples: whole organism, organism part, cell, total RNA.", + "required": true, + "ontology": null, + "CVList": [ + "whole organism", + "organism part", + "RNA", + "DNA", + "cell" + ] + } + ] +} \ No newline at end of file diff --git a/templates/arrayexpress/nucleic acid sequencing_v1.1.0.json b/templates/arrayexpress/nucleic acid sequencing_v1.1.0.json new file mode 100644 index 0000000..aa58ea2 --- /dev/null +++ b/templates/arrayexpress/nucleic acid sequencing_v1.1.0.json @@ -0,0 +1,115 @@ +{ + "metadata": { + "name": "nucleic acid sequencing", + "group": "arrayexpress", + "group_order": 4, + "temporary_name": "4_arrayexpress_nucleic_acid_sequencing", + "template_version": "1.1.0", + "isa_config": "genome_seq_default_v2015-07-02", + "isa_measurement_type": "genome sequencing", + "isa_technology_type": "nucleotide sequencing", + "isa_protocol_type": "nucleic acid sequencing", + "repo_schema_id": "ENA General experiment information 2021", + "organism": "any", + "level": "assay" + }, + "data": [ + { + "name": "protocol type", + "description": "type of assay or experimental step performed.", + "required": true, + "ontology": null, + "CVList": ["nucleic acid sequencing"] + }, + { + "name": "sequencing instrument", + "description": "a parameter to report the sequencing instrument model and make", + "required": "false", + "ontology": null, + "CVList": [ + "454 GS", + "454 GS 20", + "454 GS FLX", + "454 GS FLX+", + "454 GS FLX Titanium", + "454 GS Junior", + "HiSeq X Five", + "HiSeq X Ten", + "Illumina Genome Analyzer", + "Illumina Genome Analyzer II", + "Illumina Genome Analyzer IIx", + "Illumina HiScanSQ", + "Illumina HiSeq 1000", + "Illumina HiSeq 1500", + "Illumina HiSeq 2000", + "Illumina HiSeq 2500", + "Illumina HiSeq 3000", + "Illumina HiSeq 4000", + "Illumina iSeq 100", + "Illumina MiSeq", + "Illumina MiniSeq", + "Illumina NovaSeq 6000", + "NextSeq 500", + "NextSeq 550", + "PacBio RS", + "PacBio RS II", + "Sequel", + "Ion Torrent PGM", + "Ion Torrent Proton", + "Ion Torrent S5", + "Ion Torrent S5 XL", + "AB 3730xL Genetic Analyzer", + "AB 3730 Genetic Analyzer", + "AB 3500xL Genetic Analyzer", + "AB 3500 Genetic Analyzer", + "AB 3130xL Genetic Analyzer", + "AB 3130 Genetic Analyzer", + "AB 310 Genetic Analyzer", + "MinION", + "GridION", + "PromethION", + "BGISEQ-500", + "DNBSEQ-T7", + "DNBSEQ-G400", + "DNBSEQ-G50", + "DNBSEQ-G400 FAST", + "unspecified" + ] + }, + { + "name": "quality scorer", + "description": "Name and version of the quality scoring software.", + "required": "false", + "ontology": null, + "CVList": null + }, + { + "name": "base caller", + "description": "Name and version of the base or color calling software.", + "required": "false", + "ontology": null, + "CVList": null + }, + { + "name": "Assay Name", + "description": "User-defined name for an assay.", + "required": true, + "ontology": null, + "CVList": null + }, + { + "name": "Technology type", + "description": "", + "required": true, + "ontology": null, + "CVList": ["sequencing assay"] + }, + { + "name": "Raw Data File", + "description": "or Array Data File: Name (or URI) of the raw data file generated by an assay.", + "required": true, + "ontology": null, + "CVList": null + } + ] +} diff --git a/templates/arrayexpress/plant_v1.0.0.json b/templates/arrayexpress/plant_v1.1.0.json similarity index 60% rename from templates/arrayexpress/plant_v1.0.0.json rename to templates/arrayexpress/plant_v1.1.0.json index 4d1c3bd..5d5f391 100644 --- a/templates/arrayexpress/plant_v1.0.0.json +++ b/templates/arrayexpress/plant_v1.1.0.json @@ -1,275 +1,436 @@ -[ +{ + "metadata": { + "name": "plant", + "group": "arrayexpress", + "group_order": 1, + "temporary_name": "1_arrayexpress_plant", + "template_version": "1.1.0", + "isa_config": "studySample_default_v2015-07-02", + "isa_measurement_type": "Sample", + "isa_technology_type": "NA", + "isa_protocol_type": "sample collection", + "repo_schema_id": "Annotare-default.properties", + "organism": "plant", + "level": "study" + }, + "data":[ { "name": "Source Name", "description": "Sources are considered as the starting biological material used in a study.", - "dataType": "String", "required": true }, { "name": "organism", "description": "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. E.g Drosophila melanogaster.", "required": true, - "ontology": "http://purl.obolibrary.org/obo/OBI_0100026", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/OBI_0100026" + } }, { "name": "organism part", "description": "The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm).", "required": true, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000635", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000635" + } }, { "name": "developmental stage", "description": "A developmental stage is spatiotemporal region encompassing some part of the life cycle of an organism, e.g. blastula stage", "required": true, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000399", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000399" + } }, { "name": "age", "description": "A temporal measurement of the time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting).", "required": true, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000246", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000246" + } }, { "name": "genotype", "description": "The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.", "required": true, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000513", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000513" + } }, { "name": "cultivar", "description": "A cultivated plant variety selected and given a name because it has desirable characteristics that distinguish it from otherwise similar plants of the same species.", "required": true, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0005136", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0005136" + } }, { "name": "cultured cell", "description": "A cell in vitro that is or has been maintained or propagated as part of a cell culture.", "required": false, - "ontology": "http://purl.obolibrary.org/obo/CL_0000010", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/CL_0000010" + } }, { "name": "cell type", "description": "A cell type is a distinct morphological or functional form of cell. Examples are epithelial, glial etc.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000324", - "dataType": "ontology term" - }, + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000324" + } + }, { "name": "clinical history", "description": "Is an information entity about the material's (i.e., the patient's) medical record as background information relevant to the experiment.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000352", - "dataType": "onntology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000352" + } }, { "name": "chemical entity", "description": "A drug, solvent, chemical, etc., with a property that can be measured such as concentration. A molecular entity consisting of two or more chemical elements.", "required": false, - "ontology": "http://purl.obolibrary.org/obo/CHEBI_24431", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/CHEBI_24431" + } }, { "name": "diet", "description": "The customary allowance of food and drink taken by a person or an animal from day to day, particularly one especially planned to meet specific requirements of the individual, including or excluding certain items of food; a prescribed course of eating and drinking in which the amount and kind of food, as well as the times at which it is to be taken, are regulated for therapeutic purposes or selected with reference to a particular state of health. Regular course of eating and drinking adopted by a person or animal. This does not include DIET THERAPY, a specific diet prescribed in the treatment of a disease.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0002755", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0002755" + } }, { "name": "disease", "description": "A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. [ OGMS:0000031 ]", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000408", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000408" + } }, { "name": "disease staging", "description": "The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression. E.g. Dukes C stage describing colon cancer.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000410", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000410" + } }, { "name": "dose", "description": "The total quantity or strength of a substance administered at one time.