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Add WIP R scripts for alignment ontology
Ref #120 This isn't yet done but it's close.
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| http://purl.dataone.org/odo/salmon_000127 | ||
| http://purl.dataone.org/odo/salmon_000128 | ||
| http://purl.dataone.org/odo/salmon_000129 | ||
| http://purl.dataone.org/odo/salmon_000130 | ||
| http://purl.dataone.org/odo/salmon_000131 | ||
| http://purl.dataone.org/odo/salmon_000132 | ||
| http://purl.dataone.org/odo/salmon_000133 | ||
| http://purl.dataone.org/odo/salmon_000142 | ||
| http://purl.dataone.org/odo/salmon_000186 | ||
| http://purl.dataone.org/odo/salmon_000187 | ||
| http://purl.dataone.org/odo/salmon_000188 | ||
| http://purl.dataone.org/odo/salmon_000189 | ||
| http://purl.dataone.org/odo/salmon_000200 | ||
| http://purl.dataone.org/odo/salmon_000216 | ||
| http://purl.dataone.org/odo/salmon_000235 | ||
| http://purl.dataone.org/odo/salmon_000239 | ||
| http://purl.dataone.org/odo/salmon_000240 | ||
| http://purl.dataone.org/odo/salmon_000241 | ||
| http://purl.dataone.org/odo/salmon_000242 | ||
| http://purl.dataone.org/odo/salmon_000243 | ||
| http://purl.dataone.org/odo/salmon_000480 | ||
| http://purl.dataone.org/odo/salmon_000481 | ||
| http://purl.dataone.org/odo/salmon_000492 | ||
| http://purl.dataone.org/odo/salmon_000493 | ||
| http://purl.dataone.org/odo/salmon_000504 | ||
| http://purl.dataone.org/odo/salmon_000520 | ||
| http://purl.dataone.org/odo/salmon_000525 | ||
| http://purl.dataone.org/odo/salmon_000527 | ||
| http://purl.dataone.org/odo/salmon_000529 | ||
| http://purl.dataone.org/odo/salmon_000569 | ||
| http://purl.dataone.org/odo/salmon_000570 | ||
| http://purl.dataone.org/odo/salmon_000582 | ||
| http://purl.dataone.org/odo/salmon_000630 | ||
| http://purl.dataone.org/odo/salmon_000642 | ||
| http://purl.dataone.org/odo/salmon_000647 | ||
| http://purl.dataone.org/odo/salmon_000659 | ||
| http://purl.dataone.org/odo/salmon_000663 | ||
| http://purl.dataone.org/odo/salmon_000665 | ||
| http://purl.dataone.org/odo/salmon_000666 | ||
| http://purl.dataone.org/odo/salmon_000667 | ||
| http://purl.dataone.org/odo/salmon_000668 | ||
| http://purl.dataone.org/odo/salmon_000669 | ||
| http://purl.dataone.org/odo/salmon_000670 | ||
| http://purl.dataone.org/odo/salmon_000671 | ||
| http://purl.dataone.org/odo/salmon_000680 | ||
| http://purl.dataone.org/odo/salmon_000681 | ||
| http://purl.dataone.org/odo/salmon_000691 | ||
| http://purl.dataone.org/odo/salmon_000692 | ||
| http://purl.dataone.org/odo/salmon_000693 | ||
| http://purl.dataone.org/odo/salmon_000694 | ||
| http://purl.dataone.org/odo/salmon_000695 | ||
| http://purl.dataone.org/odo/salmon_000696 | ||
| http://purl.dataone.org/odo/salmon_000697 | ||
| http://purl.dataone.org/odo/salmon_000698 | ||
| http://purl.dataone.org/odo/salmon_000699 | ||
| http://purl.dataone.org/odo/salmon_000700 | ||
| http://purl.dataone.org/odo/salmon_000701 | ||
| http://purl.dataone.org/odo/salmon_000705 | ||
| http://purl.dataone.org/odo/salmon_000709 | ||
| http://purl.dataone.org/odo/salmon_000710 | ||
| http://purl.dataone.org/odo/salmon_000711 | ||
| http://purl.dataone.org/odo/salmon_000712 | ||
| http://purl.dataone.org/odo/salmon_000713 | ||
| http://purl.dataone.org/odo/salmon_000718 | ||
| http://purl.dataone.org/odo/salmon_000719 | ||
| http://purl.dataone.org/odo/salmon_000720 | ||
| http://purl.dataone.org/odo/salmon_000721 | ||
| http://purl.dataone.org/odo/salmon_000727 | ||
| http://purl.dataone.org/odo/salmon_000728 | ||
| http://purl.dataone.org/odo/salmon_000729 | ||
| http://purl.dataone.org/odo/salmon_000754 | ||
| http://purl.dataone.org/odo/salmon_000755 | ||
| http://purl.dataone.org/odo/salmon_000777 | ||
| http://purl.dataone.org/odo/salmon_000780 | ||
| http://purl.dataone.org/odo/salmon_000782 | ||
| http://purl.dataone.org/odo/salmon_000783 | ||
| http://purl.dataone.org/odo/salmon_000785 |
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salmon/misc/find-deprecated-iris/find-deprecated-iris.Rproj
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| Version: 1.0 | ||
|
|
||
| RestoreWorkspace: Default | ||
| SaveWorkspace: Default | ||
| AlwaysSaveHistory: Default | ||
|
|
||
| EnableCodeIndexing: Yes | ||
| UseSpacesForTab: Yes | ||
| NumSpacesForTab: 2 | ||
| Encoding: UTF-8 | ||
|
|
||
| RnwWeave: knitr | ||
| LaTeX: pdfLaTeX | ||
|
|
||
| AutoAppendNewline: Yes | ||
| StripTrailingWhitespace: Yes |
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| library(dataone) | ||
| library(xml2) | ||
|
|
||
| knb <- MNode("https://knb.ecoinformatics.org/knb/d1/mn/v2") | ||
| iris <- readLines("./deprecated_iris.txt") | ||
|
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| get_instances_single <- function(node, pid, iri) { | ||
| message("Getting instances of ", iri, " in ", pid) | ||
|
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| out_path <- tempfile() | ||
| writeBin(getObject(node, pid), out_path) | ||
| xml_doc <- xml2::read_xml(out_path) | ||
|
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| annotations <- xml2::xml_find_all(xml_doc, "//annotation") | ||
|
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| matching_annotations <- Filter(function(annotation) { | ||
| iri == xml2::xml_text(xml2::xml_find_first(annotation, "valueURI")) | ||
