Guided Phenotype Upload Workflow



  1. Intro
  2. Breeding Program
  3. Locations
  4. Accessions
  5. Trials
  6. Observations
  7. Finish
  1. Introduction

    This workflow will guide your through the basic steps required for adding one or more phenotyping / field trials to the database:



    Download Templates  


  2. Breeding Program(s)

    Trials are associated with a single Breeding Program. Before a Trial can be added, the Breeding Program must already exist in the database.

    Check the table below to see if your Breeding Program has already been created.



    Breeding Programs:

    NameDescription
    Agricultural Biotechnology Research Institute, FaisalabadShahid Nazir
    Agriculture and Agri-Food CanadaRon Knox
    Agriculture and Agri-Food Canada AlbertaDean Spaner
    Agriculture and Agri-Food Canada ManitobaStephen Fox
    Agriculture and Agri-Food Canada SaskatchewanRon Depauw
    AgriPro-Syngenta
    Allele Based Breeding CooperativeABB trials performed by various Universities
    Cereal Research Institute Non-Profit Ltd.Akos Mesterhazy
    CIMMYTHans Braun
    Clemson
    Colorado State UniversityEsten Mason
    Cornell UniversityMark Sorrells
    Designing Future WheatCristobal Uauy
    Dow AgroSciencesClay Sneller
    Durum Genome Sequencing ConsortiumInternational Durum Wheat Genome Sequencing Consortium
    EVIGEZ Czech Republic
    Five State CooperativeCooperative trials of elite SRWW lines
    Genesis SeedsClay Sneller
    Gortzen
    Gulf Atlantic Wheat Nursery CooperativeCooperative trials of elite SRWW lines
    Hard Winter Wheat Fusarium Head Blight Nursery CooperativeCooperative nursery of HWW FHB trials
    Kansas State UniversityEduard Akhunov
    Kansas State University - HaysEduard Akhunov
    KWS CerealsClay Sneller
    Limagrain Cereal Seed
    LMGLimagrain Cereal Seed
    Louisiana State University
    Michigan State University
    Montana State UniversityLuther Talbert
    National Agricultural Research Development InstituteMarianna Ittu
    National SGCNational Small Grains Collection
    National Small Grains CollectionHarold Bockelman
    National Small Grains Collection - BarleyHarold Bockelman
    Nebraska USDA
    North Carolina State University
    North Dakota State University
    Ohio State University
    Oklahoma State UniversityBrett Carver
    Oregon State University
    Pioneer
    PSB Collection
    Purdue University
    Regional Scab Nursery CooperativeCooperative nursery of scab trials
    Septoria Nursery CooperativeCooperative nursery of septoria trials
    Soft Red Winter Wheat Nursery CooperativeCooperative nursery of SRWW trials
    Soft White Winter Wheat Nursery Cooperative
    South Dakota State University- Spring WheatKarl Glover
    South Dakota State University- Winter WheatSunish Sehgal
    Sunbeam ExtractClay Sneller
    TAMUTexas A&M University, Jackie Rudd
    TCAP CooperativeCooperative trials for TCAP
    Trio Hybrids
    UC DavisJorge Dubcovsky
    UniSouth Genetics
    University of Arkansas
    University of Florida
    University of Georgia
    University of GuelphClay Sneller
    University of IdahoJianli Chen
    University of Illinois
    University of Kentucky
    University of Maryland
    University of MinnesotaJim Anderson
    University of Missouri
    University of NebraskaSteve Baenziger
    University of Tennessee
    University of Wisconsin Lucia Gutierrez
    Unknown
    USDA-ARSNational
    USDA-ARS North DakotaNDG, Shiaoman Chao, Illumina genotyping lab
    Utah State UniversityMargaret Krause
    Virginia TechNicholas Santantonio
    Washington State UniversityMichael Pumphrey
    WestBredDale Clark
    Winter Wheat Scab Nursery CooperativeCooperative trials from uniform scab nurseries


    If your Breeding Program exists:

    Continue to the next step


    If your Breeding Program does not exist:

    1. Go to the Manage > Breeding Programs page
    2. Click the Add New Program button at the bottom of the page to add your Breeding Program to the database


    Detailed Instructions  


  3. Locations

    Each Trial needs to be associated with a single Location and the Location needs to exist in the database before adding a Trial. Most of our trials are associated with a location of the closest town to the field site. However, more specific locations can be used (such as a separate location for each field).

