Wilf Morlidge Jacopo de Berardinis Elliott Watkiss-Leek George Hannah Valentina Tamma Harry Rostron Andrew Ng Ewan Johnson Andrew Mitchell Terry R. Payne The AnIML Ontology The AnIML Ontology The AnIML Ontology is a OWL-based model that formalises the semantics of the Analytical Information Markup Language (AnIML) and aligns it with the Allotrope Data Format to support cross-system and cross-lab interoperability. The AnIML Ontology is a OWL-based model that formalises the semantics of the Analytical Information Markup Language (AnIML) and aligns it with the Allotrope Data Format to support cross-system and cross-lab interoperability. 1.0.0 2025-02-01 2025-02-27 aml http://www.w3id.org/animl/ontology/ This denotes the property of an object having a governing specification The inverse of the specification property which denotes that a specification is used by an object A reified data property denoting that the domain (which is conceptually a component of a series determined before the series is created) has a plotscale, which itself is a class of individuals equivalent to the possible settings of the reified data property A reified property for the concept of a role being fulfilled by an agent, in english the concept of a task / job being done by someone This is the inverse of the bag association, however it carries the connotation that the agent becomes defined by their task. This is in the same way that if a human practices medicine to fulfill a need for medical treatment, then that need becomes met, however it also makes the human a doctor. An implementation of the common 'hasPart' realtion to denote the special relation between series and datapoint specifications, wherein series specifications govern some of the attributes of their corresponding dataPointSpecifications This relationship indicates the object, conceptually the area of the animl document describing that object, that a change has been made to This relationship shows that an animl document contains all the information regarding (e.i denotes) a particular experiment This is the inverse of the denotes relation This property denotes that an object of a class has a role associated with it, this generalises asociations to several classes of objects that are now generalised as role This denotes that a category includes a parameter This denotes the relationship between a result and a category This denotes the relationship between a sample and a category This denotes the inclusion of a set of samples in a document, they are attached to the doucment as samples exist outside of the This denotes the relationship of a category object with another of the same class, where the information of one category may be a component of another broader one This denotes the property of have tags attached to you, as well as specifying the set of tags for which this is true This is distinct from the concept of data type where a classes equivalent in the animl xml was bound by an attribute to one of a set of enumerated types, we have reified that attribute and created type classes whose individuals are the possible settings of type for the relevant class. this relationship is the relation between a class and its type class This is the property linking a document and agents to their version history This property is designed to link an experiment step to is associated infrastructure This property does not make complete sense at a human level it ties a sample into the sampleincontainer situation since a sample in that situation has the property of being contained This is not the inverse of the above property, it links a sampleIncontainer situation to a container as the object doing the containing within the situation This relation indicates that it is at a particular version that a change is made This relation is to link an experimentStep to its results, and also to indicate that said results are created in the step This relation links a signature to the signableitem, conceptually an area of the animl file (or one of the files it represents), it is attached it. it also indicates that the given signable item is watermarked by the signature This denotes the inclusion of a method in an experiment step, and also indicates that a method is something that is utilised in an exmperiment step rather than being part of it This denotes the inclusion of a technique in an experiment step, and also indicates that a technique is something that is utilised in an exmperiment step rather than being part of it This represents the idea of an object containing an object, without having neccessary parthood This is used to indicate effects an attribute, or an entire element This is used to indicate which version of the animl markup language was used to create the document This is used to store the characters underlying the barcode for a sample This exists to enable human readable comments to be attached to all objects in the ontology This expresses the Id which a container is given to allow it be found in a group of containers This represents the row position of a sample in a container, within the reified sampleInContainer situation This represents the column position of a sample in a container, within the reified sampleInContainer situation This represents the email address of an agent This is any machine readable code not assigned within the system, for example if an agent has an employee number This represents a human readable physical location (typically an address, site number, or building space ref) for an agent This is a generalisation of name,model, etc meaning the human understood identifier for something This represents as a string literal the post change state of an item changed in a change This represents as a string literal the per change state of an item changed in a change This is an optional property recording the operating system of an agent, where an agent is human, or a piece of mechanical hardware this value will be none. This denotes the organisation to which an agent belongs, this can be the employer of a human agent, or the owner of a non human agent. This is an optional property denoting the phone number of an agent, where the agent is not human this will be none This property represents the actual data corresponding to a datapoint object of the individual sub class This is a natural language description justifying a change This is an optional parameter which points outside of the file to the location of storage for the raw data that was later translated into a sample or experimentStep This is a dataTime indicating the exact point in time at which an object was created This is an untyped string serving as a container for any data that may need to