diff --git a/.gitignore b/.gitignore index a8bfb77..74f019c 100644 --- a/.gitignore +++ b/.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 diff --git a/.travis.yml b/.travis.yml index df36ae3..af524bb 100644 --- a/.travis.yml +++ b/.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 diff --git a/LICENSE b/LICENSE index 8dada3e..655a633 100644 --- a/LICENSE +++ b/LICENSE @@ -1,201 +1,21 @@ - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. 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IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/README.md b/README.md index f9ea05e..1961f54 100644 --- a/README.md +++ b/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 diff --git a/testcases/Brochu 2003/paper.json b/phyx/Brochu 2003/paper.json similarity index 100% rename from testcases/Brochu 2003/paper.json rename to phyx/Brochu 2003/paper.json diff --git a/testcases/Fisher et al, 2007/paper.json b/phyx/Fisher et al, 2007/paper.json similarity index 100% rename from testcases/Fisher et al, 2007/paper.json rename to phyx/Fisher et al, 2007/paper.json diff --git a/testcases/Hillis and Wilcox, 2005/T4419.nexml b/phyx/Hillis and Wilcox, 2005/T4419.nexml similarity index 100% rename from testcases/Hillis and Wilcox, 2005/T4419.nexml rename to phyx/Hillis and Wilcox, 2005/T4419.nexml diff --git a/testcases/Hillis and Wilcox, 2005/paper.json b/phyx/Hillis and Wilcox, 2005/paper.json similarity index 100% rename from testcases/Hillis and Wilcox, 2005/paper.json rename to phyx/Hillis and Wilcox, 2005/paper.json diff --git a/testcase2owl/paper-context.json b/phyx2owl/paper-context.json similarity index 100% rename from testcase2owl/paper-context.json rename to phyx2owl/paper-context.json diff --git a/testcase2owl/phyloref/Identified.py b/phyx2owl/phyloref/Identified.py similarity index 100% rename from testcase2owl/phyloref/Identified.py rename to phyx2owl/phyloref/Identified.py diff --git a/testcase2owl/phyloref/Phylogeny.py b/phyx2owl/phyloref/Phylogeny.py similarity index 100% rename from testcase2owl/phyloref/Phylogeny.py rename to phyx2owl/phyloref/Phylogeny.py diff --git a/testcase2owl/phyloref/PhylogenyGroup.py b/phyx2owl/phyloref/PhylogenyGroup.py similarity index 100% rename from testcase2owl/phyloref/PhylogenyGroup.py rename to phyx2owl/phyloref/PhylogenyGroup.py diff --git a/testcase2owl/phyloref/Phyloreference.py b/phyx2owl/phyloref/Phyloreference.py similarity index 100% rename from testcase2owl/phyloref/Phyloreference.py rename to phyx2owl/phyloref/Phyloreference.py diff --git a/testcase2owl/phyloref/PhyloreferenceTestCase.py b/phyx2owl/phyloref/PhyloreferenceTestCase.py similarity index 100% rename from testcase2owl/phyloref/PhyloreferenceTestCase.py rename to phyx2owl/phyloref/PhyloreferenceTestCase.py diff --git a/testcase2owl/phyloref/Specifier.py b/phyx2owl/phyloref/Specifier.py similarity index 100% rename from testcase2owl/phyloref/Specifier.py rename to phyx2owl/phyloref/Specifier.py diff --git a/testcase2owl/phyloref/TUMatch.py b/phyx2owl/phyloref/TUMatch.py similarity index 100% rename from testcase2owl/phyloref/TUMatch.py rename to phyx2owl/phyloref/TUMatch.py diff --git a/testcase2owl/phyloref/TaxonomicUnit.py b/phyx2owl/phyloref/TaxonomicUnit.py similarity index 100% rename from testcase2owl/phyloref/TaxonomicUnit.py rename to phyx2owl/phyloref/TaxonomicUnit.py diff --git a/testcase2owl/phyloref/__init__.py b/phyx2owl/phyloref/__init__.py similarity index 100% rename from testcase2owl/phyloref/__init__.py rename to phyx2owl/phyloref/__init__.py diff --git a/testcase2owl/phyloref/owlterms.py b/phyx2owl/phyloref/owlterms.py similarity index 100% rename from testcase2owl/phyloref/owlterms.py rename to phyx2owl/phyloref/owlterms.py diff --git a/testcase2owl/testcase2owl.py b/phyx2owl/phyx2owl.py similarity index 98% rename from testcase2owl/testcase2owl.py rename to phyx2owl/phyx2owl.py index 6698870..7ff8b12 100644 --- a/testcase2owl/testcase2owl.py +++ b/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, diff --git a/testcase2owl/tests/test_taxonomic_units.py b/phyx2owl/tests/test_taxonomic_units.py similarity index 100% rename from testcase2owl/tests/test_taxonomic_units.py rename to phyx2owl/tests/test_taxonomic_units.py diff --git a/testcases_too_slow/Wojciechowski, 2013/paper.json b/phyx_too_slow/Wojciechowski, 2013/paper.json similarity index 100% rename from testcases_too_slow/Wojciechowski, 2013/paper.json rename to phyx_too_slow/Wojciechowski, 2013/paper.json diff --git a/testcases/Fisher et al, 2007/README.md b/testcases/Fisher et al, 2007/README.md deleted file mode 100644 index af6046e..0000000 --- a/testcases/Fisher et al, 2007/README.md +++ /dev/null @@ -1,29 +0,0 @@ -# Fisher *et al.*, 2007 - -* Based on [Fisher *et al.*, 2007](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) - * Tree [available on TreeBase](https://treebase.org/treebase-web/search/study/taxa.html?id=1624). - -* Input file: [`paper.json`](paper.json) -* To create ontology: - * `python ../../testcase2owl/testcase2owl.py paper.json -o paper_as_owl.json` - * `rdfpipe -i json-ld paper_as_owl.json -o xml > paper.owl` - * (On Windows, you need to end with `... | Set-Content -Encoding UTF8 fisher_et_al_2007.owl`) - -* Output file: `paper.owl` - * This file can be opened in Protege; phyloreferences are instances of the - Phyloreference class and should contain a single node from which this clade - descends. - -## Current test status - -* Albifolium: resolved correctly. -* Arthrocormus: resolved correctly. -* Calymperaceae: resolved correctly. -* Calymperes: resolved correctly. -* Exodictyon: resolved correctly. -* Exostratum: resolved correctly. -* Leucophanella: **no nodes resolved**, as it specifies *Syrrhopodon revolutus* as an internal specifier, but this specifier does not exist in this phylogeny. -* Leucophanes: resolved correctly. -* Mitthyridium: resolved correctly. -* Syrrhopodon: resolved correctly. -* Trachymitrium: resolved correctly. diff --git a/testcases/Fisher et al, 2007/T748.nexml b/testcases/Fisher et al, 2007/T748.nexml deleted file mode 100644 index 5ab1540..0000000 --- a/testcases/Fisher et al, 2007/T748.nexml +++ /dev/null @@ -1,634 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/testcases/Fisher et al, 2007/old_labeled.json b/testcases/Fisher et al, 2007/old_labeled.json deleted file mode 100644 index 1bedc01..0000000 --- a/testcases/Fisher et al, 2007/old_labeled.json +++ /dev/null @@ -1,4441 +0,0 @@ -{ - "@context": "../paper-context.json", - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#", - "@type": [ - "tbd:Publication", - "owl:Ontology" - ], - "citation": "Fisher KM, Wall DP, Yip KL, Mishler BD (2007) The Bryologist 