From 2bf1b9cf2412b215407e4bdd751088361590b622 Mon Sep 17 00:00:00 2001 From: Tiger Zhang Date: Fri, 10 Nov 2017 10:27:36 -0600 Subject: [PATCH 1/5] finished article --- .../realrichardparker-PMC4174215.ttl | 98 +++++++++++++++++++ 1 file changed, 98 insertions(+) create mode 100644 data/individuals-realrichardparker/realrichardparker-PMC4174215.ttl diff --git a/data/individuals-realrichardparker/realrichardparker-PMC4174215.ttl b/data/individuals-realrichardparker/realrichardparker-PMC4174215.ttl new file mode 100644 index 000000000..aa0e82f30 --- /dev/null +++ b/data/individuals-realrichardparker/realrichardparker-PMC4174215.ttl @@ -0,0 +1,98 @@ + +@prefix xsd: . +@prefix rdf: . +@prefix rdfs: . +@prefix owl: . + +@prefix ca: . +@prefix doap: . +@prefix vivo: . + +@prefix bioj: . +@prefix citec: . +@prefix bioj-cited: . +@prefix pmcid: . +@prefix pmcid-cited: . +@prefix dc: . +#done +# https://howisonlab.github.io/softcite-pdf-files/pdf-files/pmc_oa_files/PMC4174215.pdf +pmcid:PMC4174215 rdf:type bioj:article ; + + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:coded_no_in_text_mentions ; + citec:isPresent false; # true/false + ] ; + ] ; + + + citec:has_in_text_mention pmcid:PMC4174215_TZ01 ; # name in text mention like pmcid:PMC3028497_JC01, no quotes +. +pmcid:PMC4174215_TZ01 rdf:type citec:in_text_mention ; # use in text mention name + citec:full_quote """ IBM SPSS version 20 predictive analytics software + was used in the analysis of all the statistical + tests. """ ; # use triple quotes + + citec:on_pdf_page 3 ; # integer + + citec:spans_pages false ; # true/false + + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:mention_type ; + rdfs:label """software""";# software | algorithm | hardware | other ; # put one in triple quotes + ca:certainty 10 ; # integer + ca:memo """SPSS is a well known statistical analysis software""" ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:software_was_used ; + citec:isPresent true; # true/false + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:software_name ; + citec:isPresent true ; # true/false + rdfs:label """SPSS""" ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:version_number ; + citec:isPresent true ; # true/false + rdfs:label """version 20""" ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:version_date ; + citec:isPresent false ; # true/false + #rdfs:label FIXME ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:url ; + citec:isPresent false ; # true/false + # rdfs:label FIXME ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:creator ; + citec:isPresent true ; # true/false + rdfs:label """IBM""" ; # use triple quotes + ] ; + ] ; + # citec:has_reference pmcid-citedFIXME: ; # name reference like pmcid-cited:a2004-40-NAT_GENET_Author-YYYY, no quotes +. From 17621c615cf67a130f3269ba506b01d650bc7f4c Mon Sep 17 00:00:00 2001 From: Tiger Zhang Date: Fri, 10 Nov 2017 11:06:07 -0600 Subject: [PATCH 2/5] finished two articles, no mentions --- .../realrichardparker-PMC1904263.ttl | 31 +++++++++++++++++++ .../realrichardparker-PMC4192806.ttl | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 data/individuals-realrichardparker/realrichardparker-PMC1904263.ttl create mode 100644 data/individuals-realrichardparker/realrichardparker-PMC4192806.ttl diff --git a/data/individuals-realrichardparker/realrichardparker-PMC1904263.ttl b/data/individuals-realrichardparker/realrichardparker-PMC1904263.ttl new file mode 100644 index 000000000..dcac423c5 --- /dev/null +++ b/data/individuals-realrichardparker/realrichardparker-PMC1904263.ttl @@ -0,0 +1,31 @@ + +@prefix xsd: . +@prefix rdf: . +@prefix rdfs: . +@prefix owl: . + +@prefix ca: . +@prefix doap: . +@prefix vivo: . + +@prefix bioj: . +@prefix citec: . +@prefix bioj-cited: . +@prefix pmcid: . +@prefix pmcid-cited: . +@prefix dc: . +#done no mentions of software, lots of hardware mentions though +# https://howisonlab.github.io/softcite-pdf-files/pdf-files/pmc_oa_files/PMC1904263.pdf +pmcid:PMC1904263 rdf:type bioj:article ; + + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:coded_no_in_text_mentions ; + citec:isPresent true; # true/false + ] ; + ] ; + + + # citec:has_in_text_mention FIXME ; # name in text mention like pmcid:PMC3028497_JC01, no quotes +. diff --git a/data/individuals-realrichardparker/realrichardparker-PMC4192806.ttl b/data/individuals-realrichardparker/realrichardparker-PMC4192806.ttl new file mode 100644 index 000000000..39fc7b17b --- /dev/null +++ b/data/individuals-realrichardparker/realrichardparker-PMC4192806.ttl @@ -0,0 +1,31 @@ + +@prefix xsd: . +@prefix rdf: . +@prefix rdfs: . +@prefix owl: . + +@prefix ca: . +@prefix doap: . +@prefix vivo: . + +@prefix bioj: . +@prefix citec: . +@prefix bioj-cited: . +@prefix pmcid: . +@prefix pmcid-cited: . +@prefix dc: . +#done no mentions of software, couple of hardware +# https://howisonlab.github.io/softcite-pdf-files/pdf-files/pmc_oa_files/PMC4192806.pdf +pmcid:PMC4192806 rdf:type bioj:article ; + + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:coded_no_in_text_mentions ; + citec:isPresent true; # true/false + ] ; + ] ; + + + # citec:has_in_text_mention FIXME ; # name in text mention like pmcid:PMC3028497_JC01, no quotes +. From 01da9f0de0ea3793f9ba3733388e5863cc5f1a46 Mon Sep 17 00:00:00 2001 From: Tiger Zhang Date: Fri, 10 Nov 2017 11:16:33 -0600 Subject: [PATCH 3/5] finished article, no mentions --- .../realrichardparker-PMC3607915.ttl | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 data/individuals-realrichardparker/realrichardparker-PMC3607915.ttl diff --git a/data/individuals-realrichardparker/realrichardparker-PMC3607915.ttl b/data/individuals-realrichardparker/realrichardparker-PMC3607915.ttl new file mode 100644 index 000000000..fa3f3e867 --- /dev/null +++ b/data/individuals-realrichardparker/realrichardparker-PMC3607915.ttl @@ -0,0 +1,31 @@ + +@prefix xsd: . +@prefix rdf: . +@prefix rdfs: . +@prefix owl: . + +@prefix ca: . +@prefix doap: . +@prefix vivo: . + +@prefix bioj: . +@prefix citec: . +@prefix bioj-cited: . +@prefix pmcid: . +@prefix pmcid-cited: . +@prefix dc: . +#done, no software mentions +# https://howisonlab.github.io/softcite-pdf-files/pdf-files/pmc_oa_files/PMC3607915.pdf +pmcid:PMC3607915 rdf:type bioj:article ; + + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:coded_no_in_text_mentions ; + citec:isPresent true; # true/false + ] ; + ] ; + + + #citec:has_in_text_mention FIXME ; # name in text mention like pmcid:PMC3028497_JC01, no quotes +. From 8b24e65fd4d660fea14af8e27aac754511628351 Mon Sep 17 00:00:00 2001 From: Tiger Zhang Date: Fri, 10 Nov 2017 11:24:22 -0600 Subject: [PATCH 4/5] finished article --- .../realrichardparker-PMC5081317.ttl | 96 +++++++++++++++++++ 1 file changed, 96 insertions(+) create mode 100644 data/individuals-realrichardparker/realrichardparker-PMC5081317.ttl diff --git a/data/individuals-realrichardparker/realrichardparker-PMC5081317.ttl b/data/individuals-realrichardparker/realrichardparker-PMC5081317.ttl new file mode 100644 index 000000000..8c715ade9 --- /dev/null +++ b/data/individuals-realrichardparker/realrichardparker-PMC5081317.ttl @@ -0,0 +1,96 @@ + +@prefix xsd: . +@prefix rdf: . +@prefix rdfs: . +@prefix owl: . + +@prefix ca: . +@prefix doap: . +@prefix vivo: . + +@prefix bioj: . +@prefix citec: . +@prefix bioj-cited: . +@prefix pmcid: . +@prefix pmcid-cited: . +@prefix dc: . +#done +# https://howisonlab.github.io/softcite-pdf-files/pdf-files/pmc_oa_files/PMC5081317.pdf +pmcid:PMC5081317 rdf:type bioj:article ; + + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:coded_no_in_text_mentions ; + citec:isPresent false; # true/false + ] ; + ] ; + + + citec:has_in_text_mention pmcid:PMC5081317_TZ01 ; # name in text mention like pmcid:PMC3028497_JC01, no quotes +. +pmcid:PMC5081317_TZ01 rdf:type citec:in_text_mention ; # use in text mention name + citec:full_quote """The analysis of the collected data was with IBM SPSS statistics package ver. 20.0 (IBM, Armonk, NY, USA). """ ; # use triple quotes + + citec:on_pdf_page 3 ; # integer + + citec:spans_pages false ; # true/false + + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:mention_type ; + rdfs:label """software""";# software | algorithm | hardware | other ; # put one in triple quotes + ca:certainty 10 ; # integer + ca:memo """SPSS is a well known statistical analysis software""" ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:software_was_used ; + citec:isPresent true; # true/false + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:software_name ; + citec:isPresent true ; # true/false + rdfs:label """IBM SPSS statistics package""" ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:version_number ; + citec:isPresent true ; # true/false + rdfs:label """ver. 20.0 """ ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:version_date ; + citec:isPresent false ; # true/false + # rdfs:label FIXME ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:url ; + citec:isPresent false ; # true/false + # rdfs:label FIXME ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:creator ; + citec:isPresent true ; # true/false + rdfs:label """IBM""" ; # use triple quotes + ] ; + ] ; + # citec:has_reference pmcid-citedFIXME: ; # name reference like pmcid-cited:a2004-40-NAT_GENET_Author-YYYY, no quotes +. From 13344e3719f906b3a7e8a30a34ef5c9bd9a3209a Mon Sep 17 00:00:00 2001 From: Tiger Zhang Date: Fri, 10 Nov 2017 11:47:56 -0600 Subject: [PATCH 5/5] finished article --- .../realrichardparker-PMC4255760.ttl | 228 ++++++++++++++++++ 1 file changed, 228 insertions(+) create mode 100644 data/individuals-realrichardparker/realrichardparker-PMC4255760.ttl diff --git a/data/individuals-realrichardparker/realrichardparker-PMC4255760.ttl b/data/individuals-realrichardparker/realrichardparker-PMC4255760.ttl new file mode 100644 index 000000000..1e948f554 --- /dev/null +++ b/data/individuals-realrichardparker/realrichardparker-PMC4255760.ttl @@ -0,0 +1,228 @@ + +@prefix xsd: . +@prefix rdf: . +@prefix rdfs: . +@prefix owl: . + +@prefix ca: . +@prefix doap: . +@prefix vivo: . + +@prefix bioj: . +@prefix citec: . +@prefix bioj-cited: . +@prefix pmcid: . +@prefix pmcid-cited: . +@prefix dc: . +#done +# https://howisonlab.github.io/softcite-pdf-files/pdf-files/pmc_oa_files/PMC4255760.pdf +pmcid:PMC4255760 rdf:type bioj:article ; + + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:coded_no_in_text_mentions ; + citec:isPresent false; # true/false + ] ; + ] ; + + + citec:has_in_text_mention pmcid:PMC4255760_TZ01 ; # name in text mention like pmcid:PMC3028497_JC01, no quotes + citec:has_in_text_mention pmcid:PMC4255760_TZ02 ; + citec:has_in_text_mention pmcid:PMC4255760_TZ03 ; +. +pmcid:PMC4255760_TZ01 rdf:type citec:in_text_mention ; # use in text mention name + citec:full_quote """After electrophoresis in a 1.5% agarose gel, ethidiumbromide–stained bands were visualized by ultraviolet transillumi-nation, and the fluorescence intensity was semiquantified using aBio2239 gel analysis system (Bio-Print, Chicago, IL)""" ; # use triple quotes + + citec:on_pdf_page 3 ; # integer + + citec:spans_pages false ; # true/false + + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:mention_type ; + rdfs:label """software""";# software | algorithm | hardware | other ; # put one in triple quotes + ca:certainty 3 ; # integer + ca:memo """Name and contexnt make Bio2239 sound like software, however googling for Bio2239 finds nothing""" ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:software_was_used ; + citec:isPresent true; # true/false + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:software_name ; + citec:isPresent true ; # true/false + rdfs:label """Bio2239""" ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:version_number ; + citec:isPresent false ; # true/false + # rdfs:label FIXME ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:version_date ; + citec:isPresent false ; # true/false + # rdfs:label FIXME ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:url ; + citec:isPresent false ; # true/false + # rdfs:label FIXME ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:creator ; + citec:isPresent true ; # true/false + rdfs:label """Bio-Print""" ; # use triple quotes + ] ; + ] ; + # citec:has_reference pmcid-citedFIXME: ; # name reference like pmcid-cited:a2004-40-NAT_GENET_Author-YYYY, no quotes +. +pmcid:PMC4255760_TZ02 rdf:type citec:in_text_mention ; # use in text mention name + citec:full_quote """The intensity of immunohistochemical staining wasanalyzed using Image-Pro-Plus image analysis software.""" ; # use triple quotes + + citec:on_pdf_page 3 ; # integer + + citec:spans_pages false ; # true/false + + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:mention_type ; + rdfs:label """software""";# software | algorithm | hardware | other ; # put one in triple quotes + ca:certainty 10 ; # integer + ca:memo """Image-Pro-Plus is a well knwon image analysis software, also explicit mention of word software""" ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:software_was_used ; + citec:isPresent true; # true/false + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:software_name ; + citec:isPresent true ; # true/false + rdfs:label """Image-Pro-Plus""" ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:version_number ; + citec:isPresent false ; # true/false + #rdfs:label FIXME ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:version_date ; + citec:isPresent false ; # true/false + # rdfs:label FIXME ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:url ; + citec:isPresent false ; # true/false + # rdfs:label FIXME ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:creator ; + citec:isPresent false ; # true/false + #rdfs:label FIXME ; # use triple quotes + ] ; + ] ; + #citec:has_reference pmcid-citedFIXME: ; # name reference like pmcid-cited:a2004-40-NAT_GENET_Author-YYYY, no quotes +. +pmcid:PMC4255760_TZ03 rdf:type citec:in_text_mention ; # use in text mention name + citec:full_quote """Data were analyzed using SPSS 17.0 software (SPSS Inc,Chicago, IL) and are presented as meanstandard deviation.""" ; # use triple quotes + + citec:on_pdf_page 3 ; # integer + + citec:spans_pages false ; # true/false + + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:mention_type ; + rdfs:label """software""";# software | algorithm | hardware | other ; # put one in triple quotes + ca:certainty 10 ; # integer + ca:memo """SPSS is awell known statistical analysis software, explicit mention of version nuber and word software""" ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:software_was_used ; + citec:isPresent true; # true/false + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:software_name ; + citec:isPresent true ; # true/false + rdfs:label """SPSS""" ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:version_number ; + citec:isPresent true ; # true/false + rdfs:label """17.0""" ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:version_date ; + citec:isPresent false ; # true/false + # rdfs:label FIXME ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:url ; + citec:isPresent false ; # true/false + # rdfs:label FIXME ; # use triple quotes + ] ; + ] ; + ca:isTargetOf + [ rdf:type ca:CodeApplication ; + ca:hasCoder "realrichardparker" ; + ca:appliesCode [ rdf:type citec:creator ; + citec:isPresent true ; # true/false + rdfs:label """SPSS Inc""" ; # use triple quotes + ] ; + ] ; + # citec:has_reference pmcid-citedFIXME: ; # name reference like pmcid-cited:a2004-40-NAT_GENET_Author-YYYY, no quotes +.