Umayer Reza, Xuelian Zhang, Torsten Hahmann. (2024). OnNER: An Ontology for Semantic Representation of Named Entities in Scholarly Publications.
Torsten Hahmann <http://orcid.org/0000-0002-5331-5052>
Umayer Reza <https://orcid.org/0000-0003-4013-3513>
Xuelian Zhang <https://orcid.org/0000-0002-0708-4070>
OnNER is designed to capture and represent named entities — terms identified and labeled using named entity recognition (NER) methods — along with relevant semantic context, such as their location within a document, from scholarly publications. The ontology is aligned with Basic Formal Ontology (BFO) and Information Artifact Ontology (IAO), and it also incorporates relevant high-level concepts from Relation Ontology (RO), Ontology for Biomedical Investigations (OBI), and NCBI organismal classification (NCBITaxon).
Spatial Knowledge and Artificial Intelligence (SKAI) Lab, University of Maine
OnNER: An Ontology for Semantic Representation of Named Entities in Scholarly Publications
A relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process.
realized in
A relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process.
realizes
A relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence.
role of
A relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
has role
P has output C iff C is a participant in P, C is present at the end of P, and C is not present in the same state at the beginning of P.
has output
C is output of P iff C is a participant in P, C is present at the end of P, and C is not present in the same state at the beginning of P.
output of
The relation between a publication and the bibliographic record or bibliographic reference describing it.
is referenced by
The relation between a bibliographic record or a bibliographic reference and the publication being referenced.
references
The citing entity cites the cited entity, either directly and explicitly (as in the reference list of a journal article), indirectly (e.g. by citing a more recent paper by the same group on the same topic), or implicitly (e.g. as in artistic quotations or parodies, or in cases of plagiarism).
cites
The cited entity (the subject of the RDF triple) is cited by the citing entity (the object of the triple).
is cited by
A structured element contains another generic element.
contains
An element that is contained by another structured element.
is contained by
The relationship between a responsible agent (e.g., a person or an NER system) holding an NER labeler role and a status assigned by that agent to a labeled term (also known as a named entity).
assigner of status
[NER-Model-A] assigns [Status-A-1-1] to the labeled term [Hemicellulose].
The relationship between a person holding a publication author role and a document (e.g., a scholarly publication) that the person has written.
author of publication
The relationship of a bibliographic entry with a bibliography which contains that bibliographic entry.
bibliographic entry contained by
The relationship between a bibliographic entry which provides the location of a scholarly publication on the web and that scholarly publication itself.
bibliographic entry references scholarly publication
The relationship between the detailed source information for locating a resource (e.g., a bibliographic reference) on the web and a text fragment citing that resource.
cited by
The relationship between a text fragment citing a resource and a detailed source information for locating the cited resource (e.g., a bibliographic reference) on the web.
The relationship of a content with the container of that content.
contained by
The relationship of a container with the content of that container.
The relationship of a bibliography with a bibliographic entry which is contained by that bibliography.
contains bibliographic entry
The relationship of a document part or a scholarly publication with another document part that is contained by the former, regardless of direct or indirect containment.
contains document part
The relationship of a document part or a scholarly publication with another document part that is contained by the former directly.
directly contains document part
The relationship of a text fragment with a labeled term which is contained by that text fragment directly.
directly contains labeled term
The relationship of a document part with another document part or a scholarly publication that contains the former, regardless of direct or indirect containment.
document part contained by
The relationship of a document part with another document part or a scholarly publication that contains the former directly.
document part directly contained by
The relationship between a floating document element (e.g., a figure, a table, or a listing) referenced by a text fragment (e.g., a paragraph, a caption, or a formula) and that text fragment itself.
floating document part referenced by text fragment
The relationship between a label of a labeled term (also known as a named entity) and a labeling schema to which that label belongs.
from labeling schema
The relationship between a person and an organization with which that person is affiliated.
has affiliation
The relationship between a floating document element (e.g., a figure, a table, or a listing) and an accompanying text fragment (e.g., a caption) which describes that floating document element.
has caption
The relationship between a status of a labeled term (also known as a named entity) and a label assigned to that labeled term.
has labeled term label
The relationship between a labeled term (also known as a named entity) and a status assigned to that labeled term.
has labeled term status
The relationship between a person and a role which distinguishes that person as an author of a particular publication.
has publication author role
The relationship between an agent (e.g., a person or an NER system) and a role which grants the privilege of NER labeling to that agent.
has NER labeler role
The relationship of a labeled term with a text fragment which contains that labeled term directly.
labeled term directly contained by
The relationship between an ordered document element (e.g., a section or a paragraph) and another ordered document element that immediately follows the first.
next document part
The relationship between a document (e.g., a scholarly publication) and a person holding a publication author role who has written that document.
publication authored by
The relationship between two document parts or between a document part and a scholarly publication, where one is referenced by the other.
referenced by
The relationship between two document parts or between a document part and a scholarly publication, where one references the other.
