What to Expect When You're Reference Processing

eXtyles Bibliographic Reference Processing is a powerful tool, and it can save editors a significant amount of time editing a reference list, because references that are fully color coded and restructured need only be lightly proofed. However, it is important to understand the limitations of Reference Processing so that the editor’s role in an eXtyles workflow is clear. This section will describe what you can expect eXtyles to do and not to do during reference processing and what the implications are for USGS editors.


In this section

What You Can Expect Reference Processing to Do

eXtyles Reference Processing performs two primary functions: (1) it identifies the semantically distinct elements of the reference entry and applies meaningful, color-coded character styles to each element and (2) it restructures book (<bok>, <edb>) and journal (<jrn>) references to conform to USGS editorial style.

In addition to the editorial benefit, the automated identification of reference elements and application of character styles is used to produce granular tagging of the reference entry in the XML exported from Word by eXtyles.

Glossary of Terms Used in This Guide

Restructure The process by which eXtyles edits a reference to conform to USGS editorial style. eXtyles will automatically restructure references of a certain type (e.g., journal and book).
Tag A Word field that eXtyles adds during reference processing to the start and end of each reference. The tag defines the reference type (e.g., <jrn> for journal). More information about tags can be found here
Color Coding The character styles that are applied to semantically distinct elements of the reference. The character styles have different colored shading to facilitate easy visual proofing of the reference.


Book and Journal References

eXtyles will fully tag references that it identifies as books (<bok>, <edb>) and journals (<jrn>). When your references appear as in the examples to the right, without any added eXtyles warnings (in the form of Word comments), you can safely assume that eXtyles has correctly identified the various elements of the reference and restructured them according to USGS editorial style.

Further, the color of the character styles that eXtyles applies to these references enables the editor to quickly proof the reference entry. In these examples, it is easy to see that the reference elements have been correctly identified and the references have been accurately edited.


Book and Journal Reference Examples

Conference Proceedings

eXtyles will also attempt to fully color code those references it identifies as conference proceedings (<conf>). However, because of the variety of formats that conference proceedings can take, eXtyles will not restructure these references. Your editors will still need to edit <conf> references to conform to USGS editorial style, and care will need to be taken to ensure that any color coding that has been applied is correctly retained during manual editing.


Conference Reference Example

Electronic References, Legal Documents, and Theses/Dissertations

Because of the variety of formats in which references to certain types of documents can take, eXtyles will not fully color code or restructure references that it identifies as electronic (<eref>), legal (<lgl>), and thesis (<ths>).

Note that eXtyles will still try to identify and color code certain elements of these types of references. For every reference, eXtyles will attempt to color code: (1) author given name, (2) author surname, and (3) publication date. Additionally, for some references (e.g., conferences and theses and dissertations), eXtyles will also attempt to color code the document title and URL or DOI. It is critical that for every reference the author name(s) and date are color coded, which enables eXtyles to perform accurate citation matching; however, if eXtyles has failed to color code other parts of the reference (e.g., the title), it is not essential that you manually apply color coding to those elements.

Also, because eXtyles will not restructure these types of references, your editors will still need to manually copyedit references that are tagged as <eref>, <lgl>, and <ths>.

Electronic, Legal, and Thesis/Dissertation Reference Examples



Other and Unknown References

Other

Most types of references not covered by the previously described tags will fall into the <other> category, including working papers, patents, maps, and other documents. The example shows a reference to a map (atlas) that has been correctly tagged as <other>.

Unknown

eXtyles will provide a message after Bibliographic Reference Processing has completed that will include the number of <unknown> references eXtyles identified:

It is important to note whether there are <unknown> references in the document, because they will need to be carefully reviewed to see whether the reference is, in fact, something known (like a journal) and was not correctly identified because of an error in the source content. 

Other (Map) Reference Example

Unknown Reference Example


For example, the following reference is, to the human eye, clearly a journal article:

Cohn, T.A., W.L. Lane, and Baier, W.G., 1997, An algorithm, for computing moments based flood quantile estimates when historical flood information is available, Water Resour. Res., 33(9), 2,089-2,096.

