http://purl.obolibrary.org/obo/miapa.owl
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.
URI | http://edamontology.org/operation_0004 |
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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 |
URI | http://edamontology.org/operation_0323 |
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Super-classes |
edam:operation_0004c obo:CDAO_0000014c |
Sub-classes |
edam:operation_0539c |
URI | http://edamontology.org/operation_0539 |
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Super-classes |
edam:operation_0323c |
Sub-classes |
obo:MIAPA_0000038c |
URI | http://edamontology.org/operation_2928 |
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Super-classes |
edam:operation_0004c obo:CDAO_0000032c |
URI | http://purl.obolibrary.org/obo/IAO_0000010 |
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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 |
URI | http://purl.obolibrary.org/obo/IAO_0000028 |
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Super-classes |
obo:IAO_0000030c |
Sub-classes |
obo:IAO_0000129c |
URI | http://purl.obolibrary.org/obo/IAO_0000030 |
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Sub-classes |
obo:IAO_0000033c obo:IAO_0000028c obo:IAO_0000064c |
URI | http://purl.obolibrary.org/obo/IAO_0000033 |
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Super-classes |
obo:IAO_0000030c |
Sub-classes |
obo:IAO_0000104c |
URI | http://purl.obolibrary.org/obo/IAO_0000064 |
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Super-classes |
obo:IAO_0000030c |
Sub-classes |
obo:MIAPA_0000037c swo2:SWO_0000592c |
In range of |
swo2:SWO_0000740op |
URI | http://purl.obolibrary.org/obo/IAO_0000104 |
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Super-classes |
obo:IAO_0000033c |
Sub-classes |
obo:IAO_0000010c |
URI | http://purl.obolibrary.org/obo/IAO_0000129 |
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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 |
URI | http://purl.obolibrary.org/obo/MIAPA_0000001 |
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Super-classes |
obo:CDAO_0000110c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000002 |
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Super-classes |
obo:CDAO_0000110c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000003 |
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Super-classes |
(prov:Activityc and ub285bL119C13c and ub285bL124C13c) |
URI | http://purl.obolibrary.org/obo/MIAPA_0000009 |
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Super-classes |
(prov:Activityc and ub285bL164C13c) |
URI | http://purl.obolibrary.org/obo/MIAPA_0000010 |
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Super-classes |
prov:Planc |
Sub-classes |
obo:CDAO_0000007c |
Members |
obo:MIAPA_0000012 obo:MIAPA_0000013 |
URI | http://purl.obolibrary.org/obo/MIAPA_0000015 |
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Super-classes |
swo2:SWO_0000592c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000016 |
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Super-classes |
obo:IAO_0000010c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000020 |
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Super-classes |
obo:IAO_0000010c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000022 |
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Super-classes |
obo:IAO_0000010c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000024 |
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Super-classes |
obo:IAO_0000010c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000025 |
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Super-classes |
obo:IAO_0000010c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000026 |
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Super-classes |
obo:IAO_0000010c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000027 |
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Super-classes |
obo:IAO_0000010c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000028 |
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Super-classes |
obo:IAO_0000010c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000032 |
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Super-classes |
obo:CDAO_0000020c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000033 |
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Super-classes |
obo:CDAO_0000020c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000034 |
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Super-classes |
obo:CDAO_0000020c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000037 |
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Super-classes |
obo:IAO_0000064c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000038 |
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Super-classes |
edam:operation_0539c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000039 |
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Super-classes |
(prov:Collectionc and ub285bL319C13c and obo:CDAO_0000118c and ub285bL310C13c) (prov:Collectionc and ub285bL319C13c and obo:CDAO_0000118c and ub285bL310C13c) |
URI | http://purl.obolibrary.org/obo/MIAPA_0000040 |
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Super-classes |
