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Version: 2.0
Template Description: This template aims to provide a uniform, well-defined format for the recording of phenotype data. The template allows a high degree of customization. Almost any trait can be incorporated. The format is adapted from the ICIS fieldbook. In principle the template allows the storage of raw experimental data. However in most cases, e.g. for the publication of the data in the GCP Central Registry, the data would preferable be cleaned and summarized up to a level where it would be of more immediate use to other users. This template aims to provide a uniform, well-defined format for the recording of phenotype data. The template allows a high degree of customization. Almost any trait can be incorporated. The format is adapted from the ICIS fieldbook. In principle the template allows the storage of raw experimental data. However in most cases, e.g. for the publication of the data in the GCP Central Registry, the data would preferable be cleaned and summarized up to a level where it would be of more immediate use to other users.
Introduction
This template aims to provide a uniform, well-defined format for the recording of phenotype data. The template allows a high degree of customization. Almost any trait can be incorporated. The format is adapted from the ICIS fieldbook. In principle the template allows the storage of raw experimental data. However in most cases, e.g. for the publication of the data in the GCP Central Registry, the data would preferable be cleaned and summarized up to a level where it would be of more immediate use to other users.
Mappings for this template
Sections available in this template
| Section Name | Description | Conditions |
| Source | Information on the source of the dataset, the species it concerns and the name and version of the dataset | Mandatory
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| Experiment | General experiment data | Mandatory
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| Quality Assessment | Information about the quality measures used | Mandatory
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| Experimental Sites | Description of the experimental sites. | Mandatory
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| Factors and Variates | Description of the factors (e.g. identifiers, treatments etc) and the variates (e.g. traits) used. | Mandatory
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| Data | The data matrix. | Mandatory
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| Accessions | | Optional
Multiple sheets allowed
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| Institutions | List of institute codes used in passport data sections and their corresponding decoded name and addresses. | Optional
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Source
Section Description: Information on the source of the dataset, the species it concerns and the name and version of the dataset
see section: source in GCPDataSubmissionTemplate2.0
for the following fields
institute, principalInvestigator, projectCode, projectName, emailContact, species, ploidy, datasetName, version, creationDate, remark
Experiment
Section Description: General experiment data
| Field Name | Description | Conditions |
| Purpose of Experiment | Purpose of the experiment
Example: Standard genebank evaluation. | Mandatory
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| Experimental Design | Test describing the design of the experiment
Example: Randomized complete block | Mandatory
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| Missing Data | Information about missing data. Must be in the form missing data symbol=description. Multiple missing data symbols can be separated with a semi colon.
Example: 9=For each marker there are upto five possible alleles, 9 is uses to represent the absence of 2nd, 3rd, 4th and/or 5th alllele. | Mandatory
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| Remark | none | Optional
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Quality Assessment
Section Description: Information about the quality measures used
see section: qualityAssessment in GCPDataSubmissionTemplate2.0
for the following fields
qualityMeasure, standard, control, errorEstimator
Experimental Sites
Section Description: Description of the experimental sites.
| Field Name | Description | Conditions |
| Site ID | Unique site identifier where the experiment was executed. For multi-location experiments provide a Site ID and description for each site.
Example: s1 | Mandatory
Unique
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| Country | Code of the country where experimental site is located. Use 3-letter ISO 3166-1 extended country codes.
Example: PHL | Optional
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| Primary Admin Subdivision | Name of the primary administrative subdivision of a country in which the site is located (e.g. state or province names).
Example: Bulakan | Optional
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| Secondary Admin Subdivision | Name of the secondary administrative subdivision of the country in which the site is located (e.g. county or department name). | Optional
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| Locality | Location information below the country level (or any other more detailed sub-country levels used) that describes where the site is located.
Example: Santa Maria | Optional
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| Name experimental site | Name experimental site
Example: Santa Maria experimental fields, sector IV | Mandatory
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| Latitude string | Latitude of collecting site. Degree (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.
Example: 10----S
Example: 011530N
Example: 4531--S | Optional
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| Longitude string | Longitude of collecting site. Degree (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.
