Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology

Classes

activity^c back to ToC or Class ToC

IRI: http://www.w3.org/ns/prov#Activity

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.

has sub-classes: Operation^c

algorithm^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000064

has super-classes: i a o 0000030^c
has sub-classes: Likelihood method^c, Parsimony method^c
is in range of: implements^op

Alignment construction^c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2928

has super-classes: Operation^c; c d a o 0000032

AMPHORA^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000028

has super-classes: software^c

BEAST^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000044

has super-classes: software^c

Consensus tree^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000002

has super-classes: c d a o 0000110

directive information entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000033

has super-classes: i a o 0000030^c
has sub-classes: plan specification^c

entity^c back to ToC or Class ToC

IRI: http://www.w3.org/ns/prov#Entity

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).

has sub-classes: plan^c

Gene tree^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000001

has super-classes: c d a o 0000110

GTR+CAT^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000033

has super-classes: c d a o 0000020

GTR+GAMMA^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000032

has super-classes: c d a o 0000020

Likelihood method^c back to ToC or Class ToC

IRI: http://www.ebi.ac.uk/efo/swo/SWO_0000592

has super-classes: algorithm^c
has sub-classes: Maximum likelihood method^c

MAFFT^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000020

has super-classes: software^c

Manual procedure^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000009

has super-classes: activity^c and (was influenced by^op some person^c)

Maximum likelihood method^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000015

has super-classes: Likelihood method^c

MrBayes^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000041

has super-classes: software^c

MUSCLE^c back to ToC or Class ToC

IRI: http://www.ebi.ac.uk/swo/SWO_0000060

has super-classes: software^c

Operation^c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0004

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.

has super-classes: activity^c
has sub-classes: Alignment construction^c, Phylogenetic tree construction^c

Parameter specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000010

has super-classes: plan^c
has members: default parametersⁿⁱ, unspecified parametersⁿⁱ

Parsimony method^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000037

has super-classes: algorithm^c

PAUP*^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000025

has super-classes: software^c

person^c back to ToC or Class ToC

IRI: http://www.w3.org/ns/prov#Person

has super-classes: agent

Phylogenetic tree construction^c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0323

has super-classes: Operation^c; c d a o 0000014
has sub-classes: Phylogenetic tree construction (method centric)^c

Phylogenetic tree construction (method centric)^c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0539

has super-classes: Phylogenetic tree construction^c
has sub-classes: Phylogenetic tree construction (pruning and grafting)^c

Phylogenetic tree construction (pruning and grafting)^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000038

has super-classes: Phylogenetic tree construction (method centric)^c

PhyML^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000027

has super-classes: software^c

plan^c back to ToC or Class ToC

IRI: http://www.w3.org/ns/prov#Plan

has super-classes: entity^c
has sub-classes: Parameter specification^c

plan specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000104

has super-classes: directive information entity^c
has sub-classes: software^c

PRANK^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000024

has super-classes: software^c

RAxML^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000016

has super-classes: software^c

SetOfNetworks^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000039

has super-classes: collection and (had member only c d a o 0000006); c d a o 0000118 and (c d a o 0000198 only c d a o 0000006)

SetOfTrees^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000040

has super-classes: collection and (had member only c d a o 0000110); SetOfNetworks^c and (c d a o 0000198 only c d a o 0000110)

SINA^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000022

has super-classes: software^c

software^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000010

has super-classes: plan specification^c; software agent^c
has sub-classes: AMPHORA^c, BEAST^c, MAFFT^c, MUSCLE^c, MrBayes^c, PAUP*^c, PRANK^c, PhyML^c, RAxML^c, SINA^c, TNT^c
is in domain of: implements^op

software agent^c back to ToC or Class ToC

IRI: http://www.w3.org/ns/prov#SoftwareAgent

has super-classes: agent
has sub-classes: software^c

Software procedure^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000003

has super-classes: activity^c and (used^op some plan^c) and (was influenced by^op some software agent^c)

symbol^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000028

has super-classes: i a o 0000030^c
has sub-classes: version number^c

TNT^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000026

has super-classes: software^c

version number^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000129

has super-classes: symbol^c
is in range of: has version^op
has members: 1.5.1ⁿⁱ, 10ⁿⁱ, 3.2ⁿⁱ, 3.7ⁿⁱ, 4.0b10ⁿⁱ, 6.712bⁿⁱ, 7.2.6, Pthreads-based and SSE3-vectorizedⁿⁱ, 7.2.7ⁿⁱ, 7.2.8ⁿⁱ

