USER MANUAL FOR THE IDEA INTERFACE

Preface

The following is a manual to guide the user through the features of the new IDEA. IDEA stands for Interbull Data Exchange Area. IDEA is a restricted area accessible only to member countries through the Interbull website.

• Last updated May 16 , 2012

LOG IN

To enter the main page of IDEA go to https://idea.interbull.org You will be required to provide a username and password to log in.

Your username is equal to the intial of your name followed by your surname. For example, the user name for Thomas White will be twhite. If your surname contains special character, such as ö, ä, å etch, write it with the corresponding ASCII letters, i.e. o,a, etc.

Your username is associated to the organization you belong to. IDEA has a table linking together usernames and organizations for the persons that have had so far regular contacts with the Centre. If you wish for one of your co-worker to have access to IDEA, simply notify the Centre with his/her name and email address.

Access to IDEA is, therefore, set to an individual access. If you used to share your password in the past, it is your responsability to change it to a new password.

First time log in

You will receive a temporary password from Interbull Centre. Use your username, as described above, and your temporary password to log in.

AFTER YOU LOG IN

Welcome to IDEA start!!!

The first thing you need to do is to change the temporary password to one of your choice.You can do it right on "IDEA start" by clicking on "Change your password". You can also update your email address by clicking on "Change email"

The Menu List appears in the top navigation pane with several menu items that will allow you to interact with the database. In this section we give you an explanation of their functions.

IDEA Start

The IDEA Start menu gives you access to the main functions available in the database. Currently these functions are solely related to the pedigree handling, but new functions for handling of conventional MACE, genotypes etc, will also be accessible from here whenever their modules will be implemented.

The available pedigree functions are: Query, Uploads, Conflicts, Statistics.

Software

The Software menu gives you access to the Interbull checking programs. By clicking on Software a drop down menu will open and you will be able to choose the type of checking program you are interested in, i.e. Pedigree, Proofs or GenoList.

Pedigree's Checking Programs

Two Pythons programs are available for checking pedigree, they are CheckPedigree.py and CheckLinks.py. Under Software|Pedigree you will find information on each of the programs together with the latest version of the program to download. Please note that the programs check their internal version with the value stored on the Interbull server. You will have to download the most recent version if there is a mismatch. This implies that you have to have access to an internet connection to be able to run the programs.

Pedigree

The Pedigree menu gives you access to the main pedigree functions which are: Animal Query, Uploads, Conflicts and Statistics. These functions are also accessible from the IDEA Start menu.

Animal Query

If you want to get pedigree information on a particular animal, click on Animal Query menu link.The page that will open contains an Animal lookup,by inserting an International ID in the Animal lookup and then clicking on Lookup! will show the information related to your query.

The central part of the page will show the international ID of the animal you were interested, followed by its name, birth date and birth date status, animal status, date of last update and who performed the last update. A description of all possible birthdate and animal status are presented in Table 1.

Table 1: Birthdate and Animal status

Above the animal information, you will see the animal's parents and grand-parents. The animal's parents are displayed together with their name, birth date and birth date status and animal status. Grandparents are displayed as active links, clicking on their ID will update the Animal Query withe their pedigree information, if available in the system.

Below the animal information, you will find a table listing all animal's offspring together with their name and birth date. The table, by default, shows the first 200 offsprings associated to that particular animal ID. You can however modify the number of entries by clicking on the harrow beside "entries". Likewise, if you are only interested on a specific offspring, you can search for it by inserting its IID in the "search" space. Each header in the table is an active buttom, this means that by clicking on them you have the possibility to sort the content of the table in the way that suits you better.

Each ID reported in the parents and offspring section is an active link, therefore clicking on any displayed ID will update the page with that animal’s pedigree information.

If you enter an alias ID in the Animal lookup space you will see the official IID associated to that alias id.

 ADD PICTURE OF ANIMAL QUERY

Table 2: Different types of organization and their authority level

Pedigree Upload

The Uploads menu link is set up for uploading of pedigree and link (cross-reference) files. These files have to be created according to the format reported in APPENDIX I, file format 200 for dairy pedigree, file format 601 for beef pedigree and file format 202 for link files, valid for both dairy and beef. The content of your files needs to be checked by running two pythons programs: CheckPedigree.py and CheckLinks.py. If the programs find no errors in the format or in the content of your files than they will produce two zip files, IB-org_code-yyyymmddThhmmss.zip (containing the file200 or file601) and IB202-org_code-yyyymmddThhmmss.zip (containing the file202). These files are the only files that can be uploaded into IDEA, any other file will be rejected.

