SEARCH

SEARCH BY CITATION

Summary

  1. Top of page
  2. Summary
  3. Review Criteria
  4. Keeping up the traditional way – the ‘search’
  5. A shotgun approach – eTOCs
  6. Intelligent harvesting – the automated targeted search
  7. Separating the wheat from the chaff
  8. New ‘workflow’ tools
  9. What to do with your harvest
  10. Summary
  11. References

Background:  There is a virtual avalanche of medical information available to clinicians and researchers. The traditional ‘search’ can be substantially augmented by proactive ‘harvesting.’

Aims:  To describe how to search and harvest the medical literature.

Materials & Methods:  Survey of selected resources available on the internet.

Results:  PubMed remains the backbone of the traditional literature search. The availability of automated delivery of electronic tables of contents (‘eTOCs’), electronic feeds of targeted search results, and workflow tools allows relevant articles to find the reader. Electronic storage and retrieval tools make it possible to manage this information and make day-to-day clinical and research activities more efficient.

Discussion:  Searching and harvesting the medical literature is made easier with the advent of the internet and email. In addition, there are internet resources that screen and filter potential articles of interest. Managing one’s electronic library of PDF documents requires attention to appropriately naming files and the use of indexing programs.

Conclusion:  In addition to readers searching for relevant citations, these citations themselves can be searching for readers. Clinicians and researchers can take advantage of this and efficiently harvest the medical literature with a modest investment of time.


Review Criteria

  1. Top of page
  2. Summary
  3. Review Criteria
  4. Keeping up the traditional way – the ‘search’
  5. A shotgun approach – eTOCs
  6. Intelligent harvesting – the automated targeted search
  7. Separating the wheat from the chaff
  8. New ‘workflow’ tools
  9. What to do with your harvest
  10. Summary
  11. References

Resources available on the internet and used by the authors.

Message for the Clinic

Internet resources such as PubMed, the electronic delivery of tables of contents, news feeds, automated customized search tools, and sites that vet articles of interest make it easier to keep up with the medical literature.

Harvesting the medical literature, in contrast to simple searching, is the ongoing process of keeping up with the virtual flood of information that comes our way. It involves setting aside a little time each day or each week to download, skim, classify and store articles, preferably electronically, for potential future use. For the individual clinician or researcher, the harvest targets can be idiosyncratic, but the common processes are the same, and a major challenge remains to separate the wheat from the chaff. Popular harvesting tools are the automated delivery of electronic tables of contents (eTOCs) and automated delivery of carefully scripted search-engine-generated mini-lists of articles of interest. A bonus of having a bountiful harvest of stored articles is that it will make searching for answers a more pleasant task when you know you had collected this information earlier and had stored it in a way that is easily retrievable.

As discussed in a prior article (1), journals now almost universally publish materials online, often prior to print publication, and in almost all cases prior to when the printed journal arrives in one’s physical mailbox. This presents a challenge and an opportunity. How does one keep up, and how can one winnow down the torrent into a trickle and still be up-to-date? The ultimate goal is to have the relevant articles find you, rather than the other way around.

Keeping up the traditional way – the ‘search’

  1. Top of page
  2. Summary
  3. Review Criteria
  4. Keeping up the traditional way – the ‘search’
  5. A shotgun approach – eTOCs
  6. Intelligent harvesting – the automated targeted search
  7. Separating the wheat from the chaff
  8. New ‘workflow’ tools
  9. What to do with your harvest
  10. Summary
  11. References

Using an online search website such as PubMed (http://pubmed.gov/), it is easy to locate the journal article entry and a link to the publisher’s site. Many journal articles are available for free download for everyone. Clinicians with hospital or university affiliations can get broader access to more journal titles. Physicians in New York State in the US have free access, upon registration, to the New York State Library and its full text electronic journal holdings (http://www.nysl.nysed.gov/).

This sounds convenient, but the major problem with this approach is that you have to have a question in mind to do the search. This approach does not help you when your goal is simply to keep up in a general sense, with topics that interest you and are critical to your day-to-day work. For clinicians and researchers, this means keeping up on new information about specific disease states and therapeutic modalities. Researchers may want to add topics such as different research methodologies or theoretical constructs.

Additional tips on conducting a search can be found elsewhere (2–4).