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000428", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000428" + } }, { "name": "ecotype", "description": "A biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000434", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000434" + } }, { "name": "enviromental history", "description": "Information concerning the envinonrment a material entity has been exposed to, such as an organism from a lake.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0004444", - "dataType": "organism term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0004444" + } }, { "name": "enviromental stress treatment", "description": "Environmental stress is a treatment where some aspect of the environment is perturbed in order to stress the organism or culture, e.g. change in temperature, change in watering regime.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000470", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000470" + } }, { "name": "fraction", "description": "Definition: A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator). [Wikipedia]", "required": false, - "ontology": "http://purl.obolibrary.org/obo/UO_0000191", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/UO_0000191" + } }, { "name": "genetic modification", "description": "A genetic modification of the genome of an organism which may occur naturally by spontaneous mutation, or be introduced by some experimental means. Examples of genetic modification include specification of a transgene or the gene knocked-out or details of transient transfection.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000510", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000510" + } }, { "name": "growth condition", "description": "A role that a material entity can play which enables particular conditions used to grow organisms or parts of the organism. This includes isolated environments such as cultures and open environments such as field studies.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000523", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000523" + } }, { "name": "immunoprecipitate", "description": "The precipitate antibody bound target molecules generated when precipitating an antigen out of a solution during the process of immunoprecipitation.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000541", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000541" + } }, { "name": "individual", "description": "An individual used a specimen in an experiment, from which a material sample was derived.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000542", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000542" + } }, { "name": "infection", "description": "The state of being infected such as from the introduction of a foreign agent such as serum, vaccine, antigenic substance or organism.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000544", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000544" + } }, { "name": "inferred cell type", "description": "A cell type classification that is determined as result of a single-cell analysis, such as cell clustering or trajectory analysis.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0010196", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0010196" + } }, { "name": "injury", "description": "Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. [ NCIT:C3671 ]", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000546", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000546" + } }, { "name": "irradiate", "description": "The process of treating a material with radiation.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000554", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000554" + } }, { "name": "karyotype", "description": "A karyotype is the number and appearance of chromosomes in the nucleus of a eukaryotic cell.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0004426", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0004426" + } }, { "name": "phenotype", "description": "The observable form taken by some character (or group of characters) in an individual or an organism, excluding pathology and disease. The detectable outward manifestations of a specific genotype.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000651", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000651" + } }, { "name": "RNA interference", "description": "The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes.", "required": false, - "ontology": "http://purl.obolibrary.org/obo/GO_0016246", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/GO_0016246" + } }, { "name": "replicate", "description": "A role played by a a biological sample in the context of an experiment where the intent is that biological or technical variation is measured.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000683", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000683" + } }, { "name": "sampling site", "description": "A site from which a sample, i.e. a statistically representative of the whole, is extracted from the whole. e.g. a liver sample.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000688", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000688" + } }, { "name": "sex", "description": "The assemblage of physical properties or qualities by which male is distinguished from female; the physical difference between male and female; the distinguishing peculiarity of male or female. An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny.", "required": false, - "ontology": "http://purl.obolibrary.org/obo/PATO_0000047", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/PATO_0000047" + } }, { "name": "single cell identifier", "description": "A unique identifier for a single cell specimen.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0010197", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0010197" + } }, { "name": "specimen with known storage state", "description": "A specimen for which it is known whether it has been subjected to storage of a specified type.", "required": false, - "ontology": "http://purl.obolibrary.org/obo/OBI_0001472", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/OBI_0001472" + } }, { "name": "strain", "description": "A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics.", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0005135", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0005135" + } }, { "name": "time", "description": "", "required": false, - "ontology": "http://www.ebi.ac.uk/efo/EFO_0000721", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://www.ebi.ac.uk/efo/EFO_0000721" + } }, { "name": "tumor grading", "description": "An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. Determination of the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus.", "required": false, - "ontology": "http://purl.obolibrary.org/obo/OBI_0600002", - "dataType": "ontology term" + "ontology": { + "name": "efo", + "version": "1", + "description": "Experimental Factor Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/OBI_0600002" + } }, { "name": "material type", "description": "Used as an attribute column following Source Name, Sample Name, Extract Name, or Labeled Extract Name. This column contains terms describing the type of each material, for examples: whole organism, organism part, cell, total RNA.", "required": true, "ontology": null, - "dataType": "string", "CVList": ["whole organism, organism part, RNA, DNA, cell"] }, { @@ -277,14 +438,13 @@ "description": "type of assay or experimental step performed.", "required": true, "ontology": null, - "dataType": "string", "CVList": ["sample collection"] }, { "name": "Sample Name", "description": "Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.", "required": true, - "ontology": null, - "dataType": "string" + "ontology": null } -] \ No newline at end of file +] +} \ No newline at end of file diff --git a/templates/ena/all_organisms_v1.1.0.json b/templates/ena/all_organisms_v1.1.0.json new file mode 100644 index 0000000..6e1114f --- /dev/null +++ b/templates/ena/all_organisms_v1.1.0.json @@ -0,0 +1,552 @@ +{ + "metadata": { + "name": "all organisms", + "group": "ena", + "group_order": 1, + "temporary_name": "1_ena_all_organisms", + "template_version": "1.1.0", + "isa_config": "genome_seq_default_v2015-07-02", + "isa_measurement_type": "genome sequencing", + "isa_technology_type": "nucleotide sequencing", + "isa_protocol_type": "sample collection", + "repo_schema_id": "ERC000011.xml 2021", + "organism": "any", + "level": "study" + }, + "data": [ + { + "name": "Source