    Check the table below to see if the Location(s) of your Trial(s) have already been created.



    Locations:

    NameAbbreviationCountryTrials
    Aberdeen, IDABEIDUnited States of America36 trials
    Aberdeen, SDABESDUnited States1 trials
    Agar, SDAGASDUnited States1 trials
    Akron, COAKRCOUnited States of America18 trials
    Alliance, NEALLNEUnited States of America28 trials
    Altus, OKALTOKUnited States of America8 trials
    Ames, IAAMEIAUnited States of America10 trials
    Archer, WYARCWYUnited States of America17 trials
    Ardmore, OKARDOKUnited States of America1 trials
    Arlington, WIARLWIUnited States of America1 trials
    Baton Rouge, LABATLAUnited States of America6 trials
    Bay, ARBAYARUnited States of America9 trials
    Becker, MNBECMNUnited States1 trials
    Belle Mina, ALBELALUnited States of America4 trials
    Belleville, ILBELILUnited States of America21 trials
    Bellfield, NDBELNDUnited States of America2 trials
    Beresford, SDBERSDUnited States of America5 trials
    Billings, MTBILMTUnited States of America1 trials
    Bison, SDBISSDUnited States of America8 trials
    Blacksburg, VABLAVAUnited States of America50 trials
    Blackville, SCBLASCUnited States of America1 trials
    Bozeman, MTBOZMTUnited States of America41 trials
    Britton, SDBRISDUnited States of America1 trials
    Brookfield Twp, Huron Co, MIBROMIUnited States7 trials
    Brookings, SDBROSDUnited States of America71 trials
    Brookston, INBROINUnited States of America14 trials
    Brownstown, ILBROILUnited States of America37 trials
    Burlington, COBURCOUnited States of America15 trials
    Bushland, TXBUSTXUnited States of America15 trials
    Bushland, TX - DrylandBUSTX-DRYUnited States of America0 trials
    Bushland, TX - IrrigatedBUSTX-IRRUnited States15 trials
    Calhoun, KYCALKYUnited States of America1 trials
    Carmi, ILCARILUnited States6 trials
    Carrington, NDCARNDUnited States of America14 trials
    Casselton, NDCASNDUnited States of America8 trials
    Castle Co, DECASDEUnited States of America1 trials
    Castroville, TXCASTXUnited States of America2 trials
    Centralia, ILCENILUnited States of America1 trials
    Champaign, ILCHAILUnited States of America21 trials
    Charleston, MOCHAMOUnited States of America1 trials
    Chillicothe, TXCHITXUnited States of America13 trials
    Claire City, SDCLASDUnited States1 trials
    Clarkston, MICLAMIUnited States of America1 trials
    Clarksville, MDCLAMDUnited States of America6 trials
    Clay Center, NECLANEUnited States of America21 trials
    Cleveland, MSCLEMSUnited States of America8 trials
    Clinton, MICLIMIUnited States of America1 trials
    Clovis, NMCLONMUnited States of America20 trials
    Colby, KSCOLKSUnited States of America15 trials
    Columbia, MOCOLMOUnited States of America94 trials
    Crawfordsville, IACRAIAUnited States of America10 trials
    Crookston, MNCROMNUnited States of America23 trials
    Crowley, LACROLAUnited States of America1 trials
    Custar, OHCUSOHUnited States24 trials
    Dakota Lakes, SDDAKSDUnited States of America28 trials
    Danforth, ILDANILUnited States1 trials
    Davis, CADAVCAUnited States of America29 trials
    DeKalb, ILDEKILUnited States of America19 trials
    Debre-Zeit, EthiopiaDEBETEthiopia1 trials
    Deckerville, MIDECMIUnited States of America8 trials
    Deerfield, MIDEEMIUnited States2 trials
