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miappe.obo
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miappe.obo
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format-version: 1.2
ontology: miappe
property_value: owl:versionInfo "MIAPPE version 1.1" xsd:string
[Term]
id: MIAPPE:0000
name: Investigation
def: "Investigations are research programmes with defined aims. They can exist at various scales (for example, they could encompass a grant-funded programme of work, the various components comprising a peer-reviewed publication, or a single experiment)."
comment: "Cardinality: 1 per MIAPPE submission"
[Term]
id: MIAPPE:0001
name: Investigation unique ID
def: "Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution."
comment: "Example: EBI:12345678. Format: Unique identifier. Cardinality: 0-1"
is_a: MIAPPE:0000 ! Investigation
[Term]
id: MIAPPE:0002
name: Investigation title
def: "Human-readable string summarising the investigation."
comment: "Example: Adaptation of Maize to Temperate Climates: Mid-Density Genome-Wide Association Genetics and Diversity Patterns Reveal Key Genomic Regions, with a Major Contribution of the Vgt2 (ZCN8) Locus.. Format: Free text (short). Cardinality: 1"
is_a: MIAPPE:0000 ! Investigation
[Term]
id: MIAPPE:0003
name: Investigation description
def: "Human-readable text describing the investigation in more detail."
comment: "Example: The migration of maize from tropical to temperate climates was accompanied by a dramatic evolution in flowering time. To gain insight into the genetic architecture of this adaptive trait, we conducted a 50K SNP-based genome-wide association and diversity investigation on a panel of tropical and temperate American and European representatives.. Format: Free text. Cardinality: 0-1"
is_a: MIAPPE:0000 ! Investigation
[Term]
id: MIAPPE:0004
name: Submission date
def: "Date of submission of the dataset presently being described to a host repository."
comment: "Example: 2012-12-17. Format: Date/Time (ISO 8601, optional time zone). Cardinality: 0-1"
is_a: MIAPPE:0000 ! Investigation
[Term]
id: MIAPPE:0005
name: Public release date
def: "Date of first public release of the dataset presently being described."
comment: "Example: 2013-02-25. Format: Date/Time (ISO 8601, optional time zone). Cardinality: 0-1"
is_a: MIAPPE:0000 ! Investigation
[Term]
id: MIAPPE:0006
name: License
def: "License for the reuse of the data associated with this investigation. The Creative Commons licenses cover most use cases and are recommended."
comment: "Example: CC BY-SA 4.0, Unreported. Format: Unique identifier. Cardinality: 0-1"
is_a: MIAPPE:0000 ! Investigation
[Term]
id: MIAPPE:0007
name: MIAPPE version
def: "The version of MIAPPE used."
comment: "Example: 1.1. Format: Version number. Cardinality: 1"
is_a: MIAPPE:0000 ! Investigation
[Term]
id: MIAPPE:0008
name: Associated publication
def: "An identifier for a literature publication where the investigation is described. Use of DOIs is recommended."
comment: "Example: doi:10.1371/journal.pone.0071377. Format: DOI. Cardinality: 0+"
is_a: MIAPPE:0000 ! Investigation
[Term]
id: MIAPPE:0009
name: Study
def: "A study (or experiment) comprises a series of assays (or measurements) of one or more types, undertaken to answer a particular biological question."
comment: "Cardinality: 1+ per investigation"
[Term]
id: MIAPPE:0010
name: Study unique ID
def: "Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution."
comment: "Example: EBI:12345678 http://phenome-fppn.fr/maugio/2013/t2351. Format: Unique identifier. Cardinality: 0-1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0011
name: Study title
def: "Human-readable text summarising the study"
comment: "Example: 2002 evaluation of flowering time for a panel of 375 maize lines at the experimental station of Maugio (France). . Format: Free text (short). Cardinality: 1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0012
name: Study description
def: "Human-readable text describing the study"
comment: "Example: 2002 evaluation of male and female flowering time for a panel of 375 maize lines representing the worldwide genetic diversity at the experimental station of Maugio, France. . Format: Free text. Cardinality: 0-1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0013
name: Start date of study
def: "Date and, if relevant, time when the experiment started"
comment: "Example: 2002-04-04 2006-09-27T10:23:21+00:00. Format: Date/Time (ISO 8601, optional time zone). Cardinality: 1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0014
name: End date of study
def: "Date and, if relevant, time when the experiment ended"
comment: "Example: 2002-11-27. Format: Date/Time (ISO 8601, optional time zone). Cardinality: 0-1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0015
name: Contact institution
def: "Name and address of the institution responsible for the study."
comment: "Example: UMR de Génétique Végétale, INRA – Université Paris-Sud – CNRS, Gif-sur-Yvette, France. Format: Free text (short). Cardinality: 1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0016
name: Geographic location (country)
def: "The country where the experiment took place, either as a full name or preferably as a 2-letter code."
comment: "Example: FR. Format: Country name or 2-letter code (ISO 3166). Cardinality: 1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0017
name: Experimental site name
def: "The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place."
