The MatWerk ontology represents research data and related activities of the MSE community. A first version of the ontology will be simplified, focusing on (i) community structure: researchers, research projects, universities, and institutions; (ii) infrastructure: software, workflows, ontologies, schemas, APIs, instruments, facilities, educational resources; and (iii) data: repositories, databases, scientific publications, published datasets and reference data.
The purpose of the MatWerk Ontology is to represent the scientific and infrastructural status of the Materials Science and Engineering (MSE) community. It will be used as a backbone for the MSE Knowledge Graph.
definition
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explains the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
A shortened form of a word or phrase. [Definition Source: NCI]
abbreviation
The non-unique initials or abbreviated name used for identification. [Definition Source: NCI]
acronym
Media Type or Extent
UDC
A media type or extent.
The set of conceptual resources specified by the Universal Decimal Classification.
[MIME] http://www.iana.org/assignments/media-types/
Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME].
The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types.
Format
has format
The file format, physical medium, or dimensions of the resource.
has_broad_synonym
has_exact_synonym
has_narrow_synonym
has_related_synonym
Note that this should be a super-property of hasRelatedSynonym, hasExactSynonym etc; however, we cannot state this and remain in OWL-DL
has_synonym
The property is a relationship between a resource and the best practice.
best practice
best practice of
The property relates a city or a state to a country where it is located.
country
country of
The property relates a city to a federal state where it is located.
federal state
federal state of
The property relates a thing to an organisation or a project that provided funding for it. The sub-properties are used to specify more specific funding relationships.
funder
funder of
The property relates a resource or a project to the organisation that provided funding for it.
funding organisation
funding organisation of
The property relateds a resource to the project that provided funding for it.
funding project
funding project of
The property is a relationship between a thing and a place its located at.
location
location of
The property relates a data collection to the type of object it contains.
object type
object type of
The property is a parental relationship between organisations.
parent organisation
The property links software to a programming language it is written in.
programming language
programming language of
The property is a relationship between a resource and an organisation or a person responsible for publishing it.
publisher
publisher of
The property is a relationship between related projects. The property is symmetric.
related project
The property relates a resource to its semantic expressivity spectrum.
semantic expressivity
semantic expressivity of
The property relates a resource to the standard it relies on.
standard
standard of
subsidiary organization
A relation between a dataset and the material it contains data on.
about material
A relation between a research group or large-scale facility and the organization it belongs to.
belongs to
A relation between a resource and the specification it conforms to.
conforms to specification
a relation between a person and an organization to which the person is affiliated.
has affiliation
A relation between a resource and a person, who is the author.
has author
A relation between a thing and its contact point, which can be a person or website.
has contact point
has contributor
A relation between a dataset and a person or organization, who has created the data.
A relation between a resource or large-scale facility and the academic discipline of the produced work.
has discipline
A relation between a resource and its documentation.
has documentation
A relation between a person and an academic discipline or research topic, in which this person is an expert.
has expertise in
The file format of the resource
A relation between a research group and its leader.
has leader
A relation between an academic event and a person, who participates in teaching capacity in the event.
has lecturer
A relation between an instrument and its documentation.
has manual
A relation between a research project and its members.
has member
A relation between an instrument and the organization that acts as its owner.
has owner
A relation between two different resources, which indicates both are associated.
has related resource
A relation between a software and the website of the repository where it is stored.
has repository
A relation between a person (the bearer) and a role, in which the role specifically depends on the bearer for its existence.
has role
A relation between a semantic resource and its SPARQL Endpoint.
has SPARQL endpoint
A relation between a research project and the topic of the research question it investigates.
has topic
a relation between a thing and its website.
has website
A relation between an organization or person and the resource of which it is a contributor.
is contributor of
is leader of
member of
A relation between an educational resource or academic event and the tools required to participate.
required tool
A relation between a work and a cited software.
software citation
A relation between a resource and method it implements, uses or describes.
uses method
A relation between an instrument and the technology it implements.
uses technology
A relation between a research group and the topic in which it conducts research.
working on topic
Cytoscape plugins would be linked to the Cytoscape application via uses software, while Microsoft Excel is linked to Microsoft Office via has_part.
