|
Name
(alphabetical by first name, faculty at top)
|
Position | Affiliation | ||
|
Faculty
(alphabetical by first name)
|
||||
| David Paltiel |<EMAIL_ADDRESS>| Professor | Yale Public Health and Yale Management | |
| Forrest Crawford |<EMAIL_ADDRESS>| Associated Professor | Yale School of Public Health | |
| Gregg Gonsalves |<EMAIL_ADDRESS>| Assistant Professor, Epidemiology of Microbial Diseases | Yale School of Public Health | |
| Jeffrey Eaton |<EMAIL_ADDRESS>| Faculty of Medicine, School of Public Health | Imperial College London | |
| Josh Salomon |
<EMAIL_ADDRESS>|
Professor of Medicine | Stanford School of Medicine | |
| Meagan Fitzpatrick |<EMAIL_ADDRESS>| Assistant Professor | University of Maryland School of Medicine | |
| Nick Menzies |<EMAIL_ADDRESS>| Assistant Professor | Harvard TH Chan School of Public Health | |
| Reza Yaesoubi |<EMAIL_ADDRESS>| Assistant Professor of Public Health (Health Policy) | Yale School of Medicine | |
|
Fellows, students, and staff (alphabetical by first name)
|
||||
| Adam Beckman |<EMAIL_ADDRESS>| MD-MBA Student | Harvard Medical School and Harvard Business School | |
| Alyssa Bilinski |<EMAIL_ADDRESS>| PhD Student | Harvard Graduate School of Arts and Sciences | |
| Anna York |<EMAIL_ADDRESS>| Post-Doctoral Associate | Yale School of Public Health | |
| Anne Williamson |<EMAIL_ADDRESS>| MD student | Barts and the London School of Medicine | |
| Bianca Mulaney |<EMAIL_ADDRESS>| MD student | Stanford School of Medicine | |
| Christian Testa |<EMAIL_ADDRESS>| Data Analyst and Programmer | Harvard School of Public Health | |
| Emma Clarke-Deelder |<EMAIL_ADDRESS>| PhD Student | Population Health Sciences at Harvard | |
| Evan MacKay |<EMAIL_ADDRESS>| MPhil Student | University of Cambridge | |
| Hanna Ehrlich |<EMAIL_ADDRESS>| PhD Student | Yale University | |
| Jinyi Zhu |<EMAIL_ADDRESS>| PhD Student | Harvard University | |
| John Giardina |<EMAIL_ADDRESS>| PhD Student | Harvard University | |
| Katie Rich |<EMAIL_ADDRESS>| MD Student | Harvard University | |
| Kayoko Shioda |<EMAIL_ADDRESS>| PhD Student | Yale University | |
| Lin Zhu |<EMAIL_ADDRESS>| Research Engineer | Stanford | |
| Elizabeth White |<EMAIL_ADDRESS>| PhD Student | Yale University | |
| Luke Massa |<EMAIL_ADDRESS>| Software Engineer | TripAdvisor | |
| Maile Phillips |<EMAIL_ADDRESS>| PhD Student | Yale University | |
| Margret Erlendsdottir |<EMAIL_ADDRESS>| MD/PhD student |
Yale School
of Public Health (Biostatistics) and Yale School of Medicine
|
|
| Melanie Chitwood |<EMAIL_ADDRESS>| Research Associate | Yale Epidemiology of Microbial Diseases | |
| Monica Farid |<EMAIL_ADDRESS>| PhD Student | Health Policy (Economics), Harvard University | |
| Nicole Swartwood |<EMAIL_ADDRESS>| Research Analyst | Harvard University, Global Health and Population | |
| Nikhil Deshmukh |<EMAIL_ADDRESS>| CTO | Jobstep | |
| Raphael Sherak |<EMAIL_ADDRESS>| MD Student | Albert Einstein College of Medicine | |
| Ruthie Birger |<EMAIL_ADDRESS>| Post-Doctoral Associate | Yale Epidemiology of Microbial Diseases | |
| Samantha Burn |<EMAIL_ADDRESS>| PhD student | Health Policy (Economics), Harvard | |
| Soheil Eshghi |<EMAIL_ADDRESS>| Post-Doctoral Associate | Yale School of Public Health | |
| Stephanie Perniciaro |<EMAIL_ADDRESS>| Post-Doctoral Associate | Yale Epidemiology of Microbial Diseases | |
| Suzan Iloglu |<EMAIL_ADDRESS>| Post-Doctoral Associate | Yale School of Public Health | |
| Thomas Thornhill |<EMAIL_ADDRESS>| Research Assistant | Yale School of Public Health | |
| Tyler Copple |<EMAIL_ADDRESS>| Software Engineer | Yale School of Public Health | |
| Yu-Han Kao |<EMAIL_ADDRESS>| Research Affiliate | Yale Epidemiology of Microbial Diseases | |
| Yuli Lily Hsieh |<EMAIL_ADDRESS>| PhD Student | Health Policy (Decision Sciences), Harvard University |


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Processing and testing software provide technical support for the manufacture of first-class casting molds.
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BrAPI JSON-LD Dictionary
brapi:PUI
Object Contexts:
MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology.
Object Contexts:
MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology.
brapi:URL
Object Contexts:
DEFINITION MISSING
brapi:abbreviation
Object Contexts:
An abbreviation which represents this location
Object Contexts:
An abbreviation which represents this program
Object Contexts:
an abbreviation for the name of this breeding method
brapi:accessionNames
Object Contexts:
MCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space.
brapi:accessionNumber
Object Contexts:
MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869").
Object Contexts:
This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection
brapi:acquisitionDate
Object Contexts:
MCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or "00" [double zero].
Object Contexts:
The date this germplasm was acquired by the genebank MCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or "00" [double zero].
brapi:acquisitionSourceCode
Object Contexts:
MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. 10) Wild habitat 11) Forest or woodland 12) Shrubland 13) Grassland 14) Desert or tundra 15) Aquatic habitat 20) Farm or cultivated habitat 21) Field 22) Orchard 23) Backyard, kitchen or home garden (urban, peri-urban or rural) 24) Fallow land 25) Pasture 26) Farm store 27) Threshing floor 28) Park 30) Market or shop 40) Institute, Experimental station, Research organization, Genebank 50) Seed company 60) Weedy, disturbed or ruderal habitat 61) Roadside 62) Field margin 99) Other (Elaborate in REMARKS field)
brapi:active
Object Contexts:
Is this study currently active
Object Contexts:
Is this trail currently active
brapi:additionalInfo
Additional arbitrary info
Object Contexts:
DEFINITION MISSING
Object Contexts:
Additional arbitrary information specific to a particular Vendor. Look for the Vendors specific API documentation for more details
brapi:alternateIDs
Object Contexts:
MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon.
brapi:alternate_bases
Object Contexts:
The bases that appear instead of the reference bases. Multiple alternate alleles are possible.
brapi:alternativeAbbreviations
Object Contexts:
Other frequent abbreviations of the trait, if any. These abbreviations do not have to follow a convention
brapi:amount
Object Contexts:
Current balance of seeds in this lot. Could be a count (seeds, bulbs, etc) or a weight (kg of seed).
Object Contexts:
The amount of units being transfered. Could be a count (seeds, bulbs, etc) or a weight (kg of seed).
brapi:analysis
Object Contexts:
Set of Analysis descriptors for this VariantSet
brapi:analysisDbId
Object Contexts:
Unique identifier for this analysis description
brapi:analysisName
Object Contexts:
A human readable name for this analysis
brapi:ancestralData
Object Contexts:
MCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'.
brapi:assemblyPUI
Object Contexts:
The remaining information is about the source of the sequences Public id of this reference set, such as `GRCH_37`.
brapi:attribute
Object Contexts:
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour"
brapi:attributeDbId
Object Contexts:
The ID which uniquely identifies this attribute within the given database server
brapi:attributeName
Object Contexts:
A human readable name for this attribute
brapi:authors
Object Contexts:
Ontology's list of authors (no specific format)
brapi:availableFormats
Object Contexts:
When the data for a VariantSet is retrieved, it can be retrieved in a variety of data formats and file formats. dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc) fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response.
brapi:bibliographicalReference
Object Contexts:
Bibliographical reference describing the method. MIAPPE V1.1 (DM-91) Reference associated to the method - URI/DOI of reference describing the method.
brapi:biologicalStatusOfAccessionCode
MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. 100) Wild 110) Natural 120) Semi-natural/wild 130) Semi-natural/sown 200) Weedy 300) Traditional cultivar/landrace 400) Breeding/research material 410) Breeders line 411) Synthetic population 412) Hybrid 413) Founder stock/base population 414) Inbred line (parent of hybrid cultivar) 415) Segregating population 416) Clonal selection 420) Genetic stock 421) Mutant (e.g. induced/insertion mutants, tilling populations) 422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) 423) Other genetic stocks (e.g. mapping populations) 500) Advanced or improved cultivar (conventional breeding methods) 600) GMO (by genetic engineering) 999) Other (Elaborate in REMARKS field)
brapi:biologicalStatusOfAccessionDescription
Object Contexts:
Supplemental text description for 'biologicalStatusOfAccessionCode'
brapi:breedingInstitutes
Object Contexts:
DEFINITION MISSING
brapi:breedingMethodDbId
Object Contexts:
the unique identifier for this breeding method
Object Contexts:
The unique identifier for the breeding method used to create this germplasm
brapi:breedingMethodName
Object Contexts:
human readable name of the breeding method
brapi:callSetCount
Object Contexts:
The number of CallSets included in this VariantSet
brapi:callSetDbId
Object Contexts:
The ID of the call set this variant call belongs to. If this field is not present, the ordering of the call sets from a `SearchCallSetsRequest` over this `VariantSet` is guaranteed to match the ordering of the calls on this `Variant`. The number of results will also be the same.
