openmhealth / schemas Goto Github PK

https://github.com/openmhealth/schemas/blob/master/schema/clinical/physical-activity-1.0.json and the web page at http://www.openmhealth.org/developers/schemas/#activity-name seem to say that an activity name should be taken from the list provided at http://www.startwalkingnow.org/documents/PA_Intensity_table_2_1.pdf . however, while this list contains activities, it is not clear which values to use in the activity_name property. if it is a goal to make these values machine-readable, then they should be well-defined, and ideally they actually should be URIs so that they can be used as context-free identifiers. what is the idea which values to use, and where does the "walking" value in the example come from? thanks!

Same failure on Mac via command line and in Idea IntelliJ

$ javac -version
javac 1.7.0_71

$ gradle --version

Gradle 2.3

Build time: 2015-02-16 05:09:33 UTC
Build number: none
Revision: 586be72bf6e3df1ee7676d1f2a3afd9157341274

Groovy: 2.3.9
Ant: Apache Ant(TM) version 1.9.3 compiled on December 23 2013
JVM: 1.7.0_71 (Oracle Corporation 24.71-b01)
OS: Mac OS X 10.10.3 x86_64

$ gradle clean
Download https://jcenter.bintray.com/com/jfrog/bintray/gradle/gradle-bintray-plugin/1.1/gradle-bintray-plugin-1.1.pom
Download https://jcenter.bintray.com/org/codehaus/groovy/modules/http-builder/http-builder/0.7.2/http-builder-0.7.2.pom
Download https://jcenter.bintray.com/org/apache/httpcomponents/httpclient/4.2.1/httpclient-4.2.1.pom
Download https://jcenter.bintray.com/org/apache/httpcomponents/httpcomponents-client/4.2.1/httpcomponents-client-4.2.1.pom
Download https://jcenter.bintray.com/net/sf/json-lib/json-lib/2.3/json-lib-2.3.pom
Download https://jcenter.bintray.com/net/sourceforge/nekohtml/nekohtml/1.9.16/nekohtml-1.9.16.pom
Download https://jcenter.bintray.com/org/apache/httpcomponents/httpcore/4.2.1/httpcore-4.2.1.pom
Download https://jcenter.bintray.com/org/apache/httpcomponents/httpcomponents-core/4.2.1/httpcomponents-core-4.2.1.pom
Download https://jcenter.bintray.com/xerces/xercesImpl/2.9.1/xercesImpl-2.9.1.pom
Download https://jcenter.bintray.com/com/jfrog/bintray/gradle/gradle-bintray-plugin/1.1/gradle-bintray-plugin-1.1.jar
Download https://jcenter.bintray.com/org/codehaus/groovy/modules/http-builder/http-builder/0.7.2/http-builder-0.7.2.jar
Download https://jcenter.bintray.com/org/apache/httpcomponents/httpclient/4.2.1/httpclient-4.2.1.jar
Download https://jcenter.bintray.com/net/sf/json-lib/json-lib/2.3/json-lib-2.3-jdk15.jar
Download https://jcenter.bintray.com/net/sourceforge/nekohtml/nekohtml/1.9.16/nekohtml-1.9.16.jar
Download https://jcenter.bintray.com/org/apache/httpcomponents/httpcore/4.2.1/httpcore-4.2.1.jar
Download https://jcenter.bintray.com/xerces/xercesImpl/2.9.1/xercesImpl-2.9.1.jar

FAILURE: Build failed with an exception.

• Where:
  Build file '/Users/alan_cooper/Documents/GitHub/AperitasCloud/openmhealth/schemas/java-schema-sdk/build.gradle' line: 83

• What went wrong:
  A problem occurred evaluating project ':java-schema-sdk'.

  Could not find property 'bintray_user' on com.jfrog.bintray.gradle.BintrayExtension_Decorated@1177f25c.

• Try:
  Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

BUILD FAILED

Total time: 11.848 secs

Hello,
I'm Seng Chan You (please call me 'Chan'), who is one of the active collaborators of OHDSI (www.ohdsi.org).
Recently, I started to build data conversion conventions for Patient Generated Health Data (PGHD) in OHDSI (http://forums.ohdsi.org/t/patient-generated-health-data-pghd-working-group/).
Jon Duke introduced this amazing project to me.

