bep

PopulationAbundance function

Abstract

The purpose of this BEP is to add populationAbundance(TAX:|) or pop(TAX:|) to the BEL Language.

A populationAbundance function would allow biologists and toxicologists to capture population changes in a taxon, e.g., a species, subspecies, or phylum, OR a cell population, e.g. adipocytes, epithelial, muscle cells. There is currently no way to capture this information using BEL 2.0.0. This would be especially useful for microbiome, cell biology and ecology/toxicology.

Preamble

BEP-Id: BEP0001

Status: Draft

Version: 1

Authors: William Hayes ([email protected])

Created-Date: 2018-04-23

Type: Standards Track

BEL-Version: 2.0.0+

Rationale and Goals

Population abundance is not currently captured by the BEL Language. In order to support microbiome, environmental biologists, toxicologists, and others, BEL needs the ability to describe effects on entire populations of organisms and cells.

Use Cases

Adding a populationAbundance() function would allow capturing Taxon and Cell population level changes due to environment or treatments.

# Penicillin decreases the population of Streptococcus entericus
a(CHEBI:penicillin) decreases pop(TAX:1123302)

# California Mule Deer increases population of gray wolves
pop(TAX:598490) increases pop(TAX:9612)

# Firmicutes bacteria increases obesity
pop(TAX:1239) increases path(MESH:Obesity)

# A heterogeneous population of microbiome bacteria
composite(pop(TAX:xxxx), pop(TAX:yyyy)) increases ...

# A drug decreases the population of adipocytes
a(CHEBI:metformin) decreases pop(MESH:"Adipocytes, White")

# P. falciparum invasion of RBCs increases malaria
complex(pop(NCBI:txid5833), pop(CL:erythrocyte)) increases path(DO:malaria)

#S. typhimurium in complex with L-ficolin (an opsonin) enhances phagocytosis [PMID:8576206]
complex(pop(NCBI:txid90371), p(HGNC:FCN2)) increases bp(GO:phagocytosis)

Discussion

• Should we use this for cell populations as well? E.g., (PMID 19404966) “The number of Th17 cells increased during SLE flare”. Is there a need for distinct entity types for populations of cells and taxonomic groups, i.e., different needs for modifying functions?
• Similar to other BEL abundance types, should the loc() modifier apply? E.g., pop(TAX:”Demodex folliculorum”, loc(UBERON:”hair follicle”))
• Almost all other BEL abundance types can participate in complexes. Should pop() participate in complexes? Or do we need a new entity or relationship to represent physical interactions between populations and/or populations and other abundances?How should symbiotic or parasitic relationships be represented?

Specification

The new language feature is:

populationAbundance(|) pop(|)

composite(pop(), pop(), …)

translocation(pop(), fromLoc(), toLoc() )

pop(MESH:”Adipocytes, White”, loc())

Taxon is currently supported by the BEL.bio API using the NCBI Taxonomy (TAX) namespace. Cell is supported by CELL, part of MESH and other Cell-tagged namespaces

Backwards Compatibility

This proposed feature is for 2.0.0+ and will be added to the language so does not require any efforts to migrate older BEL knowledge.

Reference Implementation

The reference implementation will target the next minor point release of the BEL language after approval (e.g. 2.1.0) and will consist of adding the populationAbundance() function to the BEL Specification yaml file.

functions:
  info:
    populationAbundance:
      type: primary
      abbreviation: pop
      categories:
      - abundance
      description: Denotes the abundance of a taxon.
      name: populationAbundance
  signatures:
    populationAbundance:
      func_type: primary
      name: populationAbundance
        signatures:
          - arguments:
            - type: NSArg
              position: 1
              values:
              - Species
              - Cell
            - optional: true
              type: Modifier
              values:
              - location

    translocation:
      func_type: primary
      name: translocation
      signatures:
      - arguments:
        - type: Function
          position: 1
          values:
          - proteinAbundance
          - rnaAbundance
          - microRNAAbundance
          - complexAbundance
          - populationAbundance
        - type: Modifier
          position: 2
          values:
          - fromLoc
        - type: Modifier
          position: 3
          values:
          - toLoc


    compositeAbundance:
      func_type: primary
      name: compositeAbundance
      notes: Cannot embed a composite function inside a compositeAbundance
        function, you can use named complexes inside composite functions
      signatures:
      - arguments:
        - multiple: true
          optional: true
          type: Function
          values:
          - abundance
          - activity
          - proteinAbundance
          - geneAbundance
          - microRNAAbundance
          - rnaAbundance
          - complexAbundance
          - populationAbundance
        - multiple: true
          optional: true
          type: NSArg
          values:
          - Complex

    complexAbundance:
      description: |
        Can have multiple, named complexes (Entities of entity_type: Complex) as
        well as multiple abundance or proteinAbundance function arguments with
        a location Modifier.
      func_type: primary
      name: complexAbundance
      notes: |
        Cannot embed a complex function inside a complexAbundance function,
        you can use named complexes inside complex functions
      signatures:
      - arguments:
        - multiple: true
          optional: true
          type: Function
          values:
          - abundance
          - proteinAbundance
          - geneAbundance
          - microRNAAbundance
          - rnaAbundance
          - populationAbundance
        - multiple: true
          optional: true
          type: NSArg
          values:
          - Complex
        - optional: true
          type: Modifier
          values:
          - location

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