From 85d1be90794e3f6bf766475968475d6855be1ceb Mon Sep 17 00:00:00 2001 From: Stuart Chalk Date: Sat, 1 May 2021 06:45:50 -0400 Subject: [PATCH] april 2021 update --- data/202104/sjc040121.jsonld | 1 + data/202104/sjc040221.jsonld | 1 + data/202104/sjc040321.jsonld | 1 + data/202104/sjc040421.jsonld | 1 + data/202104/sjc040521.jsonld | 1 + data/202104/sjc040621.jsonld | 1 + data/202104/sjc040721.jsonld | 1 + data/202104/sjc040821.jsonld | 1 + data/202104/sjc040921.jsonld | 1 + data/202104/sjc041021.jsonld | 1 + data/202104/sjc041121.jsonld | 1 + data/202104/sjc041221.jsonld | 1 + data/202104/sjc041321.jsonld | 1 + data/202104/sjc041421.jsonld | 1 + data/202104/sjc041521.jsonld | 1 + data/202104/sjc041621.jsonld | 1 + data/202104/sjc041721.jsonld | 1 + data/202104/sjc041821.jsonld | 1 + data/202104/sjc041921.jsonld | 1 + data/202104/sjc042021.jsonld | 1 + data/202104/sjc042121.jsonld | 1 + data/202104/sjc042221.jsonld | 1 + data/202104/sjc042321.jsonld | 1 + data/202104/sjc042421.jsonld | 1 + data/202104/sjc042521.jsonld | 1 + data/202104/sjc042621.jsonld | 1 + data/202104/sjc042721.jsonld | 1 + data/202104/sjc042821.jsonld | 1 + data/202104/sjc042921.jsonld | 1 + data/202104/sjc043021.jsonld | 1 + health-data.ipynb | 29 +++++++++++++++++++++++++++-- healthdata.csv | 11 ++++++++++- requirements.txt | 1 + writesd.py | 4 +--- 34 files changed, 69 insertions(+), 6 deletions(-) create mode 100644 data/202104/sjc040121.jsonld create mode 100644 data/202104/sjc040221.jsonld create mode 100644 data/202104/sjc040321.jsonld create mode 100644 data/202104/sjc040421.jsonld create mode 100644 data/202104/sjc040521.jsonld create mode 100644 data/202104/sjc040621.jsonld create mode 100644 data/202104/sjc040721.jsonld create mode 100644 data/202104/sjc040821.jsonld create mode 100644 data/202104/sjc040921.jsonld create mode 100644 data/202104/sjc041021.jsonld create mode 100644 data/202104/sjc041121.jsonld create mode 100644 data/202104/sjc041221.jsonld create mode 100644 data/202104/sjc041321.jsonld create mode 100644 data/202104/sjc041421.jsonld create mode 100644 data/202104/sjc041521.jsonld create mode 100644 data/202104/sjc041621.jsonld create mode 100644 data/202104/sjc041721.jsonld create mode 100644 data/202104/sjc041821.jsonld create mode 100644 data/202104/sjc041921.jsonld create mode 100644 data/202104/sjc042021.jsonld create mode 100644 data/202104/sjc042121.jsonld create mode 100644 data/202104/sjc042221.jsonld create mode 100644 data/202104/sjc042321.jsonld create mode 100644 data/202104/sjc042421.jsonld create mode 100644 data/202104/sjc042521.jsonld create mode 100644 data/202104/sjc042621.jsonld create mode 100644 data/202104/sjc042721.jsonld create mode 100644 data/202104/sjc042821.jsonld create mode 100644 data/202104/sjc042921.jsonld create mode 100644 data/202104/sjc043021.jsonld diff --git a/data/202104/sjc040121.jsonld b/data/202104/sjc040121.jsonld new file mode 100644 index 0000000..951f317 --- /dev/null +++ b/data/202104/sjc040121.jsonld @@ -0,0 +1 @@ +{"@context": ["https://stuchalk.github.io/scidata/contexts/scidata_subject.jsonld", "https://stuchalk.github.io/scidata/contexts/scidata_activity.jsonld", "https://stuchalk.github.io/scidata/contexts/scidata.jsonld", {"sdo": "https://stuchalk.github.io/scidata/ontology/scidata.owl#", "w3i": "https://w3id.org/skgo/modsci#", "qudt": "http://qudt.org/vocab/unit/", "obo": "http://purl.obolibrary.org/obo/", "dc": "http://purl.org/dc/terms/", "xsd": "http://www.w3.org/2001/XMLSchema#", "loinc": "https://loinc.org/", "ss": "http://semanticscience.org/resource/", "afp": "http://purl.allotrope.org/ontologies/process#"}, {"@base": "https://github.com/stuchalk/fair-health-data/data/sjc040121/"}], "@id": "dataset91", "generatedAt": "05-01-21 06:44:28", "version": "1", "@graph": {"@id": "https://github.com/stuchalk/fair-health-data/data/sjc040121/", "@type": "sdo:scidataFramework", "uid": "https://github.com/stuchalk/fair-health-data/data/sjc040121/", "title": "Health data for Stuart J. 