I want to build PGHD schema in OHDSI compatible with open mHealth. If there is anyone who can help me for this, please let me know.

Thank you for all your contribution!

Are the schemas written in the OpenAPI Format that can be used in the Swagger Spec?

I don't see it specifically mentioned anywhere that the schemas are described.

Conforming to the Swagger Spec would be very helpful for standardizing the data schemas and API on a conventional format and integrating with popular third-party vendors (e.g. Google Cloud Endpoints)

Thanks!

I look for cholesterol related schema. I was not able to find anything. Did I miss anything? Is it planned?

HKCategoryTypeIdentifierMindfulSession appears to be missing from schemas/schema/granola/hk-category-type-1.1.json.

It is part of HKCategoryTypeIdentifier in HealthKit (here), but it's not included in the schema.

@bewest asked on commit 1a0c459:

Howdy, I have a project displaying continuous glucose values derived from CGM in real time. The CGM produces, raw (the voltage measured at sensor in interstitial fluid), "filtered", and estimated bg, as well as records of "calibration" measures (manually input). We also get activity from insulin pumps (including similar manual and automated glucose measurements), in addition to the classic "finger-stick" meters, which are the only real sources of "truth" on finger-stick values.

My question is how to best differentiate between these types of records?
I'd love to re-use and share schemas and get our app in the registry.
Here's the app https://github.com/nightscout/cgm-remote-monitor, bewest/sgvdata#2

Ideally, somewhere in my app, I can have a directory full of schemas/models, and let the machinery do the rest in terms of oauth, display, etc...

Hi there,

I was looking at one of your schemas and noticed a broken link reference.

Schema: http://www.openmhealth.org/documentation/#/schema-docs/schema-library/schemas/omh_activity-name

Broken link: http://www.startwalkingnow.org/documents/PA_Intensity_table_2_1.pdf

That seems to be the only reference to that link and domain.

Hello,
I have seen that the sleep episode schema already includes the number of awakenings, but I suggest that adding the Wake Time After Sleep Onset (WASO) (see also https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246141/) could be a useful addition to quantify sleep fragmentation.

Mainstream APIs already have fields like "timeAwake" or "wakeupduration" so also updating the shims should be quite easy.

Let me know what you think of that

Pull in GPS data to help with analytics

All the schemas to be uri-referenciable from other schemas correctly, should have an id.

for example, the body-weight-1.0.json schema, by including the id "http://www.openmhealth.org/schema/omh/body-weight-1.0.json, would allow mass-unit-value-1.x.json to be correctly resolved, and hence the schema will be considered valid by validators when remotely referenced in other schemas. (e.g. http://www.jsonschemavalidator.net)

{
  "$schema": "http://json-schema.org/draft-04/schema#",
  "id": "http://www.openmhealth.org/schema/omh/body-weight-1.0.json",
  "description": "This schema represents a person's body weight, either a single body weight measurement, or for the result of aggregating several measurements made over time (see Numeric descriptor schema for a list of aggregate measures)",
  "type": "object",
  "references": [
    {
      "description": "The SNOMED code represents Body weight measure (observable entity)",
      "url": "http://purl.bioontology.org/ontology/SNOMEDCT/363808001"
    }
  ],
  "definitions": {
    "mass_unit_value": {
      "$ref": "mass-unit-value-1.x.json"
    },
    "time_frame": {
      "$ref": "time-frame-1.x.json"
    },
    "descriptive_statistic": {
      "$ref": "descriptive-statistic-1.x.json"
    }
  },
  "properties": {
    "body_weight": {
      "$ref": "#/definitions/mass_unit_value"
    },
    "effective_time_frame": {
      "$ref": "#/definitions/time_frame"
    },
    "descriptive_statistic": {
      "$ref": "#/definitions/descriptive_statistic"
    }
  },
  "required": [
    "body_weight"
  ]
}