Publications Database Manual

Logging In | Updating Existing Publication | Create New Publication | Primary | Secondary | Abstract | Exporting Data | Scholar | Webpages | Miscellaneous

General Information

https://nefsc-publications.fisheries.noaa.gov/

No login needed for searching, filtering, and exporting.

The landing page is a list of the most recent publications, including in press and accepted titles. The page is auto-generated. I copy and paste it into our staff publications page whenever something changes.

Access the main search page by clicking the SEARCH ALL menu button. That will bring up all publications in reverse chron order, starting with in press and accepted titles. The filters at the top let you narrow things down by author, title, year, division, and branch.

You can sort the SEARCH ALL table by clicking on linked table headings (year, author, outlet, etc.).

To search only peer-reviewed titles, select “Primary Publications” from the top menu. Here you can search/filter by author, title word, and year. 

Reports/Secondary are also broken down into CRDs, Tech Memos, etc. There are very few conference abstracts in the database but they have a menu link under secondary. The search is limited to author, title word, and year. The Stock Assessments search includes a species field and year only.

The “Branch/Program” page is specifically for recreating/exporting to existing publication webpages. Not all programs have them, but other lists can be produced as needed by using the SEARCH ALL page.

Working in the Database

Logging In

  1. Click user login link on footer right

  2. Accept conditions

  3. Enter username and password

  4. Click Log In button

See “General Information” above for information on navigating the site.

Basic Instructions

Gather Information

Multiple sources to get publication updates:

  1. Jon Hare's weekly (Monday) email. He usually includes at least once new/accepted/in-press publication at the very bottom.
  2. Jarita's report to HQ (irregular; whenever someone sends her an update).
  3. Google Scholar alerts.
  4. Editorial will periodically send out emails asking NEC staff to check the site and request of any corrections and additions.

It's important to search the database before adding anything new, to avoid duplication. Go to SEARCH ALL and search on the NEFSC author name, but you can also use "Search All Authors," entering the primary author then sorting the table by author.

IMPORTANT: When copying-and-pasting information into a field, be sure to delete any spaces at the beginning or end of the text. Empty spaces throw off sort order.

Update Existing Publication

To check on the status of “In press” and “Accepted” publications, Go to the SEARCH ALL page. Those items appear at the top. 

  1. Click on the DOI or link (if available) to see if the article has moved forward from “accepted” to “in press” (usually indicated by “article has been edited” or words to that effect) or from “in press” to “published” (assigned to a volume/issue).

  2. If there’s no link, highlight the title and right-click to do a Google search. Some journals don’t do pre-print (like Fishery Bulletin) so you may not find the article until it’s been published. Some move more slowly than others. Keep checking.

  3. BE SURE that you’re looking at the journal site, not ResearchGate, PubMed, or some other citation-gathering site. Check the site name against the outlet in the database.

  4. If there’s a change, click on the “title” link in the database table to open the node.

  5. Click the “edit” tab and make the changes (remember to double-check the published title; this can change during the editing phase).

  6. Go to the bottom of the form and click “Save.”

Creating a New Publication

To add a publication, click the “Add Publication” link under user menu (footer right). The “Create Publication” form will appear.

Choose the publication type: Primary, Report, or Abstract. The form will change based on your choices.

  1. Primary: Choose journal, book, or chapter (this applies to books as well as other types of publications, like proceedings or sections in professional papers). Go to instructions for “Primary” below.

  2. Report: Choose most appropriate from dropdown then go to instructions for “Reports (Secondary)” below. 

  3. Abstracts: Oral or poster presentations not published in proceedings. I’ve been pretty lax about adding these, as people don’t report them and hunting them down is a pain.

NOTE: ID numbers are auto-assigned once you save the publication.

Primary

This category includes peer-reviewed publications; mostly journal articles but also books and book chapters.

We use Council of Science Editors (CSE) style for citations.

Full Authorship

ALL authors in the order they appear in the publication. Format should be CSE style, which is pretty barebones (as few periods and commas as possible):

Last First MI, Last First MI Jr, Last First MI

Don’t enter a final period; that is automated. If you put one here you’ll end up with two periods.

Year

Four-digit year of publication. For articles not yet published enter “Accepted” or “In press” (exactly as they appear here; otherwise grouping will get messed up) depending on their current status. 

Final period is automated.

NOTE: For “early view” or “online first” publications, do not enter the year until the article is assigned to a volume/issue. Print publication is the official publication date, no matter how early the article appears online. For online-only journals use the web publication date (there’s usually a volume and article # assigned).

Title

Enter the full title EXACTLY as it appears in the journal. Sometimes titles change between acceptance and publication so be sure to check before adding/updating. 

Final period is automated.

Journal

Use official journal abbreviation only! Many journals are already included in the taxonomy so just start to type and see if the journal appears. If it doesn’t, there are many websites that provide the information; just type the journal name plus “abbreviation” into Google. Here’s an example site: https://www.vims.edu/library/quick_links/jnlabbrev.php

CSE Style: no periods at all. J Ecol Evol or Trans Am Fish Soc

Final period (before volume info) is automated.

Volume-Issue-Pages

Usually formatted with the volume number followed by the issue in parens, followed by a colon and space, followed by page range or article number: 34(2): 61-68 or 52: 14832

Final period is automated.

Link

Usually the DOI; if no DOI, then best web link. This field is automatically generated as a link. If the article is not available online or if it’s a book or book chapter, leave it blank. No period.

NEFSC Author(s)

Start to enter staff member name starting with last name. 

  • If person has already been entered, their full name should appear after a few keystrokes.

  • If not, complete the entry to add them to the list.
    Format: Lastname Firstname MiddleInitial (Garner Laura S -- no period).
    The person's name will get added to the taxonomy. 