This property allows the linkage of two different pieces of software such that one directly executes or uses the other. The has_part relationship should instead be used to describe related but independent members of a larger software package, and 'uses platform' relationship should be used to describe which operating system(s) a particular piece of software can use.
uses software
is software for
Provides a method of asserting what type of interactions are possible for the class in question. The interface must be from the 'software interface' hierarchy.
The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between software and a software license.
The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between a software license and the software which implements it.
is license for
'is compatible license of' provides a method of marking two software licenses as compatible and without conflicts, e.g. that the Apache License version 2 is compatible with GNU GPL version 3. If two licenses are connected with this property, it means code released under one license can be released with code from the other license in a larger program.
http://www.gnu.org/licenses/gpl-faq.html#WhatDoesCompatMean, accessed 12 June 2013.
is compatible license of
A citation or reference to another creative work, such as another publication, web page, scholarly article, etc.
citation
Operating systems supported (Windows 7, OS X 10.6, Android 1.6).
operatingSystem
A person or organization that supports a thing through a pledge, promise, or financial contribution. E.g. a sponsor of a Medical Study or a corporate sponsor of an event.
sponsor
has part
has sub event
is part of
is sub event of
A relation between company that makes goods for sale.
has manufacturer
is manufacturer of
URL of a thing.
url
A data property linking an entity to its description.
description
email address
A data property indicating the acronym of an entity, often represented as an abbreviation of the initials of the name or title of the entity.
has acronym
A data property relating a work to its Digital Object Identifier (DOI).
A data property relating a SPARQL EndPoint with its URL.
has endpoint URL
A data property relating a person to their Open Researcher and Contributor ID (ORCID).
A data property linking a person with information about that person.
has personal information
A data property indicating the postal address of an entity.
has postal address
A data property indicating the postal code of an entity.
A data property relating a research project with a unique identifier, defined in a given context.
has project identifier
A data property relating an organization to its identifier within the Research Organization Registry (ROR).
A data property linking something, for example a piece of equipment, to its serial number.
has serial number
A number or string that identifies different variants or releases of a resource.
has version
A data property relating an instrument with the model information.
instrument model
A flag to indicate an organized event or educational resource can be accessed online.
is online
A data property used for defining something with keywords.
keywords
The gender of this Agent (typically but not necessarily 'male' or 'female').
The date on which the CreativeWork was created or the item was added to a DataFeed.
dateCreated
Date of first broadcast/publication.
datePublished
A flag to signal that the item, event, or place is accessible for free.
free
duration
end date
start date
A matter individual that stands for a real world object representing an amount of a physical substance (or mixture of substances) in different states of matter or phases.
An instance of a material (e.g. nitrogen) can represent different states of matter. The fact that the individual also belongs to other classes (e.g. Gas) would reveal the actual form in which the material is found.
Material usually means some definite kind, quality, or quantity of matter, especially as intended for use.
Material
Architecture, Art History, Musicology, Media Studies, Performing Arts
An academic discipline, a research field or domain of a resource, e.g. a data portal or a field of study of a person.
academic discipline
Berlin, Hannover, Kyiv
A city or a town where the thing is located.
city
RISM catalogue of musical sources
A tangible collection of valuables published or curated by an organisation or a person.
collection
NFDI consortia grouped by a discipline based in a science-led process managed by the German Research Foundation (DFG).
consortium
A country where the thing is located.
Bach digital, KultSam, MusiXplora
An online platform that provides access to data collections and datasets.
data portal
A dataset is associated with a structured information about a resource.
dataset
Sachsen, Berlin
A federal state where the thing is located.
book, photograph, music sheet
A resource that identifies the type of object in a data collection.
Universit\u00e4tsbibliothek Leipzig, S\u00e4chsisches Wirtschaftsarchiv, Museen der Stadt K\u00f6ln
An organisation of some kind, e.g. research organisation or business organisation
organization
Harald Sack, Tabea Tietz, Sasha Bruns, Etienne Posthumus
A resource that represents a single person.
person
A spatial region, e.g. country, city or district.
place
A formal language used for implementing a software.
