The SEPIO ontology is in its early stages of development, undergoing iterative refinement as new requirements emerge and alignment with existing standards is explored. The SEPIO core file imports two files which can be resolved at the URLs below:
IAO ontology-metadata import: https://raw.githubusercontent.com/monarch-initiative/SEPIO-ontology/master/src/ontology/imports/ontology-metadata.owl
bfo mireot: https://raw.githubusercontent.com/monarch-initiative/SEPIO-ontology/master/src/ontology/mireots/bfo-mireot.owl
consider
Used to capture development notes and design decisions or questions. All annotations using this property should be removed before publishing / releasing the ontology to the public (but ideally retained in some place as valuable documentation).
SEPIO_editor_note
usage note
in_value_set
sepio_preferred_label
Annotation indicating whether a property represents a "shortcut" relation that can be used to directly link two objects that are indirectly linked through a longer path of two or more edges. Shortcut relations can be logically expanded to be expressed in terms of this longer path, e.g.
has_evidence_from_source = has_evidence_line o has_evidence_item o source.
is_shortcut
An account of the resource.
Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource."
description
database_cross_reference
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
has_part
has part
Paraphrase of elucidation: 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
Is_about is a (currently) primitive relation that relates an information artifact to an entity.
is_about
A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale.
Deprecate unless there is a use case requireing this relation.
obsolete_has_category_label
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
has participant
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process
capable of
p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
Chris Mungall
consumes
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
Chris Mungall
produces
has output
Is member of is a mereological relation between a item and a collection.
member of
Has member is a mereological relation between a collection and an item.
has member
Chris Mungall
input of
Chris Mungall
output of
A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.
is_evidence_supported_by
is_evidence_with_support_from
A relationship between an assertion or proposition and an evidence line used in evaluating its validity.
Consider re-use of http://purl.obolibrary.org/obo/RO_0002558 ! 'has evidence'.
Definition = "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x."
See also http://semanticscience.org/resource/SIO_000772 ! 'has evidence'.
has_evidence
has_evidence_line
A relation between a proposition and information that supports its validity, based on the evaluation of some agent.
Mapping to related terms:
Consider: http://semanticscience.org/resource/SIO_000206 ! 'is supported by'
has_supporting_evidence_line
A relation between a proposition and information that contradicts its validity, based on the evaluation and conclusion of some agent.
Mapping to related terms:
Consider: http://semanticscience.org/resource/SIO_000774 ! 'is refuted by'
has_conflicting_evidence
has_refuting_evidence_line
has_disputing_evidence_line
A relation between a proposition and information that was used to evaluate a particular proposition, but failed to provide conclusive support for or against its validity.
Mapping to related terms:
Consider: http://semanticscience.org/resource/SIO_000207 ! 'is disputed by'
A relation between a proposition and information that does not conclusively support or contradict its validity, based on evaluation of some agent.
has_inconclusive_evidence_line
A relation holding between a proposition and an assertion in which it is expressed.
is_asserted_in
A particular proposition can be asserted in more than one assertion - in cases where assertions made by different agents, or on different occasions, put forth the same proposition as true.
proposition_asserted_in
Consider use of http://purl.obolibrary.org/obo/RO_0002217 ! actively participates in.
Definition = "actively participates in y if and only if x participates in y and x realizes some active role"
has_agent
Decided that a more generic has_subject property should suffice to cover links from either an assertion or a proposition to an entity representing the subject of the statement made.
But wanted to maintain the text in the comment here for future reference/use.
Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents.
As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_subject :thing1).
The assertion_has_subject property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the subject of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_subject).
This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association.
assertion_has_subject
Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents.
As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_object :thing1).
The assertion_has_object property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the object of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_object).
This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association.
assertion_has_object
Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents.
As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_predicate :thing1).
The assertion_has_predicate property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the predicate of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_predicate).
This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association.
assertion_has_predicate
A relation holding between an assertion and the proposition that it puts forth as true.
Mapping to related terms:
Consider: http://purl.org/see/rdo#is_assertion_asserting
assertsProposition
In practice, SEPIO recommends that data is captured at the assertion level, and post-processed as needed to aggregate assertions making the same claim under a single proposition using this property.
asserts_proposition
A relation holding between a planned process, or the artifact it generates, and a plan specification that specifies all or part of the process (e.g. a protocol, guideline, rule set)
Consider SIO:00339 (a relation between a product and the information content entity that specifies it.)
In SEPIO, this property is most often used to link an assertion (the generated artifact) to an 'assertion method' that may specified how it was created. This assertion method may describe what types of data may be used as evidence, what weight to give a particular type of evidence, and how to combine different lines of evidence in generating the final assertion.
is_specified_by
Consider RO:0000087 ! has_role (def = a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence). However, this property is defined as a relation between an independent continuant and a role. In BFO, dependent continuants (such as information) cannot bear roles.
has_role
A relation holding between an evidence line and an individual information entity that contributes to the argument it represents.
has_supporting_information
has_evidence_item
If we start using the 'study data set' class in a similar way to organize data items from a partiular study, we should create a similar property chain that traverses the property we use to link study data sets to their data item parts.
Can this just be "has part" . . .or is a specific/unique relation needed here to avoid unwanted entailments?
This property chain ensures that any evidence items that are organized into groups using a 'study finding' object will still be classified as evidence items for the relevant evidence line, and returned by queries for evidence items for a particular evidence line.
A relation that links an evidence line to any activities (studies, assays, computational tasks, curation) that generated evidence items contributing to it.
has_evidence_item_output_from
has_supporting_activity
true
evidence_has_supporting_activity
has_equivalent_proposition
is_equilavent_to
has_consistent_proposition
is_consistent_with
Previosly implemented property chains:
is_asserted_in o strongly_contradicts o asserts -> strongly_contradicts
asserts o strongly_contradicts o is_asserted_in -> strongly_contradicts
But these broke reasoner - "the given hierarchy is not regular" error message". Apparently breaks rule that "in property chains of 3 or larger, the inner property must not also appear as the composite property". (https://arxiv.org/pdf/1212.2902.pdf)
has_contradicting_proposition
Relation between two propositions that make opposing claims (e.g. proposition1 holds that variant1 is pathogenic for disease1, and proposition2 holds that variant1 is benign for disease1).
strongly_contradicts
has_inconsistent_proposition
contradicts
Relationship between a statement or proposition and a document in which it is expressed (e.g. a publication, report, or database record).
is_expressed_in
Relationship between a document (e.g. a publication, report, database record) and an assertion or proposition that is stated in its content.
expresses
Grouping class to hold exploratory relationships linking assertions or propositions based on the compatability or degree of agreement in their meaning. Has utility toward inferring links between evidence lines and propositions.
has_concordance
propositional relationships
has_compatability
A relation between a planned process and a parameter that it measures as part of an assay or observation.
measures_parameter
conflicts_with
aligns_with
A relation that holds between an evidence line and a citable document from which information supporting the evidence line was obtained (i.e. a "supporting reference").
Note that this relation only links an evidence line to publications actually consulted by the asserting agent to find and interpret evidence items. There may be other publications that describe the same evidence item that the asserting agent did not consult, which would not qualify as supporting references.
For example, consider a GO curator's use of sequence data for the rat Vegfa gene in a line of evidence supporting their assertion that the human VEGFA ortholog exhibited the same angiogeneic activity. There may be multiple publications that report this same rat gene sequence, but only the publication that the curator consulted in making this assertion would qualify as a supporting reference for this evidence line.
For this resaon, we are not able to create a property chain declaring "has_evidence_item o is_described_by -> has_evidence_item_described_by". . . because this would entail that any publication describing this rat Vegfa gene sequence was a supporting reference for the assertion.
has_supporting_reference
Keeping the label has_supporting_reference instead of has_evidence_item_described_by because the later follows the pattern we use for true shortcut relations (i.e. that can be defined using property chains). For reasons outlined in the editor note, this is not such a shortcut relation.
evidence_has_supporting_reference
is_inconsistent_with
As an example, consider the assertion that "Variant X causes Disease Y". At an abstract level this represents a bfo: information content entity (or frbr:Work). This abstract assertion can be concretized / encoded various formats - e.g. a free-text sentence, an rdf graph, a blob of json, or stanza of XML. Each such manifestation might use a different model or structure to represent this knowledge. Each such concrete form is considered a separate resource/digital artifact at the 'manifestation' level, but each expresses the same knowledge.