comment: "Example: INRA, UE Diascope - Chemin de Mezouls - Domaine expérimental de Melgueil - 34130 Mauguio - France. Format: Free text (short). Cardinality: 1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0018
name: Geographic location (latitude)
def: "Latitude of the experimental site in degrees, in decimal format."
comment: "Example: +43.619264. Format: Degrees in the decimal format (ISO 6709). Cardinality: 0-1 (1 if longitude is provided)"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0019
name: Geographic location (longitude)
def: "Longitude of the experimental site in degrees, in decimal format."
comment: "Example: +3.967454. Format: Degrees in the decimal format (ISO 6709). Cardinality: 0-1 (1 if latitude is provided)"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0020
name: Geographic location (altitude)
def: "Altitude of the experimental site, provided in metres (m)."
comment: "Example: 100 m. Format: Numeric + unit abbreviation. Cardinality: 0-1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0021
name: Description of the experimental design
def: "Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be 'unknown'/'NA', 'aggregated/reduced data', or simply 'none'."
comment: "Example: Lines were repeated twice at each location using a complete block design. In order to limit competition effects, each block was organized into four sub-blocks corresponding to earliness groups based on a priori information. . Format: Free text. Cardinality: 1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0022
name: Type of experimental design
def: "Type of experimental design of the study, in the form of an accession number from the Crop Ontology."
comment: "Example: CO_715:0000145. Format: Crop Ontology term (subclass of "CO_715:0000003"). Cardinality: 0-1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0023
name: Observation unit level hierarchy
def: "Hierarchy of the different levels of repetitions between each others"
comment: "Example: block>rep>plot. Format: Formatted text (level>level). Cardinality: 0-1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0024
name: Observation unit description
def: "General description of the observation units in the study."
comment: "Example: Observation units consisted in individual plots themselves consisting of a row of 15 plants at a density of approximately six plants per square meter. NA. Format: Free text. Cardinality: 1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0025
name: Description of growth facility
def: "Short description of the facility in which the study was carried out."
comment: "Example: field environment condition NA. Format: Free text (short). Cardinality: 1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0026
name: Type of growth facility
def: "Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology."
comment: "Example: CO_715:0000162. Format: Crop Ontology term (subclass of 'CO_715:0000005'). Cardinality: 0-1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0027
name: Cultural practices
def: "General description of the cultural practices of the study."
comment: "Example: Irrigation was applied according needs during summer to prevent water stress.. Format: Free text. Cardinality: 0-1"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0028
name: Map of experimental design
def: "Representation of the experimental design."
comment: "Example: https://urgi.versailles.inra.fr/files/ephesis/181000503/181000503_plan.xls. Format: URL or File name (of gis or tabular file like csv or tsv). Cardinality: 0+"
is_a: MIAPPE:0009 ! Study
[Term]
id: MIAPPE:0029
name: Person
def: "A human involved in the investigation or specifically any of its studies."
comment: "Cardinality: 1+ per investigation / 0+ per study"
[Term]
id: MIAPPE:0030
name: Person name
def: "The name of the person (either full name or as used in scientific publications)"
comment: "Example: Ines Chaves. Format: Name. Cardinality: 1"
is_a: MIAPPE:0029 ! Person
[Term]
id: MIAPPE:0031
name: Person email
def: "The electronic mail address of the person."
comment: "Example: ichaves@itqb.unl.pt. Format: email address. Cardinality: 0-1"
is_a: MIAPPE:0029 ! Person
[Term]
id: MIAPPE:0032
name: Person ID
def: "An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended."
comment: "Example: orcid.org/0000-0001-6494-0008; orcid.org/0000-0002-7054-800X. Format: Unique identifier. Cardinality: 0-1"
is_a: MIAPPE:0029 ! Person
[Term]
id: MIAPPE:0033
name: Person role
def: "Type of contribution of the person to the investigation"
comment: "Example: data submitter; author; corresponding author. Format: Free text (short). Cardinality: 1+"
is_a: MIAPPE:0029 ! Person
[Term]
id: MIAPPE:0034
name: Person affiliation
def: "The institution the person belongs to"
comment: "Example: ITQB, Portugal; grid.10772.33. Format: Free text (short). Cardinality: 1+"
is_a: MIAPPE:0029 ! Person
[Term]
id: MIAPPE:0035
name: Data File
def: "A file or digital object holding observation data recorded during one or more assays of the study, typically in tabular form. Multiple data files may be provided per study, and each file can include observations for several observation units and several observed variables."
comment: "Cardinality: 0+ per study"
[Term]
id: MIAPPE:0036
name: Data file link
def: "Link to the data file (or digital object) in a public database or in a persistent institutional repository; or identifier of the data file when submitted together with the MIAPPE submission."
comment: "Example: http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32551/. Format: URL or File name. Cardinality: 1"
is_a: MIAPPE:0035 ! Data File
[Term]
id: MIAPPE:0037
name: Data file description
def: "Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."