A shotgun approach – eTOCs

  1. Top of page
  2. Summary
  3. Review Criteria
  4. Keeping up the traditional way – the ‘search’
  5. A shotgun approach – eTOCs
  6. Intelligent harvesting – the automated targeted search
  7. Separating the wheat from the chaff
  8. New ‘workflow’ tools
  9. What to do with your harvest
  10. Summary
  11. References

Not too long ago medical librarians would spend part of their time making photocopies of tables of contents of relevant journals as they arrived in the mail. These would then get distributed to the members of the staff who made arrangements to receive these sheets and they would then circle the titles of the articles they wanted to obtain copies of. The clinician without access to such a service would be restricted to have only those journals he or she has subscribed to, or is receiving as a member benefit from their professional association. Some of these journals entered into reciprocity agreements where they would publish each other’s tables of contents, so that readers would have some idea of what else was available.

In today’s internet world, anyone can now subscribe, for free, for delivery of eTOCs. All of the major publishers and some of the smaller ones as well enable users to register for a free personal account on their websites. Once you have an account, you will be able to sign up for eTOCs. Often, you can sign up for individual journal alerts from a journal’s home page. Alternatively, many publishers provide a place on their website where users can manage all of their alerts. Look for a tab or link labelled ‘Alerts’ or ‘E-Alerts’.

As a result of consolidation in the scholarly publishing industry in recent years, a large proportion of medical journals are now published by a handful of the largest publishers (Elsevier, LWW, Springer, Wiley-Blackwell) (see Table 1). Each of these offers an eTOC service on its website. If you locate a favourite journal’s home page via an internet search, you can often quickly determine whether an alerting option is available.

Table 1.   Selected internet resources
Publishing houses
 BioMed Central (Springer)http://www.biomedcentral.com/
 Informaworld (Taylor & Francis)http://www.informaworld.com/
 LWWonline (Wolters Kluwer)http://www.lwwonline.com/
 Nature.com (Nature Publishing Group)http://www.nature.com/
 ScienceDirect (Elsevier)http://www.sciencedirect.com/
 SpringerLink (Springer)http://springerlink.com/
 Wiley InterScience (Wiley-Blackwell)http://www.interscience.wiley.com/
Aggregators
 Amedeo Medical Literature Guidehttp://www.amedeo.com/
 EBSCOhosthttp://www.ebscohost.com/
 HighWire Presshttp://highwire.stanford.edu/
 IngentaConnecthttp://www.ingentaconnect.com/
 MedPageTodayhttp://www.medpagetoday.com/
 MD Consulthttp://www.mdconsult.com/
 MDLinxhttp://www.mdlinx.com/
 myNCBIhttp://www.ncbi.nlm.nih.gov/sites/myncbi/
 OvidSPhttp://www.ovid.com/
 PeerView Institutehttp://www.peerview-institute.org/ntk/ntk.nsf/html/index.html/
Newsletters
 Journal Watchhttp://www.jwatch.org/
 M.J. Powershttp://alertpubs.com/
 The Medical Letterhttp://themedicalletter.com/
Evidence based medicine resources
 ACP Journal Clubhttp://www.acpjc.org/
 AHRQ (Agency for Healthcare Research and Quality)http://www.ahrq.gov/
 Bandolierhttp://www.medicine.ox.ac.uk/bandolier/
 BMJ Evidence Centrehttp://group.bmj.com/products/evidence-centre/evidence-updates
 The Cochrane Collaborationhttp://www.cochrane.org/
 Essential Evidence Plushttp://www.essentialevidenceplus.com/
 Faculty of 1000 Medicinehttp://www.f1000medicine.com/
 McMaster Online Rating of Evidencehttp://hiru.mcmaster.ca/More/
Workflow tools
 CiteULikehttp://www.citeulike.org/
 Connoteahttp://www.connotea.org/
 del.icio.ushttp://delicious.com/
 Digghttp://digg.com/
 Facebookhttp://www.facebook.com/
 Mendeleyhttp://www.mendeley.com/

Another good source of eTOCs is HighWire Press, an online publishing platform which currently hosts 1,245 journals from over 140 scholarly publishers. From the HighWire home page, you can easily browse the journals by topic or by title, and alerts can easily be managed by selecting the Alerts tab.