Object Contexts:
The call set ID.
brapi:callSetName
Object Contexts:
The name of the call set this variant call belongs to. If this field is not present, the ordering of the call sets from a `SearchCallSetsRequest` over this `VariantSet` is guaranteed to match the ordering of the calls on this `Variant`. The number of results will also be the same.
Object Contexts:
The call set name.
brapi:calls
Object Contexts:
Array of available calls on this server
brapi:categories
Object Contexts:
List of possible values with optional labels
brapi:ciend
Object Contexts:
Similar to "cipos", but for the variant's end position (which is derived from start + svlen).
brapi:cipos
Object Contexts:
In the case of structural variants, start and end of the variant may not be known with an exact base position. "cipos" provides an interval with high confidence for the start position. The interval is provided by 0 or 2 signed integers which are added to the start position. Based on the use in VCF v4.2
brapi:clientId
Object Contexts:
A unique, alpha-numeric ID which identifies the client to the vendor. Used to connect the order to the correct billing and contact info.
A unique, alpha-numeric ID which identifies the client to the vendor. Used to connect the order to the contract, billing, and contact info.
brapi:clientPlateBarcode
(Optional) The value of the bar code attached to this plate
brapi:clientPlateId
The ID which uniquely identifies this plate to the client making the request
brapi:clientSampleBarCode
Object Contexts:
(Optional) The value of the bar code attached to this sample
brapi:clientSampleId
Object Contexts:
The ID which uniquely identifies this sample to the client making the request
brapi:clientSampleIds
Object Contexts:
The list of sampleDbIds included in the file
brapi:code
Object Contexts:
The 2 digit code representing the type of storage this germplasm is kept in at a genebank. MCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.)  Collecting date of the sample [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or "00" [double zero].
brapi:collectingInfo
Object Contexts:
Information about the collection of this germplasm
brapi:collectingInstitutes
Object Contexts:
Institutes which collected the sample
brapi:collectingMissionIdentifier
Object Contexts:
MCPD (v2.1) (COLLMISSID) 4.2 Identifier of the collecting mission used by the Collecting Institute (4 or 4.1) (e.g. "CIATFOR_052", "CN_426").
brapi:collectingNumber
Object Contexts:
MCPD (v2.1) (COLLNUMB) 3. Original identifier assigned by the collector(s) of the sample, normally composed of the name or initials of the collector(s) followed by a number (e.g. "ab109909"). This identifier is essential for identifying duplicates held in different collections.
brapi:collectingSite
Object Contexts:
Information about the location where the sample was collected
brapi:collection
Object Contexts:
A specific panel/collection/population name this germplasm belongs to.
brapi:collector
Object Contexts:
The name or identifier of the entity which collected the observation
brapi:column
The Column identifier for this samples location in the plate
brapi:comments
Object Contexts:
Additional comments
Object Contexts:
Generic comments about this sample for the vendor
brapi:commonCropName
Object Contexts:
Common name for the crop which this program is for
Object Contexts:
Common name for the crop associated with this study
Object Contexts:
Common name for the crop associated with this trial
Object Contexts:
Crop name (examples: "Maize", "Wheat")
Object Contexts:
The common name of the crop
Object Contexts:
the common name of a crop (for multi-crop systems)
Object Contexts:
MCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: "malting barley", "mas".
Object Contexts:
Common name for the crop MCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: "malting barley", "mas".
brapi:commonCropNames
Object Contexts:
Common name for the crop which this program is for
brapi:concentration
Object Contexts:
DEFINITION MISSING
brapi:contactDbId
Object Contexts:
The ID which uniquely identifies this contact MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended.
brapi:contactEmail
Object Contexts:
A contact email address for this server management
brapi:contacts
Object Contexts:
List of contact entities associated with this study
Object Contexts:
List of contact entities associated with this trial
brapi:contextOfUse
Object Contexts:
Indication of how trait is routinely used. (examples: ["Trial evaluation", "Nursery evaluation"])
brapi:coordinateDescription
Object Contexts:
Describes the precision and landmarks of the coordinate values used for this location. (ex. the site, the nearest town, a 10 kilometers radius circle, +/- 20 meters, etc)
brapi:coordinateUncertainty
Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown.
Object Contexts:
MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated with the coordinates in metres. Leave the value empty if the uncertainty is unknown.
brapi:coordinates
Object Contexts:
DEFINITION MISSING
brapi:copyright
Object Contexts:
The copyright information of this image. Example 'Copyright 2018 Bob Robertson'
Object Contexts:
Ontology copyright
brapi:countryCode
Object Contexts:
[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.
brapi:countryName
Object Contexts:
The full name of the country where this location is MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.
brapi:countryOfOrigin
Object Contexts:
MCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers" variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note: Descriptors 14 to 16 below should be completed accordingly only if it was "collected".
brapi:countryOfOriginCode
Object Contexts:
3-letter ISO 3166-1 code of the country in which the sample was originally collected MCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note- Descriptors 14 to 16 below should be completed accordingly only if it was "collected".
brapi:created
Object Contexts:
The time at which this record was created, in ISO 8601 format.
Object Contexts:
The date this call set was created
Object Contexts:
The timestamp when this variant was created.
brapi:createdDate
Object Contexts:
The time stamp for when this seed lot was created
brapi:crossAttributeName
Object Contexts:
the human readable name of a cross attribute
brapi:crossAttributeValue
Object Contexts:
the value of a cross attribute
brapi:crossAttributes
Object Contexts:
Set of custom attributes associated with a cross
brapi:crossName
Object Contexts:
the human readable name for a cross
brapi:crossType
the type of cross
brapi:crossingProjectDbId
the unique identifier for a crossing project
Object Contexts:
The crossing project used to generate this germplasm
brapi:crossingProjectDescription
Object Contexts:
the description for a crossing project
brapi:crossingProjectName
the human readable name for a crossing project
brapi:crossingYear
Object Contexts:
The year the parents were originally crossed
brapi:culturalPractices
Object Contexts:
MIAPPE V1.1 (DM-28) Cultural practices - General description of the cultural practices of the study.
brapi:data
Matrix of observation data recorded for different observation variables across different observation units
brapi:dataFormat
Object Contexts:
The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy)
Object Contexts:
dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)
brapi:dataLinks
Object Contexts:
List of links to extra data files associated with this study. Extra data could include notes, images, and reference data.
brapi:dataType
Object Contexts:
DEFINITION MISSING
brapi:dataTypes
Object Contexts:
The possible data formats returned by the available call
brapi:datafiles
Object Contexts:
The datafiles contains a list of file URLs and metadata. These files contain additional information related to the returned object and can be retrieved by a subsequent call. This could be a supplementary data file, an informational file, the uploaded file where the data originated from, a generated file representing the whole dataset in a particular format, or any other related file.
brapi:datasetAuthorships
Object Contexts:
License and citation information for the data in this trial
brapi:datasetPUI
Object Contexts:
DEFINITION MISSING
brapi:date
Object Contexts:
A list of dates when the event occured MIAPPE V1.1 (DM-68) Event date - Date and time of the event.
brapi:dateCreated
Object Contexts:
Timestamp when the entity was first created
brapi:dateModified
Object Contexts:
Timestamp when the entity was last updated
brapi:decimalPlaces
Object Contexts:
For numerical, number of decimal places to be reported
brapi:defaultDisplayName
Object Contexts:
Human readable name used for display purposes
brapi:defaultValue
Object Contexts:
Variable default value. (examples: "red", "2.3", etc.)
brapi:description
Object Contexts:
The general description of this data link
Object Contexts:
Human-readable value of the environment parameter (defined above) constant within the experiment
Object Contexts:
Method description MIAPPE V1.1 (DM-90) Method description - 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)
Object Contexts:
description of this person
Object Contexts:
MIAPPE V1.1 (DM-22) Description of the experimental design - 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'.
Object Contexts:
MIAPPE V1.1 (DM-26) Description of growth facility - Short description of the facility in which the study was carried out.
Object Contexts:
The human readable description of an image.
