Fixing broken links on About pages

README.md

@@ -1 +1,175 @@
-# pharos-documentation
+[![Pharos](https://github.com/viralemergence/pharos-database/blob/prod/img/pharos-banner.png)](https://pharos.viralemergence.org/)
+
+This repository is part of the [Pharos project](https://pharos.viralemergence.org/)
+which is split into three repositories:
+
+| Repository                                                                       | Purpose                                            |
+| -------------------------------------------------------------------------------- | -------------------------------------------------- |
+| [`pharos-frontend`](https://github.com/viralemergence/pharos-frontend)           | Frontend application and deployment infrastructure |
+| [`pharos-api`](https://github.com/viralemergence/pharos-api)                     | API and deployment infrastructure                  |
+| [`pharos-database`](https://github.com/viralemergence/pharos-database)           | SQL database and deployment infrastructure         |
+| [`pharos-documentation`](https://github.com/viralemergence/pharos-documentation) | Markdown files used to generate about pages        |
+
+</br>
+</br>
+</br>
+<h1 align="center">
+  Pharos Documentation
+</h1>
+
+## 🚀 Deployment Status
+
+CI/CD deployments are not triggered by any changes in this repository, deployments of all
+content in the `publish` bransh of this repository occur when changes are pushed or builds
+are triggered in the [`pharos-frontend`](https://github.com/viralemergence/pharos-frontend)
+repository.
+
+| Branch  | CI/CD Status                                                                                                                                                                                                                                                 | Url                                                                              |
+| ------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------- |
+| Prod    | [![CircleCI](https://dl.circleci.com/status-badge/img/circleci/39PL8myokkHY7obZPJeFEC/VSEyuiVS42F6DmyCLZcbdW/tree/prod.svg?style=svg)](https://dl.circleci.com/status-badge/redirect/circleci/39PL8myokkHY7obZPJeFEC/VSEyuiVS42F6DmyCLZcbdW/tree/prod)       | [pharos.viralemergence.org/](https://pharos.viralemergence.org/)                 |
+| Staging | [![CircleCI](https://dl.circleci.com/status-badge/img/circleci/39PL8myokkHY7obZPJeFEC/VSEyuiVS42F6DmyCLZcbdW/tree/staging.svg?style=svg)](https://dl.circleci.com/status-badge/redirect/circleci/39PL8myokkHY7obZPJeFEC/VSEyuiVS42F6DmyCLZcbdW/tree/staging) | [staging-pharos.viralemergence.org/](https://staging-pharos.viralemergence.org/) |
+| Review  | [![CircleCI](https://dl.circleci.com/status-badge/img/circleci/39PL8myokkHY7obZPJeFEC/VSEyuiVS42F6DmyCLZcbdW/tree/review.svg?style=svg)](https://dl.circleci.com/status-badge/redirect/circleci/39PL8myokkHY7obZPJeFEC/VSEyuiVS42F6DmyCLZcbdW/tree/review)   | [dev-pharos.viralemergence.org/](https://review-pharos.viralemergence.org/)      |
+| Dev     | [![CircleCI](https://dl.circleci.com/status-badge/img/circleci/39PL8myokkHY7obZPJeFEC/VSEyuiVS42F6DmyCLZcbdW/tree/dev.svg?style=svg)](https://dl.circleci.com/status-badge/redirect/circleci/39PL8myokkHY7obZPJeFEC/VSEyuiVS42F6DmyCLZcbdW/tree/dev)         | [dev-pharos.viralemergence.org/](https://dev-pharos.viralemergence.org/)         |
+
+Automated deployment schedule: AirtableCMS data is ingested, "About" content is ingested, and full site is built weekly on `Staging` site.
+
+</br>
+
+## 👩‍💻 Overview
+
+This repository contains the markdown files which are used to create the
+[`/about/` pages](https://pharos.viralemergence.org/about/) on
+[pharos.viralemergence.org/about/](https://pharos.viralemergence.org/about/).
+
+These pages contain documentation, instructions, user agreements, and other
+content to help users.
+
+## To contribute a documentation change:
+
+1. Team members with access may push changes to the `main` branch
+1. Contributors outside the core team may create a fork, and open a PR to this repository
+1. PR with changes should be made against the `publish` branch
+1. Once approved and merged, the documentation changes will show up on the `staging` site during the next automatic build
+1. To push changes to the `prod` site, a team member with appropriate permissions should trigger a build in [`pharos-frontend`](https://github.com/viralemergence/pharos-frontend).
+
+</br>
+
+## Markdown
+
+Quick help with Markdown formatting syntax can be found on
+the [Commonmark help page](https://commonmark.org/help/).
+
+The full
+[commonmark spec can be found here](https://spec.commonmark.org/0.30/).
+
+</br>
+
+## Directory, File and Page Structure
+
+The directory structure in this repository maps to the
+sidebar and page structure of the site. Pages created in
+this project will be transformed into pages, using the
+name of the file as the url; for example `about.md` becomes
+[https://pharos.viralemergence.org/about/](https://pharos.viralemergence.org/about/).
+
+When files are in directories, such as `/guide-for-users/`,
+then the metadata from the readme file is used to create
+a section in the sidebar which links to the url based on
+the directory name.
+
+### Frontmatter:
+
+Metadata for documentation pages is pulled from the
+"frontmatter" which is the small section demarcated by
+three hyphens `---` at the top of each markdown file.
+
+We support two frontmatter fields:
+
+#### `title`
+
+This field sets the title of the generated page and the
+link text for the sidebar link which points to it.
+
+#### `order`
+
+This field sets the sidebar order of the page, relative
+to its section (directory) The `order` field from the
+`README.md` file in each directory sets the order of the
+section in the parent list.
+
+</br>
+
+## Linking
+
+_Files in this repository should not be renamed now that
+the site is live, because it will break internal links
+(which we can fix) and external links and SEO (which we
+cannot fix)_. If renaming a file is extremely important,
+please reach out to
+[[email protected]](mailto:[email protected]).
+
+There are two types of links which must be handled
+separately; internal links to other pages on pharos, and
+external links to other websites.
+
+Incorrect links confuse users and damage SEO (How Google
+ranks Pharos in their results) so it is important for
+links to be correct and maintained.
+
+### Internal links (Links to Pharos pages)
+
+To link to a page on the Pharos site, you need to only
+use the path, not the entire link.
+
+For example, to link to the user agreement page at
+`https://pharos.viralemergence.org/user-agreement/`
+you need to take just the last part of the link, after
+the `.org`: just `/user-agreement/`.
+
+The link should look like this in markdown:
+
+`[user agreement](/user-agreement/)`
+
+### External links (links to non-Pharos sites)
+
+To link outside the pharos site, it is important to
+include the full and complete link, including the
+`https://` in the beginning.
+
+For example, to link to [example.org](https://example.org),
+the link in markdown should look like this:
+
+`[example.org](http://example.org)`.
+
+If the `https://` is ommitted from the front of the
+link, it will be interpreted as an internal link.
+
+### Email links
+
+To add an email address into a documentation page, you
+should create a `mailto` link like this:
+
+`[[email protected]](mailto:[email protected]?subject=Example)`
+
+This syntax will render like this:
+
+[[email protected]](mailto:[email protected]?subject=Example)
+
+Clicking the link will open the user's default email
+program and will fill in the subject line with the
+text after the `?subject=` section of the
+link if it is provided (optional!).
+
+</br>
+
+## Under the hood
+
+Markdown files in this repository are parsed using
+[micromark](https://github.com/micromark/micromark) which
+is compliant with
+[the commonmark standard](https://commonmark.org/help/) so
+commonmark documentation should be used as the reference
+for markdown syntax in this project.
+
+The full
+[commonmark spec can be found here](https://spec.commonmark.org/0.30/).

