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Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology

Metadata

URI
http://purl.obolibrary.org/obo/miapa.owl
Creator(s)
Hilmar Lapp
Phylotastic Tree Annotation Team
Imports
obo:cdao.owl
http://www.w3.org/ns/prov-o
Ontology RDF
RDF (turtle)

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.

Table of Contents

  1. Classes
  2. Object Properties
  3. Datatype Properties
  4. Named Individuals
  5. Namespaces
  6. Legend

Overview

Pictures say 1,000 words
Figure 1: Ontology overview

Classes

Operationc # Classes

URI http://edamontology.org/operation_0004
Description

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.

Super-classes prov:Activityc
Sub-classes edam:operation_0323c
edam:operation_2928c

Phylogenetic tree constructionc # Classes

URI http://edamontology.org/operation_0323
Super-classes edam:operation_0004c
obo:CDAO_0000014c
Sub-classes edam:operation_0539c

Phylogenetic tree construction (method centric)c # Classes

URI http://edamontology.org/operation_0539
Super-classes edam:operation_0323c
Sub-classes obo:MIAPA_0000038c

Alignment constructionc # Classes

URI http://edamontology.org/operation_2928
Super-classes edam:operation_0004c
obo:CDAO_0000032c

softwarec # Classes

URI http://purl.obolibrary.org/obo/IAO_0000010
Super-classes prov:SoftwareAgentc
obo:IAO_0000104c
Sub-classes obo:MIAPA_0000026c
obo:MIAPA_0000041c
swo:SWO_0000060c
obo:MIAPA_0000020c
obo:MIAPA_0000022c
obo:MIAPA_0000016c
obo:MIAPA_0000044c
obo:MIAPA_0000027c
obo:MIAPA_0000025c
obo:MIAPA_0000024c
obo:MIAPA_0000028c
In domain of swo2:SWO_0000740op

symbolc # Classes

URI http://purl.obolibrary.org/obo/IAO_0000028
Super-classes obo:IAO_0000030c
Sub-classes obo:IAO_0000129c

IAO_0000030c # Classes

URI http://purl.obolibrary.org/obo/IAO_0000030
Sub-classes obo:IAO_0000033c
obo:IAO_0000028c
obo:IAO_0000064c

directive information entityc # Classes

URI http://purl.obolibrary.org/obo/IAO_0000033
Super-classes obo:IAO_0000030c
Sub-classes obo:IAO_0000104c

algorithmc # Classes

URI http://purl.obolibrary.org/obo/IAO_0000064
Super-classes obo:IAO_0000030c
Sub-classes obo:MIAPA_0000037c
swo2:SWO_0000592c
In range of swo2:SWO_0000740op

plan specificationc # Classes

URI http://purl.obolibrary.org/obo/IAO_0000104
Super-classes obo:IAO_0000033c
Sub-classes obo:IAO_0000010c

version numberc # Classes

URI http://purl.obolibrary.org/obo/IAO_0000129
Super-classes obo:IAO_0000028c
In range of swo:SWO_0004000op
Members obo:MIAPA_0000043
obo:MIAPA_0000017
obo:MIAPA_0000031
obo:MIAPA_0000029
obo:MIAPA_0000019
obo:MIAPA_0000030
obo:MIAPA_0000036
obo:MIAPA_0000021
obo:MIAPA_0000042

Gene treec # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000001
Super-classes obo:CDAO_0000110c

Consensus treec # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000002
Super-classes obo:CDAO_0000110c

Software procedurec # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000003
Super-classes (prov:Activityc and ub285bL119C13c and ub285bL124C13c)

Manual procedurec # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000009
Super-classes (prov:Activityc and ub285bL164C13c)

Parameter specificationc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000010
Super-classes prov:Planc
Sub-classes obo:CDAO_0000007c
Members obo:MIAPA_0000012
obo:MIAPA_0000013

Maximum likelihood methodc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000015
Super-classes swo2:SWO_0000592c

RAxMLc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000016
Super-classes obo:IAO_0000010c

MAFFTc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000020
Super-classes obo:IAO_0000010c

