README.md
In NiklasTR/microbiomefhir:
microbiomeFHIR - turn a patient’s microbiome OTU data into FHIR
library(microbiomefhir)
library(tidyverse)
library(curatedMetagenomicData)
library(phyloseq)
library(here)
DISCLAIMER: This is an alpha build,
The microbiomfhir package allows the conversion of a patient’s OTU table
into a structured FHIR DiagnosticReport. At this point the package only
supports the import of phyloseq
objects.
Planned features
- integrate SNOMED API calls to code for bacterial species
- integrate PROCEDURE ressource to annotate more experiment related
information
- change patient and sample submission details
- process multiple profiles into separate reports
Installation Instructions
The package is currenlty available via GitHub
devtools::install_github("https://github.com/NiklasTR/microbiomefhir")
The package has, among others, the following requirements:
- tidyverse toolbox
- phyloseq
- curatedMetagenomicData
Example
Let’s use the package’s built-in function to collect an example from
Levi Waldron’s excellent curated Metagenomic Data
ressource.
pseq <- load_example()
Here is a glimpse at one of the OTU table profiles. We can see the
patient identifier as the column name. Each row represents a taxonomic
unit (from kingdom - Bacteria down to many species).
otu_table(pseq)[,1] %>% head()
## OTU Table: [6 taxa and 1 samples]
## taxa are rows
## LomanNJ_2013.metaphlan_bugs_list.stool:OBK1122
## k__Bacteria 100.00000
## p__Bacteroidetes 83.55662
## p__Firmicutes 15.14819
## p__Proteobacteria 1.29520
## c__Bacteroidia 83.55662
## c__Clostridia 14.93141
We can simply export the patient’s OTU table into a FHIR
DiagnosticReport:
parse_json(pseq, file = here("output/my_first_microbiome_fhir_report.json"))
We can take a closer look at out output JSON file.
readLines(here("output/my_first_microbiome_fhir_report.json"), 150)
## [1] "{"
## [2] " \"resourceType\": [\"DiagnosticReport\"],"
## [3] " \"id\": [\"101\"],"
## [4] " \"meta\": {"
## [5] " \"tag\": ["
## [6] " {"
## [7] " \"system\": \"http://example.org/fhir/CodeSystem/workflow-codes\","
## [8] " \"code\": \"01\","
## [9] " \"display\": \"Needs Review\""
## [10] " }"
## [11] " ]"
## [12] " },"
## [13] " \"text\": {"
## [14] " \"status\": [\"generated\"],"
## [15] " \"div\": [\"<div Lorem Ipsum; ????<\\/p><\\/div>\"]"
## [16] " },"
## [17] " \"contained\": {"
## [18] " \"resourceType\": [\"Specimen\"],"
## [19] " \"id\": [\"stool\"],"
## [20] " \"accessionIdentifier\": ["
## [21] " {"
## [22] " \"system\": \"http://example.org/specimens/2019\","
## [23] " \"value\": \"X352356\""
## [24] " }"
## [25] " ],"
## [26] " \"status\": [\"unavailable\"],"
## [27] " \"type\": ["
## [28] " {"
## [29] " \"coding\": ["
## [30] " {"
## [31] " \"system\": \"http://snomed.info/sct\","
## [32] " \"code\": \"119339001\","
## [33] " \"display\": \"Stool specimen\""
## [34] " }"
## [35] " ]"
## [36] " }"
## [37] " ],"
## [38] " \"subject\": ["
## [39] " {"
## [40] " \"reference\": \"Patient/example\""
## [41] " }"
## [42] " ],"
## [43] " \"receivedTime\": [\"2019-08-16T07:03:00Z\"],"
## [44] " \"collection\": ["
## [45] " {"
## [46] " \"collector\": {"
## [47] " \"display\": \"Patient\""
## [48] " },"
## [49] " \"collectedDateTime\": \"2011-08-16T06:15:00Z\","
## [50] " \"method\": {"
## [51] " \"coding\": ["
## [52] " {"
## [53] " \"system\": \"http://hl7.org/fhir/v2/0488\","
## [54] " \"code\": \"SWA\""
## [55] " }"
## [56] " ]"
## [57] " }"
## [58] " }"
## [59] " ],"
## [60] " \"issued\": [null],"
## [61] " \"valueCodeableConcept\": ["
## [62] " {"
## [63] " \"coding\": {}"
## [64] " }"
## [65] " ],"
## [66] " \"valueQuantity\": ["
## [67] " {}"
## [68] " ],"
## [69] " \"12\": ["
## [70] " {"
## [71] " \"resourceType\": \"Observation\","
## [72] " \"id\": \"k__Bacteria\","
## [73] " \"status\": \"final\","
## [74] " \"subject\": {"
## [75] " \"display\": \"Roel\""
## [76] " },"
## [77] " \"issued\": \"2019-08-16 