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 22, 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 my password". You can also update your email address by clicking on "Change my 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, Duplicates, 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: Query, Uploads, Conflicts, Duplicates and Statistics.

Animal Query

If you want to get pedigree information on a particular animal, click on the 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. If the animal is involved in any type of conflicts, i.e. birthdate conflict or potential duplicate, this information will be listed among the animal's information as well.

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, birth date and sex. 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, name or birth date in the "search" space. Each header in the table is an active buttom, this means that by clicking on it 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 as well, 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.

Table 2: Different types of organization and their authority level

Pedigree Upload

The Upload 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 be rejected.

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

To upload your file, browse it 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 link 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. All files entering IDEA must be created with 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.

Potential Duplicates

By clicking on “Duplicates” you will access a table listing all potential duplicates associated to your organization.

The table presents 8 columns: First Animal, Second Animal, Auth. Orgs, Feedback, and 4 action columns such as No Opinion (NO), 1st, 2nd, Not duplicates (ND).

In the First and Second Animal's column you will find information related to the pair of animals considered as potential duplicate. Each animal in the table is presented with its sire, dam, birthdate and name so to make it easier for you to realize if the animals are indeed duplicates or not.

The Auth. Orgs. column shows the organization(s) that are authoritative for the pair. In general, if your organization is authoritative for both animals involved in the conflict you have complete control over the pair. If your organization is authoritative only for one of the two animals then your selected action will appear in the "Feedback" column. The action will be processed only if the other authoritative organization agrees with your selected action.

For each pair you can choose among the following actions: No opinion (NO), 1st animal (1st), second animal (2nd), Not duplicates (ND).

Let's see in details what will happen for each action:

• You are authoritative for both IDs and select "1st": you indicate that the AID appearing in the first animal column is the official ID. By clicking "Submit changes" the ID listed in the "second animal ID" will become an alias of the first animal ID. Likewise if you select "2nd".
• You are authoritative for both IDs and select ND: you indicate that the two IDs are not duplicates. The two IDs will be marked as two different animals, dropped from your list of potential duplicates and they will never reappear.
• You are authoritative for both IDs and select NO: you indicate that you cannot say if the animals are duplicates or not. The pair selected in such way will remain in your potential duplicate page.
• You are authoritative only for one ID: Your choice will appear in the "Feedback" column and will be visible by you and by the other organization involved. An action will be performed only if the other organization agrees with your selection. In case the other organization disagrees the pair will remain in both your duplicate page.

By default your choice is always set to NO (No Opinion). In this way you can decide which pairs to process first, in fact by leaving the selection on NO will leave the pairs inaltered.

Once you have done processing the potential duplicates do not forget to click "Submit Changes" so that your selection(s) can be registered in the database, or they will get lost.

By clicking on "Reset to original values" will set your selection to the latest submitted one.

By default the table will show you the first 200 entries. You can modified the number by clicking on the "show entries" above the table.You can advance to the next group of animals by clicking on "Next/Previous". Also each header is an active header therefore you can sort the content of the table as it better suits you. You can even search for a given ID using the search box.

Statistics menu

By clicking on "Statistics" you will get access to your "Request of Pedigree", "Corrected Animals" file, statistics on overall number of animals pending verification by other organizations and overall number of animals pending verification by your organization.

Request of Pedigree

You can either view or download your request of pedigree. the file has the format shown in Appendix IV. This 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 by verifying their pedigree.

Verification Process: How does it work?

For each animal listed in your “Request of Pedigree” file you have to upload its pedigree information as it appears in your own database, using a file format 200 or 601 and CheckPedigree.py. 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's 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 reported animal ID is correct then you will have to:

• Upload a pedigree file (file200 or 601 previously inspected by CheckPedigree.py) as it appears in your own database.

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 previously checked by CheckLinks.py. The file202 will provide the cross-reference link between the reported animal's id and the animal's 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) and create 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 and you know to which organization it should belong:

• Prepare two file202 containing two entries for the same animal: first file sets the wrong ID to UUUUUUUUUUUUUUUUUUU then second file links the wrong ID to the new organization's ID.

N.B. it is extremely important that you upload these file in the right order, i.e. first the link that sets the AID to invalid (first file202) and then the link creating the cross-reference with the other AID (second file202).

Example:

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

USA prepares two file202 that will look like:

first file202: 202 BSWUSAM000803611398 UUUUUUUUUUUUUUUUUUU

second file202: 202 BSWUSAM000803611398 BSWDEUM000803611398

In this way the USA ID will get status INVALID and will be linked to the DEU ID.

Scenario 4

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

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

Doing so the animal’s international ID will be marked as invalid.

Example:

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

202 BSWUSAM000000000008 UUUUUUUUUUUUUUUUUUU

Invalid IDs

Anytime an AID is submitted to the database with a link to UUUUUUUUUUUUUUUUUUU it will be marked as invalid. This means that its authoritative organization did not find any records of it in its database. Nevertheless such AIDs can still be valid AIDs in other countries, especially if the animal is an old animal or if it was sold as a calf or embryos. Therefore such AID will still be extracted from the database and it could partecipate into a gentic evaluation if it appears itself connected to a genetic proofs or connected via the pedigree to an animal with proofs.

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 the animals you have reported and got corrected by their authoritative organizations.You can either view or download the file. The file format is specified in Appendix V.

Once you have gone through the file and applied the necessary corrections in your own database, you can reset the content of the file by clicking on "Reset these to the latest updates". By doing so the content of the file will be emptied and only changes from the day after your reset day will be listed.

Animals submitted by your organization and awaiting verification by authoritative 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 authoritative organization, the status of the animals and the overall count. By clicking on "Download" you will be able to download the list. The file has format as descripted in APPENDIX VI.

N.B. Animals associated to your organization and with animal status set to AUTO_CREATED are parents for which you have not provided a pedigree record. To have them dropped from this table you have to upload a pedigree file for these animals.

View statistics for animals that need verification from you

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 reporting organization, the country it belongs to and the overall count. This table is useful to monitor your verification process.

Pedigree Conflicts

Although your national pedigree file has been already checked by the CheckPedigree.py for pedigree conflicts, there is the possibility that the international pedigree still shows some birthdates conflicts.To check for that click on "Conflicts", you will access a table showing all conflicts where your organization is involved.

The table contains the "first animal" and the "second animal" involved in the conflict together with their relationship status, i.e. parent, grand-parent, offspring.

As every tables in IDEA, each header is an active header so you can sort the content of teh table as it better fits you. Also you can modify the number of entries shown or search for a particular animal's ID.

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

APPENDIX I: Organization Codes as provided by Interbull Centre

APPENDIX II: File Format 200 for Dairy Pedigree

APPENDIX IIa:File Format 601 for Beef Pedigree

APPENDIX III: Format File202 Correcting International 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: Animals Pending Verification

APPENDIX VII: 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.

Q.

How do I know if I have any animal to verify? A. By clicking on “Statistic/View statistics for animals that need verification from you” the table will show you the number of animals you need to verify and their reporting organization.

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

A. Download from the statistic 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.py. If you notice that the IID of the animals is wrong or is an alias ID then you also have to submit a file202 previously checked by CheckLinks.py.

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, checked by CheckLinks.py, 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.py and also provide a file202, previously checked by CheckLinks.py, 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” a croos-reference record is created. 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 verified 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 and marked as invalid.