| Code | Comment | Example |
|---|---|---|
| codable | Applies to article. Enter true if the article is codable. For example, if the article is in a foreign language and does not have an English translation then it would be uncodable and you would enter false.
If you reply false, delete the rest of the codes in the article block and move on to a new article. | |
| standard_type | Reply true if the article appears to be a normal research article (literature review, experiment, qualitative study, etc.). An abstract or reference list is usually indicative of the file being a standard research article. Enter false for other content like letters to the editor, post-mortems, book reviews, committee or workshop reports, abstract collections, etc.
Continue coding regardless of whether or not the article is standard. | |
| memo | Use this space to record any interesting issues that come up in the paper. Put the memo in triple quotes. You can insert a memo anywhere you need by using the memo snippet. | - Sentence has two mentions, one for Staden, one for GDE. Each in text mention is coded separately. |
| has_in_text_mention | 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 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. | - Your first mention, if your initials are AB and the article title is pmcid:2002-22-AM_J_BOT would read pmcid:2002-22-AM_J_BOT_AB01
- Your fourth mention would read pmcid:2002-22-AM_J_BOT_AB04 |
| coded_no_in_text_mentions | 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). | |
| full_quote | Applies to both in text mentions and references. 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. | - 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. |
| on_pdf_page | Applies to both in text mentions and references. 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. | - 5 |
| spans_pages | Applies to both in text mentions and references. This code indicates whether or not the quote starts on one page but continues to a secont page.
If the in text mention or reference starts and stops on different PDF pages, enter true. If it is only on one page, enter false. | |
| mention_type | Applies to in-text mentions. 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.
If you are unsure if a mention of some sort of technology is software, do a web search around that mention. Or read more in the context paper. Or find some other possible means to judge what the mention is actually referring to. - Use "software" if the mention is software. Note that if a programming language is mentioned, like "Java", "Perl", "R", etc., mark it as "software". As programming languages are themselves software being used to create software. If the mention is of a script written in a language, for example, "We used Perl scripts to...", then it should be coded as 2 mentions. One for the language "Perl", one for the scripts. But the scripts should be coded as no software_name. - Use "algorithm" if the mention is referring to an algorithm, a computerized problem-solving process, or a function. - Use "hardware" if the mention is referring to a piece of hardware or a physical instrument (that may or may not have software installed on it). - Use "database" if the mention is referring to an actual data collection/dataset (i.e., the real data). In some cases the data is "wrapped" in software components such as an interface. Make sure what the mention refers to is the data inside the database or a functioning database supported by a software framework. - Use "web platform" if the mention is referring to an online platform with a web interface. This category could include web services such as "Google", "Amazon", or "Sportify". But exception exists. For example, MediaWiki can refer to the technology platform that Wikipedia and Wikitionary run on. It can also be downloaded by individuals for specific use in academic work. In the latter scenario, MediaWiki is used more as software rather than a web platform. - 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. If you do not categorize the mention as software (e.g. it is hardware), then you can stop coding the in text selection after this code and delete all other codes that follow. | |
| software_was_used | Applies to in text mentions. 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. | |
| software_name | Applies to both in text mentions and references. 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). Do not include the version number in the label. Delete the label line if no software name is provided in the in text mention. If the software is mentioned both by name and by abbreviation in the same excerpt, it should be coded as two separate mentions that differ in software_name only in-text_mention name only. | - PC-ORD
- Staden - GDE |
| version_number | Applies to both in text mentions and references. 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. If there is a "v" or the word "version" before the number in the article, include that in your label. Dates do not count as version numbers-use version date instead. Delete the label line if no version number is provided in the in text mention. | - v34
- beta 0.3 - version 2.0 - 1.3.9 |
| version_date | Applies to both in text mentions and references. This code provides a date used to indicate a version of the software.
If you are coding an in-text mention, enter true if a date is provided that tells you when the software itself was created. When coding an in-text mention, this is is not the date of a cited paper's publication. That means that if the only date in the in-text mention is part of a citation (e.g. "(Jones, 2004)"), then you will enter false. If you are coding a reference and the reference includes a date of any kind, enter true. 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. Delete the label line if no date is provided in the in text mention. | - May 2012
- 2004-02-11 |
| url | Applies to both in text mentions and references. 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. Delete the label line if no URL is provided in the in text mention. If the URL is embedded, meaning that you see text that is a hyperlink but not the actual URL, mark this code as false. | - http://timat2.sourceforge.net |
| creator | Applies to both in text mentions and references. 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. Delete the label line if no creator is provided in the in text mention. | - 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 '....we used custom imaging software (Jones, 2004),' then your rdfs:label is Jones. - 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. |
| has_reference | Applies to in text mentions. 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 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, delete this code altogether. | - pmcid-cited:2002-22-AM_J_BOT_Staden-1996
- pmcid-cited:2002-22-AM_J_BOT_Staden-1996b |
| reference_type | This code is only applied to reference selections. It 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). | - 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. |