about.md

@@ -5,12 +5,12 @@ order: 1
 
 # About Verena
 
-[Verena (the Viral Emergence Research Initiative)](viralemergence.org) was founded in 2019 by Colin Carlson and Greg Albery, and established as a U.S. National Science Foundation Biology Integration Institute in 2022. Our mission is to use the science of the host-virus network to advance efforts to predict, prevent, and prepare for disease emergence. The Institute's work includes a mix of data synthesis, algorithm-in-the-loop machine learning, model-guided experiments, and boots-on-the-ground partnerships. All of our data and code is 100% open, giving you the tools you need to study viral emergence from anywhere in the world. Using that platform, we're training the next generation of scientists, from K-12 up through graduate and postgraduate mentorship.
+[Verena (the Viral Emergence Research Initiative)](https://www.viralemergence.org/) was founded in 2019 by Colin Carlson and Greg Albery, and established as a U.S. National Science Foundation Biology Integration Institute in 2022. Our mission is to use the science of the host-virus network to advance efforts to predict, prevent, and prepare for disease emergence. The Institute's work includes a mix of data synthesis, algorithm-in-the-loop machine learning, model-guided experiments, and boots-on-the-ground partnerships. All of our data and code is 100% open, giving you the tools you need to study viral emergence from anywhere in the world. Using that platform, we're training the next generation of scientists, from K-12 up through graduate and postgraduate mentorship.
 
 ## About PHAROS
 
 The Pathogen Harmonized Observatory (PHAROS) is an open-access database of wildlife disease surveillance. The platform's objectives are to enable data sharing across borders and projects in real-time; to incentivize the sharing of negative data; and to help bring open science into fields like One Health and disease ecology. PHAROS is as much a data rescue project as a forward-looking database: for decades, researchers have immortalized genetic sequence data while the line list data from animal disease surveillance is lost to the grey literature, supplemental files, or unpublished spreadsheets. With your help, we hope we can change that.
 
