need a biolink-model term for mouse strain

[justaddcoffee]

I'm looking for a biolink model term to represent mouse strain (C57black, BALB/c). This doesn't seem to exist now in biolink-model. I'm guessing this same term might be used to describe subspecies in other species besides mouse - human subpopulations, yeast strains, etc. Could we make a term for this, or could someone point me to the most appropriate term?

[justaddcoffee]

@deepakunni3 per our convo, there is the term "population of individual organisms", which might be the right one here...

[cmungall]

There is an argument for including a subclass for strain/breed https://www.ebi.ac.uk/ols/ontologies/geno/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGENO_0000112

[TomConlin]

more fodder

#
#           biospecimen         https://en.wikipedia.org/wiki/Biological_specimen
#       specimen            https://en.wikipedia.org/wiki/Zoological_specimen
#       organism            https://en.wikipedia.org/wiki/Organism
#   strain              https://en.wikipedia.org/wiki/Strain_(biology)
#   breed               https://en.wikipedia.org/wiki/Breed
#   cultivar            https://en.wikipedia.org/wiki/Cultivar
#   hybrid              https://en.wikipedia.org/wiki/Hybrid_(biology)
#   landrace            https://en.wikipedia.org/wiki/Landrace

forma               https://en.wikipedia.org/wiki/Form_(botany)
varietas            https://en.wikipedia.org/wiki/Variety_(botany)
subspecies          https://en.wikipedia.org/wiki/Subspecies

[deepakunni3]

There is an argument for including a subclass for strain/breed https://www.ebi.ac.uk/ols/ontologies/geno/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGENO_0000112

@cmungall Do we want to add a subclass for strain/breed?

[deepakunni3]

We could treat strain as an organism taxon for an organism class. What about breed, cultivar, landrace, etc.? These ought to be addressed by reusing organism taxon

[RichardBruskiewich]

In crop science (plants), there are global standards which tag different kinds of subpopulations, eg. landraces, cultivar, etc. See http://aims.fao.org/vest-registry/metadata-sets/faoipgri-multi-crop-passport-descriptors

[TomConlin]

others

#           biospecimen         https://en.wikipedia.org/wiki/Biological_specimen
#       specimen            https://en.wikipedia.org/wiki/Zoological_specimen
#       organism            https://en.wikipedia.org/wiki/Organism
#   strain              https://en.wikipedia.org/wiki/Strain_(biology)
#   breed               https://en.wikipedia.org/wiki/Breed
#   cultivar            https://en.wikipedia.org/wiki/Cultivar
#   hybrid              https://en.wikipedia.org/wiki/Hybrid_(biology)
#   landrace            https://en.wikipedia.org/wiki/Landrace

forma               https://en.wikipedia.org/wiki/Form_(botany)
varietas            https://en.wikipedia.org/wiki/Variety_(botany)

[RichardBruskiewich]

Once again, in the world of (crop) plants, the various terms - landrace, hybrid, cultivar, etc. - have less to do with the biology of the plant than it has to do with their sociological, geographical or technical origin. There are, of course, typical genetic features of interest in each of these plants even if they are the same species. In many crop plants, for example, rice, there are major ancient subtypes - Oryza sativa japonica, Oryza sativa indica, etc. - as well as many subpopulations specific to environments and regions. All of these categories could, in principle, be tagged as "Strains" although the term is not commonly used in (crop) plant science.

I suspect that if we simple introduce the Biolink model subclass "Strain" to designate a genetically distinct instance of a species (taxon), then we will adequately cover alot of ground. Beyond that, all the rest is what we call "germplasm documentation".

[nlharris]

Should this still be assigned to @mbrush?

[sierra-moxon]

The Alliance probably has some work we can reuse here. In particular, the concepts of genotypes, strains, backgrounds and genotypes with sequence targeting reagents should be "groupable" into a higher level class.

[sierra-moxon]

the model has:

  population of individual organisms:
    description: >-
      A collection of individuals from the same taxonomic class
      distinguished by one or more characteristics.  Characteristics can
      include, but are not limited to, shared geographic location, genetics,
      phenotypes [Alliance for Genome Resources]
    local_names:
      ga4gh: population
      agr: population
    mixins:
      - thing with taxon
    is_a: organismal entity
    exact_mappings:
      - PCO:0000001
      - SIO:001061
      # UMLS Semantic Type "Population Group"
      - STY:T098
      - OBI:0000181
    id_prefixes:
      - HANCESTRO
    in_subset:
      - model_organism_database