Note that in addition to email alerts, some content providers also offer an alerting option known as Really Simple Syndication or RSS. RSS is a notification system that alerts you to new web content. These alerts come in the form of RSS ‘feeds’, and your computer must have an RSS feed reader for you to view the updates. A feed reader can easily be installed, if necessary. Recent versions of Microsoft’s email application, Outlook, have a built-in RSS reader, which makes the process very simple. If you use this reader, then the feeds can be treated as email messages. If a publisher or other web provider offers both kinds of alerts, it is just a matter a preference which you choose. You can try out an RSS feed to see how you like it, and then switch to email instead if you prefer. The email/RSS alternative also applies to other kinds of alerts mentioned below.

Intelligent harvesting – the automated targeted search

  1. Top of page
  2. Summary
  3. Review Criteria
  4. Keeping up the traditional way – the ‘search’
  5. A shotgun approach – eTOCs
  6. Intelligent harvesting – the automated targeted search
  7. Separating the wheat from the chaff
  8. New ‘workflow’ tools
  9. What to do with your harvest
  10. Summary
  11. References

There is now a way for relevant articles to find the interested reader, rather than the reader searching for the relevant articles. Free online services can be used to formulate a general question and set up an automated search. The subscriber would then receive on a periodic basis in their email inbox a list of relevant articles that matched their specifications. These specifications can be further refined, and the number of new articles can be reduced to a more manageable amount. Abstracts are usually available free by a click of the mouse, and for many, access to the full text is also free. There are many options for setting up this kind of topical alerting. Just a few examples will be discussed here.

One powerful resource to consider is My NCBI – NCBI stands for National Center for Biotechnology Information – which enables you to customise a personal profile so you can best take advantage of PubMed (and other NCBI databases). A link to My NCBI can be found in the left margin of the PubMed front page. With a My NCBI account, you can store keyword searches which will be run against PubMed on a regular basis. Whenever there are new results that match your search specifications, they will be emailed to you automatically. My NCBI also allows you to store and manage bibliographies and other collections of PubMed citations.

Some information service providers have set up an array of subject categories from which you can choose. Once you register with the service, and then select the topic(s) you are interested in, the alerts are automatically sent to you on a regular basis. A good example of this type of service is Amedeo, which also allows you to select which journals will be used to generate your alert results. The Amedeo website is provided by Flying Publisher, which also collects free medical resources at http://www.freemedicaljournals.com/ and at http://www.freebooks4doctors.com/.

BioMed Central is a publisher of online journals, many of which are ‘open access’, or freely available to anyone. If you register with the BioMed Central website, it offers several ways to harvest publications that might be of interest to you. First, you can sign up to be alerted when new articles are published in a particular journal. Second, you can specify one or more areas of interest in medicine and science, and receive topical alerts based on your specifications. Finally, you can store keyword searches which will generate alerts when new matches are found.

Commercial database vendors, such as Ovid and EBSCO, can also be a good harvesting source. If you are affiliated with a hospital or academic institution, you may be able to access a variety of research databases. In general, these systems enable you to create a personal account where you can store customised search strategies. These can be as broad or as specific as you want them to be, and you can usually configure the automatic alerts in a variety of ways.

Elsevier is a commercial publisher, but free registration on its ScienceDirect content platform enables anyone to sign up for targeted alerts in a wide range of subjects. As the categories are ready-made, you simply add a Topic Alert to your profile to begin receiving email (or RSS) updates. You can easily manage all of your selections (including subject alerts, new issue alerts and customised search alerts) under the Alerts tab on the ScienceDirect site. The sheer number of journals published by Elsevier makes this a rich source of new content. Free access is provided to article abstracts, when available, but you will normally need a license (i.e. online subscription) to view the full text.

This brings us to the general question of how to obtain the full text of articles that you want to read. Here are several possibilities to consider. (i) First, check whether the article is freely available online. Some journals are entirely open access, and some make selected articles open access. Also, authors sometimes post the manuscript version of their articles on their institutional or personal website. By entering a segment of an article title in quotation marks (“like this”) into Google, you can often quickly determine whether an article can be freely downloaded. (ii) When you cannot obtain a digital copy yourself, you may be able to take advantage of your institutional affiliation and request a copy from a hospital or university medical library. If you are eligible for this service, a librarian should be able to supply requested articles without much delay. Some articles may be available using in-house library resources, while others may be obtained through inter-library exchange. (iii) If you do not have access to a medical library, another option is to contact the corresponding author and request a copy. Success will depend on the responsiveness of the author, but a simple email message often leads to a fast and gratifying result. (iv) When all else fails, you may have the option of purchasing a digital copy of the desired article, either from the publisher or from another vendor. Typically, individual articles are priced in the $10–$25 range, but sometimes they are more expensive than that.

