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
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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. 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. Before you start, please check if the intended publication is in the PubDB. 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
Page Numbers, Volume Number, Issue Number are optional if you entered those information in the
Citation line as follows: Med Image Anal. 2008 Oct;12(5):603-15.
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
Publisher: Enter the name of the Journal or the conference.
PMCID: Enter the PubMed Central (PMC) ID when is available.
Publisher:
Links:
Keywords: Enter the keywords associated with your 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.
- Click on the Administration link at the top navigation bar.
- Select Import
- In the Set a PubMed term to mirror field: enter the PubMed ID#
- Click on Mirror>>
- At the bottom of the page check-mark the Import box
- Click on Import Selection
- There will be a message in red, Import successful
- At the bottom of the page click on Modify
- You have to manually enter the citation from PubMed as PubMed doesn't export the citation but generates it on the fly. See the new NIH Public Access Policy.
- Enter the PMCID number if it is available on the PubMed page.
- Both first and last names of the authors should be entered
- 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.
- 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:
- Select All Publications from the top navigation bar
- Find the publication to be removed
- In the most right column click on the Remove link
OR
- Select the publication to be removed
- 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