110(1):46-73.", - "comments": "None.", - "curator": "Gaurav Vaidya ", - "http://example.org/TBD#hasExternalSpecifier": { - "@id": "tbd:hasExternalSpecifier", - "@type": "owl:ObjectProperty" - }, - "http://example.org/TBD#hasInternalSpecifier": { - "@id": "tbd:hasInternalSpecifier", - "@type": "owl:ObjectProperty" - }, - "http://example.org/TBD#hasNode": { - "@id": "tbd:hasNode", - "@type": "owl:ObjectProperty" - }, - "http://example.org/TBD#hasSpecifier": { - "@id": "tbd:hasSpecifier", - "@type": "owl:ObjectProperty" - }, - "http://example.org/TBD#inPhylogeny": { - "@id": "tbd:inPhylogeny", - "@type": "owl:ObjectProperty" - }, - "http://phylotastic.org/terms/tnrs.rdf#matchedName": { - "@id": "tnrs:matchedName", - "@type": "owl:DatatypeProperty" - }, - "http://phylotastic.org/terms/tnrs.rdf#submittedName": { - "@id": "tnrs:submittedName", - "@type": "owl:DatatypeProperty" - }, - "owl:imports": [ - "https://www.w3.org/2004/02/skos/core", - "http://raw.githubusercontent.com/hlapp/phyloref/master/phyloref.owl" - ], - "phylogenies": [ - { - "labeledNodeData": [ - { - "label": [ - "Arthrocormus schimperi", - "Arthrocormus" - ], - "skos:closeMatch": [ - "http://www.theplantlist.org/tpl1.1/record/tro-35179022", - "http://www.tropicos.org/Name/35179022", - 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(1846) -- Mishler 7/24/98 (5) Queensland, Australia (UC)", - "tnrs:matchedName": "Arthrocormus schimperi" - } - ], - "label": "Arthrocormus", - "manchesterSyntax": "Node and ((Node that tnrs:matchedName value \"Arthrocormus schimperi\"^^xsd:string) or has_Descendant some (Node that tnrs:matchedName value \"Arthrocormus schimperi\"^^xsd:string) and (has_Sibling some ((Node that tnrs:matchedName value \"Exostratum blumii\"^^xsd:string) or has_Descendant some (Node that tnrs:matchedName value \"Exostratum blumii\"^^xsd:string))))" - }, - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref9", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "nomen cladi conversum, Exostratum blumii (Nees ex Hampe) L. Ellis, Lindbergia 11: 22. (1985)\nStem-based definition:\n\ninternal specifier: Type: Exostratum blumii (Nees ex Hampe) L. Ellis, Lindbergia 11: 22. (1985)\ninternal specifier: Mishler 7/24/98(3), Queensland, Australia (uc)\nexternal specifier: Type: Arthrocormus schimperi (Dozy & Molk.) Dozy & Molk. (= Mielichhoferia schimperi Dozy & Molk.), Musci Frond. Ined. Archip. Ind. 75. (1846)\nIncluded terminal clade:\n\nblumii", - "equivalentClass": { - "@type": "owl:Class", - "intersectionOf": [ - { - "@type": "owl:Class", - "unionOf": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref9_specifier1", - "@type": [ - "owl:Class", - "tbd:InternalSpecifier" - ], - "unionOf": [ - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Exostratum blumii", - "onProperty": "tnrs:matchedName" - } - ] - } - ] - }, - { - "@type": "owl:Restriction", - "onProperty": "obo:CDAO_0000174", - "someValuesFrom": { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref9_specifier1", - "@type": [ - "owl:Class", - "tbd:InternalSpecifier" - ], - "unionOf": [ - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Exostratum blumii", - "onProperty": "tnrs:matchedName" - } - ] - } - ] - } - } - ] - }, - { - "@type": "owl:Restriction", - "onProperty": "phyloref:has_Sibling", - "someValuesFrom": { - "@type": "owl:Class", - "unionOf": { - "@type": "owl:Class", - "unionOf": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref9_specifier3", - "@type": [ - "owl:Class", - "tbd:ExternalSpecifier" - ], - "unionOf": [ - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Arthrocormus schimperi", - "onProperty": "tnrs:matchedName" - } - ] - } - ] - }, - { - "@type": "owl:Restriction", - "onProperty": "obo:CDAO_0000174", - "someValuesFrom": { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref9_specifier3", - "@type": [ - "owl:Class", - "tbd:ExternalSpecifier" - ], - "unionOf": [ - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Arthrocormus schimperi", - "onProperty": "tnrs:matchedName" - } - ] - } - ] - } - } - ] - } - } - } - ] - }, - "externalSpecifiers": [ - { - "dc:description": "Type: Arthrocormus schimperi (Dozy & Molk.) Dozy & Molk. (= Mielichhoferia schimperi Dozy & Molk.), Musci Frond. Ined. Archip. Ind. 75. (1846)", - "tnrs:matchedName": "Arthrocormus schimperi" - } - ], - "hasExternalSpecifier": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref9_specifier3" - } - ], - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref9_specifier1" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref9_specifier1" - }, - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref9_specifier3" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Type: Exostratum blumii (Nees ex Hampe) L. Ellis, Lindbergia 11: 22. (1985)", - "tnrs:matchedName": "Exostratum blumii" - }, - { - "dc:description": "Mishler 7/24/98(3), Queensland, Australia (uc)" - } - ], - "label": "Exostratum", - "manchesterSyntax": "Node and ((Node that tnrs:matchedName value \"Exostratum blumii\"^^xsd:string) or has_Descendant some (Node that tnrs:matchedName value \"Exostratum blumii\"^^xsd:string) and and (has_Sibling some ((Node that tnrs:matchedName value \"Arthrocormus schimperi\"^^xsd:string) or has_Descendant some (Node that tnrs:matchedName value \"Arthrocormus schimperi\"^^xsd:string))))" - }, - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref10", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "nomen cladi conversum, Exodictyon Cardot, Rev. Bryol. Lich\u00c3\u00a9nol. 26: 6. (1899), excl. parte, emend Ellis in Lindbergia 11: 16 (1985)\n\nStem-based definition:\n\ninternal specifier: Type: Exodictyon Cardot, Rev. Bryol. Lich\u00c3\u00a9nol. 26: 6. (1899), excl. parte, emend Ellis in Lindbergia 11: 16 (1985)\ninternal specifier: Wall 2527, Fiji (uc)\nexternal specifier: Type: Leucophanes octoblepharoides Brid., Bryol. Univ. 1: 763. (1826)\nIncluded terminal clade:\n\nincrassatum", - "equivalentClass": { - "@type": "owl:Class", - "intersectionOf": [ - { - "@type": "owl:Class", - "unionOf": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref10_specifier1", - "@type": [ - "owl:Class", - "tbd:InternalSpecifier" - ], - "unionOf": [ - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Exodictyon incrassatum (Mitt.) Cardot", - "onProperty": "tnrs:submittedName" - } - ] - }, - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Exodictyon incrassatum", - "onProperty": "tnrs:matchedName" - } - ] - } - ] - }, - { - "@type": "owl:Restriction", - "onProperty": "obo:CDAO_0000174", - "someValuesFrom": { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref10_specifier1", - "@type": [ - "owl:Class", - "tbd:InternalSpecifier" - ], - "unionOf": [ - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Exodictyon