comment: "Example: FASTA tab-delimited column headers headers: 1. A 2. B 3. C. Format: Free text (short). Cardinality: 1"
is_a: MIAPPE:0035 ! Data File
[Term]
id: MIAPPE:0038
name: Data file version
def: "The version of the dataset (the actual data)."
comment: "Example: 1.0. Format: Software version number. Cardinality: 1"
is_a: MIAPPE:0035 ! Data File
[Term]
id: MIAPPE:0039
name: Biological Material
def: "The biological material being studied (e.g. plants grown from a certain bag or seed, or plants grown in a particular field). The original source of that material (e.g., the seeds or the original plant cloned) is called the material source, which, when held by a material repository, should have its stock identified."
comment: "Cardinality: 1+ per study; 0+ per observation unit"
[Term]
id: MIAPPE:0040
name: Biological material ID
def: "Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc… This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below."
comment: "Example: INRA:W95115_inra_2001; INRA:inra_kernel_2351; Rothamsted:rres_GK090847. Format: Unique identifier. Cardinality: 1"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0041
name: Organism
def: "An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended. "
comment: "Example: NCBITAXON:4577 . Format: Unique identifier. Cardinality: 1"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0042
name: Genus
def: "Genus name for the organism under study, according to standard scientific nomenclature."
comment: "Example: Zea Solanum. Format: Genus name. Cardinality: 0-1"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0043
name: Species
def: "Species name (formally: specific epithet) for the organism under study, according to standard scientific nomenclature."
comment: "Example: mays lycosperium x pennellii. Format: Species name. Cardinality: 0-1"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0044
name: Infraspecific name
def: "Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: ‘subsp.’ (subspecies); ‘convar.’ (convariety); ‘var.’ (variety); ‘f.’ (form); ‘Group’ (cultivar group)."
comment: "Example: vinifera Pinot noir B73 subspecies:vinifera ; cultivar:Pinot noir var:B73 subsp. vinifera var. Pinot Noir var. B73. Format: Free text, or key-value pair list, or MCPD-compliant format. Cardinality: 0-1"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0045
name: Biological material latitude
def: "Latitude of the studied biological material. [Alternative identifier for in situ material]"
comment: "Example: +39.067. Format: Degrees in the decimal format (ISO 6709). Cardinality: 0-1 (1 if longitude is provided)"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0046
name: Biological material longitude
def: "Longitude of the studied biological material. [Alternative identifier for in situ material]"
comment: "Example: -8.73. Format: Degrees in the decimal format (ISO 6709). Cardinality: 0-1 (1 if latitude is provided)"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0047
name: Biological material altitude
def: "Altitude of the studied biological material, provided in meters (m). [Alternative identifier for in situ material]"
comment: "Example: 10 m. Format: Numeric + unit abbreviation. Cardinality: 0-1"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0048
name: Biological material coordinates uncertainty
def: "Circular uncertainty of the coordinates, preferably provided in meters (m). [Alternative identifier for in situ material]"
comment: "Example: 200 m. Format: Numeric. Cardinality: 0-1"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0049
name: Biological material preprocessing
def: "Description of any process or treatment applied uniformly to the biological material, prior to the study itself. Can be provided as free text or as an accession number from a suitable controlled vocabulary."
comment: "Example: EO:0007210 - PVY(NTN); transplanted from study http://phenome-fppn.fr/maugio/2013/t2351 observation unit ID: pot:894. Format: Plant Environment Ontology and/or free text. Cardinality: 0+"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0050
name: Material source ID (Holding institute/stock centre, accession)
def: "An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material. Where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, the material can be defined as follows: 'mother_accession X father_accession', or, if father is unknown, as 'mother_accession X UNKNOWN'. For in situ material, the region of provenance may be used when an accession is not available."
comment: "Example: INRA:W95115_inra ICNF:PNB-RPI. Format: Unique identifier. Cardinality: 0-1"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0051
name: Material source DOI
def: "Digital Object Identifier (DOI) of the material source"
comment: "Example: doi:10.15454/1.4658436467893904E12. Format: DOI. Cardinality: 0-1"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0052
name: Material source latitude
def: "Latitude of the material source. [Alternative identifier for in situ material]"
comment: "Example: +39.067. Format: Degrees in the decimal format (ISO 6709). Cardinality: 0-1 (1 if longitude is provided)"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0053
name: Material source longitude
def: "Longitude of the material source. [Alternative identifier for in situ material]"
comment: "Example: -8.73. Format: Degrees in the decimal format (ISO 6709). Cardinality: 0-1 (1 if latitude is provided)"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0054
name: Material source altitude
def: "Altitude of the material source, provided in metres (m). [Alternative identifier for in situ material]"
comment: "Example: 10 m. Format: Numeric + unit abbreviation. Cardinality: 0-1"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0055
name: Material source coordinates uncertainty
def: "Circular uncertainty of the coordinates, provided in meters (m). [Alternative identifier for in situ material]"
comment: "Example: 200 m. Format: Numeric + unit abbreviation. Cardinality: 0-1"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0056
name: Material source description
def: "Description of the material source"
comment: "Example: Branches were collected from a 10-year-old tree growing in a progeny trial established in a loamy brown earth soil.. Format: Free text. Cardinality: 0-1"
is_a: MIAPPE:0039 ! Biological Material
[Term]
id: MIAPPE:0057
name: Environment
def: "Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below)."
