Bit Stomach

A command line application that processes performance data to make assertions about performer attributes.

An animated SVG screen cast demonstration is in the screen cast directory.

Input Requirements

The application expects a spek, tabular input data, and annotation functions.

Input Spek

JSON-LD description of project. It includes:

• any apriori assertions about performers.
• description of performance data column names and uses.
• descriptions of performance measures and comparators.

Input Data

Tabular data (csv) with performance data.
These usually include: performer, timepoint, and performance value or counts.

Annotation Specification

An R file containing functions which provide situation specific interpretation of the performance values.
Specified by collaborator or domain expert.
Format and use of annotations is convention instead of configuration.

• The annotate_X functions need to return a table with the id column and one column per annotation.
• The short name of the annotation can be used.
• It is looked up and resolved to an IRI per the mapping in package_constants.R
• A cache of values can be generated by providing a setup_cache function.
• See vert-ramp-affirmation project for exampe vignettes.

Snippet of an annotation.r that assesses the positive gap annotation. The setup_cache has been omitted for brevity.

library(dplyr, warn.conflicts = FALSE)
library(rlang, warn.conflicts = FALSE)
library(tidyr, warn.conflicts = FALSE)

annotate_positive_gap <- function(data, spek){
  rate <- cache$rate_col_sym
  time <- cache$time_col_sym
  id <- cache$id_col_sym

  data %>%
    dplyr::filter(!!time == max(!!time)) %>%
    group_by(!!id) %>%
    summarize(positive_gap = (!!rate > cache$comparator))
}

Resulting Annotations

Functions to process input data and determine if attribute is present or not.
Each function is called with the performance data and a column spec as args. It is expected to return a table of the id and boolean value of the attribute. Returned table must be grouped by id. e.g the result of annotate_capability_barier:

id	positive_gap
Alice	TRUE
Bob	FALSE
Carol	FALSE

The IRI is substituted for the attribute short name.

id	http://purl.obolibrary.org/obo/psdo_0000104
Alice	TRUE

The performer and attribute is emitted as part of the output JSON-LD.

{
  "@id": "_:pAlice",
  "http://purl.obolibrary.org/obo/RO_0000091": [
    {
      "@type": "http://purl.obolibrary.org/obo/psdo_0000104",
      "http://example.com/slowmo#RegardingMeasure": {
        "@id": "_:m1"
      }
    }
  ],
  "@type": "http://purl.obolibrary.org/obo/psdo_0000085"
}