07:03:00\","
## [78] " \"valueCodeableConcept\": {"
## [79] " \"coding\": ["
## [80] " {"
## [81] " \"system\": \"http://snomed.info/sct\","
## [82] " \"display\": \"Bacteria\""
## [83] " }"
## [84] " ]"
## [85] " },"
## [86] " \"valueQuantity\": {"
## [87] " \"value\": 100,"
## [88] " \"unit\": \"percent\","
## [89] " \"code\": \"%\""
## [90] " }"
## [91] " }"
## [92] " ],"
## [93] " \"13\": ["
## [94] " {"
## [95] " \"resourceType\": \"Observation\","
## [96] " \"id\": \"p__Bacteroidetes\","
## [97] " \"status\": \"final\","
## [98] " \"subject\": {"
## [99] " \"display\": \"Roel\""
## [100] " },"
## [101] " \"issued\": \"2019-08-16 07:03:00\","
## [102] " \"valueCodeableConcept\": {"
## [103] " \"coding\": ["
## [104] " {"
## [105] " \"system\": \"http://snomed.info/sct\","
## [106] " \"display\": \"Bacteroidetes\""
## [107] " }"
## [108] " ]"
## [109] " },"
## [110] " \"valueQuantity\": {"
## [111] " \"value\": 83.5566,"
## [112] " \"unit\": \"percent\","
## [113] " \"code\": \"%\""
## [114] " }"
## [115] " }"
## [116] " ],"
## [117] " \"14\": ["
## [118] " {"
## [119] " \"resourceType\": \"Observation\","
## [120] " \"id\": \"p__Firmicutes\","
## [121] " \"status\": \"final\","
## [122] " \"subject\": {"
## [123] " \"display\": \"Roel\""
## [124] " },"
## [125] " \"issued\": \"2019-08-16 07:03:00\","
## [126] " \"valueCodeableConcept\": {"
## [127] " \"coding\": ["
## [128] " {"
## [129] " \"system\": \"http://snomed.info/sct\","
## [130] " \"display\": \"Firmicutes\""
## [131] " }"
## [132] " ]"
## [133] " },"
## [134] " \"valueQuantity\": {"
## [135] " \"value\": 15.1482,"
## [136] " \"unit\": \"percent\","
## [137] " \"code\": \"%\""
## [138] " }"
## [139] " }"
## [140] " ],"
## [141] " \"15\": ["
## [142] " {"
## [143] " \"resourceType\": \"Observation\","
## [144] " \"id\": \"p__Proteobacteria\","
## [145] " \"status\": \"final\","
## [146] " \"subject\": {"
## [147] " \"display\": \"Roel\""
## [148] " },"
## [149] " \"issued\": \"2019-08-16 07:03:00\","
## [150] " \"valueCodeableConcept\": {"
NiklasTR/microbiomefhir documentation built on June 23, 2019, 2:06 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
microbiomeFHIR - turn a patient’s microbiome OTU data into FHIR
library(microbiomefhir)
library(tidyverse)
library(curatedMetagenomicData)
library(phyloseq)
library(here)
DISCLAIMER: This is an alpha build,
The microbiomfhir package allows the conversion of a patient’s OTU table into a structured FHIR DiagnosticReport. At this point the package only supports the import of phyloseq objects.
Planned features
- integrate SNOMED API calls to code for bacterial species
- integrate PROCEDURE ressource to annotate more experiment related information
- change patient and sample submission details
- process multiple profiles into separate reports
Installation Instructions
The package is currenlty available via GitHub
devtools::install_github("https://github.com/NiklasTR/microbiomefhir")
The package has, among others, the following requirements:
- tidyverse toolbox
- phyloseq
- curatedMetagenomicData
Example
Let’s use the package’s built-in function to collect an example from Levi Waldron’s excellent curated Metagenomic Data ressource.
pseq <- load_example()
Here is a glimpse at one of the OTU table profiles. We can see the patient identifier as the column name. Each row represents a taxonomic unit (from kingdom - Bacteria down to many species).
otu_table(pseq)[,1] %>% head()
## OTU Table: [6 taxa and 1 samples]
## taxa are rows
## LomanNJ_2013.metaphlan_bugs_list.stool:OBK1122
## k__Bacteria 100.00000
## p__Bacteroidetes 83.55662
## p__Firmicutes 15.14819
## p__Proteobacteria 1.29520
## c__Bacteroidia 83.55662
## c__Clostridia 14.93141
We can simply export the patient’s OTU table into a FHIR DiagnosticReport:
parse_json(pseq, file = here("output/my_first_microbiome_fhir_report.json"))
We can take a closer look at out output JSON file.