    Dickinson, NDDICNDUnited States of America13 trials
    Dixon Springs, ILDIXILUnited States of America16 trials
    Draper, SDDRASDUnited States1 trials
    Dundee, MIDUNMIUnited States of America1 trials
    East Lansing, MIEASMIUnited States of America59 trials
    El Centro, CAEL CAUnited States of America4 trials
    Elkville, ILELKILUnited States of America3 trials
    Enid, OKENIOKUnited States of America1 trials
    Etter, TXETTTXUnited States of America0 trials
    Evansville, INEVAINUnited States of America6 trials
    Example, NY - 50EXANY-50United States of America1 trials
    Example, NY - FOEXANY-FOUnited States of America1 trials
    Faith, SDFAISDUnited States of America3 trials
    Fargo, NDFARNDUnited States of America1 trials
    Farmington, NMFARNMUnited States of America16 trials
    Fayetteville, ARFAYARUnited States of America12 trials
    Flora, ILFLOILUnited States of America1 trials
    Florence, SCFLOSCUnited States of America3 trials
    Forman, NDFORNDUnited States of America6 trials
    Fort Cobb, OKFOROKUnited States of America8 trials
    Fort Collins, COFORCOUnited States of America20 trials
    Frankenmuth, MIFRAMIUnited States20 trials
    Fremont, OHFREOHUnited States11 trials
    Ft. Branch, INFT.INUnited States of America4 trials
    Fundulea, RomaniaFUNRORomania13 trials
    Garden City, KSGARKSUnited States of America12 trials
    Geddes, SDGEDSDUnited States of America3 trials
    Glenlea, MB, CanadaGLEMBCanada4 trials
    Goodland, KSGOOKSUnited States of America5 trials
    Goodwell, OKGOOOKUnited States of America17 trials
    Granite, OKGRAOKUnited States of America2 trials
    Grant, NEGRANEUnited States of America2 trials
    Greeley, COGRECOUnited States of America2 trials
    Greensburg, INGREINUnited States of America2 trials
    Griffin, GAGRIGAUnited States of America15 trials
    Halcomb, KYHALKYUnited States46 trials
    Hamel, ILHMLILUnited States of America1 trials
    Hampshire, ILHAMILUnited States of America2 trials
    Havre, MTHAVMTUnited States of America1 trials
    Hayes, SDHAYSDUnited States of America9 trials
    Hays, KSHAYKSUnited States of America20 trials
    Henderson, KYHENKYUnited States of America1 trials
    Hettinger, NDHETNDUnited States of America22 trials
    Highland, ILHIGILUnited States9 trials
    Highmore, SDHIGSDUnited States of America5 trials
    Hildreth, NEHILNEUnited States of America1 trials
    Hillman, MIHILMIUnited States of America1 trials
    Home Twp, MIHOTMIUnited States of America2 trials
    Hopkinsville, KYHOPKYUnited States of America1 trials
    Horse Heaven, WAHORWAUnited States of America1 trials
    Hugoton, KSHUGKSUnited States of America2 trials
    Huntley, MTHUNMTUnited States of America9 trials
    Hutchinson, KSHUTKSUnited States of America12 trials
    Ida Twp, MIIDAMIUnited States of America4 trials
    Independence, KSINDKSUnited States of America2 trials
    Ingham, MIINGMIUnited States of America3 trials
    Irvington, ILIRVILUnited States of America2 trials
    Ithaca, NEITHNEUnited States of America8 trials
    Ithaca, NYITHNYUnited States of America30 trials
    Ithaca, NY - CaldwellITHNY-CALUnited States of America13 trials
    Ithaca, NY - HelferITHNY-HELUnited States17 trials
    Ithaca, NY - KetolaITHNY-KETUnited States17 trials
    Ithaca, NY - McGowanITHNY-MCGUnited States6 trials
    Ithaca, NY - SnyderSNYNYUnited States11 trials
    Julesburg, COJULCOUnited States of America16 trials