comment: "Cardinality: 0-1 per study"
[Term]
id: MIAPPE:0058
name: Environment parameter
def: "Name of the environment parameter constant within the experiment. "
comment: "Example: sowing density rooting medium composition; pH. Format: Free text (see Appendix I). Cardinality: 1+"
is_a: MIAPPE:0057 ! Environment
[Term]
id: MIAPPE:0059
name: Environment parameter value
def: "Value of the environment parameter (defined above) constant within the experiment."
comment: "Example: 300 seeds per m2 Clay 50% plus sand; 6.5. Format: Free text. Cardinality: 1 per parameter"
is_a: MIAPPE:0057 ! Environment
[Term]
id: MIAPPE:0060
name: Experimental Factor
def: "The object of a study is to ascertain the impact of one or more factors on the biological material. Thus, a factor is, by definition a condition that varies between observation units, which may be biotic (pest, disease interaction) or abiotic (treatment and cultural practice) in nature. Depending on the level of the data, an experimental factor can be either 'what is the factor applied to the plant' (i.e. Unwatered), or the 'environmental characterisation' (i.e. if no rain on unwatered plant : Drought ; if rain on unwatered plant: Irrigated) "
comment: "Cardinality: 0+ per study; 0+ per observation unit"
[Term]
id: MIAPPE:0061
name: Experimental Factor type
def: "Name/Acronym of the experimental factor."
comment: "Example: Watering. Format: Free text (see Appendix II). Cardinality: 1"
is_a: MIAPPE:0060 ! Experimental Factor
[Term]
id: MIAPPE:0062
name: Experimental Factor description
def: "Free text description of the experimental factor. This includes all relevant treatments planification and protocol planned for all the plants targeted by a given experimental factor. "
comment: "Example: Daily watering 1 L per plant. . Format: Free text. Cardinality: 0-1"
is_a: MIAPPE:0060 ! Experimental Factor
[Term]
id: MIAPPE:0063
name: Experimental Factor values
def: "List of possible values for the factor."
comment: "Example: Watered; Unwatered. Format: Free text. Cardinality: 2+ per factor"
is_a: MIAPPE:0060 ! Experimental Factor
[Term]
id: MIAPPE:0064
name: Event
def: "An event is discrete occurrence at a particular time in the experiment (which can be natural, such as rain, or unnatural, such as planting, watering, etc). Events may be the realization of Factors or parts of Factors, or may be confounding to Factors. Can be applied at the whole study level or to only a subset of observation units."
comment: "Cardinality: 0+ per study/observation unit"
[Term]
id: MIAPPE:0065
name: Event type
def: "Short name of the event."
comment: "Example: Planting Fertilizing. Format: Free text (short). Cardinality: 1"
is_a: MIAPPE:0064 ! Event
[Term]
id: MIAPPE:0066
name: Event accession number
def: "Accession number of the event type in a suitable controlled vocabulary (Crop Ontology)."
comment: "Example: CO_715:0000007 CO_715:0000011. Format: Crop Ontology term (subclass of CO_715:0000006). Cardinality: 0-1"
is_a: MIAPPE:0064 ! Event
[Term]
id: MIAPPE:0067
name: Event description
def: "Description of the event, including details such as amount applied and possibly duration of the event. "
comment: "Example: Sowing using seed drill Fertilizer application: Ammonium nitrate at 3 kg/m2. Format: Free text. Cardinality: 0-1"
is_a: MIAPPE:0064 ! Event
[Term]
id: MIAPPE:0068
name: Event date
def: "Date and time of the event."
comment: "Example: 2006-09-27T10:23:21+00:00 2006-10-27; 2006-11-13; 2016-11-21. Format: Date/Time (ISO 8601, optional time zone). Cardinality: 1+"
is_a: MIAPPE:0064 ! Event
[Term]
id: MIAPPE:0069
name: Observation Unit
def: "Observation units are objects that are subject to instances of observation and measurement. An observation unit comprises one or more plants, and/or their environment. There can be pure environment observation units with no plants. Synonym: Experimental unit."
comment: "Cardinality: 1+ per study"
[Term]
id: MIAPPE:0070
name: Observation unit ID
def: "Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. "
comment: "Example: plot:894. Format: Unique identifier. Cardinality: 1"
is_a: MIAPPE:0069 ! Observation Unit
[Term]
id: MIAPPE:0071
name: Observation unit type
def: "Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. The observation unit type cannot be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). Alternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead."
