initial commit of ontology sources of efo using ontology-starter-kit

.gitignore

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+*.tmp
+src/ontology/mirror
+src/ontology/mirror/*
+src/ontology/efo.obo
+src/ontology/efo.owl
+semantic.cache

.travis.yml

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+## REMEMBER TO SET UP YOUR GITHUB REPO FOR TRAVIS
+## Go to: https://travis-ci.org/EBISPOT for details
+language: java
+jdk:
+  - oraclejdk8
+
+before_script:
+  - mkdir -p bin
+  - export PATH=$PATH:$PWD/bin
+  - wget http://build.berkeleybop.org/userContent/owltools/owltools -O bin/owltools
+  - wget http://build.berkeleybop.org/userContent/owltools/ontology-release-runner -O bin/ontology-release-runner
+  - wget http://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar -O bin/owltools-runner-all.jar
+  - wget http://build.berkeleybop.org/userContent/owltools/owltools-oort-all.jar -O bin/owltools-oort-all.jar
+  - wget http://build.berkeleybop.org/job/robot/lastSuccessfulBuild/artifact/bin/robot -O bin/robot
+  - wget http://build.berkeleybop.org/job/robot/lastSuccessfulBuild/artifact/bin/robot.jar -O bin/robot.jar
+  - wget --no-check-certificate https://raw.githubusercontent.com/cmungall/pattern2owl/master/apply-pattern.py -O bin/apply-pattern.py
+  - chmod +x bin/*
+
+# command to run tests
+script: cd src/ontology && make test
+
+#after_success:
+#  coveralls
+
+# whitelist
+branches:
+  only:
+    - master
+    - test-travis
+
+### UNCOMMENT THIS AND ADD YOUR DETAILS:
+#notifications:
+#  email:
+#    - [email protected]

CONTRIBUTING.md

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+## Before you write a new request, please consider the following: 
+
+- **Does the term already exist?** Before submitting suggestions for new ontology terms, check whether the term exist, either as a primary term or a synonym term. You can search using [OLS](http://www.ebi.ac.uk/ols/ontologies/efo)
+
+## Guidelines for creating GitHub tickets with contributions to the ontology:
+
+1. **Write a detailed request:** Please be specific and include as many details as necessary, providing background information, and if possible, suggesting a solution. GOC editors will be better equipped to address your suggestions if you offer details regarding *'what is wrong'*, *'why'*, and *'how to fix it'*.
+
+2. **Provide examples and references:** Please include PMIDs for new term requests, and include also screenshots, or URLs illustrating the current ontology structure for other types of requests. 
+
+3. **For new term request:** Be sure to provide suggestions for label (name), definition, references, position in hierarchy, etc.
+
+4. **For updates to relationships:** Provide details of the current axioms, why you think they are wrong or not sufficient, and what exactly should be added or removed.
+
+On behalf of the efo editorial team, Thanks!

README.md

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+[![Build Status](https://travis-ci.org/EBISPOT/efo.svg?branch=master)](https://travis-ci.org/EBISPOT/efo)
+[![DOI](https://zenodo.org/badge/13996/EBISPOT/efo.svg)](https://zenodo.org/badge/latestdoi/13996/EBISPOT/efo)
+
+# efo
+
+This ontology... YOUR DESCRIPTION HERE
+
+## Versions
+
+### Stable release versions
+
+The latest version of the ontology can always be found at:
+
+http://purl.obolibrary.org/obo/efo.owl
+
+(note this will not show up until the request has been approved by obofoundry.org)
+
+### Editors' version
+
+Editors of this ontology should use the edit version, [src/ontology/efo-edit.owl](src/ontology/efo-edit.owl)
+
+## Contact
+
+Please use this GitHub repository's [Issue tracker](https://github.com/EBISPOT/efo/issues) to request new terms/classes or report errors or specific concerns related to the ontology.
+
+## Acknowledgements
+
+This ontology repository was created using the [ontology starter kit](https://github.com/INCATools/ontology-starter-kit)

issue_template.md

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+For new term requests, please provide the following information:
+
+## Preferred term label
+
+(e.g., Asplenia)
+
+## Synonyms
+
+(e.g., Absent spleen)
+
+## Textual definition
+
+the definition should be understandable even for non-specialists. Include a PubMed ID to refer to any relevant article that provides additional information about the suggested term.
+
+## Suggested parent term
+
+Please look in the hierarchy in a browser such as [OLS](http://www.ebi.ac.uk/ols/ontologies/efo)
+
+## Attribution
+
+If you would like a nanoattribution, please indicate your ORCID id

src/metadata/README.md

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+Metadata files for the OBO Library
+
+ * [efo.yml](efo.yml)
+     * Determines how your purl.obolibrary.org/obo/efo/ redirects will be handled
+     * Go here: https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config
+     * Click [New File](https://github.com/OBOFoundry/purl.obolibrary.org/new/master/config)
+     * Paste in the contents of [efo.yml](efo.yml)
+     * Click "Commit new file"
+     * IMPORTANT: remember to make a pull request
+     * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library*
+ * [efo.md](efo.md)
+     * Determines how your metadata is shown on OBO Library, OLS and AberOWL
+     * Go here: https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology
+     * Click [New File](https://github.com/OBOFoundry/OBOFoundry.github.io/new/master/ontology)
+     * Paste in the contents of [efo.md](efo.md)
+     * Click "Commit new file"
+     * IMPORTANT: remember to make a pull request
+     * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library*
+
+For more background see:
+
+ * http://obofoundry.org/
+ * http://obofoundry.org/faq/how-do-i-edit-metadata.html

