YamBase

Intro
File format
Upload inventory
Fix missing seedlots problem
Try submitting inventory again

What is a seedlot inventory?
- Seedlots represent physical seed in packets.
- This seed can be from crosses or for named accessions.
- Seedlots can have a specific location, box, weight(g), and count.
- Seedlots can belong to breeding programs and organizations.
- Seedlots can be used in trials (e.g. they were planted in a plot) and they can be harvested from a plot or plant (e.g. a cross was performed and seeds were collected.)
- A seedlot inventory consists of giving a location and current weight(g) to your seedlots. The seedlot name is the unique identifier for each seedlot and so should be encoded in a barcode on each seedlot packet.
- You can use the "Inventory" Android Application to scan seedlot barcodes and record weight. If you prefer you can create your own CSV file and upload that, if you do not want to use the Inventory Application. For info about the format of the file to upload, go to the next tab.
- It is also possible to manually enter a transaction by going to the seedlot detail page and clicking "Add New Transaction".
Make sure you are collecting seedlot inventory in the following format

The "Seed Inventory" Android Application will export this same exact format by default.
Select your file and upload seedlot inventory

Upload File (.csv):
Fixing the missing seedlot(s) problem
- Seedlots must exist in the database prior to updating or adding inventory. The reason for this is that the inventory does not give information about the content (a named accession or a cross name) and this information is required for a seedlot to exist in the database. We also want to be careful about adding new seedlots into the database because we do not want data to be incorrectly linked to duplicates.
- When adding seedlots into the database, you can upload an Excel file or you can add seedlots one at a time.
Seedlot Inventory Upload Error Messages
Submit your inventory again. You should have corrected all errors by now, but if not please take a look at the errors in the red box below. You can continue to modify your file and then click Upload until it works.

There exist these problems in your file:

Finished! Your seedlot inventory is in the database

The seedlot inventory file was uploaded successfully

You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just updated.
You can print barcodes for the seedlots.

Finished! Your seedlot inventory is in the database

The seedlot inventory file was uploaded successfully

You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just updated.
You can print barcodes for the seedlots.

Seedlots may be uploaded in a CSV file (.csv)
(Excel .xls and .xlsx format not supported)

Header:
The first row (header) should contain the following:

box_id	seed_id	inventory_date	inventory_person	weight_gram

Required fields:

box_id (the name of the box that the seedlot is in. also called box_name.)
seed_id (unique identifier for the seedlot. must exist in the database. also called seedlot_name)
inventory_date (a timestamp for when the seedlot was inventoried)
inventory_person (the name of the person doing the inventory. can be any name. also called operator_name)
weight_gram (the weight in grams of the seedlot)

Intro
What seedlots do you have?
File format
Upload seedlots
Fix errors in file
Try submitting seedlots again

What are seedlots?
- Seedlots represent physical plant materials in packets/containers.
- Plant material in a seedlot can be seed, root, clone, plant, tissue culture or gametophype.
- If you would like to set a default material type for seedlots, please contact us.
- These plant materials can be from crosses or for named accessions.
- Seedlots can have a specific location, box, weight_gram, and count.
- Seedlots can belong to breeding programs and organizations.
- Seedlots can be used in trials (e.g. they were planted in a plot) and they can be harvested from a plot or plant (e.g. a cross was performed and seeds were collected.)
Seedlots fall into two categories

Select One:
Make sure your file matches the correct file format
Provide basic information about the seedlots and upload your file

Material Type:

Breeding Program:

Location of seedlot storage:

Organization Name:

Upload File:

Upload File:
Fix all errors in your file
- Accessions must exist in the database prior to adding seedlots of them. The reason for this is that an accession can be exist in many seedlots and therefore exists as a separate entity in the database. We also want to be careful about adding new accessions into the database because we do not want incorrectly duplicated data.
- When adding accessions into the database, you can use either a list of accessions or an Excel file.
- Crosses must exist in the database before adding your seed lots. The reason for this is that a cross can produce many seed lots and so the cross must exists as a separate entity in the database. We also want to be careful about adding new crosses into the database because we do not want data to be incorrectly linked to duplicates.
- When adding crosses into the database, you can upload an Excel file or you can add seedlots one at a time.
Seedlot Upload Error Messages
Submit your seedlots again. You should have corrected all errors by now, but if not please take a look at the errors in the red box below. You can continue to modify your file and then click Upload until it works.