SINAc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000022
Super-classes obo:IAO_0000010c

PRANKc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000024
Super-classes obo:IAO_0000010c

PAUP*c # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000025
Super-classes obo:IAO_0000010c

TNTc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000026
Super-classes obo:IAO_0000010c

PhyMLc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000027
Super-classes obo:IAO_0000010c

AMPHORAc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000028
Super-classes obo:IAO_0000010c

GTR+GAMMAc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000032
Super-classes obo:CDAO_0000020c

GTR+CATc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000033
Super-classes obo:CDAO_0000020c

WAGc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000034
Super-classes obo:CDAO_0000020c

Parsimony methodc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000037
Super-classes obo:IAO_0000064c

Phylogenetic tree construction (pruning and grafting)c # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000038
Super-classes edam:operation_0539c

SetOfNetworksc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000039
Super-classes (prov:Collectionc and ub285bL319C13c and obo:CDAO_0000118c and ub285bL310C13c)
(prov:Collectionc and ub285bL319C13c and obo:CDAO_0000118c and ub285bL310C13c)

SetOfTreesc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000040
Super-classes (obo:MIAPA_0000039c and ub285bL334C13c and prov:Collectionc and ub285bL343C13c)
(obo:MIAPA_0000039c and ub285bL334C13c and prov:Collectionc and ub285bL343C13c)

MrBayesc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000041
Super-classes obo:IAO_0000010c

BEASTc # Classes

URI http://purl.obolibrary.org/obo/MIAPA_0000044
Super-classes obo:IAO_0000010c

Locationc # Classes

URI http://purl.org/dc/terms/Location
In range of geo:locationop

Specimenc # Classes

URI http://purl.org/dsw/Specimen

Likelihood methodc # Classes

URI http://www.ebi.ac.uk/efo/swo/SWO_0000592
Super-classes obo:IAO_0000064c
Sub-classes obo:MIAPA_0000015c

MUSCLEc # Classes

URI http://www.ebi.ac.uk/swo/SWO_0000060
Super-classes obo:IAO_0000010c

Activityc # Classes

URI http://www.w3.org/ns/prov#Activity
Description

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.

Sub-classes edam:operation_0004c
obo:CDAO_0000032c
obo:CDAO_0000014c

Entityc # Classes

URI http://www.w3.org/ns/prov#Entity
Description

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).

Sub-classes prov:Planc

Personc # Classes

URI http://www.w3.org/ns/prov#Person
Super-classes prov:Agentc

Planc # Classes

URI http://www.w3.org/ns/prov#Plan
Super-classes prov:Entityc
Sub-classes obo:MIAPA_0000010c

SoftwareAgentc # Classes

URI http://www.w3.org/ns/prov#SoftwareAgent
Super-classes prov:Agentc
Sub-classes obo:IAO_0000010c

Object Properties

edgeLengthop # OPs

URI http://purl.obolibrary.org/obo/MIAPA_0000008
Description

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.

Super-properties obo:CDAO_0000193
Range(s) obo:CDAO_0000046c

referencesop # OPs

URI http://purl.org/dc/terms/references
Description

For MIAPA reporting, recommended for referencing sequence and other identifiers for a TU as applicable.

derivedFromop # OPs

URI http://purl.org/dsw/derivedFrom
Description

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).

toTaxonop # OPs

URI http://rs.tdwg.org/ontology/voc/TaxonConcept#toTaxon
Description

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.

implementsop # OPs

URI http://www.ebi.ac.uk/efo/swo/SWO_0000740
Inverse properties swo:SWO_0000085op
Domain(s) obo:IAO_0000010c
Range(s) obo:IAO_0000064c

is implemented byop # OPs

URI http://www.ebi.ac.uk/swo/SWO_0000085

has versionop # OPs

URI http://www.ebi.ac.uk/swo/SWO_0004000
Range(s) obo:IAO_0000129c

locationop # OPs

URI http://www.w3.org/2003/01/geo/wgs84_pos#location
Description

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(s) dcterms:Locationc

usedop # OPs

URI http://www.w3.org/ns/prov#used
Description

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.

