Archiving FS Software?

https://data.fs.usda.gov/research/services/westernstubservices/productsservicesentry?product_id=&treesearch_id=52214

nev3mU_4Aspe

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"

https://addons.mozilla.org/en-US/firefox/addon/open-multiple-urls/?src=api

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

Put this in one column:

https://www.treesearch.fs.fed.us/search.php?in_words_phrases=

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

Copy and paste both columns here:

http://textmechanic.com/text-tools/basic-text-tools/find-and-replace-text/

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:

https://www.treesearch.fs.fed.us/search.php?in_words_phrases=Phenology+of+Pacific+Northwest+tree+species

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:

https://www.treesearch.fs.fed.us/pubs/53128

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:

https://www.treesearch.fs.fed.us/search.php?in_words_phrases=Annotated+bibliography+of+the+red+tree+vole+(Arborimus+longicaudus),+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)

Example:

https://www.treesearch.fs.fed.us/search.php?in_words_phrases=Annotated+bibliography+of+the+red+tree+vole

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)

TreeSearch_ID

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."

https://www.treesearch.fs.fed.us/pubs/49896

https://www.treesearch.fs.fed.us/pubs/49900

https://www.treesearch.fs.fed.us/pubs/50056

https://www.treesearch.fs.fed.us/pubs/50057

https://www.treesearch.fs.fed.us/pubs/50067

https://www.treesearch.fs.fed.us/pubs/50115

https://www.treesearch.fs.fed.us/pubs/50198

https://www.treesearch.fs.fed.us/pubs/50199

https://www.treesearch.fs.fed.us/pubs/50200

https://www.treesearch.fs.fed.us/pubs/50263

https://www.treesearch.fs.fed.us/pubs/50332

https://www.treesearch.fs.fed.us/pubs/50397

https://www.treesearch.fs.fed.us/pubs/50400

https://www.treesearch.fs.fed.us/pubs/50402

https://www.treesearch.fs.fed.us/pubs/50464

https://www.treesearch.fs.fed.us/pubs/50468

https://www.treesearch.fs.fed.us/pubs/50503

https://www.treesearch.fs.fed.us/pubs/50530

https://www.treesearch.fs.fed.us/pubs/50567

https://www.treesearch.fs.fed.us/pubs/50656

https://www.treesearch.fs.fed.us/pubs/50697

https://www.treesearch.fs.fed.us/pubs/50788

https://www.treesearch.fs.fed.us/pubs/50789

https://www.treesearch.fs.fed.us/pubs/50790

https://www.treesearch.fs.fed.us/pubs/50791

https://www.treesearch.fs.fed.us/pubs/50882

https://www.treesearch.fs.fed.us/pubs/50909

https://www.treesearch.fs.fed.us/pubs/50910

https://www.treesearch.fs.fed.us/pubs/50914

https://www.treesearch.fs.fed.us/pubs/50915

https://www.treesearch.fs.fed.us/pubs/50916

https://www.treesearch.fs.fed.us/pubs/50917

https://www.treesearch.fs.fed.us/pubs/50918

https://www.treesearch.fs.fed.us/pubs/50919

https://www.treesearch.fs.fed.us/pubs/50935

https://www.treesearch.fs.fed.us/pubs/50952

https://www.treesearch.fs.fed.us/pubs/50970

https://www.treesearch.fs.fed.us/pubs/50985

https://www.treesearch.fs.fed.us/pubs/51057

https://www.treesearch.fs.fed.us/pubs/51058

https://www.treesearch.fs.fed.us/pubs/51076

https://www.treesearch.fs.fed.us/pubs/52016

https://www.treesearch.fs.fed.us/pubs/52017

https://www.treesearch.fs.fed.us/pubs/52019