There exist these problems in your file:

Finished! Your seedlots are now in the database

The seedlot file was uploaded successfully

You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just created.
You can print barcodes for the seedlots.

Finished! Your seedlots are now in the database

The seedlot file was uploaded successfully

You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just created.
You can print barcodes for the seedlots.

Header:
The first row (header) should contain the following:

seedlot_name	accession_name	operator_name	amount	weight_gram	description	box_name	quality	source

Required fields:

seedlot_name (must be unique)
accession_name (must exist in the database. the accession_name is the unique identifier for the named genotype)
operator_name (the name of the person who oversaw the inventory process. can be any name.)
amount (number of materials in seedlot. can be provided in conjunction with weight_gram. must provide a value for amount or weight_gram or both.)
AND/OR
weight_gram (weight in grams of seedlot. can be provided in conjunction with amount. must provide a value for amount or weight_gram or both.)
box_name (the box name that the plant material is located in. can be any name.)

Optional fields:

description (information about why this seedlot is being added)
quality (status of the seedlot, for example "ok", "moldy", "insect damage" etc.
source (an alternate source, such as a plot, subplot, or plant identifier from which the seed was collected)

Seedlots may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).

Optional columns may be left out, if not used in your data.

Header:
The first row (header) should contain the following:

seedlot_name	cross_unique_id	operator_name	amount	weight_gram	description	box_name	quality

Required fields:

seedlot_name (must be unique)
cross_unique_id (must exist in the database. a cross_unique_id can represent a cross between accessions e.g. AxB, but a cross can also represent a cross between specific plots in the field if you have this information)
operator_name (the name of the person who oversaw the inventory process. can be any name.)
amount (number of materials in seedlot. can be provided in conjunction with weight_gram. must provide a value for amount or weight_gram or both.)
AND/OR
weight_gram (weight in grams of seedlot. can be provided in conjunction with amount. must provide a value for amount or weight_gram or both.)
box_name (the box name that the plant material is located in. can be any name.)

Optional fields:

description (information about why this seedlot is being added)
quality (brief description of quality, e.g., "ok", "moldy", "insect damage", etc)

Seedlots may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).

Optional columns may be left out, if not used in your data.

Using Lists
Uploading a File

File format information
Spreadsheet format

Upload File:

Email Alert:

Use Fuzzy Search:

Note: Use the fuzzy search to match similar names to prevent uploading of duplicate accessions. Fuzzy searching is much slower than regular search. Only a curator can disable the fuzzy search.

Append Synonyms:

When checked, add synonyms of existing accession entries to the synonyms already stored in the database. When not checked, remove any existing synonyms of existing accession entries and store only the synonyms in the upload file.

Accessions may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).

Optional columns may be left out, if not used in your data.

Header:
The first row (header) must contain the accession_name and species_name columns. Additional information can be included by selecting optional column(s) (see below). :

accession_name	species_name	population_name	synonym	description	PUI	accession number	acquisition date	biological status of accession code	country of origin	donor	donor PUI	donor institute	genome_structure	institute code	institute name	introgression_backcross_parent	introgression_chromosome	introgression_end_position_bp	introgression_map_version	introgression_parent	introgression_start_position_bp	location_code	ncbi_taxonomy_id	notes	number_of_insertions	organization	ploidy_level	released_variety_name	seed source	state	transgenic	type of germplasm storage code	variety

Comma Separated Fields:

