9 Search Results for "Bateman, John"

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
Position
DOI: 10.4230/TGDK.1.1.5
Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities

Authors: Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.
Cite as

Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma. Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 5:1-5:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{chen_et_al:TGDK.1.1.5,
  author =	{Chen, Jiaoyan and Dong, Hang and Hastings, Janna and Jim\'{e}nez-Ruiz, Ernesto and L\'{o}pez, Vanessa and Monnin, Pierre and Pesquita, Catia and \v{S}koda, Petr and Tamma, Valentina},
  title =	{{Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{5:1--5:33},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.5},
  URN =		{urn:nbn:de:0030-drops-194791},
  doi =		{10.4230/TGDK.1.1.5},
  annote =	{Keywords: Knowledge graphs, Life science, Knowledge discovery, Explainable AI}
}
Document
Invited Talk
DOI: 10.4230/OASIcs.CMN.2016.1
From Narrative to Visual Narrative to Audiovisual Narrative: the Multimodal Discourse Theory Connection (Invited Talk)

Authors: John A. Bateman

Published in: OASIcs, Volume 53, 7th Workshop on Computational Models of Narrative (CMN 2016)

Abstract
Models of narrative have been proposed from many perspectives and most of these nowadays promote further the notion that narrative is a transmedial phenomenon: i.e., stories can be told making use of distinct and multiple forms of expressions. This raises a range of theoretical and practical questions, as well as rendering the task of providing computational models of narrative both more interesting and more challenging. Central to this endeavour are issues concerned with the potential mutual conditioning of narrative forms and the media employed. Methods are required for isolating narrative properties and mechanisms that may be generalised across media, while at the same time appropriately respecting differences in medial affordances. In this discussion paper I set out a corresponding approach to characterising narrative that draws on a fine-grained formal characterisation of multimodal discourse developed on the basis of both functional and formal linguistic models of discourse, generalised to the multimodal case. After briefly setting out the theoretical principles on which the account builds, I position narrative with respect to the framework and give an example of how audiovisual narratives such as film are accounted for. It will be suggested that a common anchoring in a well specified notion of discourse as an intrinsically multimodal phenomenon offers beneficial new angles on how narratives can be modelled, as well as establishing bridges between humanistic understandings of narrative and complementary computational accounts of narratives involving communicative goal-based planning.
Cite as

John A. Bateman. From Narrative to Visual Narrative to Audiovisual Narrative: the Multimodal Discourse Theory Connection (Invited Talk). In 7th Workshop on Computational Models of Narrative (CMN 2016). Open Access Series in Informatics (OASIcs), Volume 53, pp. 1:1-1:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@InProceedings{bateman:OASIcs.CMN.2016.1,
  author =	{Bateman, John A.},
  title =	{{From Narrative to Visual Narrative to Audiovisual Narrative: the Multimodal Discourse Theory Connection}},
  booktitle =	{7th Workshop on Computational Models of Narrative (CMN 2016)},
  pages =	{1:1--1:11},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-020-0},
  ISSN =	{2190-6807},
  year =	{2016},
  volume =	{53},
  editor =	{Miller, Ben and Lieto, Antonio and Ronfard, R\'{e}mi and Ware, Stephen G. and Finlayson, Mark A.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.CMN.2016.1},
  URN =		{urn:nbn:de:0030-drops-67028},
  doi =		{10.4230/OASIcs.CMN.2016.1},
  annote =	{Keywords: Narrative, computational modelling, discourse, multimodality}
}
Document
DOI: 10.4230/DagSemProc.10131.1
10131 Executive Summary and Abstracts Collection – Spatial Representation and Reasoning in Language: Ontologies and Logics of Space

Authors: John Bateman, Anthony G. Cohn, and James Pustejovsky

Published in: Dagstuhl Seminar Proceedings, Volume 10131, Spatial Representation and Reasoning in Language : Ontologies and Logics of Space (2011)

Abstract
The goal of this seminar was to bring together researchers from diverse disciplines to address the spatial semantics of natural language, the interface between spatial semantics and geospatial representations, and the role of ontologies in reasoning about spatial concepts in language and thought.
Cite as

John Bateman, Anthony G. Cohn, and James Pustejovsky. 10131 Executive Summary and Abstracts Collection – Spatial Representation and Reasoning in Language: Ontologies and Logics of Space. In Spatial Representation and Reasoning in Language : Ontologies and Logics of Space. Dagstuhl Seminar Proceedings, Volume 10131, pp. 1-14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2011)

