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README and docs edited for readability

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tgbugs committed Oct 14, 2017
1 parent 6bd108d commit e63acacbb2e8d4a05d974cec314db374def3f2af
Showing with 33 additions and 15 deletions.
  1. +1 −1 README.md
  2. +19 −10 docs/development setup.md
  3. +13 −4 docs/processes.md
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@@ -9,7 +9,7 @@ the [log](https://github.com/SciCrunch/NIF-Ontology/commits/master) or
run `git log` for a quick overview.
# Documentation
Please see [docs](docs/) for documentation about how to develop NIFSTD
Please see [docs/](docs/) for documentation about how to develop NIFSTD
using this repository.
Please see the [GitHub wiki](https://github.com/SciCrunch/NIF-Ontology/wiki)
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@@ -1,22 +1,31 @@
# Intro
This file documents
the steps needed to create
a working development environment
for NIFSTD.
NIFSTD development uses this repo, git (GitHub), pyontutils (Python3.6), Protege, ELK, FACT++, and InterLex.
NIFSTD development also uses SciGraph (Java8), and OWLAPI (see pyontutils for more information).
## git
If you have not used git before please follow [this guide](https://help.github.com/articles/set-up-git/).
**We do not accept pull requests with commits that do not have an email address.** Please be sure to
Set up git. [This guide can be helpful.](https://help.github.com/articles/set-up-git/).
**We only accept pull requests with commits that have an email address.**
Please be sure to
[set your commit email](https://help.github.com/articles/setting-your-commit-email-address-in-git/).
**NOTE:** If you have not participated in open source development before I often
recommend creating a new email specifically for all development related activities.
If you have never used git before check out the
[git bootcamp guides](https://help.github.com/categories/bootcamp/)
and if you have never used GitHub before check out the
[GitHub guides](https://guides.github.com/).
## repo
If you do not have push rights to
[SciCrunch/NIF-Ontology](https://github.com/SciCrunch/NIF-Ontology),
[SciCrunch/NIF-Ontology](https://github.com/SciCrunch/NIF-Ontology), please
[fork](https://github.com/SciCrunch/NIF-Ontology#fork-destination-box)
the repo so that you can push somewhere that can submit
[pull requests](https://github.com/SciCrunch/NIF-Ontology/pull/new/master).
@@ -42,22 +51,22 @@ Download and install the latest version of Protege [here](http://protege.stanfor
**NIFSTD is a very large ontology which requires more memory than the Protege defaults.**
Modify how your OS's equivalent of `run.sh` launches java to `jre/bin/java -Xmx8G -Xms500M \`
Modify `run.sh` (or equivalent) so that it launches java with `jre/bin/java -Xmx8G -Xms500M \`
(or similar).
## Reasoners (ELK, FACT++)
You can obtain copies of ELK and FACT++ but launching protege and in the
menu bar File -> Check for plugins and select ELK and FACT++. **NOTE:**
that sometimes the plugin repos don't resolve, if that happens try again.
Otherwise you can get the reasoner plugins and put them in `Protege-*/plugins/`.
## Reasoners
You can obtain copies of ELK and FACT++ by launching protege and going to
menu bar `File -> Check for plugins` and selecting ELK and FACT++.
**NOTE:** sometimes the plugin repos don't load, if that happens try again.
Otherwise you can download the reasoner plugins and put them in `Protege-*/plugins/`.
### ELK
Get the latest version of `elk-distribution-*-protege-plugin.zip` from https://github.com/liveontologies/elk-reasoner/releases.
Or get the latest version of https://mvnrepository.com/artifact/org.semanticweb.elk/elk-owlapi.
### FACT++
Get the latest version of `uk.ac.manchester.cs.owl.factplusplus-*.jar` from https://bitbucket.org/dtsarkov/factplusplus/downloads/.
## InterLex
[InterLex](https://interlex.org/) provides all new identifiers for NIFSTD.
[InterLex](http://interlex.org/) provides all new identifiers for NIFSTD.
You will need a [SciCrunch account](https://scicrunch.org/register) in order to
access the InterLex web api and to use InterLex to create new terms.
**NOTE:** At the moment only curators can add terms so let us know if you need access.
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@@ -1,14 +1,22 @@
# Intro
This file documents
the development processes
that have not (yet) been automated
and
the practices that developers should follow
when working on NIFSTD.
All of these processes expect the full NIF-Ontology development
environment to have been set up according to [development setup.md](development%20setup.md).
All relative filepaths listed in code sections start from the base
folder of this repository `../` from the location of this file.
# DO NOT PUSH TO MASTER
The `master` branch serves the 'live' resolvable ontology files.
The `uri.neuinfo.org` resolver points to the `master` branch on GitHub
(see [the resolver config](https://github.com/tgbugs/pyontutils/blob/088b2f8f28be5e55278e3cde1e0e8a4f3ccfc94f/resolver/nif-ont-resolver.conf#L20-L24)).
Please do not push to the master branch.
Therefore, please do not push to the master branch.
Please submit a pull request (even if it is from another branch
in the SciCrunch org repo) so that we can run all the requisite
@@ -69,8 +77,9 @@ patch -p2 -i ../dev-reasoner.patch
# Then
protege # can be launched as you see fit
```
1. In protege menu bar File -> Open `ttl/nif.ttl`
2. Make sure reasoner is set to ELK (menu bar Reasoner -> ELK 0.4.3)
1. In protege menu bar `File -> Open` and choose `ttl/nif.ttl`
(after first load `File -> Open recent` is faster).
2. Make sure reasoner is set to ELK (menu bar `Reasoner -> ELK 0.4.3`)
3. Ctrl-R
Protege does not have to be run from `ttl/` in order to find `ttl/catalog-v001.xml`,

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