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Posts: 6
Registered: ‎10-25-2016
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Emailed OVIDSP reference list into Endnote

Hi!

 

I am doing a systematic review and have the following question: 

 

I had to search through a few OVID SP databases in the British Library as our university does not have access to them. At the library I could not export references, but only email them to myself. I now have some thousands of references in an txt email attachment, but they dont seem to follow any of the filters Endnote provides.

 

Does anyone know how to import the emailed references into endnotes (without too much tweaking, as there are so many).

 

BW,

Pauline

 

 

FYI: the text file looks like this (just first 2 items): 

 

1.
Tillage system and cover crop management impacts on soil quality and vegetable crop performance in organically managed production in Tennessee.
Butler, D. M.  Bates, G. E.  Inwood, S. E. E.
HortScience; 2016. 51(8):1038-1044. many ref.
[Journal article]
AN: 20163341551
Research is lacking on the impact of alternative reduced tillage (RT) systems on vegetable crop performance and soil quality, especially in organic production systems, where weed control cannot rely on synthetic herbicides. A 2-year field study was implemented in Aug. 2010 in Knoxville, TN, to evaluate cover crop-based systems for organic vegetable production either with or without spring tillage. Treatments, all organically managed, included (1) Till (+ACC), spring tillage of a winter cover crop with aboveground cover crop biomass (ACC) retained and soil covered by polyethylene mulch; (2) Till (-ACC), spring tillage of a winter cover crop with aboveground cover crop biomass (ACC) removed before tillage and soil covered by polyethylene mulch; and (3) RT system with no spring tillage and mechanically terminated winter cover crop residue on the soil surface. Vegetable crops of eggplant (Solanum melongena L.) and watermelon [Citrullus lanatus (Thunb.) Matsum. et Nakai] were planted in 2011 and 2012, respectively. Crop yield, cover crop biomass accumulation, soil N and C dynamics, and weed density were assessed. Marketable eggplant yield and marketable watermelon yield did not differ among treatments, but weed density was higher in the RT system. Measures of soil quality after 2 years of the study indicated that particulate organic matter-carbon (POM-C) and -nitrogen (POM-N) were highest in the RT treatment, a significant increase as compared with values at the beginning of the study. As a measure of the active fraction of soil organic matter, this indicates that the RT system may best maintain and improve soil quality in similar regional organic vegetable cropping systems. As indicated by measures of soil quality and crop yield, removal of aboveground cover crop biomass did not negatively impact the Till (-ACC) system as compared with the Till (+ACC).
Publisher
American Society for Horticultural Science
Location of Publisher
Alexandria
Country of Publication
USA


2.
Summer cover crops and lettuce planting time influence weed population, soil nitrogen concentration, and lettuce yields.
Kruse, R.  Nair, A.
HortTechnology; 2016. 26(4):409-416. 23 ref.
[Journal article]
AN: 20163341520
Cover crops can be used as a sustainable weed management tool in crop production systems. Cover crops have the ability to suppress weeds, reduce soil erosion, increase soil organic matter, and improve soil physical, chemical, and biological properties. In the north-central region of the United States, including Iowa, much cover crop research has been conducted in row crop systems, mainly with corn (Zea mays) and soybean (Glycine max) where cover crops are planted at the end of the growing season in September or October. There is little information available on the use of cover crops in vegetable cropping systems, particularly on the use of summer cover crops for fall vegetable production. The choice of the cover crop will significantly impact the entire fall vegetable production enterprise. Vegetable growers need information to identify the right cover crop for a particular slot in the cropping system and to understand how cover crops would affect weed suppression, soil properties, and successive vegetable crop yield. The time interval between cover crop termination and vegetable planting critically affects the growth and successive yield of the vegetable crop. This study investigated how short-duration summer cover crops impact weed suppression, soil properties, and 'Adriana' lettuce (Lactuca sativa) yield. The study also examined appropriate planting times of lettuce transplants after soil incorporation of cover crops. The experimental design was a randomized complete block split-plot design with four replications. Whole plots consisted of cover crop treatments: 'Mancan' buckwheat (Fagopyrum esculentum), 'Iron & Clay' cowpea/southernpea (Vigna unguiculata), black oats (Avena strigosa), 'Grazex II' sorghum-sudangrass (Sorghum bicolor ssp. drummondii), and a control (no-cover crop) where weeds were left to grow unchecked. The subplot treatment consisted of two lettuce transplanting times: planted immediately or 8 days after cover crop soil incorporation. Fall-planted butterhead lettuce was used. Data were collected on cover crop biomass, weed biomass, soil nutrient concentration, lettuce growth, and yield. All cover crops significantly reduced weed biomass during the fallow period as compared with the control treatment. Highest degree of weed suppression (90% as compared with the no-cover crop control treatment) was provided by buckwheat. Southernpea, a legume, increased soil nitrogen (N) concentration and contributed to higher lettuce yield and improved quality. Southernpea also enhanced lettuce growth and led to an earlier harvest than other treatments. Sorghum-sudangrass showed evidence of detrimental effects to the marketable lettuce crop. This was not due to N immobilization but presumably due to alleopathic properties. There is no clear pattern within any cover crop treatment that lettuce planting time following cover crop termination affects plant growth; however, planting early or soon after cover crop incorporation ensures more growing degree days and daylight, thus leading to timely harvest of a higher quality product. This study demonstrates that cover crops can successfully be integrated into vegetable cropping systems; however, cover crop selection is critical.
Publisher
American Society for Horticultural Science
Location of Publisher
Alexandria
Country of Publication
USA

