NCBI Gene & PubMed, Lecture 1 | Part 3 By Dr. Muhammad Naveed
NCBI, Gene, PubMed:
NCBI's Gene resources include collections of curated nucleotide sequences used as references, sequence clusters to predict and study homologs, and various databases and tools for the study of gene expression.
Entrez Gene (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) is NCBI's database for gene-specific information. It does not include all known or predicted genes; instead Entrez Gene focuses on the genomes that have been completely sequenced, that have an active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. The content of Entrez Gene represents the result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is updated as new information becomes available. Entrez Gene is a step forward from NCBI's LocusLink, with both a major increase in taxonomic scope and improved access through the many tools associated with NCBI Entrez.
PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintain the database as part of the Entrez system of information retrieval.
From 1971 to 1997, online access to the MEDLINE database had been primarily through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home- and office-based MEDLINE searching. The PubMed system was offered free to the public starting in June 1997.
Content
In addition to MEDLINE, PubMed provides access to:
older references from the print version of Index Medicus, back to 1951 and earlier
references to some journals before they were indexed in Index Medicus and MEDLINE, for instance Science, BMJ, and Annals of Surgery
very recent entries to records for an article before it is indexed with Medical Subject Headings (MeSH) and added to MEDLINE
a collection of books available full-text and other subsets of NLM records [4]
PMC citations
NCBI Bookshelf
Many PubMed records contain links to full text articles, some of which are freely available, often in PubMed Central[5] and local mirrors, such as UK PubMed Central.[6]
Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog.
As of 27 January 2020, PubMed has more than 30 million citations and abstracts dating back to 1966, selectively to the year 1865, and very selectively to 1809. As of the same date, 20 million of PubMed's records are listed with their abstracts, and 21.5 million records have links to full-text versions (of which 7.5 million articles are available, full-text for free).[8] Over the last 10 years (ending 31 December 2019), an average of nearly 1 million new records were added each year. Approximately 12% of the records in PubMed correspond to cancer-related entries, which have grown from 6% in the 1950s to 16% in 2016.[9] Other significant proportion of records correspond to "chemistry" (8.69%), "therapy" (8.39%), and "infection" (5%).[citation needed]
In 2016, NLM changed the indexing system so that publishers are able to directly correct typos and errors in PubMed indexed articles.
PubMed has been reported to include some articles published in predatory journals. MEDLINE and PubMed policies for the selection of journals for database inclusion are slightly different. Weaknesses in the criteria and procedures for indexing journals in PubMed Central may allow publications from predatory journals to leak into PubMed.
#NCBI #PubMed #Gene
NCBI's Gene resources include collections of curated nucleotide sequences used as references, sequence clusters to predict and study homologs, and various databases and tools for the study of gene expression.
Entrez Gene (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) is NCBI's database for gene-specific information. It does not include all known or predicted genes; instead Entrez Gene focuses on the genomes that have been completely sequenced, that have an active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. The content of Entrez Gene represents the result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is updated as new information becomes available. Entrez Gene is a step forward from NCBI's LocusLink, with both a major increase in taxonomic scope and improved access through the many tools associated with NCBI Entrez.
PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintain the database as part of the Entrez system of information retrieval.
From 1971 to 1997, online access to the MEDLINE database had been primarily through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home- and office-based MEDLINE searching. The PubMed system was offered free to the public starting in June 1997.
Content
In addition to MEDLINE, PubMed provides access to:
older references from the print version of Index Medicus, back to 1951 and earlier
references to some journals before they were indexed in Index Medicus and MEDLINE, for instance Science, BMJ, and Annals of Surgery
very recent entries to records for an article before it is indexed with Medical Subject Headings (MeSH) and added to MEDLINE
a collection of books available full-text and other subsets of NLM records [4]
PMC citations
NCBI Bookshelf
Many PubMed records contain links to full text articles, some of which are freely available, often in PubMed Central[5] and local mirrors, such as UK PubMed Central.[6]
Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog.
As of 27 January 2020, PubMed has more than 30 million citations and abstracts dating back to 1966, selectively to the year 1865, and very selectively to 1809. As of the same date, 20 million of PubMed's records are listed with their abstracts, and 21.5 million records have links to full-text versions (of which 7.5 million articles are available, full-text for free).[8] Over the last 10 years (ending 31 December 2019), an average of nearly 1 million new records were added each year. Approximately 12% of the records in PubMed correspond to cancer-related entries, which have grown from 6% in the 1950s to 16% in 2016.[9] Other significant proportion of records correspond to "chemistry" (8.69%), "therapy" (8.39%), and "infection" (5%).[citation needed]
In 2016, NLM changed the indexing system so that publishers are able to directly correct typos and errors in PubMed indexed articles.
PubMed has been reported to include some articles published in predatory journals. MEDLINE and PubMed policies for the selection of journals for database inclusion are slightly different. Weaknesses in the criteria and procedures for indexing journals in PubMed Central may allow publications from predatory journals to leak into PubMed.
#NCBI #PubMed #Gene
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