Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology
type: Ontology
creator: Phylotastic Tree Annotation Team
rights: http://creativecommons.org/publicdomain/zero/1.0/
description: The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies. This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA.
creator: Hilmar Lapp
imports: cdao.owl
imports: prov-o

CDAO_0000193
comment: For providing MIAPA-compliant edge lengths, one should normally use its subproperty miapa:edgeLength. The alternative is to use the miapa:'has edge length' data property or one of its subproperties.

edgeLength
type: ObjectProperty
comment: This object property is one way for providing MIAPA-compliant edge lengths. The object is an instance of the appropriate cdao:EdgeLength subclass, which its value described by cdao:has_Value. The alternative is to use the miapa:'has edge length' data property or one of its subproperties.
range: CDAO_0000046
sub property of: CDAO_0000193

references
type: ObjectProperty
comment: For MIAPA reporting, recommended for referencing sequence and other identifiers for a TU as applicable.

derivedFrom
type: ObjectProperty
comment: For MIAPA reporting, recommended to associate the taxonomic unit to a specimen. Use a unique identifier for the specimen, or create an instance of type dsw:Specimen described by the "Darwin Core triplet" (dwc:institutionCode, dwc:collectionCode, dwc:catalogNumber).
IAO_0000112: :otu1 a cdao:TU ; dsw:derivedFrom [ a dsw:Specimen ; dwc:institutionCode "MVZ" ; dwc:collectionCode "Birds" ; dwc:catalogNumber "35287" ; ] .

toTaxon
type: ObjectProperty
comment: For MIAPA reporting, recommended as the property relating an OTU to a taxonomic concept (an entry in a taxonomy, such as an NCBI taxonomy reference) that has been obtained through taxonomic name or other kinds of name resolution or reconciliation procedures.

implements
type: ObjectProperty
domain: software
range: algorithm
inverse of: is implemented by

is implemented by
type: ObjectProperty

has version
type: ObjectProperty
range: version number

location
type: ObjectProperty
comment: For MIAPA reporting, recommended as the property for indicating a spatial location for OTUs and/or specimens. An exact location can be described using geo:lat, geo:long, and geo:alt. These are the same terms DBpedia uses (see http://wiki.dbpedia.org/Datasets#h18-17). Inexact locations known by name can be described using dc:description.
range: Location

used
type: ObjectProperty
comment: For provenance reporting in MIAPA, the property linking an activity that generated an output (such as a tree inference procedure involving software) to the parameter specification that was the plan for executing the software.
sub property of: wasInfluencedBy

wasAssociatedWith
type: ObjectProperty
comment: For provenance reporting in MIAPA, the property linking the activity that generated an output to the agent that was involved in (responsible for) it. For software procedures, this will be a SoftwareAgent, and for manual procedures it will be a Person.
sub property of: wasInfluencedBy

wasDerivedFrom
type: ObjectProperty
comment: For MIAPA reporting, recommended as the property relating a phylogenetic tree to the data matrix (or matrices) from which it was derived.
sub property of: wasInfluencedBy

wasGeneratedBy
type: ObjectProperty
comment: For provenance reporting in MIAPA, the property linking the tree or the data matrix to the activity that generated it.
sub property of: wasInfluencedBy

branch length
type: DatatypeProperty
comment: This data property is one way for providing MIAPA-compliant edge lengths, in this case branch lengths. The alternative is using the miapa:edgeLength (or its superproperty cdao:has_Annotation) object property, with an instance of the appropriate cdao:EdgeLength subclass as the object, which itself may have its value described by cdao:has_Value.
sub property of: has edge length

bootstrap value
type: DatatypeProperty
comment: This data property is one way for providing MIAPA-compliant edge lengths, in this case bootstrap values. The alternative is using the miapa:edgeLength (or its superproperty cdao:has_Annotation) object property, with an instance of the appropriate cdao:EdgeLength subclass as the object, which itself may have its value described by cdao:has_Value.
sub property of: CDAO_0000214

posterior probability
type: DatatypeProperty
comment: This data property is one way for providing MIAPA-compliant edge lengths, in this case posterior probabilities. The alternative is using the miapa:edgeLength (or its superproperty cdao:has_Annotation) object property, with an instance of the appropriate cdao:EdgeLength subclass as the object, which itself may have its value described by cdao:has_Value.
sub property of: CDAO_0000214

has edge length
type: DatatypeProperty

value
type: DatatypeProperty
comment: For provenance reporting in MIAPA, the property for giving the literal value of a provenance entity, specifically the value of parameter specifications (which are instances of prov:Plan, a subclass of prov:Entity).

