larsw@orangina:~/Data/Pinus$ getpapers -q Pinus -k 1000 -o . -xn info: Searching using eupmc API info: Running in no-execute mode, so nothing will be downloaded info: Found 4566 open access results warn: This version of getpapers wasn't built with this version of the EuPMC api in mind warn: getpapers EuPMCVersion: 5.1.1 vs. 5.2.1 reported by api larsw@orangina:~/Data/Pinus$ getpapers -q Pinus -k 1000 -o . -x info: Searching using eupmc API info: Found 4566 open access results warn: This version of getpapers wasn't built with this version of the EuPMC api in mind warn: getpapers EuPMCVersion: 5.1.1 vs. 5.2.1 reported by api info: Limiting to 1000 hits Retrieving results [==============================] 100% (eta 0.0s) info: Done collecting results info: Saving result metadata info: Full EUPMC result metadata written to eupmc_results.json info: Individual EUPMC result metadata records written info: Extracting fulltext HTML URL list (may not be available for all articles) info: Fulltext HTML URL list written to eupmc_fulltext_html_urls.txt warn: Article with pmcid "PMC5444476" was not Open Access (therefore no XML) warn: Article with pmcid "PMC4114966" was not Open Access (therefore no XML) warn: Article with pmcid "PMC5496519" was not Open Access (therefore no XML) warn: Article with pmcid "PMC3900274" was not Open Access (therefore no XML) warn: Article with pmcid "PMC5021648" was not Open Access (therefore no XML) warn: Article with pmcid "PMC4211101" was not Open Access (therefore no XML) warn: Article with pmcid "PMC3512621" was not Open Access (therefore no XML) warn: Article with pmcid "PMC5026301" was not Open Access (therefore no XML) warn: Article with pmcid "PMC3239991" was not Open Access (therefore no XML) warn: Article with pmcid "PMC3240041" was not Open Access (therefore no XML) warn: Article with pmcid "PMC3239982" was not Open Access (therefore no XML) info: Got XML URLs for 989 out of 1000 results info: Downloading fulltext XML files Downloading files [==============================] 100% (989/989) [484.5s elapsed, eta 0.0] info: All downloads succeeded! larsw@orangina:~/Data/Pinus$ norma --project . -i fulltext.xml -o scholarly.html --transform nlm2html !.!!UNKNOWN nlm: mlabeledtr: .!...UNKNOWN nlm: chem-struct: ..!UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: UNKNOWN nlm: preformat: .....!..!.....UNKNOWN nlm: mmultiscripts: UNKNOWN nlm: mprescripts: UNKNOWN nlm: none: UNKNOWN nlm: mmultiscripts: UNKNOWN nlm: mprescripts: UNKNOWN nlm: none: ....UNKNOWN nlm: overline: UNKNOWN nlm: overline: ...UNKNOWN nlm: alt-text: ..........UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: UNKNOWN nlm: nlm-citation: ....UNKNOWN nlm: alt-text: ...UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: UNKNOWN nlm: statement: .........!.!.UNKNOWN nlm: anonymous: .UNKNOWN nlm: alt-text: ...UNKNOWN nlm: alt-text: ......UNKNOWN nlm: alt-text: UNKNOWN nlm: alt-text: UNKNOWN nlm: alt-text: UNKNOWN nlm: alt-text: UNKNOWN nlm: alt-text: ..UNKNOWN nlm: issue-sponsor: UNKNOWN nlm: string-conf: .........UNKNOWN nlm: data-title: UNKNOWN nlm: version: .UNKNOWN nlm: alt-text: UNKNOWN nlm: alt-text: UNKNOWN nlm: alt-text: UNKNOWN nlm: alt-text: .UNKNOWN nlm: city: UNKNOWN nlm: state: UNKNOWN nlm: city: UNKNOWN nlm: state: UNKNOWN nlm: city: UNKNOWN nlm: state: UNKNOWN nlm: city: UNKNOWN nlm: state: UNKNOWN nlm: city: UNKNOWN nlm: state: .UNKNOWN nlm: mroot: UNKNOWN nlm: mroot: ..UNKNOWN nlm: alt-text: UNKNOWN nlm: alt-text: UNKNOWN nlm: alt-text: UNKNOWN nlm: alt-text: UNKNOWN nlm: alt-text: UNKNOWN nlm: alt-text: UNKNOWN nlm: city: UNKNOWN nlm: city: UNKNOWN nlm: city: .....UNKNOWN nlm: mlabeledtr: UNKNOWN nlm: mlabeledtr: UNKNOWN nlm: mlabeledtr: UNKNOWN nlm: mlabeledtr: UNKNOWN nlm: mlabeledtr: UNKNOWN nlm: mlabeledtr: ..!.UNKNOWN OBJECT-ID TYPE: : 10.3389/fpls.2016.02050 UNKNOWN nlm: city: UNKNOWN nlm: city: UNKNOWN nlm: data-title: UNKNOWN nlm: version: UNKNOWN nlm: data-title: UNKNOWN nlm: version: UNKNOWN nlm: data-title: UNKNOWN nlm: data-title: UNKNOWN nlm: version: ..UNKNOWN nlm: glyph-ref: UNKNOWN nlm: city: UNKNOWN nlm: city: UNKNOWN nlm: city: UNKNOWN nlm: data-title: UNKNOWN nlm: version: .UNKNOWN nlm: city: UNKNOWN nlm: state: UNKNOWN nlm: city: UNKNOWN nlm: state: UNKNOWN nlm: city: UNKNOWN nlm: state: ..UNKNOWN nlm: city: UNKNOWN nlm: state: UNKNOWN nlm: city: UNKNOWN nlm: state: ..!.....UNKNOWN nlm: city: UNKNOWN nlm: state: UNKNOWN nlm: city: UNKNOWN nlm: city: UNKNOWN nlm: state: UNKNOWN nlm: data-title: UNKNOWN nlm: city: UNKNOWN nlm: state: UNKNOWN nlm: city: UNKNOWN nlm: state: UNKNOWN nlm: city: UNKNOWN nlm: state: UNKNOWN nlm: city: UNKNOWN nlm: state: UNKNOWN nlm: city: UNKNOWN nlm: state: larsw@orangina:~/Data/Pinus$ ami2-species --project . -i scholarly.html --sp.species --sp.type genus ..................................................................................................... larsw@orangina:~/Data/Pinus$ ami2-species --project . -i scholarly.html --sp.species --sp.type binomial ..................................................................................................... larsw@orangina:~/Data/Pinus$ ami2-sequence --project . --filter file\(\*\*/results.xml\) -o sequencesfiles.xml ..................................................................................................... larsw@orangina:~/Data/Pinus$ ctj rdf -p . info: CProject To JSON (ctj) config: info: Input directory: /home/larsw/Data/Pinus info: Output directory: /home/larsw/Data/Pinus info: Output format: turtle [===============================] Parsing directory 1000/1000: PMC5541149 (eta 0.0s) info: Directories parsed! [===============================] Formatting rdf item 9080/9080: :12a5c27ec8207bb9cd2590209fabfc42 (eta 0.0s) info: Saving output... info: Saving output succeeded!