Name", + "description": "Sources are considered as the starting biological material used in a study.", + "dataType": "String", + "required": "true" + }, + { + "name": "tax_id", //First field on an ENA sample file. It is the number ID + "description": "NCBI Taxonomy Identifier. This is appropriate for individual organisms and some environmental samples.", + "dataType": "Ontology term", + "required": true, + "ontology": { + "name": "NCBITAXON", + "version": "", + "description": "NCBI organismal classification", + "rootTermURI": "http://purl.obolibrary.org/obo/ncbitaxon.owl"} + }, + { + "name": "organism", + "description": "Provide a taxonomic information associated to the Source Biological material (for example, Species, genus, strain,....). Ideally, provide NCBI TaxID or NEWT identifier", //Changed to the description from ENA + "dataType": "Ontology term", + "required": false, + "ontology": { + "name": "NCBITAXON", + "version": "", + "description": "NCBI organismal classification", + "rootTermURI": "http://purl.obolibrary.org/obo/ncbitaxon.owl"} + }, + { + "name": "cell_type", + "description": "cell type from which the sample was obtained", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "dev_stage", + "description": "if the sample was obtained from an organism in a specific developmental stage, it is specified with this qualifier", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "germline", + "description": "the sample described presented in the entry has not undergone somatic genomic rearrangement as part of an adaptive immune response; it is the unrearranged molecule that was inherited from the parental germline", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "tissue_lib", + "description": "tissue library from which sample was obtained", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "tissue_type", + "description": "tissue type from which the sample was obtained", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "collection_date", + "description": "date that the specimen was collected", + "dataType": "^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$", + "required": false, + "ontology": null + }, + { + "name": "isolation_source", + "description": "describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "lat_lon", + "description": "geographical coordinates of the location where the specimen was collected", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "collected_by", + "description": "name of persons or institute who collected the specimen", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "geographic location (country and/or sea)", + "description": "The geographical origin of the sample as defined by the country or sea. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).", + "required": false, + "ontology": "http://insdc.org/country.html", + "dataType": "string", + "CVList": [ + "Afghanistan", + "Albania", + "Algeria", + "American Samoa", + "Andorra", + "Angola", + "Anguilla", + "Antarctica", + "Antigua and Barbuda", + "Arctic Ocean", + "Argentina", + "Armenia", + "Aruba", + "Ashmore and Cartier Islands", + "Atlantic Ocean", + "Australia", + "Austria", + "Azerbaijan", + "Bahamas", + "Bahrain", + "Baker Island", + "Baltic Sea", + "Bangladesh", + "Barbados", + "Bassas da India", + "Belarus", + "Belgium", + "Belize", + "Benin", + "Bermuda", + "Bhutan", + "Bolivia", + "Borneo", + "Bosnia and Herzegovina", + "Botswana", + "Bouvet Island", + "Brazil", + "British Virgin Islands", + "Brunei", + "Bulgaria", + "Burkina Faso", + "Burundi", + "Cambodia", + "Cameroon", + "Canada", + "Cape Verde", + "Cayman Islands", + "Central African Republic", + "Chad", + "Chile", + "China", + "Christmas Island", + "Clipperton Island", + "Cocos Islands", + "Colombia", + "Comoros", + "Cook Islands", + "Coral Sea Islands", + "Costa Rica", + "Cote d'Ivoire", + "Croatia", + "Cuba", + "Curacao", + "Cyprus", + "Czech Republic", + "Democratic Republic of the Congo", + "Denmark", + "Djibouti", + "Dominica", + "Dominican Republic", + "East Timor", + "Ecuador", + "Egypt", + "El Salvador", + "Equatorial Guinea", + "Eritrea", + "Estonia", + "Ethiopia", + "Europa Island", + "Falkland Islands (Islas Malvinas)", + "Faroe Islands", + "Fiji", + "Finland", + "France", + "French Guiana", + "French Polynesia", + "French Southern and Antarctic Lands", + "Gabon", + "Gambia", + "Gaza Strip", + "Georgia", + "Germany", + "Ghana", + "Gibraltar", + "Glorioso Islands", + "Greece", + "Greenland", + "Grenada", + "Guadeloupe", + "Guam", + "Guatemala", + "Guernsey", + "Guinea", + "Guinea-Bissau", + "Guyana", + "Haiti", + "Heard Island and McDonald Islands", + "Honduras", + "Hong Kong", + "Howland Island", + "Hungary", + "Iceland", + "India", + "Indian Ocean", + "Indonesia", + "Iran", + "Iraq", + "Ireland", + "Isle of Man", + "Israel", + "Italy", + "Jamaica", + "Jan Mayen", + "Japan", + "Jarvis Island", + "Jersey", + "Johnston Atoll", + "Jordan", + "Juan de Nova Island", + "Kazakhstan", + "Kenya", + "Kerguelen Archipelago", + "Kingman Reef", + "Kiribati", + "Kosovo", + "Kuwait", + "Kyrgyzstan", + "Laos", + "Latvia", + "Lebanon", + "Lesotho", + "Liberia", + "Libya", + "Liechtenstein", + "Lithuania", + "Luxembourg", + "Macau", + "Macedonia", + "Madagascar", + "Malawi", + "Malaysia", + "Maldives", + "Mali", + "Malta", + "Marshall Islands", + "Martinique", + "Mauritania", + "Mauritius", + "Mayotte", + "Mediterranean Sea", + "Mexico", + "Micronesia", + "Midway Islands", + "Moldova", + "Monaco", + "Mongolia", + "Montenegro", + "Montserrat", + "Morocco", + "Mozambique", + "Myanmar", + "Namibia", + "Nauru", + "Navassa Island", + "Nepal", + "Netherlands", + "New Caledonia", + "New Zealand", + "Nicaragua", + "Niger", + "Nigeria", + "Niue", + "Norfolk Island", + "North Korea", + "North Sea", + "Northern Mariana Islands", + "Norway", + "Oman", + "Pacific Ocean", + "Pakistan", + "Palau", + "Palmyra Atoll", + "Panama", + "Papua New Guinea", + "Paracel Islands", + "Paraguay", + "Peru", + "Philippines", + "Pitcairn Islands", + "Poland", + "Portugal", + "Puerto Rico", + "Qatar", + "Republic of the Congo", + "Reunion", + "Romania", + "Ross Sea", + "Russia", + "Rwanda", + "Saint Helena", + "Saint Kitts and Nevis", + "Saint Lucia", + "Saint Pierre and Miquelon", + "Saint Vincent and the Grenadines", + "Samoa", + "San Marino", + "Sao Tome and Principe", + "Saudi Arabia", + "Senegal", + "Serbia", + "Seychelles", + "Sierra Leone", + "Singapore", + "Sint Maarten", + "Slovakia", + "Slovenia", + "Solomon Islands", + "Somalia", + "South Africa", + "South Georgia and the South Sandwich Islands", + "South Korea", + "Southern Ocean", + "Spain", + "Spratly Islands", + "Sri Lanka", + "Sudan", + "Suriname", + "Svalbard", + "Swaziland", + "Sweden", + "Switzerland", + "Syria", + "Taiwan", + "Tajikistan", + "Tanzania", + "Tasman Sea", + "Thailand", + "Togo", + "Tokelau", + "Tonga", + "Trinidad and Tobago", + "Tromelin Island", + "Tunisia", + "Turkey", + "Turkmenistan", + "Turks and Caicos Islands", + "Tuvalu", + "USA", + "Uganda", + "Ukraine", + "United Arab Emirates", + "United Kingdom", + "Uruguay", + "Uzbekistan", + "Vanuatu", + "Venezuela", + "Viet Nam", + "Virgin Islands", + "Wake Island", + "Wallis and Futuna", + "West Bank", + "Western Sahara", + "Yemen", + "Zambia", + "Zimbabwe", + "not applicable", + "not collected", + "not provided", + "restricted access" + ] + }, + { + "name": "geographic location (region and locality)", + "description": "The geographical origin of the sample as defined by the specific region name followed by the locality name.", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "identified_by", + "description": "name of the expert who identified the specimen taxonomically", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "environmental_sample", + "description": "identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism", + "dataType": "string", + "required": false, + "ontology": null, + "CVList": ["No", "Yes"] + }, + { + "name": "mating_type", + "description": "mating type of the organism from which the sequence was obtained; mating type is used for prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "sex", + "description": "sex of the organism from which the sample was obtained", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "lab_host", + "description": "scientific name of the laboratory host used to propagate the source organism from which the sample was obtained", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "host scientific name", + "description": "Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "bio_material", + "description": "identifier