CDCB Database Queries¶
This query shows genotype usability and can be used to fix errors, when applicable.
- Correct a pedigree
- Submit the animal ID or sample ID
- Click "Show to see errors and conflicts"
- If errors are shown, a FIX_FMT1 option might be displayed.
- Suggestions are displayed to help the user resolve the conflicts
- If the suggestions are correct, simply click on “submit changes.”
- Once the change is processed, the pedigree is updated and conflicts are cleared (note changes are effective usually after next update program.
- Correct an unlikely grandsire
- The MGS and PGS likelihood is indicated at the top of the page. If either is unlikely, the box can be clicked to show more information and all possible options (e.g. modify the pedigree of the animal or the parent's).
- Select the appropriate animal to modify and the appropriate replacement ID. Note that setting a parent to "blank" (unknown) is allowed
- Withdraw unusable genotype
Withdrawing genotypes is an extreme and exceptional measure, and restricted to genotypes that will never be used again. For example, when the genotyping of an animal of a different species got erroneously submitted to CDCB. Withdrawing a genotype means that the user accepts that there is no possibility the genotype will be used in the future. A genotype can be withdrawn by selecting "W" in the "Use Ind" column. "Use Ind" refers to Genomic usability code.
Genotype Move/Swap APP¶
This query is used to re-assign an animal to another animal. Animal ID and sample IDs can be used. “S+” in front of ID means that the ID that is following S+ is a sample ID.
- How to "move" a genotype assignation.
- If a genotype has not been assigned to an animal, only the sample IDs or the mixed IDs can be used to identify the target genotype.
- If a genotype has been assigned to an animal, all 3 options (animal ID, sample ID and mixed IDs) can be used.
- The next screen will show the information of the queried animal(s). By clicking on ‘TO’ animal ID, a drop down with the other queried animals will be displayed
- Once the source and destination animals have been correctly indentified, click on “Reassign Genotypes”.
Sample IDs can be modified before submitting by changing sample ID information in the respective column.
CDCB Nomination¶CDCB-Nomination is used to nominate animals or to change a nomination status of nomination that was done previously. The status that you can change (update) using this query are:
- Parentage indicator code (PI)
You can only change PI from N to a correct genomic fee code of this animal. Animals with parentage only indicator (PI=P) will receive a fee code 8 and a service fee will be charged. In other words, users are not allowed to change a non-N-fee code to another fee code once it has been assigned. In case of need to make this change, please open a ticket on the CDCB customer service portal.
- Nominator ID
Updates/corrects nomination information (please be aware that genomic fee code cannot be changed once an evaluation has been calculated). The "SOLD" function in this query can be used to change a requesterID after the nomination process has been completed. However, only the current nominator who has already agreed to pay (or paid) the fee can change the requesterID field.
To change the requesterID, Click the '$=>' link in the 'Sold' column, and choose the appropriate nominator from the drop down. An email notification will be sent to both nominators (the previous and the current) to notify the change.
Group/HerdID will be used to determine the correct genomic fee code for the corresponding animal. Therefore, it is important to provide updated and accurate information. Please read carefully all documents in CDCB Fee Schedule for Genomic Evaluation Fees
Check FMT1 records¶This query checks if the format1 matches the information currently stored in the CDCB cooperator database.
The procedure is:
- Enter the format1 text into the text box (or provide a file containing format1 records) and click submit
- A response is provided in a new text box:
- The information flagged as “In” contains the record provided by the user
- If “matched” is shown at the bottom of the box, it means that the pedigree provided matches the information in the CDCB cooperator database.
Checks the animal pedigree and provides information about errors and dam pedigree/progeny/calving dates.
The query accepts individual Animal IDs ( 2-Breed 3-Country 12-ID_Num ) or plain ASCII text file as input.
Affiliate specific genotype reports¶In this section, nominator-specific genomic reports are provided:
- Lists genotypes with fee code=N loaded in the past 6 month
Animals assigned "N" genomic fee code, that do not receive an evaluation.
- Fee codes for genotypes loaded since the last invoice
Summary of fee codes by animal/sample ID in the last invoicing period.
- Lists parentage only genotypes since the previous genomic run
Animals assigned a parentage only genomic fee code, that do not receive an evaluation.
- Reports missing animal ID for a requester
A list of sample IDs, date of genotype loaded and chip type for genotypes loaded without valid nomination (no animal ID found). No evaluation will be generated for those animas.
- Conflicts for genotypes loaded in the past 45 days
Genomic error codes for animals loaded in the past 45 days. Genomic conflicts prevents animals to receive an evaluation.
- Check for missing pedigree of animals nominated in the past 75 days
Animals not yet genotyped but nominated with unknown parents or unknown grandparents.
- List conflicting genotypes within animal (Negative key)
List of animals with negative key genotypes, which are not included in the evaluations.
- Animals with genotypes that conflict with imputed dam genotypes
As reported by title.
- Parentage verification records for genotypes loaded in the past 45 days
Parentage verification, discovery (and - if applicable - suggestions) for genotypes loaded in the past 45 days.
Get CDCB Fee from herdcode¶
This query shows the genomic fee code and the type of provided records (e.g. the information used to assign the fee) for a given Herd ID. This is the information that the CDCB system will use to correct the fee submitted by the nominator
Retrieve Parentage Validation Record¶
This query outputs the parentage verification records for the requested animals.
Get herd code and CDCB Fee for specified animal ID¶
This query shows the genomic fee code for a given animal ID.