After uploading, the same checks performed by the checking programs will be performed once again inside IDEA therefore any manipulation of the zip files would be useless as the files will get rejected.

Access to the programs and their instruction is via the Software menu link.

To upload your files, browse them using the Browse buttom and upload it by clicking on Upload.

Whithin few minutes you will receive an email with the outcome of your uploading: if it was successful or if it failed for some reasons.

Attached to the confirmation email you will find two files called "processed.txt" and "not_processed.txt". The "processed.txt" contains all animals that have been inserted in the database and, eventually, other information such as:

• Automatically created due to parent link (see Table 1).
• The birth date is in conflict with birth date(s) of related animal(s)
• Country estimated birth date has been re-estimated by IBC due to conflicting birth dates

The "not_processed.txt" contains all animals that have been skipped and therefore not included in the database. Reasons for exclusion can be:

• Identical data already exists on the server
• No authority over existing animal

Creation of cross reference in the database

The creation of cross references in the database is made by uploading of a IB202-org_code-yyyymmddThhmmss.zip (file202 previously checked by CheckLinks.py). Two IDs will be always considered as two different animals until a proper file202 is uploaded.

In IDEA you can create cross-reference for the following situations:

• linking your domestic animals, i.e. animals for which you are the authoritative organization;
• correcting the ID of your foreign animals (if you are the first reporting organization, see Table 2);
• adding national IDs to a given international ID.

Please be advised that IDEA does not discern between international and national aliases as it solely relies on the international ID.

In IDEA you can now submit cross-references for animals outside your authority. In this case the pair you are trying to link together will be treated as potential duplicates and listed in the corresponding authoritative organization's potential duplicates page, with your choice highlighted.The linking will be performed only if the authoritative organization agrees with your choice.

The table below summarizes all possible linking scenarioes together with an explanation of what will happen inside IDEA.

Table 3: Possible linking actions

AID1 and AID2 are according to the format of file202, therefore AID1=wrong/alias AID and AID2=international AID.

In case of records that fit in the conditions for more than one case, the first case in the table takes precedence.

Name of the animal

The official name of an animal is equal to the name provided by each official organization. To avoid sudden changes in names or name missing it is extremely important that each authoritative organization always provide a name record, whenever available, for every uploading and be consistent with the name, i.e. do not provide the full name for the first uploading and a short version of it for the next, otherwise the name of the animal will get overwritten.

Please note that IDEA is based on a UTF-8 character encoding. It is recommended that all files entering IDEA would use a UTF-8 character encoding as well.

How do I change/add a name for a given animal?

Only authoritative organization or first reporting organization, while the record is till unverified, can modify the name of an animal. To do so simply upload a pedigree file with the new name information and the changes will be recorded in the database.

Statistics menu link

Clicking on the Download button you will be able to get information about pedigree, proofs, parameters, forms, retrieve a list of animals waiting for your validation (as you appear to be their authoritative organization) or check the list of invalid international ID. Many of the features contained in this tab are still under development but you can already get access to the list of animals waiting for your validation as well as check the invalid international id.

Retrieve your "Request of Pedigree"

By clicking on here you will be directed into an ascii file following the format shown in Appendix IV. You can save the file by clicking on “File/Save As” in the tool bar.The ascii file contains a list of all animals as loaded by reporting countries and for which you appear as the authoritative organization. This means that only you have the right to say if the pedigree record is correct or not.

Verification Process: How does it work?

For each animal listed in your “Request of Pedigree” file yhave to upload its pedigree information as it appears in your own database, using file format 200 and checkpedigree.pl.By doing so you are verifying the reported information as the system considers verified only the information provided by the authority organization. When you are verifying an animal record you might find yourself in front of four possible scenarios, below you find instructions on what to do for each of them.

Scenario 1

If you find that the animal ID reported is correct then you will have to:

• Upload a pedigree file (file200 previously inspected by CheckPedigree.pl) as it appears in your own database, weather the reported pedigree information is correct or not.

Scenario 2

If you notice that an animal has been reported with an incorrect international id then you will have to:

• Upload a pedigree record for that animal using its correct id
• AND upload a file202. The file202 will provide the cross-reference link between the reported animal id and the animal id you verified.

Example:

A country submitted a pedigree for the animal BSWUSAF000000569466 using the ID BSWUSAF000000659466.

As it is an USA animal, the animal will appear in the USA list of Request of Pedigree. When looking at the record USA notices that two numbers have been misplaced. So USA will upload a pedigree file using the correct id for the animal (BSWUSAF000000569466) together with a file202 which will look like:

202 BSWUSAF000000659466 BSWUSAF000000569466

Scenario 3

If you realize that a given animal has been erroneously associated to your organization then:

• If you know the right authoritative organization, upload a pedigree file containing the new international ID of that animal. Doing so the animal will be sent for validation to the organization associated to the country you specified in its international ID.