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Mentor
Posts: 2,087
Registered: ‎09-30-2009
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Re: Emailed OVIDSP reference list into Endnote

In order for Endnote to import the.txt file there needs to be an import filter that corresponds to the text file’s field data format. It might be possible to build one but would need to see the actual.txt file to identify the hidden characters. Could you attach a sample of a few records from the.txt file (and saved as a.txt)? New users to the forum may not have immediate privileges to attach files so if you are unable to do so check the private message section (look for the envelope icon below the “Go To” drop down menu on the upper right hand side of this page) for my email address and send me the file.

 

BTW, are all the records journal articles or a mix of reference sources/type?

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User
Posts: 6
Registered: ‎10-25-2016
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Re: Emailed OVIDSP reference list into Endnote

Sure, I have attached 1 (of the many) emails with 200 references I had to send to myself (because it exceeded the size I coudl attach to this answer I have just left in the first 10 and the last 10).

 

they contain different formats, journal articles, books, conference papers etc. 

 

Would be great if you could help me!

 

 

 

Pauline

 

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User
Posts: 6
Registered: ‎10-25-2016
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Re: Emailed OVIDSP reference list into Endnote

Apologies, the attached gives a better overview of what the files look like (more recent year)

 

P

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Mentor
Posts: 2,087
Registered: ‎09-30-2009
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Re: Emailed OVIDSP reference list into Endnote

Thanks for the text file. The primary challenge to importing these records into Endnote is that the records do not include “tags” which label the start of each field (and which would be used to identify which Endnote field to funnel the information to). These records contain only hard returns to mark the end of a data line. So the file is going to require: 1) editing the data to insert/change character delimiters; 2) creating tags in the data file to mark each field; and 3) creating an Endnote filter to enable importing the data. A further complication is that you mentioned co-mingling of reference types within the same data file but the records might be able to be corrected once they’re imported into Endnote.

 

Am testing a workaround which uses both MS Word and MS Excel – do you have both programs?

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Posts: 6
Registered: ‎10-25-2016
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Re: Emailed OVIDSP reference list into Endnote

Naturally Smiley Happy

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Mentor
Posts: 2,087
Registered: ‎09-30-2009
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Re: Emailed OVIDSP reference list into Endnote

[ Edited ]

Here’s the workaround which encompasses: 1) editing the text file (using MS Word); 2) adding “tags” to the data lines (using MS Excel); and 3) importing the “tagged” file into Endnote using the filter constructed for the file. Note that editing the text file, adding tags, and using the constructed filter is based on your text file of 30 records. It’s possible future modifications may be needed if other records deviate from the structure of the original 30.