(obo:MIAPA_0000039c and ub285bL334C13c and prov:Collectionc and ub285bL343C13c) (obo:MIAPA_0000039c and ub285bL334C13c and prov:Collectionc and ub285bL343C13c) |
URI | http://purl.obolibrary.org/obo/MIAPA_0000041 |
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Super-classes |
obo:IAO_0000010c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000044 |
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Super-classes |
obo:IAO_0000010c |
URI | http://purl.org/dc/terms/Location |
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In range of |
geo:locationop |
URI | http://www.ebi.ac.uk/efo/swo/SWO_0000592 |
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Super-classes |
obo:IAO_0000064c |
Sub-classes |
obo:MIAPA_0000015c |
URI | http://www.ebi.ac.uk/swo/SWO_0000060 |
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Super-classes |
obo:IAO_0000010c |
URI | http://www.w3.org/ns/prov#Activity |
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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 |
URI | http://www.w3.org/ns/prov#Entity |
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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 |
URI | http://www.w3.org/ns/prov#Person |
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Super-classes |
prov:Agentc |
URI | http://www.w3.org/ns/prov#Plan |
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Super-classes |
prov:Entityc |
Sub-classes |
obo:MIAPA_0000010c |
URI | http://www.w3.org/ns/prov#SoftwareAgent |
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Super-classes |
prov:Agentc |
Sub-classes |
obo:IAO_0000010c |
URI | http://purl.obolibrary.org/obo/MIAPA_0000008 |
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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 |
URI | http://purl.org/dc/terms/references |
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Description |
For MIAPA reporting, recommended for referencing sequence and other identifiers for a TU as applicable. |
URI | http://purl.org/dsw/derivedFrom |
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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). |
URI | http://rs.tdwg.org/ontology/voc/TaxonConcept#toTaxon |
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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. |
URI | http://www.ebi.ac.uk/efo/swo/SWO_0000740 |
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Inverse properties | swo:SWO_0000085op |
Domain(s) | obo:IAO_0000010c |
Range(s) | obo:IAO_0000064c |
URI | http://www.ebi.ac.uk/swo/SWO_0004000 |
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Range(s) | obo:IAO_0000129c |
URI | http://www.w3.org/2003/01/geo/wgs84_pos#location |
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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 |
URI | http://www.w3.org/ns/prov#used |
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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 |
URI | http://www.w3.org/ns/prov#wasAssociatedWith |
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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 |
URI | http://www.w3.org/ns/prov#wasDerivedFrom |
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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 |
URI | http://www.w3.org/ns/prov#wasGeneratedBy |
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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 |
URI | http://purl.obolibrary.org/obo/MIAPA_0000004 |
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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 |
URI | http://purl.obolibrary.org/obo/MIAPA_0000006 |
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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 |
URI | http://purl.obolibrary.org/obo/MIAPA_0000007 |
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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 |
URI |
http://purl.obolibrary.org/obo/MIAPA_0000012
|
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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). |
URI |
http://purl.obolibrary.org/obo/MIAPA_0000013
|
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URI |
http://purl.obolibrary.org/obo/MIAPA_0000017
|
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URI |
http://purl.obolibrary.org/obo/MIAPA_0000019
|
---|
URI |
http://purl.obolibrary.org/obo/MIAPA_0000021
|
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URI |
http://purl.obolibrary.org/obo/MIAPA_0000029
|
---|
URI |
http://purl.obolibrary.org/obo/MIAPA_0000030
|
---|
URI |
http://purl.obolibrary.org/obo/MIAPA_0000031
|
---|
URI |
http://purl.obolibrary.org/obo/MIAPA_0000036
|
---|
URI |
http://purl.obolibrary.org/obo/MIAPA_0000042
|
---|
URI |
http://purl.obolibrary.org/obo/MIAPA_0000043
|
---|
http://purl.obolibrary.org/obo/miapa.owl
http://purl.org/dc/elements/1.1/
http://purl.org/dc/terms/
http://purl.org/dsw/
http://edamontology.org/
http://www.w3.org/2003/01/geo/wgs84_pos#
http://purl.obolibrary.org/obo/
http://www.w3.org/2002/07/owl#
http://www.w3.org/ns/prov#
http://www.w3.org/1999/02/22-rdf-syntax-ns#
http://www.w3.org/2000/01/rdf-schema#
https://schema.org/
http://www.w3.org/2004/02/skos/core#
http://www.ebi.ac.uk/swo/
http://www.ebi.ac.uk/efo/swo/
http://www.w3.org/2001/XMLSchema#
c | Classes |
op | Object Properties |
fp | Functional Properties |
dp | Data Properties |
dp | Annotation Properties |
p | Properties |
ni | Named Individuals |