readLines(here("output/my_first_microbiome_fhir_report.json"), 150)
## [1] "{"
## [2] " \"resourceType\": [\"DiagnosticReport\"],"
## [3] " \"id\": [\"101\"],"
## [4] " \"meta\": {"
## [5] " \"tag\": ["
## [6] " {"
## [7] " \"system\": \"http://example.org/fhir/CodeSystem/workflow-codes\","
## [8] " \"code\": \"01\","
## [9] " \"display\": \"Needs Review\""
## [10] " }"
## [11] " ]"
## [12] " },"
## [13] " \"text\": {"
## [14] " \"status\": [\"generated\"],"
## [15] " \"div\": [\"<div Lorem Ipsum; ????<\\/p><\\/div>\"]"
## [16] " },"
## [17] " \"contained\": {"
## [18] " \"resourceType\": [\"Specimen\"],"
## [19] " \"id\": [\"stool\"],"
## [20] " \"accessionIdentifier\": ["
## [21] " {"
## [22] " \"system\": \"http://example.org/specimens/2019\","
## [23] " \"value\": \"X352356\""
## [24] " }"
## [25] " ],"
## [26] " \"status\": [\"unavailable\"],"
## [27] " \"type\": ["
## [28] " {"
## [29] " \"coding\": ["
## [30] " {"
## [31] " \"system\": \"http://snomed.info/sct\","
## [32] " \"code\": \"119339001\","
## [33] " \"display\": \"Stool specimen\""
## [34] " }"
## [35] " ]"
## [36] " }"
## [37] " ],"
## [38] " \"subject\": ["
## [39] " {"
## [40] " \"reference\": \"Patient/example\""
## [41] " }"
## [42] " ],"
## [43] " \"receivedTime\": [\"2019-08-16T07:03:00Z\"],"
## [44] " \"collection\": ["
## [45] " {"
## [46] " \"collector\": {"
## [47] " \"display\": \"Patient\""
## [48] " },"
## [49] " \"collectedDateTime\": \"2011-08-16T06:15:00Z\","
## [50] " \"method\": {"
## [51] " \"coding\": ["
## [52] " {"
## [53] " \"system\": \"http://hl7.org/fhir/v2/0488\","
## [54] " \"code\": \"SWA\""
## [55] " }"
## [56] " ]"
## [57] " }"
## [58] " }"
## [59] " ],"
## [60] " \"issued\": [null],"
## [61] " \"valueCodeableConcept\": ["
## [62] " {"
## [63] " \"coding\": {}"
## [64] " }"
## [65] " ],"
## [66] " \"valueQuantity\": ["
## [67] " {}"
## [68] " ],"
## [69] " \"12\": ["
## [70] " {"
## [71] " \"resourceType\": \"Observation\","
## [72] " \"id\": \"k__Bacteria\","
## [73] " \"status\": \"final\","
## [74] " \"subject\": {"
## [75] " \"display\": \"Roel\""
## [76] " },"
## [77] " \"issued\": \"2019-08-16 07:03:00\","
## [78] " \"valueCodeableConcept\": {"
## [79] " \"coding\": ["
## [80] " {"
## [81] " \"system\": \"http://snomed.info/sct\","
## [82] " \"display\": \"Bacteria\""
## [83] " }"
## [84] " ]"
## [85] " },"
## [86] " \"valueQuantity\": {"
## [87] " \"value\": 100,"
## [88] " \"unit\": \"percent\","
## [89] " \"code\": \"%\""
## [90] " }"
## [91] " }"
## [92] " ],"
## [93] " \"13\": ["
## [94] " {"
## [95] " \"resourceType\": \"Observation\","
## [96] " \"id\": \"p__Bacteroidetes\","
## [97] " \"status\": \"final\","
## [98] " \"subject\": {"
## [99] " \"display\": \"Roel\""
## [100] " },"
## [101] " \"issued\": \"2019-08-16 07:03:00\","
## [102] " \"valueCodeableConcept\": {"
## [103] " \"coding\": ["
## [104] " {"
## [105] " \"system\": \"http://snomed.info/sct\","
## [106] " \"display\": \"Bacteroidetes\""
## [107] " }"
## [108] " ]"
## [109] " },"
## [110] " \"valueQuantity\": {"
## [111] " \"value\": 83.5566,"
## [112] " \"unit\": \"percent\","
## [113] " \"code\": \"%\""
## [114] " }"
## [115] " }"
## [116] " ],"
## [117] " \"14\": ["
## [118] " {"
## [119] " \"resourceType\": \"Observation\","
## [120] " \"id\": \"p__Firmicutes\","
## [121] " \"status\": \"final\","
## [122] " \"subject\": {"
## [123] " \"display\": \"Roel\""
## [124] " },"
## [125] " \"issued\": \"2019-08-16 07:03:00\","
## [126] " \"valueCodeableConcept\": {"
## [127] " \"coding\": ["
## [128] " {"
## [129] " \"system\": \"http://snomed.info/sct\","
## [130] " \"display\": \"Firmicutes\""
## [131] " }"
## [132] " ]"
## [133] " },"
## [134] " \"valueQuantity\": {"
## [135] " \"value\": 15.1482,"
## [136] " \"unit\": \"percent\","
## [137] " \"code\": \"%\""
## [138] " }"
## [139] " }"
## [140] " ],"
## [141] " \"15\": ["
## [142] " {"
## [143] " \"resourceType\": \"Observation\","
## [144] " \"id\": \"p__Proteobacteria\","
## [145] " \"status\": \"final\","
## [146] " \"subject\": {"
## [147] " \"display\": \"Roel\""
## [148] " },"
## [149] " \"issued\": \"2019-08-16 07:03:00\","
## [150] " \"valueCodeableConcept\": {"
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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