Example:

Animal BSWUSAM000803611398 is sent to USA for validation but USA realizes the animal belong to DEU instead.

USA uploads a file200 (checked by CheckPedigree.pl) for the animal BSWDEUM000803611398

Scenario 4

If you do not know anything about that animal and it does not appear in your database then you have to:

• Upload a file202 containing “UUUUUUUUUUUUUUUUUUU” in the “correct IID” field.

Doing so the animal’s international ID will be considered as invalid and listed in the limbo (for the limbo see below)

Example:

Animal BSWUSAM000000000008 cannot be found in the USA database.The file 202 will be:

202 BSWUSAM000000000008 UUUUUUUUUUUUUUUUUUU

You will have to upload your files using the uploading pedigree tool you find in the upload tab.

Corrected Foreign Animals

In this file you find information on the validation activity over an IID, and its pedigree, done by each authoritative organization on your foreign animals. Therefore by checking it you can get the corrected IDs, or pedigrees, of some of the animals you have been reported that have been corrected by their authoritative organizations.You can open the file by clicking on the link or save it directly on your computer. The file format is specified in Appendix V.

The content of the file will be completely updated after extraction of the pedigree for each Interbull evaluation. You therefore have the time between extractions to check the file and eventually do the necessary correction in your own database.

Invalid IDs

By clicking on the limbo tab you will get access to the list of international IDs that were not recognized by their authoritative organizations and therefore set to unknown. The list is available for you to double check your database and eventually update it accordingly.

Download Pedigree

After every Interbull evaluations the international pedigree for the six breeds evaluated at the Centre will be available for download. By clicking on Download Pedigree you will have access to the international pedigree used in the latest Interbull evaluation. You will be entitled to have access only to the international pedigree of the official breed(s) with which you participate to the Interbull evaluation.You will be able to either look at the pedigree or saved it on your own computer.

Conflicts Menu Link

The Statistics menu link contains general information about your pedigree.

Overview of verified/unverified animals submitted by your organization

The table shows the general situation of your pedigree data as it is in the database at the time of your log in. The table contains the country of the authoritative organization, the number of animals that have already been validated by it and the number of animals that are still waiting for validation, for all the breeds you have submitted. By clicking on the drop down menu you can select a particular breed among your own and have the same statistics recalculated just for that breed.

N.B. among all the animals in the “animal” field that you have uploaded, the ones having your country code in their international ID are considered validated by default because you are their authoritative organization, therefore there should not be any animals still pending validation by your country in this table. If this is not the case it means that there are some parents without an entry in the animal field and could not be validated because the validation procedure takes place in the animal field. To prevent this to happen, you will have to upload pedigree records for the animals and their parents as well.

Summary of animals waiting for verification by your organization

This table contains the list of all animals submitted to the Interbull database by other organizations for which you appear to be the authoritative organization and therefore you need to provide the correct information (see verification procedure above) . The table contains the total number of records, the reporting organization’s name and its country code. This table is useful for you to monitor your verifying ID tasks.

Pedigree Conflicts

Although your national pedigree file has been already checked by the CheckPedigree.pl for pedigree conflicts, there is the possibility that the international pedigree still shows some birthdays conflicts.To check for that click on Pedigree Conflicts bottom, you will be directed into a new page showing all conflicts where your organization is involved. Below is an explenation of the Pedigree Conflicts page content:

The IID listed is the one of an animal in which pedigree there is one of more conflicts. The type of conflicts are shown in the Conflict path column, where S, D, SD means that the sire, the dam or the sire of the dam birthdate is conflicting with the animal’s birthdate.

The cross (x) in the “Strange” column indicates that all animals involved in the conflict have already been verified by their own authoritative organization.

Clicking on “Details” will open a new page showing more details on the animals in conflict.

How to handle animal's conflicts?

Sometimes a conflict could be due to unverified animals, if this is the case please proceed on verifying the animals double checking that the new birthdate you are going to provide will no more be in conflict.

If you do not know how to fix the conflict you should contact Interbull Centre deciding what action you, as the authoritative organization for that animal, want to take.

So, in general, to fix a conflict you should:

• Upload new pedigree file of the conflicting animal with a new no-conflicting birthdate

• In case you do not know how to fix it you should contact Interbull Centre

Pedigree Duplicates

By clicking on “Pedigree Duplicates” you will see a list of potential duplicates associated to your organization. The list shows five pairs at the time.