Operation
type: Class
subclass of: Activity
comment: For the purposes of MIAPA annotation and cross-ontology interoperability, instances of edam:Operation are instances of a prov:Activity. They need to be further classified as to whether they are maipa:'Manual procedure' or miapa:'Software procedure' instances.

Phylogenetic tree construction
type: Class
subclass of: Operation
subclass of: CDAO_0000014

Phylogenetic tree construction (method centric)
type: Class
subclass of: Phylogenetic tree construction

Alignment construction
type: Class
subclass of: Operation
subclass of: CDAO_0000032

CDAO_0000007
subclass of: Parameter specification
comment: For MIAPA-compliant reporting, the model description is a kind of miapa:'Parameter specification', and this a kind of prov:Plan. Alternatively, we could model this as dc:isPartOf some prov:Plan.

CDAO_0000014
subclass of: Activity
IAO_0000115: A procedure that generates the tree.
comment: For provenance annotation in MIAPA, the activity that generated the tree should be asserted as an instance of cdao:TreeProcedure.

Axiom
IAO_0000116: See https://github.com/miapa/miapa/issues/5
annotated source: CDAO_0000014
annotated property: subClassOf
annotated target: Activity

CDAO_0000032
subclass of: Activity
IAO_0000115: A procedure that generates the alignment.
comment: For provenance annotation in MIAPA, the activity that generated the alignment should be asserted as an instance of cdao:AlignmentProcedure.

Axiom
IAO_0000116: To be proposed to and fixed in CDAO. That would then make the has_type some EdgeLengthType restriction obsolete.
annotated source: CDAO_0000046
annotated target: CDAO_0000063
annotated property: equivalentClass

Axiom
IAO_0000116: To be proposed to and fixed in CDAO. That would then make the has_type some EdgeLengthType restriction obsolete.
annotated source: CDAO_0000046
annotated target: CDAO_0000063
annotated property: equivalentClass

software
type: Class
subclass of: plan specification
subclass of: SoftwareAgent

symbol
type: Class
subclass of: IAO_0000030

directive information entity
type: Class
subclass of: IAO_0000030

algorithm
type: Class
subclass of: IAO_0000030

plan specification
type: Class
subclass of: directive information entity

version number
type: Class
subclass of: symbol

Gene tree
type: Class
subclass of: CDAO_0000110

Consensus tree
type: Class
subclass of: CDAO_0000110

Software procedure
type: Class
subclass of: Class
  intersection of: Activity
  intersection of: Restriction
    on property: used
    some values from: Plan
  intersection of: Restriction
    on property: wasInfluencedBy
    some values from: SoftwareAgent
IAO_0000115: A procedure (a type of prov:Activity) that involves running software to generate the output, and is therefore associated with a piece of software, and uses a parameter specification as the plan for running the software.

Manual procedure
type: Class
subclass of: Class
  intersection of: Activity
  intersection of: Restriction
    on property: wasInfluencedBy
    some values from: Person
IAO_0000115: A procedure (a type of prov:Activity) that involves a person making manual manipulations to data, such as manually editing an alignment. An alignment procedure can involve both running software and manual editing to generate the output, and therefore ManualProcedure and SoftwareProcedure are not disjoint.

Parameter specification
type: Class
subclass of: Plan

Maximum likelihood method
type: Class
subclass of: Likelihood method
IAO_0000116: Should be pushed down to SWO.

RAxML
type: Class
subclass of: software
IAO_0000116: Should be pushed down to SWO.

MAFFT
type: Class
subclass of: software
IAO_0000116: Should be pushed down to SWO.

SINA
type: Class
subclass of: software
IAO_0000116: Should be pushed down to SWO.

PRANK
type: Class
subclass of: software
IAO_0000116: Should be pushed down to SWO.

PAUP*
type: Class
subclass of: software
IAO_0000116: Should be pushed down to SWO.

TNT
type: Class
subclass of: software
IAO_0000116: Should be pushed down to SWO.

PhyML
type: Class
subclass of: software
IAO_0000116: Should be pushed down to SWO.

AMPHORA
type: Class
subclass of: software
IAO_0000116: Should be pushed down to SWO.

