The PubMed database is available on the Entrez retrieval system, and was developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM). PubMed provides free access to MEDLINE, NLM's database of more than 13 million bibliographic citations and abstracts in the fields of biomedicine, nursing, dentistry, veterinary medicine, health care systems, and preclinical sciences. PubMed also includes access to additional selected life sciences journals not in MEDLINE. PubMed's LinkOut feature http://www.ncbi.nlm.nih.gov/entrez/linkout/ provides access to a wide variety of relevant web-accessible online resources, including full-text publications, biological databases, consumer health information, and research tools. Links are also available to the molecular biology databases maintained by NCBI. New citations are typically added to PubMed Tuesday through Saturday.
Recent develoments :
Two new NCBI databases, Journals and MeSH, were created to provide additional search features for PubMed. The Related Articles algorithm was modified to better calculate citations that are closely related to a selected article. Icons were added to the PubMed Summary page display to indicate whether or not a link to the free full-text article is available. An e-mail feature, cancer subset, and several new indexes were added including: Corporate Author, Comments/Corrections, Place of Publication, Grant Number, and Ahead of Print. In addition, the LinkOut library program now includes print as well as electronic holdings data.
NCBI continued development of PubMed, with enhancements including the addition of over 1.7 million OLDMEDLINE citations. These citations were originally printed in the hardcopy indexes published from 1950 through 1965. The MeSH database was enhanced with terms that are identified by MeSH as pharmacological actions and a direct link was added to the Clinical Queries page. The Clinical Queries page was also revised and the filter strategies were updated. The History page now includes a menu from the search statements number to provide an easier way to combine, delete and retrieve History statements. The truncation limit in PubMed was increased from 150 variations of a truncated term to 600. Entrez programming software used by PubMed was enhanced to improve the way in which PubMed interprets users' queries. A new Entrez NCBI database, NLM Catalog, was developed to provide additional search features for books, journals and audiovisuals in the NLM collections.
Déjà vu (1) is a manually curated repository of duplicate citations found in several databases, including Medline. In the scientific research community plagiarism and multiple publications of the same data are considered unacceptable practices undermining the public confidence in scientific integrity.
Déjà vu is a database of duplicate citations (abstracts and titles) that are computationally identified with the text similarity searching tool eTBLAST and manually confirmed (2;3). Duplications are recorded along with user provided commentary and evidence to affirm or deny a given document’s putative categorization. The availability of a search tool by which journal submissions can be compared to existing databases to identify potential duplicate citations, and this database of duplicate citations increases the ability of the scientific community to identify duplications and provides means to help prevent the multiple publication of a scientific study. The Déjà vu database is freely accessible at http://spore.swmed.edu/dejavu. The tool eTBLAST is also freely available at http://invention.swmed.edu/etblast/etblast.shtml.
Recent develoments :
To extend our database content, we are currently identifying duplicate citations in all Medline. At the current rate of finding and manual validation, we expect to find around 10,000 duplicates with different authors (potential cases of plagiarisms) and a total of 70,000 duplicates in other categories. While these duplicates are currently manually verified, they are added to the database daily.
This work was supported by the P.O’B. Montgomery Distinguished Chair (HG) and the Hudson Foundation (HG) as well as the National Institute of Health/ National Library of Medicine grant R01 LM009758-01 (HG). We wish to thank Dr Wayne Fisher, Tara Long and Dr Jonathan D. Wren for helpful comments and discussions.
1. Errami,M., Hicks,M.J., Fisher,W., Trusty,D., Wren,J.D. and Garner,H.R. Déjà vu - A Study of Duplicate Citations in Medline (2007). In press.
2. Errami,M., Wren,J.D., Hicks,J.M. and Garner,H.R. (2007). eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications. Nucleic Acids Res. 35: W12-W15.
3. Lewis,J., Ossowski,S., Hicks,J., Errami,M. and Garner,H.R. (2006). Text similarity: an alternative way to search MEDLINE. Bioinformatics (Oxford, England). 22: 2298-304.
Pathway and Literature Strainer (PaLS) highlights those members on a user inputted list that share descriptors from PubMed, GO, KEGG and Reactome.
BioLit is a web sever resource that integrates scientific publications with existing biological databases. To perform this link, BioLit searches the full text of the article for metadata such as database identifiers and ontology terms.
BIOSMILE is a web-based NCBI PubMed search tool. Users input keywords to be searched and BIOSMILE retrieves matching PubMed abstracts.
E3Miner is a web-based text mining tool that extracts and incorporates comprehensive knowledge about ubiquitin-protein ligases (E3) with their underlying mechanisms. This tool integrates available E3 data from the published literature as well as from the biological databases.
The Protein Interaction information Extraction system (PIE) is a configurable web server for extraction of protein-protein interactions from literature. Both co-occurrence of proteins in text and predefined phrase patterns for protein-protein interactions are employed in a machine learning framework.
PolySearch allows users to conduct comprehensive and associative queries, such as given X, find all Y's, where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also identifies, highlights and ranks abstracts, paragraphs or sentences.
PubChem contains the chemical structures of small organic molecules and information on their biological activities. PubChem can be searched by keywords, chemical properties, and structural similarity. PubChem s chemical structure records are linked to other NCBI databases including PubMed.
It goes to the library. You go to the pub; receive email alerts for current contents of PubMed and GenBank; e.g. use accession number of htg record as query to receive sequence updates (as the version number changes).
The acronym database provides free access to medical/biological acronyms. It has 100,000+ acronyms and the users can also contribute by rating the entries quality. In the backend, it is generated from medline data.
Molecular Biology Database Collection with links to databases with short descriptions of each.
Entrez-searchable database of biomedical literature citations with links to molecular resources at the NCBI.
PubMed Central (PMC) is the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature.
The Directory of Open Access Journals provides a listing of open-access journals and a searchable database of article abstracts from them. It aims to incorporate journals from all subjects and languages.