src/metadata/efo.md

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+---
+layout: ontology_detail
+id: efo
+title: efo
+jobs:
+  - id: https://travis-ci.org/EBISPOT/efo
+    type: travis-ci
+build:
+  checkout: git clone https://github.com/EBISPOT/efo.git
+  system: git
+  path: "."
+contact:
+  email: [email protected]
+  label: Chris Mungall
+description: efo is an ontology...
+domain: stuff
+homepage: https://github.com/EBISPOT/efo
+products:
+  - id: efo.owl
+  - id: efo.obo
+dependencies:
+tracker: https://github.com/EBISPOT/efo/issues
+license:
+  url: http://creativecommons.org/licenses/by/3.0/
+  label: CC-BY
+---
+
+Enter a detailed description of your ontology here

src/metadata/efo.yml

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+# PURL configuration for http://purl.obolibrary.org/obo/efo
+
+idspace: EFO
+base_url: /obo/efo
+
+products:
+- efo.owl: https://raw.githubusercontent.com/EBISPOT/efo/master/efo.owl
+- efo.obo: https://raw.githubusercontent.com/EBISPOT/efo/master/efo.obo
+
+term_browser: ontobee
+example_terms:
+- EFO_0000000
+
+entries:
+
+- prefix: /releases/
+  replacement: https://raw.githubusercontent.com/EBISPOT/efo/v
+
+- prefix: /tracker/
+  replacement: https://github.com/EBISPOT/efo/issues
+
+- prefix: /about/
+  replacement: http://www.ontobee.org/ontology/EFO?iri=http://purl.obolibrary.org/obo/
+
+## generic fall-through, serve direct from github by default
+- prefix: /
+  replacement: https://raw.githubusercontent.com/EBISPOT/efo/master/

src/ontology/Makefile

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+# ----------------------------------------
+# Standard Constants
+# ----------------------------------------
+# these can be overwritten on the command line
+
+OBO=http://purl.obolibrary.org/obo
+ONT=efo
+BASE=$(OBO)/$(ONT)
+SRC=$(ONT)-edit.owl
+RELEASEDIR=../..
+ROBOT= robot
+OWLTOOLS= owltools
+USECAT= --use-catalog
+SPARQLDIR = ../sparql
+
+# ----------------------------------------
+# Top-level targets
+# ----------------------------------------
+
+all: sparql_test all_imports $(ONT).owl $(ONT).obo
+test: sparql_test all
+prepare_release: all
+	cp $(ONT).owl $(ONT).obo $(RELEASEDIR) &&\
+	mkdir -p $(RELEASEDIR)/imports &&\
+	cp imports/*{owl,obo} $(RELEASEDIR)/imports &&\
+	git add $(RELEASEDIR)/imports/*{obo,owl} &&\
+	(test -f subsets/*owl && cp subsets/*{owl,obo} $(RELEASEDIR)/subsets && git add $(RELEASEDIR)/subsets/* || echo "no subsets") &&\
+	echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on github"
+
+# ----------------------------------------
+# Main release targets
+# ----------------------------------------
+
+# by default we use Elk to perform a reason-relax-reduce chain
+# after that we annotate the ontology with the release versionInfo
+$(ONT).owl: $(SRC)
+	$(ROBOT)  reason -i $< -r ELK relax reduce -r ELK annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $@
+$(ONT).obo: $(ONT).owl
+	$(ROBOT) convert -i $< -f obo -o $(ONT).obo.tmp && mv $(ONT).obo.tmp $@
+
+# ----------------------------------------
+# Import modules
+# ----------------------------------------
+# Most ontologies are modularly constructed using portions of other ontologies
+# These live in the imports/ folder
+# These can be regenerated with make all_imports
+
+IMPORTS = 
+IMPORTS_OWL = $(patsubst %, imports/%_import.owl,$(IMPORTS)) $(patsubst %, imports/%_import.obo,$(IMPORTS))
+
+# Make this target to regenerate ALL
+all_imports: $(IMPORTS_OWL)
+
+# Use ROBOT, driven entirely by terms lists NOT from source ontology
+imports/%_import.owl: mirror/%.owl imports/%_terms.txt
+	$(ROBOT) extract -i $< -T imports/$*_terms.txt --method BOT -O $(BASE)/$@ -o $@
+.PRECIOUS: imports/%_import.owl
+
+# we use owltools for making the obo file until: https://github.com/ontodev/robot/issues/64
+imports/%_import.obo: imports/%_import.owl
+	$(OWLTOOLS) $(USECAT) $< -o -f obo $@
+
+# clone remote ontology locally, perfoming some excision of relations and annotations
+mirror/%.owl: $(SRC)
+	$(OWLTOOLS) $(OBO)/$*.owl --remove-annotation-assertions -l -s -d --remove-dangling-annotations  -o $@
+.PRECIOUS: mirror/%.owl
+
+# ----------------------------------------
+# Release
+# ----------------------------------------
+# copy from staging area (this directory) to top-level
+release: $(ONT).owl $(ONT).obo
+	cp $^ $(RELEASEDIR) && cp imports/* $(RELEASEDIR)/imports
+
+# ----------------------------------------
+# Sparql queries: Q/C
+# ----------------------------------------
+
+# these live in the ../sparql directory, and have suffix -violation.sparql
+# adding the name here will make the violation check live
+VCHECKS = equivalent-classes trailing-whitespace owldef-self-reference xref-syntax nolabels
+
+# run all violation checks
+VQUERIES = $(foreach V,$(VCHECKS),$(SPARQLDIR)/$V-violation.sparql)
+sparql_test: $(SRC)
+	robot verify -i $< --queries $(VQUERIES) -O reports/
+
+# ----------------------------------------
+# Sparql queries: Reports
+# ----------------------------------------
+
+REPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms
+REPORT_ARGS = $(foreach V,$(REPORTS),-s $(SPARQLDIR)/$V.sparql reports/$V.tsv)
+all_reports: $(SRC)
+	robot query -f tsv -i $< $(REPORT_ARGS)