Object Contexts:
Human readable description of Ontology
Object Contexts:
A human readable description of the analysis
Object Contexts:
Optional free text description of this reference set.
Object Contexts:
DEFINITION MISSING
Object Contexts:
human readable description of the breeding method
Object Contexts:
A supplemental text description of the storage type
brapi:descriptiveOntologyTerms
Object Contexts:
A list of terms to formally describe the image. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL.
brapi:determinedDate
Object Contexts:
The date the value of this attribute was determined for a given germplasm
brapi:documentationLinks
Object Contexts:
links to various ontology documentation
brapi:documentationURL
Object Contexts:
A URL to the human readable documentation of this object
brapi:donorAccessionNumber
Object Contexts:
MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.
Object Contexts:
The accession number assigned by the donor MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.
brapi:donorAccessionPui
Object Contexts:
PUI (DOI mostly) of the accession in the donor system.
brapi:donorInfo
Object Contexts:
Information about the donor
brapi:donorInstitute
Object Contexts:
DEFINITION MISSING
brapi:donorInstituteCode
Object Contexts:
The institute code for the donor institute MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.
brapi:donors
Object Contexts:
List of donor institutes
brapi:elevation
Object Contexts:
MCPD (v2.1) (ELEVATION) 16. Elevation of collecting site expressed in metres above sea level. Negative values are allowed.
brapi:email
Object Contexts:
The contacts email address MIAPPE V1.1 (DM-32) Person email - The electronic mail address of the person.
brapi:emailAddress
Object Contexts:
email address for this person
brapi:end
Object Contexts:
This field is optional and may be ignored if there is no relevant map or reference to be associated with. The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated by `start + referenceBases.length`.
brapi:endDate
Object Contexts:
The date the study ends MIAPPE V1.1 (DM-15) End date of study - Date and, if relevant, time when the experiment ended
Object Contexts:
The date this trial ends
brapi:entity
Object Contexts:
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the entity is the part of the plant that the trait refers to e.g., for "grain colour", entity = "grain"
brapi:entryType
Object Contexts:
The type of entry for this observation unit. ex. "CHECK", "TEST", "FILLER"
brapi:environmentParameters
Object Contexts:
Environmental parameters that were kept constant throughout the study and did not change between observation units.
brapi:environmentType
Object Contexts:
Describes the general type of environment of the location. (ex. forest, field, nursery, etc)
brapi:eventDbId
Object Contexts:
Internal database identifier
brapi:eventDescription
Object Contexts:
A detailed, human-readable description of this event MIAPPE V1.1 (DM-67) Event description - Description of the event, including details such as amount applied and possibly duration of the event.
brapi:eventParameters
Object Contexts:
A list of objects describing additional event parameters. Each of the following accepts a human-readable value or URI
brapi:eventType
Object Contexts:
General category for this event (e.g. Sowing, Watering, Rain). Each eventType should correspond to exactly one eventTypeDbId, if provided. MIAPPE V1.1 (DM-65) Event type - Short name of the event.
brapi:eventTypeDbId
Object Contexts:
An identifier for this event type, in the form of an ontology class reference MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology).
brapi:experimentalDesign
Object Contexts:
The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology
brapi:exposure
Object Contexts:
Describes the level of protection/exposure for things like sun light and wind.
brapi:externalReferenceIDs
Object Contexts:
List of external references for the trait to search for
brapi:externalReferenceSources
Object Contexts:
List of external references sources for the trait to search for
brapi:externalReferences
Object Contexts:
brapi:ObservationUnitNewRequest
brapi:CrossingProjectNewRequest
DEFINITION MISSING
brapi:factor
Object Contexts:
The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.
brapi:familyCode
Object Contexts:
The code representing the family
brapi:fileDescription
Object Contexts:
A human readable description of the file contents
Object Contexts:
The human readable long description for this form
brapi:fileFormat
Object Contexts:
The MIME type of the file (ie text/csv, application/excel, application/zip).
Object Contexts:
fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response.
brapi:fileMD5Hash
Object Contexts:
The MD5 Hash of the file contents to be used as a check sum
brapi:fileName
Object Contexts:
The name of the file
Object Contexts:
The human readable name for this form
Object Contexts:
Name of the file
brapi:fileSize
Object Contexts:
The size of the file in bytes
brapi:fileType
Object Contexts:
The type or format of the file. Preferably MIME Type.
Object Contexts:
Format of the file
brapi:fileURL
Object Contexts:
The absolute URL where the file is located
Object Contexts:
A URL which indicates the location of the file version of this VariantSet. Could be a static file URL or an API endpoint which generates the file.
Object Contexts:
The URL to download this form
Object Contexts:
The URL to a file with the results of a vendor analysis
brapi:filtersApplied
Object Contexts:
True if filters were applied for this variant. VCF column 7 "FILTER" any value other than the missing value.
brapi:filtersFailed
Object Contexts:
Zero or more filters that failed for this variant. VCF column 7 "FILTER" shared across all alleles in the same VCF record.
brapi:filtersPassed
Object Contexts:
True if all filters for this variant passed. VCF column 7 "FILTER" value PASS.
brapi:firstName
Object Contexts:
Persons first name
brapi:formula
Object Contexts:
For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation
brapi:fromSeedLotDbId
Object Contexts:
The identifier for the Seed Lot being transfered out of
brapi:genotype
Object Contexts:
DEFINITION MISSING
brapi:genotype_likelihood
Object Contexts:
The genotype likelihood for this variant call. Each array entry represents how likely a specific genotype is for this call as log10(P(data | genotype)), analogous to the GL tag in the VCF spec. The value ordering is defined by the GL tag in the VCF spec.
brapi:genus
Object Contexts:
MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.
Object Contexts:
Genus name for taxon. Initial uppercase letter required. MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required. MIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature.
brapi:geoCoordinates
Object Contexts:
DEFINITION MISSING
brapi:geometry
Object Contexts:
A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed.
brapi:georeferencingMethod
Object Contexts:
MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing method used (GPS, determined from map, gazetteer, or estimated using software). Leave the value empty if georeferencing method is not known.
brapi:germplasmDbId
Object Contexts:
The ID which uniquely identifies a germplasm
Object Contexts:
the unique identifier for a germplasm
Object Contexts:
The ID which uniquely identifies a germplasm within the given database server
Object Contexts:
A unique identifier which identifies a germplasm in this database
Object Contexts:
The germplasm DbId of the parent of this germplasm
Object Contexts:
the germplasm DbId of the sibling
Object Contexts:
The unique identifier of a progeny germplasm
Object Contexts:
Unique DbId of the Germplasm held in this Seed Lot
brapi:germplasmDbIds
Object Contexts:
List of IDs which uniquely identify germplasm to search for
brapi:germplasmName
Name of the germplasm. It can be the preferred name and does not have to be unique.
Object Contexts:
the human readable name for a germplasm
A human readable name for a germplasm
Object Contexts:
the human readable name of the parent of this germplasm
Object Contexts:
the germplasm name of the sibling
Object Contexts:
The human readable name of a progeny germplasm
brapi:germplasmNames
Object Contexts:
List of human readable names to identify germplasm to search for
brapi:germplasmOrigin
Object Contexts:
Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm.
brapi:germplasmPUI
Object Contexts:
MCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties.
Object Contexts:
DEFINITION MISSING
Object Contexts:
The Permanent Unique Identifier which represents a germplasm MIAPPE V1.1 (DM-41) Biological material ID - 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.
brapi:germplasmPreprocessing
Object Contexts:
Description of any process or treatment applied uniformly to the germplasm, prior to the study itself. Can be provided as free text or as an accession number from a suitable controlled vocabulary.
brapi:growthFacility
Object Contexts:
Short description of the facility in which the study was carried out.
brapi:growthStage
Object Contexts:
Growth stage at which measurement is made (examples: "flowering")
brapi:headerRow
Object Contexts:
The table is REQUIRED to have the following columns
- observationUnitDbId - Each row is related to one Observation Unit
- observationTimeStamp - Each row is has a time stamp for when the observation was taken
- At least one column with an observationVariableDbId
The table may have any or all of the following OPTIONAL columns. Included columns are decided by the server developer
- observationUnitName
- studyDbId
- studyName
- germplasmDbId
- germplasmName
- positionCoordinateX
- positionCoordinateY
- year
The table also may have any number of Observation Unit Hierarchy Level columns. For example:
- field
- plot
- sub-plot
- plant
- pot
- block
- entry
- rep
The JSON representation provides a pair of extra arrays for defining the headers of the table. The first array "headerRow" will always contain "observationUnitDbId" and any or all of the OPTIONAL column header names. The second array "observationVariables" contains the names and DbIds for the Observation Variables represented in the table. By appending the two arrays, you can construct the complete header row of the table.