The relationship between a role and a person who is distinguished as an author of a particular publication by that role.
role of publication author
The relationship between a role and an agent (e.g., a person or an NER system) that is granted the privilege of NER labeling by that role.
role of NER labeler
The relationship between a scholarly publication which is located on the web by a bibliographic entry and that bibliographic entry itself.
scholarly publication referenced by bibliographic entry
The relationship between a status assigned to a labeled term (also known as a named entity) and an agent (e.g., a person or an NER system) holding an NER labeler role responsible for assigning that status.
status assigned by
[Status-A-1-1] is assigned to the labeled term [Hemicellulose] by [NER-Model-A].
The relationship between a status assigned to a labeled term (also known as a named entity) and that labeled term itself.
status of labeled term
The relationship of an NER system with its designated owner or operator.
system belongs to
The relationship between a text fragment (e.g., a paragraph, a caption, or a formula) referencing a floating document element (e.g., a figure, a table, or a listing) and that floating document element itself.
text fragment references floating document part
A text segment containing the description of a floating document element (e.g., a figure, a table, or a listing).
caption text
A text segment containing a unique digital identifier assigned to a scholarly publication released online.
doi
A unique figure number within a document.
figure number
A text segment containing a keyword mentioned in a scholarly publication.
keyword text
A text segment containing a label assigned to a labeled term (also known as a named entity).
label text
A text segment containing a labeled term (also known as a named entity) identified within a text fragment.
labeled term text
The total number of characters in a labeled term (also known as a named entity).
length
A unique listing number within a document.
listing number
The starting position of a labeled term (also known as a named entity) within a paragraph.
offset
A text segment containing an organization's address.
organization address
A text segment containing an organization's name.
organization name
A text segment containing a paragraph.
paragraph text
A text segment containing a person's name.
person name
A unique number indicating the hierarchical position of a document part within its parent document part.
position in parent document part
A date when a publication is made publicly available or officially released to the audience.
publication date
A text segment containing the title of a scholarly publication.
publication title
A text segment indicating the venue of the conference where a scholarly publication is presented.
publication venue
A text segment containing a schema name.
schema name
A text segment containing a section number.
section number
A text segment containing a section title.
section title
A specific date and time at which a particular status is assigned to a labeled term (also known as a named entity).
status assignment date
A text segment containing the version number of an NER system.
system version
A unique table number within a document.
table number
An entity is anything that exists or has existed or will exist.
Entity
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity.
Continuant
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region.
Occurrent
B is an independent continuant = Def. B is a continuant which is such that there is no C and no T such that B s-depends_on C at T.
Independent Continuant
P is a process = Def. P is an occurrent that has temporal proper parts and for some time T, P s-depends_on some material entity at T.
Process
To say that B is a realizable entity is to say that B is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type.
Realizable Entity
A quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized.
Quality
B is a specifically dependent continuant = Def. B is a continuant & there is some independent continuant C which is not a spatial region and which is such that B s-depends_on C at every time T during the course of B’s existence.
Specifically Dependent Continuant
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
Role
B is a generically dependent continuant = Def. B is a continuant that g-depends_on one or more other entities.
Generically Dependent Continuant
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part.
Material Entity
B is a relational quality = Def. for some independent continuants C, D and for some time T: B quality_of C at T & B quality_of D at T.
Relational Quality
A generically dependent continuant that is about some thing.
Information Content Entity
A collection of information content entities intended to be understood together as a whole.
Document
An information content entity that is part of a document.
Document Part
A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
Abstract
A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
Author Role
A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a document act.
Document Act Performer Role
A subclass from NCBI Taxonomy.
Homo Sapiens
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
Organization
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
Organism
A material entity consisting of multiple components that are causally integrated.
System
A collection of bibliographic records, each of which references a publication (or a work in preparation for publication). Examples of bibliographic collections include a collection of the bibliographic records of all the publications that a single individual has authored, or a collection of those bibliographic records to be included in a research paper, where they are expressed as a reference list.
Bibliographic Collection
An expression of a bibliographic record in a specific format, that references a particular textual or data publication (or a work in preparation for publication). Each bibliographic reference is a list of items containing entities that describe aspects of the referenced work - for example authors, title, journal, publication year - selected from the bibliographic record. Note that because different journal styles may require omission of elements of the bibliographic record in references included in a paper's reference list (e.g. the title, the identifier, the names of the eighth and subsequent authors), and because errors can be introduced when an author creates a bibliographic reference, the bibliographic reference to a published work may not be a complete or fully accurate expression of the information contained within the authoritative bibliographic record for that work.
Bibliographic Reference
Text accompanying another item, such as a picture.
