Archiving FS Software?


An important note: the treesearch ID is in the "View article…" XML link that comes from Top 20 Most Recent PNW Pubs

From Subject Received Size Categories

Top 20 PNW Pubs Ozone exposure and nitrogen deposition lowers root biomass of ponderosa pine in the San Bernardino Mountains California 3/17/2017 7 KB

Top 20 PNW Pubs Area burned in alpine treeline ecotones reflects regionwide trends 3/17/2017 6 KB

Top 20 PNW Pubs Response of giant sequoia canopy foliage to elevated concentrations of atmospheric ozone 3/17/2017 8 KB

Top 20 PNW Pubs Transient nature of CO2 fertilization in arctic tundra 3/16/2017 7 KB

So, you would be able to skip a lot of the below steps?

Install Firefox

Add a new function: "Open Multiple URLS"

Opens a list of multiple URLs from a supplied list of URLS, in plain text format.

Put this in one column:

Put the names of the publications with + instead of "space" in the next column.

Copy and paste both columns here:

NOte: Is there a python command module that can do this?

COmbine them by "finding" the tab and "replacing" with nothing.

It is better to do this in a text editor Like NOtepad++ or TextWrangler but this is the best alternative I could find.

actions for "find and replace" in a text editor to prepare the data for the FirefOx link add-on:

Step 1 – prepare URL string by creating TreeSearch compatible search query: Find "space" and replace with with "+"

Step 2 – prepare URL string by combining TreeSearch text query with compatible search string: Find "tabs" (five spaces) and replace with "nothing" (i.e., delete all tabs so you have one continuous string)

The desired outcome is a whole list of URL search strings that look like this:

Copy and paste all that into a new Notepad (plain text document)

Save it.

Copy and paste all that plain text into your Firefox add-on.

You should see a result that matches your search string. There may be a few, rely on your human brain to choose the right one.

COpy and past the URL for teh correct result. For the example above, that is the following URL:

Scroll all the way back (left arrow on your browser tabs in Firefox)

Start copying and pasting URLs.

Ctrl+W as you go along will close each tab as you proceed through.

You might encounter some hitches. Example:,+Sonoma+tree+vole+(A.+pomo),+and+white-footed+vole+(A.+albipes).

Possibly failed due to non-coded parenthetical.

Executing the search again, with the problem character removed (paranthetical in this case, yeilds success)


Note "NA" if your automated search (and attempt at fixing problem searches, as above) did not retrieve results.

If there is a problem with a record, highlight it in red.

Example – a RITS record with typographical errors:

Dam Rmoval Iformation Prtal (DRIP)—A map-based resource linking scientific studies and associated geospatial information about dam removals: U.S

Dam Removal Information Portal (DRIP)—A map-based resource linking scientific studies and associated geospatial information about dam removals: U.S

Sort by TreeSearch ID (Column D)


Copy out all the URLS which contain the TreeSearch ID. In this example, it was 148 out of total 178. Two were "not found" and one was a "reject."

Copy and paste these to the online tool for "Find and Replace" used earlier (

"FInd" the string "" and "Replace" with "nothing" (i.e., no characters, nothing, zilch, nada, not even white space). The goal here is to get the TreeSearch ID all by itself.

Create a new column, "TreeSearch_ID" and paste all the TreeSearch ID’s into that column (select the first cell in the column where you wish to put this data). Double check to be sure the TreeSearch ID code matches the TreeSearch URL/

Create a new tab in your spreadsheet, "merge."

In Columnn B, paste your TreeSearch IDs.

IN column A, paste the following:

Propagate that down the entire column (easiest way is to select the right lower corner of the cell, until a ‘+’ appears, then drag it down.

Now you need to merge the two columns into a single, connected URL string.

Goal: 53842


Return to the online text editing tool ( to "Find and Replace."

This time, you are "Finding" the blank space, and "replacing" with "nothing" (again, nothing, nada, zilch to eliminate any and all blank space betweeen the TreeSearch ID in COlumn B and the URL string in Column A).

Copy one of the blank spaces (and only the blank spaces) from between id= and the TreeSearch ID. Paste that into the "find" option. It is very likely five single spaces (a tab).

In the "Replace with" box, delete everything so it’s "nada, zilch, nothing."


Copy and paste the result back to your "merge" spreadsheet in column C if you wish. Check again to be sure you did not miss anything (1:1 match between source data and new URL strings).

Go back to Sheet1 in your pub_update workbook.

Add a new column for "TreeSearch_XML"

Paste your new URL strings there.

Double check again to be sure there is a 1:1 match from original data to new data.

Save the spreadsheet.

Back in FireFox, use the "Open Multiple URLs" tab and paste in your list of TreeSearch XML.

Wait for the URLS to load.

Scroll your tabs all the way to the left and start at the beginning. You are looking for the Digital Object Identifier.

You can expedite this by searching for "DOI" in Firefox "Find" mode. (Ctrl + F)

Systematically copy the DOI and paste it into your spreadsheet.

If not available, write, NA and move on to the next one.

Clean the list to remove any "" – the goal is to have the DOI alone.

The end result is a list of Digital Object Identifiers. IN this example, I obtained

IN this case, only 96 out of the total 178 had a DOI (from my method). 52 were coded "NA."



Metadata search via crossref:

Metadata as JSON

Capture: Capture Reference

To install the Capture tool, just drag the Capture Reference button to your Bookmarks bar (also known as "Favorites Bar" or "Bookmarks Toolbar"). In some browsers, you may need to right-click and select "Add to Favorites" or "Bookmark This Link."

To use it, browse to a page you like and click the Capture Reference button in the Bookmarks bar. The Capture Reference window will open. Follow the instructions in the window.

View Bookmarks Bar

I think for now, install the Firefox web app for mendeley, then add them all.

Make a new sheet, call it "doi merge."

In column A, enter ""

In column B, enter the list of DOI.

Propagate Column A to match Column B

Unite two columns using process described already.

Maybe "CiteULike" has some kind of tool?

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About Tanner Jessel

I am a recent M.S. in Information Science graduate from the University of Tennessee School of Information Science. I was formerly a graduate research assistant funded by DataONE (Data Observation Network for Earth). Prior, I worked for four years as a content lead and biodiversity scientist with the U.S. Geological Survey's Biodiversity Informatics Program. Building on my work experience in biodiversity and environmental informatics, my work with DataONE focused on exploring the nature of scientific collaborations necessary for scientific inquiry. I also conducted research concerning user experience and usability, and assisted in development of member nodes with an emphasis on spatial data and infrastructure. I assisted with research designed to understand sociocultural issues within collaborative research communities. Through August 1, 2014, I was based at the Center for Information and Communication Studies at the University of Tennessee School of Information Science in Knoxville, Tennessee.

Posted on April 15, 2017, in Uncategorized, USFS Research. Bookmark the permalink. Leave a comment.

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