@inbook {26441, title = {Design of a Biochemistry Procedure-Oriented Ontology}, booktitle = {the Communications in Computer and Information Science book series}, volume = {1297}, year = {2020}, pages = {65-387}, publisher = {Springer}, organization = {Springer}, abstract = {

Ontologies must provide the entities, concepts, and relations required by the domain being represented. The domain of interest in this paper is the biochemistry experimental procedure. These procedures are composed of procedure steps which can be represented as sequences. Sequences are composed of totally ordered, partially ordered, and alternative subsequences. The ontology language being used is OWL-DL. OWL-DL was adopted due to its well-balanced flexibility among expressiveness (e.g., class description, cardinality restriction, etc.), completeness, and decidability. In the biochemistry procedure-oriented ontology presented here, subsequences are represented with two relations,\ directlyFollows\ and\ directlyPrecedes\ that are used to represent sequences. Alternative subsequences can be generated by composing a\ oneOf\ function in OWL-DL. Each alternative subsequence is referred to as\ optionalStepOf\ in this work. Two biochemistry procedures, Alkaline Agarose Gel Electrophoresis and Southern Blotting, are used to demonstrate the generality of this procedural ontology. Portions of these procedures are described in detail. SPARQL queries show the versatility of the ontology.

}, url = {https://doi.org/10.1007/978-3-030-66196-0_17}, author = {Mohammed Alliheedi and Yetian Wang and Robert E. Mercer} } @conference {keod20, title = {Semantic Search for Biomedical Texts using Predicate-Argument Structure}, booktitle = {Proceedings of the 12th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management - Volume 2: KEOD,}, year = {2020}, pages = {299-306}, publisher = {INSTICC}, organization = {INSTICC}, isbn = {978-989-758-474-9}, doi = {10.5220/0010150702990306}, author = {Mohammed Alliheedi. and Robert E. Mercer.} } @conference {17827, title = {Annotation of Rhetorical Moves in Biochemistry Articles}, booktitle = {Workshop on Argument Mining collocated with ACL 2019}, year = {2019}, month = {1 August 2019}, pages = {113--123}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {6th Workshop on Argument Mining, Florence, Italy}, abstract = {This paper focuses on the real world application of scientific writing and on determining rhetorical moves, an important step in establishing the argument structure of biomedical articles. Using the observation that the structure of scholarly writing in laboratory-based experimental sciences closely follows laboratory procedures, we examine most closely the Methods section of the texts and adopt an approach of identifying rhetorical moves that are procedure-oriented. We also propose a verb-centric frame semantics with an effective set of semantic roles in order to support the analysis. These components are designed to support a computational model that extends a promising proposal of appropriate rhetorical moves for this domain, but one which is merely descriptive. Our work also contributes to the understanding of argument-related annotation schemes. In particular, we conduct a detailed study with human annotators to confirm that our selection of semantic roles is effective in determining the underlying rhetorical structure of existing biomedical articles in an extensive dataset. The annotated dataset that we produce provides the important knowledge needed for our ultimate goal of analyzing biochemistry articles.}, url = {https://www.aclweb.org/anthology/W19-4514}, author = {Mohammed Alliheedi and Robert E. Mercer and Robin Cohen} } @conference {18231, title = {Biochemistry procedure-oriented ontology: A case study}, booktitle = {the 11th International Conference on Knowledge Engineering and Ontology Development}, volume = {2}, year = {2019}, month = {17 September}, pages = {164-173}, publisher = {Science and Technology Publications (SCITEPRESS)}, organization = {Science and Technology Publications (SCITEPRESS)}, address = {the 11th International Conference on Knowledge Engineering and Ontology Development, Vienna, Austria}, abstract = {Ontologies must provide the entities, concepts, and relations required by the domain being represented. The domain of interest in this paper is the biochemistry experimental procedure. The ontology language being used is OWL-DL. These procedures are composed of procedure steps which can be represented as sequences. Sequences are composed of totally ordered, partially ordered, and alternative subsequences. Subsequences can be represented with two relations, directlyFollows and directlyPrecedes that are used to represent sequences. Alternative subsequences can be generated by composing a oneOf function in OWL-DL, referred to it as optionalStepOf in this work, which is a simple generalization exclusiveOR. Alkaline Agarose Gel Electrophoresis, a biochemistry procedure, is described and examples of these subsequences are provided.}, url = {https://www.scitepress.org/PublicationsDetail.aspx?ID=cIetqK9MzqI=\&t=1}, author = {Alliheedi, Mohammed and Wang, Yetian and Robert E. Mercer} } @conference {17826, title = {Ontological Knowledge for Rhetorical Move Analysis}, booktitle = {International Conference on Computational Linguistics and Intelligent Text}, volume = {23}, year = {2019}, month = {07 April 2019}, address = { 20th International Conference on Computational Linguistics and Intelligent Text Processing, La Rochelle, France}, abstract = {
Scholarly writing in the experimental biomedical sciences follows the IMRaD (Introduction, Methods, Results, and Discussion) structure. Many Biomedical Natural Language Processing tasks take advantage of this structure. Recently, a new challenging information extraction task has been introduced as a means of obtaining these types of detailed information: identifying the argumentation structure in biomedical articles. Argumentation mining can be used to validate scientic claimsand experimental methodology, and to plot deeper chains of scienti creasoning. One subtask in identifying the argumentation structure is the identication of rhetorical moves, text segments that are rhetorical and perform specic communicative goals, in the Methods section. Based on a descriptive taxonomy of rhetorical moves structured around IMRaD, the foundational linguistic knowledge needed for a computationally feasible model of the rhetorical moves is described: semantic roles. One goal is to provide FrameNet and VerbNet-like ontologies for the specializeddo main of biochemistry. Using the observation that the structure of scholarly writing in the laboratory-based experimental sciences closely follows the laboratory procedures, we focus on the procedural verbs inthe Methods section. Occasionally, the text does not contain llers forall of the semantic role slots that are needed to perform an adequate analysis of a verb. To overcome this problem, an ontology of experimental procedures can be interrogated to provide a most likely candidate for the missing semantic role(s).