The authored_by and date_authored properties allow us connect an abstract or concrete representation of this assertion to who and when the knowledge was originally generated. This will be the same agent and date for all formats/manifestations listed above.
The created_by and date_created properties allow us to connect a representation of the abstract or concrete assertion to who and when the specific manifestation was created in a particular format. The agent/dates here will be different for each of the formats/manifestations listed above.
A relation between an information content entity (or concrete manifestation of it as a particular resource/digital artifact), and the agent that originally generated the information content.
Older note - remove before releasing:
We intentionally avoid use of a more generic "creator" property here, as this term is used in established standards such as PAV and DC to specifically describe agents who generated a specific representation of an information content entity. For example, the pav:createdBy property is used specifically to describe agents contributing to a specific representation.
SEPIO, by contrast, aims to describe the agent(s) responsible for generating the abstract information content these concretized artifacts express. For this reason, SEPIO creates the more specific "stated_by" relation to explicitly distinguish the act of making a statement (generating its information content) from the act of creating a specific digital representation of the statement (generating a particular concretized artifact).
A explicit commitment to this more abstracted level of representation is a core feature of the SEPIO model, and has implications for how instances in the data are described, identified, and distinguished in practice.
In the case that the information artifact is an assertion, the responsible agent is the one who originally generated an assertion based on their evaluation of relevant evidence. If more than one agent is involved in this process, we may consider them collectively as a group or organization representing a single agent.
authored_by
A relation describing the degree of support provided by an evidence line for a target assertion or proposition.
The value of this property is typically a term from some defined set of values that enumerates categorical degrees of evidence strength (e.g. the CIViC five-teired 'evidence level' scale). Different systems or applications can create terms representing the levels of strength they wish to define for their use case.
evidence_line_strength
A relation holding between a generated artifact and an agent who evaluated its quality, completeness, or utility.
In SEPIO, the agent responsible for a particular evidence line is linked via the "evaluated_by" property. This reflects that perspective that evaluation of the relevance, strength, and direction of an evidence line w.r.t. a particular assertion are the key acts inherent in the evidence line's "creation".
We avoid using a "creator" relation here because this label is used in established standards such as PAV and DC to specifically describe agents contributing to a specific digital representation, as opposed to agents responsible for generating the underlying information content these concrete representations express.
A explicit commitment to this more abstracted level of representation is a core feature of the SEPIO model, and has implications for how instances in the data are described, identified, and distinguished in practice.
assessed_by
evaluated_by
A relation used to indicate context in which a particular assertion or proposition applies.
has_qualifier
A relation used to link an assertion or proposition to a source where evidence for it was found (i.e. a document, document part, database, etc)
cito:cites_as_evidence
Note that this may not qualify as a proper shortcut (i.e. it may not be valid to define using a property chain) for the same reason has_supporting reference is not defined as a property chain called has_evidence_item_described_by.
true
This is a shortcut relation to be used when publications are referenced as providing support for an assertion, but it is not clear how many evidence lines are described across these publications. In such cases, discrete evidence lines cannot be created, and the has_evidence_from_source relation is used to directly link the assertion to publications providing some form of evidence information.
has_evidence_from_source
A relation used to link an assertion or proposition directly to some indicator of the strength of the total evidence supporting it.
has_total_evidence_strength
This relation links an assertion or proposition directly to some indicator of the strength of the total evidence supporting it. It is used when there is not enough information to create evidence line(s) for the assertion, but the source provides some indication of the strength of the evidence supporting it.
Note that this is different than the notion of statement confidence, which describes how confident an agent is that a statement is true. Confidence may depend on factors in addition to the strength of the evidence (e.g. who made the prior probability that the asserted proposition could be true, who made the assertion and when, etc.)
has_evidence_level
A relation between an information content entity and an agent who made a contribution to its information content, or to its subsequent modification or assessment.
SEPIO intentionally creates its own hierarchy of contributor properties, instead of re-using terms from existing standards like PAV or Dublin Core - whose domain is structured digital resources. This is because properties such as pav:createdBy specifically describe agents who generated a specific digital representation of information, while SEPIO aims to describe agents responsible for generating the abstract information content that such a concrete representation may express.
The subject of 'contributor' relations in the SEPIO are explicitly abstract in nature - considered at the level of their information content as opposed to concretizations in particular digital resources or representations. For example, the SEPIO "stated_by" relation explicitly refers toan agent originally putting forth a statement as true (generating its information content), as opposed to an agent creating a specific digital representation of the statement (generating a particular concretized artifact such as a json object returned by an API).
Should further clarification become available with respect to whether PAV or DC contributor properties accommodate the nuanced definitions we require, we will re-consider their inclusion in SEPIO. For example, the pav:authoredBy property seems to refer specifically to the agent who generated information content expressed in a resource - and thus may be appropriate in the context of SEPIO. But even here, the range of the property is a particular authored digital resource, and not the information content it expresses. DC properties such as dc:contributor and dc:creator are ambiguous as to which level of contribution they describe.
has_contributor
A relation holding between a statement and an agent that validates its truth or accuracy - typically by reviewing the provenance and data on which it is based.
validity_assessed_by
validated_by
evidence_strength_assessed_by
ClinGen not using this, as they create contrigution objects and assign roles to capture such information. Can bring it back if there is need in some other use case/application.
obsolete_evidence_assessed_by
A relation holding between an artifact and a contribution made by a particular agent to its creation, modification, assessment, or destruction.
Consider sup-properties specific to the type of contribuion make, to support property chains for inferring a direct realtiomnship between the artifact/entitiy contributed to, and a related agent or date. At present, we could only support:
- qualified_contribution o date_of_contribution -> dc:date
Want to be able to support inferences such as:
- qualified_creation o date_of_contribution -> date_created
- qualified_evaluation o date_of_contribution -> date_evaluated
- qualified_modification o date_of_contribution -> date_modified
has_contribution
Analogous to PROV qualified Attribution - use to capture additional information about the contribution made by an agent, such as a role they played, or organization on behalf of which the contribution was made.
qualified_contribution
a relation between an information entity and an indicator of degree of confidence that the information it represents is true.
trust_rating
Confidence in an information entity can mean different things for different types of information. For example, for assertions this reflects the confidence an agent has that the proposition it puts forth is true. For things like data items, it reflects the confidence an agent has that the data accurately reflects the aspect of reality its was intended to measure.
confidence_level
a relation between an agent and an other agent, typically an organization, on whose behalf a Contribution is made.
performed_on_behalf_of
performed_for
A relation between one entity and an informtion content entity that provides a description of it.
Consider: http://semanticscience.org/resource/SIO_000557 ! 'is described by'
is_described_by
A relation indicating whether an evidence line supports or disputes a target proposition (or represents inconclusive evidence that is not sufficient for either).
evidenceDirection
evidence_direction
contributesTo
A relation between an agent and an entity toward which the agent made a contribution.
contributes_to
A shortcut relation that directly relates an assertion and an evidence item that contributes to one or more of its evidence lines (i.e. a piece of information that is used as evidence for or against its validity).
assertion_has_evidence_item
has_evidence_information
has_evidence_supported_by
This relation can be used to link an assertion directly to evidence items that support it. Evidence items are typically organized into 'evidence lines' that group them according to the argument(s) to which they contribute. This shortcut relation supports use cases where it is desirable to elide over this level of organization and create direct links from an assertion to the fundamental pieces of information that represent evidence supporting it.