Freisch\u00fctz digital, Corpus Vitrearum Medii Aevi
A scientific or business endeavour that aims to conclude an investigation or to answer a research question.
project
A ressource that identifies a resource provided to the nfdi.
provided resource
MusiXplora: Visual analysis of a musicological encyclopedia, Textkategorien in kompositorischen Werkstattdokumenten
A published scholarly work that reports on ongoing activity about or within a resource, e.g. a dataset.
publication
The most generic kind of a resource and may be associated with any kind of creative work, e.g. datasets, books, movies, photographs; offered products and services, e.g. data portals, data curation, data digitization; and intangible things, e.g. subjects of creative works, topics of events, offers, a list of enumerations.
resource
controlled vocabulary, ontology, taxonomy
An entity that identifies the level of the semantic expressivity of a resource. Five instances are now included in nfdicore.
Expertise, advertisement, curation
A resource that identifies the type of a service.
service type
A computer software provided by an organisation or a person.
software
A set of requirements, guidelines, standards contributed by an organisation or a person.
specification
An international standard and norm that can be used to evaluate or create services.
Groovy on Grails, Angular
A technology, e.g. a web application or a programming framework used in a resource.
technological means
A collection of webpages contributed by an organisation or a person.
website
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length). If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
Examples include the formats defined by the list of Internet Media Types.
File Format
A digital resource format.
Media Type
A file format or physical medium.
A database containing chemistry data.
chemistry database
A computational workflow is a workflow which describes the complex multi-step methods that are used for data collection, data preparation, analytics, predictive modelling, and simulation that lead to new data products.
computational workflow
A role which inheres in a bearer and is realised when this person acts as the contact point regarding a contribution.
contact person
A contact point is a person, website or e-mail which provides information concerning a resource.
Point of contact
contact point
A database containing crystal structures and data on structural and mathematical crystallography, solid state physics and structural chemistry.
crystallography database
A role which inheres in a bearer and is realised when this bearer has participated in the gathering of data.
The bearer in this definition might be a person or a software agent. Data may consist of subject data, object data or both.
data collector
A structured collection of logically related data usually stored and retrieved using computer-based means.
database
Documentation is any communicable material that is used to describe, explain or instruct regarding some attributes of an object, system or procedure, such as its parts, assembly, installation, maintenance and use
documentation
An organized event with the purpose of teaching knowledge to others by displaying educational materials.
A resource or material that can be used for teaching and learning puposes.
educational resource
An Electronic Lab Notebook is a software tool that digitally replicates paper lab notebooks traditionally used in the sciences to record experimental results. It allows scientists to access, search, and share results from an experiment.
Electronic Laboratory Notebook
electronic lab notebook
Experimental workflow is a workflow that describes an experimental process, including the design, preparation, measurement, and analysis of the data.
experimental workflow
A repository that is created and managed using a Git version control system.
A role which inheres in a bearer and is realized when this person holds the responsibility for the operations of a group of agents.
The responsibilities of a group leader might include, among others, guiding, motivating, supporting and coordinating the group in different scopes (i.e. scientific, administrative, financial). In scientific projects (i.e. within the NFDI context) the group in this definition will be a research group, institute or department. In most cases the group leader is also the supervisor to the group
group leader
A facility that provides access to large-scale scientific equipment and allows scientists to carry out state-of-the-art research.
large-scale facility
An academic event which is intented to deliver instruction on a specific topic, most commonly to an audience of university students.
A database containing data of experimental and computational properties of materials
materials database
A metadata schema is a specification which establishes the elements needed to describe a data resource in a formalized and concise manner.
metadata schema
A method is a systematic procedure, technique, or mode of inquiry employed by or proper to a particular discipline or art.
Approach
Procedure
Technique
method
A repository which contains ontologies.
ontology repository
A patent is an exclusive right granted for an invention, which is a product or a process that provides, in general, a new way of doing something, or offers a new technical solution to a problem. To get a patent, technical information about the invention must be disclosed to the public in a patent application.
patent
A data repository which contains interatomic potentials or pseudopotentials for atomistic models.
potentials repository
Software which carries out a (planned) process on digital data,
Depending on the temporal relation of the carried out process to an analysis process, the process might either be termed "pre-processing" (e.g. converting file formats) or "post-processing" (e.g. spatial filtering of images).
processing software
A role which inheres in a bearer and is realized when a person is responsible for 1) the coordination of project resources and 2) the operations carried out within it.
