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biocide and biocide_admin_method illustrate inconsistent modelling with paired method slots #879

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turbomam opened this issue Dec 18, 2024 · 1 comment

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@turbomam
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turbomam commented Dec 18, 2024

Upon further review, there may be two general patterns of "pairs with a method". See additional comments below. Here is one worked example:

biocide:
  annotations:
    Expected_value: name;name;timestamp
  description: List of biocides (commercial name of product and supplier) and date of administration
  title: biocide administration
  examples:
    - value: ALPHA 1427;Baker Hughes;2008-01-23
  keywords:
    - administration
  string_serialization: '{text};{text};{timestamp}'
  slot_uri: MIXS:0001011
  recommended: true
biocide_admin_method:
  annotations:
    Expected_value: measurement value;frequency;duration;duration
    Preferred_unit: milligram per liter
  description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)
  title: biocide administration method
  keywords:
    - administration
    - method
  string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'
  slot_uri: MIXS:0000456
  recommended: true

vs

cur_vegetation:
  annotations:
    Expected_value: current vegetation type
  description: Vegetation classification from one or more standard classification systems, or agricultural crop
  title: current vegetation
  keywords:
    - vegetation
  range: string
  slot_uri: MIXS:0000312
cur_vegetation_meth:
  description: Reference or method used in vegetation classification
  title: current vegetation method
  keywords:
    - method
    - vegetation
  slot_uri: MIXS:0000314
  range: string
  pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
  structured_pattern:
    syntax: ^{PMID}|{DOI}|{URL}$
    interpolated: true
    partial_match: true
@turbomam
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turbomam commented Dec 18, 2024

This list only concerns slots with "meth" in their names. There are additional slots whose description mention "method".

method citations

  • al_sat_meth
  • cur_vegetation_meth
  • heavy_metals_meth
  • horizon_meth
  • local_class_meth
  • micro_biomass_meth
  • ph_meth
  • photosynt_activ_meth
  • prev_land_use_meth
  • samp_collect_method
  • soil_texture_meth
  • soil_type_meth
  • tot_org_c_meth
  • water_cont_soil_meth

method descriptions:

  • add_recov_method
  • anim_water_method
  • biocide_admin_method
  • chem_treat_method
  • plant_water_method
  • sim_search_meth
  • urine_collect_meth

unclear (minimally elaborated string ranges)

  • alkalinity_method (example = titration)
  • heat_sys_deliv_meth (example = radiant)
  • samp_sort_meth no example or pattern
  • sc_lysis_method (example = ambion single cell lysis kit)
  • urine_collect_meth (example = catheter)

ontology term range

  • seq_meth

@turbomam turbomam changed the title biocide and biocide_admin_method are inconsistent with other term pairs where one is about the method by which the other was determined biocide and biocide_admin_method illustrate inconsistent modelling with paired method slots Dec 18, 2024
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