for the biological material from which the sample was obtained, with optional institution code and collection code for the place where it is currently stored.", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "culture_collection", + "description": "institution code and identifier for the culture from which the sample was obtained, with optional collection code.", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "specimen_voucher", + "description": "identifier for the specimen from which the sample was obtained", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "cultivar", + "description": "cultivar (cultivated variety) of plant from which sample was obtained", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "ecotype", + "description": "a population within a given species displaying genetically based, phenotypic traits that reflect adaptation to a local habitat.", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "isolate", + "description": "individual isolate from which the sample was obtained", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "sub_species", + "description": "name of sub-species of organism from which sample was obtained", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "variety", + "description": "variety (= varietas, a formal Linnaean rank) of organism from which sample was derived.", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "sub_strain", + "description": "name or identifier of a genetically or otherwise modified strain from which sample was obtained, derived from a parental strain (which should be annotated in the strain field; sub_strain from which sample was obtained", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "cell_line", + "description": "cell line from which the sample was obtained", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "serotype", + "description": "serological variety of a species characterized by its antigenic properties", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "serovar", + "description": "serological variety of a species (usually a prokaryote) characterized by its antigenic properties", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "strain", + "description": "Name of the strain from which the sample was obtained.", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "protocol type", + "description": "type of assay or experimental step performed.", + "dataType": "string", + "required": true, + "ontology": null, + "CVList": ["sample collection"] + }, + { + "name": "Sample Name", + "description": "Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.", + "dataType": "String", + "required": true + } +] +} \ No newline at end of file diff --git a/templates/ena/library construction_v1.1.0.json b/templates/ena/library construction_v1.1.0.json new file mode 100644 index 0000000..eb68675 --- /dev/null +++ b/templates/ena/library construction_v1.1.0.json @@ -0,0 +1,99 @@ +{ + "metadata": { + "name": "library construction", + "group": "ena", + "group_order": 3, + "temporary_name": "3_ena_library_construction", + "template_version": "1.1.0", + "isa_config": "genome_seq_default_v2015-07-02", + "isa_measurement_type": "genome sequencing", + "isa_technology_type": "nucleotide sequencing", + "isa_protocol_type": "library construction", + "repo_schema_id": "ENA General experiment information 2021", + "organism": "any", + "level": "assay" + }, + "data": [ + { + "name": "protocol type", + "description": "type of assay or experimental step performed.", + "required": true, + "ontology": null, + "CVList": ["library construction"] + }, + { + "name": "library source", + "description": "The LIBRARY_SOURCE specifies the type of source material that is being sequenced. (SRA 1.2 documentation)", + "dataType": "String", + "required": false, + "ontology": null, + "CVList": [ + "GENOMIC", + "GENOMIC SINGLE CELL", + "TRANSCRIPTOMIC", + "TRANSCRIPTOMIC SINGLE CELL", + "METAGENOMIC", + "METATRANSCRIPTOMIC", + "SYNTHETIC", + "VIRAL RNA", + "OTHER" + ] + }, + { + "name": "library strategy", + "description": "Sequencing technique intended for this library (SRA 1.2 documentation)", + "dataType": "List", + "required": false, + "ontology": null, + "CVList": ["AMPLICON", "CLONE", "WGS", "OTHER"] + }, + { + "name": "library selection", + "description": "Whether any method was used to select for or against, enrich, or screen the material being sequenced. (SRA 1.2 documentation)", + "dataType": "List", + "required": false, + "ontology": null, + "CVList": [ + "RANDOM", + "PCR", + "RANDOM PCR", + "RT-PCR", + "HMPR", + "MF", + "repeat fractionation", + "size fractionation", + "MSLL", + "cDNA", + "cDNA_randomPriming", + "cDNA_oligo_dT", + "PolyA", + "Oligo-dT", + "Inverse rRNA", + "Inverse rRNA selection", + "ChIP", + "ChIP-Seq", + "MNase", + "DNase", + "Hybrid Selection", + "Reduced Representation", + "Restriction Digest", + "5-methylcytidine antibody", + "MBD2 protein methyl-CpG binding domain", + "CAGE", + "RACE", + "MDA", + "padlock probes capture method", + "other", + "unspecified" + ] + }, + { + "name": "library layout", + "description": "specifies whether to expect single, paired, or other configuration of reads.", + "dataType": "List", + "required": false, + "ontology": null, + "CVList": ["SINGLE", "PAIRED"] + } + ] +} \ No newline at end of file diff --git a/templates/ena/nucleic acid extraction_v1.1.0.json b/templates/ena/nucleic acid extraction_v1.1.0.json new file mode 100644 index 0000000..8a081a0 --- /dev/null +++ b/templates/ena/nucleic acid extraction_v1.1.0.json @@ -0,0 +1,41 @@ +{ + "metadata": { + "name": "nucleic acid extraction", + "group": "ena", + "group_order": 2, + "temporary_name": "2_ena_nucleic_acid_extraction", + "template_version": "1.1.0", + "isa_config": "genome_seq_default_v2015-07-02", + "isa_measurement_type": "genome sequencing", + "isa_technology_type": "nucleotide sequencing", + "isa_protocol_type": "nucleic acid extraction", + "repo_schema_id": "ENA General experiment information 2021", + "organism": "any", + "level": "assay" + }, + "data": [ + { + "name": "sample volume or weight for DNA extraction", + "description": "Volume (mL) or weight (g) of sample processed for DNA extraction", + "required": false, + "ontology": null, + "dataType": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?", + "unit": ["mL","g"] + }, + { + "name": "protocol type", + "description": "type of assay or experimental step performed.", + "required": true, + "ontology": null, + "CVList": ["nucleic acid extraction"] + }, + { + "name": "Extract Name", + "description": "User-defined names for each portion of extracted material.", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null + } + ] +} \ No newline at end of file diff --git a/templates/ena/nucleic acid sequencing_v1.1.0.json b/templates/ena/nucleic acid sequencing_v1.1.0.json new file mode 100644 index 0000000..fbfd113 --- /dev/null +++ b/templates/ena/nucleic acid sequencing_v1.1.0.json @@ -0,0 +1,113 @@ +{ + "metadata": { + "name": "nucleic acid sequencing", + "group": "ena", + "group_order": 4, + "temporary_name": "4_ena_nucleic_acid_sequencing", + "template_version": "1.1.0", + "isa_config": "genome_seq_default_v2015-07-02", + "isa_measurement_type": "genome sequencing", + "isa_technology_type": "nucleotide sequencing", + "isa_protocol_type": "nucleic acid sequencing", + "repo_schema_id": "ENA General experiment information 2021", + "organism": "any", + "level": "assay" + }, + "data": [ + { + "name": "protocol type", + "description": "type of assay or experimental step performed.", + "required": true, + "ontology": null, + "CVList": ["nucleic acid sequencing"] + }, + { + "name": "sequencing instrument", + "description": "a parameter to report the sequencing instrument model and make", + "dataType": "List", + "required": false, + "ontology": null, + "CVList": [ + " 454 GS", + " 454 GS 20", + " 454 GS FLX", + " 454 GS FLX+", + " 454 GS FLX Titanium", + " 454 GS Junior", + " HiSeq X Five", + " HiSeq X Ten", + " Illumina Genome Analyzer", + " Illumina Genome Analyzer II", + " Illumina Genome Analyzer IIx", + " Illumina HiScanSQ", + " Illumina HiSeq 1000", + " Illumina HiSeq 1500", + " Illumina HiSeq 2000", + " Illumina HiSeq 2500", + " Illumina HiSeq 3000", + " Illumina HiSeq 4000", + " Illumina iSeq 100", + " Illumina MiSeq", + " Illumina MiniSeq", + " Illumina NovaSeq 6000", + " NextSeq 500", + " NextSeq 550", + " PacBio RS", + " PacBio RS II", + " Sequel", + " Ion Torrent PGM", + " Ion Torrent Proton", + " Ion Torrent S5", + " Ion Torrent S5 XL", + " AB 3730xL Genetic Analyzer", + " AB 3730 