Searching the literature

Pubmed / Entrez
Essentially all biologically relevant literature is indexed by the National Library of Medicine, and linked to the Pubmed database. The entry point of choice for a search is Entrez, which, in addition to searching in Pubmed also searches a wide variety of other databases, including Genbank.

Sophisticated searches are possible in Pubmed, using the advanced search page. See the Pubmed Tutorial.

Be sure to look at the "Related articles" links on the right of entries, which are very often spot on relevant.

Some literature is missing from Pubmed, notably agricultural data (See Agricola for this) and literature pre-1960 or so. The coverage varies with the journal indexed, so a given article may not be present. Other indices, such as Web of Science are more useful for very old references.

Hubmed provides an alternative, more user-friendly interface to Pubmed. Almost Everything About Hubmed is a tutorial on its use.

eTBlast searches Pubmed using a paragraph of input text as the search index, often yielding more exact matches to the articles you want.

See also Hardcore PubMeding (advanced PubMed searching) here on OpenWetWare.

Biosis / Biological Abstracts
An alternative to Pubmed is the commercial Biosis (Biological Abstracts) service. Biosis is only available through institutional subscription. At MIT, link to Biosis through the Vera electronic access system. Biosis indexes a slightly older and wider range of material than Pubmed, including poster abstracts for all of the major conferences, such as ASM. They also index many book chapters. Biosis is closely integrated with the Web of Science (same publisher).

Web of Science
The Science Citation Index or Web of Science from ISI Web of Knowledge is an extremely useful tool for searching forward in time from a relevant article. The bibliography of a research paper provides excellent links backward in time to relevant prior work; the science citation index provides a similar mechanism forward in time. Each article, when published, is mined for its references. SCI allows users to search for future articles which reference the article in question. Access is limited, as this is a commercial service. MIT users can access SCI from the Vera home page, A Web of Science tutorial is available here. Briefly, you almost always want a "Cited Reference Search." For the article you are searching from, enter the author name, first initial, and * as a wild card for any middle initial. Skip the journal, but enter the year of publication and hit Search. Locate the article you are searching from. In general there may be many instances with slightly varying references, typically due to errors and inconsistencies in the bibliographies. Be sure to check both the listing with and without middle initials. Press "Finish Search" to identify the articles which reference your article.

Science Citation Index is also useful in finding titles and references to articles which are not otherwise indexed, including Ph.D. theses, book chapters, patents, and web pages. Pubmed does not index these, while SCI does, since it indexes all references from indexed articles.

Navigating the journal pages
Pubmed indexes several types of books as if they were journals. Libraries are inconsistent about the corresponding cataloging. Notable examples are the Annual Reviews books, which are indexed as journals in Pubmed but shelved and cataloged as books at MIT (but not at Countway). An even more annoying example is the Methods in Molecular Biology series published by Humana Press. Here, Pubmed indexes the series as a journal, failing to give you the book title or author. The books are cataloged by topic and author at both MIT and Harvard. Methods in Enzymology is indexed as a journal in Pubmed, and is kept in the reference section at the MIT Science Library (or, for many important volumes, on TK's bookshelves). Recently Methods in Enzymology has been scanned and is accessible online.

Open Access Journals
Many journal articles are now available through Pubmed Central, hot linked from the PubMed page. All NIH researchers are now required to submit new journal articles to Pubmed Central after 1 year.

Many journals now provide open access. A convenient list of open access journals is here: Directory of Open Access Journals.

MIT
University libraries house paper collections of many important journals. The MIT collections can be searched with Barton, the online catalog. Search Barton under "Journals" for information about the paper collections accessible at MIT libraries. Almost all biology related materials are in the basement of the Science Library at Hayden. Searches in Barton often fail when using the standard Pubmed journal abbreviation. Barton is poor in identifying the accessible online journals for MIT researchers. The Vera index of electronic resources captures some, but not all, of the online resources. Some of these resources can only be accessed by linking through the Vera page. Vera recognizes the Pubmed journal abbreviations much more readily than Barton. In some cases, MIT has access to journals which are neither indexed in Barton nor listed in Vera. The only way of knowing is to access the journal web site directly and see if you have full access to the articles.

Sometimes, but not always, there are links from the NCBI Pubmed site directly to the publisher's web site. Following these links often allows access to the article, but N.B. the point made earlier about required linking through Vera. If you think this is a mess and confusing, you are right.

Most journals have current content accessible on line. MIT may or may not have access to it. MIT access changes with time, and just because you have access today does not mean you will tomorrow. Elsevier journals, in particular, are essentially all accessible this year, through special arrangement. Next year they will not be. Content older than 1995 or so is normally inaccessible online, with important exceptions. The ASM is putting back issues of all of its journals online, including J Bact. Science and PNAS have back issues online. The Science back issues are (ironically) not accessible through the Science home page; you need to follow the JSTOR link in Vera to find older articles in Science. Nature is particularly annoying (remember this when you publish!!). They keep the last 5 years accessible online, and, if MIT pays enough, they can access older issues online. Currently MIT pays for the last 10 years.

