Bruno Vasques Costa Cyril Pommier Daniel Faria Evangelia Papoutsoglou Guillaume Cornut Hanna Cwiek-Kupczynska Ines Chaves Manuel Ruiz Marie Angélique Laporte Pascal Neveu Pierre Larmande has BrAPI synonym has exact synonym has ISA synonym has MIAPPE synonym has ontology recommendation has related synonym derives from has affiliation has biological material has contact institution has country has country of origin has data file has environment has environment parameter has event has factor has factor value has growth facility has location has material source has method has modality has observation has observation level has observation level hierarchy has observed subject has part has participating institution has person with role has role has scale has spatial distribution has spatial distribution type has experimental design has sublevel has superlevel has trait has variable is modality of is role of is role of person in is subject of observation part of has abbreviation has address The altitude of a location in metres has altitude has associated publication has collection date An ISO 3166-1 country code with either 2 or 3 letters (alpha-2 or alpha-3). has country code has cultural practices An external identifier that is specifically a DOI, given either as just the DOI code (string) or as an URI. The entity <=> DOI relation should be bijective. has DOI An external identifier that is specifically a database identifier. has database identifier has date-time has description The location of the file in the form of a URI or, if the file is contained within a local MIAPPE submission (e.g. ISA-Tab), a path or file name. has digital location The e-mail address of a person has e-mail contact has end date-time Used in BrAPI Phenotypes call has entry number Used in BrAPI Phenotypes call has entry type A map of the experimental design of the study, in gis or excel has experimental design map An identifier from another public resource, such as an ontology or database, either in the form of an accession number, or in the form of a URI. An external identifier should be globally unique. has external identifier has genus A unique identifier for a germplasm. has germplasm accession number has identifier 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). has infraspecific name A code or acronym of an institution. has institute code An identifier used internally, either only in the MIAPPE submission itself, or also on a non-public database whence the information was retrieved. An internal identifier need only be unique among entities of the same type within a MIAPPE submission. has internal identifier The latitude of a location in degrees, in the decimal system has latitude has license The longitude of a location in degrees, in the decimal system has longitude has MIAPPE version An identifier used specifically for biological materials (and their sources) which can be internal or external. For material sources, it usually follows one of two forms: a key-value pair comprising the name/identifer of the repository from which the material was sourced plus the accession number of the repository for that material, or, where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, "mother_accession X father_accession" (father_accession can be "UNKNOWN"). has material identifier has title has name has observation unit description has plant anatomical entity has plant structure development stage has preprocessing has public release date has season has specific epithet has species has species authority has start date-time has submission date has subtaxon has subtaxon authority An external identifier for a taxon that is either an NCBI Taxon identifier or an equivalent. has taxon identifier has time scale has type has uncertainty has value has version is active 1 1 GPS location 1 1 1 1 1 1 germplasm An organism that was the subject of the study and/or was observed in an observation unit. biological material 1 organism A country in the world that either presently exists (i.e. is recognized in status by most entities) or existed at the time of the study. country 1 1 1 A description of and link to a file or data stream holding some or all of the data described by the MIAPPE submission. data file The set of environmental parameters or experimental conditions that were kept constant during the study and did not change betweeen observation units or assays. environment 1 1 A parameter of the environment which is represented by a name and a value. environment parameter 1 1 1 time factor A discrete change to the state of one or more observation units that happened at a given point in time, be it deliberate or inadvertent. event 1 http://www.cropontology.org/rdf/CO_715:0000006 2 1 1 A condition that varies between observation units, by taking different values or modalities, assessing the effect of which is the goal of the study. A factor may be biotic (pest, disease interaction) or abiotic (treatment, cultural practice) in nature. It must have at least two values or modalities. factor 1 1 A value or modality of a factor. factor value 1 1 A facility in which plants can be grown, such as a field or greenhouse. growth facility 1 http://www.cropontology.org/rdf/CO_715:0000005 1 An institution (academic or industrial) involved in the investigation or study. institution 1 1 1 1 trial A research programme with defined aims, which can vary in scale from a single experiment, to a grant-funded programme or various components comprising a peer-reviewed publication. investigation 1 investigation title 1 investigation unique ID A physical location, typically on planet Earth, identified by GPS coordinates and/or name and address. location 1 1 1 1 An organism from which the organism(s) used in the study were derived. It should be identified with a unique external identifier (such as germplasm accession number) and possibly a DOI. material source 1 1 1 1 method 1 http://www.cropontology.org/ (Method) 1 1 1 named location 1 1 observation 1 observation level observation level hierarchy 1 1 experiment unit observation unit 1 1 1 1 1 1 observation variable assay observed variable 1 http://www.cropontology.org/rdf/Variable 1 1 1 person 1 role 1 1 1 1 1 1 sample 1 http://purl.obolibrary.org/obo/PO_0025131 1 http://purl.obolibrary.org/obo/PO_0009012 1 1 scale 1 http://www.cropontology.org/ (Scale) spatial coordinate 1 1 spatial distribution 1 spatial distribution type 1 1 experimental design 1 http://www.cropontology.org/rdf/CO_715:0000003 1 1 1 1 1 1 1 1 1 1 1 1 1 experiment A study (or experiment) comprises a series of assays (or measurements) of one or more types, undertaken to answer a particular biological question. It is recommended that a Study have a description. study 1 study title 1 study unique ID 1 1 Name of the (plant or environmental) trait under observation trait 1 http://purl.obolibrary.org/obo/to.owl http://www.cropontology.org/ (traits) altitude The global spatial coordinate altitude (in meters) column The local spatial coordinate identifying the column latitude The global spatial coordinate latitude (in degrees in the decimal system) longitude The global spatial coordinate latitude (in degrees in the decimal system) row The local spatial coordinate identifying the row x The local spatial coordinate x (numeric, discrete) x (m) The local spatial coordinate x (in meters) y The local spatial coordinate y (numeric, discrete) y (m) The local spatial coordinate y (in meters) z The local spatial coordinate z (numeric, discrete) z (m) The local spatial coordinate z (in meters)