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Merge pull request #27 from Knowledge-Graph-Hub/landing-page
Further improvements to landing page(s)
2 parents aca276a + 1b518e1 commit fd5dbbb

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docs/MANIFEST.yaml

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docs/_config.yml

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docs/_config_header.yml

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# Welcome to Jekyll!
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#
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# This config file is meant for settings that affect your whole blog, values
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# which you are expected to set up once and rarely edit after that. If you find
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# yourself editing this file very often, consider using Jekyll's data files
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# feature for the data you need to update frequently.
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#
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# For technical reasons, this file is *NOT* reloaded automatically when you use
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# 'bundle exec jekyll serve'. If you change this file, please restart the server process.
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#
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# If you need help with YAML syntax, here are some quick references for you:
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# https://learn-the-web.algonquindesign.ca/topics/markdown-yaml-cheat-sheet/#yaml
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# https://learnxinyminutes.com/docs/yaml/
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#
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# Site settings
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# These are used to personalize your new site. If you look in the HTML files,
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# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
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# You can create any custom variable you would like, and they will be accessible
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# in the templates via {{ site.myvariable }}.
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title: Knowledge Graph Hub
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description: >- # this means to ignore newlines until "baseurl:"
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KG-Hub - a collection of Biological and Biomedical Knowledge Graphs
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#baseurl: / # the subpath of your site, e.g. /blog
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domain: knowledge-graph-hub.github.io
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url: https://knowledge-graph-hub.github.io/
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# Build settings
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theme: minima
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#plugins:
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# - jekyll-feed
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# Exclude from processing.
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# The following items will not be processed, by default.
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# Any item listed under the `exclude:` key here will be automatically added to
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# the internal "default list".
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#
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# Excluded items can be processed by explicitly listing the directories or
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# their entries' file path in the `include:` list.
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#
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# exclude:
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# - .sass-cache/
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# - .jekyll-cache/
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# - gemfiles/
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# - Gemfile
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# - Gemfile.lock
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# - node_modules/
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# - vendor/bundle/
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# - vendor/cache/
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# - vendor/gems/
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# - vendor/ruby/

docs/_includes/manifest_table.html

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<table class="table">
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<tbody>
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<tr>
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<th>ID</th>
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<th>Title</th>
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<th>Description</th>
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<th>Version</th>
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</tr>
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{% for product in site.manifest %}
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<tr>
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<td>
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<a href= {{ product.id }} > {{ product.id }} </a>
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</td>
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<td>
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{{ product.title }}
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</td>
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<td>
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{{ product.description }}
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</td>
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<td>
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{{ product.version }}
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</td>
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</tr>
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{% endfor %}
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</tbody>
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</table>

docs/_includes/project_table.html

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<table class="table">
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<tbody>
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<tr>
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<th>Name</th>
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<th>Description</th>
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<th>Graph</th>
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<th>Source Code</th>
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</tr>
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{% for project in site.projects %}
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<tr>
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<td>
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{{ project.id }}
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</td>
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<td>
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{{ project.description }}
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</td>
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<td>
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<a href= {{ project.url }} > {{ project.url }} </a>
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</td>
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<td>
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<a href= {{ project.repository }} > {{ project.repository }} </a>
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</td>
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</tr>
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{% endfor %}
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</tbody>
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</table>

docs/all_graphs.html

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---
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layout: page
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title: All Graphs
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permalink: /all_graphs/
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---
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<div class="content">
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<div class="col-md-12">
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<h3>All Graphs on KG-Hub</h3>
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<li><a href="https://kg-hub.berkeleybop.io/MANIFEST.yaml">See the list of all graphs</a></li>
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<li><a href="https://kg-hub.berkeleybop.io/">Browse all files on KG-Hub</a></li>
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<br>
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<p>The table below lists all graphs on KG-Hub, including both full KGs and intermediate products.</p>
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</div>
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<div class="col-md-12">
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<div class="row">
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<div class="col-md-12">
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{% include manifest_table.html %}
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</div>
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</div>
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</div>
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</div>