incrassatum (Mitt.) Cardot", - "onProperty": "tnrs:submittedName" - } - ] - }, - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Exodictyon incrassatum", - "onProperty": "tnrs:matchedName" - } - ] - } - ] - } - } - ] - }, - { - "@type": "owl:Restriction", - "onProperty": "phyloref:has_Sibling", - "someValuesFrom": { - "@type": "owl:Class", - "unionOf": { - "@type": "owl:Class", - "unionOf": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref10_specifier2", - "@type": [ - "owl:Class", - "tbd:ExternalSpecifier" - ], - "unionOf": [ - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Leucophanes octoblepharoides", - "onProperty": "tnrs:matchedName" - } - ] - } - ] - }, - { - "@type": "owl:Restriction", - "onProperty": "obo:CDAO_0000174", - "someValuesFrom": { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref10_specifier2", - "@type": [ - "owl:Class", - "tbd:ExternalSpecifier" - ], - "unionOf": [ - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Leucophanes octoblepharoides", - "onProperty": "tnrs:matchedName" - } - ] - } - ] - } - } - ] - } - } - } - ] - }, - "externalSpecifiers": [ - { - "dc:description": "Type: Leucophanes octoblepharoides Brid., Bryol. Univ. 1: 763. (1826)", - "tnrs:matchedName": "Leucophanes octoblepharoides" - } - ], - "hasExternalSpecifier": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref10_specifier2" - } - ], - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref10_specifier1" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref10_specifier1" - }, - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref10_specifier2" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Type: Exodictyon Cardot, Rev. Bryol. Lich\u00c3\u00a9nol. 26: 6. (1899), excl. parte, emend Ellis in Lindbergia 11: 16 (1985) -- Wall 2527, Fiji (uc)", - "tnrs:matchedName": "Exodictyon incrassatum", - "tnrs:submittedName": "Exodictyon incrassatum (Mitt.) Cardot" - } - ], - "label": "Exodictyon", - "manchesterSyntax": "Node and ((Node that tnrs:submittedName value \"Exodictyon incrassatum (Mitt.) Cardot\"^^xsd:string or tnrs:matchedName value \"Exodictyon incrassatum\"^^xsd:string) or has_Descendant some (Node that tnrs:submittedName value \"Exodictyon incrassatum (Mitt.) Cardot\"^^xsd:string or tnrs:matchedName value \"Exodictyon incrassatum\"^^xsd:string) and (has_Sibling some ((Node that tnrs:matchedName value \"Leucophanes octoblepharoides\"^^xsd:string) or has_Descendant some (Node that tnrs:matchedName value \"Leucophanes octoblepharoides\"^^xsd:string))))" - }, - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref11", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "nomen cladi conversum, Leucophanes octoblepharoides Brid., Bryol. Univ. 1: 763. (1826)\n\nStem-based definition:\n\ninternal specifier: Type: Leucophanes octoblepharoides Brid., Bryol. Univ. 1: 763. (1826)\ninternal specifier: Type: Leucophanes seychellarum Besch., Ann. Sci. Nat., Bot., VI, 9: 337. (1880)\nexternal specifier: Wall 2527, Fiji (uc)\nIncluded terminal clades:\n\nconfertus, glaucum, octoblepharoides, seychellarum", - "equivalentClass": { - "@type": "owl:Class", - "intersectionOf": [ - { - "@type": "owl:Class", - "unionOf": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref11_specifier1", - "@type": [ - "owl:Class", - "tbd:InternalSpecifier" - ], - "unionOf": [ - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Leucophanes octoblepharoides", - "onProperty": "tnrs:matchedName" - } - ] - } - ] - }, - { - "@type": "owl:Restriction", - "onProperty": "obo:CDAO_0000174", - "someValuesFrom": { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref11_specifier1", - "@type": [ - "owl:Class", - "tbd:InternalSpecifier" - ], - "unionOf": [ - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Leucophanes octoblepharoides", - "onProperty": "tnrs:matchedName" - } - ] - } - ] - } - } - ] - }, - { - "@type": "owl:Class", - "unionOf": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref11_specifier2", - "@type": [ - "owl:Class", - "tbd:InternalSpecifier" - ], - "unionOf": [ - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Leucophanes seychellarum", - "onProperty": "tnrs:matchedName" - } - ] - } - ] - }, - { - "@type": "owl:Restriction", - "onProperty": "obo:CDAO_0000174", - "someValuesFrom": { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref11_specifier2", - "@type": [ - "owl:Class", - "tbd:InternalSpecifier" - ], - "unionOf": [ - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Leucophanes seychellarum", - "onProperty": "tnrs:matchedName" - } - ] - } - ] - } - } - ] - }, - { - "@type": "owl:Restriction", - "onProperty": "phyloref:has_Sibling", - "someValuesFrom": { - "@type": "owl:Class", - "unionOf": { - "@type": "owl:Class", - "unionOf": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref11_specifier3", - "@type": [ - "owl:Class", - "tbd:ExternalSpecifier" - ], - "unionOf": [ - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Exodictyon incrassatum", - "onProperty": "tnrs:matchedName" - } - ] - } - ] - }, - { - "@type": "owl:Restriction", - "onProperty": "obo:CDAO_0000174", - "someValuesFrom": { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref11_specifier3", - "@type": [ - "owl:Class", - "tbd:ExternalSpecifier" - ], - "unionOf": [ - { - "@type": "owl:Class", - "intersectionOf": [ - { - "@id": "obo:CDAO_0000140" - }, - { - "@type": "owl:Restriction", - "hasValue": "Exodictyon incrassatum", - "onProperty": "tnrs:matchedName" - } - ] - } - ] - } - } - ] - } - } - } - ] - }, - "externalSpecifiers": [ - { - "dc:description": "Wall 2527, Fiji (uc) -- Exodictyon incrassatum (Mitt.) Cardot", - "tnrs:matchedName": "Exodictyon incrassatum" - } - ], - "hasExternalSpecifier": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref11_specifier3" - } - ], - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref11_specifier1" - }, - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref11_specifier2" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref11_specifier1" - }, - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref11_specifier2" - }, - { - "@id": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2#file1_tree1_phyloref11_specifier3" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Type: Leucophanes octoblepharoides Brid., Bryol. Univ. 1: 763. (1826)", - "tnrs:matchedName": "Leucophanes octoblepharoides" - }, - { - "dc:description": "Type: Leucophanes seychellarum Besch., Ann. Sci. Nat., Bot., VI, 9: 337. (1880)", - "tnrs:matchedName": "Leucophanes seychellarum" - } - ], - "label": "Leucophanes", - "manchesterSyntax": "Node and ((Node that tnrs:matchedName value \"Leucophanes octoblepharoides\"^^xsd:string) or has_Descendant some (Node that tnrs:matchedName value \"Leucophanes octoblepharoides\"^^xsd:string) and (Node that tnrs:matchedName value \"Leucophanes seychellarum\"^^xsd:string) or has_Descendant some (Node that tnrs:matchedName value \"Leucophanes seychellarum\"^^xsd:string) and (has_Sibling some ((Node that tnrs:matchedName value \"Exodictyon incrassatum\"^^xsd:string) or has_Descendant some (Node that tnrs:matchedName value \"Exodictyon incrassatum\"^^xsd:string))))" - } - ] - } - ], - "url": "https://doi.org/10.1639/0007-2745%282007%29110%5B46%3APOTCWA%5D2.0.CO%3B2", - "year": 2007 -} \ No newline at end of file diff --git a/testcases/Fisher et al, 2007/reason.py b/testcases/Fisher et al, 2007/reason.py deleted file mode 100644 index 7b71451..0000000 --- a/testcases/Fisher et al, 2007/reason.py +++ /dev/null @@ -1,30 +0,0 @@ -#!