Example: 0762510W
Example: 076----W | Optional
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| Latitude decimal | Latitude of collecting site. | Optional
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| Longitude decimal | Longitude of collecting site. | Optional
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| Elevation | Elevation of experimental site expressed in meters above sea level. Negative values are allowed.
Example: 763
Example: 200 | Optional
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| Coordinate error distance | The upper limit of the distance (in meters) from the given latitude and longitude describing a circle within which the whole of the described locality must lie. Use NULL where the uncertainty is unknown, cannot be estimated, or is not applicable (because there are no coordinates).
Example: 250 | Optional
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| Institution | The Institute where the experiment was done. If FAO institute code does not exist create a temporary code which starts with an asterisk followed by the 3-letter ISO country code representing the country where the institute is located and the institute's acronym (e.g. '*NLDIFG').
Example: MEX002 | Optional
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| Remark | none | Optional
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Factors and Variates
Section Description: Description of the factors (e.g. identifiers, treatments etc) and the variates (e.g. traits) used.
| Field Name | Description | Conditions |
| Type | Indicate either FACTOR or VARIATE as type. FACTORS can be identifiers, treatments etc. The factor <b>GermplasmID is obligatory</b>. Use VARIATE for any of the traits being evaluated.
Example: FACTOR
Example: VARIATE | Mandatory
Unique
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| Label | Column label used for the factor or variate. Germplasm ID is obligatory. Additional factors such as variety names or accession names can be listed to facilitate crosschecking with passport data. Treatments can also be defined as factors (e.g. 'irrigation'). Likewise the column labels for the variates (traits) are listed here.
Example: AccName | Mandatory
Unique
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| Description | Description of the factor or variate.
Example: Accession name | Mandatory
Unique
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| Property | Property of the factor or variate.
Example: Accession name | Optional
Unique
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| Scale | Scale that is used to express the value of the factor or variate (if appropriate). | Optional
Unique
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| Method | Description of method.
Example: Either a registered or other formal designation given to the accession. First letter uppercase. Multiple names separated with semicolon without space. | Mandatory
Unique
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| Data Type | Indicates data type. Must be one of character, integer or decimal
Example: character | Mandatory
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Data
Section Description: The data matrix.
| Field Name | Description | Conditions |
| Site ID | Unique site identifier where the experiment was executed. Sites are described in worksheet �Experimental sites’. <b>Must<b> relate to the a Site ID in the Experiment Sites section.
Example: s1 | Mandatory
Unique
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| Germplasm ID | A unique alphanumeric value which identifies the germplasm. This global identifier links data across domains. The format proposed is concatenation of holdingInstitute:collectionName:localUniqueID.
Example: PHL000:Rice collection:00001 | Mandatory
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| Data | none
Example: IR999 | Mandatory
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Accessions
Section Description: none
see section: generalPassportData in GCPPassportTemplate2.0
for the following fields
germplasmID, holdingInstitute, collectionName, localUniqueID, genus, species, countryOfOrigin
| Field Name | Description | Conditions |
| Country of origin | Code of the country in which the sample was originally collected. Use 3-letter ISO 3166-1 extended country codes. | Optional
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Institutions
Section Description: List of institute codes used in passport data sections and their corresponding decoded name and addresses.
see section: institutions in GCPDataSubmissionTemplate2.0
for the following fields
faoInstituteCode, organizationName, street, cityState, zipCode, country, institutionalEmail, institutionalTelephone, fax, url, primaryContactName
Copyright (c) 2004-2006 CIMMYT, CIMMYT, IPGRI - Rome, IPGRI - Rome, IRRI, IRRI, IRRI, IRRI, IRRI
Developed by Richard Bruskiewich (IRRI), Guy Davenport (CIMMYT), Tom Hazekamp (IPGRI - Rome), Tom Hazekamp (IPGRI - Rome), Graham McLaren (IRRI), Thomas Metz (IRRI), Thomas Payne (CIMMYT), Arllet Portugal (IRRI), Genevieve Aquino (IRRI)
This work is licensed under a Creative Commons Attribution-ShareAlike 2.5 License.
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