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First, the 'head' button was depressed and held down while moving the device across the forehead from left to right at a distance of ~1 cm away. The 'head' button was then released. The reading on the display was recorded in the Notes app on an iPhone."}, {"@id": "activity/1/", "@type": "obo:NCIT_C43431", "exercise": "road running", "exerciseref": "obo:NCIT_C94737", "url": "https://connect.garmin.com/modern/activity/6697879972"}]}, "system": {"@id": "system/", "@type": "sdo:system", "facets": [{"@id": "subject/1/", "@type": "sdo:subject", "species": "homo sapien", "speciesref": "obo:NCBITaxon_9606", "gender": "male", "ethnicity": "caucasian", "nationality": "english"}, {"@id": "condition/1/", "@type": "sdo:condition", "quantity": "temperature", "property": "room temperature", "propertyref": "loinc:60832-3", "value": {"@id": "condition/1/numericvalue/1/", "@type": "sdo:numericvalue", "number": "75", "unit": "qudt:DEG_F"}}]}, "dataset": {"@id": "dataset/", "@type": "sdo:dataset", "scope": "specimen/1/", "datapoint": [{"@id": "datapoint/1/", "@type": "sdo:datapoint", "source": ["measurement/2/", "measurement/3/", "measurement/4/"], "property": "VO2 max", "propertyref": "loinc:94122-9", "activity": "activity/1/", "textstring": {"@id": "datapoint/1/numericvalue/1/", "@type": "sdo:numericvalue", "value": "51", "unit": "qudt:MilliL-PER-KiloGM-MIN"}}, {"@id": "datapoint/2/", "@type": "sdo:datapoint", "source": ["measurement/3/", "measurement/4/"], "property": "calories burned", "propertyref": "loinc:93825-8", "value": {"@id": "datapoint/2/numericvalue/1/", "@type": "sdo:numericvalue", "number": "607", "unit": "qudt:KiloCAL"}}, {"@id": "datapoint/3/", "@type": "sdo:datapoint", "source": "measurement/4/", "property": "running distance", "propertyref": "loinc:93817-5", "value": {"@id": "datapoint/3/numericvalue/1/", "@type": "sdo:numericvalue", "number": "5.01", "unit": "qudt:MI_US"}}, {"@id": "datapoint/4/", "@type": "sdo:datapoint", "source": "measurement/5/", "property": "exercise duration", "propertyref": "loinc:55411-3", "value": {"@id": "datapoint/4/numericvalue/1/", "@type": "sdo:numericvalue", "number": 39.9, "unit": "qudt:MIN"}}, {"@id": "datapoint/5/", "@type": "sdo:datapoint", "source": "measurement/1/", "property": "body temperature", "propertyref": "loinc:18688-2", "conditions": "condition/1/", "value": {"@id": "datapoint/5/numericvalue/1/", "@type": "sdo:numericvalue", "number": "96.6", "unit": "qudt:DEG_F"}}, {"@id": "datapoint/6/", "@type": "sdo:datapoint", "source": "measurement/2/", "property": "body weight", "propertyref": "loinc:18690-8", "textstring": {"@id": "datapoint/6/numericvalue/1/", "@type": "sdo:numericvalue", "number": "182.1", "unit": "qudt:LB"}}, {"@id": "datapoint/7/", "@type": "sdo:datapoint", "source": "measurement/3/", "property": "resting heart rate", "propertyref": "loinc:40443-4", "number": {"@id": "datapoint/7/numericvalue/1/", "@type": "sdo:numericvalue", "value": "42", "unit": "qudt:BEAT-PER-MIN"}}], "datagroup": [{"@id": "datagroup/1/", "@type": "sdo:datagroup", "source": ["resource/3/", "event/1/"], "datapoints": ["datapoint/1/", "datapoint/2/", "datapoint/3/", "datapoint/4/"]}]}}, "sources": [{"@id": "source/1/", "@type": "dc:source", "citation": "Chalk Health Study 2021", "url": "https://github.com/stuchalk/fair-health-data"}], "rights": [{"@id": "rights/1/", "@type": "dc:rights", "holder": "Stuart J. Chalk", "license": "https://creativecommons.org/licenses/by-nc-nd/4.0/"}]}} \ No newline at end of file diff --git a/health-data.ipynb b/health-data.ipynb index 