/usr/bin/python - -import owlready2 - -owlready2.onto_path.append("C:/Users/Gaurav/code/phyloref/curation-workflow/phylorefs/Fisher et al, 2007") - -# onto = owlready2.get_ontology("file:///Users/Gaurav/code/phyloref/curation-workflow/phylorefs/Fisher et al, 2007/fisher_tweaked.owl") -onto = owlready2.get_ontology("file://./fisher_tweaked.owl") -onto.load(format="rdfxml") - -# Speak CDAO -obo = owlready2.get_ontology("http://purl.obolibrary.org/obo/cdao.owl").load() -cdao = obo.get_namespace("http://purl.obolibrary.org/obo/") -class_Node = cdao.CDAO_0000140 - -# Find me all nodes and all classes they belong to. -nodes = onto.search(is_a = class_Node) - -for node in nodes: - print(" - " + str(node) + ": " + str(node.is_a)) - -with onto: - owlready2.sync_reasoner() - -nodes = onto.search(is_a = class_Node) -for node in nodes: - print(" - " + str(node) + ": " + str(node.is_a)) - - -onto.save("reasoned.nt", format="ntriples") diff --git a/testcases/Hillis and Wilcox, 2005/README.md b/testcases/Hillis and Wilcox, 2005/README.md deleted file mode 100644 index 8b5180b..0000000 --- a/testcases/Hillis and Wilcox, 2005/README.md +++ /dev/null @@ -1,34 +0,0 @@ -# Hillis and Wilcox, 2005 - -* Based on [Hillis and Wilcox, 2005](http://www.sciencedirect.com/science/article/pii/S1055790304003240) - * Tree [available on TreeBase](https://treebase.org/treebase-web/search/study/trees.html?id=1269) - -* Input file: [`paper.json`](paper.json) -* To create ontology: - * `python ../../testcase2owl/testcase2owl.py paper.json -o paper_as_owl.json` - * `rdfpipe -i json-ld paper_as_owl.json -o xml > paper.owl` - * (On Windows, you need to end with `... | Set-Content -Encoding UTF8 hillis_and_wilcox_2005.owl` - -* Output file: `paper.owl` - * This file can be opened in Protege; phyloreferences are instances of the - Phyloreference class, and should contain a single node from which that - clade descends. - -## Current test status - -1. Amerana: **no nodes resolved**. -2. Aquarana: **no nodes resolved**. -3. Lacusirana: **no nodes resolved**. -4. Laurasiarana: **no nodes resolved**. -5. Levirana: resolved correctly. -6. Lithobates: **no nodes resolved**. -7. Nenirana: resolved correctly. -8. Novirana: resolved correctly. -9. Pantherana: **no nodes resolved**. -10. Ranula: resolved correctly. -11. Scurrilirana: **no nodes resolved**. -12. Sierrana: **no nodes resolved**. -13. Stertirana: resolved correctly. -14. Torrentirana: resolved correctly. -15. Trypheropsis: resolved correctly. -16. Zweifelia: resolved correctly. diff --git a/testcases/Hillis and Wilcox, 2005/S1186A3750.treorg b/testcases/Hillis and Wilcox, 2005/S1186A3750.treorg deleted file mode 100644 index 5aa6bb0..0000000 --- a/testcases/Hillis and Wilcox, 2005/S1186A3750.treorg +++ /dev/null @@ -1,75 +0,0 @@ -NEXUS -[File created by TreeBASE: 7/26/07 21:06:31] -[Analysis accession#: S1186A3750] - -BEGIN TREES; - TITLE S1186A3750; - TRANSLATE - 1 Rana_sphenocephela_utricularia, - 2 Rana_chiricahuensis_KU_194419, - 3 Rana_chiricahuensis_KU_194442, - 4 Rana_luteiventris_MVZ191016, - 5 Rana_luteiventris_MVZ225749, - 6 Rana_palmipes_AMNHA118801, - 7 Rana_catesbiana_DMH84R2, - 8 Rana_sylvatica_DMH84R43, - 9 Rana_catesbiana_X12841, - 10 Rana_palmipes_KU204425, - 11 Rana_sp4_AMNH_A_124167, - 12 Rana_pipiens_JSF1119, - 13 Rana_septentrionales, - 14 Rana_sierramadrensis, - 15 Rana_sp5_LACM_146764, - 16 Rana_sp6_LACM_146810, - 17 Rana_pipiens_Y10945, - 18 Rana_subaquavocalis, - 19 Rana_macroglossa_b, - 20 Rana_magnaocularis, - 21 Rana_sp1_QCAZ13219, - 22 Rana_sp2_KU_204420, - 23 Rana_sp3_KU_194559, - 24 Rana_sp7_KU_194492, - 25 Rana_sp8_KU_195346, - 26 Rana_sphenocephela, - 27 Rana_warszewitshii, - 28 Rana_neovolcanica, - 29 Rana_yavapaiensis, - 30 Rana_berlandieri, - 31 Rana_macroglossa, - 32 Rana_spectabilis, - 33 Rana_tarahumarae, - 34 Rana_heckscheri, - 35 Rana_montezumae, - 36 Rana_omiltemana, - 37 Rana_virgatipes, - 38 Rana_temporaria, - 39 Rana_clamitans, - 40 Rana_okaloosae, - 41 Rana_palustris, - 42 Rana_psilonota, - 43 Rana_pustulosa, - 44 Rana_sylvatica, - 45 Rana_vaillanti, - 46 Rana_vibicaria, - 47 Rana_zweifelii, - 48 Rana_areolata, - 49 Rana_cascadae, - 50 Rana_maculata, - 51 Rana_forreri, - 52 Rana_juliani, - 53 Rana_muscosa, - 54 Rana_taylori, - 55 Rana_tlaloci, - 56 Rana_aurora, - 57 Rana_blairi, - 58 Rana_boylii, - 59 Rana_capito, - 60 Rana_grylio, - 61 Rana_sevosa, - 62 Rana_bwana, - 63 Rana_dunni, - 64 Rana_onca, - ; - TREE Tree3378 = [&R] (38,((58,(4,5)),(53,(56,49))),(((44,8),((13,(60,((40,39),(34,(9,7))))),37)),(((50,(46,27)),((((6,10),21),62),(45,52))),((14,((42,47),(33,43))),(((12,17),((63,35),(22,((3,18),2)))),((41,(48,(61,59))),(((32,(36,23)),((((55,28),30),57),(26,1))),(51,(((20,24),((29,64),25)),(((31,19),54),((11,15),16))))))))))); - -END; diff --git a/testcases/Hillis and Wilcox, 2005/T4419-annotated.nexml b/testcases/Hillis and Wilcox, 2005/T4419-annotated.nexml deleted file mode 100644 index 43485e2..0000000 --- a/testcases/Hillis and Wilcox, 2005/T4419-annotated.nexml +++ /dev/null @@ -1,770 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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Napo: Misahuall\u00c3\u00ad" - }, - "ownerInstitutionCode": "KU", - "skos:closeMatch": "https://www.ncbi.nlm.nih.gov/nuccore/AY779211" - }, - "inPhylogeny": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1", - "label": "Rana palmipes KU204425", - "matchedName": [ - "Rana palmipes" - ], - "siblings": [ - "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_node124" - ], - "submittedName": "Rana palmipes KU204425" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_node124", - "@type": [ - [ - "obo:CDAO_0000140", - "owl:Thing" - ] - ], - "children": [], - "hasBasisOfRecord": { - "GenBankID": "AY779210", - "catalogNumber": "A-118801", - "locatedAt": { - "verbatimLocality": "AMNH A-118801: Venezuela: Prov. Amazonas: Neblina Base Camp on R\u00c3\u00ado