| }, annotations) | ||
|
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| # Note: This assumes attribute and just go with it | ||
| unique(vapply(matching_annotations, function(annotation) { | ||
| parent <- xml2::xml_parent(annotation) | ||
| attributeName <- xml2::xml_text(xml2::xml_find_first(parent, "attributeName")) | ||
| attributeDefintion <- xml2::xml_text(xml2::xml_find_first(parent, "attributeDefinition")) | ||
|
|
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| propertyURI <- xml2::xml_find_first(annotation, "propertyURI") | ||
| valueURI <- xml2::xml_find_first(annotation, "valueURI") | ||
|
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| propertyURILabel <- xml2::xml_attr(propertyURI, "label") | ||
| propertyURIValue <- xml2::xml_text(propertyURI) | ||
| valueURILabel <- xml2::xml_attr(valueURI, "label") | ||
| valueURIValue <- xml2::xml_text(valueURI) | ||
|
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| # Create an easy to survey string describing the attribute and the | ||
| # annotation | ||
| paste0(attributeName, " (", attributeDefintion, ") <-> ", valueURILabel, " (", valueURIValue, ")") | ||
| }, "", USE.NAMES = FALSE)) | ||
| } | ||
|
|
||
| get_instances <- function(node, pid, iris) { | ||
| unique(vapply(iris, function(iri) { | ||
| get_instances_single(node, pid, iri) | ||
| }, "")) | ||
| } | ||
|
|
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| debug_iri <- function(node, iri) { | ||
| message("Debugging ", iri) | ||
|
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| ids <- unlist(query( | ||
| node, | ||
| list( | ||
| q = paste0('sem_annotation:"', iri, '"'), | ||
| fl = "identifier" | ||
| ) | ||
| ), use.names = FALSE) | ||
|
|
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| result <- unique(unlist(lapply(ids, function(id) { | ||
| get_instances(node, id, iri) | ||
| }))) | ||
|
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| result | ||
| } | ||
|
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| debug_iris <- function(node, iris) { | ||
| result <- lapply(iris, function(iri) { | ||
| debug_iri(knb, iri) | ||
| }) | ||
|
|
||
| names(result) <- iris | ||
|
|
||
| result | ||
| } | ||
|
|
||
|
|
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| <http://purl.dataone.org/odo/salmon_000129> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000129> . | ||
| <http://purl.dataone.org/odo/salmon_000130> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000130> . | ||
| <http://purl.dataone.org/odo/salmon_000131> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000131> . | ||
| <http://purl.dataone.org/odo/salmon_000132> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000132> . | ||
| <http://purl.dataone.org/odo/salmon_000133> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000133> . | ||
| <http://purl.dataone.org/odo/salmon_000142> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000142> . | ||
| <http://purl.dataone.org/odo/salmon_000186> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000186> . | ||
| <http://purl.dataone.org/odo/salmon_000187> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000187> . | ||
| <http://purl.dataone.org/odo/salmon_000188> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000188> . | ||
| <http://purl.dataone.org/odo/salmon_000189> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000189> . | ||
| <http://purl.dataone.org/odo/salmon_000200> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000200> . | ||
| <http://purl.dataone.org/odo/salmon_000216> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000216> . | ||
| <http://purl.dataone.org/odo/salmon_000235> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000235> . | ||
| <http://purl.dataone.org/odo/salmon_000239> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000239> . | ||
| <http://purl.dataone.org/odo/salmon_000240> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000240> . | ||
| <http://purl.dataone.org/odo/salmon_000241> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000241> . | ||
| <http://purl.dataone.org/odo/salmon_000242> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000242> . | ||
| <http://purl.dataone.org/odo/salmon_000243> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000243> . | ||
| <http://purl.dataone.org/odo/salmon_000480> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000480> . | ||
| <http://purl.dataone.org/odo/salmon_000481> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000481> . | ||
| <http://purl.dataone.org/odo/salmon_000492> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000492> . | ||
| <http://purl.dataone.org/odo/salmon_000493> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000493> . | ||
| <http://purl.dataone.org/odo/salmon_000504> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000504> . | ||
| <http://purl.dataone.org/odo/salmon_000520> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000520> . | ||
| <http://purl.dataone.org/odo/salmon_000525> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000525> . | ||
| <http://purl.dataone.org/odo/salmon_000527> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000527> . | ||
| <http://purl.dataone.org/odo/salmon_000529> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000529> . | ||
