Patr sequence source misannotated in chain_sequence.tsv

[ArnNag]

Sequences for Patr chains are annotated as having the Source "IPD", though their accessions refer to GenBank. Some of these do indeed have relevant entries in the IPD-MHC.

[rvita]

Hi, Thanks for the question. For any given protein chain, there may exist many different accessions. When we cite "IPD", it is because we used the accession selected by IPD as the official sequence for that particular protein chain, and which aligns with the IPD identifier. MRO considers the Immuno Polymorphism Database (IPD) as the definitive source for MHC nomenclature and expertise, therefore, we prefer to use their sequence assignments. For some species not yet in IPD, we will instead go to GenBank ourselves and find a representative entry. Here is a link to the IPD Patr protein entries that we use: https://www.ebi.ac.uk/ipd/mhc/allele/list/?query=eq(organism.name,Patr)#panelAdvanced

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On Mon, Feb 16, 2026 at 4:07 PM Arnav Nagle ***@***.***> wrote: *ArnNag* created an issue (IEDB/MRO#160) <#160> These sequences are annotated as having the Source "IPD", though their accessions refer to GenBank. Some of these do indeed have relevant entired in the IPD-MHC. — Reply to this email directly, view it on GitHub <#160>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADKDY42P7QFLLCUBCSOCK7D4MJLUTAVCNFSM6AAAAACVK4BDPOVHI2DSMVQWIX3LMV43ASLTON2WKOZTHE2TAMBWGUYDQOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Randi Vita, M.D. Lead Ontology and Quality Manager Immune Epitope Database and Analysis Project La Jolla Institute for Allergy & Immunology 9420 Athena Circle La Jolla, Ca 92037 ***@***.*** www.immuneepitope.org 858-752-6912

[ArnNag]

To be more specific, the accession provided in the table is an accession for GenBank, not an accession for IPD, even though it is annotated as such. Here's an example:
Patr-A*01:01 chain Patr-A*01:01 IPD AAF72774.1 [sequence]

This is the only row corresponding to Patr-A*01:01 in the table.
Moreover, since you mention that the IPD sequence is preferred, there is indeed an sequence in the IPD for this allele with accession NHP00705. This is not referenced anywhere in the table. This is the case for several Patr alleles.

[rvita]

Hi, at the time we added those chains to MRO, we imported the names, accessions, and sequences from the IPD's download file. This was done several years ago and we have never attempted to re sync with any changes that may have taken place at IPD, primarily due to no user requests and limited staff. We do have versioning in MRO, but I am not sure if IPD does. We could perform an update to match the current data on IPD's site, but I'd need to look into if we have anyone available to work on it at this time. Also note that we previously noted a few differences between what is shown on their public site vs what was in the download file. I'll see if I can get an estimate of when we'd have someone who could run those updates.

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On Tue, Feb 17, 2026 at 12:08 PM Arnav Nagle ***@***.***> wrote: *ArnNag* left a comment (IEDB/MRO#160) <#160 (comment)> To be more specific, the accession provided in the table is an accession for GenBank, not an accession for IPD, even though it is annotated as such. Here's an example: Patr-A*01:01 chain Patr-A*01:01 IPD AAF72774.1 [sequence] This is the only row corresponding to Patr-A*01:01 in the table. Moreover, since you mention that the IPD sequence is preferred, there is indeed an sequence in the IPD for this allele with accession NHP00705. This is not referenced anywhere in the table. This is the case for several Patr alleles. — Reply to this email directly, view it on GitHub <#160 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADKDY42BHBWSTLGTTAIJ6W34MNYL7AVCNFSM6AAAAACVK4BDPOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTSMJWHAZTQMJRHE> . You are receiving this because you commented.Message ID: ***@***.***>

-- Randi Vita, M.D. Lead Ontology and Quality Manager Immune Epitope Database and Analysis Project La Jolla Institute for Allergy & Immunology 9420 Athena Circle La Jolla, Ca 92037 ***@***.*** www.immuneepitope.org 858-752-6912

[rvita]

Hi, we discussed the issue of outdated protein accessions in MRO and have several possible solutions, depending on your specific needs, your interest, and skill set. We currently do not have a bioinformatics post-doc who is available to work on MRO. If you have a specific, smaller set of MRO terms that you have identified and need updated for your immediate work, and if you send me that list, I can manually update them. Or if you need a larger set of terms updated, and you can provide me with the MRO term (and/or identifiers) and the new chain accessions for each chain, we can push an automated update using those values. Or if you are familiar and comfortable working with open source ontologies, MRO is an open project and you can push changes to a test build, I can review that build, and if it looks good, we can push your changes directly to MRO. If working with ontologies is something you are not familiar with, but that you'd like to learn about, I can point you to some excellent resources to get you started. Or if you just need immediate access to the chain accessions that IPD/IMGT currently cites, they have a downloadable file accessible via their website (which is what we used to automate the seeding of MRO several years ago), I can point you to that file. Please describe your needs and let me know what you think will work best for you. Thanks, Randi