However, eXtyles tags it during Reference Processing as <unknown>:

This is because the commas in the four-digit page range prevent eXtyles from being able to confidently identify the reference as a journal (<jrn>). You will want to remove the commas from the page range and reprocess this reference so that it is correctly tagged as <jrn> and so that you can take advantage of Reference Restructuring and Crossref Linking and Correction. (See Manually Editing References for more information.)

Note

eXtyles Auto-Redact will remove commas from four-digit page numbers. Because Auto-Redact is run before Reference Processing, you should rarely see incorrect tagging of references as a result of this type of format

Once the user removes the commas from the page range, deletes the <unknown> tags, and re-runs Reference Processing, the reference will be processed correctly:

Reference Processing and USGS Publications

eXtyles Reference Processing will tag, color code, and restructure USGS active publications, such as Professional Papers, Techniques and Methods, Circulars, and so on. These publications should be tagged as <bok>, as in the examples.

However, there are some formatting conventions that will cause eXtyles to unsuccessfully identify and process a reference to a USGS publication. Following are the most common causes of eXtyles processing issues.

Format of Author Given Names

As of early 2018, USGS editorial style has been updated to use initials for author given names in a reference list, regardless of whether the author uses one or two (or more) given names. When this style is used, eXtyles will generally have no problem properly color-coding author names during Bibliographic Reference Processing.

However, the former USGS editorial style of using a mixture of initials and spelled-out given names within a single reference may appear in documents that were authored prior to the editorial style update. Because you may continue to encounter this editorial style, the following information is provided, which explains eXtyles behavior with regard to this style, and how you can achieve properly color-coded references when this style is used.

The mixture of initials and spelled-out given names in a single reference falls outside of eXtyles’s automation capabilities. When such a mix of styles is used, eXtyles is unable to disambiguate the components of the authors’ names, and will fail to fully color code and restructure the reference. For example, this reference:

McGuire, V.L., Johnson, Michael, Schieffer, R.L., Stanton, J.S., Sebree, S.K., and Verstraeten, I.M., 2003, Water in storage and approaches to ground-water management, High Plains aquifer, 2000: U.S. Geological Survey Circular 1243, 51 p.

will result in the following after Bibliographic Reference Processing:

You can see that eXtyles was unable to proceed with color coding and restructuring after the first author’s name. This is because the second author’s given name (Johnson, Michael) is spelled out, and eXtyles is consequently unable to safely disambiguate the given names from the surnames in the rest of the author list. Rather than incorrectly restructure the reference, eXtyles stops color coding, and adds a helpful warning in the form of a Word comment.

There are a couple of ways to resolve this: (1) prior to running Reference Processing the author given names can be edited to conform to a consistent style (either initials or spelled out), or (2) the reference can be edited after Reference Processing, and then reference processing can be re-run.

To perform the second option, you will need to manually change the author’s spelled-out given name to M. and remove the eXtyles tags (<bok>):

After re-running Reference Processing the result is a correctly tagged and color-coded reference:

USGS Publications Reference Examples

Plate, Sheet, and Scale Information for Non-Map Publications

As discussed in the previous section “Other and Unknown References,” eXtyles will tag references it identifies as maps as <other>, and only color code the author names and publication date. eXtyles will not restructure references identified as <other>.

Occasionally, non-map USGS publications contain maps and, consequently, sheet and scale (and plate) information can appear in a reference to that publication. For example, the following Professional Paper contains map, sheet, and scale information:

Christiansen, R.L. 2001, The Quaternary and Pliocene Yellowstone Plateau volcanic field of Wyoming, Idaho, and Montana: U.S. Geological Survey Professional Paper 729–G, 145 p.; 3 map sheets, scale 1:125,000. [Also available at http://pubs.usgs.gov/pp/pp729g]

During Reference Processing, the reference will be processed the way eXtyles, correctly, handles other maps:

But because this publication is actually a Professional Paper, <other> might not be appropriate. In order for eXtyles to tag this reference as <bok>, the map, sheet, and scale information needs to be moved to a place that will allow eXtyles to identify the reference as a Professional Paper and not a map. The information could either be removed from the reference entirely or moved to within the bracketed comment. If the latter option is selected, the reference will process like the following:

Then, so that the reference conforms to USGS editorial style, move the sheet and scale information back to outside of the brackets, and remove the color coding by selecting the sheet and scale information and hitting Ctrl + Space (which formats the content as plain text). The correctly edited reference looks like this:



<other> or <bok>: What's the Difference?