Accessing PubMed through the Vera link here tags articles with full text accessible to MIT with an "SFX" tag. Some (BUT NOT ALL!) of the accessible journal articles are listed in this way. It does not, for example, pick up access to older articles in Science, held at JSTOR.

Journals articles which are not accessible either in print or online at MIT can be obtained through interlibrary loan. Documents requested in this way are scanned and delivered by .pdf email/download within a few days typically. This is a free service to the MIT community. If you are too lazy to copy articles yourself out of the available print collection, Web=Docs will do it for a charge of $6.00/article and deliver by email.

MIT libraries are freely accessible. Access to online resources is limited to on-campus computers, or VPN proxy connections to the MIT network. Visitors are able to connect to the MIT networks for a few weeks with minimal overhead.

Harvard
Hollis is the primary index for Harvard libraries, and is very good at locating journals. Hollis typically is effective in noting online access to subscribed journals, although sometimes access is available even though no catalog entry is present. Countway library is the primary location for most journals, although some plant oriented literature is found only in the Botanical Library collection. Access to Countway is limited to the Harvard community. MIT graduate students and staff can obtain Countway access by request at the Hayden (MIT) reference desk. The terrific feature of the Countway collection is that it very extensive and goes back to pre-history. Recently, cutbacks in the library budget has resulted in cancellation of several journals.

If you access Pubmed through the Countway Library web page (click on Digital Libraries, PubMed with full text), you access a version of PubMed with hot links to "Find it at Harvard," providing direct access to many (but not all!!) of the full text articles.

The Patent Literature
The US Patent Office maintains an excellent search site for patents and published patent applicatons. One thing to know about this is that inventor names are listed in full, and that the wild-card character for the search is a dollar sign, rather than a star. Searches such as in/knight-t$ will find all of the inventions for Tom Knight, e.g.  But note that some of the patents will list Knight-Jr-Thomas-F as the inventor. Beware.

The result of the USPTO search will be HTML versions of the patent or patent application. The diagrams and scanned images are not easily available from USPTO. They can, however, be downloaded for free from the web site Free Patents Online or Pat2PDF as a PDF document. European patents are also available on the first site.

Google also offers a patent search.

The Patent Lens offers good search, full text, and important information about patent expiration.

Peer to Patent offers community patent review as part of a pilot project with the USPTO initially on software patents. WikiPatents also offers community patent review and the ability to sell and license your patents.

There are no copyrights on patent documents. They can be freely uploaded and distributed in any form.

Scirus Search
Scirus: a science-specific search engine.

JSTOR
JSTOR - older articles

Google Scholar
Casts a wider net by indexing some non-standard publications along with the typical peer-reviewed work. Be sure to set your preferences to select your university in order to have links appear for direct downloads from journals subscribed to by your instituion. Also capable of finding forward citations (e.g. what other papers cite this paper), and so functions like a free version of Web of Science.

mapLit
mapLit: a new search interface to Pubmed

Automatic Updates
Permanent searches can be uploaded to the My NCBI web site, and run automatically, with results emailed periodically. This is an effective way of keeping up to date with recent literature in narrowly focused areas. Set up the search after logging into the My NCBI site (free registration).

Another service available is the free Pubcrawler which also searches Genbank files for new sequence data.

Online Techniques Forums
There are several online forums addressing the general topic of molecular biology technique. Protocol Online captures a set of online protocols, and an active community forum on techniques. Biotechniques, a free print journal of techniques, runs a less active forum. It is worthwhile subscribing to Biotechniques, if only to gain access to their online archives of articles, inaccessible in other ways. There is a very active Chinese forum here. If you are not fluent in Chinese, you might try the Chinese/Japanese/Korean character interpreting web frame, Popjisyo.

Check out Siphs and Connotea.

Two other forums at BioWWW and Biology Online.

See also MolecularStation and Scientist Solutions.

The International Society of Dumplings and Ramachandran Plots forum is centered on protein and biomolecule crystallization techniques.

Check out also the Bite Sized Bio forum here.

Endnote and Bibliography Creation
BibDesk is a nice graphical BibTeX bibliography database manager for Mac OS X. Even if you don't use LaTeX to write papers (and therefore BibTeX to do your references), BibDesk is a pretty convenient (and free!) program for keeping track of your pdfs since it will auto-name and auto-file them for you. It is under quite active development and thus bug fixes and new features are available on a regular basis. It is mostly painless to save pubmed citations and open them in BibDesk.

Refworks is a commercial tool for maintaining, sharing and distributing web-accessible bibliographies. It provides easy uploading of Endnote databases and read-only or shared modification by others. MIT site licenses Refworks. Shared read-only bibliographies are accessible without licensing.

CiteULike is a free service to help academics to share, store, and organise the academic papers they are reading

Connotea is also a free web-service to share, store and organise scientific publications, references or more generally web-links.

Zotero - from the website "Zotero [zoh-TAIR-oh] is a free, easy-to-use Firefox extension to help you collect, manage, and cite your research sources. It lives right where you do your work — in the web browser itself."

Mendeley - "is free social software for managing and sharing research papers. It is also a Web 2.0 site for discovering research trends and connecting to like-minded academics."