In a project, a project leader might engage, motivate and support the team by establishing and maintaining productive operations
project leader
A role which inheres in a bearer and is realized when that person is responsible for 1) helping to define the project scope, goals and deliverables, 2) taking care of the budget, documentation and staffing, 3) reporting and documenting the progress, and 4) managing a project and meeting deadlines.
project manager
A role which inheres in a bearer and is realized when this bearer participates in the planning, operation or dissemination of a project.
project member
A central location in which data is stored and managed.
repository
A group of people who work in a university or research institute and carry research on one or more topics.
research group
Software which was created for a research purpose.
Scientific software
Software components (e.g., operating systems, libraries, dependencies, packages, scripts, etc.) that are used for research but were not created during or with a clear research intent should be considered software in research and not Research Software. This differentiation may vary between disciplines. Research software might be source code files, algorithms, scripts, computational workflows and executables
research software
A research topic is a specific field of study within a broader academic discipline.
Research area
Research field
Research subject
research topic
A machine-actionable controlled vocabularies to describe the meaning of the content and express relations among them.
An academic event where recuring meetings are held on a particular research topic, usually attended by academic and research staff.
Seminar
A repository which contains software and its components, including libraries, scripts, etc.
software repository
A SPARQL endpoint is a web service that provides an access point for receiving and processing SPARQL protocol requests
SPARQL endpoint
An academic event where a school session is conducted in summer enabling students to accelerate progress toward a diploma or degree, to make up credits lost through absence or failure, or to round out professional education.
Summer School
A role which inheres in a bearer and is realized when a person is responsible for 1) the coordination and 2) the operations of another person, group or department.
In a project with more than one member, the project leader might engage, motivate and support the team by establishing and maintaining productive operations. Note that a project leader is not necessarily the group leader.
supervisor
An academic event where the objective is to teach skills needed for a particular task or job.
Training Course
Software which creates graphical representations of data, features of data or data sets.
Graphics software
visualization software
A service that supports interoperable machine-to-machine interaction over a network.
web service
A workflow is a specification which describes a repeatable sequence of steps needed to create or produce a work.
workflow
A workflow environment is a software that manages and allows the user to create and interact with computational workflows.
workflow environment
This type covers computer programming languages such as Scheme and Lisp, as well as other language-like computer representations. Natural languages are best represented with the Language type.
ComputerLanguage
An organization such as a school, NGO, corporation, club, etc.
Organization
An enterprise (potentially individual but typically collaborative), planned to achieve a particular aim. Use properties from Organization, subOrganization/parentOrganization to indicate project sub-structures.
Project
A service provided by an organization, e.g. delivery service, print services, etc.
Service
Computer software, or generally just software, is any set of machine-readable instructions (most often in the form of a computer program) that conform to a given syntax (sometimes referred to as a language) that is interpretable by a given processor and that directs a computer's processor to perform specific operations.
Modified in parts from https://en.wikipedia.org/wiki/Software
AL 7.9.22: There are some reasoning oddities associated with marking IAO and SWO software as equivalent; once these are sorted out, the equivalence statement will take the place of this current parent-child relationship.
A licence is a legal instrument (usually by way of contract law, with or without printed material) governing the use or redistribution of the resource containing the licence.
Modified from http://en.wikipedia.org/wiki/Software_license
licence
An operating system is a piece of software which is responsible for managing software that runs on a computer and the interactions of that software with the hardware and system resources.
Mac OS is software which is used as the operating system for the Macintosh personal computer created by Apple Inc.
http://en.wikipedia.org/wiki/History_of_Mac_OS, accessed 25 March 2015.
Mac OS
The mode of interaction with a piece of software.
A web service is a software interface which works as a method of communication between two electronic devices over the World Wide Web and which is provided at a particular network address. There are two major classes of Web services: REST-compliant Web services, and arbitrary (or application-specific) Web services.
Modified from http://www.w3.org/TR/ws-arch/, accessed 6 June 2013; Modified from http://en.wikipedia.org/wiki/Web_service, accessed 6 June 2013.
An application programming interface is a set of routines, protocols, and tools for building software applications. An API expresses a software component in terms of its operations, inputs, outputs, and underlying types. An API defines functionalities that are independent of their respective implementations, which allows definitions and implementations to vary without compromising each other. The API specifies how software components should interact.
http://en.wikipedia.org/wiki/Application_programming_interface, accessed 25 November 2014.