comment: "Example: plot. Format: Free text. Cardinality: 1"
is_a: MIAPPE:0069 ! Observation Unit
[Term]
id: MIAPPE:0072
name: External ID
def: "Identifier for the observation unit in a persistent repository, comprises the name of the repository and the identifier of the observation unit therein. The EBI Biosamples repository can be used. URI are recommended when possible."
comment: "Example: Biosamples:SAMEA4202911. Format: Unique identifier. Cardinality: 0+"
is_a: MIAPPE:0069 ! Observation Unit
is_a: MIAPPE:0075 ! Sample
[Term]
id: MIAPPE:0073
name: Spatial distribution
def: "Type and value of a spatial coordinate (georeference or relative) or level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. Levels of observation must be consistent with those listed in the Study section."
comment: "Example: latitude:+2.341; row:4 ; X:3; Y:6; Xm:35; Ym:65; block:1; plot:894. Format: Formatted text (Key:value). Cardinality: 0+"
is_a: MIAPPE:0069 ! Observation Unit
[Term]
id: MIAPPE:0074
name: Observation Unit factor value
def: "List of values for each factor applied to the observation unit."
comment: "Example: Watered. Format: Free text. Cardinality: 0+"
is_a: MIAPPE:0069 ! Observation Unit
[Term]
id: MIAPPE:0075
name: Sample
def: "A sample is a portion of plant tissue harvested, non-harvested or extracted from an observation unit for the purpose of sub-plant observations and/or molecular studies. A sample must be used when there is a physical sample that needs to be stored and traced. Otherwise, observations made at the sub-plant level should be recorded as plant level observations using the observed variables to characterize the object of the observation (e.g. Berry sugar content, Fruit weight, Grain Protein content, Leaf 1 width, Leaf 2 width, Leaf 2 length)."
comment: "Cardinality: 0+ per observation unit"
[Term]
id: MIAPPE:0076
name: Sample ID
def: "Unique identifier for the sample."
comment: "Example: CEA:BE00034067. Format: Unique identifier. Cardinality: 1"
is_a: MIAPPE:0075 ! Sample
[Term]
id: MIAPPE:0077
name: Plant structure development stage
def: "The stage in the life of a plant structure during which the sample was taken, in the form of an accession number to a suitable controlled vocabulary (Plant Ontology, BBCH scale)"
comment: "Example: PO:0025094 BBCH-17. Format: Plant Ontology term (subclass or PO:0009012) or BBCH scale term. Cardinality: 0-1"
is_a: MIAPPE:0075 ! Sample
[Term]
id: MIAPPE:0078
name: Plant anatomical entity
def: "A description of the plant part (e.g. leaf) or the plant product (e.g. resin) from which the sample was taken, in the form of an accession number to a suitable controlled vocabulary (Plant Ontology)."
comment: "Example: PO:0000003 PO:0025161. Format: Plant Ontology term (subclass of PO:0025131) . Cardinality: 1"
is_a: MIAPPE:0075 ! Sample
[Term]
id: MIAPPE:0079
name: Sample description
def: "Any information not captured by the other sample fields, including quantification, sample treatments and processing."
comment: "Example: Distal part of the leaf ; 100 mg of roots taken from 10 roots at 20°C, conserved in vacuum at 20 mM NaCl salinity, stored at -60 °C to -85 °C.. Format: Free text. Cardinality: 0-1"
is_a: MIAPPE:0075 ! Sample
[Term]
id: MIAPPE:0080
name: Collection date
def: "The date and time when the sample was collected / harvested"
comment: "Example: 2005-08-15T15:52:01+00:00. Format: Date/Time. Cardinality: 1"
is_a: MIAPPE:0075 ! Sample
[Term]
id: MIAPPE:0082
name: Observed Variable
def: "An observed variable describes how a measurement has been made. It typically takes the form of a measured characteristic of the observation unit (plant or environmental trait), associated to the method and unit of measurement. Multiple variables with the same combination of trait, method and scale can be used in association with different plant parts (leaf 1, leaf 2), when this distinction is necessary for observations referring to different parts of the same observation unit."
comment: "Cardinality: 1+ per study"
[Term]
id: MIAPPE:0083
name: Variable ID
def: "Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: <trait abbreviation>_<method abbreviation>_<scale abbreviation>). A variable ID must be unique within a given investigation."
comment: "Example: Ant_Cmp_Cday. Format: Unique identifier. Cardinality: 1"
is_a: MIAPPE:0082 ! Observed Variable
[Term]
id: MIAPPE:0084
name: Variable name
def: "Name of the variable."
comment: "Example: Anthesis computed in growing degree days. Format: Free text. Cardinality: 0-1"
is_a: MIAPPE:0082 ! Observed Variable
[Term]
id: MIAPPE:0085
name: Variable accession number
def: "Accession number of the variable in the Crop Ontology"
comment: "Example: CO_322:0000794. Format: Crop Ontology term. Cardinality: 0-1"
is_a: MIAPPE:0082 ! Observed Variable
[Term]
id: MIAPPE:0086
name: Trait
def: "Name of the (plant or environmental) trait under observation"
comment: "Example: Anthesis time Reproductive growth time. Format: Free text. Cardinality: 1"
is_a: MIAPPE:0082 ! Observed Variable
[Term]
id: MIAPPE:0087
name: Trait accession number
def: "Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology)."