    Kalispell, MTKALMTUnited States of America3 trials
    Kennebec, SDKENSDUnited States of America8 trials
    Kibler, ARKIBARUnited States of America4 trials
    Kimball, MNKIMMNUnited States of America4 trials
    Kinston, NCKINNCUnited States of America34 trials
    Knoxville, TNKNOTNUnited States of America4 trials
    Lafayette, INLAFINUnited States of America50 trials
    Lahoma, OKLAHOKUnited States of America17 trials
    Lake Wheeler, NCLAKNCUnited States of America2 trials
    Lamberton, MNLAMMNUnited States of America9 trials
    Langdon, NDLANNDUnited States of America18 trials
    Laporte, MILAPMIUnited States of America1 trials
    Larned, KSLARKSUnited States of America1 trials
    Laurel Springs, NCLAUNCUnited States of America4 trials
    Le Center, MNLE MNUnited States of America8 trials
    Lethbridge, ABLETABCanada12 trials
    Lexington, KYLEXKYUnited States of America74 trials
    Lexington, NCLEXNCUnited States of America0 trials
    Lincoln, NELINNEUnited States of America47 trials
    Lind, WALINWAUnited States of America8 trials
    Lisbon, NDLISNDUnited States of America5 trials
    Logan Co, KYLOGKYUnited States of America19 trials
    Mandan, NDMANNDUnited States of America7 trials
    Manhattan, KSMANKSUnited States of America41 trials
    Maricopa, AZMARAZUnited States of America10 trials
    Martin, SDMARSDUnited States of America11 trials
    Mason, MIMASMIUnited States33 trials
    McCook, NEMCCNEUnited States of America2 trials
    McGregor, TXMCGTXUnited States of America3 trials
    McLaughlin, SDMCLSDUnited States of America2 trials
    Mead, NEMEANEUnited States of America23 trials
    Merrill, MIMERMIUnited States of America2 trials
    Mexico CityMexico0 trials
    Mexico, MOMEXMOUnited States of America1 trials
    Middletown, DEMIDDEUnited States of America1 trials
    Minot, NDMINNDUnited States of America15 trials
    Moccasin, MTMOCMTUnited States of America17 trials
    Morden, MB, CanadaMORMBCanada2 trials
    Mount Holly, VAMOHVAUnited States4 trials
    Mt Vernon, SDMT SDUnited States of America1 trials
    Mt. Vernon, WAMT.WAUnited States of America39 trials
    Mulkeytown, ILMULILUnited States of America1 trials
    NWBranch, OHNWBOHUnited States of America22 trials
    Nairn, ONNAIONCanada3 trials
    Napoleon, OHNAPOHUnited States of America8 trials
    Neoga, ILNEOILUnited States of America6 trials
    New Haven, INNEWINUnited States of America1 trials
    Newport, ARNEWARUnited States of America7 trials
    Newton, MSNEWMSUnited States of America4 trials
    Njoro, KenyaNJOKEKenya1 trials
    North Platte, NENORNEUnited States of America34 trials
    Norwich, UKNUK0 trials
    Nottawa, MINOTMIUnited States of America1 trials
    Oconto, WIOCOWIUnited States of America6 trials
    Oelrichs, SDOELSDUnited States of America4 trials
    Onida, SDONISDUnited States of America8 trials
    Othello, WAOTHWAUnited States2 trials
    Ottawa, ONOTTONCanada1 trials
    Owensville, INOWEINUnited States of America2 trials
    Palmer, KSPALKSUnited States of America5 trials
    Pendleton, ORPENORUnited States of America7 trials
    Perry, ILPERILUnited States of America22 trials
    Pierre, SDPIESDUnited States of America8 trials
    Pine Bluffs, WYPINWYUnited States of America1 trials
    Plains, GAPLAGAUnited States of America16 trials
    Plankinton, SDPLASDUnited States of America2 trials
