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Support alternate versions #61

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Support alternate versions #61

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e74ef4d
Added an alternate versions PubMed example XML.
gaurav Apr 6, 2020
fcbc34f
Added tool to identify alternate versions.
gaurav Apr 8, 2020
8b1cc35
Added SLURM job file for IdentifyVersions.
gaurav Apr 8, 2020
5be6d2f
Updated PMID to include the version number.
gaurav Apr 30, 2020
0fc1c91
Added dct:isVersionOf to keep links to the original article.
gaurav Apr 30, 2020
3c2620b
Updated tests to include versioned PMID URLs.
gaurav Apr 30, 2020
f707608
Added a basic test to make sure we get four separate versions.
gaurav May 5, 2020
5038246
Cleaned up code with scalafix and scalafmt.
gaurav May 5, 2020
7a7fdc0
Removed unnecessary identify versions code.
gaurav May 5, 2020
4d3aa39
Fixed tests.
gaurav Apr 1, 2021
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8 changes: 8 additions & 0 deletions src/main/scala/org/renci/chemotext/Main.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -120,6 +120,14 @@ object PubMedTripleGenerator extends LazyLogging {
pmidIRI,
RDF.`type`,
ResourceFactory.createResource(s"$FaBiONamespace/Article")
),
(
// <pmidIRI> dct:isVersionOf <pmid IRI without version>
ResourceFactory.createStatement(
pmidIRI,
DCTerms.isVersionOf,
ResourceFactory.createResource(pubMedArticleWrapped.pmidIRI)
)
)
) ++ (
// <pmidIRI> fabio:hasPublicationYear "2019"^xsd:gYear
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5 changes: 5 additions & 0 deletions src/main/scala/org/renci/chemotext/PubMedArticleWrapper.scala
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Expand Up @@ -71,6 +71,7 @@ object PubMedArticleWrapper {
class PubMedArticleWrapper(val article: Node) {
// The following methods extract particular fields from the wrapped PubMed article.
val pmid: String = (article \ "MedlineCitation" \ "PMID").text
val version: String = (article \ "MedlineCitation" \ "PMID" \ "@Version").text
val title: String = (article \\ "ArticleTitle").map(_.text).mkString(" ")
val abstractText: String = (article \\ "AbstractText").map(_.text).mkString(" ")
val journalNodes: NodeSeq = (article \\ "Article" \ "Journal")
Expand Down Expand Up @@ -145,6 +146,10 @@ class PubMedArticleWrapper(val article: Node) {

// Generate an IRI for this PubMedArticleWrapper.
val iriAsString: String = {
val PMIDNamespace = "https://www.ncbi.nlm.nih.gov/pubmed"
s"$PMIDNamespace/$pmid.$version"
}
val pmidIRI: String = {
val PMIDNamespace = "https://www.ncbi.nlm.nih.gov/pubmed"
s"$PMIDNamespace/$pmid"
}
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