This repository has been archived by the owner on Dec 13, 2019. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 10
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Adds draft version of Overview Detail Content (currently
disabled/hidden). - Adds GSoC phenopacket-scraper links - Adds BOSC2016 and Force2016 links. - Deletes unused JPG. - Updates words. - Adds Planteome logo - Improves carousel scrolling smoothness. - Carousel links now open new windows/tabs.
- Loading branch information
Showing
14 changed files
with
620 additions
and
151 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,18 +1,38 @@ | ||
# PhenoPackets | ||
|
||
[![](https://phenopackets.org/site/PhenoPackets_Logo.png)](https://phenopackets.org) | ||
|
||
[![Build Status](https://travis-ci.org/phenopackets/phenopacket-format.svg?branch=master)](https://travis-ci.org/phenopackets/patient-phenotype-submission-format) | ||
[![DOI](https://zenodo.org/badge/13996/phenopackets/phenopacket-format.svg)](https://zenodo.org/badge/latestdoi/13996/phenopackets/patient-phenotype-submission-format) | ||
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.46742.svg)](https://doi.org/10.5281/zenodo.46742) | ||
|
||
|
||
## Overview | ||
|
||
PhenoPackets is an open standard for representing and sharing detailed descriptions of phenotypic abnormalities and characteristics of individual patients, organisms, diseases, and publications. This repository serves as the primary documentation about the PhenoPacket Exchange Format (PXF), including the JSON and YAML representations. Other repositories (see [Implementations](#implementations) below) contain Java, JavaScript, Python and other language-specific tools and implementations. | ||
|
||
### Motivation | ||
|
||
The health of an individual organism results from a complex interplay between its genes and environment. Although great strides have been made in standardizing the representation of genetic information for exchange, there are no comparable standards to represent phenotypes (e.g. patient symptoms and disease features) and environmental factors. Phenotypic abnormalities of individual organisms are currently described in diverse places and in diverse formats: publications, databases, health records, registries, clinical trials, and even social media. However, the lack of standardization, accessibility, and computability among these contexts makes it extremely difficult to effectively extract and utilize these data, hindering the understanding of genetic and environmental contributions to disease. | ||
|
||
The health of an individual organism results from a complex interplay between its genes and environment. Although great strides have been made in standardizing the representation of genetic information for exchange, there are no comparable standards to represent phenotypes (e.g. patient symptoms and disease features) and environmental factors (Figure 1). Phenotypic abnormalities of individual organisms are currently described in diverse places and in diverse formats: publications, databases, health records, registries, clinical trials, and even social media. However, the lack of standardization, accessibility, and computability among these contexts makes it extremely difficult to effectively extract and utilize these data, hindering the understanding of genetic and environmental contributions to disease. | ||
|
||
## Documentation | ||
|
||
See the [Wiki](https://github.com/phenopackets/phenopacket-format/wiki/Getting-Started) for documentation | ||
See the [Phenopackets.org site](https://phenopackets.org) for the public-facing project documentation. | ||
|
||
Or, see the detailed Markdown-based [documentation](https://github.com/phenopackets/phenopacket-format/blob/master/docs/content/Overview.md) via GitHub. | ||
|
||
The [Wiki](https://github.com/phenopackets/phenopacket-format/wiki/Getting-Started) has additional documentation, although it may be out-of-date. | ||
|
||
## Implementations | ||
|
||
Or jump straight into the [reference implementation](https://github.com/phenopackets/phenopacket-reference-implementation) | ||
- [phenopacket-reference-implementation: Java Reference Implementation](https://github.com/phenopackets/phenopacket-reference-implementation). | ||
- [phenopackets-js: JavaScript Implementation](https://github.com/phenopackets/phenopackets-js). | ||
- [phenopacket-python: Python Implementation](https://github.com/phenopackets/phenopacket-python). | ||
- [pxftools: Command-line Utility for manipulating PhenoPackets](https://github.com/phenopackets/pxftools). | ||
|
||
## TODO | ||
## Contributing | ||
|
||
See the issue tracker for a complete list. Some of the main issues of relevance: | ||