src/ontology/README-editors.md

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+These notes are for the EDITORS of efo
+
+This project was created using the [ontology starter kit](https://github.com/cmungall/ontology-starter-kit). See the site for details.
+
+For more details on ontology management, please see the [OBO tutorial](https://github.com/jamesaoverton/obo-tutorial) or the [Gene Ontology Editors Tutorial](go-protege-tutorial.readthedocs.io)
+
+## Editors Version
+
+Make sure you have an ID range in the [idranges file](efo-idranges.owl)
+
+If you do not have one, get one from the head curator.
+
+The editors version is [efo-edit.owl](efo-edit.owl)
+
+** DO NOT EDIT efo.obo OR efo.owl in the top level directory **
+
+[../../efo.owl](../../efo.owl) is the release version
+
+To edit, open the file in Protege. First make sure you have the repository cloned, see [the GitHub project](https://github.com/EBISPOT/efo) for details.
+
+## ID Ranges
+
+These are stored in the file
+
+ * [efo-idranges.owl](efo-idranges.owl)
+
+** ONLY USE IDs WITHIN YOUR RANGE!! **
+
+If you have only just set up this repository, modify the idranges file
+and add yourself or other editors. Note Protege does not read the file
+- it is up to you to ensure correct Protege configuration.
+
+
+### Setting ID ranges in Protege
+
+We aim to put this up on the technical docs for OBO on http://obofoundry.org/
+
+For now, consult the [GO Tutorial on configuring Protege](http://go-protege-tutorial.readthedocs.io/en/latest/Entities.html#new-entities)
+
+
+## Release Manager notes
+
+You should only attempt to make a release AFTER the edit version is
+committed and pushed, and the travis build passes.
+
+to release:
+
+    cd src/ontology
+    make
+
+If this looks goo
+d type:
+
+    make prepare_release
+
+This generates derived files such as efo.owl and efo.obo and places
+them in the top level (../..). The versionIRI will be added.
+
+Commit and push these files.
+
+    git commit -a
+
+And type a brief description of the release in the editor window
+
+Finally type
+
+    git push origin master
+
+IMMEDIATELY AFTERWARDS (do *not* make further modifications) go here:
+
+ * https://github.com/EBISPOT/efo/releases
+ * https://github.com/EBISPOT/efo/releases/new
+
+The value of the "Tag version" field MUST be
+
+    vYYYY-MM-DD
+
+The initial lowercase "v" is REQUIRED. The YYYY-MM-DD *must* match
+what is in the versionIRI of the derived efo.owl (data-version in
+efo.obo).
+
+Release title should be YYYY-MM-DD, optionally followed by a title (e.g. "january release")
+
+Then click "publish release"
+
+__IMPORTANT__: NO MORE THAN ONE RELEASE PER DAY.
+
+The PURLs are already configured to pull from github. This means that
+BOTH ontology purls and versioned ontology purls will resolve to the
+correct ontologies. Try it!
+
+ * http://purl.obolibrary.org/obo/efo.owl <-- current ontology PURL
+ * http://purl.obolibrary.org/obo/efo/releases/YYYY-MM-DD.owl <-- change to the release you just made
+
+For questions on this contact Chris Mungall or email obo-admin AT obofoundry.org
+
+# Travis Continuous Integration System
+
+Check the build status here: [![Build Status](https://travis-ci.org/EBISPOT/efo.svg?branch=master)](https://travis-ci.org/EBISPOT/efo)
+
+Note: if you have only just created this project you will need to authorize travis for this repo. Go to [https://travis-ci.org/profile/EBISPOT](https://travis-ci.org/profile/EBISPOT) for details
+

src/ontology/catalog-v001.xml

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+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+    <group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base=""/>
+</catalog>