Mawarinuma" - }, - "ownerInstitutionCode": "AMNH", - "skos:closeMatch": "https://www.ncbi.nlm.nih.gov/nuccore/AY779210" - }, - "inPhylogeny": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1", - "label": "Rana palmipes AMNHA118801", - "matchedName": [ - "Rana palmipes" - ], - "siblings": [ - "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_node123" - ], - "submittedName": "Rana palmipes AMNHA118801" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_node118", - "@type": [ - [ - "obo:CDAO_0000140", - "owl:Thing" - ] - ], - "children": [ - "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_node125", - "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_node126" - ], - "inPhylogeny": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1", - "siblings": [ - "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_node117" - ] - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_node125", - "@type": [ - [ - "obo:CDAO_0000140", - "owl:Thing" - ] - ], - "children": [], - "hasBasisOfRecord": { - "GenBankID": "AY779214", - "catalogNumber": "195299", - "locatedAt": { - "verbatimLocality": "KU 195299: Mexico: Oaxaca: 5.6 mi NE Tapanatepec" - }, - "ownerInstitutionCode": "KU", - "skos:closeMatch": "https://www.ncbi.nlm.nih.gov/nuccore/AY779214" - }, - "inPhylogeny": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1", - "label": "Rana vaillanti", - "matchedName": [ - "Rana vaillanti" - ], - "siblings": [ - "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_node126" - ], - "submittedName": "Rana vaillanti" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_node126", - "@type": [ - [ - "obo:CDAO_0000140", - "owl:Thing" - ] - ], - "children": [], - "hasBasisOfRecord": { - "GenBankID": "AY779215", - "catalogNumber": "60324", - "locatedAt": { - "verbatimLocality": "TNHC 60324: Belize: Cayo District: Little Vaqueros Creek" - }, - "ownerInstitutionCode": "TNHC", - "skos:closeMatch": "https://www.ncbi.nlm.nih.gov/nuccore/AY779215" - }, - "inPhylogeny": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1", - "label": "Rana juliani", - "matchedName": [ - "Rana juliani" - ], - "siblings": [ - "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_node125" - ], - "submittedName": "Rana juliani" - } - ], - "newick": "((((Rana_luteiventris_MVZ225749,Rana_luteiventris_MVZ191016),Rana_boylii),(Rana_muscosa,(Rana_cascadae,Rana_aurora)))Amerana,Rana_temporaria,((((Rana_septentrionales,(((Rana_heckscheri,(Rana_catesbiana_X12841,Rana_catesbiana_DMH84R2)),(Rana_clamitans,Rana_okaloosae)),Rana_grylio)),Rana_virgatipes)Aquarana,(Rana_sylvatica_DMH84R43,Rana_sylvatica)),(((((Rana_pustulosa,Rana_tarahumarae),(Rana_psilonota,Rana_zweifelii))Zweifelia,Rana_sierramadrensis)Torrentirana,(((Rana_palustris,(Rana_areolata,(Rana_capito,Rana_sevosa)))Nenirana,(((((Rana_magnaocularis,Rana_sp7_KU_194492),(Rana_sp8_KU_195346,(Rana_onca,Rana_yavapaiensis))),((Rana_sp6_LACM_146810,(Rana_sp5_LACM_146764,Rana_sp4_AMNH_A_124167)),(Rana_taylori,(Rana_macroglossa,Rana_macroglossa_b)))),Rana_forreri),((Rana_spectabilis,(Rana_sp3_KU_194559,Rana_omiltemana)),((((Rana_tlaloci,Rana_neovolcanica),Rana_berlandieri),Rana_blairi),(Rana_sphenocephela_utricularia,Rana_sphenocephela))))Scurrilirana),((((Rana_chiricahuensis_KU_194419,(Rana_subaquavocalis,Rana_chiricahuensis_KU_194442)),Rana_sp2_KU_204420),(Rana_dunni,Rana_montezumae))Lacusirana,(Rana_pipiens_JSF1119,Rana_pipiens_Y10945))Stertirana)Pantherana),((Rana_maculata,(Rana_warszewitshii,Rana_vibicaria)Trypheropsis)Levirana,((Rana_bwana,(Rana_sp1_QCAZ13219,(Rana_palmipes_KU204425,Rana_palmipes_AMNHA118801))),(Rana_vaillanti,Rana_juliani))Lithobates)Ranula)Sierrana)Novirana);" - } - ], - "phylorefs": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref1", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "Laurasiarana, new clade name. Definition: The clade stemming from the most recent common ancestor of Rana temporaria Linne 1758 and Rana aurora Baird and Girard 1852.", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional1" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref1_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref1_specifier2" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref1_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref1_specifier2" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana temporaria Linne 1758", - "tnrs:matchedName": "Rana temporaria" - }, - { - "dc:description": "Rana aurora Baird and Girard 1852", - "tnrs:matchedName": "Rana aurora" - } - ], - "label": "Laurasiarana" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref2", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "Amerana Dubois 1992 (converted clade name). Definition: The clade stemming from the most recent common ancestor of Rana aurora Baird and Girard 1852, Rana boylii Baird 1854, Rana cascadae Slater 1939, Rana muscosa Camp 1917, and Rana pretiosa Baird and Girard 1853.", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional5" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref2_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref2_specifier2" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref2_specifier3" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref2_specifier4" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref2_specifier5" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref2_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref2_specifier2" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref2_specifier3" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref2_specifier4" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref2_specifier5" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana aurora Baird and Girard 1852", - "tnrs:matchedName": "Rana aurora" - }, - { - "dc:description": "Rana boylii Baird 1854", - "tnrs:matchedName": "Rana boylii" - }, - { - "dc:description": "Rana cascadae Slater 1939", - "tnrs:matchedName": "Rana cascadae" - }, - { - "dc:description": "Rana muscosa Camp 1917", - "tnrs:matchedName": "Rana muscosa" - }, - { - "dc:description": "Rana pretiosa Baird and Girard 1853", - "tnrs:matchedName": "Rana pretiosa" - } - ], - "label": "Amerana" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref3", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "Novirana, new clade name. Definition: The clade stemming from the most recent common ancestor of Rana catesbeiana Shaw 1802 and Rana pipiens Schreber 1782.", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional6" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref3_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref3_specifier2" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref3_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref3_specifier2" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana catesbeiana Shaw 1802", - "tnrs:matchedName": "Rana catesbeiana" - }, - { - "dc:description": "Rana pipiens Schreber 1782", - "tnrs:matchedName": "Rana pipiens" - } - ], - "label": "Novirana" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref4", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "Aquarana Dubois 1992 (converted clade name). Definition: The clade stemming from the most recent common ancestor of Rana catesbeiana Shaw 1802, Rana clamitans Latreille 1802, Rana grylio Stejneger 1901, Rana heckscheri Wright 1924, Rana okaloosae Moler 1985, Rana septentrionalis Baird 1854, and Rana virgatipes Cope1891. The species used in the definition are those species that were included by Dubois within this group.", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional12" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref4_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref4_specifier2" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref4_specifier3" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref4_specifier4" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref4_specifier5" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref4_specifier6" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref4_specifier7" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref4_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref4_specifier2" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref4_specifier3" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref4_specifier4" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref4_specifier5" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref4_specifier6" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref4_specifier7" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana catesbeiana Shaw 1802", - "tnrs:matchedName": "Rana catesbeiana" - }, - { - "dc:description": "Rana clamitans Latreille 1802", - "tnrs:matchedName": "Rana clamitans" - }, - { - "dc:description": "Rana grylio Stejneger 1901", - "tnrs:matchedName": "Rana grylio" - }, - { - "dc:description": "Rana heckscheri Wright 1924", - "tnrs:matchedName": "Rana heckscheri" - }, - { - "dc:description": "Rana okaloosae Moler 1985", - "tnrs:matchedName": "Rana okaloosae" - }, - { - "dc:description": "Rana septentrionalis Baird 1854", - "tnrs:matchedName": "Rana septentrionalis" - }, - { - "dc:description": "Rana virgatipes Cope1891", - "tnrs:matchedName": "Rana virgatipes" - } - ], - "label": "Aquarana" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref5", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "Sierrana Dubois 1992 (converted clade name). Definition: The clade stemming from the most recent common ancestor of Rana julianiHillis and de S\u00c3\u00a1, 1988, Rana maculata Brocchi 1877, and Rana sierramadrensis Taylor 1939.", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional14" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref5_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref5_specifier2" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref5_specifier3" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref5_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref5_specifier2" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref5_specifier3" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana juliani Hillis and de S\u00c3\u00a1, 1988", - "tnrs:matchedName": "Rana juliani" - }, - { - "dc:description": "Rana maculata Brocchi 1877", - "tnrs:matchedName": "Rana maculata" - }, - { - "dc:description": "Rana sierramadrensis Taylor 1939", - "tnrs:matchedName": "Rana sierramadrensis" - } - ], - "label": "Sierrana" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref6", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "Ranula Peters 1859 (converted clade name). Definition: The clade stemming from the most recent common ancestor of Rana palmipes Spix 1824 and Rana warszewitschii (Schmidt) 1857.", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional15" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref6_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref6_specifier2" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref6_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref6_specifier2" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana palmipes Spix 1824", - "tnrs:matchedName": "Rana palmipes" - }, - { - "dc:description": "Rana warszewitschii (Schmidt) 1857", - "tnrs:matchedName": "Rana warszewitschii" - } - ], - "label": "Ranula" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref7", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "Levirana Cope 1894 (converted clade name). Definition: The clade stemming from the most recent common ancestor of Rana maculata Brocchi 1877 and Rana vibicaria (Cope) 1894.", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional16" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref7_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref7_specifier2" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref7_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref7_specifier2" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana maculata Brocchi 1877", - "tnrs:matchedName": "Rana maculata" - }, - { - "dc:description": "Rana vibicaria (Cope) 1894", - "tnrs:matchedName": "Rana vibicaria" - } - ], - "label": "Levirana" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref8", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "Trypheropsis Cope 1868 (converted clade name). Definition: The clade stemming from the most recent common ancestor of Rana warszewitschii (Schmidt) 1857 and Rana vibicaria (Cope) 1894.", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional17" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref8_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref8_specifier2" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref8_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref8_specifier2" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana warszewitschii (Schmidt) 1857", - "tnrs:matchedName": "Rana warszewitschii" - }, - { - "dc:description": "Rana vibicaria (Cope) 1894", - "tnrs:matchedName": "Rana vibicaria" - } - ], - "label": "Trypheropsis" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref9", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "Lithobates Fitzinger 1843 (converted clade name). Definition: The clade stemming from the most recent common ancestor of Rana palmipes Spix 1824, Rana vaillanti Brocchi 1877, Rana bwanaHillis and de S\u00c3\u00a1 1988, and Rana julianiHillis and de S\u00c3\u00a1 