Object Contexts:
The table is REQUIRED to have the following columns
- observationUnitDbId - Each row is related to one Observation Unit
- At least one column with an observationVariableDbId
The table may have any or all of the following OPTIONAL columns. Included columns are decided by the server developer
- observationUnitName
- studyDbId
- studyName
- germplasmDbId
- germplasmName
- positionCoordinateX
- positionCoordinateY
- year
The table also may have any number of Observation Unit Hierarchy Level columns. For example:
- field
- plot
- sub-plot
- plant
- pot
- block
- entry
- rep
The JSON representation provides a pair of extra arrays for defining the headers of the table. The first array "headerRow" will always contain "observationUnitDbId" and any or all of the OPTIONAL column header names. The second array "observationVariables" contains the names and DbIds for the Observation Variables represented in the table. By appending the two arrays, you can construct the complete header row of the table.
brapi:imageFileName
Object Contexts:
The name of the image file. Might be the same as 'imageName', but could be different.
brapi:imageFileSize
Object Contexts:
The size of the image in Bytes.
brapi:imageHeight
Object Contexts:
The height of the image in Pixels.
brapi:imageLocation
Object Contexts:
DEFINITION MISSING
brapi:imageName
Object Contexts:
The human readable name of an image. Might be the same as 'imageFileName', but could be different.
brapi:imageTimeStamp
Object Contexts:
The date and time the image was taken
brapi:imageURL
Object Contexts:
The complete, absolute URI path to the image file. Images might be stored on a different host or path than the BrAPI web server.
brapi:imageWidth
Object Contexts:
The width of the image in Pixels.
brapi:instituteAddress
Object Contexts:
The street address of the institute representing this location MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study.
Object Contexts:
MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.
brapi:instituteCode
Object Contexts:
MCPD (v2.1) (BREDCODE) 18. FAO WIEWS code of the institute that has bred the material. If the holding institute has bred the material, the breeding institute code (BREDCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. Multiple values are separated by a semicolon without space.
Object Contexts:
MCPD (v2.1) (COLLCODE) 4. FAO WIEWS code of the institute collecting the sample. If the holding institute has collected the material, the collecting institute code (COLLCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. Multiple values are separated by a semicolon without space.
Object Contexts:
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.
Object Contexts:
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with "obsolete" codes, see "Common formatting rules (v)".
Object Contexts:
MCPD (v2.1) (DUPLSITE) 25. FAO WIEWS code of the institute(s) where a safety duplicate of the accession is maintained. Follows INSTCODE standard.
Object Contexts:
The code for the Institute that has bred the material. MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with "obsolete" codes, see "Common formatting rules (v)".
brapi:instituteName
Object Contexts:
The name of the institution which this contact is part of MIAPPE V1.1 (DM-35) Person affiliation - The institution the person belongs to
Object Contexts:
Each institute/laboratory can have several experimental field MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study.
Object Contexts:
MCPD (v2.1) (BREDNAME) 18.1 Name of the institute (or person) that bred the material. This descriptor should be used only if BREDCODE can not be filled because the FAO WIEWS code for this institute is not available. Multiple names are separated by a semicolon without space.
Object Contexts:
MCPD (v2.1) (COLLNAME) 4.1 Name of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled because the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.
Object Contexts:
MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available.
Object Contexts:
MCPD (v2.1) (DUPLINSTNAME) 25.1 Name of the institute where a safety duplicate of the accession is maintained.
Object Contexts:
The name of the institution which bred the material
brapi:institution
Object Contexts:
Name of institution submitting the variable
brapi:isDerived
Object Contexts:
A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.
Object Contexts:
A reference set may be derived from a source if it contains additional sequences, or some of the sequences within it are derived (see the definition of `isDerived` in `Reference`).
brapi:key
Object Contexts:
Specifies the relationship between the event and the given property. E.g. fertilizer, operator
Object Contexts:
DEFINITION MISSING
brapi:label
Object Contexts:
A text label for a category
brapi:language
Object Contexts:
2 letter ISO 639-1 code for the language of submission of the variable.
brapi:lastName
Object Contexts:
Persons last name
brapi:lastUpdate
Object Contexts:
The date and time when this study was last modified
brapi:lastUpdated
Object Contexts:
The timestamp for the last update to this Seed Lot (including transactions)
brapi:latitudeDecimal
Object Contexts:
MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975).
brapi:latitudeDegrees
Object Contexts:
MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes (2 digits), and seconds (2 digits) followed by N (North) or S (South) (e.g. 103020S). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 10
brapi:leadPersonDbId
Object Contexts:
The unique identifier of the program leader
brapi:leadPersonName
Object Contexts:
The name of the program leader
brapi:length
Object Contexts:
The length of this reference's sequence.
brapi:levelName
Object Contexts:
A name for this level
brapi:levelOrder
Object Contexts:
`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9).
brapi:licence
Object Contexts:
Ontology licence
brapi:license
Object Contexts:
The usage license associated with the study data
Object Contexts:
MIAPPE V1.1 (DM-7) License - License for the reuse of the data associated with this investigation. The Creative Commons licenses cover most use cases and are recommended.
brapi:linkageGroupCount
Object Contexts:
The number of linkage groups present in this genomic map
brapi:linkageGroupName
The Uniquely Identifiable name of this linkage group
brapi:listDescription
Object Contexts:
Description of a List
brapi:listName
Object Contexts:
Human readable name of a List
brapi:listOwnerName
Object Contexts:
Human readable name of a List Owner. (usually a user or person)
brapi:listOwnerPersonDbId
Object Contexts:
The unique identifier for a List Owner. (usually a user or person)
brapi:listSize
Object Contexts:
The number of elements in a List
brapi:listSource
Object Contexts:
The description of where a List originated from
brapi:listType
Object Contexts:
DEFINITION MISSING
brapi:location
Object Contexts:
Physical location of this server (ie. City, Country)
brapi:locationDbId
Object Contexts:
The unique identifier for a Location
Object Contexts:
The ID which uniquely identifies a location, associated with this study
Object Contexts:
DbId of the storage location
brapi:locationDbIds
Object Contexts:
The location ids to search for
brapi:locationDescription
Object Contexts:
MCPD (v2.1) (COLLSITE) 14. Location information below the country level that describes where the accession was collected, preferable in English. This might include the distance in kilometres and direction from the nearest town, village or map grid reference point, (e.g. 7 km south of Townsville).
brapi:locationName
A human readable name for this location MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place.
Object Contexts:
The human readable name of a location associated with this study
brapi:locationNames
Object Contexts:
A human readable names to search for
brapi:locationType
Object Contexts:
The type of location this represents (ex. Breeding Location, Storage Location, etc)
brapi:longitudeDecimal
Object Contexts:
MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in decimal degrees. Positive values are East of the Greenwich Meridian; negative values are West of the Greenwich Meridian (e.g. +120.9123).
brapi:longitudeDegrees
Object Contexts:
MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West) (e.g. 0762510W). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 076
brapi:mailingAddress
Object Contexts:
physical address of this person
brapi:mainAbbreviation
Object Contexts:
Main abbreviation for trait name. (examples: "Carotenoid content" => "CC")
brapi:mapDbId
Object Contexts:
The ID which uniquely identifies this genomic map
Object Contexts:
The unique ID of the map
brapi:mapName
Object Contexts:
A human readable name for this genomic map
Object Contexts:
The human readable name of the map
brapi:mapPUI
Object Contexts:
The DOI or other permanent identifier for this genomic map
brapi:markerCount
Object Contexts:
The number of markers present in this genomic map
Object Contexts:
The number of markers associated with this linkage group
brapi:max
Object Contexts:
Maximum value (used for field data capture control).
brapi:maxPosition
Object Contexts:
The maximum position of a marker within this linkage group
brapi:md5checksum
Object Contexts:
The MD5 checksum uniquely representing this `Reference` as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM).