The following fields can take comma-separated values to indicate there are several values for the accession: organization_name, synonym , PUI, accession number, acquisition date, biological status of accession code, country of origin, donor, donor PUI, donor institute, genome_structure, institute code, institute name, introgression_backcross_parent, introgression_chromosome, introgression_end_position_bp, introgression_map_version, introgression_parent, introgression_start_position_bp, location_code, ncbi_taxonomy_id, notes, number_of_insertions, organization, ploidy_level, released_variety_name, seed source, state, transgenic, type of germplasm storage code, variety

Required Fields:

accession_name (must be unique)
species_name (must exist in the database)

Optional Fields:

description - a free text description of the stock.
population_name (a population is a grouping of accessions. If the population already exists in the database, the accession will be added to it; otherwise, a new population will be created). Multiple populations can be specified, using the pipe symbol (|) as the separator (for example, pop1|pop2|pop3)
synonym (an accession can be known by many names including local popular names. a synonym name can be used instead of the accession_name throughout the database; because of this, synonyms must themselves be unique. e.g. accession_synonym1,accession_synonym001)
PUI (permanent unique identifier(s) of the accession)
accession number (accession number(s) for accession from germplasm bank)
acquisition date (date(s) of acquisition YYYYMMDD for accession)
biological status of accession code (code(s) indicating the state of accession)
country of origin (the country(s) of origin)
donor (the accession_name(s) of the donor accession and should be used in conjunction with donor institute and donor PUI)
donor PUI (the permanent unique identifier(s) of the donor accession)
donor institute (the institute(s) of the donor accession(s))
genome_structure (genome structure(s) for accession which take into account ploidy and ancestral genome info e.g. AAA or AB)
institute code ( the institute code(s) of origin)
institute name (the institute name(s) of origin)
introgression_backcross_parent (the backcross parent for introducing an introgression into the accession being added)
introgression_chromosome (the chromosome number that the introgression is on)
introgression_end_position_bp (the end position of the introgression in base pairs)
introgression_map_version (the map version for identifying the start and stop position of the introgression. e.g. AGPv2)
introgression_parent (if the accession you are adding has an introgression that originated from one of the parents you can specify the parent here)
introgression_start_position_bp (the start position of the introgression in base pairs)
location_code (location code(s) for the accession)
ncbi_taxonomy_id (no definition available)
notes (free text for notes)
number_of_insertions (number of transgene insertions in a transgenic plant)
organization (the name(s) of the organization(s) which use this accession e.g. NARO)
ploidy_level (no definition available)
released_variety_name (offical variety name of the accession or stock)
seed source (origin(s) of seed source)
state (the state(s) of origin)
transgenic (indicates if accession is transgenic. Please indicate 1 if transgenic and empty if otherwise.)
type of germplasm storage code (code(s) indicating the type of germplasm storage)
variety (variety(s) can be defined as a group of individuals or plants having similar traits that can be reproduced true to type from generation to generation)

Accessions may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).

Optional columns may be left out, if not used in your data.

Intro
Crossing experiment
Upload your crosses

Introduction
- Crosses can be of different types (biparental, self, open, backcross, sib, polycross, bulk, bulk_open, bulk_self, doubled_haploid, or dihaploid_induction)
- An individual cross can be linked to a female plot or plant, as well as a male plot or plant.
- A cross can have a number of properties associated to it, such as number of flowers, pollination date, etc.
- A cross can produce seed, which goes into a seedlot.
- A cross can ultimately produce progeny, which then become named accessions in the database.
Select a crossing experiment for your crosses
If you are uploading an Intercross file and using auto-generated cross unique IDs, please use manage Intercross section

Crossing experiments are for grouping crosses together. The grouping is most often done for crosses derived from the same field trial, the same year, or for crosses that have the same breeding objective.

You are uploading crosses for crossing experiment:

Enter basic information about the crosses and upload your file

File format information
Spreadsheet format

Upload File:

Crosses may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).

