Surgical Planning Laboratory - Brigham & Women's Hospital - Boston, Massachusetts USA - a teaching affiliate of Harvard Medical School

Surgical Planning Laboratory

Contents

Help page for the Publication Database

For the Impatient

  • To add materials you need an account.
  • To request an account, contact Marianna (marianna at bwh.harvard.edu)

Introduction

The SPL Publication Database or PubDB is a repository for scientific papers and data published by the SPL and its affiliated programs. PubDB is a computational infrastructure intended to facilitate the outreach activities of scientists in our programs. Scientists participating in our programs need more flexibility than Pubmed currently offers. Most importantly, Pubmed does not cover all journals that we use to report on our NIH funded research. The SPL PubDB enables us to comply with a recently signed law: The president signed a law "directing the National Institutes of Health (NIH) to provide the public with open online access to findings from its funded research" around Dec 26 2007. See here for a short discussion of this law. The new NIH Public Access Policy effective April 7, 2008. The NIH Public Access Policy ensures that the public has access to the published results of NIH funded research. It requires scientists to submit final peer-reviewed journal manuscripts that arise from NIH funds to the digital archive PubMed Central upon acceptance for publication. To help advance science and improve human health, the Policy requires that these papers are accessible to the public on PubMed Central no later than 12 months after publication.

PubDB was developed by Kitware under contract with the SPL and some of its affiliated programs. It is based on a commercial package.

SPL hosted Publications Database
Click here to go to the Publication Database.


Features

  • Uploading follows a self-serve model. If you have problems with an upload (button on the same row as the search), our webmaster, Marianna Jakab (marianna at bwh.harvard.edu) can help.
  • The database can Import form PubMed and export in formats that are compatible with endnote and bibtex.
  • The database is not limited to PubMed papers but can also accommodate other peer reviewed publications.
  • The database can hold files and data (pdf, jpg, gif, png, tgz, etc.)
  • The database holds information about the grants acknowledged by a paper
  • Links can be inserted in the Abstract

Upload

Uploading follows a self-serve model. If you have problems with an upload (button on the same row as the search), our webmaster, Marianna (marianna at bwh.harvard.edu) can help. Please do not upload Abstracts and Posters in the database. We have the Abstract Database for that purpose. Before you start, please check whether the intended publication is in the PubDB or not. Enter information in the following fields manually as completely as you can. PubDB allows to upload a variety of materials, including the full paper, high res versions of figures and data that was used to do the research.

Main collection: Based on the most relevant supporting grants/sponsors
Secondary Collections: Additional supports
Title: Enter the title of the publication
Institution: Enter at least the institution of the principal author. The database allows multiple institutions. Click on the Add more link.
Authors: Enter the authors' first and last names one by one. Click on the Add more link.
Authors' list: You may enter the authors' name as a list, following the pattern: firstname, lastname; firstname, lastname
Abstract: You may insert HTML tags in the abstract to create a link to another publication in the database. For instance: <a href="http://www.spl.harvard.edu/pubdb/item/view/1265">SPL Brain Atlas</a>
Date: Enter the date of the publication
Journal: Name of the Journal
Presented at: If the entry is a presentation at conferences
Page Numbers, Volume Number, Issue Number: enter these informations
Citation: Enter as completely as possible, as follows: Journal Name. Date; Volume(issue):page numbers.
PubMed ID: Enter the PubMed ID, strongly recommended as the database makes a link from this number back to PubMed. See the new NIH Public Access Policy
PMCID: Enter the PubMed Central (PMC) ID when is available.
Publisher: Name of the publishing company.
Keywords: Enter the keywords associated with the publication.
Sponsors: Enter the names of any sponsors, funding codes and grant supports from the actual paper.

Now you can add associated files to this publication:
Click on the Next>> button, which takes you to the Upload a picture page where you can upload a representative image from the publication. Name your image, using the following naming convention: PrincipalAuthorLastName-JournalYear-fig#.png. Select your image, using the browser and check mark the "I certify that I have the right to distribute this picture and I allow Kitware Inc. to use this picture." box and click on Upload. Use the figure caption (including the figure number) as a description of the image and click on Save description.

Click on the Next>> button, which takes you to the Add files to publication page. Name the associated pdf file, using the following naming convention: PrincipalAuthorLastName-JournalYear.pdf Select the pdf file, using the browser and check mark the "I certify that I have the right to distribute this file." box and click on Upload. Finally click on the Finish Submission>> button. *Your submitted publication has to be approved by the editor. We are going to look at your submission as soon as we can. will appear at the upper left corner. Now it is waiting in a queue for an approval by the Database administrator. If you want to speed up the approval process you may send an e-mail to Marianna (marianna at bwh.harvard.edu).

Import from PubMed

Log in to the Publication Database, by clicking on Log in at the top navigation bar. If you do not have an account, contact Marianna (marianna at bwh.harvard.edu) for help.

  1. Click on the Administration link at the top navigation bar.
  2. Select Import
  3. In the Set a PubMed term to mirror field: enter the PubMed ID#
  4. Click on Mirror>>
  5. At the bottom of the page check-mark the Import box
  6. Click on Import Selection
  7. There will be a message in red, Import successful
  8. At the bottom of the page click on Modify
  9. The citation from PubMed need to be entered manually as PubMed doesn't export the citation but generates it on the fly. See the new NIH Public Access Policy.
  10. The PMCID number is imported automatically, if available
  11. Click on the Next>> button, which takes you to the Upload a picture page where you can upload a representative image from the publication. Name your image, using the following naming convention: PrincipalAuthorLastName-JournalYear-fig#.png. Select your image, using the browser and check mark the I certify that I have the right to distribute this picture and I allow Kitware Inc. to use this picture. box and click on Upload. Use the figure caption (including the figure number) as a description of the image and click on Save description.

Click on the Next>> button, which takes you to the Add files to publication page. If the Free PMC Article is available upload that instead of the Journal Article. Name the associated pdf file, using the following naming convention: PrincipalAuthorLastName-JournalYear.pdf Select the pdf file, using the browser and check mark the "I certify that I have the right to distribute this file." box and click on Upload. Finally click on the Finish Submission>> button.

Remove Publication form the Database

Log in to the Publication Database, by clicking on Log in at the top navigation bar. If you do not have an account, contact Marianna (marianna at bwh.harvard.edu) for help.

There are two ways of deleting publication form the database:

  1. Select All Publications from the top navigation bar
  2. Find the publication to be removed
  3. In the most right column click on the Remove link

OR

  1. Select the publication to be removed
  2. At the lower left corner click on the Delete Publication link

Insert Links in the Abstract

External links can be inserted in an abstract using HTML by following this template:

 <a href="http://link_to_a_web_page">Text of my link</a>

Publication Statistics

The publication database records the IP address of each downloaded publication (or relevant part of a publication) and trace back the geolocation from the IP address. The geolocation might not be accurate since IP addresses may change and/or be relocated. Therefore, some locations might not show up on the map but the publication count will be increased. Moreover, if papers are downloaded from the same location, only one pin will appear on the map for the given location.

What is the Publication Database?

The Publication Database (PubDB) is developed by Kitware Inc. and is part of the MIDAS framework.

The publication database:

  • Stores, organizes and easily searchs your publications
  • Conforms to the Open Archives Initiative (OAI)
  • Supports the Corporation for National Research Initiatives (CNRI) handle system
  • Built on top of open-source DSpace technology
  • Automatically harvested by Google Scholar
  • Image Gallery
  • Automatic generation and export of citations as bibtex

For more information about PuDB please visit the Kitware product page

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