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@InProceedings{bateman_et_al:DagSemProc.10131.1,
  author =	{Bateman, John and Cohn, Anthony G. and Pustejovsky, James},
  title =	{{10131 Executive Summary and Abstracts Collection – Spatial Representation and Reasoning in Language: Ontologies and Logics of Space}},
  booktitle =	{Spatial Representation and Reasoning in Language : Ontologies and Logics of Space},
  pages =	{1--14},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2011},
  volume =	{10131},
  editor =	{John A. Bateman and Anthony G. Cohn and James Pustejovsky},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10131.1},
  URN =		{urn:nbn:de:0030-drops-29216},
  doi =		{10.4230/DagSemProc.10131.1},
  annote =	{Keywords: Language of space, spatial ontologies, reasoning about space and time, mapping language to GIS}
}
Document
DOI: 10.4230/DagSemProc.10131.2
How can spatial language be learned?

Authors: Kenneth D. Forbus

Published in: Dagstuhl Seminar Proceedings, Volume 10131, Spatial Representation and Reasoning in Language : Ontologies and Logics of Space (2011)

Abstract
How languages are learned is one of the deepest mysteries of cognitive science. This question can be addressed from multiple perspectives. This position paper considers two of them: (1) How do people learn spatial language? (2) Given the wide range of spatial terms in language, how might we bootstrap the linguistic capabilities of intelligent systems that need spatial language to achieve wide and accurate coverage? We discuss each question in turn.
Cite as

Kenneth D. Forbus. How can spatial language be learned?. In Spatial Representation and Reasoning in Language : Ontologies and Logics of Space. Dagstuhl Seminar Proceedings, Volume 10131, pp. 1-3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2011)

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@InProceedings{forbus:DagSemProc.10131.2,
  author =	{Forbus, Kenneth D.},
  title =	{{How can spatial language be learned?}},
  booktitle =	{Spatial Representation and Reasoning in Language : Ontologies and Logics of Space},
  pages =	{1--3},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2011},
  volume =	{10131},
  editor =	{John A. Bateman and Anthony G. Cohn and James Pustejovsky},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10131.2},
  URN =		{urn:nbn:de:0030-drops-27336},
  doi =		{10.4230/DagSemProc.10131.2},
  annote =	{Keywords: Sketch understanding, analogy, spatial language, spatial reasoning}
}
Document
DOI: 10.4230/DagSemProc.10131.3
How should depiction be represented and reasoned about?

Authors: Kenneth D. Forbus

Published in: Dagstuhl Seminar Proceedings, Volume 10131, Spatial Representation and Reasoning in Language : Ontologies and Logics of Space (2011)

Abstract
Interpreting a scene requires understanding how its visual properties and context yield evidence about the spatial and conceptual properties of what it depicts. Depiction is intimately tied to spatial language, since describing a scene linguistically, or imagining a scene described in language, involves connecting linguistic and spatial knowledge. We focus here on scenes described via sketching.
Cite as

Kenneth D. Forbus. How should depiction be represented and reasoned about?. In Spatial Representation and Reasoning in Language : Ontologies and Logics of Space. Dagstuhl Seminar Proceedings, Volume 10131, pp. 1-3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2011)

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@InProceedings{forbus:DagSemProc.10131.3,
  author =	{Forbus, Kenneth D.},
  title =	{{How should depiction be represented and reasoned about?}},
  booktitle =	{Spatial Representation and Reasoning in Language : Ontologies and Logics of Space},
  pages =	{1--3},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2011},
  volume =	{10131},
  editor =	{John A. Bateman and Anthony G. Cohn and James Pustejovsky},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10131.3},
  URN =		{urn:nbn:de:0030-drops-27318},
  doi =		{10.4230/DagSemProc.10131.3},
  annote =	{Keywords: Sketch understanding, analogy, spatial language, spatial reasoning}
}
Document
DOI: 10.4230/DagSemProc.10131.4
Interpreting Place Descriptions for Navigation Services

Authors: Yunhui Wu and Stephan Winter

Published in: Dagstuhl Seminar Proceedings, Volume 10131, Spatial Representation and Reasoning in Language : Ontologies and Logics of Space (2011)

Abstract
We see a need for research bringing spatial intelligence into the fundamental mechanisms of parsing and interpreting place descriptions. An intelligent navigation service will have capabilities to imitate human route communication behavior (Winter and Wu, 2009), thus, at least the capabilities to make sense of place descriptions.
Cite as