comment: "Example: CO_322:0000030 TO:0000366. Format: Term from Plant Trait Ontology, Crop Ontology, or XML Environment Ontology. Cardinality: 0-1"
is_a: MIAPPE:0082 ! Observed Variable
[Term]
id: MIAPPE:0088
name: Method
def: "Name of the method of observation"
comment: "Example: Growing degree days to anthesis. Format: Free text. Cardinality: 1"
is_a: MIAPPE:0082 ! Observed Variable
[Term]
id: MIAPPE:0089
name: Method accession number
def: "Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology)."
comment: "Example: CO_322:0000189. Format: Term from Plant Trait Ontology, Crop Ontology, or XML Environment Ontology. Cardinality: 0-1"
is_a: MIAPPE:0082 ! Observed Variable
[Term]
id: MIAPPE:0090
name: Method description
def: "Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number)"
comment: "Example: Days to anthesis for male flowering was measured in thermal time (GDD: growing degree-days) according to Ritchie J, NeSmith D (1991;Temperature and crop development. Modeling plant and soil systems American Society of Agronomy Madison, Wisconsin USA) with TBASE=8°C and T0=30°C. Plant height was measured at 5 years with a ruler, one year after Botritis inoculation.. Format: Free text. Cardinality: 0-1"
is_a: MIAPPE:0082 ! Observed Variable
[Term]
id: MIAPPE:0091
name: Reference associated to the method
def: "URI/DOI of reference describing the method."
comment: "Example: http://doi.org/10.2134/agronmonogr31.c2. Format: URI or DOI. Cardinality: 0-1"
is_a: MIAPPE:0082 ! Observed Variable
[Term]
id: MIAPPE:0092
name: Scale
def: "Name of the scale associated with the variable"
comment: "Example: °C day. Format: Unique identifier. Cardinality: 1"
is_a: MIAPPE:0082 ! Observed Variable
[Term]
id: MIAPPE:0093
name: Scale accession number
def: "Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."
comment: "Example: CO_322:0000510. Format: Crop Ontology term. Cardinality: 0-1"
is_a: MIAPPE:0082 ! Observed Variable
[Term]
id: MIAPPE:0094
name: Time scale
def: "Name of the scale or unit of time with which observations of this type were recorded in the data file (for time series studies)."
comment: "Example: Growing degree day (GDD) Date/Time. Format: Free text. Cardinality: 0+"
is_a: MIAPPE:0082 ! Observed Variable
[Term]
id: MIAPPE:0095
name: Growth facility
is_a: MIAPPE:0058 ! Environment parameter
[Term]
id: MIAPPE:0096
name: Air temperature
def: "List of hourly air temperature throughout the experiment."
comment: "Example: 22 °C. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0097
name: Organ temperature
def: "List of hourly organ temperatures throughout the experiment"
comment: "Example: 18 °C. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0098
name: Change over the course of experiment
def: "Difference between the maximum air temperature recorded and the minimum."
comment: "Example: 0.75 °C. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0099
name: Photon flux density (PPFD) measured at plant or canopy level
def: "List of hourly Photosynthetic photon flux density (PPFD) throughout the experiment."
comment: "Example: PPFD: 89061 mol m-2 sd-1; . Format: Text"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0100
name: Average length of the light period
def: "Average length of the light period in h."
comment: "Example: 16. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0101
name: Light intensity
def: "Intensity of total light"
comment: "Example: [μmol m–2 s–1]. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0102
name: Range in peak light intensity
def: "Range in peak light intensity for the whole experiment."
comment: "Example: [μmol m–2 s–1]. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0103
name: Fraction of outside light intercepted by growth facility components and surrounding structures
def: "Fraction of outside light intercepted by growth facility components and surrounding structures."
comment: "Example: Number between 0 and 1. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0104
name: Type of lamps used
def: "Nature of the light source for controlled environments. XEO: 00137"
comment: "Example: fluorescent tubes; high intensity discharge (HID) lamps; light emitting diodes (LED). Format: Text"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0105
name: R/FR ratio
def: "Red light to far red light ratio. XEO:00036"
comment: "Example: [mol mol–1]. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0106
name: Daily UV-A radiation
def: "Intensity of UVA radiation (320-400 nm); XEO:00037"
comment: "Example: [W m-2]. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0107
name: Daily UV-B radiation
def: "Intensity of UVB radiation (290-320 nm); XEO:00038"
comment: "Example: [W m-2]. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0108
name: Total daily irradiance
def: "Intensity of total light (XEO:00034) averaged over the experiment."
comment: "Example: [W m-2]. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0109
name: Atmospheric CO2 concentration
def: "Denotes whether the atmospheric CO2 concentrations were controlled during the experiment."