Object Contexts:
Order-independent MD5 checksum which identifies this `ReferenceSet`. To compute this checksum, make a list of `Reference.md5checksum` for all `Reference` s in this set. Then sort that list, and take the MD5 hash of all the strings concatenated together. Express the hash as a lower-case hexadecimal string.
brapi:md5sum
Object Contexts:
MD5 Hash Check Sum for the file to confirm download without error
brapi:message
Object Contexts:
A short message concerning the status of this request/response
brapi:messageType
Object Contexts:
The logging level for the attached message
brapi:method
Object Contexts:
DEFINITION MISSING
brapi:methodClass
Object Contexts:
Method class (examples: "Measurement", "Counting", "Estimation", "Computation", etc.)
brapi:methodName
Object Contexts:
Human readable name for the method MIAPPE V1.1 (DM-88) Method Name of the method of observation
brapi:methods
Object Contexts:
The possible HTTP Methods to be used with the available call
brapi:middleName
Object Contexts:
Persons middle name
brapi:mimeType
Object Contexts:
The file type of the image. Examples 'image/jpeg', 'image/png', 'image/svg', etc
brapi:min
Object Contexts:
Minimum value (used for data capture control) for numerical and date scales
brapi:mlsStatus
Object Contexts:
MCPD (v2.1) (MLSSTAT) 27. The status of an accession with regards to the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture. Leave the value empty if the status is not known 0 No (not included) 1 Yes (included) 99 Other (elaborate in REMARKS field, e.g. "under development")
brapi:modality
Object Contexts:
The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc MIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor.
brapi:name
Object Contexts:
The full name of this contact person MIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications)
Object Contexts:
The name of the external data link MIAPPE V1.1 (DM-38) Data file description - 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.
brapi:nextPageToken
Object Contexts:
The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there are not any additional results.
brapi:numberOfSamples
The total number of samples contained in this request. Used for billing and basic validation of the request.
brapi:objective
Object Contexts:
The primary objective of the program
brapi:observationDbIds
Object Contexts:
A list of observation Ids this image is associated with, if applicable.
brapi:observationLevel
Object Contexts:
DEFINITION MISSING
brapi:observationLevelRelationships
Object Contexts:
Observation levels indicate the granularity level at which the measurements are taken. `levelName` defines the level `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are at the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify this observation unit by each level of the hierarchy where it exists
brapi:observationLevels
Object Contexts:
Observation levels indicate the granularity level at which the measurements are taken. `levelName` defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are at the bottom of the hierarchy (ie plant > 6).
brapi:observationTimeStamp
Object Contexts:
The date and time when this observation was made
brapi:observationUnitDbId
Object Contexts:
The related observation unit identifier, if relevant.
The ID which uniquely identifies an observation unit
Object Contexts:
the unique identifier for an observation unit
brapi:observationUnitDbIds
Object Contexts:
A list of the affected observation units. If this parameter is not given, it is understood that the event affected all units in the study
brapi:observationUnitName
A human readable name for an observation unit
Object Contexts:
the human readable name for an observation unit
brapi:observationUnitPUI
Object Contexts:
A Permanent Unique Identifier for an observation unit MIAPPE V1.1 (DM-72) External ID - 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.
brapi:observationUnitPosition
Object Contexts:
DEFINITION MISSING
brapi:observationUnitsDescription
Object Contexts:
MIAPPE V1.1 (DM-25) Observation unit description - General description of the observation units in the study.
brapi:observationVariableDbId
Object Contexts:
The ID which uniquely identifies an observation variable
Variable unique identifier
brapi:observationVariableDbIds
Object Contexts:
The DbIds of Variables to search for
brapi:observationVariableName
Object Contexts:
A human readable name for an observation variable
Variable name (usually a short name)
brapi:observationVariableNames
Object Contexts:
The names of Variables to search for
brapi:observationVariables
The list of observation variables which have values recorded for them in the data matrix. Append to the 'headerRow' for complete header row of the table.
brapi:offset
Object Contexts:
The offset position (0-based) of the given sequence from the start of this `Reference`. This value will differ for each page in a request.
brapi:ontologyDbId
Ontology database unique identifier
brapi:ontologyName
Ontology name
brapi:ontologyReference
Object Contexts:
DEFINITION MISSING
brapi:orcid
Object Contexts:
The Open Researcher and Contributor ID for this contact person (orcid.org) MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended.
brapi:orderId
Object Contexts:
The order id returned by the vendor when the order was successfully submitted.
Object Contexts:
A unique, alpha-numeric ID which identifies the order
brapi:organismName
Object Contexts:
Scientific organism name
brapi:organizationName
Object Contexts:
The name of the organization that manages this server and data
brapi:organizationURL
Object Contexts:
The URL of the organization that manages this server and data
brapi:page
Object Contexts:
Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.
brapi:pageSize
The size of the pages to be returned. Default is `1000`.
Object Contexts:
The number of data elements returned, aka the size of the current page. If the requested page does not have enough elements to fill a page at the requested page size, this field should indicate the actual number of elements returned.
brapi:pageToken
Object Contexts:
Used to request a specific page of data to be returned. Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively.
brapi:parameterName
Object Contexts:
Name of the environment parameter constant within the experiment
brapi:parameterPUI
Object Contexts:
URI pointing to an ontology class for the parameter
brapi:parent1
DEFINITION MISSING
brapi:parent2
DEFINITION MISSING
brapi:parentType
Object Contexts:
The type of parent ex. 'MALE', 'FEMALE', 'SELF', 'POPULATION', etc.
Object Contexts:
The type of parent the parent is. ex. 'MALE', 'FEMALE', 'SELF', 'POPULATION', etc.
Object Contexts:
Given a germplasm A having a progeny B and C, 'parentType' for progeny B item refers to the 'parentType' of A toward B.
brapi:parents
Object Contexts:
List of parent nodes in the pedigree tree.
brapi:pedigree
Object Contexts:
The cross name and optional selection history.
Object Contexts:
The string representation of the pedigree.
brapi:phaseSet
Object Contexts:
If this field is populated, this variant call's genotype ordering implies the phase of the bases and is consistent with any other variant calls on the same contig which have the same phase set string.
brapi:phoneNumber
Object Contexts:
phone number of this person
brapi:plannedCrossName
Object Contexts:
the human readable name for a cross
brapi:plateDbId
Object Contexts:
The ID which uniquely identifies a plate of samples
brapi:plateName
Object Contexts:
The human readable name of a plate
brapi:plates
Array of new plates to be submitted to a vendor
brapi:pollinationTimeStamp
Object Contexts:
the timestamp when the pollination took place
brapi:position
Object Contexts:
The position of a marker within a linkage group
brapi:positionCoordinateX
Object Contexts:
The X position coordinate for an observation unit. Different systems may use different coordinate systems.
brapi:positionCoordinateXType
Object Contexts:
The type of positional coordinate used. Must be one of the following values LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details LATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details PLANTED_ROW - The physical planted row number PLANTED_INDIVIDUAL - The physical counted number, could be independant or within a planted row GRID_ROW - The row index number of a square grid overlay GRID_COL - The column index number of a square grid overlay MEASURED_ROW - The distance in meters from a defined 0-th row MEASURED_COL - The distance in meters from a defined 0-th column
brapi:positionCoordinateY
Object Contexts:
The Y position coordinate for an observation unit. Different systems may use different coordinate systems.
brapi:positionCoordinateYType
Object Contexts:
The type of positional coordinate used. Must be one of the following values LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details LATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details PLANTED_ROW - The physical planted row number PLANTED_INDIVIDUAL - The physical counted number, could be independant or within a planted row GRID_ROW - The row index number of a square grid overlay GRID_COL - The column index number of a square grid overlay MEASURED_ROW - The distance in meters from a defined 0-th row MEASURED_COL - The distance in meters from a defined 0-th column
brapi:progeny
Object Contexts:
List of germplasm entities which are direct children of this germplasm
brapi:programDbId
Object Contexts:
A program identifier to search for
Object Contexts:
The ID which uniquely identifies a program
Object Contexts:
The ID which uniquely identifies a program within the given database server
Object Contexts:
the unique identifier for a program
Object Contexts:
Unique DbId of the breeding Program this Seed Lot belongs to
brapi:programDbIds
Object Contexts:
A program identifier to search for
brapi:programName
Human readable name of the program
Object Contexts:
The human readable name of a program
Object Contexts:
the human readable name for a program
brapi:programNames
Object Contexts:
A name of a program to search for
brapi:provenance
Object Contexts:
The description of the origin or ownership of this linked data. Could be a formal reference to software, method, or workflow.
brapi:publicReleaseDate
Object Contexts:
MIAPPE V1.1 (DM-6) Public release date - Date of first public release of the dataset presently being described.
brapi:publicationPUI
Object Contexts:
DEFINITION MISSING
brapi:publicationReference
Object Contexts:
DEFINITION MISSING
brapi:publications
Object Contexts:
MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended.
brapi:publishedDate
Object Contexts:
The date this genome was published
brapi:rdfValue
Object Contexts:
The type of the value given above, e.g. http://xmlns.com/foaf/0.1/Agent
brapi:referenceBases
Object Contexts:
The reference bases for this variant. They start at the given start position.
brapi:referenceDbId
Object Contexts:
The reference ID. Unique within the repository.
brapi:referenceName
Object Contexts:
The unique name of this reference within the Reference Set (e.g. '22').
Object Contexts:
The reference on which this variant occurs. (e.g. `chr_20` or `X`)
brapi:referenceSetDbId
Object Contexts:
The reference set ID. Unique in the repository.