Genetic Analyzer", + " AB 3500xL Genetic Analyzer", + " AB 3500 Genetic Analyzer", + " AB 3130xL Genetic Analyzer", + " AB 3130 Genetic Analyzer", + " AB 310 Genetic Analyzer", + " MinION", + " GridION", + " PromethION", + " BGISEQ-500", + " DNBSEQ-T7", + " DNBSEQ-G400", + " DNBSEQ-G50", + " DNBSEQ-G400 FAST", + " unspecified" + ] + }, + { + "name": "quality scorer", + "description": "ENA term if applicable", + "dataType": "Ontology term", + "required": false, + "ontology": null, + "CVList": null + }, + { + "name": "base caller", + "description": "ENA term if applicable", + "dataType": "Ontology term", + "required": false, + "ontology": null, + "CVList": null + }, + { + "name": "Assay Name", + "description": "assayname", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null + }, + { + "name": "Raw Data File", + "description": "raw data", + "dataType": "String", + "required": false, + "ontology": null, + "CVList": null + } + ] +} diff --git a/templates/ena/all_organisms_v1.0.0.json b/templates/ena/older versions/all_organisms_v1.0.0.json similarity index 100% rename from templates/ena/all_organisms_v1.0.0.json rename to templates/ena/older versions/all_organisms_v1.0.0.json diff --git a/templates/ena/library construction_v1.0.0.json b/templates/ena/older versions/library construction_v1.0.0.json similarity index 100% rename from templates/ena/library construction_v1.0.0.json rename to templates/ena/older versions/library construction_v1.0.0.json diff --git a/templates/ena/nucleic acid extraction_v1.0.0.json b/templates/ena/older versions/nucleic acid extraction_v1.0.0.json similarity index 100% rename from templates/ena/nucleic acid extraction_v1.0.0.json rename to templates/ena/older versions/nucleic acid extraction_v1.0.0.json diff --git a/templates/ena/nucleic acid sequencing_v1.0.0.json b/templates/ena/older versions/nucleic acid sequencing_v1.0.0.json similarity index 100% rename from templates/ena/nucleic acid sequencing_v1.0.0.json rename to templates/ena/older versions/nucleic acid sequencing_v1.0.0.json diff --git a/templates/ena/plant_v1.0.0.json b/templates/ena/older versions/plant_v1.0.0.json similarity index 100% rename from templates/ena/plant_v1.0.0.json rename to templates/ena/older versions/plant_v1.0.0.json diff --git a/templates/ena/sequence assembly_v1.0.0.json b/templates/ena/older versions/sequence assembly_v1.0.0.json similarity index 100% rename from templates/ena/sequence assembly_v1.0.0.json rename to templates/ena/older versions/sequence assembly_v1.0.0.json diff --git a/templates/ena/plant_v1.1.0.json b/templates/ena/plant_v1.1.0.json new file mode 100644 index 0000000..c8efab6 --- /dev/null +++ b/templates/ena/plant_v1.1.0.json @@ -0,0 +1,1105 @@ +{ + "metadata": { + "name": "plant", + "group": "ena", + "group_order": 1, + "temporary_name": "1_ena_plant", + "template_version": "1.1.0", + "isa_config": "genome_seq_default_v2015-07-02", + "isa_measurement_type": "genome sequencing", + "isa_technology_type": "nucleotide sequencing", + "isa_protocol_type": "sample collection", + "repo_schema_id": "ERC000037.xml 2021", + "organism": "plant", + "level": "study" + }, + "data": [ + { + "name": "Source Name", + "description": "Sources are considered as the starting biological material used in a study.", + "dataType": "String", + "required": true + }, + { + "name": "tax_id", //First field on an ENA sample file. It is the number ID + "description": "NCBI Taxonomy Identifier. This is appropriate for individual organisms and some environmental samples.", + "dataType": "Ontology term", + "required": true, + "ontology": { + "name": "NCBITAXON", + "version": "", + "description": "NCBI organismal classification", + "rootTermURI": "http://purl.obolibrary.org/obo/ncbitaxon.owl"} + }, + { + "name": "organism", + "description": "Scientific name of sample that distinguishes its taxonomy. Please use a name or synonym that is tracked in the INSDC Taxonomy database. Also, this field can be used to confirm the TAXON_ID setting.", //Changed to the description from ENA + "dataType": "Ontology term", + "required": false, + "ontology": { + "name": "NCBITAXON", + "version": "", + "description": "NCBI organismal classification", + "rootTermURI": "http://purl.obolibrary.org/obo/ncbitaxon.owl"} + }, + { + "name": "ploidy", + "description": "The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2013-10-28) please refer to http://purl.bioontology.org/ontology/PATO. Mandatory for MIGS of eukaryotes.", + "dataType": "string", + "required": true, + "ontology": { + "name": "PATO", + "version": "", + "description": "Phenotype And Trait Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/PATO_0001374"} + }, + { + "name": "number of replicons", + "description": "Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.", + "dataType": "[+-]?[0-9]+", + "required": true, + "ontology": null + }, + { + "name": "extrachromosomal elements", + "description": "Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).", + "dataType": "[+-]?[0-9]+", + "required": false, + "ontology": null + }, + { + "name": "estimated size", + "description": "The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.", + "dataType": "[+-]?[0-9]+", + "required": true, + "ontology": null, + "unit": ["bp"] + }, + { + "name": "collected_by", + "description": "name of persons or institute who collected the specimen", + "dataType": "string", + "required": false, + "ontology": null, + }, + { + "name": "collection date", + "description": "The date of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.", + "dataType": "(^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not collected$)|(^not provided$)|(^restricted access$)", + "required": true, + "ontology": null + }, + { + "name": "geographic location (altitude)", + "description": "The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.", + "dataType": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?", + "required": false, + "ontology": null + }, + { + "name": "geographic location (country and/or sea)", + "description": "The geographical origin of the sample as defined by the country or sea. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).", + "required": true, + "ontology": "http://insdc.org/country.html", + "dataType": "string", + "CVList": [ + "Afghanistan", + "Albania", + "Algeria", + "American Samoa", + "Andorra", + "Angola", + "Anguilla", + "Antarctica", + "Antigua and Barbuda", + "Arctic Ocean", + "Argentina", + "Armenia", + "Aruba", + "Ashmore and Cartier Islands", + "Atlantic Ocean", + "Australia", + "Austria", + "Azerbaijan", + "Bahamas", + "Bahrain", + "Baker Island", + "Baltic Sea", + "Bangladesh", + "Barbados", + "Bassas da India", + "Belarus", + "Belgium", + "Belize", + "Benin", + "Bermuda", + "Bhutan", + "Bolivia", + "Borneo", + "Bosnia and Herzegovina", + "Botswana", + "Bouvet Island", + "Brazil", + "British Virgin Islands", + "Brunei", + "Bulgaria", + "Burkina Faso", + "Burundi", + "Cambodia", + "Cameroon", + "Canada", + "Cape Verde", + "Cayman Islands", + "Central African Republic", + "Chad", + "Chile", + "China", + "Christmas Island", + "Clipperton Island", + "Cocos Islands", + "Colombia", + "Comoros", + "Cook Islands", + "Coral Sea Islands", + "Costa Rica", + "Cote d'Ivoire", + "Croatia", + "Cuba", + "Curacao", + "Cyprus", + "Czech Republic", + "Democratic Republic of the Congo", + "Denmark", + "Djibouti", + "Dominica", + "Dominican Republic", + "East Timor", + "Ecuador", + "Egypt", + "El Salvador", + "Equatorial Guinea", + "Eritrea", + "Estonia", + "Ethiopia", + "Europa Island", + "Falkland Islands (Islas Malvinas)", + "Faroe Islands", + "Fiji", + "Finland", + "France", + "French Guiana", + "French Polynesia", + "French Southern and Antarctic Lands", + "Gabon", + "Gambia", + "Gaza Strip", + "Georgia", + "Germany", + "Ghana", + "Gibraltar", + "Glorioso Islands", + "Greece", + "Greenland", + "Grenada", + "Guadeloupe", + "Guam", + "Guatemala", + "Guernsey", + "Guinea", + "Guinea-Bissau", + "Guyana", + "Haiti", + "Heard Island and McDonald Islands", + "Honduras", + "Hong Kong", + "Howland Island", + "Hungary", + "Iceland", + "India", + "Indian Ocean", + "Indonesia", + "Iran", + "Iraq", + "Ireland", + "Isle of Man", + "Israel", + "Italy", + "Jamaica", + "Jan Mayen", + "Japan", + "Jarvis Island", + "Jersey", + "Johnston Atoll", + "Jordan", + "Juan de Nova Island", + "Kazakhstan", + "Kenya", + "Kerguelen Archipelago", + "Kingman Reef", + "Kiribati", + "Kosovo", + "Kuwait", + "Kyrgyzstan", + "Laos", + "Latvia", + "Lebanon", + "Lesotho", + "Liberia", + "Libya", + "Liechtenstein", + "Lithuania", + "Luxembourg", + "Macau", + "Macedonia", + "Madagascar", + "Malawi", + "Malaysia", + "Maldives", + "Mali", + "Malta", + "Marshall