ALL Metrics
-
Views
-
Downloads
Get PDF
Get XML
Cite
Export
Track
Software Tool Article

Abstract Sifter: a comprehensive front-end system to PubMed

[version 1; peer review: 2 approved]
PUBLISHED 21 Dec 2017
Author details Author details
OPEN PEER REVIEW
REVIEWER STATUS

This article is included in the Cheminformatics gateway.

Abstract

The Abstract Sifter is a Microsoft Excel based application that enhances existing search capabilities of PubMed. The Abstract Sifter assists researchers to search effectively, triage results, and keep track of articles of interest. The tool implements an innovative “sifter” functionality for relevance ranking, giving the researcher a way to find articles of interest quickly. The tool also gives researchers a view of the literature landscape for a set of entities such as chemicals or genes. The Abstract Sifter is available as a Microsoft Excel macro-enabled workbook application.

Keywords

PubMed, document retrieval, Microsoft Excel, Visual Basic for Applications, chemistry, toxicology, biology

Introduction

Scientists in the biological and medical domains can spend considerable time searching for relevant articles in PubMed, and tools that make the searching more effective will save time and resources (Khare et al., 2014). Here, we present a tool, the Abstract Sifter, built to improve efficiency in searching PubMed. Specifically, this tool was designed with the following objectives: 1) To make it quicker and easier to find relevant articles in PubMed; 2) To visualize the “literature landscape”, which can help focus on key relevant articles; 3) To make it easier to evaluate and take notes on abstracts; and 4) To facilitate collaboration on literature tasks.

Methods

The Abstract Sifter application is a Microsoft Excel macro-enabled workbook that has been tested in Excel 2013 and 2016 on the Windows platform. Visual Basic for Applications (VBA) was used to develop the features that go beyond native Excel functionality. For the retrieval of PubMed query results, Entrez Programming Utilities (E-utilities) (Sayers, 2016) are called from VBA. These utilities were developed by the National Center for Biotechnology Information (NCBI) to allow software developers to query PubMed and other NCBI databases and retrieve the results for incorporation into local applications (2017). Through implementation as an Excel workbook, the Abstract Sifter can easily be shared with collaborators.

Use case

The Abstract Sifter application workbook contains seven sheets: ReadMe, Main, Abstract, Notes, Log, and Landscape, and SampleQueries. The Main sheet is where the basic functions operate, including the novel functionality called “sifting”. To start, the end-user clicks on the Query PubMed button at the top of the screen and enters any PubMed query of interest. For the example in Figure 1a, the end-user has entered the simple query “chlorpyrifos”. However, these queries can be more complex. In fact, any query run in PubMed can be executed in the Sifter. When the query entry is finished, the user then clicks on Submit and the query is sent to the NCBI PubMed E-utility. The first response returned by the E-utility is the number of articles found that satisfy the query. The citations are downloaded from PubMed by the Abstract Sifter, parsed by pattern matching algorithms coded in VBA. All citations are thus parsed for title, abstract, authors, publication year, journal, and PubMed identifier, and the data is inserted into rows in the Main sheet. Every new search will clear results from the previous query. For performance purposes, if the number of articles exceeds 5,000, the query will not be run and the user is encouraged to re-word the query to return fewer records.

1292c746-1135-4f62-a8b7-8dd0f14d27b6_figure1.gif

Figure 1.

1a. Abstract Sifter Main sheet and 1b. Abstract sheet view.

The results of the query stored in the Main sheet can be browsed like any other data in a spreadsheet. The sifter feature provides a novel and effective way to narrow search results with large number of citations to find articles of interest. For example, the query for “chlorpyrifos” returned over 4,000 PubMed citations. If a researcher is looking for neurological effects in studies where rats were dosed with chlorpyrifos, the researcher could type the term “mg/kg” in the spreadsheet cell B3, “rat” in C3, and “brain” in D3 (Figure 1a inset). The Abstract Sifter returns the number of occurrences of each term found in the title and abstract combined. The Main sheet’s citations can be sorted by these counts. Sifting by entering terms and sorting can be repeated. Similarly, new PubMed queries can be run, altered, and rerun. Double-clicking on any cell in the row (except the cell containing the PMID) takes the end-user to the Abstract sheet where the title and abstract of that citation are shown (Figure 1b). The sifter terms are highlighted by giving each the color of the term on the Main sheet. Together, these query and sifting capabilities provide a powerful search tool.

The Abstract Sifter also incorporates functionality to allow the end-user to take notes on citations. On the Abstract sheet, for instance, the user can click on the button Add Note. A form appears that provides the opportunity to add short notes (tags) or long notes or to specify one of three categories (yes, no, or maybe) (Figure 2a). How these values are used is a decision of the end-user. When the user clicks on OK, a row is inserted into the Notes sheet with the citation information along with the notes. Alternatively, the end-user can take notes on more than one article at a time from the Main sheet. To do this, the end-user selects multiple rows of interest and then clicks on Take Group Notes. Each of the selected citations will be inserted into the Notes sheet with the entered notes and tags (Figure 2b).