Object Contexts:
The ID of the reference set that describes the sequences used by the variants in this set.
brapi:referenceSetName
Object Contexts:
The reference set name.
brapi:remarks
Object Contexts:
MCPD (v2.1) (REMARKS) 28. The remarks field is used to add notes or to elaborate on descriptors with value 99 or 999 (= Other). Prefix remarks with the field name they refer to and a colon (:) without space (e.g. COLLSRC:riverside). Distinct remarks referring to different fields are separated by semi-colons without space.
brapi:requiredServiceInfo
Object Contexts:
A map of additional data required by the requested service. This includes things like Volume and Concentration.
brapi:row
The Row identifier for this samples location in the plate
brapi:safetyDuplicateInstitutes
Object Contexts:
DEFINITION MISSING
brapi:sampleBarcode
Object Contexts:
A unique identifier physically attached to the sample
brapi:sampleDbId
Object Contexts:
The Biosample entity the call set data was generated from.
brapi:sampleDescription
Object Contexts:
Description of a sample MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing.
brapi:sampleGroupDbId
Object Contexts:
The ID which uniquely identifies a group of samples
brapi:sampleName
Object Contexts:
The name of the sample
brapi:samplePUI
Object Contexts:
A permanent unique identifier for the sample (DOI, URL, UUID, etc) MIAPPE V1.1 (DM-81) External ID - An identifier for the sample in a persistent repository, comprising the name of the repository and the accession number of the observation unit therein. Submission to the EBI Biosamples repository is recommended. URI are recommended when possible.
brapi:sampleSubmissionFormat
DEFINITION MISSING
brapi:sampleTimestamp
Object Contexts:
The date and time a sample was collected from the field MIAPPE V1.1 (DM-80) Collection date - The date and time when the sample was collected / harvested
brapi:sampleType
Object Contexts:
The type of sample taken. ex. 'DNA', 'RNA', 'Tissue', etc
Object Contexts:
The type of Samples being submitted
brapi:samples
DEFINITION MISSING
brapi:scale
Object Contexts:
DEFINITION MISSING
brapi:scaleName
Object Contexts:
Name of the scale MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable
brapi:scientificName
Object Contexts:
Full scientific binomial format name. This includes Genus, Species, and Sub-species
brapi:scientificType
Object Contexts:
The general type of data. For example- Genotyping, Phenotyping raw data, Phenotyping reduced data, Environmental, etc
brapi:scientist
Object Contexts:
Name of scientist submitting the variable.
brapi:season
Object Contexts:
Name of the season. ex. 'Spring', 'Q2', 'Season A', etc.
Object Contexts:
DEFINITION MISSING
brapi:seasonDbId
Object Contexts:
The ID which uniquely identifies a season. For backward compatibility it can be a string like '2012', '1957-2004'
brapi:seasons
Object Contexts:
List of seasons over which this study was performed.
brapi:seedLotDbId
Object Contexts:
The unique identifier for the originating Seed Lot
brapi:seedLotDescription
Object Contexts:
A general description of this Seed Lot
brapi:seedLotName
Object Contexts:
A human readable name for this Seed Lot
brapi:seedSource
Object Contexts:
The source of the seed
brapi:seedSourceDescription
Object Contexts:
Description of the material source
brapi:sequence
Object Contexts:
A sub-string of the bases that make up this reference. Bases are represented as IUPAC-IUB codes; this string matches the regular expression `[ACGTMRWSYKVHDBN]*`.
brapi:serverDescription
Object Contexts:
A description of this server
brapi:serverName
Object Contexts:
The name of this server
brapi:service
Object Contexts:
The name of the available call as recorded in the documentation
brapi:serviceDescription
Object Contexts:
Description of the vendor platform
brapi:serviceId
Object Contexts:
Unique identifier for this service
brapi:serviceIds
Object Contexts:
A list of unique, alpha-numeric ID which identify the requested services to be applied to this order. A Vendor Service defines what platform, technology, and markers will be used. A list of available service IDs can be retrieved from the Vendor Specs.
brapi:serviceName
Object Contexts:
The human readable name of a platform
brapi:servicePlatformMarkerType
Object Contexts:
The type of markers used in this services platform
brapi:servicePlatformName
Object Contexts:
The technology platform used by this service
brapi:services
Object Contexts:
List of platform specifications available at the vendor
brapi:shipmentForms
Object Contexts:
Array of paper forms which need to be printed and included with the physical shipment
brapi:siblings
Object Contexts:
List of sibling germplasm
brapi:siteStatus
Object Contexts:
Description of the accessibility of the location (ex. Public, Private)
brapi:slope
Object Contexts:
Describes the approximate slope (height/distance) of the location.
brapi:software
Object Contexts:
The software run to generate this analysis.
brapi:sourceAccessions
Object Contexts:
All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) which must include a version number, e.g. `GCF_000001405.26`.
Object Contexts:
All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, e.g. `NC_000001.11`.
brapi:sourceCollection
Object Contexts:
The description of the source where this material was originally collected (wild, nursery, etc)
brapi:sourceDivergence
Object Contexts:
The `sourceDivergence` is the fraction of non-indel bases that do not match the reference this message was derived from.
brapi:sourceName
Object Contexts:
The human readable name of the taxonomy provider
brapi:sourceURI
Object Contexts:
The URI from which the sequence was obtained. Specifies a FASTA format file/string with one name, sequence pair. In most cases, clients should call the `getReferenceBases()` method to obtain sequence bases for a `Reference` instead of attempting to retrieve this URI.
Object Contexts:
Specifies a FASTA format file/string.
brapi:spatialReferenceSystem
Object Contexts:
MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial reference system upon which the coordinates given in decimal latitude and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 datum.
brapi:species
DEFINITION MISSING
Object Contexts:
MCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: "sp."
Object Contexts:
Specific epithet portion of the scientific name in lowercase letters. MCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: "sp." MIAPPE V1.1 (DM-44) Species - Species name (formally: specific epithet) for the organism under study, according to standard scientific nomenclature.
brapi:speciesAuthority
Object Contexts:
MCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name.
Object Contexts:
The authority organization responsible for tracking and maintaining the species name MCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name.
brapi:speciesName
Object Contexts:
Scientific species name
brapi:specificRequirements
Object Contexts:
Additional arbitrary requirements for a particular platform
brapi:start
Object Contexts:
This field is optional and may be ignored if there is no relevant map or reference to be associated with. The start position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases. Genomic positions are non-negative integers less than reference length. Variants spanning the join of circular genomes are represented as two variants one on each side of the join (position 0).
brapi:startDate
Object Contexts:
The date this study started MIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started
Object Contexts:
The date this trial started
brapi:status
Object Contexts:
Trait status (examples: "recommended", "obsolete", "legacy", etc.)
Object Contexts:
Variable status. (examples: "recommended", "obsolete", "legacy", etc.)
Object Contexts:
The status field contains a list of informational status messages from the server. If no status is reported, an empty list should be returned. See Error Reporting for more information.
brapi:storageLocation
Object Contexts:
Description the storage location
brapi:storageTypeCodes
Object Contexts:
MCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) 10) Seed collection 11) Short term 12) Medium term 13) Long term 20) Field collection 30) In vitro collection 40) Cryo-preserved collection 50) DNA collection 99) Other (elaborate in REMARKS field)
brapi:storageTypes
Object Contexts:
The type of storage this germplasm is kept in at a genebank.
brapi:studyCode
Object Contexts:
A short human readable code for a study
brapi:studyDbId
Object Contexts:
The study in which the event occurred
Object Contexts:
The ID which uniquely identifies a study within the given database server
Object Contexts:
The ID of the dataset this variant set belongs to.
brapi:studyDbIds
Object Contexts:
List of study identifiers to search for
brapi:studyDescription
Object Contexts:
The description of this study MIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study
brapi:studyName
Object Contexts:
The human readable name for a study MIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study
Object Contexts:
The human readable name for a study
brapi:studyNames
Object Contexts:
List of study names to filter search results
brapi:studyPUI
Object Contexts:
A permanent unique identifier associated with this study data. For example, a URI or DOI
brapi:studyType
Object Contexts:
The type of study being performed. ex. "Yield Trial", etc
brapi:submissionDate
Object Contexts:
MIAPPE V1.1 (DM-5) Submission date - Date of submission of the dataset presently being described to a host repository.
brapi:submissionId
Object Contexts:
A unique, alpha-numeric ID which identifies a set of plates which have been successfully submitted.
brapi:submissionTimestamp
Object Contexts:
Timestamp when the Variable was added (ISO 8601)
brapi:subtaxa
Object Contexts:
Subtaxon can be used to store any additional taxonomic identifier. MCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: "subsp." (for subspecies); "convar." (for convariety); "var." (for variety); "f." (for form); "Group" (for "cultivar group"). MIAPPE V1.1 (DM-44) Infraspecific name - 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).
brapi:subtaxaAuthority
Object Contexts:
The authority organization responsible for tracking and maintaining the subtaxon information MCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level.
brapi:subtaxon
Object Contexts:
MCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: "subsp." (for subspecies); "convar." (for convariety); "var." (for variety); "f." (for form); "Group" (for "cultivar group").
brapi:subtaxonAuthority
Object Contexts:
MCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level.
brapi:svlen
Object Contexts:
Length of the - if labeled as such in variant_type - structural variation. Based on the use in VCF v4.2
brapi:synonym
Object Contexts:
Alternative name or ID used to reference this germplasm
brapi:synonyms
Object Contexts:
Other trait names
Object Contexts:
Other variable names
Object Contexts:
List of alternative names or IDs used to reference this germplasm
brapi:takenBy
Object Contexts:
The name or identifier of the entity which took the sample from the field
brapi:taxonId
Object Contexts:
The identifier (name, ID, URI) of a particular taxonomy within the source provider
brapi:taxonIds
Object Contexts:
The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as "ncbiTaxon" preferably with a purl. The rank of this ID should be species. MIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended.
brapi:taxonomyOntologyReference
Object Contexts:
DEFINITION MISSING
brapi:term
Object Contexts:
Ontology term - the label of the ontology term the termId is pointing to.
brapi:termURI
Object Contexts:
Ontology term identifier - the CURIE for an ontology term. It differs from the standard GA4GH schema's :ref:`id ` in that it is a CURIE pointing to an information resource outside of the scope of the schema or its resource implementation.
brapi:timestamp
Object Contexts:
DEFINITION MISSING
brapi:tissueType
Object Contexts:
The type of tissue sampled. ex. 'Leaf', 'Root', etc. MIAPPE V1.1 (DM-78) Plant anatomical entity - 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).
