Hello! This looks like an interesting tool, and I would like to take a shot at providing it (and all its platform-specific builds) on conda-forge. We'd be able to support building the "big three" x86-64 platforms, as well as some additional ones, for modern pythons (e.g. 3.8+).

Like a lot of "system-style" package managers, conda-forge prefer to use a "canonical" source distribution (such as a .tar.gz uploaded to PyPI). Lacking that, a GitHub release tarball is usually fine, but the cryptography sums can change over time. So the big request here is either:

• upload an sdist to go with the .whl
• add a tag for when 0.2.1 was shipped

And:

• add an explicit LICENSE to the repo (and probably as-released metadata)

If broader distribution is interesting to the maintainers of this package, we always love to have upstream maintainers join the maintainer team, but certainly not required! Once everything "works," it's mostly a matter of pressing "merge" on automated PRs that update version numbers and crypto hashes when new upstream releases come out.

Thanks again!

It looks like axiom annotations are not included.

it would be good to decide in advance how this should be stored with the current pseudo-lisp datastructures. Functional syntax and owlx place annotations as the first argument which is IMHO weird and may be particularly hard to work with using the current untyped structures.

I think the best options are:

• break with s-expressions and use a mixed dict/list structure
• place axiom annotations as the last argument, and ALWAYS include them, even if [], that way the s-expressions can be evaluated unambiguously

I tried to load a number of disjointness axioms using py-horned-owl, but the resulting disjointness axioms do not contain the target class:

>>> onto_dis = pyhornedowl.open_ontology("chebi-disjoints.owl")
>>> onto_dis.get_axioms_for_iri("http://purl.obolibrary.org/obo/CHEBI_15356")
['AxiomKind::DisjointClasses']

what I would expect is something like

['AxiomKind::DisjointClasses', 'http://purl.obolibrary.org/obo/CHEBI_23509']

Motivation: I would like to use the Rust version of @balhoff's Whelk, whelk.rs

Previously I was thinking the way to go would be to write a pyo3 wrapper onto whelk.rs. However, it may make more sense to have a generic wrapper for reasoners, with py-horned-owl providing the interface, just as there is one reasoner API for the OWLAPI

(it might be nice to have some features the owlapi ones lack though, that give access to some of the neater features of whelk)

Hello @jannahastings,

I built some windows wheels using github actions. One can find them here: https://github.com/Eugenio2192/py-horned-owl/releases
I did them using a branch of your latest release and the development version of https://github.com/phillord/horned-owl
I have been using them and so far they have been working properly.

I could adapt this github action: https://github.com/Eugenio2192/py-horned-owl/blob/build/.github/workflows/build.yml to what you consider apropiate for release.

AFAICT there is no datatype info on literals, and no way to determine if the value is a node or a literal when it stringifies as a URL

E.g. in GO:

['AxiomKind::AnnotationAssertion', 'http://purl.obolibrary.org/obo/GO_0019098', 'http://purl.obolibrary.org/obo/IAO_0000233', 'https://github.com/geneontology/go-ontology/issues/23491']

is the last argument a node, a plain literal, a string, an xsd:anyURI...?

Looks like it is intentionally conflating these:

I suggest an additional argument for literals

This probably belongs to the horned-owl itself but I discovered it here so I write it here first in case you find a root cause in this library.

So I have been using this in parallel with ROBOT to try out some automatic checks and I noticed that if I read a owx file written by ROBOT(OWLAPI) and then read it in into py-horned-owl and then save it without altering it I get an inconsistency that makes the file not undestandable by OWLAPI. The xml Namespaces are not appearing. See this example:

This is the header of the output of OWLAPI:

<?xml version="1.0"?>
<Ontology xmlns="http://www.w3.org/2002/07/owl#"
     xml:base="http://openenergy-platform.org/ontology/oeo/oeo-physical/"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     ontologyIRI="http://openenergy-platform.org/ontology/oeo/oeo-physical/"
     versionIRI="http://openenergy-platform.org/ontology/oeo/dev/oeo-physical.omn">
    <Prefix name="owl" IRI="http://www.w3.org/2002/07/owl#"/>
    <Prefix name="rdf" IRI="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
    <Prefix name="xml" IRI="http://www.w3.org/XML/1998/namespace"/>
    <Prefix name="xsd" IRI="http://www.w3.org/2001/XMLSchema#"/>
    <Prefix name="rdfs" IRI="http://www.w3.org/2000/01/rdf-schema#"/>

This is the output of horned-owl:

<?xml version="1.0"?>
<Ontology xmlns="http://www.w3.org/2002/07/owl#">
    <Prefix name="owl" IRI="http://www.w3.org/2002/07/owl#"/>
    <Prefix name="rdf" IRI="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
    <Prefix name="xml" IRI="http://www.w3.org/XML/1998/namespace"/>
    <Prefix name="xsd" IRI="http://www.w3.org/2001/XMLSchema#"/>
    <Prefix name="rdfs" IRI="http://www.w3.org/2000/01/rdf-schema#"/>

When I try to convert this last version to something else using OWLAPI I get an empty file.

I don't see the generation of these Namespaces happening anywhere here:

https://github.com/phillord/horned-owl/blob/e33ea9e98df83773ddead0bbe438955690b6b73c/src/io/owx/writer.rs#L228

So the root cause may be there. If you think the same I can just bring this issue to @phillord

Currently the library is not build for ARM architecture and hence not available for use on e.g. M2 Macs.

https://jannahastings.github.io/py-horned-owl/generated/pyhornedowl.open_ontology.html#pyhornedowl.open_ontology

Says "Only .owl and .owx files are currently supported."

.owl could be any syntax, but it looks like this means OWL layered as RDF/XML.

Are there any plans to support other syntaxes? I believe these are supported in the rust layer.

https://github.com/phillord/horned-owl/tree/main/src/io/ofn

For saving, only .owx is supprted:

https://jannahastings.github.io/py-horned-owl/generated/pyhornedowl.PyIndexedOntology.html#pyhornedowl.PyIndexedOntology.save_to_file