}, url = {https://www.cys.cic.ipn.mx/ojs/index.php/CyS/article/view/3282}, author = {Mohmmed Alliheedi and Robert E. Mercer and Sandor Haas-Neill} } @mastersthesis {21964, title = {Procedurally Rhetorical Verb-Centric Frame Semantics as a Knowledge Representation for Argumentation Analysis of Biochemistry Articles}, year = {2019}, type = {PhD thesis}, abstract = {The central focus of this thesis is rhetorical moves in biochemistry articles. Kanoksilapatham has provided a descriptive theory of rhetorical moves that extends Swales{\textquoteright} CARS model to the complete biochemistry article. The thesis begins the construction of a computational model of this descriptive theory. Attention is placed on the Methods section of the articles. We hypothesize that because authors{\textquoteright} argumentation closely follows their experimental procedure, procedural verbs may be the guide to understanding the rhetorical moves. Our work proposes an extension to the normal (i.e., VerbNet) semantic roles especially tuned to this domain. A major contribution is a corpus of Method sections that have been marked up for rhetorical moves and semantic roles. The writing style of this genre tends to occasionally omit semantic roles, so another important contribution is a prototype ontology that provides experimental procedure knowledge for the biochemistry domain. Our computational model employs machine learning to build its models for the semantic roles and rhetorical moves, validated against a gold standard reflecting the annotation of these texts by human experts. We provide significant insights into how to derive these annotations, and as such have contributions as well to the general challenge of producing markups in the domain of biomedical science documents, where specialized knowledge is required.}, url = {http://hdl.handle.net/10012/15021}, author = {Alliheedi, Mohammed} } @conference {17825, title = {Semantic Roles: Towards Rhetorical Moves in Writing About Experimental Procedures}, booktitle = {Canadian Conference on Artificial Intelligence}, volume = {11489}, year = {2019}, pages = {518-524}, publisher = {springer}, organization = {springer}, address = {The 32nd Canadian Conference on Artificial Intelligence, Kingston, ON}, abstract = {Scholarly writing in the experimental biomedical sciences follows the IMRaD (Introduction, Methods, Results, and Discussion) structure. Many Biomedical Natural Language Processing tasks take advantage of this structure. The task of interest in this paper is the identification of semantic roles of procedural verbs as a first step toward identifying rhetorical moves, text segments that are rhetorical and perform specific communicative goals, in the Methods section. Based on a descriptive taxonomy of rhetorical moves structured around IMRaD, the foundational linguistic knowledge needed for a computationally feasible model of the rhetorical moves is described: semantic roles. Using the observation that the structure of scholarly writing in the laboratory-based experimental sciences closely follows the laboratory procedures, we focus on the procedural verbs in the Methods section. Our goal is to provide FrameNet and VerbNet-like information for the specialized domain of biochemistry. This paper presents the semantic roles required to achieve this goal.}, url = {https://link.springer.com/chapter/10.1007/978-3-030-18305-9_54}, author = {Mohammed Alliheedi and Robert E. Mercer} } @conference {15090, title = {Rhetorical Figuration as a Metric in Text Summarization}, booktitle = {Canadian Conference on Artificial Intelligence}, volume = {8436}, year = {2014}, pages = {13-22}, publisher = {springer}, organization = {springer}, edition = {1}, address = {27th Canadian Conference on Artificial Intelligence, Canadian AI 2014, Montr{\'e}al, QC, Canada, May 6-9, 2014. Proceedings}, url = {https://link.springer.com/chapter/10.1007/978-3-319-06483-3_2}, author = {Alliheedi, Mohammed and DiMarco, Chrysanne} } @mastersthesis {15091, title = {Multi-document Summarization System Using Rhetorical Information}, year = {2012}, type = {Masters thesis}, abstract = {
Over the past 20 years, research in automated text summarization has grown significantly in the field of natural language processing. The massive availability of scientific and technical information on the Internet, including journals, conferences, and news articles has attracted the interest of various groups of researchers working in text summarization. These researchers include linguistics, biologists, database researchers, and information retrieval experts. However, because the information available on the web is ever expanding, reading the sheer volume of information is a significant challenge. To deal with this volume of information, users need appropriate summaries to help them more efficiently manage their information needs. Although many automated text summarization systems have been proposed in the past twenty years, none of these systems have incorporated the use of rhetoric. To date, most automated text summarization systems have relied only on statistical approaches. These approaches do not take into account other features of language such as antimetabole and epanalepsis. Our hypothesis is that rhetoric can provide this type of additional information. This thesis addresses these issues by investigating the role of rhetorical figuration in detecting the salient information in texts. We show that automated multi-document summarization can be improved using metrics based on rhetorical figuration. A corpus of presidential speeches, which is for different U.S. presidents speeches, has been created. It includes campaign, state of union, and inaugural speeches to test our proposed multi-document summarization system. Various evaluation metrics have been used to test and compare the performance of the produced summaries of both our proposed system and other system. Our proposed multi-document summarization system using rhetorical figures improves the produced summaries, and achieves better performance over MEAD system in most of the cases especially in antimetabole, polyptoton, and isocolon. Overall, the results of our system are promising and leads to future progress on this research.
}, url = {https://uwspace.uwaterloo.ca/handle/10012/6820}, author = {Alliheedi, Mohammed} }