Object Contexts:
The type of tissue in this sample. List of accepted tissue types can be found in the Vendor Specs.
brapi:tissueTypeOntologyReference
Object Contexts:
DEFINITION MISSING
brapi:toSeedLotDbId
Object Contexts:
The identifier for the Seed Lot being transfered into
brapi:topography
Object Contexts:
Describes the topography of the land at the location. (ex. Plateau, Cirque, Hill, Valley, etc)
brapi:totalCount
Object Contexts:
The total number of elements that are available on the server and match the requested query paramters.
brapi:totalPages
Object Contexts:
The total number of pages of elements available on the server. This should be calculated with the following formula. totalPages = CEILING( totalCount / requested_page_size)
brapi:trait
Object Contexts:
DEFINITION MISSING
brapi:traitClass
Object Contexts:
Trait class. (examples: "morphological", "phenological", "agronomical", "physiological", "abiotic stress", "biotic stress", "biochemical", "quality traits", "fertility", etc.)
brapi:traitDescription
Object Contexts:
The description of a trait
brapi:traitName
Object Contexts:
The human readable name of a trait MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation
brapi:transactionDescription
Object Contexts:
A general description of this Seed Lot Transaction
brapi:transactionTimestamp
Object Contexts:
The time stamp for when the transaction occured
brapi:treatments
Object Contexts:
List of treatments applied to an observation unit. MIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit.
brapi:trialDbId
The ID which uniquely identifies a trial
Object Contexts:
The ID which uniquely identifies a trial within the given database server
brapi:trialDbIds
Object Contexts:
The ID which uniquely identifies a trial to search for
brapi:trialDescription
Object Contexts:
The human readable description of a trial MIAPPE V1.1 (DM-4) Investigation description - Human-readable text describing the investigation in more detail.
brapi:trialName
The human readable name of a trial
Object Contexts:
The human readable name of a trial MIAPPE V1.1 (DM-3) Investigation title - Human-readable string summarising the investigation.
brapi:trialNames
Object Contexts:
The human readable name of a trial to search for
brapi:trialPUI
Object Contexts:
A permanent identifier for a trial. Could be DOI or other URI formatted identifier.
brapi:type
Object Contexts:
The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.) MIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation
Object Contexts:
DEFINITION MISSING
Object Contexts:
The literal string "Feature"
Object Contexts:
The literal string "Point"
Object Contexts:
The literal string "Polygon"
Object Contexts:
The type of analysis.
Object Contexts:
The type of map this represents, usually "Genetic"
Object Contexts:
A descriptive classification for this synonym
brapi:unit
Object Contexts:
Unit of the value for this parameter
Object Contexts:
The units used to describe the data in this map
brapi:unitPUI
Object Contexts:
URI pointing to an ontology class for the unit
brapi:units
Object Contexts:
Units (example: "ng/ul")
Object Contexts:
Description of the things being counted in this Seed Lot (seeds, bulbs, kg, tree, etc)
Object Contexts:
Description of the things being transfered in this transaction (seeds, bulbs, kg, etc)
brapi:updated
Object Contexts:
The time at which this record was last updated, in ISO 8601 format.
Object Contexts:
The time at which this call set was last updated
Object Contexts:
The time at which this variant was last updated.
brapi:uploadedBy
Object Contexts:
The name or id of the user who uploaded the observation to the database system
brapi:url
Object Contexts:
MIAPPE V1.1 (DM-37) Data file link - 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.
brapi:userID
Object Contexts:
A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.
brapi:validValues
Object Contexts:
DEFINITION MISSING
brapi:value
Object Contexts:
Numerical or categorical value
Object Contexts:
The actual value for a category
Object Contexts:
The value of the property for this event. E.g. nitrogen, John Doe
Object Contexts:
The value of the data collected as an observation
Object Contexts:
Value (example: "2.3")
Object Contexts:
The value of this attribute for a given germplasm
brapi:valuePUI
Object Contexts:
URI pointing to an ontology class for the parameter value
brapi:values
Object Contexts:
Repeated field of dynamically typed values.
brapi:variantCount
Object Contexts:
The number of Variants included in this VariantSet
brapi:variantDbId
Object Contexts:
The ID of the variant this call belongs to.
Object Contexts:
Internal db identifier
Object Contexts:
The variant ID.
brapi:variantName
Object Contexts:
The name of the variant this call belongs to.
Object Contexts:
The human readable name for a marker
brapi:variantNames
Object Contexts:
Names for the variant, for example a RefSNP ID.
brapi:variantSetDbId
Object Contexts:
An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted.
Object Contexts:
The variant set ID.
brapi:variantSetIds
Object Contexts:
The IDs of the variant sets this call set has calls in.
brapi:variantSetName
Object Contexts:
The variant set name.
brapi:variantType
Object Contexts:
The "variant_type" is used to denote e.g. structural variants. Examples: DUP : duplication of sequence following "start" DEL : deletion of sequence following "start"
brapi:vendorAddress
Object Contexts:
The street address of the vendor
brapi:vendorCity
Object Contexts:
The name of the city where the vendor is located
brapi:vendorContact
Object Contexts:
DEFINITION MISSING
brapi:vendorContactName
Object Contexts:
The name or identifier of the primary vendor contact
brapi:vendorCountry
Object Contexts:
The name of the country where the vendor is located
brapi:vendorDescription
Object Contexts:
A description of the vendor
brapi:vendorEmail
Object Contexts:
The primary email address used to contact the vendor
brapi:vendorName
Object Contexts:
The human readable name of the vendor
brapi:vendorPhone
Object Contexts:
The primary phone number used to contact the vendor
brapi:vendorURL
Object Contexts:
The primary URL for the vendor
brapi:version
Object Contexts:
MIAPPE V1.1 (DM-39) Data file version - The version of the dataset (the actual data).
Ontology version (no specific format)
Object Contexts:
DEFINITION MISSING
brapi:versions
Object Contexts:
The supported versions of a particular call
brapi:volume
Object Contexts:
DEFINITION MISSING
brapi:well
The Well identifier for this samples location in the plate. Usually a concatenation of Row and Column, or just a number if the samples are not part of an ordered plate.
brapi:year
Object Contexts:
The 4 digit year of the season.


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The Shear class¶
-
class
galsim.
Shear
(*args, **kwargs)[source]¶ A class to represent shears in a variety of ways.
The Shear object can be initialized in a variety of ways to represent shape distortions. A shear is an operation that transforms a circle into an ellipse with minor-to-major axis ratio b/a, with position angle beta, while conserving the area (see below for a discussion of the implications of this choice). Given the multiple definitions of ellipticity, we have multiple definitions of shear:
- reduced shear
\(|g| = \frac{a - b}{a + b}\)
- distortion
\(|e| = \frac{a^2 - b^2}{a^2 + b^2}\)
- conformal shear
\(\eta = \log(b/a)\)
- minor-to-major axis ratio
\(q = \frac{b}{a}\)
These can be thought of as a magnitude and a real-space position angle \(\beta\), or as two components, e.g., \(g_1\) and \(g_2\), with:
\[\begin{split}g_1 &= |g| \cos(2 \beta) \\ g_2 &= |g| \sin(2 \beta)\end{split}\]Note: \(\beta\) is _not_ the phase of a complex valued shear. Rather, the complex shear is \(g_1 + i g_2 = g \exp(2 i \beta)\). Likewise for \(\eta\) or \(e\). The phase of the complex value is \(2 \beta\).
