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softcite-coding-scheme.ttl
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@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix ca: <http://floss.syr.edu/ontologies/2008/4/contentAnalysis.owl#> .
@prefix softcite: <http://james.howison.name/ontologies/softcite#> .
@prefix bioj: <http://james.howison.name/ontologies/bio-journal-sample#> .
@prefix citec: <http://james.howison.name/ontologies/software-citation-coding#> .
@prefix bioj-cited: <http://james.howison.name/ontologies/bio-journal-sample-citation#> .
@prefix dc: <http://dublincore.org/documents/2012/06/14/dcmi-terms/> .
#STRUCTURE OF YOUR CODED FILE (using snippets)
#ARTICLE BLOCK
# bioj:a2004-46-NATURE rdf:type bioj:article ;
# bioj:has_supplement bioj:a2004-46-NATURE-supp1 ; #SUPPLEMENT NAME
# bioj:has_supplement bioj:a2004-46-NATURE-supp2 ; #INCREMENT SUPPLEMENT NAME
#
# bioj:has_in_text_mention bioj:a2004-46-NATURE-C01 ; # YOUR INITIALS 01
# bioj:has_in_text_mention bioj:a2004-46-NATURE-C02 ; # INCREMENT YOUR INITIALS
#.
# citec:coded_no_in_text_mentions TRUE ; #ALTERNATIVE TO ABOVE 2 LINES IF NO MENTION
#IN TEXT MENTION BLOCK
# bioj:a2004-46-NATURE-C01 rdf:type citec:in_text_mention ;
# citec:full_quote "The molecule is rich in proline residues (13%) and analysis of its amino acid sequence with PONDR [21] indicates that in the absence of other viral components at least the N-terminal half of the subunit would be disordered.";
# citec:on_pdf_page 4 ;
# ca:isTargetOf
# [ rdf:type ca:CodeApplication ;
# ca:hasCoder "yourusername" ;
# ca:appliesCode [ rdf:type citec:in-text_mention ];
# ] ;
#CITATION BLOCK
#Codes apply to the article or a selection from the article. A selection may be an in text mention or a reference. Many codes below apply to both in text mentions and references, but may be used slightly differently because those contexts are slightly different. If you're currently coding an in text mention do not refer to the citations to gather more information and vice versa.
#You will read the article, highlight in text mentions (a selection) and their corresponding references, if present (another selection). Those selections will then be coded using the options below.
#BELOW CODES ARE IN ARTICLE BLOCK
citec:has_supplement
ca:comment "Testing sync" ;
rdf:type ca:ContentAnalysisCode ;
rdfs:comment """Applies to article. Enter true if the article references supplementary materials or if the supplementary materials were assigned to you. Enter false if there is no mention or supplementary materials assigned with this article.""" ;
ca:example """ """ ;
ca:codingOrder 1 ;
ca:codingRound 1 ;
# ca:scope "article" ; # in-text_mention | reference
#SCOPE IS COMMENTED OUT BECAUSE THIS IS ADDED TO generateSnippet.py MANUALLY
ca:template """citec:isPresent FIXME""" ;
.
citec:has_in_text_mention
rdf:type ca:ContentAnalysisCode ;
rdfs:comment """Applies to article. This code is applied to each in text mention of software.
Use this code multiple times, once for each mention. Name the mention so that it is the article title, preceded by an a and followed by an underscore, then your initials, then a number. Start that number at 01 and increment one each time you find a new mention. Doesn't have to match the order the mentions are in the PDF.
Do not use this code if there were no software mentions (use coded_no_in_text_mentions instead).
If you find a mention in a footnote, code the footnote as one mention and the sentence the footnote linked to as another.""" ;
ca:example """- Your first mention, if your initials are AB and the article title is 2002-22-AM_J_BOT would read a2002-22-AM_J_BOT_AB01
- Your fourth mention would read a2002-22-AM_J_BOT_AB04""";
ca:codingOrder 2 ;
ca:codingRound 1 ;
#ca:scope "article" ; # in-text_mention | reference
#SCOPE IS COMMENTED OUT BECAUSE THIS IS ADDED TO generateSnippet.py MANUALLY
ca:template """<FIXME>""" ;
.
citec:coded_no_in_text_mentions
rdf:type ca:ContentAnalysisCode ;
rdfs:comment """Applies to article. This code is used if the article made no mention of software.
Reply true if there was no mention of software in the article. Reply false if there was a mention (i.e. it's false if you have responses for has_in_text_mention above).""" ;
ca:example """ """ ;
ca:codingOrder 3 ;
ca:codingRound 1 ;
#ca:scope "article" ; # in-text_mention | reference
#SCOPE IS COMMENTED OUT BECAUSE THIS IS ADDED TO generateSnippet.py MANUALLY
ca:template """FIXME;""" ;
.
citec:memo
rdfs:type ca:ContentAnalysisCode ;
rdfs:comment """Use this space to record any interesting issues that come up in the paper.""" ;
ca:example """- Sentence has two mentions, one for Staden, one for GDE. Each in text mention is coded separately.""" ;
ca:codingOrder 0.5 ;
ca:codingRound 1 ;
# ca:scope "article" ; # in-text_mention | reference
#SCOPE IS COMMENTED OUT BECAUSE THIS IS ADDED TO generateSnippet.py MANUALLY
ca:template """FIXME;""" ;
.
