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Documents authored by Balhoff, James P.

Artifact
Software
DOI: 10.4230/artifacts.22615
Whelk reasoner

Authors: James P. Balhoff and Christopher J. Mungall

Abstract
Cite as

James P. Balhoff, Christopher J. Mungall. Whelk reasoner (Software, Source code). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@misc{dagpub-supp--paper-21724-urlgithub.com-INCATools-whelk,
   title = {{Whelk reasoner}}, 
   author = {Balhoff, James P. and Mungall, Christopher J.},
   note = {Software, version 1.2.1., swhId: \href{https://archive.softwareheritage.org/swh:1:dir:f8919707e053212b2c74bc63988a06ffe03fb796;origin=https://github.com/INCATools/whelk;visit=swh:1:snp:900616057d4dbe7b6bcfee048b79dd78b399df31;anchor=swh:1:rev:6186eaa434399203d6fad9ff47d0e0df61acb98c}{\texttt{swh:1:dir:f8919707e053212b2c74bc63988a06ffe03fb796}} (visited on 2024-12-18)},
   url = {https://github.com/INCATools/whelk},
   doi = {10.4230/artifacts.22615},
}
Artifact
Software
DOI: 10.4230/artifacts.22530
Horned-OWL

Authors: Phillip Lord, Björn Gehrke, Martin Larralde, Janna Hastings, Filippo De Bortoli, James A. Overton, James P. Balhoff, and Jennifer Warrender

Abstract
Cite as

Phillip Lord, Björn Gehrke, Martin Larralde, Janna Hastings, Filippo De Bortoli, James A. Overton, James P. Balhoff, Jennifer Warrender. Horned-OWL (Software, Source Code). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@misc{dagstuhl-artifact-22530,
   title = {{Horned-OWL}}, 
   author = {Lord, Phillip and Gehrke, Bj\"{o}rn and Larralde, Martin and Hastings, Janna and De Bortoli, Filippo and Overton, James A. and Balhoff, James P. and Warrender, Jennifer},
   note = {Software (visited on 2024-12-18)},
   url = {https://github.com/phillord/horned-owl},
   doi = {10.4230/artifacts.22530},
}
Document
Resource Paper
DOI: 10.4230/TGDK.2.2.7
Whelk: An OWL EL+RL Reasoner Enabling New Use Cases

Authors: James P. Balhoff and Christopher J. Mungall

Published in: TGDK, Volume 2, Issue 2 (2024): Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 2, Issue 2

Abstract
Many tasks in the biosciences rely on reasoning with large OWL terminologies (Tboxes), often combined with even larger databases. In particular, a common task is retrieval queries that utilize relational expressions; for example, “find all genes expressed in the brain or any part of the brain”. Automated reasoning on these ontologies typically relies on scalable reasoners targeting the EL subset of OWL, such as ELK. While the introduction of ELK has been transformative in the incorporation of reasoning into bio-ontology quality control and production pipelines, we have encountered limitations when applying it to use cases involving high throughput query answering or reasoning about datasets describing instances (Aboxes). Whelk is a fast OWL reasoner for combined EL+RL reasoning. As such, it is particularly useful for many biological ontology tasks, particularly those characterized by large Tboxes using the EL subset of OWL, combined with Aboxes targeting the RL subset of OWL. Whelk is implemented in Scala and utilizes immutable functional data structures, which provides advantages when performing incremental or dynamic reasoning tasks. Whelk supports querying complex class expressions at a substantially greater rate than ELK, and can answer queries or perform incremental reasoning tasks in parallel, enabling novel applications of OWL reasoning.
Cite as

James P. Balhoff and Christopher J. Mungall. Whelk: An OWL EL+RL Reasoner Enabling New Use Cases. In Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 2, pp. 7:1-7:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{balhoff_et_al:TGDK.2.2.7,
  author =	{Balhoff, James P. and Mungall, Christopher J.},
  title =	{{Whelk: An OWL EL+RL Reasoner Enabling New Use Cases}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{7:1--7:17},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.2.7},
  URN =		{urn:nbn:de:0030-drops-225918},
  doi =		{10.4230/TGDK.2.2.7},
  annote =	{Keywords: Web Ontology Language, OWL, Semantic Web, ontology, reasoner}
}
Document
Resource Paper
DOI: 10.4230/TGDK.2.2.9
Horned-OWL: Flying Further and Faster with Ontologies

Authors: Phillip Lord, Björn Gehrke, Martin Larralde, Janna Hastings, Filippo De Bortoli, James A. Overton, James P. Balhoff, and Jennifer Warrender

Published in: TGDK, Volume 2, Issue 2 (2024): Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 2, Issue 2

Abstract
Horned-OWL is a library implementing the OWL2 specification in the Rust language. As a library, it is aimed at processes and manipulation of ontologies, rather than supporting GUI development; this is reflected heavily in its design, which is for performance and pluggability; it builds on the Rust idiom, treating an ontology as a standard Rust collection, meaning it can take direct advantage of the data manipulation capabilities of the Rust standard library. The core library consists of a data model implementation as well as an IO framework supporting many common formats for OWL: RDF, XML and the OWL functional syntax; there is an extensive test library to ensure compliance to the specification. In addition to the core library, Horned-OWL now supports a growing ecosystem: the py-horned-owl library provides a Python front-end for Horned-OWL, ideal for scripting ontology manipulation; whelk-rs provides reasoning services; and horned-bin provides a number of command line tools. The library itself is now mature, supporting the entire OWL2 specification, in addition to SWRL rules, and the ecosystem is emerging into one of the most extensive for manipulation of OWL ontologies.
Cite as

Phillip Lord, Björn Gehrke, Martin Larralde, Janna Hastings, Filippo De Bortoli, James A. Overton, James P. Balhoff, and Jennifer Warrender. Horned-OWL: Flying Further and Faster with Ontologies. In Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 2, pp. 9:1-9:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{lord_et_al:TGDK.2.2.9,
  author =	{Lord, Phillip and Gehrke, Bj\"{o}rn and Larralde, Martin and Hastings, Janna and De Bortoli, Filippo and Overton, James A. and Balhoff, James P. and Warrender, Jennifer},
  title =	{{Horned-OWL: Flying Further and Faster with Ontologies}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{9:1--9:14},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.2.9},
  URN =		{urn:nbn:de:0030-drops-225932},
  doi =		{10.4230/TGDK.2.2.9},
  annote =	{Keywords: Web Ontology Language, OWL, Semantic Web}
}
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