The following are all examples of valid calls to initialize a Shear object:
>>> s = galsim.Shear() # empty constructor sets ellipticity/shear to zero >>> s = galsim.Shear(g1=0.05, g2=0.05) >>> s = galsim.Shear(g1=0.05) # assumes g2=0 >>> s = galsim.Shear(e1=0.05, e2=0.05) >>> s = galsim.Shear(e2=0.05) # assumes e1=0 >>> s = galsim.Shear(eta1=0.07, eta2=-0.1) >>> s = galsim.Shear(eta=0.05, beta=45.0*galsim.degrees) >>> s = galsim.Shear(g=0.05, beta=0.25*numpy.pi*galsim.radians) >>> s = galsim.Shear(e=0.3, beta=30.0*galsim.degrees) >>> s = galsim.Shear(q=0.5, beta=0.0*galsim.radians) >>> s = galsim.Shear(0.05 + 0.03j) # Uses the g1,g2 reduced shear definition
There can be no mixing and matching, e.g., specifying
g1
ande2
. It is permissible to only specify one of two components, with the other assumed to be zero. If a magnitude such ase
,g
,eta
, orq
is specified, thenbeta
is also required to be specified. It is possible to initialize a Shear with zero reduced shear by specifying no args or kwargs, i.e.galsim.Shear()
.In addition, for use cases where extreme efficiency is required, you can skip all the normal sanity checks and branches in the regular Shear constructor by using a leading underscore with the complex shear
g1 + 1j * g2
:>>> s = galsim._Shear(0.05 + 0.03j) # Equivalent to galsim.Shear(g1=0.05, g2=0.03)
Analagous to the construction options, one can access the shear in the same variety of definitions.
- Attributes
g1 – The first component of the shear in the “reduced shear” definition.
g2 – The second component of the shear in the “reduced shear” definition.
g – The magnitude of the shear in the “reduced shear” definition.
e1 – The first component of the shear in the “distortion” definition.
e2 – The second component of the shear in the “distortion” definition.
e – The magnitude of the shear in the “distortion” definition.
eta1 – The first component of the shear in the “conformal shear” definition.
eta2 – The second component of the shear in the “conformal shear” definition.
eta – The magnitude of the shear in the “conformal shear” definition.
q – The minor-to-major axis ratio
beta – The position angle as an
Angle
instanceshear – The reduced shear as a complex number g1 + 1j * g2.
Note
Since we have defined a Shear as a transformation that preserves area, this means that it is not a precise description of what happens during the process of weak lensing.
The coordinate transformation that occurs during the actual weak lensing process is such that if a galaxy is sheared by some \((\gamma_1, \gamma_2)\), and then sheared by \((-\gamma_1, -\gamma_2)\), it will in the end return to its original shape, but will have changed in area due to the magnification,
\[\mu = \frac{1}{(1-\kappa)^2 - (\gamma_1^2 + \gamma_2^2)}\]which is not equal to 1 for non-zero shear even for convergence \(\kappa=0\).
Application of a
Shear
using theGSObject.shear
method does not include this area change. To properly incorporate the effective change in area due to shear, it is necessary to either:define the Shear object, use the
GSObject.shear
method, and separately use theGSObject.magnify
method, oruse the
GSObject.lens
method that simultaneously magnifies and shears.
-
property
e
¶ The magnitude of the shear in the “distortion” definition.
-
property
e1
¶ The first component of the shear in the “distortion” definition.
-
property
e2
¶ The second component of the shear in the “distortion” definition.
-
property
esq
¶ The square of the magnitude of the shear in the “distortion” definition.
-
property
eta
¶ The magnitude of the shear in the “conformal shear” definition.
-
property
eta1
¶ The first component of the shear in the “conformal shear” definition.
-
property
eta2
¶ The second component of the shear in the “conformal shear” definition.
-
property
g
¶ The magnitude of the shear in the “reduced shear” definition.
-
property
g1
¶ The first component of the shear in the “reduced shear” definition.
-
property
g2
¶ The second component of the shear in the “reduced shear” definition.
-
getMatrix
()[source]¶ Return the matrix that tells how this shear acts on a position vector:
If a field is sheared by some shear, s, then the position (x,y) -> (x’,y’) according to:
\[\begin{split}\left( \begin{array}{c} x^\prime \\ y^\prime \end{array} \right) = S \left( \begin{array}{c} x \\ y \end{array} \right)\end{split}\]and \(S\) is the return value of this function
S = shear.getMatrix()
.Specifically, the matrix is
\[\begin{split}S = \frac{1}{\sqrt{1-g^2}} \left( \begin{array}{cc} 1+g_1 & g_2 \\ g_2 & 1-g_1 \end{array} \right)\end{split}\]
-
property
q
¶ The minor-to-major axis ratio
-
rotationWith
(other)[source]¶ Return the rotation angle associated with the addition of two shears.
The effect of two shears is not just a single net shear. There is also a rotation associated with it. This is easiest to understand in terms of the matrix representations:
If
shear3 = shear1 + shear2
is a sum of two shears, and the corresponding shear matrices are \(S_1\), \(S_2\), and \(S_3\), then \(S_3 R = S_1 S_2\), where \(R\) is a rotation matrix:\[\begin{split}R = \left( \begin{array}{cc} cos(\theta) & -sin(\theta) \\ sin(\theta) & cos(\theta) \end{array} \right)\end{split}\]and \(\theta\) is the return value (as a
galsim.Angle
) fromshear1.rotationWith(shear2)
.
-
property
shear
¶ The reduced shear as a complex number g1 + 1j * g2.
-
galsim.
_Shear
(shear)[source]¶ Equivalent to
galsim.Shear(shear)
, but without the overhead of the normal sanity checks and other options for how to specify the shear.- Parameters
shear – The complex shear g1 + 1j * g2.
- Returns
a
galsim.Shear
instance


Situated on the west coast of Ireland, Westport is a charming, planned town, built in the Georgian style and has an attractive walk alongside the river Carrow Beg. It is a major tourist destination because of its magnificent scenery.
This small port, Westport Quays, although once busy, is no longer used commercially. Westport Bay provides many sheltered anchorages whatever the weather but beware of the fish farms and shellfish beds.
Cruisers who need pilotage information can contact the Mayo Sailing Club or Glenans Irish Sailing Club. SSCA members can contact Alex Blackwell based in Westport and acting as the SSCA Cruising Station for Ireland.
Last updated February 2011.


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HAVANA A film review by Wayne V. Citrin Copyright 1990 Wayne V. Citrin
It's December 1958, and a gambler (Robert Redford) is on his way to Havana to earn some money playing high-stakes poker, as he regularly does. On the boat, he does a favor for a beautiful woman (Lena Olin - THE UNBEARABLE LIGHTNESS OF BEING, ENEMIES, A LOVE STORY). Their paths cross again in Havana, and Redford spends the rest of the film pursuing both Olin and the big score. But the Batista government is on its last legs, the rebels are about to win, and the revolution ultimately upsets Redford's plans for both Olin and the score.
HAVANA starts off encouragingly, with a beautifully edited montage of scenes designed to make Havana seem sensual, exciting, and dangerous. This atmosphere is sustained for about an hour into the film, and then the love story takes over and things fall flat. Apart, Redford and Olin are fine. Redford (looking much older than I've ever seen him) is a convincing man of the world, and Olin's performance has considerable depth, giving the feeling that her character's political convictions are genuine. But when they get together, the chemistry isn't there. This is unfortunate, because it becomes obvious fairly early on that HAVANA is a remake of CASABLANCA, with Redford and Olin in the Bogart and Bergman roles. In the scenes without Olin, Redford pulls this off fairly well, but when he has to be tender with Olin it just seems lame and out of character. It's no spoiler to say that the film develops in much the same way CASABLANCA does, although the price that Redford is forced to pay at the end is much less than Bogart ultimately had to pay, which I felt trivialized the ending. The conclusion contains some rather incoherent events relating to the CIA's involvement in Batista's government, which I felt blunted the impact of the film (the incoherence, that is, not the presence of the CIA itself).
HAVANA does a very good job of presenting what the atmosphere and feel of the city must have been like at that time, at least to a visiting American. There's not much discussion of how the city must have seemed to poor Cubans and rebels, although that wasn't the point of the film and could be excused. The film does a good job of contrasting the decadence of the city with the war in the countryside and the brutality of the secret police that underlies everyday life.
The film was shot in Santo Domingo, and the filmmakers were impressively successful in reproducing the feeling of familiarity and strangeness that Havana must have presented to Americans of the late 1950s. Americans don't think much about Havana anymore; we're reminded here that the city was a (long) ferry ride away, and that Americans once considered the place not entirely foreign soil.
The supporting cast is good. Alan Arkin does an excellent job as Redford's friend, a casino manager with no illusions about what's coming. (This is the Claude Rains part.) The husband of the Olin character, played by Raul Julia in an uncredited role (due to a dispute over the billing to which Julia was entitled) is good in the Paul Henried part, and the actor who plays the chief of police (whose name I didn't catch) is also good.
In short, the film is not bad, but it's no CASABLANCA (although there's no shame in that). It needed a more convincing love story, and the ending should have both hurt more and been more exhilarating, in the manner of CASABLANCA.
I'd give it two-and-a-half stars (out of four).
Wayne
.
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