1292c746-1135-4f62-a8b7-8dd0f14d27b6_figure2.gif

Figure 2.

2a. Taking Group notes. 2b. Viewing Notes sheet. 2c. Highlighting noted citations.

Often, after entering a number of notes, the user will forget which citations have been read and evaluated and for which notes have been taken. By clicking on the Highlight Noted PMIDs button either on the Main or Notes sheet, the PubMed identifier (PMID) on the Main sheet will be set to the color specified in the Note form (Figure 2c). Using the built-in Excel filtering feature, the color can be selected or sorted on to view Noted citations.

The Notes sheet itself can be viewed and edited and rows can be deleted. Entries on the Notes sheet can be exported to PubMed where they can then be downloaded in a number of different formats, including a format for direct import into citation management software. The button to export to a citation manager via PubMed is labelled Get references and appears on the Notes sheet.

Another unique feature of the Abstract Sifter is the Landscape sheet functionality. The Landscape sheet is an alternative to the Main sheet as an entry point, and provides the end-user a visualization of literature for a set of chemicals. To use this functionality, the end-user enters chemical name queries in Column C of the Landscape sheet after Row 4. An example in which the end-user has entered seven chemical queries is shown in Figure 3. The chemical queries can be extended with CAS registry numbers or synonyms. Next, the end-user enters subject matter query text in Row 3, Columns E and higher. In the example depicted in Figure 3, the end-user has entered several subject matter queries, starting with “neoplasms OR cancer”.

1292c746-1135-4f62-a8b7-8dd0f14d27b6_figure3.gif

Figure 3. Landscape sheet.

The end-user can then select cells in the intersection region (E5 through J11 in Figure 3) and click on the button Update Article Counts. This action causes the tool to iterate through the cells, build a query using the chemical terms in column C appended to the effect terms in Row 3, and then send the query to PubMed for execution. The counts of the articles satisfying each query are returned from PubMed and are inserted into the corresponding cells. To see the PubMed records, the user double-clicks on a cell in the intersection region. This action starts the PubMed query process and sends the results to the Main page for sifting. More chemicals, entries and/or and additional queries can be added by the user on this Landscape sheet. Buttons are available on the Landscape sheet to help with formatting results, such as applying heat-map coloring to the article counts. The SampleQueries sheet has some text that can be used as a starting point for Landscape queries. To use, the end-user selects rows and clicks on the Send Queries to Landscape button to have the queries appended to Row 3 on the Landscape page.

The Log sheet contains a row for each query run. The query text is inserted into the row along with date and time information and the number of records returned. Queries can be easily rerun by double-clicking on the query text in column C.

Discussion

The Abstract Sifter can facilitate many PubMed literature tasks by enabling rapid identification, triage, and tracking of relevant articles. The literature landscape viewing and navigating capabilities give researchers distinctive insight into characteristics of a literature corpus.

Software availability

The Abstract Sifter Excel workbook and user documentation are available at: https://github.com/USEPA/CompTox-Chemistry-Dashboard-Abstract-Sifter/

Archived source code as at the time of publication: http://dx.doi.org/10.5281/zenodo.1040961 (nancycolebaker, 2017)

License: CC0 1.0 Public Domain Dedication.

Comments on this article Comments (4)

Version 1
VERSION 1 PUBLISHED 21 Dec 2017
  • Author Response 25 Jan 2022
    Nancy Baker, Leidos, Research Triangle Park, NC, USA
    25 Jan 2022
    Author Response
    To find the newest version, go to the EPA Comptox Chemicals Dashboard downloads page:
    https://comptox.epa.gov/dashboard/downloads

    Scroll down to Abstract Sifter to find link to a zip file with the ... Continue reading
  • Author Response 30 Jan 2019
    Nancy Baker, Leidos, Research Triangle Park, NC, USA
    30 Jan 2019
    Author Response
    Dear Users of the Abstract Sifter, 

    Some important enhancements and fixes have been made to the tool.  Please download the new version at 

    ftp://newftp.epa.gov/COMPTOX/Sustainable_Chemistry_Data/Chemistry_Dashboard/Abstract_Sifter/AbstractSifter_v1.zip

    (Even though the ... Continue reading
  • Author Response 02 Jan 2018
    Nancy Baker, Leidos, Research Triangle Park, NC, USA
    02 Jan 2018
    Author Response
    Thanks to feedback from helpful users, the user guide has been updated and corrected.  Be sure to download the latest version.
    Competing Interests: I am an author on this work.
  • Reader Comment 27 Dec 2017
    Emma Schymanski, LCSB, University of Luxembourg, Luxembourg
    27 Dec 2017
    Reader Comment
    I was made aware of the Abstract Sifter by the authors prior to this publication - while this article is quite short, the user documentation contains more information and steps ... Continue reading
Author details Author details
Competing interests
Grant information
Copyright
Download
 