 ## About "Pharos"
 
-Pharos is an island that was the home of the Lighthouse of Alexandria until the 1400s. The lighthouse is the symbol of the Verena team; this one _specifically_ is also a tongue-in-cheek reference to the Library of Alexandria, and how easily knowledge can be lost when we don't take steps to ensure its survival.
+Pharos is an island that was the home of the Lighthouse of Alexandria until the 1400s. The lighthouse is the symbol of the Verena team; this one _specifically_ is also a tongue-in-cheek reference to the Library of Alexandria, and how easily knowledge can be lost when we don't take steps to ensure its survival.

guide-for-users/README.md

@@ -9,7 +9,7 @@ If you are a scientist working with open-access wildlife disease data, we welcom
 
 ## User agreement
 
-- Familiarize yourself with our [user agreement](/data-use/)
+- Familiarize yourself with our [user agreement](/user-agreement/)
 
 ## Set up an account
 
@@ -69,7 +69,7 @@ Publishing your data adds it to the public PHAROS database, which means that you
 
 - A citation to any PHAROS data used must appear either in the full text or references of the paper 
 
-- Read the [attribution requirement] (https://staging-pharos.viralemergence.org/research-with-pharos/attribution/) for more details 
+- Read the [attribution requirement](/research-with-pharos/attribution/) for more details
 
 
 

guide-for-users/data-we-accept.md

@@ -39,16 +39,16 @@ Example projects that could contribute data would include:
 
 ## Data we don't accept
 
-- **Human clinical data.** We do not accept any data on human disease surveillance. We encourage you to consider whether the [global.health](global.health) project to build an open database of human epidemiological line data would be appropriate for your needs.
+- **Human clinical data.** We do not accept any data on human disease surveillance. We encourage you to consider whether the [global.health](https://global.health/) project to build an open database of human epidemiological line data would be appropriate for your needs.
 
 - **Livestock or companion animal disease data.** At this time, we don't accept data on any captive, domestic, or livestock animal disease. These tend to fall under the jurisdiction of the World Organization for Animal Health, which shares data submitted by member states through the [WAHIS](https://wahis.woah.org/#/home) system. Data on feral cats, dogs, or other domesticated species is currently permissible.
 
 - **Animal disease in captivity.** No experimental infections in laboratory settings, infection data from zoo animals, wildlife trade supply chain data, etc.
 
 - **Data on livestock select agents.** We ask that you not deposit any original data (i.e., data not already published elsewhere) for any animal pathogens on the [USDA Veterinary Services list of Select Agents](https://www.selectagents.gov/sat/list.htm).
 
-- **Pathogen genetic or genomic sequence data.** There are other repositories that are more appropriate for these data, and we strongly encourage you to deposit data in submissions that are cross-linked. Any nucleotide sequence can be deposited in NCBI's [GenBank](https://www.ncbi.nlm.nih.gov/genbank/submit/) database; some pathogen sequence data (e.g., for influenza, SARS-CoV-2, and monkeypox) can also be deposited in [GISAID](gisaid.org). Metagenomic or metatranscriptomic data - including any samples meant to describe an entire animal microbiome - should be deposited in the [NCBI Sequence Read Archive](https://www.ncbi.nlm.nih.gov/sra/docs/submit/).
+- **Pathogen genetic or genomic sequence data.** There are other repositories that are more appropriate for these data, and we strongly encourage you to deposit data in submissions that are cross-linked. Any nucleotide sequence can be deposited in NCBI's [GenBank](https://www.ncbi.nlm.nih.gov/genbank/submit/) database; some pathogen sequence data (e.g., for influenza, SARS-CoV-2, and monkeypox) can also be deposited in [GISAID](https://gisaid.org/). Metagenomic or metatranscriptomic data - including any samples meant to describe an entire animal microbiome - should be deposited in the [NCBI Sequence Read Archive](https://www.ncbi.nlm.nih.gov/sra/docs/submit/).
 
-- **Data on pathogen free-living stages or most environmental samples.** These are appropriate for several other databases, including [GBIF](gbif.org). All records submitted to PHAROS should include an association with a host; do not submit data that document occurrences of e.g., questing ticks, hunting leeches, soil samples of environmentally-persistent bacteria, etc. Exceptions on environmental samples can be made if host associations are still known (e.g., parasites in nest boxes, or fecal samples from monitored animal populations).
+- **Data on pathogen free-living stages or most environmental samples.** These are appropriate for several other databases, including [GBIF](https://www.gbif.org/). All records submitted to PHAROS should include an association with a host; do not submit data that document occurrences of e.g., questing ticks, hunting leeches, soil samples of environmentally-persistent bacteria, etc. Exceptions on environmental samples can be made if host associations are still known (e.g., parasites in nest boxes, or fecal samples from monitored animal populations).
 
-- **Data you've digitized from the literature or accessed from other public sources (that isn't yours).** For now, we're not allowing data rescue or digitization projects into PHAROS. This is an ethics question, not a feasibility question: We're currently deciding the best way to recover large quantities of data from the published literature, while also honoring the principles around credit and equity that have shaped our approach. We will seek input from the community on this issue in the future, and may eventually develop a revised policy.
+- **Data you've digitized from the literature or accessed from other public sources (that isn't yours).** For now, we're not allowing data rescue or digitization projects into PHAROS. This is an ethics question, not a feasibility question: We're currently deciding the best way to recover large quantities of data from the published literature, while also honoring the principles around credit and equity that have shaped our approach. We will seek input from the community on this issue in the future, and may eventually develop a revised policy.