A property chain (has_evidence_line o has_evidence_item -> has_evidence_with_item) is defined that can be used to infer this direct edge, facilitating interoperability between data sets that do and don't implement evidence lines to organize evidence items.
has_evidence_line_with_item
A relationship that holds between an assertion and a term that summarizes its asserted conclusion.
asserted_outcome
assertedConclusion
asserted_conclusion
Deprecate until there is a specific use case requiring this relation.
obsolete_has_quantifier
A relation that holds between a study finding and a data item it describes (i.e. a data item generated by the study whose results are described by the finding).
describes_supporting_data
describes_study_data
evidenceItemFor
evidence_item_for
As an example, consider the assertion that "Variant X causes Disease Y". At an abstract level this represents a bfo: information content entity (or frbr:Work). This abstract assertion can be concretized / encoded various formats - e.g. a free-text sentence, an rdf graph, a blob of json, or stanza of XML. Each such manifestation might use a different model or structure to represent this knowledge. Each such concrete form is considered a separate resource/digital artifact at the 'manifestation' level, but each expresses the same knowledge.
The authored_by and date_authored properties allow us connect an abstract or concrete representation of this assertion to who and when the knowledge was originally generated. This will be the same agent and date for all formats/manifestations listed above.
The created_by and date_created properties allow us to connect a representation of the abstract or concrete assertion to who and when the specific manifestation was created in a particular format. The agent/dates here will be different for each of the formats/manifestations listed above.
A relation between a particular information resource / digital artifact and an agent who made a primary contribution to its original creation.
With respect to information resources, this property is used to capture a creator of a particular representation/manifestation of the information content - e.g. as a web resource or digital artifact. To describe the creator of the information content carried by such a digital artifact or resource, us the 'authored_by' property.
created_by
A relation that holds between a statement or proposition which can be captured in part or in whole as a directional relationship between two entities, and the entity that representing the subject of this relationship.
has_subject
A relation that holds between a statement or proposition which can be captured in part or in whole as a directional relationship between two entities, and the property serving as the predicate in this relationship.
has_predicate
A relation that holds between a statement or proposition which can be captured in part or in whole as a directional relationship between two entities, and the entity that representing the object or value of this relationship.
has_object
A shortcut relation that links an assertion directly to a term representing the type of evidence that supports it.
true
Relation expands to has_evidence_line o rdf:type -> has_evidence_type
has_evidence_type
ExploratoryObjectProperty
A relation holding between a plan specification and a planned process it specifies, or the artifact the process generates.
specifies_creation_of
A relation describing the quality of the data used as evidence by an agent making an assertion.
This property is used to indicate the inherent quality of a piece of data, based on the rigor of the experiment that produced it. It is not a direct indicator of the strength of evidence the data may provide for an assertion.
The value of this property is typically a term from some defined set of values that enumerates categorical degrees of quality (e.g. the CIViC five star 'trust rating' scale) Different systems or applications can create terms representing the levels of quality they wish to define for their use case.
evidence_item_quality
evidence_for
is_evidence_line_for
A relationship between an information resource found in some information system, and the agent (person, organization, computational agent) who is responsible for sharing/providing it to that information system.
Note that this property connects a resource to an agent, not to some other information resource from which it came (e.g. another database or an API from which the resource in question was obtained). Use the 'source' property to capture this type of relationship.
Consider: pav:providedBy
provided_by
Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents.
This property is defined by OBAN to specifically link 'associations', which are proposition-level entities, to their object (sensu RDF). It is therefore a more specific relation than its has_object parent, which can be used to link a statement or proposition to its object.
association has object
Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents.
This property is defined by OBAN to specifically link 'associations', which are proposition-level entities, to the property representing the predicate of the reified triple. It is therefore a more specific relation than its has_predicate parent, which can be used to link a statement or proposition to its predicate.
association has predicate
Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents.
This property is defined by OBAN to specifically link 'associations', which are proposition-level entities, to their subject (sensu RDF). It is therefore a more specific relation than its has_subject parent, which can be used to link a statement or proposition to its subject.
association has subject
An agent that originated or gave existence to the work that is expressed by the digital resource.
The author of the content of a resource may be different from the creator of the resource representation (although they are often the same). See pav:createdBy for a discussion.
pav:authoredBy is more specific than its superproperty dct:creator - which might or might not be interpreted to also cover the creation of the representation of the artifact.
The author is usually not a software agent (which would be indicated with pav:createdWith, pav:createdBy or pav:importedBy), unless the software actually authored the content itself; for instance an artificial intelligence algorithm which authored a piece of music or a machine learning algorithm that authored a classification of a tumor sample.
The date of authoring can be expressed using pav:authoredOn - note however in the case of multiple authors that there is no relationship in PAV identifying which agent contributed when or what. If capturing such lineage is desired, it should be additionally expressed using PROV relationships like prov:qualifiedAttribution or prov:wasGeneratedBy.
Authored by
SEPIO creates this relation distinct from existing PAV and PROV relations (e.g. pcav:createdBy), which are too specific about whether a relation refers to the agent who created the abstract information content, vs who serialized and documented in concrete form.
http://purl.org/dc/terms/creator
An agent primary responsible for making the digital artifact or resource representation.
This property is distinct from forming the content, which is indicated with pav:contributedBy or its subproperties; pav:authoredBy, which identifies who authored the knowledge expressed by this resource; and pav:curatedBy, which identifies who curated the knowledge into its current form.
pav:createdBy is more specific than its superproperty dct:creator - which might or might not be interpreted to cover this creator.
For instance, the author wrote 'this species has bigger wings than normal' in his log book. The curator, going through the log book and identifying important knowledge, formalizes this as 'locus perculus has wingspan > 0.5m'. The creator enters this knowledge as a digital resource in the knowledge system, thus creating the digital artifact (say as JSON, RDF, XML or HTML).
A different example is a news article. pav:authoredBy indicates the journalist who wrote the article. pav:contributedBy can indicate the artist who added an illustration. pav:curatedBy can indicate the editor who made the article conform to the news paper's style. pav:createdBy can indicate who put the article on the web site.
The software tool used by the creator to make the digital resource (say Protege, Wordpress or OpenOffice) can be indicated with pav:createdWith.
The date the digital resource was created can be indicated with pav:createdOn.
The location the agent was at when creating the digital resource can be made using pav:createdAt.
Created by
Specifies an agent specialist responsible for shaping the expression in an appropriate format. Often the primary agent responsible for ensuring the quality of the representation.
The curator may be different from the author (pav:authoredBy) and creator of the digital resource (pav:createdBy).
The curator may in some cases be a software agent, for instance text mining software which adds hyperlinks for recognized genome names.
The date of curating can be expressed using pav:curatedOn - note however in the case of multiple curators that there is no relationship in PAV identifying which agent contributed when or what. If capturing such lineage is desired, it should be additionally expressed using PROV relationships like prov:qualifiedAttribution or prov:wasGeneratedBy
Curated by
Derived from a different resource.
Derivation conserns itself with derived knowledge. If this resource has the same content as the other resource, but has simply been transcribed to fit a different model (like XML -> RDF or SQL -> CVS), use pav:importedFrom. If a resource was simply retrieved, use pav:retrievedFrom. If the content has however been further refined or modified, pav:derivedFrom should be used.
Details about who performed the derivation (e.g. who did the refining or modifications) may be indicated with pav:contributedBy and its subproperties.
Derived from
The original source of imported information.
Import means that the content has been preserved, but transcribed somehow, for instance to fit a different representation model by converting formats. Examples of import are when the original was JSON and the current resource is RDF, or where the original was an document scan, and this resource is the plain text found through OCR.
The imported resource does not have to be complete, but should be consistent with the knowledge conveyed by the original resource.
If additional knowledge has been contributed, pav:derivedFrom would be more appropriate.
If the resource has been copied verbatim from the original representation (e.g. downloaded), use pav:retrievedFrom.
To indicate which agent(s) performed the import, use pav:importedBy. Use pav:importedOn to indicate when it happened.
Imported from
The URI where a resource has been retrieved from.
The retrieving agent is usually a software entity, which has done the retrieval from the original source without performing any transcription.