Islands", + "Martinique", + "Mauritania", + "Mauritius", + "Mayotte", + "Mediterranean Sea", + "Mexico", + "Micronesia", + "Midway Islands", + "Moldova", + "Monaco", + "Mongolia", + "Montenegro", + "Montserrat", + "Morocco", + "Mozambique", + "Myanmar", + "Namibia", + "Nauru", + "Navassa Island", + "Nepal", + "Netherlands", + "New Caledonia", + "New Zealand", + "Nicaragua", + "Niger", + "Nigeria", + "Niue", + "Norfolk Island", + "North Korea", + "North Sea", + "Northern Mariana Islands", + "Norway", + "Oman", + "Pacific Ocean", + "Pakistan", + "Palau", + "Palmyra Atoll", + "Panama", + "Papua New Guinea", + "Paracel Islands", + "Paraguay", + "Peru", + "Philippines", + "Pitcairn Islands", + "Poland", + "Portugal", + "Puerto Rico", + "Qatar", + "Republic of the Congo", + "Reunion", + "Romania", + "Ross Sea", + "Russia", + "Rwanda", + "Saint Helena", + "Saint Kitts and Nevis", + "Saint Lucia", + "Saint Pierre and Miquelon", + "Saint Vincent and the Grenadines", + "Samoa", + "San Marino", + "Sao Tome and Principe", + "Saudi Arabia", + "Senegal", + "Serbia", + "Seychelles", + "Sierra Leone", + "Singapore", + "Sint Maarten", + "Slovakia", + "Slovenia", + "Solomon Islands", + "Somalia", + "South Africa", + "South Georgia and the South Sandwich Islands", + "South Korea", + "Southern Ocean", + "Spain", + "Spratly Islands", + "Sri Lanka", + "Sudan", + "Suriname", + "Svalbard", + "Swaziland", + "Sweden", + "Switzerland", + "Syria", + "Taiwan", + "Tajikistan", + "Tanzania", + "Tasman Sea", + "Thailand", + "Togo", + "Tokelau", + "Tonga", + "Trinidad and Tobago", + "Tromelin Island", + "Tunisia", + "Turkey", + "Turkmenistan", + "Turks and Caicos Islands", + "Tuvalu", + "USA", + "Uganda", + "Ukraine", + "United Arab Emirates", + "United Kingdom", + "Uruguay", + "Uzbekistan", + "Vanuatu", + "Venezuela", + "Viet Nam", + "Virgin Islands", + "Wake Island", + "Wallis and Futuna", + "West Bank", + "Western Sahara", + "Yemen", + "Zambia", + "Zimbabwe", + "not applicable", + "not collected", + "not provided", + "restricted access" + ] + }, + { + "name": "geographic location (latitude)", + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "dataType": "(^.*[+-]?[0-9]+.?[0-9]*.*$)|(^not collected$)|(^not provided$)|(^restricted access$)", + "required": true, + "ontology": null + }, + { + "name": "geographic location (longitude)", + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "dataType": "(^.*[+-]?[0-9]+.?[0-9]*.*$)|(^not collected$)|(^not provided$)|(^restricted access$)", + "required": true, + "ontology": null + }, + { + "name": "geographic location (region and locality)", + "description": "The geographical origin of the sample as defined by the specific region name followed by the locality name.", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "identified_by", + "description": "name of the expert who identified the specimen taxonomically", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "geographic location (depth)", + "description": "Depth is defined as the vertical distance below surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly. Depth can be reported as an interval for subsurface samples.", + "dataType": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?", + "required": false, + "ontology": null + }, + { + "name": "environment (biome)", + "description": "Biomes are defined based on factors such as plant structures, leaf types, plant spacing, and other factors like climate. Biome should be treated as the descriptor of the broad ecological context of a sample. Examples include: desert, taiga, deciduous woodland, or coral reef. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO", + "dataType": "string", + "required": false, + "ontology": { + "name": "ENVO", + "version": "", + "description": "Environment Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/ENVO_00000428"} + }, + { + "name": "environment (feature)", + "description": "Environmental feature level includes geographic environmental features. Compared to biome, feature is a descriptor of the more local environment. Examples include: harbor, cliff, or lake. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO", + "dataType": "string", + "required": false, + "ontology": { + "name": "ENVO", + "version": "", + "description": "Environment Ontology", + "rootTermURI": ""} + }, + { + "name": "geographic location (elevation)", + "description": "The elevation of the sampling site as measured by the vertical distance from mean sea level.", + "dataType": "[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?", + "required": false, + "ontology": null + }, + { + "name": "source material identifiers", + "description": "A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "isolation and growth condition", + "description": "Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.", + "dataType": "string", + "required": true, + "ontology": null + }, + { + "name": "propagation", + "description": "This field is specific to different taxa. For plants: sexual/asexual, for phages: lytic/lysogenic, for plasmids: incompatibility group (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice. Mandatory for MIGS of eukaryotes, plasmids and viruses.", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "plant structure", + "description": "name of plant structure that the sample was obtained from; for Plant Ontology (PO) terms see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051); if an individual flower is sampled the sex of it can be recorded here", + "dataType": "string", + "required": true, + "ontology": { + "name": "PO", + "version": "", + "description": "Plant Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/PO_0009011"} + }, + { + "name": "plant developmental stage", + "description": "developmental stage at the time of sample collection; for Plant Ontology (PO) (v 20) terms, see http://purl.bioontology.org/ontology/PO, e.g. hypocotyl emergence stage (PO_0007043)", + "dataType": "string", + "required": true, + "ontology": { + "name": "PO", + "version": "", + "description": "Plant Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/PO_0009012"} + }, + { + "name": "sampled age", + "description": "age of subject at the time of sample collection; relevant scale depends on species and study; e.g. 2 weeks old", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "sample phenotype", + "description": "phenotype of the plant from which the sample was obtained, such as colour of corolla, fruit diameter, circular leaf shape; Plant Trait Ontology (TO), Phenotypic Quality Ontology (PATO), or other ontology is recommended; e.g. stem epidermis colour (TO:1000018)", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "sample health state", + "description": "health status of the subject at the time of sample collection", + "dataType": "string", + "required": false, + "ontology": null, + "CVList": ["diseased", "healthy"] + }, + { + "name": "sample disease status", + "description": "list of diseases with which the subject has been diagnosed at the time of sample collection; can include multiple diagnoses; the value of the field depends on subject; e.g. Charcoal rot (Macrophomina phaseolina), Late wilt (Cephalosporium maydis)", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "sample disease stage", + "description": "stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "sample wet mass", + "description": "measurement of wet mass at the time of sample collection; e.g. 0.23 g", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "sample dry mass", + "description": "measurement of dry mass at the time of sample collection; e.g. 0.05g", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "sample height", + "description": "height of subject at the time of sampling, if different from the length; e.g. 0.75m", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "sample length", + "description": "length of subject at the time of sampling, if different from the height; e.g. 2m", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "growth facility", + "description": "type of facility where the sampled plant was grown", + "dataType": "string", + "required": false, + "ontology": null, + "CVList": ["experimental garden", "field", "glasshouse", "growth chamber", "open top chamber", "other"] + }, + { + "name": "sample capture status", + "description": "Reason for the sample collection.", + "dataType": "string", + "required": false, + "ontology": null, + "CVList": [ + "active surveillance in response to