comment: "Example: controlled; uncontrolled. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0110
name: Average CO2 during the light and dark periods
def: "Concentration of CO2 in the air during the light and dark periods (XEO:00023)"
comment: "Example: light period: 390 mLL-1; dark period: 450 mLL-1. Format: Text"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0111
name: Vapour pressure deficit
def: "Vector of hourly VPD throughout the experiment .The Vapour Pressure Deficit in the air defines the difference between the maximal amount of water in the air minus the actual amount during the light period in kPa (XEO:00021)"
comment: "Example: 2 kPa. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0112
name: Average relative humidity during the light period
def: "The relative humidity describes the amount of water vapor in the air, generally expressed as the percentage of the maximum water vapor during the light period (XEO:00020)"
comment: "Example: 30%. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0113
name: Average VPDair during the dark period.
def: "The Vapour Pressure Deficit in the air defines the difference between the maximal amount of water in the air minus the actual amount during the light period in kPa (XEO:00021)"
comment: "Example: 2.7 kPa. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0114
name: Average relative humidity during the dark period
def: "The relative humidity describes the amount of water vapor in the air, generally expressed as the percentage of the maximum water vapor during the dark period (XEO:00020)"
comment: "Example: 33%. Format: Numeric"
is_a: MIAPPE:0095 ! Growth facility
[Term]
id: MIAPPE:0115
name: Rooting conditions
is_a: MIAPPE:0058 ! Environment parameter
[Term]
id: MIAPPE:0116
name: Rooting medium
def: "An abiotic plant treatment (EO:0007191) involving the use of a solid or liquid substrate for growing plants or tissue-cultured plant samples."
comment: "Example: hydroponic plant culture media; in vitro liquid growth medium; in vitro solid growth medium; soil environment. Format: Plant Environment Ontology:'EO_0007147'"
is_a: MIAPPE:0115 ! Rooting conditions
[Term]
id: MIAPPE:0117
name: Container type
def: "Type of container used to grow/treat the plants.XEO:00040"
comment: "Example: pot; Petri dish; well; tray. Format: Text"
is_a: MIAPPE:0115 ! Rooting conditions
[Term]
id: MIAPPE:0118
name: Container volume
def: "Volume that is available to the roots. XEO:00113"
comment: "Example: [L]. Format: Numeric"
is_a: MIAPPE:0115 ! Rooting conditions
[Term]
id: MIAPPE:0119
name: Container height
def: "Height of the container."
comment: "Example: [m]. Format: Numeric"
is_a: MIAPPE:0115 ! Rooting conditions
[Term]
id: MIAPPE:0120
name: Number of plants per containers
def: "Number of plants per container. XEO:00112"
comment: "Example: X/container. Format: Numeric"
is_a: MIAPPE:0115 ! Rooting conditions
[Term]
id: MIAPPE:0121
name: Plot size
def: "Description of experimental sites."
comment: "Example: higher-level landform; land element and position; slope; ..... Format: Crop Ontology:'CO_715:0000058'"
is_a: MIAPPE:0115 ! Rooting conditions
[Term]
id: MIAPPE:0122
name: Sowing density
def: "Sowing density."
comment: "Example: x/plot. Format: Natural Resource and Environment Ontology"
is_a: MIAPPE:0115 ! Rooting conditions
[Term]
id: MIAPPE:0123
name: Rooting medium replenishment
def: "Frequency and volume of replenishment or addition of the rooting medium."
comment: "Format: Text"
is_a: MIAPPE:0115 ! Rooting conditions
[Term]
id: MIAPPE:0124
name: pH
def: "Value of soil pH, separated by a colon, the depth (cm) from where soil sample was taken. Multiple values are separated by semicolon. "
comment: "Example: 7.7:40-60; 6.5; 4.3:10-20. Format: Text"
is_a: MIAPPE:0115 ! Rooting conditions
[Term]
id: MIAPPE:0125
name: Porosity
def: "A permeability quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices. PATO:0000973"
comment: "Example: [%]. Format: Numeric"
is_a: MIAPPE:0115 ! Rooting conditions
[Term]
id: MIAPPE:0126
name: Medium temperature
def: "Temperature of the replenishment medium. "
comment: "Example: [°C]. Format: Numeric"
is_a: MIAPPE:0115 ! Rooting conditions
[Term]
id: MIAPPE:0127
name: Soil penetration strength
def: "Soil penetration strength as measured by the standard penetration test (SPT; ISO 22476-3), the cone penetrometer test (CPT), in-situ vane shear tests, and shear wave velocity measurements."
