Merge pull request #35 from phyloref/update-README

Since the name and role of this repository has changed (#19), we no longer refer to these as testcases but as PHYX files. I've updated the README file to reflect this (closes #30) and renamed some of the directories in this repository to make their purpose clearer, as well as cleaning out some out-of-date information that no longer needs to be stored outside the PHYX file itself. Individual lists of phyloreferences have been removed, and will eventually be replaced by an automatically generated table that provides information on the types of included phyloreferences (#34).

.gitignore

@@ -1,3 +1,10 @@
+# Ignore files produced by the test suite
+phyx/*/paper_as_owl.json
+phyx/*/paper.owl
+
+# Ignore files produced by pytest
+.pytest_cache/
+
 # Ignore Mac-specific files
 .DS_Store
 

.travis.yml

@@ -8,5 +8,5 @@ install:
 
 # command to run tests
 script:
-  - cd testcase2owl; python -m pytest; cd ..
-  - travis_wait 120 py.test ./tests
+  - cd phyx2owl; python -m pytest; cd ..
+  - travis_wait 40 py.test ./tests

LICENSE

@@ -1,201 +1,21 @@
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README.md

@@ -1,25 +1,40 @@
-# Phyloreferencing Curation Workflow
-The Phyloreferencing curation workflow serves three main purposes:
+# Clade Ontology
 
-1. It provides a set of exemplar curated phyloreferences in JSON and OWL.
-2. It provides a test space for trying different approaches to generating phyloreferences from JSON to OWL, although these will be moved into their own repositories if they prove to be successes.
-3. It provides a test suite of phyloreferences along with expected resolved nodes, allowing reasoning to be continually tested as ontologies and software tools are updated.
+The Clade Ontology is an ontology of exemplar phyloreferences curated from peer-reviewed publications. Phyloreferences in this ontology include their verbatim clade definition and the phylogeny upon which they were initially defined. The ontology therefore acts as both a catalogue of computable clade definitions as well as a test suite of phyloreferences that can be tested to determine if each phyloreference resolves as expected. This ontology is expressed in the [Web Ontology Language (OWL)]. The executable software code in this repository is available for reuse under the terms of the [MIT license].
 
-[![Build Status](https://travis-ci.org/phyloref/curation-workflow.svg?branch=master)](https://travis-ci.org/phyloref/curation-workflow)
+[![Build Status](https://travis-ci.org/phyloref/clade-ontology.svg?branch=master)](https://travis-ci.org/phyloref/clade-ontology)
 
-## Currently curated phyloreferences
+## Executing phyloreferences as a test suite
 
-| Curated paper | DOI | Phyloreferences | Status |
-|---------------|-----|-----------------|--------|
-| [Fisher et al, 2007](testcases/Fisher%20et%20al,%202007) | [doi](https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2) | 11 phyloreferences | All resolved correctly, but one resolved to a different node from paper | 
-| [Hillis and Wilcox, 2005](testcases/Hillis%20and%20Wilcox,%202005) | [doi](https://doi.org/10.1016/j.ympev.2004.10.007) | 16 phyloreferences | All resolved correctly, but in two cases the correct resolution was no nodes |
+To generate all OWL files and test all phyloreferences, you will need [pytest], which you can install by running `pip install -r requirements.txt`. Note that you will also need to have [Java] installed to test the phyloreferences.
 
-## Executing phyloreferences as a test suite
+Once pytest and all other required libraries are installed, you can execute all tests by running `py.test tests/` in the root directory of this project. We support two optional marks:
+
+ * `py.test tests/ -m json` executes the scripts to create OWL representations of the test suite. This tests the content of the JSON file and ensures that they can be converted into OWL.
+ * `py.test tests/ -m owl` reasons over the created OWL files and ensures that the expected nodes are correctly resolved by the phyloreferences.
+
+## Data workflow
+
+Curated phyloreferences produced by the [Curation Tool] as Phyloreference eXchange (PHYX) files are currently stored in the [`phyx`] directory (see [Brochu 2003] as an example). When executed as a test suite, these files are converted into the Web Ontology Language (OWL) in the following steps:
+
+1. PHYX files are converted to JSON-LD files using the [`phyx2owl`] Python tool. This tool translate phylogenies stored in [the Newick format] into a series of statements describing individual nodes and their relationships, and translates phyloreferences into OWL class restrictions that describes the nodes they resolve to.
+2. The produced JSON-LD files can be transformed by any standards-compliant converter into OWL files. In the test suite, we use the  [`rdfpipe`] tool included in the [`rdflib`] Python library.
+3. Any compliant [OWL 2 DL reasoner] should be able to reason over this OWL file and provide information on which nodes each phyloreference resolved to. In the test suite, we use [`jphyloref`], a Java application that uses the [JFact++ OWL reasoner] to reason over input OWL files. `jphyloref` can also read the annotations that indicate where each phyloreference was expected to resolve on any of the included phylogenies, and test whether phyloreferences resolved to the expected nodes.
 
-You can execute and test all phyloreferences by running `py.test` in the root directory
-of this project. We support two marks:
+We are currently working on a complete workflow that would allow us to [merge separate PHYX files into a single Clade Ontology] available as a single OWL file available for individual download. At the moment, therefore, OWL files need to be generated by running the test suite on your own computer.
 
- * `py.test -m json` executes the scripts to create OWL representations of the test suite.
-   This tests the content of the JSON file and ensures that they can be converted into OWL.
- * `py.test -m owl` reasons over the created OWL files and ensures that the expected nodes 
-   are correctly resolved by the phyloreferences.
+[Web Ontology Language (OWL)]: https://en.wikipedia.org/wiki/Web_Ontology_Language
+[MIT license]: ./LICENSE
+[pytest]: https://docs.pytest.org/
+[Java]: https://java.com/
+[Curation Tool]: https://github.com/phyloref/curation-tool
+[`phyx`]: ./phyx/
+[Brochu 2003]: ./phyx/Brochu%202003/paper.json
+[`phyx2owl`]: ./phyx2owl/
+[the Newick format]: https://en.wikipedia.org/wiki/Newick_format
+[`rdfpipe`]: http://rdflib.readthedocs.io/en/stable/apidocs/rdflib.tools.html#module-rdflib.tools.rdfpipe
+[`rdflib`]: http://rdflib.readthedocs.io/
+[OWL 2 DL reasoner]: https://www.w3.org/TR/2012/REC-owl2-direct-semantics-20121211/
+[`jphyloref`]: https://github.com/phyloref/jphyloref
+[JFact++ 1.2.4 OWL reasoner]: http://jfact.sourceforge.net/
+[merge separate PHYX files into a single Clade Ontology]: https://github.com/phyloref/clade-ontology/projects/3

testcase2owl/testcase2owl.py → phyx2owl/phyx2owl.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 """
-testcase2owl.py: Converts a Phyloreference curated test case into a 
+phyx2owl.py: Converts a Phyloreference curated test case into a
 JSON-LD file with node information. It carries out two conversions:
 
  1. Converts all phylogenies into a node-based representation in OWL,