  • To add another author to a publication, insert a comma after the previous author then start to type the next last name, as above.

Affiliation

More fields will appear depending on what you select as Division and/or Branch. You may select more than one division, branch, or program depending on where the authors are based. 

NOTE: This field is not required because some older publications aren’t affiliated with our current structure, but with new publications it functions as a tag, and should be filled out to populate various lists.

Reports (Secondary)

Instructions vary depending on what you choose from the “Secondary” dropdown in the first (Submission Type) field:

  • Conference Proceedings or Chaptered Report

  • NEFSC Ref or Lab Document (applies to all ref doc series across Center, historical and current -- select this whenever you add a CRD)

  • NOAA Technical Memorandum (applies to all TMs across the agency and history; SPO, OPR, etc. No matter what series of TM you’re adding, select this)

  • Other Agency or Program Document (NAFO, Sea Grant, ICES, other NGOs)

  • Other Government Document (non-NOAA; i.e., NASA)

Fill in fields as under “Primary” except:

  • Another dropdown will appear in case the submission is a stock assessment, TRAC document, etc. Select one if applicable. 

  • If you select stock assessment from the program document dropdown, a “Species” field will appear. This field will auto-populate once you start typing in a species (common) name. If the species you want doesn’t appear, you can add it by typing it into the field.

  • Conference proceedings have an additional field because sometimes there are more details: editors, conference proceedings, tech memo chapters, etc. This information goes into the “Details” field if needed. Be sure to use CSE format.

  • I have more work to do on field dependencies (i.e., right now the “Details” field appears only if “Conference Proceedings” is selected; I should add that to more selections). Dependencies can be tricky and need to be slapped around a bit to work correctly.

Series

  • CRDs: Even though you selected “NEFSC Ref or Lab Document” in the top field, you need to fill in “Northeast Fish Sci Cent Ref Doc” here. THIS IS FOR TAGGING REASONS.

  • TMs: Same goes for Tech Memos. Even though you selected “NOAA Technical Memorandum” in the top field, you need to fill in the precise series here (for example, “NOAA Tech Memo NMFS NE”). Again, because TAGGING.

Abstracts

I don’t know if we need to keep track of these anymore, but just in case:

From “Submission Type,” choose “Abstract”
The default (most common) abstract type is “Oral presentation,” but be sure to check what type it is.

Full Authorship
Year
Title
Presented at: Full name of conference; location of conference; beginning through end dates of conference.
Journal: Sometimes journals publish conference proceedings (J Shellfish Res usually publishes the Milford Aquaculture Seminar abstracts, for example)
Vol-Issue-Page: Full details on where the abstract appears in print, if applicable
Link: Sometimes abstracts are published online; for example, ICES conferences
NEFSC Author & Affiliation: see above

Exporting Data

Using the Export Function

I set up the View Export module mainly for leadership so they can see what their staff has produced, or for authors to put into a CV. It doesn’t always work well so it’s only on the main SEARCH page.

Theoretically, you can filter the data using the filters at the top of the page (for instance, by author, by year, by division, etc.) then export the filtered data as a Word or Excel document, or a CSV, Text, or XML file. If you sort the list (alpha, by year, etc.), the ordering doesn’t come through in the export.

In Word the data comes through in a table. I use Word’s “convert to text” function if I have to export, but I’ve set up most public-intended pages as lists in the database to avoid that issue. 

Updating Web Pages

For pages that are formatted as lists, it’s usually easiest to copy the data by highlighting it, then pasting it into the page, or copy and paste only new information onto the existing page. The drawback is that most lists are multiple pages so you have to copy one page at a time. Details are in the "Webpages" section below.

Google Scholar Alerts

This is one of the ways I keep track of NEFSC publications. It's come in very handy.

1. Go to Google Scholar.

2. Enter "Northeast Fisheries Science Center" into the search field.

3. You'll get this screen:

4. Select a time period (since 2020 is probably best).

5. Uncheck "include patents."

6. Click "Create alert.

7. You'll get this screen:

8. Make whatever adjustments and click "Create Alert" button.

9. You're done. Alerts will show up sporadically in your inbox. You’ll need to sift through them for our staff authors and make sure they’re not already in the database.

Publication Webpages

Currently, with the database not accessible to the public, I copy and paste new information into existing pages. If the database is made public we’ll need to update a bunch of links on the HQ site. The biggest pages (TMs, CRDs, SAW) are resource pages with links to pages on our apps server.

Recent Publications

The landing page of the database is a recreation of the old publications landing page, which listed our most recent publications (including in-press and accepted). After an update, I copy the list from the landing page and paste it over the existing content on our “Staff Publications” page.

Gail and Frady can edit this page. Since it’s the only publications page on the HQ site, I don’t think Jarita needs to be added but it should be updated whenever something changes -- usually when an accepted or in-press manuscript is added or published.

NEFSC-published Series

The following lists are on the apps server, linked from resource pages in the HQ site. I put pre-IR publications on the apps server initially, then update links in the database and on the apps page when the documents become available in the IR. 

IMPORTANT: Once a document is in the IR, I remove it from the apps page and DELETE THE DOCUMENT from the apps directory to avoid having duplicate versions of the same document floating around the web.

NEFSC Reference Documents

NOAA Tech Memos NMFS-NE

Stock Assessment Documents

TRAC Documents

Branch Publications

In the database under “By Division/Branch.” They’re broken out by branch and program (only for groups that have existing publication lists on the HQ site) in the main menu dropdown. I still need to compare their pages with the database lists.

Miscellaneous Pages

Below are non-publication webpages and tasks that I update/perform as needed.