    Platte, SDPLTSDUnited States of America7 trials
    Pleasant Twp, OHPLTOHUnited States of America1 trials
    Plymouth, NCPLYNCUnited States of America4 trials
    Pomeroy, WAPOMWAUnited States of America2 trials
    Portageville, MOPORMOUnited States of America13 trials
    Princeton, INPRIINUnited States of America1 trials
    Princeton, KYPRNKYUnited States of America46 trials
    Princetown, KYPRIKYUnited States0 trials
    Prosper, NDPRONDUnited States of America23 trials
    Prosper, TXPROTXUnited States of America13 trials
    Pullman, WAPULWAUnited States of America44 trials
    Queenstown, MDQUEMDUnited States of America4 trials
    Quincy, FLQUIFLUnited States of America10 trials
    Raleigh, NCRALNCUnited States of America1 trials
    Ridgetown, ONRIDONUnited States of America22 trials
    Rodney, ONRODONUnited States of America1 trials
    Roseau, MNROSMNUnited States of America7 trials
    Rosemount, MNROSEMN17 trials
    Salina, KSSALKSUnited States of America15 trials
    Salisbury, MDSALMDUnited States of America13 trials
    Salisbury, NCSALNCUnited States of America4 trials
    Sample, NY - 50SAMNY-50United States of America1 trials
    Sample, NY - FOSAMNY-FOUnited States of America1 trials
    Saskatoon, SK, CanadaSASSKCanada1 trials
    Schochoh, KYSCHKYUnited States of America7 trials
    Selby, SDSELSDUnited States13 trials
    Sidney, MTSIDMTUnited States of America1 trials
    Sidney, NESIDNEUnited States of America31 trials
    South Charleston, OHSCHOHUnited States of America1 trials
    South Shore, SDSOUSDUnited States7 trials
    St. Jacob, ILSTJILUnited States8 trials
    St. Paul, MNST.MNUnited States of America37 trials
    Stillwater, OKSTIOKUnited States of America17 trials
    Storage A0 trials
    Sturgis, SDSTUSDUnited States of America12 trials
    Stuttgart, ARSTUARUnited States of America8 trials
    Sussex Co, DESUSDEUnited States of America2 trials
    Szeged, HungarySZEHUHungary4 trials
    Tipton, INTIPINUnited States of America4 trials
    Tipton, OKTIPOKUnited States of America2 trials
    Tripp County, SDTRISDUnited States of America4 trials
    Urbana, ILURBILUnited States128 trials
    VCBranch, OHVCBOHUnited States24 trials
    Vincennes, INVININUnited States of America4 trials
    Vivian, SDVIVSDUnited States of America2 trials
    Volga, SDVOLSDUnited States1 trials
    Wabash, INWABINUnited States of America3 trials
    Wall, SDWALSDUnited States of America14 trials
    Walla Walla, WAWALWAUnited States of America4 trials
    Walsh, COWALCOUnited States of America10 trials
    Warsaw, VAWARVAUnited States of America22 trials
    Waseca, MNWASMNUnited States of America9 trials
    Watertown, SDWATSDUnited States of America2 trials
    West Lafayette, INWESINUnited States of America102 trials
    Wichita, KSWICKSUnited States of America21 trials
    Williston, NDWILNDUnited States of America27 trials
    Windfall, INWININUnited States of America1 trials
    Winfield, KSWINKSUnited States of America17 trials
    Winner intensive, SDWINSDUnited States of America2 trials
    Winner, SDWIISDUnited States of America44 trials
    Winnsboro, LAWINLAUnited States of America15 trials
    Wishek, NDWISNDUnited States of America5 trials
    Woodford Co, KYWOOKYUnited States50 trials
    Woodford, KYWODKYUnited States of America14 trials
    Wooster, OHWOOOHUnited States of America150 trials
    Yaqui Valley, Sonora, MexicoYAQSOMexico4 trials