Retrieval indicates that this resource has the same representation as the original resource. If the resource has been somewhat transformed, use pav:importedFrom instead.
The time of the retrieval should be indicated using pav:retrievedOn. The agent may be indicated with pav:retrievedBy.
Retrieved from
Source accessed at
The resource is related to a given source which was accessed or consulted (but not retrieved, imported or derived from). This access can be detailed with pav:sourceAccessedBy and pav:sourceAccessedOn.
For instance, a curator (pav:curatedBy) might have consulted figures in a published paper to confirm that a dataset was correctly pav:importedFrom the paper's supplementary CSV file.
Another example: I can access the page for tomorrow weather in Boston (http://www.weather.com/weather/tomorrow/Boston+MA+02143) and I can blog ‘tomorrow is going to be nice’. The source does not make any claims about the nice weather, that is my interpretation; therefore the blog post has pav:sourceAccessedAt the weather page.
Web address of the resource
has_url
SEPIO creates a relation separate from existing PAV and PROV relations (e.g. pav:createdOn) which are too specific about whether a relation refers to the date on which the abstract information content was created, or when it was serialized and documented as a concrete digital artifact or resource with a particular format.
created_on
Consider:
1. http://purl.org/dc/terms/created
2. http://purl.org/pav/createdOn ! Created on
Def: The date of creation of the resource representation. The agents responsible can be indicated with pav:createdBy. This property is normally used in a functional way, indicating the time of creation, although PAV does not formally restrict this. pav:lastUpdateOn can be used to indicate minor updates that did not affect the creating date.
3. prov:generatedAtTime: The time at which an entity was completely created and is available for use.
obsolete_date_created
The date that a particular resource or artifact was last modified or updated.
date_last_updated
http://purl.org/dc/terms/modified ! Date Modified
Definition: Date on which the resource was changed.
Examples of modification include adding or removing content to/from a document, updating information in a data record, fixing errors in a manuscript, etc. The important thing is that the modification retains the identity of the artifact.
date_modified
The date that a particular resource or artifact was last evaluated - typically to assess its quality, completeness, accuracy, conformance, etc.
Evaluating an artifact does not involve its modification - however the suggestion of alterations can be a separate outcome of an evaluation. If the artifact is modified by the agent during or subsequent to the evaluation, this date can be captured using the date_modified property.
date_evaluated
The date that a particular resource or artifact was formally submitted to be reviewed and/or included in some larger resource (e.g. database, registry, collection, etc.).
http://purl.org/dc/terms/dateSubmitted
date_submitted
Consider: http://www.w3.org/ns/prov#startedAtTime
start_date
date_created_before
Relation between a report and a string of text that it contains
has_textual_part
A relation holding between an information content entity and the date on which the information it expresses was initially generated.
Consider http://purl.org/pav/authoredOn
date_authored
occurredAtTime
process_date
time_of_activity
activity_date
Consider: http://www.w3.org/ns/prov#endedAtTime
end_date
Consider: http://purl.org/pav/curatedOn
Definition: The date this resource was curated.
pav:curatedBy gives the agent(s) that performed the curation.
This property is normally used in a functional way, indicating the last curation date, although PAV does not formally restrict this.
The value is of type xsd:dateTime, for instance "2013-03-26T14:49:00+01:00"^^xsd:dateTime. The timezone information (Z for UTC, +01:00 for UTC+1, etc) SHOULD be included unless unknown. If the time (or parts of time) is unknown, use 00:00:00Z. If the day/month is unknown, use 01-01, for instance, if we only know September 1983, then use "1983-09-01T00:00:00Z"^^xsd:dateTime.
obsolete_date_curated
Consider: http://purl.org/pav/lastUpdateOn
date_updated
The date that a particular resource or digital artifact was formally validated as meeting some standard for quality, completeness, relevance, etc..
date_validated
A quantitative value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about.
This property has a similar intent as assertion_confidence_level, but used for quantitative numerical values.
The 'confidence score' property does not only include statistical measures such as p-values that explicitly indicate a level of confidence. It also includes any quantitative score against which a threshold for making an assertion is defined - where the distance of this score from this threshold can be interpreted as an indicator of how much confidence we might have that the asserted conclusion is true.
For example, many silico prediction tools such as SIFT interrogate biological sequence data to calculate a score that reflects the likelihood that a particular sequence variant negatively impacts gene product function. A variant is interpreted to be 'Tolerated', 'Damaging', or 'Deleterious' based on how its score compares against pre-defined thresholds. Here, we may have less confidence that a variant with a score just above the 'Damaging' threshold is truly damaging, versus a variant whose score is well above the threshold.
confidence_score
A relation used to link a statement to some quantitative measure about the statement itself (e.g. a confidence score)
statement quantifier
A relation used to qualify the meaning of a statement.
Most commonly used with a "NOT" value to negate a statement - i.e. indicate that the claim implied by its strucuted representation is not true. For example, the negation qualifier on the following OBAN-style association would make the claim that BRCA2 is NOT linked to the phenotype 'abnormal lymphocyte count':
<:assertion1> a OBAN:association;
OBAN:association_has_object HP_0040088 (abnormal lymphocyte count);
OBAN:association_has_predicate RO:0002200 (has_phenotype);
OBAN:association_has_subject HGNC:1101 (BRCA2);
SEPIO:0000346(quallifier) "NOT".
statement qualifier
date_created_after
probabilistic quantifier
A numerical value that quantifies the strength of evidence provided by a line of evidence. This is a counterpart to the evidence_line_strength object property - for use when the strength of evidence is captured using a quantitiative score/measure.
evidence_line_strength_score
occurred_in
process_location
activity_location
ExploratoryDataProperty
ObsoleteDataProperty
Date that a particular representation/manifestation of an information content entity was created - e.g. as a web resource or digital artifact.
To describe the date that the information content carried by a digital artifact or resource as generated, use the 'date_authored' property.
date_created
http://www.w3.org/ns/prov#value
'This property serves the same purpose as rdf:value, but has been reintroduced to avoid some of the definitional ambiguity in the RDF specification (specifically, 'may be used in describing structured values'). The editor's definition comes from http://www.w3.org/TR/rdf-primer/#rdfvalue'
has_value
An account of a resource.
description
A point or period of time associated with an event in the lifecycle of an information entity or resource.
Consider: http://purl.org/pav/contributedOn
date
identifier
title
doi
digital object identifier (doi)
The version number of a resource. This is a freetext string, typical values are "1.5" or "21". The URI identifying the previous version can be provided using prov:previousVersion.
This property is normally used in a functional way, although PAV does not formally restrict this.
version
A name for some thing.
name
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
A database is an organized collection of data, today typically in digital form.
http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Database
database
journal article
Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
a report that is published in a journal
person:Alan Ruttenberg
person:Chris Stoeckert
OBI_0000159
group:OBI
journal article
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
data item
1
- Data Items: A '548.5 mg/dl' measurement of blood glucose in mutant mice.
- Protocols: A blood glucose assay protocol that describes how the measurement was taken.
- Calculations: A 1.3951e-24 p-value statistic indicating a significant increase relative to wild-type mice.
- Assertions: An assertion stating that "Lpr1 leptin receptor mutations can lead to diabetes".
- Publications: A journal article that publishes this assertion.
- Figure/Tables: A figure or table from this article that present data supporting it.
- Software/Algorithms: A text-mining algorithm that mines the literature to identify and extract the assertion.
- Databases: The MGI (Mouse Genome Informatics) database that stores the assertion as a structured gene-disease annotation.
A generically dependent continuant that is about some thing.