Super-properties prov:wasInfluencedByop

wasAssociatedWithop # OPs

URI http://www.w3.org/ns/prov#wasAssociatedWith
Description

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.

Super-properties prov:wasInfluencedByop

wasDerivedFromop # OPs

URI http://www.w3.org/ns/prov#wasDerivedFrom
Description

For MIAPA reporting, recommended as the property relating a phylogenetic tree to the data matrix (or matrices) from which it was derived.

Super-properties prov:wasInfluencedByop

wasGeneratedByop # OPs

URI http://www.w3.org/ns/prov#wasGeneratedBy
Description

For provenance reporting in MIAPA, the property linking the tree or the data matrix to the activity that generated it.

Super-properties prov:wasInfluencedByop

wasInfluencedByop # OPs

URI http://www.w3.org/ns/prov#wasInfluencedBy

Datatype Properties

branch lengthdp # DPs

URI http://purl.obolibrary.org/obo/MIAPA_0000004
Description

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.

Super-properties obo:MIAPA_0000014dp

bootstrap valuedp # DPs

URI http://purl.obolibrary.org/obo/MIAPA_0000006
Description

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.

Super-properties obo:CDAO_0000214

posterior probabilitydp # DPs

URI http://purl.obolibrary.org/obo/MIAPA_0000007
Description

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.

Super-properties obo:CDAO_0000214

has edge lengthdp # DPs

URI http://purl.obolibrary.org/obo/MIAPA_0000014

valuedp # DPs

URI http://www.w3.org/ns/prov#value
Description

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).

Named Individuals

default parametersni

Class(es)
obo:MIAPA_0000010
URI http://purl.obolibrary.org/obo/MIAPA_0000012
Description 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 parametersni

Class(es)
obo:MIAPA_0000010
URI http://purl.obolibrary.org/obo/MIAPA_0000013

7.2.8ni

Class(es)
obo:IAO_0000129
URI http://purl.obolibrary.org/obo/MIAPA_0000017

3.7ni

Class(es)
obo:IAO_0000129
URI http://purl.obolibrary.org/obo/MIAPA_0000019

6.712bni

Class(es)
obo:IAO_0000129
URI http://purl.obolibrary.org/obo/MIAPA_0000021

4.0b10ni

Class(es)
obo:IAO_0000129
URI http://purl.obolibrary.org/obo/MIAPA_0000029

7.2.7ni

Class(es)
obo:IAO_0000129
URI http://purl.obolibrary.org/obo/MIAPA_0000030

10ni

Class(es)
obo:IAO_0000129
URI http://purl.obolibrary.org/obo/MIAPA_0000031

7.2.6, Pthreads-based and SSE3-vectorizedni

Class(es)
obo:IAO_0000129
URI http://purl.obolibrary.org/obo/MIAPA_0000036

3.2ni

Class(es)
obo:IAO_0000129
URI http://purl.obolibrary.org/obo/MIAPA_0000042

1.5.1ni

Class(es)
obo:IAO_0000129
URI http://purl.obolibrary.org/obo/MIAPA_0000043

Namespaces

default (:)
http://purl.obolibrary.org/obo/miapa.owl
dc
http://purl.org/dc/elements/1.1/
dcterms
http://purl.org/dc/terms/
dsw
http://purl.org/dsw/
edam
http://edamontology.org/
geo
http://www.w3.org/2003/01/geo/wgs84_pos#
obo
http://purl.obolibrary.org/obo/
owl
http://www.w3.org/2002/07/owl#
prov
http://www.w3.org/ns/prov#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
sdo
https://schema.org/
skos
http://www.w3.org/2004/02/skos/core#
swo
http://www.ebi.ac.uk/swo/
swo2
http://www.ebi.ac.uk/efo/swo/
xsd
http://www.w3.org/2001/XMLSchema#

Legend

cClasses
opObject Properties
fpFunctional Properties
dpData Properties
dpAnnotation Properties
pProperties
niNamed Individuals