outbreak", + "active surveillance not initiated by an outbreak", + "farm sample", + "market sample", + "other", + "pet sample", + "zoo sample" + ] + }, + { + "name": "genotype", + "description": "name or code for genotype of organism", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "genetic modification", + "description": "A genetic modification of the genome of an organism which may occur naturally by spontaneous mutation, or be introduced by some experimental means. Examples of genetic modification include specification of a transgene or the gene knocked-out or details of transient transfection.", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "organism common name", + "description": "common name of the subject organism, e.g. maize", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "subspecific genetic lineage rank", + "description": "further information about the genetic distinctness of this lineage by recording additional information i.e. variety, cultivar, ecotype, inbred line,; it can also contain alternative taxonomic information", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "subspecific genetic lineage name", + "description": "name of the infraspecific rank, e.g ecotype Col-0", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "biological status", + "description": "the level of genome modification; controlled vocabulary: wild, natural, semi-natural, inbred line, breeder's line, hybrid, clonal selection, mutant", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "organism phenotype", + "description": "most relevant phenotypic traits of the subject; for Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO, e.g. bifurcated (PATO_0001784); terms from Trait Ontology (TO), Plant Ontology (PO) or Crop Ontology (CO) are also accepted; include name/method/scale for each trait; can include multiple traits", + "dataType": "string", + "required": false, + "ontology": false + }, + { + "name": "ancestral data", + "description": "information about either pedigree or other description of ancestral information (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "source material description", + "description": "further information to clarify the nature of the specimen or population used that is not collected elsewhere, e.g. if source was derived from accessioned stock, describe how it links to the original material", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "biotic relationship", + "description": "free text description of relationship(s) between the subject organism and other organism(s) it is associate with, e.g., parasite on species X; mutualist with species Y, the target organism is the subject of the relationship, and the other organism(s) is the object", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "growth habit", + "description": "characteristic shape, appearance or growth form of a plant species", + "dataType": "string", + "required": false, + "ontology": null, + "CVList": ["erect", "prostrate", "semi-erect", "spreading"] + }, + { + "name": "plant sex", + "description": "sex of the reproductive parts on the whole plant, e.g. pistilate, staminate, monoecieous, hermaphrodite", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "climate environment", + "description": "treatment involving an exposure to a particular climate; can include multiple climates", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "gaseous environment", + "description": "use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "seasonal environment", + "description": "treatment involving an exposure to a particular season (e.g. winter, summer, rabi, rainy etc.)", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "soil_taxonomic/FAO classification", + "description": "soil classification from the FAO World Reference Database for Soil Resources", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "soil_taxonomic/local classification", + "description": "soil classification based on local soil classification system", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "soil_taxonomic/local classification method", + "description": "reference or method used in determining the local soil classification", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "soil type", + "description": "soil series name or other lower-level classification", + "dataType": "string", + "required": false, + "ontology": null, + "CVList": [ + "Acrisol", + "Albeluvisol", + "Alisol", + "Andosol", + "Anthrosol", + "Arenosol", + "Calcisol", + "Cambisol", + "Chernozem", + "Cryosol", + "Durisol", + "Ferralsol", + "Fluvisol", + "Gleysol", + "Gypsisol", + "Histosol", + "Kastanozem", + "Leptosol", + "Lixisol", + "Luvisol", + "Nitisol", + "Phaeozem", + "Planosol", + "Plinthosol", + "Podzol", + "Regosol", + "Solonchak", + "Solonetz", + "Stagnosol", + "Technosol", + "Umbrisol", + "Vertisol" + ] + }, + { + "name": "soil type method", + "description": "reference or method used in determining soil series name or other lower-level classification", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "drainage classification", + "description": "drainage classification from a standard system such as the USDA system", + "dataType": "string", + "required": false, + "ontology": null, + "CVList": ["excessively drained", "moderately well", "poorly", "somewhat poorly", "very poorly", "well"] + }, + { + "name": "texture", + "description": "the relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "texture method", + "description": "reference or method used in determining soil texture", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "soil water content", + "description": "water content measurement; e.g. 13.6%", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "soil pH", + "description": "pH measurement of the soil; e.g. 6.2", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "plant growth medium", + "description": "specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium, recommended value is a specific value from EO:plant growth medium or other controlled vocabulary", + "dataType": "string", + "required": true, + "ontology": null + }, + { + "name": "rooting conditions", + "description": "relevant rooting conditions, such as field plot size, sowing density, container dimensions, number of plants per container", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "culture rooting medium", + "description": "name or reference for the hydroponic or in vitro culture rooting medium, can be a name of a commonly used medium or reference to a specific medium; e.g. Murashige and Skoog medium, if the medium has not been formally published, use the rooting medium descriptors", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "rooting medium macronutrients", + "description": "measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170mg/L)", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "rooting medium micronutrients", + "description": "measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2mg/L)", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "rooting medium organic supplements", + "description": "organic supplements of the culture rooting medium, such as vitaimins, amino acids, organic acids, antibiotics activated charcoal; e.g. Nicotinic acid (0.5mg/L)", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "rooting medium carbon", + "description": "source of organic carbon in the culture rooting medium; e.g. sucrose", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "rooting medium regulators", + "description": "growth regulators in the culture rooting medium, such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5mg/L NAA", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "rooting medium solidifier", + "description": "specification of the solidifying agent in the culture rooting medium; e.g. agar", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "rooting medium pH", + "description": "pH measurement of the culture rooting medium; e.g. 5.5", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "air temperature regimen", + "description": "information about treatment involving an exposure to varying temperatures; should include the temperature, treatment duration, interval and total experimental duration; can include different temperature regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "antibiotic regimen", + "description": "information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment duration, interval and total experimental duration; can include multiple antibiotic regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "chemical