comment: "Example: [Pa m–2]. Format: Numeric"
is_a: MIAPPE:0115 ! Rooting conditions
[Term]
id: MIAPPE:0128
name: Water retention capacity
def: "Potential energy of water per unit mass of water in the soil.XEO:00126"
comment: "Example: [g g–1 dry weight]. Format: Numeric"
is_a: MIAPPE:0115 ! Rooting conditions
[Term]
id: MIAPPE:0129
name: Organic matter content
def: "Proportion of organic matter in the soil. XEO:00117"
comment: "Example: [%]. Format: Numeric"
is_a: MIAPPE:0115 ! Rooting conditions
[Term]
id: MIAPPE:0130
name: Nutrients
is_a: MIAPPE:0058 ! Environment parameter
[Term]
id: MIAPPE:0131
name: Medium composition
def: "Concentration of the nutrients"
comment: "Example: Ca (XEO:00058): 5 mg/L. Format: XEML Environment Ontology:'XEO_00042' + Numeric"
is_a: MIAPPE:0130 ! Nutrients
[Term]
id: MIAPPE:0132
name: Extractable N content per unit ground volume before fertiliser added
def: "Extractable N content per unit ground area before fertiliser added"
comment: "Example: [mg/m2]. Format: XEML Environment Ontology:'XEO_00054' +Numeric"
is_a: MIAPPE:0130 ! Nutrients
[Term]
id: MIAPPE:0133
name: Type and amount of fertiliser added per container/m2
def: "The current practice in field /greenhouse management for fertilization"
comment: "Example: nitrogen: [concentration]; phosphorus: [concentration]. Format: Crop Ontology:'CO_715:0000204' + Numeric"
is_a: MIAPPE:0130 ! Nutrients
[Term]
id: MIAPPE:0134
name: Concentration of [nutrient] before start of the experiment
def: "Concentration of a nutrient at the start of an experiment."
comment: "Example: Ca (XEO:00058): 5 mg/L. Format: XEML Environment Ontology:'XEO_00042' + Numeric"
is_a: MIAPPE:0130 ! Nutrients
[Term]
id: MIAPPE:0135
name: Extractable N content per unit ground area at the end of the experiment
def: "Extractable N content per unit ground area at the end of the experiment"
comment: "Example: [mg/m2]. Format: XEML Environment Ontology:'XEO_00054' +Numeric"
is_a: MIAPPE:0130 ! Nutrients
[Term]
id: MIAPPE:0136
name: Volume and timing of water added per container
def: "A defined volume of water supplied to each pot."
comment: "Example: [L]. Format: Numeric"
is_a: MIAPPE:0130 ! Nutrients
[Term]
id: MIAPPE:0137
name: Matrix potential
def: "Range in water potential for soil."
comment: "Example: -10 to -30 kPa. Format: Numeric"
is_a: MIAPPE:0130 ! Nutrients
[Term]
id: MIAPPE:0138
name: Watering regimen
def: "The treatment involving an exposure to watering frequencies."
comment: "Example: irrigation from top; irrigation from bottom; drip irrigation. Format: Text"
is_a: MIAPPE:0130 ! Nutrients
[Term]
id: MIAPPE:0139
name: Composition of nutrient solutions used for irrigation
def: "For all nutrients, including micronutrients, the ontology term with concentration."
comment: "Example: Ca (XEO:00058): 5 mg/L. Format: XEML Environment Ontology:'XEO_00042' + Numeric"
is_a: MIAPPE:0130 ! Nutrients
[Term]
id: MIAPPE:0140
name: Electrical conductivity
def: "A conductivity quality inhering in a bearer by virtue of the bearer's ability to convey electricity."
comment: "Example: [dS m–1]. Format: Numeric"
is_a: MIAPPE:0130 ! Nutrients
[Term]
id: MIAPPE:0142
name: Seasonal environment
def: "A plant treatment (EO:0001001) involving an exposure to a given conditions of regional seasons."
comment: "Example: Spring season; dry season. Format: Plant Environment Ontology:'EO_0007038'"
is_a: MIAPPE:0061 ! Experimental Factor type
[Term]
id: MIAPPE:0143
name: Air treatment regime
def: "The treatment involving an exposure to wind/air with varying degree of temperature, which may depend on the study type or the regional environment."
comment: "Example: 28/25ºC ( Day/Night ). Format: Plant Environment Ontology:'EO_0007161'"
is_a: MIAPPE:0061 ! Experimental Factor type
[Term]
id: MIAPPE:0144
name: Soil temperature regime
def: "A physical plant treatment (EO:0007316) involving an exposure to varying degree of temperature, which may depend on regional environment."
comment: "Example: 27/25ºC ( Day/Night ). Format: Plant Environment Ontology:'EO_0007161'"
is_a: MIAPPE:0061 ! Experimental Factor type
[Term]
id: MIAPPE:0145
name: Soil treatment regime
def: "The treatment (EO:0007049) involving growing plants and exposing them to soil growth media with varying contents"
comment: "Example: sand content (10% v/v). Format: Plant Environment Ontology:'EO_0007161'"
is_a: MIAPPE:0061 ! Experimental Factor type
[Term]
id: MIAPPE:0146
name: Antibiotic regime
def: "A chemical treatment (EO:0007189) involving the use of antibiotic for selection purposes."