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Normalizing Mouse Strain Names + Strain-Subject-Genotype-Phenotype data model
Link to the list of current strains used by Mouse BIRN
Overview
On Mouse BIRN, we need to regularize our use of strain names, as well as coming to consensus regarding what data needs be made accessible via the subject and/or strain identifier in the context of sharing mouse-related data amongst Mouse BIRN labs.
Goals
- We need elements in the global conceptual schema to accommodate our needs where subject/subject group, strain name (all organism taxonomy entities really), and the genotype & phenotype information we directly link to subjects and/or taxonomic identifiers.
- We need a way to normalize/cleanse our use of strain names both to avoid confusion amongst BIRN labs regarding the specific strain of a subject, as well as to stay commensurate with the strain identifiers used in the mouse research community in general.
- Taxonomic identifiers (including genus, species, strain, sub-strain, etc.) need to be derived directly from BONFIRE using the preferred names or numbers as given in BIRNLex.
Recommendations
- Mouse BIRN will adopt the MGI standards for naming of rodent strains. This standard is in accordance with the International Committee on Standardized Genetic Nomenclature for Mice. An on-line tutorial on naming of mice strains is available from Jackson Laboratories.
- New data: Standard mouse strains will be entered into BIRNLex and given a unique BIRN identifer. Each strain will have a preferred spelling entered as well. Data providers should use this spelling in their databases and map this to the unique identifier. BIRNLex will maintain a cross reference to the accession number at MGI, currently the stock number.
- BIRNLex: When the MGI geneology is made available in electronic form, the BIRNLex will utilize its hierarchy. In the meanwhile, BIRNLex will recapitulate parts of this hierarchy for strains used in BIRN. The hierarchy will allow users to retrieve all C57 derived strains for example.
- Subject data model: Bill Bug has produced a data model for entering a complete specification of the genetic pedigree of a subject. We still have to decide whether this model will be implemented in each source database or whether it will be maintained as a central registry. Maryann offered to use the model to create an OWL ontology that can be used to describe individual subjects. This preliminary model is attached below.
- Legacy data: Rob Williams and Bill Bug have reviewed the current list of strain names in Mouse BIRN databases. We are making the assumption that all mice listed as C57BL/6 are in fact C57BL/6J. As much as possible, each source should review the current data and determine whether it is accurate or not. In cases where this is not possible, the strain should be mapped to the finest level of granularity that is possible. For example, if it cannot be conclusively determined that C57 is in fact C57BL/6J then it should be mapped to C57BL/6 in BIRNLex. BIRNLex will contain information on alternative spellings and usage.
- Hybrids and transgenics: The current BIRN sources are extremely inconsistent when it comes to naming transgenic animals. It is recommended that all transgenics utilized by BIRN be registered with the MGI registry and that the current list of transgenics be aligned with the standard. Again, BIRNLex should contain an entry with the preferred name and a unique identifer.
- Users of mice and stocks obtained from the Jackson Laboratory are encouraged to use the JAX Stock Number identifier. For example, strain NZO/HlLtJ is easy to misspell in many ways (e.g., NZ0/HiLtJ) but the Stock Number JAX:002105 is a good identifier. See the Info and Models pages at the Jackson Labs Mouse Catalog for more details.
- This is a specific case of the more general issue of how the many mouse strain repositories around the world uniquely identify the stocks they maintain. The International Mouse Strain Resource (IMSR) has been established to provide the research community with a unified means to uniquely identifying established strains. They are working with the various repositories to ensure there will be unique, non-colliding identifiers for ALL strains regardless of the repository the derive from. The preferred unique identifier will either be a unique number qualified by the name of the repository - e.g., JAX:002105 given above - or the mouse strain name.
- IMSR also will maintain a search engine to help investigators locate info on all of these strains. To get a sense of how strains are being identified, perform the following search:
- enter C57 in the strain/stock designation field and hit return
- click on the strain/stock designation for any mouse from Jackson Labs (holder site = JAX)
- the Jackson Labs Mouse Catalog page for that strain will come up. There you will find the Stock Number for that strain. This is the best tag to use for uniquely identifying this strain from Jackson Labs, just as is recommended above. This same situation holds true for several of the other repositories, such as the Mutant Mouse Regional Resource Centers (Holder Site = MMRRC ), The European Mouse Mutant Archive (EMMA) (Holder Site = EM), and several others.
- Other repositories are not currently advertising their internal control numbers for strains. For these repositories, the strain name itself will be the identifier. For instance, return the search result report above and click on the strain/stock designation for a strain from Oak Ridge National Labs Mutant Mouse Database (holder site = ORNL). On the ORNL MMD report page you will find a Formal Name. This is considered the unique identifier for that particular strain maintained by ORNL.
- Note this IMSR consortium effort is still a work-in-progress. This is best reflected by the fact there may in fact be some strain names not fully conformant with the recommended syntax, and some names may not in fact be globally unique. With this in mind, it is best to include the repository designation along with the strain name when logging a unique strain identifier, just as with the numeric ID example above. For instance, ORNL strain you will find at the top of this search result report would be best be identified with the tag ORNL:(C3HeB/FeJ-Atrnmg-3Jx C57BL/6J)BC. The IMSR database indicates whether the strain name has been fully vetted. This is listed in the name designation column to the far left - N (the key for the values in that field is listed at the top of the page).
- The work-in-progress status is also made clear by the fact that some of the links on the IMSR search result page will not take you directly to the resource page for that strain. This is current (2006-08-25) true for the Frozen Embryo and Sperm Archive (FESA) at the MRC Mammalian Genetics Unit in the Harwell, England, UK (holder site = HAR) and the CARD. For HAR, you must click on the Search Embryo Bank Resources link and enter the mutant phenotype - e.g., hairy ears - in the free text box in order to get to the specific strain page. For the CARD strains from the Center for Animal Resources and Development (CARD) - one of the Japan Mouse Strain Resource Repositories, the links aren't working at the moment, though they certainly have in the past.
Planning
Action Items
- 2006-08-25
- Rob, Maryann and Bill will attempt to describe the alpha synuclein transgenic using Bill’s data model.
- MGI interactions: Bill will contact Joel Richardson and Jannan Epping from MGI to discuss BIRN’s approach and the data model.
Working Pages
- Links to related working pages
Minutes, etc.
Other important information and links
- Links to areas of interest to the topic
Updates/Progress
- Link to update documents
- Or enter individual updates here
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