https://www.treesearch.fs.fed.us/pubs/52070

https://www.treesearch.fs.fed.us/pubs/52089

https://www.treesearch.fs.fed.us/pubs/52214

https://www.treesearch.fs.fed.us/pubs/52214

https://www.treesearch.fs.fed.us/pubs/52215

https://www.treesearch.fs.fed.us/pubs/52223

https://www.treesearch.fs.fed.us/pubs/52225

https://www.treesearch.fs.fed.us/pubs/52233

https://www.treesearch.fs.fed.us/pubs/52237

https://www.treesearch.fs.fed.us/pubs/52239

https://www.treesearch.fs.fed.us/pubs/52320

https://www.treesearch.fs.fed.us/pubs/52322

https://www.treesearch.fs.fed.us/pubs/52326

https://www.treesearch.fs.fed.us/pubs/52360

https://www.treesearch.fs.fed.us/pubs/52362

https://www.treesearch.fs.fed.us/pubs/52364

https://www.treesearch.fs.fed.us/pubs/52469

https://www.treesearch.fs.fed.us/pubs/52469

https://www.treesearch.fs.fed.us/pubs/52500

https://www.treesearch.fs.fed.us/pubs/52505

https://www.treesearch.fs.fed.us/pubs/52506

https://www.treesearch.fs.fed.us/pubs/52509

https://www.treesearch.fs.fed.us/pubs/52510

https://www.treesearch.fs.fed.us/pubs/52511

https://www.treesearch.fs.fed.us/pubs/52512

https://www.treesearch.fs.fed.us/pubs/52535

https://www.treesearch.fs.fed.us/pubs/52558

https://www.treesearch.fs.fed.us/pubs/52559

https://www.treesearch.fs.fed.us/pubs/52562

https://www.treesearch.fs.fed.us/pubs/52563

https://www.treesearch.fs.fed.us/pubs/52564

https://www.treesearch.fs.fed.us/pubs/52639

https://www.treesearch.fs.fed.us/pubs/52640

https://www.treesearch.fs.fed.us/pubs/53060

https://www.treesearch.fs.fed.us/pubs/53067

https://www.treesearch.fs.fed.us/pubs/53106

https://www.treesearch.fs.fed.us/pubs/53108

https://www.treesearch.fs.fed.us/pubs/53109

https://www.treesearch.fs.fed.us/pubs/53110

https://www.treesearch.fs.fed.us/pubs/53111

https://www.treesearch.fs.fed.us/pubs/53112

https://www.treesearch.fs.fed.us/pubs/53120

https://www.treesearch.fs.fed.us/pubs/53122

https://www.treesearch.fs.fed.us/pubs/53123

https://www.treesearch.fs.fed.us/pubs/53124

https://www.treesearch.fs.fed.us/pubs/53125

https://www.treesearch.fs.fed.us/pubs/53126

https://www.treesearch.fs.fed.us/pubs/53127

https://www.treesearch.fs.fed.us/pubs/53128

https://www.treesearch.fs.fed.us/pubs/53129

https://www.treesearch.fs.fed.us/pubs/53130

https://www.treesearch.fs.fed.us/pubs/53131

https://www.treesearch.fs.fed.us/pubs/53132

https://www.treesearch.fs.fed.us/pubs/53133

https://www.treesearch.fs.fed.us/pubs/53134

https://www.treesearch.fs.fed.us/pubs/53136

https://www.treesearch.fs.fed.us/pubs/53137

https://www.treesearch.fs.fed.us/pubs/53138

https://www.treesearch.fs.fed.us/pubs/53139

https://www.treesearch.fs.fed.us/pubs/53140

https://www.treesearch.fs.fed.us/pubs/53141

https://www.treesearch.fs.fed.us/pubs/53142

https://www.treesearch.fs.fed.us/pubs/53143

https://www.treesearch.fs.fed.us/pubs/53144

https://www.treesearch.fs.fed.us/pubs/53146

https://www.treesearch.fs.fed.us/pubs/53147

https://www.treesearch.fs.fed.us/pubs/53148

https://www.treesearch.fs.fed.us/pubs/53156

https://www.treesearch.fs.fed.us/pubs/53157

https://www.treesearch.fs.fed.us/pubs/53158

https://www.treesearch.fs.fed.us/pubs/53160

https://www.treesearch.fs.fed.us/pubs/53161

https://www.treesearch.fs.fed.us/pubs/53162

https://www.treesearch.fs.fed.us/pubs/53162

https://www.treesearch.fs.fed.us/pubs/53162