Separating the wheat from the chaff

  1. Top of page
  2. Summary
  3. Review Criteria
  4. Keeping up the traditional way – the ‘search’
  5. A shotgun approach – eTOCs
  6. Intelligent harvesting – the automated targeted search
  7. Separating the wheat from the chaff
  8. New ‘workflow’ tools
  9. What to do with your harvest
  10. Summary
  11. References

A major challenge that remains is determining what is worth reading beyond the abstract and what is worth saving. On a cautionary note, restricting the choice of journals to what you consider as most worthy works only moderately well, as gems can be found in the most unlikely of places, and publication in a first-tier journal is not always a hallmark of quality (5).

Here is a bit of advice to authors: readers look at titles first. If the title does not contain the relevant words or is otherwise not very enticing, that article is often initially passed over. No abstract can redeem a poorly-crafted title if the reader never clicks on the ‘read abstract’ button.

The next hurdle is the inspection of the abstract. This usually determines whether a report is harvested or not. However, there are also commentaries available that can vet a paper. We do not have a reader rating system (yet) such as seen on amazon.com, but there are websites that purport to list and summarise the top papers of the past month or year. They also make email services available that let you know when a new list is available. One free example is Evidence Updates from the BMJ Group, which will send you personalised alerts based on your settings. All citations are highly rated for quality and clinical relevance. The BMJ Evidence Centre also offers a searchable database of archived information.

On the commercial side, there are several well-known providers that screen a variety of literature and present you with a filtered selection. One is Journal Watch, which is published by the Massachusetts Medical Society (publisher of the New England Journal of Medicine). Journal Watch does offer a variety of free email alerts – a daily, general one and a range of specialty ones (weekly) and topical ones (monthly). However, a subscription fee is charged for full access to the website and more extensive alerting options.

Some current awareness resources are published as newsletters. Good examples of this type of newsletter are The Medical Letter (biweekly) and also Treatment Guidelines from The Medical Letter (monthly). Specialty area newsletters are also available. An example for psychiatry is Psychopharm Review (formerly International Drug Therapy Newsletter). M.J. Powers & Co. publishes several newsletters on drug efficacy and safety. Many newsletters began as print-only publications, but now most can also be downloaded.

The evidence based medicine umbrella provides another option for finding prescreened literature that may be of interest. Journals such as Evidence Based Medicine and Evidence Based Mental Health (both published by BMJ) survey a range of research, and present clinically relevant highlights along with expert commentary.

Another commercial resource designed to guide users to the best publications from the vast body of literature is called Faculty of 1000 Medicine. This service makes use of a large group of experts (clinicians and researchers), who select, rate and evaluate the articles they deem to be the most important. These articles are then included in the searchable and browseable online database.

With all of the information that is now freely available online, you may be reluctant to pay for this kind of service. However, keep in mind that the kinds of filtering and organising functions provided by these services can save you a substantial amount of time and effort. Another consideration is that some of these information providers make it possible to obtain Continuing Medical Education (CME) credits in conjunction with their products. If you are affiliated with an institution that provides medical library resources, then you may be able to access one or more of these pay services through an institutional license.

Becoming a rater of articles has some perks. The McMaster Online Rating of Evidence (MORE) programme will send the rater articles that have passed certain criteria for scientific merit, arrange for CME credit and provide the highest rated articles to all raters in a given discipline. MORE’s principal objective is to ‘supply clinicians with a finite, very manageable stream of high-quality, highly relevant medical literature, replacing the ‘infinite’, unmanageable flood of articles that are of lower quality and relevance for clinical care.’

New ‘workflow’ tools

  1. Top of page
  2. Summary
  3. Review Criteria
  4. Keeping up the traditional way – the ‘search’
  5. A shotgun approach – eTOCs
  6. Intelligent harvesting – the automated targeted search
  7. Separating the wheat from the chaff
  8. New ‘workflow’ tools
  9. What to do with your harvest
  10. Summary
  11. References

A number of new tools enable you to ‘bookmark’ and share links to journal papers and other information as soon as you find it. These tools allow bookmarking while you are reading, in one click, with minimal interruption. They incorporate ‘social networking’-type functions, so you can share bookmarks with colleagues. This means you can also use your colleagues’ bookmarks as a new route to more information. These tools also allow you to ‘tag’ your bookmarks with keywords both for easy retrieval, and so you can create keyword-themed clusters of information.