ICEs are abstract entities that convey information about things in the world. ICEs represent the information encoded in physical artifacts such as photographs, books, or digital storage medium (as opposed to the physical medium itself). A particular ICE can be encoded simultaneously in many physical or digital mediums and formats. For example, only one instance of the first edition of "War and Peace" exists as an ICE, representing information conveyed in this work. But many instances of "War and Peace" exist at the level of their physical concretizations in printed books or digital devices.
information content entity
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
algorithm
report
Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)
2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
PERSON:Chris Stoeckert
GROUP: OBI
OBI_0000099
report
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
person:Allyson Lister
person:Chris Stoeckert
OBI_0000042
group:OBI
data set
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Alan Ruttenberg
method
plan specification
measurement datum
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
person:Chris Stoeckert
OBI_0000305
group:OBI
measurement datum
A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
table
figure
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
PERSON: Lawrence Hunter
figure
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
PERSON: Lawrence Hunter
document
publication
A journal article or book
A document that has been accepted by a publisher
PERSON: Lawrence Hunter
publication
patent
US Patent 6,449,603
A document that has been accepted by a patent authority
PERSON: Lawrence Hunter
patent
planned process
Injecting mice with a vaccine in order to test its efficacy
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
Bjoern Peters
branch derived
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
planned process
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
investigation
assay
p-value
A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
May be outside the scope of OBI long term, is needed so is retained
PERSON:Chris Stoeckert
WEB: http://en.wikipedia.org/wiki/P-value
p-value
standard error
A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution.
person:Chris Stoeckert
group:OBI
see P-Value
standard error
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
experimental protocol
protocol
drawing a conclusion based on data
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
Bjoern Peters
drawing a conclusion based on data
A measurement datum that is reported on a categorical scale
obsolete_categorical measurement datum
binding assay
Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen.nnThe following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture.
An assay with the objective to characterize the disposition of two or more material entities to form a complex.
PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum
PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum
binding assay
protein localization assay
An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied.
Rebecca Tauber
OBI development call
protein localization assay
The proposition that BRCA1:2685T>A causes familial breast cancer.
An abstract entity representing the sharable meaning of what is expressed in a particular assertion.
In the SEPIO model, an assertion is akin to an act in speech or text that expresses beleif in the truth of a proposition. It is the proposition that represents the semantic content of a claim, and bears truth value.
Mappings to terms from related models:
1. http://purl.org/see/rdo#proposition
A SEPIO proposition is equivalent to a 'proposition' from the Semantic EvidencE framework. "The class rdo:proposition represents propositions i.e. the sharable objects of propositional attitudes like belief or desire and the bearers of truth values. As truth bearers they are either true or false. They are taken to represent the semantic content of sentences or larger lexical entities formulated in some natural or artificial language.")
2. http://purl.org/mp/Holotype
The notion of a holotype from the Micropublications model is related to a SPEIO proposition - in that it represents a statement that is selcted to all other statements expressing the same meaning.
3. http://purl.org/oban/association
An OBAN proposition is a more type of proposition, that is structured/expressed according to the specifications laid out in the OBAN ontology.
http://plato.stanford.edu/entries/propositions
The notion of a proposition, and its relationship to an assertion, derives from the domain of logic and philosophy [12]. Propositions are abstract entities that, like numbers, are independent of space and time. They represent only the meaning that is expressed in a particular agent’s assertion, and are ‘sharable’ in that the same proposition can be expressed in many different assertions. Propositions are primary bearers of truth value, in that they are true or false.
From http://plato.stanford.edu/entries/propositions/: "Propositions are the sharable objects of the attitudes and the primary bearers of truth and falsity. This stipulation rules out certain candidates for propositions, including thought- and utterance-tokens, which presumably are not sharable, and concrete events or facts, which presumably cannot be false."
proposition
The following are three seperate assertion instances, that assert the same proposition (that BRCA1:2685T>A causes familial breast cancer)
1. Counsyl's assertion on October 5, 2009 that BRCA1:2685T>A causes familial breast cancer.
2. The ENIGMA consortium’s assertion on September 18, 2010 that BRCA1:2685T>A causes familial breast cancer.
3. A later assertion by the ENIGMA consortium on May 9, 2013, based on new evidence, that BRCA1:2685T>A causes familial breast cancer.
A statement made by a particular agent on a particular occasion that a particular proposition is true, based on the evaluation of one or more lines of evidence.
SEPIO distinguishes two high-level subtypes of statements:
1. Findings are statements that report the immediate, objective results of an experiment, observation, or study - without bias or interpretation. A finding statement results simply from the act of reporting or summarizing these direct observations, calculations, or measurements.
2. Assertions, by contrast, result from acts of interpretation and/or inference, based on information used as evidence. The statement here is a conclusion drawn from critical evaluation of this more foundational information, and its validity depends on the quality of this information and the act of interpretating as evidence.
claim
evidence-based assertion
propostional assertion
Derived from http://purl.org/see/rdo#assertion
The identity of a particular assertion is dependent upon (1) what it claims to be true (its semantic content, aka its ‘proposition’), (2) the agent asserting it, and (3) the occasion on which the assertion is made. Many agents can make assertions expressing belief in the same proposition (e.g. ENIGMA’s assertion that that BRCA1:2685T>A causes familial breast cancer is a separate instance than Counsyl’s assertion of the same underlying proposition). Likewise, a single agent can make more than one assertion of belief in the same proposition on different occasions (e.g. ENIGMA may make a separate assertion of the same proposition that BRCA1:2685T>A causes familial breast cancer at a later date, based on additional evidence).
Assertions as defined in SEPIO are the result of some logical inference made based on the interpretation of evidence. They put forth a proposition that may or may not be true - the validity of which ultimately rests on the quantity, quality, diversity, and concordance of evidence supporting it.
Statements directly reporting study results or observations are not considered assertions in this sense, as they merely report what was observed or recorded, but do not rely on a leap of logical inference (see 'study finding').
assertion
An example of an evidence line would be the argument that a finding such as "Lepr1 KO mice exhibit lower blood glucose levels than matched WT controls" makes in support of the proposition that "Lepr1 gene is involved in diabetes". The Evidence Items supporting this line of evidence could include experimental data from a study exploring blood glucose levels in Lepr1 KO mice, such as a 548.5 mg/dl measurement of blood glucose in a Lepr<tm1b/tm1b> mutant mouse, or a 1.3951e-24 p-value indicating this measure to be significantly different from wild-type mice.
Here, the finding and its supporting data exist independently of their use as evidence. An evidence line based on this finding comes into existence only when an agent interprets this finding as providing a meaningful argument for a particular proposition, in the act of making an assertion.
(This example is based on data from the IMPC record here: http://bit.ly/2t4J1TI)
An evidence line represents an independent and meaningful argument for or against a particular proposition, that is based on the interpretation of one or more pieces of information as evidence.
evidence-based argument
An evidence line is created through the interpretation of one or more pieces of information that collectively support a meaningful argument for or against a proposition. To qualify as an Evidence Line, this argument must be independently significant as evidence - i.e. it must be capable of affecting the probability of accepting the target proposition as true. This does not mean, however, that it is independently sufficient to establish belief in the proposition, as additional evidence lines may be required to ultimately accept the proposition as true.
For example, in the ACMG framework for variant interpretations establishes "absence in population databases" as a type of evidence line that can argue for the pathogenicty of a particular variant. But this argument alone is not considered sufficient to establish a variant's pathogencity, as the other types of evidence are additionally required to establish the truth of this Proposition (e.g. a line of evidence demonstrating the variant to have a deleterious effect on protein function, or showing it to segregate with disease features in a family tree).
evidence line
An act of interpreting evidence to make an assertion of belief that a particular proposition is true
Mappings to terms from related models:
Likely equivalent to http://purl.org/see/rdo#act_of_inference.
May be equivalent to http://purl.obolibrary.org/obo/ECO_0000217 ! assertion method.
act of assertion
An assertion process includes the processes of interpreting data and evaluating it as evidence for the validity of a proposition. They are affected by a particular agents on a particular occasions, and can be specified by assertion methods or guidelines.
assertion process
A planned process executed in the performance of scientific research wherein systematic investigations are performed to establish facts and reach new conclusions about phenomena in the world.