For each animal listed you will see its international IID and birthday, by clicking on its IID you will access to its pedigree information. Beside each IID you have an empty box to mark.

How to handle pedigree duplicates?

In case you realize that the animals shown in the list are indeed duplicates, mark the box associated to the official IID. If the animals are NOT duplicates mark both boxes. Then press “Submit Changes” and the changes will be saved and stored in the database.

The pairs you have processed will be dropped from your list only if you are authority for both animals in the pair. Otherwise the conflict will remain in your list until the other authoritative organization provides your same answer.

What is the meaning of the star?

Whenever you are authoritative only for one animal IID showed in the pair, your submission will be kept on a hold and showed with a star (*) until the other authoritative organation has also the opportunity to look into the matter and expressed its own opinion. There can be two different scenarios:

• You and the other authoritative organization have submitted the same information: The change will then become official in the database and the pair will drop from your list.
• You and the other authoritative information have provided different information:The “disagreement” will be mark by stars (*) in both IID. No changes will happen in the database. You should contact the other authoritative organization via Interbull Centre. The conflict remains in your list.

APPENDIX I: Organization Codes as provided by Interbull Centre

APPENDIX II: File Format 200 for Dairy Pedigree

APPENDIX IIa:File Format for Beef Pedigree

APPENDIX III: Format File202 Correcting Internationa ID by the Authoritative Organization

(Creates Cross-reference links, valid for dairy and beef users)

APPENDIX IV: Request of Pedigree for Authoritative Organization

APPENDIX V: Corrected Foreign Animals

Each record line is separated from the next by a ‘\n’

APPENDIX VI: FREQUENTLY ASKED QUESTIONS

Q. How do I know that the pedigree file I have submitted has been successfully uploaded into the database?

A. You will receive a confirmation email with some information on the data you have uploaded, i.e. total number of records and number of records validated by default, i.e. number of new domestic animals you have uploaded.The time of receiving the email depends on the size of the pedigree you have uploaded. If the size of the file is ≤100 kb it gets uploaded in real time and you will shortly after receive the confirmation email. If the size of the file is ≥100 kb it gets uploaded during Swedish night hours as the process requires more time. In that case you will receive a confirmation email the next morning, containing the above mentioned information.You are kindly asked to notify the Interbull staff if you have not received any emails 24 hours after uploading of the file.

Q. What is the difference between “Overview of verified/unverified animals.." and "Summary of animals waiting for verification..."?

A. In the first statistic you can see how the verification process is proceeding on your foreign animals. In the second statistic you get an overview of how many animals reported by other organizations are still waiting for your verification.

Q. How do I know if I have any animal to verify?

A. By clicking on “Statistic/Overview of verified/unverified animals” the table will show you the number of animals you need to verify and their reporting country.

Q. What do I do if I have animals pending verification?

A. Download from the main menu the request of pedigree file. For each of the animal listed in the file you need to provide pedigree information as they appear in your own database and upload them using a file200 format previously checked by CheckPedigree.pl. If you notice that the IID of the animals is wrong or is an alias ID then you also have to submit a file202.

Q. What I have to do if some IIDs listed in the request of pedigree cannot be found in my own database?

A. In this case you only have to submit a file202 with 19 “U”s (i.e. UUUUUUUUUUUUUUUUUUU) in the correct IID field.

Q. What do I do if I notice that an animal has been reported using a cross-reference ID instead than the official IID?

A. Provide the pedigree information for that animal as it appears in your own database using a file200 previously checked by CheckPedigree.pl and also provide a file202 putting the correct official IID in the correct IID field.

Q. Can the actual system distinguish between ID formally correct but written in a different format and the real wrong ID?

A. Anytime the authoritative organization provides a file202 the “wrong/alias ID” gets stored in a particular table called “alternative scheme table”. The system does not distinguish between “formally correct” or “real wrong” IDs. The system is built on the principle that every ID is considered as potentially wrong until it gets validated by the authoritative organization. If an authoritative organization provides a “correct ID” (cross-reference link, file202) it means that the ID provided by the reporting organization was not entirely correct so it gets replaced with the one provided by the authoritative organization. The information provided by the reporting country is not lost but stored in the alternative scheme table. In case the ID reported in the correct field is represented by the unknown ID (i.e. 19 “U”s) then that ID is treated as “real wrong” and placed in the limbo space.

Q. Can I download pedigree information from the interface?

A. After every evaluation you will be able to download the international pedigree for the breeds evaluated at the Centre and for which you participate to the Interbull evaluation.