Finished! Your crosses are now in the database

The crosses file was uploaded successfully

You may want to proceed to the cross detail page(s) for the cross(es) you just created.
You can print barcodes for the crosses.
You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).

Finished! Your crosses are now in the database

The crosses file was uploaded successfully

You may want to proceed to the cross detail page(s) for the cross(es) you just created.
You can print barcodes for the crosses.
You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).

Header:
To set up crosses in the database, please provide required information. The first row (header) must contain the following:

cross_unique_id

cross_combination

cross_type

female_parent

male_parent

Required columns:

cross_unique_id (must NOT exist in the database)
cross_combination (required in the header, but value for cross combination (e.g. female accession/male accession) may be left blank)
cross_type (must be one of the following: biparental, self, open, sib, polycross, backcross, bulk, bulk_open, bulk_self, doubled_haploid, dihaploid_induction)

biparental: An individual plant pollinated by another individual plant.
self: A self pollinated individual plant.
open: An individual plant pollinated by a group of plants or open pollinated (pollen may be from a group with known or unknown members).
backcross: An individual plant pollinated by one of its parents.
sib: Mating between individuals that have at least one parent in common. Generally between two individuals within the same plot.
polycross: Mating between individual female parent from a population and the corresponding male population.
bulk: A group of plants (usually a related family) pollinated by an individual plant (between a female population and a male accession).
bulk_open: A group of plants (usually a related family) that are pollinated by another group of plants or open pollinated (between a female population and a male population or unknown male parent).
bulk_self: A group of plants (usually a related family) that are self pollinated (each individual selfed, not combined pollen).
doubled_haploid: Plants derived from doubling the chromosome number of haploid tissue.
dihaploid_induction: Plants derived from reducing the chromosome set from 4 to 2.

female_parent: Female parent names must exist as uniquenames in the database, can be accession, plot, plant or population stock type.
male_parent: Required in the header, but value may be left blank for most cross types. Must be specified for biparental, sib, backcross, polycross and bulk cross types. When specified, male parent names must exist as uniquenames in the database, can be accession, plot, plant or population stock type.

Optional columns (additional parent info): You can add additional parent info after male_plant column by using one or more of these column headers.

female_focus_trait
male_focus_trait
female_source_trial
male_source_trial

Additional cross information:

After cross unique ids are stored in the database, you can add field crossing data (e.g. pollination date, total number of flowers pollinated, total number of fruits set) or progenies to each cross unique id.
Field crossing data and progenies can be uploaded via links in crossing experiment detail page or can be added directly in each cross detail page.

Intro
Add a crossing experiment

What are crossing experiments?

Crossing experiments group crosses. The grouping can reflect crosses done in the same field trial, crosses in a breeding program in a given year, or crosses that have the same breeding objective. This grouping can be used to encapsulate all the crosses done in a crossing block field trial that you have saved in the database (e.g. in Manage Trials your crossing block will appear as a field trial with plots)
Enter basic information about the crossing experiment

Crossing Experiment Name:

Breeding Program:

Location of crossing experiment:

Year:

Description:

Finished! Your crossing experiment is now in the database

Crossing experiment was added successfully

You may want to proceed to the crossing experiment detail page you just created.
You can add or upload crosses into your crossing experiment as they become available.
You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).

Finished! Your crossing experiment is now in the database

Crossing experiment was added successfully

You may want to proceed to the crossing experiment detail page you just created.
You can add or upload crosses into your crossing experiment as they become available.
You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).