Data generation process are typically experimental studies or observations, but can include any process generating information used to evaluate a claim. This is an organizational class that groups more specific types of such processes that are most commonly used in generating data used as evidence to support claims. These processes produce informational artifacts such as measured data values, derived statistical calculations and confidence measures, or statements representing summaries or conclusions drawn from such data.
research activity
A directive information entity that specifies an algorithm or heuristics for evaluating evidence in the process of making an assertion.
SEPIO implements several OWL individuals representing instances of commonly applied assertion methods, primarily those used in pathogenic variant classification such as the ACMG variant classification criteria.
Assertion methods can be informal guidlines or heuristics that support manual evaluation of evidence, e.g. the ACMG Variant Classification Guidelines. Assertion methods can also be formally encoded as algorithms that allow computational or statistical analysis of data as evidence in support of making an assertion - e.g. multifactorial analysis algorithms that operate on specified data to generate a quantitative score indicating the validity of a particular proposition.
assertion method
A role borne by a person, group, organization, or information processing entity (e.g. software, algorithms) in virtue of its active participation in a process leading to some outcome (e.g the generation, modification, or provision of some entity).
agent role
http://purl.org/see/rdo#agent_role
In the context of evidence and proveannce, agents are persons, groups, organizations, or software that are responsible for making assertions or generating the evidence and data that support them.
contributor role
A role inhering in any material or information artifact that is used by an agent as specified input into a planned process.
In the context of evidence and provenance for scientific claims, resources are entities that are used by agents to facilitate processes aimed at the generation of assertions or the evidence and data that support them. Examples include instruments, reagents, model systems, software, and protocols.
resource role
Mappings to related terms:
1. http://purl.obolibrary.org/obo/ECO_0000218 ! manual assertion
ECO Definition/Comment: A manual assertion could be based on evidence that is generated by and interpreted by a human or it could involve human review of computationally generated information.
obsolete_manual assertion process
An assertion process performed through algorithmic analysis by a computational agent, independent of human review.
Mappings to related terms:
1. http://purl.obolibrary.org/obo/ECO_0000203 ! automatic assertion
ECO Definition/Comment: An automatic assertion is based on computationally generated information that is not reviewed by a person prior to making the assertion. For example, one common type of automatic assertion involves creating an association of evidence with an entity based on commonness of attributes of that entity and another entity for which an assertion already exists. The commonness is determined algorithmically.
Ultimately even automated assertions require a human agent to set a confidence threshhold that determines when a computational output (e.g. a sequence similarity p-value) justifies an assesrtion being made.
obsolete_automated assertion process
The process history leading to the creation and current condition of an artifact.
Consider whether it is appropriate to place this under the BFO:history class, which may apply only to histories of "material entities or sites". And consider if we want/need to define this class at all - as it is not used to model data - only as a means to record what SEPIO considers provenance to be, and how it is different from evidence.
For scientific assertions/claims, this is the process history leading to the asseertion being made, including processes through which evidence is evaluated, and processes through which information used as evidence is created. The transitive nature of provenance means that the provenance history of informtion used as supporting data becomes provenance for an assertion that uses this information as evidence. Provenance metadata describes these processes, including accounts of who conducted these processes, what entities participated in them, and when/where they occurred.
provenance
A study that involves primary research of subjects or specimens in a natural, cliniclal, or laboratory setting.
primary research study
Formal clinical study performed using cohorts of multiple patients
clinical study
http://purl.org/net/OCRe/research.owl#Interventional_study
interventional clinical study
http://purl.org/net/OCRe/research.owl#Observational_study
observational clinical study
http://purl.org/net/OCRe/research.owl#Case_control_study
case-control clinical study
A research dtudy perfomred using an experimental model system such as a cell line, or model organism.
experimental model study
in vitro study
in vivo study
cell-based in vivo study
tissue-based in vivo study
whole organism in vivo study
organism-based in vivo study
A study based only on analysis of existing data, as found in artifacts such as community/curated databases, raw datasets, or publications.
data-driven study
secondary research study
A curation-based study that uses only one or more literature publication as input data source.
Based on ClinVar 'literature only' collection method: "for submissions that provide the interpretation of a variant from one or more publications. No additional curation has been performed by the submitter; the interpretation is from the publication(s) only."
literature-based study
Based on Clinvar 'curation' collection method: "for variants that were not directly observed by the submitter, but were interpreted by curation of multiple sources, including clinical testing laboratory reports, publications, private case data, and public databases."
curation-based study
A study based on analysis of data gathered from baseline studies of a population group of apparently unaffected individuals to assess allele frequencies
ClinVar
reference population data study
A planned proccess that executes some study design or protocol to generate scientific data that is interpreted to test or generate a hypothesis.
Explore the classification of study types here as a possibility to implement in SEPIO.
https://mcw.libguides.com/evidencebased/studies
Useful because these map to the strength of the evidence each might provide.
A research study is considered broadly to be any scientific activity aimed at answering a research question. Studies can be simple or complex, depending on the scope of the question being explored and the extent of resources deployed in doing so. They may include a full research investigation, a set of experiments, or a single experiment or assay. Regardless, that act of sumamrizing any results as a finding statement is considered part of the study.
research study
A group of individuals (organisms, specimens, samples) that are subjects in an observational or intervention study, and whose members represent experimental replicates as defined in a study design by the same independent variable specifications (i.e. subjected to the same selction criteria or set of experimental interventions).
Consider: STATO_0000193, OBI_0000174
obsolete_study group
A planned process in which existing data is collected, organized, and improved in preparation for subsequent use.
curation
A data item that quantifies the degree of support an agent believes an evidence line to provide for a particular proposition.
Consider also framing as categorical measurement values?:
A categorical measurement reflecting an agent's cognitive quantification of the degree of support (s)he believes an evidence line to provide for a particular proposition.
The strength of a line of evidence typically depends on the *type* and *quality* of the study(ies) that generate its supporting evidence items.
1. Type of Study: In a particular domain of research, certain types of studies are commonly held to produce data that is more meaningful and reliable than others, as evidence for a particular type of assertion. These more reliable studies tend to draw on experimental systems that more accurately replicate the natural phenomenon being studied, and experimental designs that reduce confounding variables and biases. For example, in vivo studies of gene function provide stronger evidence than in vitro systems that may not replicate all aspects of the biology of a living system, and randomized controlled clinical trials are held to be more reliable than retrospective or case control studies that are more susceptible to confounding factors.
2. Quality of Study: A given study can be performed to varying degrees of rigor and comprehensiveness, irrespective of the type of study it represents. This is another important factor in assessing the overall strength of evidence it may produce. Higher quality studies will have carefully defined controls, and be replicated numerous times to ensure reproducibility. Other factors that are often used as secondary indicators of the quality of research data include the quality of the journal in which it is published, and the reputation of the lab or institution performing the study.
In SEPIO, the notion of evidence quality is captured in an attribute separate from the notion of evidence strength. And the notion of study type can be represented in the type assigned to a study instance, or the evidence code used to type an evidence line (which are often based on the type of study that produced the evidence data). Evidence strength typically relies on assessment of one or both of these more fundamental attributes of evidence.
evidence strength
A study that documents observations or findings from a single patent.
case reporting
patient case study
evidence role
- the raw count data from a case-control study comparing the frequency of an allele in two cohorts or populations
- the calculated p-value as a measure of statistical significance of the difference identified in the study
- a published figure documenting these data
- an author statement summarizing the outcomes of the study (i.e. a 'study finding')
- a broader conclusion inferred from interpretation of the data reported in a study (i.e. an evidence-based 'assertion')
An information content entity that is used as evidence to evaluate the validity of a target assertion or proposition.
evidence
evidence information
'Evidence Item' is a broad term covering any information interpreted as evidence in the act of making an assertion.
Classes representing different types of evidence items are imported here from ontologies such as OBI, IAO, and STATO, and include:
- measured data values
- derived data values such as statistical calculations and confidence measures
- figures presenting or describing such data
- author statements representing summaries of or conclusions drawn from such data
- established facts in a field of research
Note that publications and reports are considered separately from 'evidence items', as a they *contain* information (data values, figures author statements) that can be used as evidence. But on its own a publication or report is merely a proxy for this information.
evidence item
creator role
assessor role
validator role
approver role
curator role
1
The actions taken by a particular agent in the creation, modification, assessment, or deprecation of an artifact.
