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 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. 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.
Select the collections: based on the supporting grants/sponsors
Enter the authors of your publication you may add them one by one or as a list, following the pattern: firstname, lastname; firstname, lastname
Title:
Institution: Enter the institution of the principal author.
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/pages/Special:PubDB_View?dspaceid=84> Archip et al., 2007</a>
Date:
Citation: You may provide a custom citation for the paper in this field.
PubMed ID: Enter the PubMed ID, we prefer this 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.
Keywords: Enter the keywords associated with your publication.
Sponsors: Enter the names of any sponsors, funding codes and grant supports from the PDF file.
Click on the Submit and Add Files button, which takes you to the page where you can upload the associated pdf file, using the following naming convention: PrincipalAuthorLastName-JournalYear.pdf and select a representative image from the publication, using the following naming convention: PrincipalAuthorLastName-JournalYear-fig#.png.
Use the figure caption as a description of the image.
Click on the Finish Submission button. "This publication is not public" will show up at the upper left corner of your entry. 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 at bwh.harvard.edu.
Import from PubMed
- Log in to the Publication Database, by clicking on "Administration". If you do not have an account, contact Marianna (marianna at bwh.harvard.edu) for help.
- 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.
- Click on the Submit and Add Files button, which takes you to the page where you can upload the associated pdf file, using the following naming convention: PrincipalAuthorLastName-JournalYear.pdf and select a representative image from the publication, using the following naming convention: PrincipalAuthorLastName-JournalYear-fig#.png. Use the figure caption as a description of the image.
- Click on the Finish Submission button.
Remove Publication form the Database
- Log in to the Publication Database, by clicking on Administration. If you do not have an account, contact Marianna (marianna at bwh.harvard.edu) for help.
- Select All Publications from the top navigation bar
- Find the publication to be removed
- In the most right column click on the Remove link
Insert Links in 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.