| <http://purl.dataone.org/odo/salmon_000569> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000569> . | ||
| <http://purl.dataone.org/odo/salmon_000570> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000570> . | ||
| <http://purl.dataone.org/odo/salmon_000582> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000582> . | ||
| <http://purl.dataone.org/odo/salmon_000630> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000630> . | ||
| <http://purl.dataone.org/odo/salmon_000642> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000642> . | ||
| <http://purl.dataone.org/odo/salmon_000659> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000659> . | ||
| <http://purl.dataone.org/odo/salmon_000663> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000663> . | ||
| <http://purl.dataone.org/odo/salmon_000665> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000665> . | ||
| <http://purl.dataone.org/odo/salmon_000666> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000666> . | ||
| <http://purl.dataone.org/odo/salmon_000667> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000667> . | ||
| <http://purl.dataone.org/odo/salmon_000668> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000668> . | ||
| <http://purl.dataone.org/odo/salmon_000669> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000669> . | ||
| <http://purl.dataone.org/odo/salmon_000670> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000670> . | ||
| <http://purl.dataone.org/odo/salmon_000671> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000671> . | ||
| <http://purl.dataone.org/odo/salmon_000680> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000680> . | ||
| <http://purl.dataone.org/odo/salmon_000681> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000681> . | ||
| <http://purl.dataone.org/odo/salmon_000691> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000691> . | ||
| <http://purl.dataone.org/odo/salmon_000692> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000692> . | ||
| <http://purl.dataone.org/odo/salmon_000693> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000693> . | ||
| <http://purl.dataone.org/odo/salmon_000694> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000694> . | ||
| <http://purl.dataone.org/odo/salmon_000695> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000695> . | ||
| <http://purl.dataone.org/odo/salmon_000696> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000696> . | ||
| <http://purl.dataone.org/odo/salmon_000697> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000697> . | ||
| <http://purl.dataone.org/odo/salmon_000698> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000698> . | ||
| <http://purl.dataone.org/odo/salmon_000699> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000699> . | ||
| <http://purl.dataone.org/odo/salmon_000700> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000700> . | ||
| <http://purl.dataone.org/odo/salmon_000701> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000701> . | ||
| <http://purl.dataone.org/odo/salmon_000705> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000705> . | ||
| <http://purl.dataone.org/odo/salmon_000709> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000709> . | ||
| <http://purl.dataone.org/odo/salmon_000710> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000710> . | ||
| <http://purl.dataone.org/odo/salmon_000711> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000711> . | ||
| <http://purl.dataone.org/odo/salmon_000712> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000712> . | ||
| <http://purl.dataone.org/odo/salmon_000713> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000713> . | ||
| <http://purl.dataone.org/odo/salmon_000718> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000718> . | ||
| <http://purl.dataone.org/odo/salmon_000719> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000719> . | ||
| <http://purl.dataone.org/odo/salmon_000720> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000720> . | ||
| <http://purl.dataone.org/odo/salmon_000721> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000721> . | ||
| <http://purl.dataone.org/odo/salmon_000727> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000727> . | ||
| <http://purl.dataone.org/odo/salmon_000728> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000728> . | ||
| <http://purl.dataone.org/odo/salmon_000729> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000729> . | ||
| <http://purl.dataone.org/odo/salmon_000754> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000754> . | ||
| <http://purl.dataone.org/odo/salmon_000755> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000755> . | ||
| <http://purl.dataone.org/odo/salmon_000777> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000777> . | ||
| <http://purl.dataone.org/odo/salmon_000780> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000780> . | ||
| <http://purl.dataone.org/odo/salmon_000782> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000782> . | ||
| <http://purl.dataone.org/odo/salmon_000783> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000783> . | ||
| <http://purl.dataone.org/odo/salmon_000785> owl:equivalentClass <http://purl.dataone.org/odo/salmon_00000785> . |
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