Caption
A brief summary of a book, a research article, thesis, review, conference proceeding or any in-depth analysis of a particular subject or discipline, the purpose of which is to help the reader quickly ascertain the publication's purpose.
A communication object comprising one or more graphics, drawings, images, or other visual representations.
Figure
A unit of information expressed in mathematical, chemical or logical symbols and language.
Formula
A self-contained unit of discourse that deals with a particular point or idea. Paragraphs contains one or more sentences. The start of a paragraph is indicated by beginning on a new line, which may be indented or separated by a small vertical space by the preceding paragraph.
Paragraph
A logical division of the text, usually numbered and/or titled, which may contain subsections.
Section
A set of data arranged in cells within rows and columns.
Table
A piece of text defined by a start point and an end point.
Text Chunk
A subclass of FRBR expression, restricted to expressions of fabio:Works. For your latest research paper, the preprint submitted to the publisher, and the final published version to which the publisher assigned a unique digital object identifier, are both expressions of the same work.
Expression
An overview of a scholarly publication, usually placed at the beginning of the document and set apart from the main text.
An atomic labeled term is a straightforward annotation where a single, continuous span of text is identified as a labeled term. Note: A labeled term is also known as named entity.
Atomic Labeled Term
The term "modulation" could be identified and labeled as a "process" within the cellulose domain.
Detailed information about the source of a cited work that helps locate the original content on the web.
Bibliographic Entry
A collection of bibliographic entries typically appearing at the end of a document.
Bibliography
A status indicating that the corresponding term has not yet been reviewed by domain experts to determine its inclusion in the domain ontology.
Candidate Status
A caption differs from a paragraph as it is part of a floating document element, such as a table or figure, and provides a description of that element.
A compoubd labed term is a more complex annotation where labed terms can be contained within other labed terms. Note: A labeled term is also known as named entity.
Compound Labeled Term
The term "nanoparticle shape" (classified as "property") could be seen as a compound labeled term consisting of "nanoparticle" (classified as "structure") and "shape" (classified as "property"), both of which are individual labeled terms.
A status indicating that the corresponding term has been reviewed by domain experts and determined its inclusion in the domain ontology.
Confirmed Status
Structural features of scholarly publications that support locating identified named entities.
Abstract, Floating Document Part, Ordered Document Part, Text Fragment, Bibliography, and Bibliographic Entry.
A marker indicating the definitive end of the main text.
End of Document
A floating document element that has the flexibility to be positioned anywhere within a publication.
A document part whose order of appearance, if changed within a publication, does not alter the semantic alignment of the publication.
Floating Document Part
Figure, Table, and Listing.
A specialized piece of text representing mathematical expressions, chemical formulas, and similar content that can appear within a paragraph or a caption.
The chemical formula of sodium hydroxide and sodium chloride are NaOH and NaCl respectively.
A special text fragment that typically accompanies the abstract and may contain one or more labeled terms.
Keyword
A concept (also known as a label) assigned to a term (also known as a named entity) to classify it within a particular context.
Label
In the cellulose domain, the term "nanoparticle shape" is classified by a concept (also known as a label) called "property".
A word or group of words in a scholarly publication identified and classified as a named entity.
Labeled Term
The term "nanoparticle shape" is identified and labeled as a "property", and the term "modulation" is identified and labeled as a "process".
Each term in the ontology is associated with a status to signify its current state within the system.
Labeled Term Status
Statuses such as Candidate, Confirmed, Accepted, Suggested, and others as needed.
A labeling schema consists of a unique set of labels customized for a particular domain or purpose.
Labeling Schema
The concepts (also known as labels) "material", "property", and "process" are part of the CelloGraph schema, designed specifically for the cellulose domain.
Listing
An essential role required for a labeler to identify and classify named entities (also known as label terms) within text.
NER Labeler Role
A system that automates the process of identifying and categorizing named entities (also known as labeled terms) within text.
NER System
A document part whose order of appearance, if changed within a publication, alters the semantic alignment of the publication.
Ordered Document Part
Section and Paragraph.
A structured entity formed by a group of individuals or legal entities with a common purpose.
A text segment, often made up of one or more sentences, that can be placed inside or outside sections and starts on a new line.
An individual human being.
Person
An essential role in identifying a person as an author.
Publication Author Role
A status indicating that the corresponding term has been reviewed by domain experts and deemed ineligible for inclusion in the domain ontology.
Rejected Status
An exclusive document format that presents original research or academic discoveries.
Scholarly Publication
A key element for organizing the main text within publications, which can be nested and can contain various other parts such as paragraphs and formulas.
A status indicating that the corresponding term has been reviewed by domain experts and proposed either a different label or a revised span, particularly if the term comprises multiple words.
Suggested Status
A text segment within a publication that carries semantic meaning.
Text Fragment
Paragraph, Caption, Formula, Keyword, and Labeled Term.