This concept is similar in meaning and usage to PROV:Attribution. Consider aligning or adopting.
Contribution instances organize information about who, when, where, how (e.g. what roles were played), and on whose behalf these actions were performed. The scope of a Contribution instance includes only the actions of a single agent in contributing to a particular artifact - which may be performed in one continuous effort, or multiple discrete sessions of work. The contributing agent can be a single individual, or an organization of multiple individuals acting together.
contribution
Findings statements tend to take the form of "We observed that . . . ", or "Assay X revelaned that . . . ", or "X was determined to be Y in a study of . . . ".
For example:
"Smith et. al observed that a positive response to imatinib treatment was two-fold higher in a cohort of leukemia patients bearing Bcr-Abl fusions compared to those lacking this driver mutaiton."
A statement summarizing the outcome of a sequencing analysis: "DNA sequencing data from patient X revealed an A->T mutation at position 2143 in gene Y".
A statement summarizing the outcome of a variant population frequency study: "The frequency of variant X was determined to be 0.00015 in a cohort of non-finnish european subjects described in the ExAC dataset."
A statement describing the immediate results of a research study, describing what was directly observed, measured, or derived through mathematical calculation.
In SEPIO, a high-level distinction is made between statements that are 'findings' vs 'assertions'. Findings are statements that report/summarize what was directly observed or calculated in a study, and are about only the immediate participants in the experiment or study. As such, findings involve no interpretation or inference from the data to draw broader conclusions. Assertions, by contrast, are statements that derive from some degree of interpretation or inference based on the evaluation of 'evidence', and often make broader claims about the types or categories to which study participants belong. This distinction is important because the provenance and validity of a 'finding' statement does not depend on subjective interpretation of 'evidence' in the same way that of an assertion does. This has modeling implications for how findings and assertions are linked to information that supports them.
In practices, instances of 'study findings' are used to group one or more data items from a particular research study that are relevant as evidence for an assertion. The utility of this class is in allowing the shared provenance of these data items to be more efficiently represented - as things like agent, date, and methods can be described once for the data set and inferred to apply to all individual data items that comprise it.
study outcome
- While the act of generating a finding is simpler, it does involve some cognitive effort that could be guided by some method (i.e., one defining what experimental context should be included in the finding statement, and how this and the observed outcomes are reported). Which means that findings are not the direct output of an assay, which merely generates data. So perhaps in SEPIO we commit to only considering research processes at the level of studies - such that even assays would potentially involve some act of summarizing the results as a finding.
- Note that at present 'study data sets' can serve the same 'organizational' purpose as 'study findings' - we should converge on one recommended way to perform this level of organization of evidence data.
A study finding is a statement that summarizes the immediate results of a particular experiment or study. It describes only what was directly observed, measured, or calculated, and optionally the experimental context of these observations. It does not describe more general conclusions that may have been inferred from such results. As such, the scope of what a finding describes is limited to the direct participants in the study - i.e. it is about only the instances observed or measured in the study. It makes no broader inference or conclusion about types or classes to which these instances belong.
This is not to say that the onserved findings are necessarily accurate or correct - only that they were indeed made in a particular study. For example, the finding that "Sequencing of DNA from patient X revealed an A->T mutation at position 2143 in gene Y" is a matter of fact - this was the outcome of the assay, even if the finding is an artifact of low sequencing coverage. Metadata about the finding (e.g. sequencing methods/reagents used, coverage or read depth) are recoded so users can judge for themselves whether the objectively reported finding accurtely reflects the biology it describes.
SEPIO distinguishes two high-level subtypes of statements:
1. Findings are statements that report the immediate, objective results of an experiment, observation, or study - without bias or interpretation. A finding statement results simply from an act of reporting or summarizing these direct observations, calculations, or measurements.
2. Assertions, by contrast, result from acts of interpretation and/or inference, based on information used as evidence. The statement here is a conclusion drawn from critical evaluation of this more foundational information, and its validity depends on the quality of this information and its interpretation as evidence.
study finding
The following is derived from https://en.wikipedia.org/wiki/Statement_(logic):
Examples of sentences that are (or make) statements:
"Socrates is a man."
"A triangle has three sides."
"Madrid is the capital of Spain."
"There are five ducks on the lake"
"The BRAF V600E mutation causes breast cancer"
Examples of sentences that are not (or do not make) statements:
"Who are you?"
"Run!"
"Greenness perambulates."
"I had one grunch but the eggplant over there."
"The King of France is wise."
"Broccoli tastes good."
The first two examples are not declarative sentences and therefore are not (or do not make) statements. The third and fourth are declarative sentences but, lacking meaning, are neither true nor false and therefore are not (or do not make) statements. The fifth and sixth examples are meaningful declarative sentences, but are not statements but rather matters of opinion or taste.
An information content entity expressing a declarative sentence that is either true or false.
From https://en.wikipedia.org/wiki/Statement_(logic) (2017-06-21):
"A statement is a declarative sentence that bears truth value, in that it can be either true or false. This definition derives from the domain of logic, where a statement is either (a) a meaningful declarative sentence that is either true or false, or (b) that which a true or false declarative sentence asserts. In the latter case, a statement is distinct from a sentence in that a sentence is only one formulation of a statement, whereas there may be many other formulations expressing the same statement . . . In (this treatment), "statement" is introduced in order to distinguish a sentence from its informational content. A statement is regarded as the information content of an information-bearing sentence. Thus, a sentence is related to the statement it bears like a numeral to the number it refers to. Statements are abstract logical entities, while sentences are grammatical entities."
----
Note that the definition in (b) describes something closer to the notion of a 'Proposition' as defined in SEPIO?
Statements are sentences (or, more precisely, the information content of sentences) that declare a definitive or proposed fact - expressing something about the world or one's experience of it that may or may not be true. The identity of a particular Statement is dependent upon (1) what it reports as true (its semantic content), (2) the Agent stating it, and (3) the occasion on which the statement is made.
The phrase "the pink elephant" describes an entity, but is not a 'statement' as it has no truth value. By contrast, the phrase "the pink elephant is in the room" is a statement as this can be evaluated for its truth.
statement
A statement describing something that was observed or recorded.
In SEPIO, a high-level distinction is made between Statements that are 'Observations' vs 'Assertions'. Observations are statements that report what is observed, and are inherently true in the sense that they reflect an agents particular experience. Assertions are statements that derive from some degree of interpretation or inference based on the evaluation of 'evidence'.
This distinction is important because the ultimate truth of observations or findings do not depend on evidence in the same way that the truth of assertions does. Accordingly, any data related to an observation is not treated as evidence, and captured as observations.
An observation reflects only what an agent observed or device recorded. It is therefore considered a matter of fact, rather than a propositional assertion that may or may not be true. This does not mean that the observations or recordings were necessarily accurate or correct - only that they were indeed made by an agent. For example, the observation that "I counted six ducks in the pond" is a matter of fact, even if there are actually seven because I missed one that was hiding in the reeds.
obsolete_observation
A statement (ie an assertion or finding) that is used as evidence to evaluate the validity of a target assertion or proposition.
Term is confusing and not required for current use cases. Main reason it was creaated is that his term is used in efforts like CIViC, and we wanted to be clear about how it fits into the SEPIO model. But this can be accomplished in documentation outside of the ontology.
Axioms:
Eq:
statement
and (contributes_to_evidence_line some 'evidence line')
Sc:
'information content entity'
has_role some 'evidence role'
Evidence Statements can be 'findings' that summarize data and outcomes from a particular study, or evidence-based 'assertions' that make a broader claim, as inferred from the interpretation and evaluation of previously generated information.
obsolete_evidence statement
Research data, or a product derived from research data such as data sets or figures, that are used as evidence to evaluate the validity of a target assertion or proposition.