mutagen", + "description": "treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment duration, interval and total experimental duration; can include multiple mutagen regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "fertilizer regimen", + "description": "information about treatment involving the use of fertilizers; should include the name fertilizer, amount administered, treatment duration, interval and total experimental duration; can include multiple fertilizer regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "fungicide regimen", + "description": "information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment duration, interval and total experimental duration; can include multiple fungicide regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "gravity", + "description": "information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; can include multiple treatments", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "growth hormone regimen", + "description": "information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment duration, interval and total experimental duration; can include multiple growth hormone regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "herbicide regimen", + "description": "information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment duration, interval and total experimental duration; can include multiple regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "humidity regimen", + "description": "information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment duration, interval and total experimental duration; can include multiple regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "mineral nutrient regimen", + "description": "information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment duration, interval and total experimental duration; can include multiple mineral nutrient regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "non-mineral nutrient regimen", + "description": "information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment duration, interval and total experimental duration; can include multiple non-mineral nutrient regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "pesticide regimen", + "description": "information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment duration, interval and total experimental duration; can include multiple pesticide regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "pH regimen", + "description": "information about treatment involving exposure of plants to varying levels of pH of the growth media; can include multiple regimen", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "radiation regimen", + "description": "information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment duration, interval and total experimental duration; can include multiple radiation regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "rainfall regimen", + "description": "information about treatment involving an exposure to a given amount of rainfall; can include multiple regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "salt regimen", + "description": "information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment duration, interval and total experimental duration; can include multiple salt regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "standing water regimen", + "description": "treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water; can include multiple regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "watering regimen", + "description": "information about treatment involving an exposure to watering frequencies; can include multiple regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "water temperature regimen", + "description": "information about treatment involving an exposure to water with varying degree of temperature; can include multiple regimens", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "plant treatment", + "description": "ontology term(s) that describes the plant treatment or relevant environmental conditions, recommend use of Plant Environment Ontology (EO) or other ontology, such as XEML Environment Ontology (XEO) or Crop Ontology (CO), more specific fields in the treatment section can be used in addition to or in place of this field", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "light regimen", + "description": "information about treatment involving an exposure to light, this includes both light intensity and quality", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "biotic regimen", + "description": "information about treatment involving use of biotic factors, such as bacteria, viruses or fungi", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "mechanical damage", + "description": "information about any mechanical damage exerted on the plant; can include multiple damages and sites", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "chemical administration", + "description": "list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI", + "dataType": "string", + "required": false, + "ontology": false + }, + { + "name": "perturbation", + "description": "type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "protocol type", + "description": "type of assay or experimental step performed.", + "dataType": "string", + "required": true, + "ontology": null, + "CVList": ["sample collection"] + }, + { + "name": "sample collection device or method", + "description": "The method or deviced employed for collecting the sample", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "sample material processing", + "description": "Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2013-10-25) terms please see http://purl.bioontology.org/ontology/OBI", + "dataType": "string", + "required": false, + "ontology": { + "name": "OBI", + "version": "", + "description": "Ontology for Biomedical Investigations", + "rootTermURI": "http://purl.obolibrary.org/obo/OBI_0000094"} + }, + { + "name": "amount or size of sample collected", + "description": "Amount or size of sample (volume, mass or area) that was collected", + "dataType": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?", + "required": false, + "ontology": null + }, + { + "name": "sample storage duration", + "description": "duration for which sample was stored", + "dataType": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?", + "required": false, + "ontology": null + }, + { + "name": "sample storage temperature", + "description": "temperature at which sample was stored, e.g. -80", + "dataType": "[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?", + "required": false, + "ontology": null + }, + { + "name": "sample storage location", + "description": "location at which sample was stored, usually name of a specific freezer/room", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "sampling time point", + "description": "", + "dataType": "string", + "required": false, + "ontology": null + }, + { + "name": "Sample Name", + "description": "Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.", + "dataType": "String", + "required": true + } +] \ No newline at end of file diff --git a/templates/ena/sequence assembly_v1.1.0.json b/templates/ena/sequence assembly_v1.1.0.json new file mode 100644 index 0000000..608b0b2 --- /dev/null +++ b/templates/ena/sequence assembly_v1.1.0.json @@ -0,0 +1,49 @@ +{ + "metadata": { + "name": "sequence assembly", + "group": "ena", + "group_order": 5, + "temporary_name": "5_ena_sequence_assembly", + "template_version": "1.1.0", + "isa_config": "genome_seq_default_v2015-07-02", + "isa_measurement_type": "genome sequencing", + "isa_technology_type": "nucleotide sequencing", + "isa_protocol_type": "sequence assembly", + "repo_schema_id": "ENA General experiment information 2021", + "organism": "any", + "level": "assay" + }, + "data": [ + { + "name": "protocol type", + "description": "type of assay or experimental step performed.", + "required": true, + "ontology": null, + "CVList": ["sequence assembly"] + }, + { + "name": "Normalization Name", + "description": "User-defined name for each normalization applied", + "dataType": "String", + "required": false, + "ontology": null, + "CVList": null + }, + { + "name": "Data Transformation Name", + "description": "a data transformation", + "dataType": "String", + "required": false, + "ontology": null, + "CVList": null + }, + { + "name": "Derived Data File", + "description": "derived data such as an assembly file", + "dataType": "String", + "required": false, + "ontology": null, + "CVList": null + } + ] +}