WAG^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000034

has super-classes: c d a o 0000020

derived from^op back to ToC or Object Property ToC

IRI: http://purl.org/dsw/derivedFrom

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).

edgeLength^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000008

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.

has super-properties: c d a o 0000193
has range: c d a o 0000046

has version^op back to ToC or Object Property ToC

IRI: http://www.ebi.ac.uk/swo/SWO_0004000

has range: version number^c

implements^op back to ToC or Object Property ToC

IRI: http://www.ebi.ac.uk/efo/swo/SWO_0000740

has domain: software^c
has range: algorithm^c
is inverse of: is implemented by^op

is implemented by^op back to ToC or Object Property ToC

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

is inverse of: implements^op

location^op back to ToC or Object Property ToC

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

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.

has range: location^c

references^op back to ToC or Object Property ToC

IRI: http://purl.org/dc/terms/references

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

to taxon^op back to ToC or Object Property ToC

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

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.

used^op back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#used

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.

has super-properties: was influenced by^op

was associated with^op back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#wasAssociatedWith

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.

has super-properties: was influenced by^op

was derived from^op back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#wasDerivedFrom

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

has super-properties: was influenced by^op

was generated by^op back to ToC or Object Property ToC

IRI: http://www.w3.org/ns/prov#wasGeneratedBy

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

has super-properties: was influenced by^op

Data Properties

bootstrap value
branch length
has edge length
posterior probability
value

bootstrap value^dp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000006

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.

has super-properties: c d a o 0000214

branch length^dp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000004

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.

has super-properties: has edge length^dp

has edge length^dp back to ToC or Data Property ToC

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

has sub-properties: branch length^dp

posterior probability^dp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000007

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.

has super-properties: c d a o 0000214

value^dp back to ToC or Data Property ToC

IRI: http://www.w3.org/ns/prov#value

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

1.5.1
10
3.2
3.7
4.0b10
6.712b
7.2.6, Pthreads-based and SSE3-vectorized
7.2.7
7.2.8
default parameters
unspecified parameters

1.5.1ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000043

belongs to: version number^c

10ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000031

belongs to: version number^c

3.2ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000042

belongs to: version number^c

3.7ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000019

belongs to: version number^c

4.0b10ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000029

belongs to: version number^c

6.712bⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000021

belongs to: version number^c

7.2.6, Pthreads-based and SSE3-vectorizedⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000036

belongs to: version number^c

7.2.7ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000030

belongs to: version number^c

7.2.8ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000017

belongs to: version number^c

default parametersⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000012

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).

belongs to: Parameter specification^c

unspecified parametersⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MIAPA_0000013

belongs to: Parameter specification^c

This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni.

Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology

Table of Content

Introduction

Classes

activityc back to ToC or Class ToC

algorithmc back to ToC or Class ToC

Alignment constructionc back to ToC or Class ToC

AMPHORAc back to ToC or Class ToC

BEASTc back to ToC or Class ToC

Consensus treec back to ToC or Class ToC

directive information entityc back to ToC or Class ToC

entityc back to ToC or Class ToC

Gene treec back to ToC or Class ToC

GTR+CATc back to ToC or Class ToC

GTR+GAMMAc back to ToC or Class ToC

Likelihood methodc back to ToC or Class ToC

MAFFTc back to ToC or Class ToC

Manual procedurec back to ToC or Class ToC

Maximum likelihood methodc back to ToC or Class ToC

MrBayesc back to ToC or Class ToC

MUSCLEc back to ToC or Class ToC

Operationc back to ToC or Class ToC

Parameter specificationc back to ToC or Class ToC

Parsimony methodc back to ToC or Class ToC

PAUP*c back to ToC or Class ToC

personc back to ToC or Class ToC

Phylogenetic tree constructionc back to ToC or Class ToC

Phylogenetic tree construction (method centric)c back to ToC or Class ToC

Phylogenetic tree construction (pruning and grafting)c back to ToC or Class ToC

PhyMLc back to ToC or Class ToC

planc back to ToC or Class ToC

plan specificationc back to ToC or Class ToC

PRANKc back to ToC or Class ToC

RAxMLc back to ToC or Class ToC

SetOfNetworksc back to ToC or Class ToC

SetOfTreesc back to ToC or Class ToC

SINAc back to ToC or Class ToC

softwarec back to ToC or Class ToC

software agentc back to ToC or Class ToC

Software procedurec back to ToC or Class ToC

symbolc back to ToC or Class ToC

TNTc back to ToC or Class ToC

version numberc back to ToC or Class ToC

WAGc back to ToC or Class ToC