 

The Endnote import result is shown in image #1 (top). A custom field (RN) was added to the Endnote library so that record numbers could be included to facilitate later troubleshooting if needed. Due to the data structure of a few records you’ll note that some of the fields within the imported records will need to be manually corrected.

 

Instructions are provided below. The constructed Endnote filter is attached for your use.

 

------------------------------------------------------------------

 

STEP 1: EDIT THE TEXT FILE (Using MS Word)

Activate MS Word then open the text file. From the MS Word ribbon turn on the “Show/Hide” function to display the hidden format characters in the text file (refer to image #1, bottom). Then use the Replace function to make the following eight changes in the text file (blank space is noted by an asterisk):

 

Find what:           .***^p     [period-blank space-blank space--blank space-paragraph mark]

Replace with        .^p     [period-paragraph mark]

Note: OK to use Replace All Comment: this removes the three blank spaces before a paragraph mark

 

Find what:           .**^p     [period-blank blank space-paragraph mark]

Replace with        .^p     [period-paragraph mark] Note: OK to use Replace All

Comment: this removes the two blank spaces before a paragraph mark

 

Find what:           .**[     [period-blank space-blank space-left bracket]

Replace with        .*[     [period-blank space-left bracket]

Note: OK to use Replace All Comment: this removes one blank space

 

Find what:           .**Conference       [period-blank space-blank space-Conference-blank space]

Replace with:      .*Conference     [blank space-blank space-Conference-blank space]

Note: OK to use Replace All

 

Find what:           .**       [period-blank space-blank space]

Replace with:      ;*     [semi colon-blank space]

Note: OK to use Replace All

Comment: this inserts a semicolon delimiter in-between multiple author names having initials. The delimiter is needed in order to have each author listed on a separate line in the Endnote “Author” field.

 

Find what:           **       [blank space-blank space]

Replace with:      ;*     [semi colon-blank space]

Note: use Find Next to place semi-colon delimiters in-between multiple author names not having initials. The records must be reviewed and replaced individually to prevent incorrect replacement from occurring.

 

Find what:           ^p*^p^p^p^p   [paragraph mark-blank space-paragraph mark-paragraph mark-paragraph mark- paragraph mark]

Replace with:      ^p       [paragraph mark]

Note: OK to use Replace All

Comment: this was to address the spacing of one record among the 30 by removing the paragraph mark to eliminate the extra blank lines between each record.

 

Find what:           ^p*^p^p   [paragraph mark-blank space-paragraph mark-paragraph mark]

Replace with:      ^p       [paragraph mark]

Note: OK to use Replace All

Comment: this removes the extra blank lines between each record and is done to address the spacing of the majority of records.

 

STEP 2: ADD TAGS TO THE DATA LINES (Using MS Excel)

Activate MS Excel then open the edited text file which activates the Text Import Wizard. Step 1 of the Text Import Wizard identifies the data format as “Fixed Width”. Click the OK button to continue. At Step 2 of the Text Import Wizard, scroll down and across the records shown in the display window and delete all break lines (refer to image #2, top). Deleting the break lines prevents the resulting data from appearing in multiple columns. Click Finish.

 

In the resulting spreadsheet, one record is comprised of 13 rows. Insert a new column in cell A-1 which will be used to hold the corresponding data tags (refer to image #2, top). . You can create whatever tags you wish but in this example abbreviations are used to coincide with the content of the data line. Note that “IG” indicates the data line is to be ignored upon import. Save the modified data as a text file.

 

 

STEP 3: IMPORT THE “TAGGED” TEXT FILE INTO ENDNOTE (USING THE MODIFIED FILTER)

First install the modified filter (attached). The filter can be installed by double-clicking on the file which will activate the Endnote program then save the file. With the filter installed next go to the Endnote toolbar and select File >Import >File. In the Import File dialog box tagged text file to import (refer to image #2, bottom).

 

The import result is shown in image #1 (top).

 

Highlighted
User
Posts: 6
Registered: ‎10-25-2016
0

Re: Emailed OVIDSP reference list into Endnote

Wow amazing! I am going to try it immediately!

 

Highlighted
User
Posts: 6
Registered: ‎10-25-2016
0

Re: Emailed OVIDSP reference list into Endnote

Worked really well! Thanks again so much!