Evidence data is not classified as a 'data item' because it is intended to cover products derived from data such as figures, tables, and data sets.
evidence datum
Term is confusing and not required for current use cases.
Axioms:
Eq: ('data item' or table or figure)
and (contributes_to_evidence_line some 'evidence line')
Sc:
'information content entity'
has_role some 'evidence role'
Instances of this class can include elemental 'data items' such as experimental measurements or derived statistical calculations or scores (e.g. a 548.5 mg/dl blood glucose level, or a 1.3951e-24 p-value), data sets containing several such values and possibly metadata about them, or tables/figures that render such data for human consumption.
The notion of 'evidence data' is meant to be contrasted with the notion of an 'evidence statement', which is a statement used as evidence. (Statements here are logical sentences with truth value that are typically supported by interpretation of more fundamental data).
obsolete_evidence data
A set of data arranged in rows and columns.
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C48693 ! Data Table
Not required for data models.
obsolete_data table
A study with the goal of assessing and documenting phenotypes exhibited by one or more patients.
Source: ClinVar (" 'Phenotyping only' is intended for variants that are submitted to ClinVar to provide individual observations with detailed phenotype data, such as submissions from clinicians or patient registries, without an interpretation from the submitter. The interpretation from the testing laboratory may be provided in a separate field.")
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/release_notes/20170803_data_release_notes.pdf
patient phenotyping study
A data item that quantifies the level of confidence an agent has that a particular piece of information is true.
confidence level
Source: ClinVar (" 'Provider interpretation' is intended for variants that were interpreted by a clinical provider. For example, the clinician may reclassify the variant using detailed patient phenotype information that was unavailable to the testing laborator")
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/release_notes/20170803_data_release_notes.pdf
provider interpretation
Organizational class that groups classes imported from the skos model to support creation and definition of value sets for particular SEPIO data model implementations.
skos terms
Consider IAO:0000104 (plan specification).
plan specification
Decided to use IAO:plan specification here. Will give this term 'method' as a SEPIO-preferred label.
An information content entity that specifies instructions for how a particular objective can be achieved.
obsolete_method
The set of data output from a study of the frequency of a particular allele in a particular population, which includes the following data (and metadata) items:
{
"ascertainment": "ExAc ascertainment method"
"population": "Non-Finnish European"
"allele": "CAR:CA011797",
"alleleCount": 66706,
"alleleNumber": 1,
"alleleFrequency": 0.00001499,
"homozygousAlleleIndividualCount": 0
}
This collection of data may be described by, but remains distinct from, a 'study finding' statement that summarizes the results in narrative form.
A data set comprised of data items produced by a single research study.
Instances of this class are used in SEPIO to group one or more data items from a particular research study that are relevant as evidence for an assertion. The utility of this class is in allowing the shared provenance of these data items to be more efficiently represented - as things like agent, date, and methods can be described once for the data set and inferred to apply to all individual data items that comprise it.
The data items comprising a study data set may include primary measurements, derived calculations, metadata about study participants and methods, or parameters of execution.
A research study is considered broadly to be any scientific activity aimed at answering a research question. Studies can be simple or complex, depending on the scope of the question being explored and the extent of resources deployed in doing so. They may include a full research investigation, a set of experiments, or a single experiment or assay.
study data set
A declarative sentence that expresses a belief or judgement that is not necessarily based on fact or knowledge.
Opinions are matters of subjective judgement or taste, and typically not able to be scientifically validated as objectively true based on empirical evidence. In this way, they are distinct from statements that have inherent truth value.
obsolete_opinion
A data item that indicates an agent's assessment of whether an evidence line supports or disputes a target proposition (or represents inconclusive evidence that is not sufficient for either).
Consider also treating this as an attribute/quality of an evidence line:
An attribute of an evidence line describing whether it supports or disputes a target proposition (or represents inconclusive evidence that is not sufficient for either).
evidence direction
A data item that indicates the quality of the data used as evidence by an agent making an assertion.
The quality of an evidence item is a measure of the rigor applied in performing the study and anlysis tasks used to produce it. Higher quality studies will have carefully defined controls, and be replicated numerous times to ensure reproducibility. Other factors that are often used as secondary indicators of the quality of research data include the quality of the journal in which it is published, and the reputation of the lab or institution performing the study. Evidence qualitty is an important factor in assessing the overall strength of evidence it may produce.
evidence quality
Recommendations are another type of statement besides assertions that can be supported by evidence. They don't put forth a proposed facts as true, but instead describe a recommended action on the foundation of evidence that it will be beneficial.
recommendation
A hypothesis is another type of statement that, like an assertion, can be supported by evidence. It puts forward a possible fact as true, but does not express an agents belief in this fact. Rather, it is a possible fact whose truth will be explored via reasoning or experimentation.
hypothesis
A document containing a collection of data or statements about some entity.
http://semanticscience.org/resource/SIO_000088 ! 'record'
'Record' here is broadly defined to include any document holding (typically) structured information about a particular entity. This can include individual records from a database or knowledgebase that hold information about the subject of the record.
Specific examples include:
- A single row of a table in a relational database.
- A JSON or XML document holding information describing some entity.
- A VCF File describing varaints in a patient, or a single row in this VCF file describinng a particular variant.
- A Uniprot knowldgebase record describing the BRCA2 protein (http://www.uniprot.org/uniprot/P51587)
- A ClinVar knwoledgebase record describing an assertion about the pathogenicity of the NM_000059.3(BRCA2):c.10G>T variant (https://www.ncbi.nlm.nih.gov/clinvar/variation/51063/)
- An EHR record for a hospital patient.
record
a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data.
Alejandra Gonzalez-Beltran
Orlaith Burke
Philippe Rocca-Serra
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic).
statistic
A z-score (also known as z-value, standard score, or normal score) is a measure of the divergence of an individual experimental result from the most probable result, the mean. Z is expressed in terms of the number of standard deviations from the mean value.
Alejandra Gonzalez-Beltran
Orlaith Burke
Philippe Rocca-Serra
https://controls.engin.umich.edu/wiki/index.php/Basic_statistics:_mean,_median,_average,_standard_deviation,_z-scores,_and_p-value#Z-Scores
z-score
A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s.
obsolete_ratio
Associations are a form of proposition, framed as a tuple linking two (or more) entities through defined relationships.
association
An idea or notion; a unit of thought.
Concept
An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.
Activity
An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity.
prov:Agent is considered equivalent to foaf:Agent (http://xmlns.com/foaf/0.1/Agent ) Def = "The Agent class is the class of agents; things that do stuff. A well known sub-class is Person, representing people. Other kinds of agents include Organization and Group."
Agents typically persons, organizations, or software that perform tasks, including making assertions, or generating information used as evidence. In the execution of such tasks, an 'agent role' is realized that inheres in the agent.
Agent
An organization is a social or legal institution such as a company, society, etc.
Consider: http://xmlns.com/foaf/0.1/Organization
Organization
Person agents are people.
Consider: http://xmlns.com/foaf/0.1/Person
Person
A software agent is running software.
Software agents are autonomous computer programs that carries out tasks. They designed to execute algorithm(s) that receive some input information and direct its processing to achieve a specified goal. Artificial intelligence is not required to be considered a software agent - only that it can autonomously execute programmed tasks.
SoftwareAgent
The Group class represents a collection of individual agents (and may itself play the role of a Agent, ie. something that can perform actions).
This concept is intentionally quite broad, covering informal and ad-hoc groups, long-lived communities, organizational groups within a workplace, etc. Some such groups may have associated characteristics which could be captured in RDF (perhaps a homepage, name, mailing list etc.).
Group
An evidence direction indicating that an evidence line provides an argument that supports the validity of a target assertion.
supporting
disputing
An evidence direction indicating that an evidence line lacks sufficient credibility, relevance, or completeness to argue for or against the validity of a target assertion.
inconclusive
source
A related resource from which the described resource is derived.
The described resource may be derived from the related resource in whole or in part. Recommended best practice is to identify the related resource by means of a string conforming to a formal identification system.