MMRRC (Mutant Mouse Resource & Research Centers)

The MMRRC is a national resource that archives and distributes genetically engineered mouse strains to the research community. This ingest captures genotype information, allele-to-genotype associations, and genotype-to-phenotype associations from the MMRRC catalog data.

Data Source

Download: https://www.mmrrc.org/about/mmrrc_catalog_data.csv

The catalog is provided as a single denormalized CSV where each row represents a strain, but with one-to-many relationships embedded: a genotype (identified by STRAIN/STOCK_ID) can have multiple alleles and multiple associated genes, and phenotypes are stored as pipe-delimited lists of Mammalian Phenotype Ontology terms (e.g. phenotype label [MP:XXXXXXX]).

Preprocessing

The denormalized catalog is normalized into three datasets before transformation:

Genotypes — Deduplicated by strain ID to produce one row per unique genotype
Allele-to-genotype — Distinct pairs of MGI allele accession IDs and strain IDs, filtering out rows with no allele accession
Genotype-to-phenotype — The pipe-delimited phenotype lists are exploded into individual MP term associations per genotype, with phenotype labels extracted from the structured text

Duplicate relationships in the original catalog (e.g. the same genotype-allele pair appearing multiple times) are deduplicated during this step.

Genotype

Creates Genotype nodes for each unique mouse strain in the MMRRC catalog. All MMRRC strains are Mus musculus, so taxon is hardcoded.

Biolink Captured:

biolink:Genotype
- id: MMRRC:{strain_id} (already in format MMRRC:XXXXXX-XXX)
- name: strain_designation - Full strain designation with genetic nomenclature
- description: Constructed from strain_type and genetic information
- xref: other_names - Includes RRID identifiers
- in_taxon: ["NCBITaxon:10090"] (Mus musculus - hardcoded)
- in_taxon_label: "Mus musculus"
- provided_by: ["infores:mmrrc"]

Example Input

strain_id,strain_designation,other_names,strain_type,state,mutation_type,chromosome,sds_url,accepted_date,research_areas,pubmed_ids
MMRRC:000002-UNC,B6.129P2-<i>Esr2<sup>tm1Unc</sup></i>/Mmnc,RRID:MMRRC_000002-UNC,CON,CA,TM,12,https://www.mmrrc.org/catalog/sds.php?mmrrc_id=2,04/24/2001,,PMID: 9861029

Example Output

Genotype(
    id="MMRRC:000002-UNC",
    name="B6.129P2-<i>Esr2<sup>tm1Unc</sup></i>/Mmnc",
    xref=["RRID:MMRRC_000002-UNC"],
    in_taxon=["NCBITaxon:10090"],
    in_taxon_label="Mus musculus",
    provided_by=["infores:mmrrc"]
)

Genotype to Phenotype

Associations between genotypes and their observed phenotypes using Mammalian Phenotype Ontology (MP) terms. Rows with empty phenotype IDs or labels are filtered out.

Biolink Captured:

biolink:GenotypeToPhenotypicFeatureAssociation
- id: Generated UUID
- subject: strain_id (Genotype ID, e.g., MMRRC:000002-UNC)
- predicate: biolink:has_phenotype
- object: phenotype_id (e.g., MP:0000063)
- aggregator_knowledge_source: ["infores:monarchinitiative"]
- primary_knowledge_source: "infores:mmrrc"
- knowledge_level: "knowledge_assertion"
- agent_type: "manual_agent"

Example Input

strain_id,phenotype_id,phenotype_label
MMRRC:000002-UNC,MP:0000063,decreased bone mineral density
MMRRC:000002-UNC,MP:0000137,abnormal vertebrae morphology

Example Output

GenotypeToPhenotypicFeatureAssociation(
    id="uuid:...",
    subject="MMRRC:000002-UNC",
    predicate="biolink:has_phenotype",
    object="MP:0000063",
    aggregator_knowledge_source=["infores:monarchinitiative"],
    primary_knowledge_source="infores:mmrrc",
    knowledge_level="knowledge_assertion",
    agent_type="manual_agent"
)

Allele to Genotype

Associations between MGI alleles and the MMRRC genotypes that carry them.

Biolink Captured:

biolink:GenotypeToVariantAssociation (using Allele as a type of Variant)
- id: Generated UUID
- subject: strain_id (Genotype ID, e.g., MMRRC:000002-UNC)
- predicate: biolink:has_sequence_variant (inverse: genotype has_sequence_variant allele)
- object: allele_id (MGI Allele ID, e.g., MGI:2152217)
- aggregator_knowledge_source: ["infores:monarchinitiative"]
- primary_knowledge_source: "infores:mmrrc"
- knowledge_level: "knowledge_assertion"
- agent_type: "manual_agent"

Design Decision

We use GenotypeToVariantAssociation with has_sequence_variant predicate rather than creating a separate AlleleToGenotypeAssociation type, as Biolink Model treats alleles as a type of sequence variant. The direction is: Genotype (subject) -> has_sequence_variant -> Allele (object), which allows us to express that this allele is part of/contributes to this genotype.

Alternative considered: Using biolink:part_of or biolink:has_part, but has_sequence_variant better captures the genetic relationship in Biolink's model.

Example Input

allele_id,allele_symbol,allele_name,strain_id,mutation_type,chromosome
MGI:2152217,Esr2<tm1Unc>,"estrogen receptor 2 (beta); targeted mutation 1, University of North Carolina",MMRRC:000002-UNC,TM,12

Example Output

GenotypeToVariantAssociation(
    id="uuid:...",
    subject="MMRRC:000002-UNC",
    predicate="biolink:has_sequence_variant",
    object="MGI:2152217",
    aggregator_knowledge_source=["infores:monarchinitiative"],
    primary_knowledge_source="infores:mmrrc",
    knowledge_level="knowledge_assertion",
    agent_type="manual_agent"
)

Citation

Mutant Mouse Resource & Research Centers (MMRRC). https://www.mmrrc.org