GTR+GAMMA
type: Class
subclass of: CDAO_0000020

GTR+CAT
type: Class
subclass of: CDAO_0000020

WAG
type: Class
subclass of: CDAO_0000020

Parsimony method
type: Class
subclass of: algorithm
IAO_0000115: A method for finding the minimum transitions to account for a character given a phylogenetic tree, and by extension, a character-based phylogeny inference method in which the inferred phylogenetic tree (the "maximum parsimony tree") is the phylogenetic tree that minimizes evolutionary transitions over all characters.
IAO_0000116: Should be pushed down to SWO.
IAO_0000119: Prosdocimi, Francisco, Brandon Chisham, Enrico Pontelli, J.D. Thompson, and Arlin Stoltzfus. 2009. “Initial Implementation of a Comparative Data Analysis Ontology.” Evolutionary Bioinformatics Online (5): 47–66. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747124/
IAO_0000119: https://www.nescent.org/wg_evoinfo/Concept_Glossary#Parsimony_Method

Phylogenetic tree construction (pruning and grafting)
type: Class
subclass of: Phylogenetic tree construction (method centric)
IAO_0000115: Phylogenetic tree construction that prunes and grafts a collection of one or more source trees to create the resulting tree.
IAO_0000116: Should be pushed down to SWO.
IAO_0000117: Hilmar Lapp

SetOfNetworks
type: Class
subclass of: Class
  intersection of: CDAO_0000118
  intersection of: Restriction
    on property: CDAO_0000198
    all values from: CDAO_0000006
subclass of: Class
  intersection of: Collection
  intersection of: Restriction
    on property: hadMember
    all values from: CDAO_0000006
IAO_0000116: To be pushed down to CDAO. This would retain though in MIAPA the equivalence to "prov:Collection and provhadMember only cdao:Network".

SetOfTrees
type: Class
subclass of: Class
  intersection of: SetOfNetworks
  intersection of: Restriction
    on property: CDAO_0000198
    all values from: CDAO_0000110
subclass of: Class
  intersection of: Collection
  intersection of: Restriction
    on property: hadMember
    all values from: CDAO_0000110
IAO_0000116: To be pushed down to CDAO. This would retain though in MIAPA the equivalence to "prov:Collection and provhadMember only cdao:Network".

MrBayes
type: Class
subclass of: software
IAO_0000116: Should be pushed down to SWO.

BEAST
type: Class
subclass of: software
IAO_0000116: Should be pushed down to SWO.

Likelihood method
type: Class
subclass of: algorithm

MUSCLE
type: Class
subclass of: software

Activity
type: Class
comment: For provenance annotation in MIAPA, instances of prov:Activity (or one of its subclasses) generate parts of the data such as the alignment and the tree. They are linked to tree or alignment through the property prov:wasGeneratedBy.

Agent
comment: For provenance annotation in MIAPA, instances of prov:Agent, or more specifically an instance of prov:Person and/or prov:SoftwareAgent, are involved in (associated with, responsible for) the prov:Activity that generated a certain piece of the data (such as an alignment, or a tree).

Entity
type: Class
comment: For provenance annotation in MIAPA, the instances of a tree and of an alignment are entities for which provenance information (how they were generated) is required to be tracked (and thus annotated).

default parameters
type: NamedIndividual
type: Parameter specification
comment: It is possible that this really should be a class instead of an individual, namely the class of all default parameter specifications (which would then have instances specific to programs).

unspecified parameters
type: NamedIndividual
type: Parameter specification

7.2.8
type: NamedIndividual
type: version number

3.7
type: NamedIndividual
type: version number

6.712b
type: NamedIndividual
type: version number

4.0b10
type: NamedIndividual
type: version number

7.2.7
type: NamedIndividual
type: version number

10
type: NamedIndividual
type: version number

7.2.6, Pthreads-based and SSE3-vectorized
type: NamedIndividual
type: version number

3.2
type: NamedIndividual
type: version number

1.5.1
type: NamedIndividual
type: version number

CDAO_0000196
comment: For MIAPA reporting, recommended to be used for referencing the corresponding tree (tip) node(s) from a data matrix row

CDAO_0000187
comment: For MIAPA reporting, this property (and/or its inverse) should be used to establish the relationship between rows of the data matrix and nodes in the tree(s).

CDAO_0000215
comment: In MIAPA-compliant reporting, can be used to provide the value for instances of cdao:EdgeLength (or one of its subclasses) used for annotating edges with lengths.