Both <other> and <bok> references will make their way through eXtyles processing without problems (e.g., Citation Matching, XML Export). However, whether the reference is left as <other> or manipulated so that eXtyles tags it as <bok> has a few key implications, both editorially and in the XML.

Editorial Implications

Crossref Linking and Correction

Crossref Linking and Correction does not check references tagged as <other>; it only checks references tagged as <jrn>, <bok>, or <edb>. Therefore, if you would like the reference to be validated against Crossref and possibly have the DOI inserted (if a match is found), the reference will have to be tagged as <bok>, and it will need to have been successfully color coded by Bibliographic Reference Processing. See the examples to the right; the <bok> example could then be edited to remove the sheet and scale information from the brackets, in compliance with USGS editorial style.

Note

Not all publications are cataloged by Crossref, and so simply changing a reference’s tags to <bok> or fully color coding a reference does not guarantee that Crossref Linking and Correction will successfully return a DOI.


Automatic Reference Restructuring

eXtyles will not attempt to restructure references tagged as <other>; however, eXtyles will attempt to restructure references tagged as <bok>. For example, in the reference example to the right, periods incorrectly enclose the publication date, and there is a period after the document title rather than a colon. The incorrect punctuation is retained in the reference tagged as <other>, while the punctuation in the reference tagged as <bok> is correctly edited.


Crossref Linking and Correction Examples

<other>

<bok>


Automatic Reference Restructuring Examples

Christiansen, R.L. 2001. The Quaternary and Pliocene Yellowstone Plateau volcanic field of Wyoming, Idaho, and Montana. U.S. Geological Survey Professional Paper 729–G, 145 p.; 3 map sheets, scale 1:125,000. [Also available at http://pubs.usgs.gov/pp/pp729g]

<other>

<bok>



XML Implications

Publication Type

References tagged as <other> will be identified as such in the XML (e.g., <mixed-citation publication-type="other">), whereas references tagged as <bok> will be identified accordingly in the XML (e.g., <mixed-citation publication-type="book">); see the below code examples.

Granularity in the XML

References tagged as <other> will not have all of the granular parts of the reference entry identified in the XML; only the author names and date will have unique tagging in the XML. Whereas references tagged as <bok> will have all of the granular parts of the reference identified as such in the XML. For example:

<other>

<ref id="r1"><mixed-citation publication-type="other">Luckey, R.R., Gutentag, E.D., and Weeks, J.B., 1981, Water-level and saturated-thickness changes, predevelopment to 1980, in the High Plains aquifer in parts of Colorado, Kansas, Nebraska, New Mexico, Oklahoma, South Dakota, Texas, and Wyoming: U.S. Geological Survey Hydrologic Investigations Atlas HA-652, 2 sheets, scale 1:2,500,000.</mixed-citation></ref>


<bok>

<ref id="r8"><mixed-citation publication-type="book"><person-group person-group-type="author"><string-name name-style="western"><surname>Qi</surname>, <given-names>S.L.</given-names></string-name></person-group>, <year>2010</year>, <source>Digital map of aquifer boundary for the High Plains aquifer in parts of Colorado, Kansas, Nebraska, New Mexico, Oklahoma, South Dakota, Texas, and Wyoming</source>: <series>U.S. Geological Survey Data Series</series> <volume>543</volume>. <comment>[Also available at http://pubs.usgs.gov/ds/543/.]</comment></mixed-citation></ref>