docs/build_site.sh

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#!/bin/bash
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# Assemble files for KG-Hub site
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# Define paths
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JEKYLL_CONFIG_HEADER_FILE="_config_header.yml"
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JEKYLL_CONFIG_FILE="_config.yml"
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PROJECT_FILE="../utils/projects.yaml"
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MANIFEST_URL="https://kg-hub.berkeleybop.io/MANIFEST.yaml"
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MANIFEST_FILE="MANIFEST.yaml"
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# Retrieve most recent MANIFEST and do some format prep
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wget -N $MANIFEST_URL
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sed -i -e 's/^/ /' $MANIFEST_FILE
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sed -i '1s/^/manifest:\n /' $MANIFEST_FILE
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# Append projects list
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echo "Adding all lists to Jekyll config."
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cat $JEKYLL_CONFIG_HEADER_FILE $PROJECT_FILE $MANIFEST_FILE > $JEKYLL_CONFIG_FILE

docs/code_of_conduct.markdown

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---
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layout: page
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title: Code of Conduct
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permalink: /code_of_conduct/
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---
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This code of conduct outlines expectations of the Knowledge Graph Hub community. The KG-Hub community is committed to providing a welcoming and inspiring environment for all community members, and we expect this code of conduct to be honored by each community member. Herein, we provide specifics regarding appropriate code of conduct, including recommendations for conflict resolution. The KG-Hub community strives to:
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## Be welcoming and patient
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We want and need all comers to contribute to our collective goals of creating a robust suite of interoperable and effective ontologies. Cooperation from all members is needed to help ensure a safe and welcoming environment for everybody. We strive to be a community that that welcomes and supports persons of all backgrounds and identities. This includes, but is not limited to, members of any race, ethnicity, culture, national origin, immigration status, social and economic class, educational level, sex, sexual orientation, gender identity and expression, age, physical size, family status, political belief, religion, and mental or physical ability.
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## Be considerate
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Your work will be used by other people, and you will depend on the work of others. Any decision you take will affect other community members. The consequences of your actions should be considered when making decisions. Remember that we're a large community, so you might not be communicating in someone else's primary language or share their area of expertise. This can present a challenge, but with thoughtful consideration, all communications between community members can be, and should be, considerate of the perspectives of others.
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## Be respectful
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Community members are likely to disagree on issues. This is to be expected within our large, diverse group of individuals. However, we aim to support, at all times, constructive discourse when disagreements arise. This may lead to frustration from time to time, but we cannot allow frustration to turn into disrespectful behavior, mannerisms, or attacks. Our collective productivity very much depends on a supportive community, where people feel comfortable or not threatened when they need to disagree or propose alternative strategies.
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## Be careful in choice of words
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Be thoughtful in your use of words, as others may interpret them differently than may have been intended. If you see others using potentially disrespectful or alienating langauge, please let them know even if it was not intended for you. Often those feeling uncomfortable may not feel comfortable doing or saying anything. It is important that we collectively self-correct.
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## Be kind to everyone
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Do not insult or put down other community members. Harassment and other exclusionary behavior are not acceptable. This includes, but is not limited to: violent threats or language directed against another person; discriminatory jokes and language; posts of sexually explicit or violent material; posts (or threat of posts) of other person’s personally identifying information (“doxing”); photography or recordings; personal insults, especially those using racist or sexist terms; unwelcome sexual attention; advocating for, or encouraging, any of the above behavior; and repeated harassment of others. Harassment also includes offensive verbal comments related to gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race, religion, deliberate intimidation, stalking, sustained disruption of talks or other events. In general, if someone asks you to stop, then stop.
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## Try to understand the cause of disagreements
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Disagreements, both social and technical, happen all the time. It is important that we constructively resolve disagreements and differing views. Remember that we are a diverse group. Diversity contributes to the strength of our community, which is composed of people from a wide range of backgrounds. However, diversity also means that different persons will have different perspectives on issues. While you may not always understand why someone holds a particular viewpoint, that does not necessarily mean that a viewpoint is wrong. Instead of blame, anger, hostility, or argumentation, focus on resolving disagreements and learning from mistakes.
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## Ethics Statement
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All members of the KG-Hub community will be expected to abide by the highest ethical standards, for example, in accordance with the NIH standards for ethical conduct (<https://oir.nih.gov/sourcebook/ethical-conduct>). Plagiarism will not be tolerated.
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## Diversity Statement
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We encourage every member of the KG-Hub community to participate, and we are committed to building a community for all. Although we may not always be successful, we seek to treat every person as fairly and equally as possible. If a community member makes a mistake, then we expect that person to own responsibility for the error and correct it. If a person has been harmed or offended as a result of another person’s action, and if a community member is witness, then both members own responsibility to listen carefully and respectfully to person who has been harmed and make every effort to not repeat the behaviour, as well as to make every effort to correct the damage.
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Although this list cannot be exhaustive, we explicitly honor diversity in age, gender, gender identity or expression, culture, ethnicity, language, national origin, political beliefs, profession, race, religion, sexual orientation, socioeconomic status, and technical ability. We will not tolerate discrimination based on any of the protected characteristics above, including participants with disabilities.
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## Conflict Resolution and Reporting Issues
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If a community member experiences or witnesses unacceptable behavior, or if any other concern arises, then please report it by contacting a member of the KG-Hub management team. If the issue involves a member of the KG-Hub management team, then please contact a different member. If these options are not sufficient, consider contacting your local ombuds office.
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All reports will be handled with discretion and will receive serious attention. Reports should include the following:
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- Name of person submitting the report. Names (real, nicknames, or pseudonyms) of any individuals involved. If there are additional witnesses, please include them as well.
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- An account of the incident and whether it is ongoing.
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- A link to any publicly available record (e.g., a mailing list archive, ticket, or a public Slack log), if applicable.
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- Any additional information that may be helpful.
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If a community member files a report, then a member of the KG-Hub management team will personally contact that person, review the incident with them, follow up with any additional questions, and make a decision with you as to how to proceed. All information will be held in confidence at the direction of the person reporting the incident.

