Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology
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.
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
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.
For MIAPA reporting, recommended for referencing sequence and other identifiers for a TU as applicable.
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).
:otu1 a cdao:TU ; dsw:derivedFrom [ a dsw:Specimen ; dwc:institutionCode "MVZ" ; dwc:collectionCode "Birds" ; dwc:catalogNumber "35287" ; ] .
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.
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.
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.
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.
For MIAPA reporting, recommended as the property relating a phylogenetic tree to the data matrix (or matrices) from which it was derived.
For provenance reporting in MIAPA, the property linking the tree or the data matrix to the activity that generated it.
branch length
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.
bootstrap value
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.
posterior probability
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 edge length
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).
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 (method centric)
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.
For provenance annotation in MIAPA, the activity that generated the tree should be asserted as an instance of cdao:TreeProcedure.
See https://github.com/miapa/miapa/issues/5
A procedure that generates the alignment.
For provenance annotation in MIAPA, the activity that generated the alignment should be asserted as an instance of cdao:AlignmentProcedure.
To be proposed to and fixed in CDAO. That would then make the has_type some EdgeLengthType restriction obsolete.
Gene tree
Consensus tree
Software procedure
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
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
Maximum likelihood method
RAxML
MAFFT
SINA
PRANK
PAUP*
TNT
PhyML
AMPHORA
GTR+GAMMA
GTR+CAT
WAG
Parsimony method
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.
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/
Phylogenetic tree construction (pruning and grafting)
Phylogenetic tree construction that prunes and grafts a collection of one or more source trees to create the resulting tree.
SetOfNetworks
To be pushed down to CDAO. This would retain though in MIAPA the equivalence to "prov:Collection and provhadMember only cdao:Network".
SetOfTrees
MrBayes
BEAST
MUSCLE
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.
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).
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
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
7.2.6, Pthreads-based and SSE3-vectorized
For MIAPA reporting, recommended to be used for referencing the corresponding tree (tip) node(s) from a data matrix row
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).
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.