Intro
Select Trial
Select Seedlots
Name Seedlots
Set Contents
Set Metadata
Confirm
Create

Introduction

This workflow will guide you through the process of creating seedlots from the accessions in a field trial. You can create one new seedlot for each plot or unique accession in the trial. You can also set the initial contents (count or weight) of the seedlot as the value of a recorded trait from the trial.
Select a Field Trial

Enter the name of the field trial from which to create the seedlots:

Trial:
Select Seedlots

Seedlots can be generated from either each accession or plot or subplot or plant in this trial.
- If you select accessions: seedlots will be created
- If you select plots: seedlots will be created
- If you select subplots: seedlots will be created
- If you select plants: seedlots will be created
Name Seedlots

Enter a template for naming each new seedlot. The following variables (surrounded by curly braces) can be used in the template and the value of that variable will be replaced.
- trial_name
- accession_name
- plot_name
- plot_number
- rep
- block
- subplot_name
- subplot_index
- plant_name
- plant_index
- index - an incrementing index number, starting with 1
Name Template:

Seedlot Names

Set Seedlot Contents

Each seedlot needs to have its initial contents (either a count or a weight) set. You can either set the same initial value for each seedlot, use the value from one of the traits recorded for this trial, or compute a new value from the recorded traits for this trial. If you are creating a seedlot for each accession and select a trait or a computed value as their initial value, then the sum of the trait values for each of the accession's plots will be used. The contents of each seedlot can be modified in the table below before its creation.

Contents Type:

Contents Value:

Constant:

Trait:

Trait Variables:

Use the following variables as substitutions for the trait values to compute a new value for the initial seedlot contents. If you are creating one seedlot per plot, then the single plot trait value will be used in the computation. If you are creating one seedlot per accession, then the sum of the trait values for each plot of that accession will be used in the computation.

Variable	Trait

Contents Formula:

NOTE: The formula is evaluated using javascript, so any basic operators (+-*/) or javascript Math functions (Math.abs(x)) can be used.

Seedlot Contents

Set Seedlot Metadata

The following metadata is required for each seedlot. Fill out the form at the top apply the metadata to all of the seedlots. Then, each seedlot can be manually modified in the table below.

Breeding Program:

Location:

Box Name:

Material Type:

Quality Issues:

Organization:

Timestamp:

Description:

Seedlot Metadata
Confirm Seedlots

Confirm the attributes for the new seedlots in the table below. If something is incorrect, navigate to the previous step and correct the information. Once all the information is correct, continue to the next step to create the seedlots.

Seedlots to Create
Create Seedlots

Creating Seedlots...

70% Complete

Seedlot Progress

Complete!

Transactions may be uploaded in an Excel file (.xls or .xlsx)
Header:
The first row (header) must contain the following:

from_seedlot_name	to_seedlot_name	amount	weight(g)	operator_name	transaction_description

Required fields:

from_seedlot_name: Must exist in the database. Seeds were taken from this seedlot.
to_seedlot_name: Must exist in the database. Seeds were added to this seedlot.
amount: Number of seeds being transaferred. Can be provided in conjunction with weight(g). Must provide a value for amount or weight(g) or both.
AND/OR
weight(g): Weight in grams of seedlot being transferred. Can be provided in conjunction with amount. Must provide a value for amount or weight(g) or both.
operator_name: Name of the person who oversaw the transaction process. Can be any name.

Optional fields:

transaction_description: Information about why this transaction is processed.

Transactions may be uploaded in an Excel file (.xls or .xlsx)
Header:
The first row (header) must contain the following:

from_seedlot_name	amount	weight(g)	operator_name	transaction_description	to_new_seedlot_name	new_seedlot_box_name	new_seedlot_description	new_seedlot_quality

Required fields:

from_seedlot_name: Must exist in the database. Seeds were taken from this seedlot.
amount: Number of seeds being transaferred. Can be provided in conjunction with weight(g). Must provide a value for amount or weight(g) or both.
AND/OR
weight(g): Weight in grams of seedlot being transferred. Can be provided in conjunction with amount. Must provide a value for amount or weight(g) or both.
operator_name: Name of the person who oversaw the transaction process. Can be any name.
to_new_seedlot_name: Must NOT exist in the database. New seedlot will be created using amount/weight of seeeds from existing seedlot.
new_seedlot_box_name: Box name that this new seedlot is stored. Can be any name.