docs/index.html

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---
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layout: home
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title: Welcome
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---
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<div class="content">
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<div class="col-md-12">
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<h3>KG-Hub: A collection of biological and biomedical Knowledge Graphs, including their component data sources.</h3>
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<h3>Learn more about KG-Hub</h3>
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<li><a href="https://kg-hub.berkeleybop.io/MANIFEST.yaml">See the list of all graphs</a></li>
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<li><a href="https://kg-hub.berkeleybop.io/">Browse all files on KG-Hub</a></li>
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<br>
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<h3>Build your own KG</h3>
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<li><a href="https://github.com/Knowledge-Graph-Hub/kg-dtm-template/blob/master/Tutorials/Getting%20Started.ipynb">Get started (from scratch)</a></li>
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<li><a href="https://github.com/Knowledge-Graph-Hub/knowledge-graph-hub-suppor">Get help from the community</a></li>
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<li><a href="https://github.com/Knowledge-Graph-Hub/kg-dtm-template/blob/master/Tutorials/Machine%20Learning%20on%20Knowledge%20Graphs.ipynb">Try machine learning on KGs</a></li>
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<br>
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<h3>KG-Hub Projects</h3>
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<p>The table below lists active KG projects.</p>
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</div>
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<div class="col-md-12">
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<div class="row">
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<div class="col-md-12">
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{% include project_table.html %}
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</div>
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</div>
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</div>
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</div>

docs/index.markdown

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utils/projects.yaml

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projects:
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- id: kg-obo
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description: "KG-OBO: OBO ontologies into KGX TSV format."
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url: "https://kg-hub.berkeleybop.io/kg-obo/"
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repository: "https://github.com/Knowledge-Graph-Hub/kg-obo"
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- id: kg-idg
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description: "KG-IDG: a Knowledge Graph for Illuminating the Druggable Genome."
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url: "https://kg-hub.berkeleybop.io/kg-idg/"
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repository: "https://github.com/Knowledge-Graph-Hub/kg-idg"
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- id: kg-covid-19
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description: "KG-COVID-19: a knowledge graph for COVID-19 and SARS-COV-2."
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url: "https://kg-hub.berkeleybop.io/kg-covid-19/"
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repository: "https://github.com/Knowledge-Graph-Hub/kg-covid-19"
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- id: kg-microbe
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description: "KG-Microbe: a knowledge graph for microbial traits."
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url: "https://kg-hub.berkeleybop.io/kg-microbe/"
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repository: "https://github.com/Knowledge-Graph-Hub/kg-microbe"
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- id: eco-kg
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description: "eco-KG: a knowledge graph of plant traits starting with Planteome and EOL TraitBank."
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url: "https://kg-hub.berkeleybop.io/eco-kg/"
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repository: "https://github.com/Knowledge-Graph-Hub/eco-kg"
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- id: monarch
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description: "Graph representation of the Monarch Initiative knowledge resource."
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url: "https://kg-hub.berkeleybop.io/monarch/"
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repository: ""
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- id: kg-ontoml
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description: "Graph representation of Monarch ontologies."
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description: "Graph representation of Monarch ontologies."
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url: "https://kg-hub.berkeleybop.io/kg-ontoml/"
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repository: "https://github.com/Knowledge-Graph-Hub/kg-ontoml"

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