Authors | Ron Jacak (rjacak) |
Jody Proescher (jproesch) | |
Gene Godbold | |
Amanda Ernlund (awe220) | |
Tina Zudock (kzudock) |
This ontology contains terms to describe the function of genes and gene products involved in pathogenesis. Genes that encode toxins, virulence factors, and antimicrobial resistance have functions that are not represented well by the terms contained within the Gene Ontology or any of the other OBO Foundry ontologies. This ontology will collect and maintain common terms and descriptions of concepts related to pathogenesis, and could help provide more intuitive descriptions of function for these types of sequences.
The PathGO project has the following filesystem structure:
. ├── CONTRIBUTING.md ├── README.md <-- file shown on main GitHub page ├── bin/ <-- utilities for managing ontology files ├── imports/ <-- imported ontologies live here ├── issue_template.md ├── pathgo.obo <-- distributable versions of the ontology (.obo, .owl) ├── pathgo.owl ├── src/ │ ├── metadata/ │ ├── ontology/ │ │ ├── Makefile │ │ ├── last_used_id.txt <-- last used term id │ │ ├── pathgo-edit.owl <-- working version of the ontologies, most recent updates live here │ │ ├── pathgo-idranges.owl │ │ ├── ... │ └── sparql/ └── static/ └── protege_new_entity_settings.png
The latest official release of the ontology can always be found at:
If/when the ontology gets approved by the OBO Foundry, official releases will also be available at:
http://purl.obolibrary.org/obo/pathgo.owl
Changes made between official releases of the ontology can be found in the "-edit" file, src/ontology/pathgo-edit.owl.
We recommend the use of GitHub Desktop (https://desktop.github.com/) and Protege (https://protege.stanford.edu/) for viewing the ontology. Individuals should download and install GitHub Desktop, select the option to "Clone a Repository from the Internet...", search for the "pathogenesis_gene_ontology" repository, and clone it. When prompted, you will be able to choose where the cloned repository files are saved. Choose an alternate location or make note of the default location, because you will need this path working with the ontology. Our recommended workflow for viewing the ontology and making changes is as follows:
PathGO would welcome suggestions and contributions from the community! Individuals can either A) recommend changes by creating an issue in the ontology project page on Github.com, or B) edit the pathgo-edit.owl file in a new branch in GitHub Desktop and petition for the changes to be merged into the official PathGO branch.
Contributors are encouraged to use Protege for ontology editing, and a Git-enabled command line environment for version control and for submitting changes for integration. Note, to edit this ontology, contributors should make changes to the "-edit" file, src/ontology/pathgo-edit.owl in a separate branch, and create a pull request from that branch.
For contributors with less or no experience with Git and command line environments, we recommend the following workflow using GitHub Desktop (https://desktop.github.com/).
Current best ontology practices include identifying terms/classes with a Uniform Resource Identifier (URI). PathGO is adopting the conventions that other ontologies within the OBO Foundry use including the use of Permanent URLs (PURLs) with a standard base prefix, as well as short-form identifiers (e.g. PATHGO:0000200) to identify terms. Users should open the Protege Preferences pane and update the "New entities" tab with the following settings:
Ensure that under "Auto-generated ID", the Prefix is set to "PATHGO_", the digit count is 7, and the start is set to the number of last used id.
Instructions on how to determine last used numeric id are currently being drafted. Users experienced with git should manually configure their git environment to use the git "hooks" located in .githooks, by executing the following command: $ git config core.hooksPath .githooks The post-receive hook therein will update the src/ontology/last_used_id.txt file after any 'git push' commands.
Please use this repository's Issue tracker to request provide feedback, recommend changes to terms/classes, and/or report errors or specific concerns related to the ontology. We would love to hear from you!
This ontology repository was created using the ontology starter kit. We thank Chris Mungall and any other developers for putting this utility together.
This material is licensed to the public under CC BY-NC 4.0. The U.S. Government has “Unlimited Rights” as granted and defined under FAR 52.227-14.
©2020 The Johns Hopkins University Applied Physics Laboratory LLC (JHU/APL). All Rights Reserved.
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