40ebc08..493af1e 100644 --- a/health-data.ipynb +++ b/health-data.ipynb @@ -98,11 +98,36 @@ "name": "stdout", "output_type": "stream", "text": [ + "Writing file sjc040121.jsonld\n", + "Writing file sjc040221.jsonld\n", + "Writing file sjc040321.jsonld\n", + "Writing file sjc040421.jsonld\n", + "Writing file sjc040521.jsonld\n", + "Writing file sjc040621.jsonld\n", + "Writing file sjc040721.jsonld\n", + "Writing file sjc040821.jsonld\n", + "Writing file sjc040921.jsonld\n", + "Writing file sjc041021.jsonld\n", + "Writing file sjc041121.jsonld\n", + "Writing file sjc041221.jsonld\n", + "Writing file sjc041321.jsonld\n", + "Writing file sjc041421.jsonld\n", + "Writing file sjc041521.jsonld\n", + "Writing file sjc041621.jsonld\n", "Writing file sjc041721.jsonld\n", "Writing file sjc041821.jsonld\n", "Writing file sjc041921.jsonld\n", "Writing file sjc042021.jsonld\n", - "Writing file sjc042121.jsonld\n" + "Writing file sjc042121.jsonld\n", + "Writing file sjc042221.jsonld\n", + "Writing file sjc042321.jsonld\n", + "Writing file sjc042421.jsonld\n", + "Writing file sjc042521.jsonld\n", + "Writing file sjc042621.jsonld\n", + "Writing file sjc042721.jsonld\n", + "Writing file sjc042821.jsonld\n", + "Writing file sjc042921.jsonld\n", + "Writing file sjc043021.jsonld\n" ] } ], @@ -129,7 +154,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [] diff --git a/healthdata.csv b/healthdata.csv index 56b7282..5a314f6 100644 --- a/healthdata.csv +++ b/healthdata.csv @@ -109,4 +109,13 @@ Day,Date,Weight,VO2 Max,Indoor Temp,Body Temp,Resting HR,Miles,Time,Pace,Calorie 108,4/18/21,181.8,51,74,96.8,43,3.01,0:23:26,7:48,147,https://connect.garmin.com/modern/activity/6628097624, 109,4/19/21,183.0,52,74,96.8,43,1.25,0:09:41,7:46,138,https://connect.garmin.com/modern/activity/6633470776, 110,4/20/21,183.9,52,74,96.3,39,2.20,0:17:40,8:01,141,https://connect.garmin.com/modern/activity/6639518367, -111,4/21/21,181.9,52,74,,41,1.01,0:07:39,7:35,128,https://connect.garmin.com/modern/activity/6645605620, \ No newline at end of file +111,4/21/21,181.9,52,74,96.6,41,1.01,0:07:39,7:35,128,https://connect.garmin.com/modern/activity/6645605620, +112,4/22/21,181.0,51,75,97.0,45,5.01,0:38:52,7:45,622,https://connect.garmin.com/modern/activity/6651264936, +113,4/23/21,181.2,51,75,96.9,45,3.50,0:27:40,7:54,417,https://connect.garmin.com/modern/activity/6657056927, +114,4/24/21,180.8,51,75,97.4,43,5.01,0:38:57,7:47,605,https://connect.garmin.com/modern/activity/6662635780, +115,4/25/21,180.0,51,75,97.1,44,5.01,0:39:19,7:51,600,https://connect.garmin.com/modern/activity/6669219022, +116,4/26/21,180.9,51,75,96.8,44,4.01,0:31:14,7:48,468,https://connect.garmin.com/modern/activity/6675219296, +117,4/27/21,180.7,51,75,96.3,,4.01,0:31:48,7:56,476,https://connect.garmin.com/modern/activity/6680747478, +118,4/28/21,181.4,51,75,97.3,44,5.00,0:39:25,7:53,593,https://connect.garmin.com/modern/activity/6686862303, +119,4/29/21,182.6,51,75,97.2,41,3.01,0:24:34,8:10,361,https://connect.garmin.com/modern/activity/6692375609, +120,4/30/21,182.1,51,75,96.6,42,5.01,0:39:54,7:58,607,https://connect.garmin.com/modern/activity/6697879972, \ No newline at end of file diff --git a/requirements.txt b/requirements.txt index 93b18bc..8fc8304 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1 +1,2 @@ PyQt5>=5.15.0 +SciDataLib>=0.2 diff --git a/writesd.py b/writesd.py index dfa4f11..453c04f 100644 --- a/writesd.py +++ b/writesd.py @@ -1,8 +1,6 @@ """python scidata JSON-LD writer""" from scidatalib.scidata import SciData from datetime import datetime -import json -import csv def createsd(data): @@ -52,7 +50,7 @@ def createsd(data): sd.version('1') # graph metadata - sd.graph_id(base) + sd.graph_uid(base) sjc = {'name': 'Stuart J. Chalk', 'email': 'stuartjchalk@gmail.com', 'orcid': '0000-0002-0703-7776'}