#BELOW CODES ARE IN SELECTION BLOCK
citec:full_quote
rdf:type ca:ContentAnalysisCode ;
rdfs:comment """This code is a quotation taken directly from the article that provides the content that mentions the software (i.e. the full quote is the selection you will code).
Highlight this quote in your pdf. Copy and paste directly from the pdf to this code; there is no need to remove hyphens from line breaks. Your selection needs to be long enough to make it easy to identify which sentence you are referring to. Do not change the indentation of your quote. Use triple quotes around the quote.""" ;
ca:example """- We used Detrended Corre-spondence Analysis in PC-ORD (McCune, 1993) to depict multivariatechanges in dominance of species neighborhoods for each focal speciesin recently burned and long-unburned sites.""";
ca:codingOrder 1 ;
ca:codingRound 2 ;
#ca:scope "both" ; # in-text_mention | reference
#SCOPE IS COMMENTED OUT BECAUSE THIS IS ADDED TO generateSnippet.py MANUALLY
ca:template """ FIXME ;""" ;
.
citec:on_pdf_page
rdf:type ca:ContentAnalysisCode ;
rdfs:comment """This code provides the page of the pdf that your selection (i.e. full quote) can be found on. This refers specifically to the pdf page, not the journal page. If selection spans pages put the first page here and set citec:spans_pages to true.""" ;
ca:example """- 5""" ;
ca:codingOrder 2 ;
ca:codingRound 2 ;
#ca:scope "both" ; # in-text_mention | reference
#SCOPE IS COMMENTED OUT BECAUSE THIS IS ADDED TO generateSnippet.py MANUALLY
ca:template """ FIXME ;""" ;
.
citec:mention_type
rdf:type ca:ContentAnalysisCode ;
rdfs:comment """This code applies to the selection and describes if the mention is software or something else and then establishes how certain you are about this. A selection should only be coded if you were sure it was software, from context, or if you had to web search. No need to record things that were clearly not software.
If you are unsure if something is software, do a web search or find some other means to establish what the mention is actually referring to.
- Use "software" if the mention is software
- Use "algorithm" if the mention is referring to a process or algorithm
- Use "hardware" if the mention is referring to a piece of hardware or a physical object (that may or may not have software installed on it)
- Use "other" if the mention is none of the above
Indicate your certainty on a scale of 1-10, where 10 is the most certain about your categorization.
Leave a memo explaining how you made your decision about what category it is.""" ;
ca:codingOrder 3 ;
ca:codingRound 2 ;
ca:scope "in-text_mention" ;
ca:template """rdfs:label FIXME software | algorithm | hardware | other;
ca:certainty FIXME1-10 ;
ca:memo FIXME ;""" ;
.
citec:software_was_used
rdfs:type ca:ContentAnalysisCode ;
rdfs:comment """This code applies to the selection and describes whether or not the authors actually made use of or developed the software being mentioned.
Reply true if the authors used or developed this software and false if they only considered using the software or simply mentioned its existence.""" ;
ca:example """ """ ;
ca:codingOrder 4 ;
ca:codingRound 2 ;
ca:scope "in-text_mention" ; # in-text_mention | reference
ca:template """citec:isPresent FIXME;""" ;
.
citec:software_name
rdfs:type ca:ContentAnalysisCode ;
rdfs:comment """This code describes the name of the software as the authors refer to it in the selection.
Reply true if there was a specific name provided, then enter the name in the label. Reply false if the name of the software was never provided (e.g. if they only mention the creator or the purpose of the software.)""" ;
ca:example """- PC-ORD
- Staden
- GDE""" ;
ca:codingOrder 5 ;
ca:codingRound 2 ;
ca:scope "both" ; # in-text_mention | reference
ca:template """citec:isPresent FIXME ;
rdfs:label FIXME ;""" ;
.
citec:version_number
rdfs:type ca:ContentAnalysisCode ;
rdfs:comment """This code provides the version number as described in the selection.
Reply true if a version is provided. Reply false if there is no way to distinguish the version.
In label, provide the version number. Dates do not count as version numbers-use version date instead. Comment out the label if no version number is provided in the in text mention.""" ;
ca:example """- v34
- beta 0.3""" ;
ca:codingOrder 6 ;
ca:codingRound 2 ;
ca:scope "both" ; # in-text_mention | reference
ca:template """citec:isPresent FIXME ;
rdfs:label FIXME ;""" ;
.
citec:version_date
rdfs:type ca:ContentAnalysisCode ;
rdfs:comment """This code provides a date used to indicate a version of the software. This is not the date of a paper's publication. If you are coding a reference and the reference includes a version date (in addition to a publication date) then you enter that here.