be included in a tag This is a parameter indicating whether a series should be seen, it is intended as a flag for external systems that may be used to display animl data A container for all the parameter and seriesSet data structures associated with something since it contains data structures, and thus is a data structure, a category may also contain another category as a sub-category This is an enumeration class, e.i a class that exists only to reify the enumeration of a property of another class, in this case the individuals for this class correspond to the possible types of a container object A container for a datapoint, despite transitively being a container for a single datapoint, this is not equivalent to a datapoint, as it is independent of an enclosing data structure A sample is any item which is used, or that data regarding which is used, in an experiment in the document, they are often the subject of referencing to indicate that they are used in an experimentstep, however their set is attached to the document itself since they exist outside the context of the experiments described This is an ordered set of series data structures, series generally appear in sets when it is necessary to express multiple dimensions of data captured over the same interval or otherwise in the same context window This is the set of tags which exist in the document An agent is a generalisation of several classes, author, software, device etc and may denote any external intentional object that acts on the system This is the concept of a role that an object in the system may need an agent to fulfil This is an enumeration class, e.i a class that exists only to reify the enumeration of a property of another class, in this case the individuals for this class correspond to the possible types of intentional objects that could interact with the system Enumeration class for encodings This denotes the conceptual object of a change to the document, and is used to link to information regarding the context of a change as well as the state of the system before and after it This is an enumeration class, e.i a class that exists only to reify the enumeration of a property of another class, in this case the individuals for this class correspond to the possible types of actions that could have been perfromed on an area of the document to consistute a change This is a reification of the situation wherein a sample is present a container, used to allow information about the position of the sample in the container to be encoded This is a subclass / special case of sample which is used to denote a sample which contains other samples, it is pointed to by the sampleincontinare situation to indicate the containing sample without allowing samples to directly contain themselves or force them to have a containerid when they may not always have one This is the root node of the document, and links into its major componentw This is a conceptual representation of an experiment in which operations occur, and a container for the ordered set of experiment steps This is the root for the largest subsections of the document, it is a representation of a single action undertaken during an experiment, and consists of several components, external supporting factors, and outputs A subclass of datapoint which contains a freely assignable value. This is a container for all the data needed to begin / which consitute, an experiment, this is expected to include a set of sample and can also include previous results, or any component of a previous experiment. this is deliberately vague so that whatever information is deemed relevant may be include, for example you may or may not wish to store the fact that a piece of machinary has finished moving an is free to be acquired. This broadly denotes the procedure employed to carry out the experiment, and typically consists of a set of parameters describing the steps involved. however since this component contains a category (a largely unrestricted data container) it may take a variety of forms This is a container for any subset of data that is output from an experimentstep, though conventionally the salient 'results' as with the other direct components of experimentstep its sturcutre allows for freely assigned data to be introduced though sub elements, allowing this to take a variety of forms This is a container for the set of samples used in the experiment A series is a data sturcture containing ordered data points, a series may contain data points of any of the three data point subclasses, but the subclass of all the datapoints in a series must be the same This is a member of a set of signatures which, when linked to a signable item, causes it to be watermarked This is a container for the set of signatures present in the document This is a loosely governed container which can be attached to an experiment step or sample to provide additional data about them, where said data is not otherwise expressable This is a subclass of experimentstep used in place of its superclass when the author wishes to denote that the experiment is an example of / specification for a type of experimentstep This is a specific version, representing the state of the document at a particular moment in time, it links to an unordered collection of changes (denoting the difference between this and the previous version), as well as indicating its own relative position by pointing to the previous and next version. it also has metadata attributes and links to the agents responsible for it This is the set of versions of a document ,as well as the structure allowing navigation between them The fundamental root element for all ontologies Determinate container type Indeterminate container type Rectangular tray container type 1536 wells container type 24 wells container type 384 wells container type 6 wells container type 96 wells container type A creation change type A deletion change type A person as a human agent type A modification change type A software agent type A hardware agent type A binary encoding data point type An auto incremented encoding data point type An individual encoding data point type Denotes the relationship contained within the context of the specification for a referenced item, a relationship which indicates the requirement for the referenced item to have been consumed in a particular technique here technique may be viewed in its form as a specification for an experiment step Denotes the requirement for a technique to consume the referenced item of a referenec in order for that item to be referenced this relationship is not entirely intuitive, but it is necessary to preserve expressivity found in the original xml