Export To
metrics
Views Downloads
F1000Research - -
PubMed Central
Data from PMC are received and updated monthly.
- -
Citations
CITE
how to cite this article
Baker N, Knudsen T and Williams AJ. Abstract Sifter: a comprehensive front-end system to PubMed [version 1; peer review: 2 approved]. F1000Research 2017, 6(Chem Inf Sci):2164 (https://doi.org/10.12688/f1000research.12865.1)
NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article.
track
receive updates on this article
Track an article to receive email alerts on any updates to this article.

Open Peer Review

Current Reviewer Status: ?
Key to Reviewer Statuses VIEW
ApprovedThe paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approvedFundamental flaws in the paper seriously undermine the findings and conclusions
Version 1
VERSION 1
PUBLISHED 21 Dec 2017
Views
27
Cite
Reviewer Report 06 Feb 2018
Qingliang (Leon) Li,  National Institutes of Health, Bethesda, MD, USA 
Approved
VIEWS 27
The authors reported an Excel front-end for PubMed search by using NCBI E-Utilities. The tool supports searching literature in PubMed, importing search results into excel, adding notes into individual literature etc. Here are some minor issues that the authors may consider to improve ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Li Q(. Reviewer Report For: Abstract Sifter: a comprehensive front-end system to PubMed [version 1; peer review: 2 approved]. F1000Research 2017, 6(Chem Inf Sci):2164 (https://doi.org/10.5256/f1000research.13943.r30158)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
Views
35
Cite
Reviewer Report 15 Jan 2018
Pauliina Damdimopoulou, Unit of Toxicological Sciences, Swetox, Karolinska Institutet, Södertälje, Sweden 
Astrud Tuck, Unit of Toxicological Sciences, Swetox, Karolinska Institutet, Södertälje, Sweden 
Approved
VIEWS 35
This article describes a Microsoft Excel workbook based tool for rapid PubMed literature searches where the results can be easily sifted and annotated. With the ever-growing body of literature, tools for finding and sorting literature become increasingly more important. I ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Damdimopoulou P and Tuck A. Reviewer Report For: Abstract Sifter: a comprehensive front-end system to PubMed [version 1; peer review: 2 approved]. F1000Research 2017, 6(Chem Inf Sci):2164 (https://doi.org/10.5256/f1000research.13943.r29810)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.

Comments on this article Comments (4)

Version 1
VERSION 1 PUBLISHED 21 Dec 2017
  • Author Response 25 Jan 2022
    Nancy Baker, Leidos, Research Triangle Park, NC, USA
    25 Jan 2022
    Author Response
    To find the newest version, go to the EPA Comptox Chemicals Dashboard downloads page:
    https://comptox.epa.gov/dashboard/downloads

    Scroll down to Abstract Sifter to find link to a zip file with the ... Continue reading
  • Author Response 30 Jan 2019
    Nancy Baker, Leidos, Research Triangle Park, NC, USA
    30 Jan 2019
    Author Response
    Dear Users of the Abstract Sifter, 

    Some important enhancements and fixes have been made to the tool.  Please download the new version at 

    ftp://newftp.epa.gov/COMPTOX/Sustainable_Chemistry_Data/Chemistry_Dashboard/Abstract_Sifter/AbstractSifter_v1.zip

    (Even though the ... Continue reading
  • Author Response 02 Jan 2018
    Nancy Baker, Leidos, Research Triangle Park, NC, USA
    02 Jan 2018
    Author Response
    Thanks to feedback from helpful users, the user guide has been updated and corrected.  Be sure to download the latest version.
    Competing Interests: I am an author on this work.
  • Reader Comment 27 Dec 2017
    Emma Schymanski, LCSB, University of Luxembourg, Luxembourg
    27 Dec 2017
    Reader Comment
    I was made aware of the Abstract Sifter by the authors prior to this publication - while this article is quite short, the user documentation contains more information and steps ... Continue reading
Alongside their report, reviewers assign a status to the article:
Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions
Sign In
If you've forgotten your password, please enter your email address below and we'll send you instructions on how to reset your password.

The email address should be the one you originally registered with F1000.

Email address not valid, please try again

You registered with F1000 via Google, so we cannot reset your password.

To sign in, please click here.

If you still need help with your Google account password, please click here.

You registered with F1000 via Facebook, so we cannot reset your password.

To sign in, please click here.

If you still need help with your Facebook account password, please click here.

Code not correct, please try again
Email us for further assistance.
Server error, please try again.