1988.", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional20" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref9_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref9_specifier2" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref9_specifier3" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref9_specifier4" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref9_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref9_specifier2" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref9_specifier3" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref9_specifier4" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana palmipes Spix 1824", - "tnrs:matchedName": "Rana palmipes" - }, - { - "dc:description": "Rana vaillanti Brocchi 1877", - "tnrs:matchedName": "Rana vaillanti" - }, - { - "dc:description": "Rana bwana Hillis and de S\u00c3\u00a1 1988", - "tnrs:matchedName": "Rana bwana" - }, - { - "dc:description": "Rana juliani Hillis and de S\u00c3\u00a1 1988", - "tnrs:matchedName": "Rana juliani" - } - ], - "label": "Lithobates" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref10", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "Torrentirana, new clade name. Definition: The clade stemming from the most recent common ancestor of Rana tarahumarae Boulenger 1917 and Rana sierramadrensis Taylor 1939", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional21" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref10_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref10_specifier2" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref10_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref10_specifier2" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana tarahumarae Boulenger 1917", - "tnrs:matchedName": "Rana tarahumarae" - }, - { - "dc:description": "Rana sierramadrensis Taylor 1939", - "tnrs:matchedName": "Rana sierramadrensis" - } - ], - "label": "Torrentirana" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref11", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "Zweifelia Dubois 1992 (converted clade name). Definition: The clade stemming from the most recent common ancestor of Rana tarahumarae Boulenger 1917 and Rana zweifeli Hillis, Frost and Webb 1984.", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional22" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref11_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref11_specifier2" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref11_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref11_specifier2" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana tarahumarae Boulenger 1917", - "tnrs:matchedName": "Rana tarahumarae" - }, - { - "dc:description": "Rana zweifeli Hillis, Frost and Webb 1984", - "tnrs:matchedName": "Rana zweifeli" - } - ], - "label": "Zweifelia" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref12", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "Pantherana Dubois 1992 (converted clade name). Definition: The clade stemming from the most recent common ancestor of Rana pipiens Schreber 1782, Rana montezumae Baird 1854, Rana palustris LeConte 1825, and Rana berlandieri Baird 1854.", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional25" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref12_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref12_specifier2" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref12_specifier3" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref12_specifier4" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref12_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref12_specifier2" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref12_specifier3" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref12_specifier4" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana pipiens Schreber 1782", - "tnrs:matchedName": "Rana pipiens" - }, - { - "dc:description": "Rana montezumae Baird 1854", - "tnrs:matchedName": "Rana montezumae" - }, - { - "dc:description": "Rana palustris LeConte 1825", - "tnrs:matchedName": "Rana palustris" - }, - { - "dc:description": "Rana berlandieri Baird 1854", - "tnrs:matchedName": "Rana berlandieri" - } - ], - "label": "Pantherana" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref13", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "dc:description": "Stertirana, new clade name. Definition: The clade stemming from the most recent common ancestor of Rana pipiens Schreber 1782 and Rana montezumae Baird 1854. Etymology: From the Latin words sterto, meaning ``snore,'' and rana, meaning ``frog,'' in reference to the snore-like element of the advertisement call of the frogs in this group. Content: Includes R. pipiens and the species in Lacusirana (see below). Type species: Rana montezumae Baird 1854.", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional26" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref13_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref13_specifier2" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref13_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref13_specifier2" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana pipiens Schreber 1782", - "tnrs:matchedName": "Rana pipiens" - }, - { - "dc:description": "Rana montezumae Baird 1854", - "tnrs:matchedName": "Rana montezumae" - } - ], - "label": "Stertirana" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref14", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "Lacusirana, new clade name. Definition: The clade stemming from the most recent common ancestor of Rana montezumae Baird 1854, R. megapoda Taylor 1942, and Rana chiricahuensis Platz and Mecham 1979. Etymology: From the Latin words lacus, meaning ``lake,'' and rana, meaning ``frog,'' in reference to the habitat of most of the species in this group. Content: In addition to the species named in the definition, this clade contains Rana dunni Zweifel 1957, Rana megapoda Taylor 1942, Rana subaquavocalis Platz 1993, Rana lemosespinaliSmith and Chiszar 2003, and a least one undescribed species from the Mexican Plateau (species 2 in Figs. 1, 2). In addition, we place Rana fisheri Stejneger 1893 in this clade based on morphological similarity. Type species: R. megapoda Taylor 1942.", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional28" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref14_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref14_specifier2" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref14_specifier3" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref14_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref14_specifier2" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref14_specifier3" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana montezumae Baird 1854", - "tnrs:matchedName": "Rana montezumae" - }, - { - "dc:description": "R. megapoda Taylor 1942", - "tnrs:matchedName": "Rana megapoda" - }, - { - "dc:description": "Rana chiricahuensis Platz and Mecham 1979", - "tnrs:matchedName": "Rana chiricahuensis" - } - ], - "label": "Lacusirana" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref15", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "Nenirana, new clade name. Definition: The clade stemming from the most recent common ancestor of Rana areolata Baird and Girard 1852 and Rana palustris Le Conte 1825. Etymology: From the Latin words nenia, meaning ``a funeral song,'' and rana, meaning ``frog,'' in reference to the low, mournful advertisement call of the species in this clade. Content: In addition to the species specified in the definition, this clade includes Rana capito LeConte 1855 and Rana sevosa Goin and Netting 1940. Hillis et al. (1983) informally termed this clade the R. areolata group. Type species: Rana areolata Baird and Girard 1852.", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional29" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref15_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref15_specifier2" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref15_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref15_specifier2" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana areolata Baird and Girard 1852", - "tnrs:matchedName": "Rana areolata" - }, - { - "dc:description": "Rana palustris Le Conte 1825", - "tnrs:matchedName": "Rana palustris" - } - ], - "label": "Nenirana" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref16", - "@type": [ - [ - "phyloref:Phyloreference", - "owl:Class" - ] - ], - "description": "Scurrilirana, new clade name. Definition: The clade stemming from the most recent common ancestor of Rana berlandieri Baird 1854, Rana sphenocephala Cope 1886, Rana forreri Boulenger 1883, R. spectabilisHillis and Frost 1985, Rana omiltemana Gunther 1900, Rana taylori Smith 1959, and Rana magnaocularis Frost and Bagnara 1976. Etymology: From the Latin words scurrilis, meaning ``jesting,'' and rana, meaning ``frog,'' in reference to the advertisement calls of most of the species in this clade, which sound like chuckling laughter. Content: In addition to the species specified in the definition, this clade includes Rana blairi Mecham, Littlejohn, Oldham, Brown, and Brown 1973, Rana chichicuahutlaCuellar et al., 1996, Rana macroglossa Brocchi 1877, Rana miadis Barbour and Loveridge 1929, Rana neovolcanicaHillis and Frost, 1985, Rana onca Cope in Yarrow 1875, Rana tlalociHillis and Frost, 1985, Rana yavapaiensis Platz and Frost 1984, and several undescribed species (species 3\u00e2\u20ac\u201c8) in Mexico and Central America. Hillis et al. (1983) informally termed this clade the beta division of the R. pipiens complex. Type species: Rana berlandieri Baird 1854.", - "equivalentClass": { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_additional35" - }, - "hasInternalSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref16_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref16_specifier2" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref16_specifier3" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref16_specifier4" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref16_specifier5" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref16_specifier6" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref16_specifier7" - } - ], - "hasSpecifier": [ - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref16_specifier1" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref16_specifier2" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref16_specifier3" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref16_specifier4" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref16_specifier5" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref16_specifier6" - }, - { - "@id": "https://doi.org/10.1016/j.ympev.2004.10.007#file2_tree1_phyloref16_specifier7" - } - ], - "internalSpecifiers": [ - { - "dc:description": "Rana berlandieri Baird 1854", - "tnrs:matchedName": "Rana berlandieri" - }, - { - "dc:description": "Rana sphenocephala Cope 1886", - "tnrs:matchedName": "Rana sphenocephala" - }, - { - "dc:description": "Rana forreri Boulenger 1883", - "tnrs:matchedName": "Rana forreri" - }, - { - "dc:description": "R. spectabilis Hillis and Frost 1985", - "tnrs:matchedName": "Rana spectabilis" - }, - { - "dc:description": "Rana omiltemana Gunther 1900", - "tnrs:matchedName": "Rana omiltemana" - 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"labeled_json", - [phylorefs_path + "/" + path + "/labeled.json" for path in dirs] + "paper_as_owl_json", + [phylorefs_path + "/" + path + "/paper_as_owl.json" for path in dirs] ) if "paper_owl" in metafunc.fixturenames: diff --git a/tests/test_json2owl.py b/tests/test_json2owl.py index 68bbc21..6adac60 100644 --- a/tests/test_json2owl.py +++ b/tests/test_json2owl.py @@ -10,22 +10,22 @@ @pytest.mark.json def test_json_to_owl(paper_json): - """ Convert paper.json file to paper.owl via labeled.owl. """ + """ Convert paper.json file to paper.owl via paper_as_owl.json. """ path = paper_json[:-11] # Switch to the path of the JSON file. current_path = os.getcwd() os.chdir(path) - # Run testcase2owl.py and rdfpipe; in case of exceptions or non-zero exit values, + # Run phyx2owl.py and rdfpipe; in case of exceptions or non-zero exit values, # report any error as a failed test. try: - output_str = subprocess.check_output('python ../../testcase2owl/testcase2owl.py paper.json -o paper_as_owl.json', + output_str = subprocess.check_output('python ../../phyx2owl/phyx2owl.py paper.json -o paper_as_owl.json', shell=True, stderr=subprocess.STDOUT ).decode('utf-8') - # Will only be run if testcase2owl.py returned zero! + # Will only be run if phyx2owl.py returned zero! assert os.system('rdfpipe -i json-ld -o xml paper_as_owl.json > paper.owl') == 0 except subprocess.CalledProcessError as err: @@ -34,13 +34,13 @@ def test_json_to_owl(paper_json): finally: os.chdir(current_path) - # Did testcase2owl report any errors? + # Did phyx2owl report any errors? if 'ERROR' in output_str: - pytest.fail(u"testcase2owl.py failed: " + output_str) + pytest.fail(u"phyx2owl.py failed: " + output_str) - # Did testcase2owl report any warnings? + # Did phyx2owl report any warnings? if 'WARNING' in output_str: - warnings.warn(u"testcase2owl.py reported warnings: " + output_str) + warnings.warn(u"phyx2owl.py reported warnings: " + output_str) @pytest.mark.owl def test_owl_to_rdf(paper_owl):