    If your Location(s) exist:

    Continue to the next step


    If your Location(s) do not exist:

    1. Go to the Manage > Locations page
    2. Click the [Upload New Locations] link in the top right corner of the page to upload a Locations Excel Template


    Detailed Instructions  


  4. Accessions

    The contents of each plot must be associated with a single Accession (germplasm line). The Accession must exist in the database before a Trial can be created. Also, you must refer to the exact spelling and letter-case of the Accession's name (or synonym) in the database when creating the Trial.

    We try very hard to avoid creating duplicate entries of an Accession based on variations in the spelling and/or characters used in the Accession name. Therefore, we highly recommend using the BrAPI Germplasm Search Tool to search for existing Accession entries in the database and any that match possible variations in spelling and/or punctuation.



    Search for existing Accession entries:



    If all of your Accessions already exist:

    Continue to the next step


    Add any new Accessions to the database:

    1. Go to the Manage > Accessions page
    2. Click the [Add Accessions or Upload Accession Info] link in the top right corner of the page
    3. Select the Uploading a File tab to upload an Accessions Excel template


    Detailed Instructions  


  5. Trials

    A Trial (a single location & year environment) must exist in the database before Trait Observations can be added. When a Trial is created, the folllowing information is added to the database:

    • Trial Metadata, such as:
      • the Breeding Program that performed the Trial
      • the Location
      • the Design Type
      • the Planting/Harvest Date(s)
    • Plot Metadata, such as:
      • the Accession grown in the Plot
      • Plot number
      • Block number
      • Rep number
      • Whether or not the Plot is used as a control
      • Row/Column position of the Plot within the field


    Upload a Multi-Trial Upload Template:

    1. Go to the Manage > Field Trials page
    2. Click the Upload Existing Trial(s) button in the top right corner of the page
    3. On Step 2, select the Multiple Trial Designs tab
    4. Upload a Multi-Trial Excel Template


    Detailed Instructions  


  6. Trait Observations

    Once the Trial(s) have been added to the database, Trait Observations can be added to the Plots within the Trial(s).

    To add Trait Observations, you will need:

    • The Plot Name (used when creating the Trial)
    • The Trait Name of each observation (from the Search > Traits page)
    • The Trait ID of each observation (from the Search > Traits page)

    It is important to note the units/scale used by the trait in the database. If your observations were recorded using a different scale, you will need to convert them to the scale used by the database first.

    File Format:

    • The first column has the header observationunit_name and contains the Plot Name (or Subplot Name or Plant Name, but it is almost always going to be the Plot Name)
    • Add an additional column for each trait being stored. The column header follows the format {Trait Name}|{Trait ID} and contains the trait values for each Plot. Unobserved plots should be left blank.


    Upload a Trait Observations Template:

    1. Go to the Manage > Phenotyping Results page
    2. Click the [Upload Spreadsheet] link in the top right corner of the page
    3. Change the Spreadsheet Format format to Simple
    4. Upload a Trait Observations Excel Template


    Detailed Instructions  


  7. Finish

    At this point your Trial(s) and Phenotyping Data have been stored in the database!


    The final step is to organize similar Trials together into Folders, which are used to group Trials into Experiments:

    1. Go to the Manage > Field Trials page
    2. Click the Refresh button above the Trial tree to load the new Trials
    3. Click the Create new folder button to create a new folder within a Breeding Program
    4. Click the Move trial(s) to folder to add one or more Trial(s) to a folder
    5. Click the Refresh button again to display the changes


Complete!
Complete!