https://www.treesearch.fs.fed.us/pubs/53163

https://www.treesearch.fs.fed.us/pubs/53165

https://www.treesearch.fs.fed.us/pubs/53166

https://www.treesearch.fs.fed.us/pubs/53167

https://www.treesearch.fs.fed.us/pubs/53169

https://www.treesearch.fs.fed.us/pubs/53170

https://www.treesearch.fs.fed.us/pubs/53175

https://www.treesearch.fs.fed.us/pubs/53176

https://www.treesearch.fs.fed.us/pubs/53187

https://www.treesearch.fs.fed.us/pubs/53244

https://www.treesearch.fs.fed.us/pubs/53245

https://www.treesearch.fs.fed.us/pubs/53246

https://www.treesearch.fs.fed.us/pubs/53247

https://www.treesearch.fs.fed.us/pubs/53248

https://www.treesearch.fs.fed.us/pubs/53249

https://www.treesearch.fs.fed.us/pubs/53356

https://www.treesearch.fs.fed.us/pubs/53379

https://www.treesearch.fs.fed.us/pubs/53385

https://www.treesearch.fs.fed.us/pubs/53641

https://www.treesearch.fs.fed.us/pubs/53642

https://www.treesearch.fs.fed.us/pubs/53644

https://www.treesearch.fs.fed.us/pubs/53646

https://www.treesearch.fs.fed.us/pubs/53647

https://www.treesearch.fs.fed.us/pubs/53647

https://www.treesearch.fs.fed.us/pubs/53651

https://www.treesearch.fs.fed.us/pubs/53708

https://www.treesearch.fs.fed.us/pubs/53841

https://www.treesearch.fs.fed.us/pubs/53841

https://www.treesearch.fs.fed.us/pubs/53842

Copy and paste these to the online tool for "Find and Replace" used earlier (textmechanic.com)

"FInd" the string "https://www.treesearch.fs.fed.us/pubs/" 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:

https://data.fs.usda.gov/research/services/westernstubservices/productsservicesentry?product_id=&treesearch_id=52214

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:

https://data.fs.usda.gov/research/services/westernstubservices/productsservicesentry?product_id=&treesearch_id= 53842

into

https://data.fs.usda.gov/research/services/westernstubservices/productsservicesentry?product_id=&treesearch_id=53842

Return to the online text editing tool (textmechanic.com) 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."

Execute.

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 "http://dx.doi.org/" – 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."

.

http://tdmsupport.crossref.org/researchers/

Example;

http://dx.doi.org/10.1016/j.jenvman.2015.12.017

http://dx.doi.org/10.1016/j.landurbplan.2015.11.007

http://dx.doi.org/10.1071/WF14166

http://dx.doi.org/10.1071/WF14170

http://dx.doi.org/10.1071/WF15092

Metadata search via crossref:

http://search.crossref.org/?q=10.1071%2FWF15092#

Metadata as JSON

https://api.crossref.org/v1/works/http://dx.doi.org/10.4996/fireecology.1202001

https://blog.mendeley.com/2011/03/21/7-ways-to-add-documents-to-mendeley/

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

https://www.mendeley.com/download-mendeley-desktop/

https://blog.mendeley.com/2011/03/21/7-ways-to-add-documents-to-mendeley/

http://service.elsevier.com/app/home/supporthub/mendeley/

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 "http://doi.org/"

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?

This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

RITS_2016_PNW_Pubs_Copy_Pasted-v02.xlsx

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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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