Optional fields:

transaction_description: Information about why this transaction is processed.
new_seedlot_description: Information about this new seedlot.
new_seedlot_quality: Status or condition of the seedlot, for example "ok", "moldy", "insect damage" etc.

Transactions may be uploaded in an Excel file (.xls or .xlsx)
Header:
The first row (header) must contain the following:

from_seedlot_name	to_plot_name	amount	weight(g)	operator_name	transaction_description

Required fields:

from_seedlot_name: Must exist in the database. Seeds were taken from this seedlot.
to_plot_name: Must exist in the database. Seeds were used for this plot. You can also record seedlot used for each plot during uploading existing trial on the Manage Trials page
amount: Number of seeds being transaferred. Can be provided in conjunction with weight(g). Must provide a value for amount or weight(g) or both.
AND/OR
weight(g): Weight in grams of seedlot being transferred. Can be provided in conjunction with amount. Must provide a value for amount or weight(g) or both.
operator_name: Name of the person who oversaw the transaction process. Can be any name.

Optional fields:

transaction_description: Information about why this transaction is processed.

Transactions may be uploaded in an Excel file (.xls or .xlsx)
Header:
The first row (header) must contain the following:

from_seedlot_name	amount	weight(g)	operator_name	transaction_description

Required fields:

from_seedlot_name: Must exist in the database. Seeds were taken from this seedlot.
amount: Number of seeds being transaferred. Can be provided in conjunction with weight(g). Must provide a value for amount or weight(g) or both.
AND/OR
weight(g): Weight in grams of seedlot being transferred. Can be provided in conjunction with amount. Must provide a value for amount or weight(g) or both.
operator_name: Name of the person who oversaw the transaction process. Can be any name.
transaction_description: Information about why this transaction is processed.

Intro
Add New Transactions

Seedlot Transactions

There are four different types of seedlot transactions: Transferring seeds from an existing seedlot to another existing seedlot, to a new seedlot, to a plot or to unspecified seedlot or plot.
- You can use upload option for all transaction types
- Seedlot list option can be used only for transferring seeds from existing seedlots to unspecified seedlots/plots.
Enter information about the transactions
Note: This option is for transferring seeds to unspecified seedlots/plots only

Unit Type:

List of Seedlots:

Finished! Your seedlot transactions were stored

New seedlot transactions were added successfully

Finished! Your seedlot transactions were stored

New seedlot transactions were added successfully

Accessions	Seedlots
Accessions		Breeding Program	Seedlot Name	Contents	Seedlot Location	Count	Weight(g)

Attribute	Value
Project Name:
Start Date:
End Date:
Event Type:
Event Description:
Event Web URL:

Notice

Before creating a new account, please check if you already have an account using the directory search.
A link will be emailed to you. Please click on it to activate the account.
All fields are required.

First Name:

Last Name:

Organization:

Username:

Username must be at least 7 characters long.

Password:

Password must be at least 7 characters long and different from your username.

Confirm Password:

Password must be at least 7 characters long and different from your username.

Email Address:

An email will be sent to this address requiring you to confirm its receipt to activate your account.

Add New Accessions for Progeny:	Number of progeny:
Use Prefix and/or Suffix:	Prefix: Suffix:

Available Seedlots

Create Seedlots from a Trial

Introduction

Select a Field Trial

Select Seedlots

Name Seedlots

Seedlot Names

Set Seedlot Contents

Seedlot Contents

Set Seedlot Metadata

Seedlot Metadata

Confirm Seedlots

Seedlots to Create

Create Seedlots

Seedlot Progress

You want to transfer seeds from existing seedlots to other existing seedlots

Please provide basic information about the new seedlots and upload your file

You want to use seeds from existing seedlots for plots

You want to remove seeds from existing seedlots to unspefified seedlots/plots