The PhenoPackets standard is still evolving, and there are many opportunities to help, including improving the expressivity of the format and providing implementations that enable. | ||
|
||
* [#54](https://github.com/phenopackets/phenopacket-format/issues/54) - the examples in this repo may be out of date | ||
* [#55](https://github.com/phenopackets/phenopacket-format/issues/55) - JSON-schema is overly complex | ||
The [Issue Tracker](https://github.com/phenopackets/phenopacket-format/issues/) is a good start. | ||
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,23 +1,73 @@ | ||
### About this `/docs` directory | ||
# About this `/docs` directory | ||
|
||
The contents of this directory are deployed via GitHub Pages. | ||
The contents of this directory are deployed via GitHub Pages as [https://phenopackets.org](https://phenopackets.org). | ||
|
||
The file `index.html` is primarily boilerplate HTML, with most of the actual | ||
web-visible content specified in Markdown files that are dynamically loaded and rendered in the browser. | ||
The CNAME file determines which site can legitimately redirect here. | ||
Currently, this is https://phenopackets.org. The CNAME in the master branch of | ||
this repo must correspond for the site to be viewable as GitHub pages. | ||
|
||
## Deployment structure | ||
|
||
#### Local Development | ||
Although the website appears seamless to a user, from an author's point of view | ||
there are two types of content, HTML and Markdown. These are divided into two | ||
directories, respectively: `/site` and `/content`. The goal behind this | ||
distinction is to encourage authors to improve and create content in Markdown, | ||
which is visible both through the fancy portal, as well as through the GitHub | ||
developer interface. | ||
|
||
### `index.html` | ||
|
||
The file `index.html` defines a basic marketing-style landing page with high-level content about PhenoPackets and several links to other aspects of the project, including the other PhenoPackets repositories. In addition, index.html has JavaScript that dynamically loads more detailed information from Markdown files, and optionally renders these Markdown files (if the user clicks the 'Details' buttons on the page). | ||
|
||
### Markdown content | ||
|
||
The directory `/content` contains several Markdown files that serve two purposes: | ||
|
||
- These files may be viewed directly via GitHub, providing a source of reusable documentation | ||
- The content of these files may be more easily edited than HTML | ||
|
||
|
||
## Editing and Adding Content | ||
|
||
The high-level content is within `index.html` and the detailed content is within the Markdown files in `/content`. | ||
|
||
### Editing index.html | ||
|
||
Please use two-column indentation and no tab stops. HTML is difficult to maintain if indentation is not uniform. | ||
|
||
Please test any changes on both narrow and wide screens. Ideally, use your browser's 'Responsive Design Mode' to allow you to see how the site looks on a mobile device. | ||
|
||
|
||
## Editing Markdown files | ||
|
||
It is important to realize that the same markdown files are rendered through the https://phenopackets.org site as well as through the GitHub portal. Relative image links from Markdown files in `/content' to image files in `/content` need to be specified with a relative prefix `![](./` as in the example below: | ||
|
||
``` | ||
cd phenopacket-format/ | ||
http-server -c-1 docs/ | ||
![](./phenopacket-ecosystem_2016-02-18a.png) | ||
``` | ||
|
||
When the `index.html` page dynamically loads the Markdown content, the JavaScript code will *adjust* the prefix above to be `![](content/`so that the page can refer to the image file relative to index.html; it's a hack, but it works as long as Markdown authors use the above convention. | ||
|
||
|
||
## Local Testing | ||
|
||
It is necessary to run a local HTTP server to be able to try out the website effectively. I recommend `http-server`, which is easy to install and use if you already have a NodeJS environment: | ||
|
||
``` | ||
npm install -g http-server | ||
``` | ||
|
||
Once you have an HTTP server, it should be started so that it serves the `phenopacket-format/docs` directory as the website base URL `/`. In addition, caching should be disabled, so that local edits can be seen upon page refresh. For example, here is how to do this with `http-server`: | ||
|
||
|
||
``` | ||
cd phenopacket-format/docs/ | ||
http-server -c-1 . | ||
``` | ||
|
||
|
||
### Credits | ||
|
||
- https://commons.wikimedia.org/wiki/File:DNA_com_GGN.jpg | ||
|
||
- [Start Bootstrap](https://startbootstrap.com/) | ||
|
||
- [Stylish Portfolio](https://startbootstrap.com/template-overviews/stylish-portfolio/) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.