Enter true if a date is provided in the selection. Enter false if no date is provided. If there is a date, enter that as the label. Use the date as provided in the paper (e.g. 2/3/2001), don't change the format.)""" ;
ca:example """ - May 2012
- 2004-02-11 """ ;
ca:codingOrder 7 ;
ca:codingRound 2 ;
ca:scope "both" ; # in-text_mention | reference
ca:template """citec:isPresent FIXME ;
rdfs:label FIXME ;""" ;
.
citec:url
rdfs:type ca:ContentAnalysisCode ;
rdfs:comment """This code provides a URL if the selection includes one.
Mark as true if there is a URL provided. Mark as false if no URL was provided. Copy and paste the URL and enter it into the label. If the URL is found in a footnote without any other text, consider the URL to be part of the selection that has the footnote. If, however, the footnote includes more text than just the URL, it becomes its own mention.""" ;
ca:example """- http://timat2.sourceforge.net""" ;
ca:codingOrder 8 ;
ca:codingRound 2 ;
ca:scope "both" ; # in-text_mention | reference
ca:template """citec:isPresent FIXME ;
rdfs:label FIXME ;""" ;
.
citec:creator
rdfs:type ca:ContentAnalysisCode ;
rdfs:comment """This code provides the creator of the software as described in the in text mention or the reference, depending on which you are coding.
Enter true if a creator is named. Enter false if no creator is provided. Copy the creator as named in the in text mention or reference and paste it as the label. If multiple creators are named, select them all and enter them into the label.
If this is an in text selection, the creator would be whoever that text indicates the software creator to be, including from an "Author-Year" style citation. If this is a reference selection, the creator is the list of authors, including 'et al.' if relevant. It is ok to have a creator on the in-text_mention and on the associated reference.""" ;
ca:example """- If your selection is, 'Software, written by xyz, was used for ...,' then your rdfs:label is xyz.
- If your selection is '....coupled to MetaMorph imaging software (Universal Imaging Corporation, Downingtown, PA),' your rdfs:label is Universal Imaging Corporation.'
- If your selection is 'MCCUNE, B. 1993. Multivariate analysis on the PC-ORD system. Oregon State University, Corvallis, Oregon. USA,' then your rdfs:label is MCCUNE, B.'""" ;
ca:codingOrder 9 ;
ca:codingRound 2 ;
ca:scope "both" ; # in-text_mention | reference
ca:template """citec:isPresent FIXME ;
rdfs:label FIXME ;""" ;
.
citec:has_reference
rdf:type ca:ContentAnalysisCode ;
rdfs:comment """This code names the reference that an in text selection cites, if it cites one.
It should be named the same thing that the reference is referred to as in its own reference block below. It should start with a, followed by the article name (e.g. 002-22-AM_J_BOT), followed by an underscore and then enough information to make it a unique name. Using the first author on the reference followed by the date is a good way to ensure uniqueness, but it is possible you will need to append the character a or the character b after the date if there are multiple references by the same author in the same year.
If there are no references, remove this code.""" ;
ca:example """- a2002-22-AM_J_BOT_Staden-1996
- a2002-22-AM_J_BOT_Staden-1996b""" ;
ca:codingOrder 1 ;
ca:codingRound 1 ;
# ca:scope "article" ; # in-text_mention | reference
#SCOPE IS COMMENTED OUT BECAUSE THIS IS ADDED TO generateSnippet.py MANUALLY
ca:template """citec:isPresent FIXME""" ;
.
citec:reference_type
rdfs:type ca:ContentAnalysisCode ;
rdfs:comment """This code is only applied to reference selections and is used to categorize the type of reference that it is. Each option is mutually exclusive.
- Apply "publication" if the reference is to a formal publication of some sort.
- Apply "user_guide" if the reference is to a user guide for the software.
- Apply "project_page" if the reference is just pointing to the software's online website.
- Apply "project_name" if the reference is informal and mentions the name of the software but provides no URL (see examples).""" ;
ca:example """- If your reference selection is 'STADEN, R. 1996. The staden sequence analysis package. Molecular Biotechnology 5:233–241,' then you would code that as a publication because it is an article in the journal Molecular Biotechnology.
- If your reference selection is 'MCCUNE, B. 1993. Multivariate analysis on the PC-ORD system. Oregon State University, Corvallis, Oregon. USA,' then you would code that as project_name because it is neither a publication, nor a user guide, nor does it link to the project's webpage. It only names the project as an entity that exists.""" ;
ca:codingOrder 10 ;
ca:codingRound 2 ;
ca:scope "reference" ; # in-text_mention | reference
ca:template """rdfs:label FIXME: publication | user_guide | project_page | project_name ;""" ;
.