License without restrictions on derivatives
A licensed is a free license according to GNU if the users have the four essential freedoms: The freedom to run the program, for any purpose (freedom 0). The freedom to study how the program works, and change it so it does your computing as you wish (freedom 1). Access to the source code is a precondition for this. The freedom to redistribute copies so you can help your neighbor (freedom 2). The freedom to distribute copies of your modified versions to others (freedom 3). By doing this you can give the whole community a chance to benefit from your changes. Access to the source code is a precondition for this. A program is free software if users have all of these freedoms. Thus, you should be free to redistribute copies, either with or without modifications, either gratis or charging a fee for distribution, to anyone anywhere. Being free to do these things means (among other things) that you do not have to ask or pay for permission to do so. “Free software” does not mean “noncommercial”. A free program must be available for commercial use, commercial development, and commercial distribution. Commercial development of free software is no longer unusual; such free commercial software is very important. You may have paid money to get copies of free software, or you may have obtained copies at no charge. But regardless of how you got your copies, you always have the freedom to copy and change the software, even to sell copies.
http://www.gnu.org/philosophy/free-sw.html, accessed 12 June 2013.
Allyson Lister: This class defines those licenses which are free licenses, but which may or may not be compatible with any version of the GNU GPL.
A license which allows any form of usage of the artifact.
free to use license
GNU AGPL
Open Data Commons
A vendor-specific license is a license which was, at least originally, created by a specific organization to be used just on the resources created within that organization. This is a hierarchy of convenience rather than of shared philosophy. Many of the licenses have since been taken up by other groups whose licensing requirements matched those of the originating organization.
Vendor-specific License
Fee-Based Commercial License is a license which, among its license clauses, states that commercial entities may use the resource for a fee.
Allyson Lister: This is a convenience class which combines multiple license clauses to create a defined class, such that any license type which meets the requirements will be inferred to fall into this category.
Fee-Based Commercial License
Non-Commercial No-Fee License is a license which, among its license clauses, states that non-commercial entities may use the resource without a purchase or usage cost.
Non-Commercial No-Fee License
Academic events are e.g. conferences and conference-like events, and all the sub-events of those which are about the topic or theme of the conference, such as talks or panels.
Academic event
A conference event.
Conference
Any kind of organised event having a start and an end date.
Organised event
A talk event.
Talk
An event which a teaching session is given to to an individual or very small group.
Tutorial
An event which is a long interactive meeting or educational session designed to create a specialized result. Workshops are smaller than conferences, and are usually only a day or two long and are dedicated to discussing a specific topic.
Workshop
Invited person to give a speech in an event.
Invited speakers
Someone who gives the main address at a formal gathering such as a conference .
Keynote speaker
A tool or implement, especially one for precision work.
Instrument
An instrument needed for operations in various laboratories, synthesis and analysis.
Laboratory Instrument
Science is a systematic enterprise that builds and organizes knowledge in the form of testable explanations and predictions about the universe.
A programming language is a formal language, which comprises a set of instructions that produce various kinds of output. Programming languages are used in computer programming to implement algorithms.
A scientific instrument is, broadly speaking, a device or tool used for scientific purposes, including the study of both natural phenomena and theoretical research.
Companies manufacturing equipment for scientific sstudies.
Technology is the collection of techniques, skills, methods, and processes used in the production of goods or services or in the accomplishment of objectives, such as scientific investigation.
A list of terms, natural language definitions and naming conventions. In comparisson to a glossary, there is a dedicated curation mechanism for new terms in a controlled vocabulary.
controlled vocabulary
A list of terms and their with natural language definitions.
glossary
A data model in a class hierarchy, where all concepts inherit their behaviour from the super-class concept. Taxonomies can be strict or non strict and can contain instances.
taxonomy
A structured list of terms and relations between the terms, as e.g. broader/narrower.
thesaurus
A set of concepts belong to a specific domain and their properties and the relations between them.
ontology
Recommended best practice is to identify the resource by means of a string conforming to a formal identification system.
Identifier
An unambiguous reference to the resource within a given context.
has title
A name given to a resource. Typically, the title will be the name by which the resource is formally known.