CiteULike and Connotea offer similar, straightforward online bookmarking and link-sharing tools, with no software to download. Both encourage you to follow a simple process to add a button to your toolbar for one-click bookmarking. A third tool, Mendeley, takes a different approach. Mendeley encourages you to install a free software download that can, if you direct it to, automatically index your existing archive of articles and information. You will have to add your own ‘tags’ to each article, and the automated indexing works better for journal articles than it does for other types of information. Mendeley can then synchronise your index with your Mendeley account online (that you will have created to download the Mendeley software), and this account gives you online bookmarking and link-sharing similar to that provided by CiteULike and Connotea, but that already incorporates your existing archive.

Some journals incorporate bookmarking with CiteULike, Connotea, Mendeley and other tools (such as Digg, del.icio.us, Facebook and more) into their journal articles online, as do newpapers and other sources of online information, usually with a series of ‘Share this Article’ or ‘Share’ buttons. So if you make discovering an article and bookmarking it routine and second nature, harvesting that information for future retrieval can become a simple, efficient part of your everyday reading.

What to do with your harvest

  1. Top of page
  2. Summary
  3. Review Criteria
  4. Keeping up the traditional way – the ‘search’
  5. A shotgun approach – eTOCs
  6. Intelligent harvesting – the automated targeted search
  7. Separating the wheat from the chaff
  8. New ‘workflow’ tools
  9. What to do with your harvest
  10. Summary
  11. References

Storage and retrieval has been discussed elsewhere (1), but certain essential components are worth repeating. When downloading a journal article, specify a descriptive name so that it will be easier to retrieve later. One possible naming convention is to name the file by title, first author, journal and year. For example, this article would be named ‘HowToHarvestLiterature CITROME IJCP2009’. An alternative would be to use ‘key words’ instead of the title, such as ‘SearchHarvestMedicalLiterature CITROME IJCP2009’. It would be placed in a file folder possibly named ‘HowToSeriesIJCP’. Whatever naming scheme you use, it is important to be consistent and take care to spell correctly to allow accurate retrieval later. Adding spaces between words and using upper or lower case is optional, but may make it easier when reviewing lists of PDF file names.

Backing up the information on a hard drive is essential, and software that exists today makes incremental back-ups quick and easy. The key concept here is ‘synchronizing’ the contents of your file folders across different computers and/or external hard drives. Free programs exist such as ‘SyncToy’ from Microsoft (available at http://www.microsoft.com/downloads/).

Unfortunately, even the best naming scheme for your PDF files and file folders will be less than adequate once you have stored a few hundred files. There are free programs available such as ‘Google Desktop’ (http://desktop.google.com/) and ‘Copernic Desktop Search’ (http://www.copernic.com/) that can index the entire contents of your hard drive. The latter program can search within PDF files (as well as inside Word documents, PowerPoint presentations, Excel spreadsheets, and importantly, emails and their attachments), so that if you do not remember all the details of the file you are seeking, you can still find it by entering into the search program some of the words, dates, or names that you think the file may contain. The search program then provides a list of possible files, sorted anyway you specify, such as by date, name or type of file format. A ‘preview’ is also shown so that you do not have to open the file directly when you are searching.

Summary

  1. Top of page
  2. Summary
  3. Review Criteria
  4. Keeping up the traditional way – the ‘search’
  5. A shotgun approach – eTOCs
  6. Intelligent harvesting – the automated targeted search
  7. Separating the wheat from the chaff
  8. New ‘workflow’ tools
  9. What to do with your harvest
  10. Summary
  11. References

Harvesting the medical literature is made easier with the advent of the internet and email (see Figure 1). Having the relevant articles find the reader is now possible. This is an ever-evolving area and the examples provided are only samples of what is available. You can leverage the capabilities of automated notification of articles of interest, so that with a modest investment of time you can keep up with the medical literature that is relevant to you and your practice.

image

Figure 1.  Flowchart: harvesting the literature

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References

  1. Top of page
  2. Summary
  3. Review Criteria
  4. Keeping up the traditional way – the ‘search’
  5. A shotgun approach – eTOCs
  6. Intelligent harvesting – the automated targeted search
  7. Separating the wheat from the chaff
  8. New ‘workflow’ tools
  9. What to do with your harvest
  10. Summary
  11. References