Yunhui Wu and Stephan Winter. Interpreting Place Descriptions for Navigation Services. In Spatial Representation and Reasoning in Language : Ontologies and Logics of Space. Dagstuhl Seminar Proceedings, Volume 10131, pp. 1-3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2011)

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@InProceedings{wu_et_al:DagSemProc.10131.4,
  author =	{Wu, Yunhui and Winter, Stephan},
  title =	{{Interpreting Place Descriptions for Navigation Services}},
  booktitle =	{Spatial Representation and Reasoning in Language : Ontologies and Logics of Space},
  pages =	{1--3},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2011},
  volume =	{10131},
  editor =	{John A. Bateman and Anthony G. Cohn and James Pustejovsky},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10131.4},
  URN =		{urn:nbn:de:0030-drops-27302},
  doi =		{10.4230/DagSemProc.10131.4},
  annote =	{Keywords: Place descriptions, natural language, navigation}
}
Document
DOI: 10.4230/DagSemProc.10131.5
The Creeping Virtuality of Place

Authors: Inderjeet Mani

Published in: Dagstuhl Seminar Proceedings, Volume 10131, Spatial Representation and Reasoning in Language : Ontologies and Logics of Space (2011)

Abstract
Places are inherently dynamic. They also mediate between entities and events of significance to us, and space. They reflect a network of associations, involving landmarks deemed salient for various reasons. These are all properties assigned to a place by a speaker, and may or may not correspond to the properties assigned to a place by any other speaker. As a result, places have a subjective quality. These properties of dynamicity and subjectivity present interesting challenges when producing mashups that align different data sources. I propose addressing this by assuming that entities, following Hornsby & Egenhofer (2000), have histories, namely sequences of time intervals when they are predicated to exist. Places are entities with spatial properties that include topological relationships to other places, represented in terms of RCC-8 or the 9-intersection calculus, as well as distance and orientation relations. This spatio-temporal integration can avail of existing annotation schemes for space and time in natural language, but it leaves some open issues related to the representation of subjectivity.
Cite as

Inderjeet Mani. The Creeping Virtuality of Place. In Spatial Representation and Reasoning in Language : Ontologies and Logics of Space. Dagstuhl Seminar Proceedings, Volume 10131, pp. 1-5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2011)

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@InProceedings{mani:DagSemProc.10131.5,
  author =	{Mani, Inderjeet},
  title =	{{The Creeping Virtuality of Place}},
  booktitle =	{Spatial Representation and Reasoning in Language : Ontologies and Logics of Space},
  pages =	{1--5},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2011},
  volume =	{10131},
  editor =	{John A. Bateman and Anthony G. Cohn and James Pustejovsky},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10131.5},
  URN =		{urn:nbn:de:0030-drops-27326},
  doi =		{10.4230/DagSemProc.10131.5},
  annote =	{Keywords: Place subjectivity dynamicity}
}
Document
DOI: 10.4230/DagSemProc.10131.6
Towards Linguistically-Grounded Spatial Logics

Authors: Joana Hois and Oliver Kutz

Published in: Dagstuhl Seminar Proceedings, Volume 10131, Spatial Representation and Reasoning in Language : Ontologies and Logics of Space (2011)

Abstract
We propose a method to analyze the amount of coverage and adequacy of spatial calculi by relating a calculus to a linguistic ontology for space by using similarities and linguistic corpus data. This allows evaluating whether and where a spatial calculus can be used for natural language interpretation. It can also lead to 'more appropriate' spatial logics for spatial language.
Cite as

Joana Hois and Oliver Kutz. Towards Linguistically-Grounded Spatial Logics. In Spatial Representation and Reasoning in Language : Ontologies and Logics of Space. Dagstuhl Seminar Proceedings, Volume 10131, pp. 1-3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2011)

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@InProceedings{hois_et_al:DagSemProc.10131.6,
  author =	{Hois, Joana and Kutz, Oliver},
  title =	{{Towards Linguistically-Grounded Spatial Logics}},
  booktitle =	{Spatial Representation and Reasoning in Language : Ontologies and Logics of Space},
  pages =	{1--3},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2011},
  volume =	{10131},
  editor =	{John A. Bateman and Anthony G. Cohn and James Pustejovsky},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10131.6},
  URN =		{urn:nbn:de:0030-drops-27296},
  doi =		{10.4230/DagSemProc.10131.6},
  annote =	{Keywords: Spatial Logics, Spatial Language}
}
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