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On Tue, Feb 17, 2026 at 12:08 PM Arnav Nagle ***@***.***> wrote: *ArnNag* left a comment (IEDB/MRO#160) <#160 (comment)> To be more specific, the accession provided in the table is an accession for GenBank, not an accession for IPD, even though it is annotated as such. Here's an example: Patr-A*01:01 chain Patr-A*01:01 IPD AAF72774.1 [sequence] This is the only row corresponding to Patr-A*01:01 in the table. Moreover, since you mention that the IPD sequence is preferred, there is indeed an sequence in the IPD for this allele with accession NHP00705. This is not referenced anywhere in the table. This is the case for several Patr alleles. — Reply to this email directly, view it on GitHub <#160 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADKDY42BHBWSTLGTTAIJ6W34MNYL7AVCNFSM6AAAAACVK4BDPOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTSMJWHAZTQMJRHE> . You are receiving this because you commented.Message ID: ***@***.***>

-- Randi Vita, M.D. Lead Ontology and Quality Manager Immune Epitope Database and Analysis Project La Jolla Institute for Allergy & Immunology 9420 Athena Circle La Jolla, Ca 92037 ***@***.*** www.immuneepitope.org 858-752-6912

[rvita]

Hi, I wanted to ask if you had any new feedback or other questions for us? Thanks, Randi

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On Tue, Mar 3, 2026 at 8:59 AM Randi Vita ***@***.***> wrote: Hi, we discussed the issue of outdated protein accessions in MRO and have several possible solutions, depending on your specific needs, your interest, and skill set. We currently do not have a bioinformatics post-doc who is available to work on MRO. If you have a specific, smaller set of MRO terms that you have identified and need updated for your immediate work, and if you send me that list, I can manually update them. Or if you need a larger set of terms updated, and you can provide me with the MRO term (and/or identifiers) and the new chain accessions for each chain, we can push an automated update using those values. Or if you are familiar and comfortable working with open source ontologies, MRO is an open project and you can push changes to a test build, I can review that build, and if it looks good, we can push your changes directly to MRO. If working with ontologies is something you are not familiar with, but that you'd like to learn about, I can point you to some excellent resources to get you started. Or if you just need immediate access to the chain accessions that IPD/IMGT currently cites, they have a downloadable file accessible via their website (which is what we used to automate the seeding of MRO several years ago), I can point you to that file. Please describe your needs and let me know what you think will work best for you. Thanks, Randi On Tue, Feb 17, 2026 at 12:08 PM Arnav Nagle ***@***.***> wrote: > *ArnNag* left a comment (IEDB/MRO#160) > <#160 (comment)> > > To be more specific, the accession provided in the table is an accession > for GenBank, not an accession for IPD, even though it is annotated as such. > Here's an example: > Patr-A*01:01 chain Patr-A*01:01 IPD AAF72774.1 [sequence] > > This is the only row corresponding to Patr-A*01:01 in the table. > Moreover, since you mention that the IPD sequence is preferred, there is > indeed an sequence in the IPD for this allele with accession NHP00705. This > is not referenced anywhere in the table. This is the case for several Patr > alleles. > > — > Reply to this email directly, view it on GitHub > <#160 (comment)>, or > unsubscribe > <https://github.com/notifications/unsubscribe-auth/ADKDY42BHBWSTLGTTAIJ6W34MNYL7AVCNFSM6AAAAACVK4BDPOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTSMJWHAZTQMJRHE> > . > You are receiving this because you commented.Message ID: > ***@***.***> > -- Randi Vita, M.D. Lead Ontology and Quality Manager Immune Epitope Database and Analysis Project La Jolla Institute for Allergy & Immunology 9420 Athena Circle La Jolla, Ca 92037 ***@***.*** www.immuneepitope.org 858-752-6912

-- Randi Vita, M.D. Lead Ontology and Quality Manager Immune Epitope Database and Analysis Project La Jolla Institute for Allergy & Immunology 9420 Athena Circle La Jolla, Ca 92037 ***@***.*** www.immuneepitope.org 858-752-6912