Denotes the relationship contained within the context of the specification for a referenced item, a relationship which indicates the requirement for the referenced item to have been derived from a particular technique here technique may be viewed in its form as a specification for an experiment step Denotes the requirement for a technique to derive the referenced item of a referenec in order for that item to be referenced this relationship is not entirely intuitive, but it is necessary to preserve expressivity found in the original xml Denotes that the 'extension' (itself a subclass of technique) exists to: extend the technqiue if you consider techniques as independent complete the specification for an experiment step, if you consider technqieus as specifications for experiment steps Denotes that a class is a container for data with corresponding units of measurement, a complex quantity may have multiple units e.i mph, or rpm Conceptually this relationship is the property of being bound to a specific data type, which forces classes representing data containers to have individuals that only contain data of specific types however it is attached to the specification for such containers, since the type of data a container may hold is governed by its specification A constant value added to the equation resulting from the combination of data with units A description of type of objects or measurements to which units may be assigned A raised power, typically used to raise the dimensionality of spacial data A coefficient upon a set of units, typically an order of magnitude A string space for the bibliography related to an object A string space for a software requirement enumeration for an object A boolean denoting whether or not a technique or extension will work without being extended A unique token used to authenticate identity of an ATDD for security purposes This is the generic superclass for specifications, those objects which represent components of animl-core classes which are governed by the relevant ATDD file,each specification may be a part of exactly one other object 1 A simple class which exists only to be a component of those classes whose only governed components are those in specification these classes (A) cannot be directly part of specification, as then it would be possible for classes in A to have part to the more complex and specialised subclasses of specification This is the subclass of specification which applies to parameters, and includes additional attribute restrictions, as well as indicating that the data in a parameter must be linked to a certain set of units This is the subclass of specification which applies to series, and includes additional attribute restrictions, as well as indicating that the data points of a series must all have a common set of units 1 Data point specification 1 This is the specification subclass for a reference, it may have either a consumedby or derived from relation to any technique (and exactly one of each relation). this is because the technique of an experimentstep governs whether a sample is produced or consumed during it. this could be considered to be a property of a sample specification, except that samples are understood to exist outside of the context of the experiment (especially since some are neither consumed or produced in the experiment) and as such the ATDD can only govern the way in which they are linked into the experiment. 1 1 This is an enumeration class, e.i a class that exists only to reify the enumeration of a property of another class, in this case the individuals for this class correspond to the possible data types for a datapoint This is an enumeration class, e.i a class that exists only to reify the enumeration of a property of another class, in this case the individuals for this class correspond to the possible kinds of scale a datapoint with units may be on. e.i it determines whether a datapoint is on a linear, logarithmic, or other kind of scale This is an ordered collection of Siunits which acts to create a compound unit This is unique in the document in that it is both an enumeration class, e.i a class that reifies the enumeration of a property of another class, and links to members of its own class to indicate its position in an ordered set. this is because it is known that its individuals must correspond to one of the limited set of Siunits, but those units can still be combined in an intractable number of ways, making direct enumeration of options impossible. This is a container for all the specification objects that exist in the ATDD governance component of a animl KB. conceptually it is also the broader specification for an experiment step, it is identical to its superclass of definition except in that it can be extended by extensions, and can have derive and consume relations, which express the ability of an ATDD to govern when samples are created or destroyed during experiment steps. as with their inverses, a technique may not have a derive and consume relation to the same reference specification. however unlike a reference specification, it may have multiple derive and consume relations over all. This relation denotes that the referenceset in the domain contains references to data within a data structure of the range class This indicates that the domain reference points to something of the range class This relation represents a reified data property, where a reference is related to the textual description of the role of the data it points to, this is an optional property distinct from function and the consumes/derives relationship, it is used when further infromation about the purpose of the data is necessary to store This relation represents a reified data property, where a reference is related to the textual description of the function of the data it points to This indicates the first position in an ordered set that a contained item will be pointed to by a reference in the domain reference set This indicates the last position in an ordered set that a contained item will be pointed to by a reference in the domain reference set This is a reference set as discussed in the header for this odp, note that it can only look within one data structure 1 This is a reference for the odp, note that it can only point to one piece of data 1 This is a reified natural language field for the use case of a set of referenced datapoints This is a reified natural language field for the 'function' of data when being referenced this is optional and works to distinguish the general purpose of data from its immediate use this is an artefact from the construction of owl that has been left in to avoid damaging expressivity