1. Data-mining
Some useful resources

2. Data Mining? “Yeah, I could use a nap…”
Hopefully sitting through this presentation won’t have this effect on you…

3. What We’ll Discuss Why search Who should do it Sources
National Library of Medicine
Includes the NLM Gateway, PubMed, ClinicalTrials.gov, MEDLINEPlus, and more
Google
FDA website
National Guidelines Clearinghouse website
Obtaining articles
As you’ll see, The National Library of Medicine has a gateway and includes PubMed, Medline, and other important resources. This presentation will go more in depth into PubMed but will also touch on some neat new features in Google, including an alert mechanism, and introduce you to some useful sources within the very robust FDA website.

4. Why Search? Find product data and competitive information
Clients often provide incomplete information
Find new data
Clients may not even be aware it exists
Learn about the latest research and where the market is headed
Can you ever have too much information about your client’s or competitor's products?
Finding new information can also lead to ideas for tactics. This is especially true in newer products that have clinical interest.
For Synercid, an antibiotic active against multi-resistant gram positive infections, looking at the literature we found an opportunity to present tactics based on case studies and patient profiles, since there were many unusual and successful cases written up. We also found several papers we later used for reprint carriers.
For Thrombin-JMI, a topical surgical hemostatic agent, we just finished a robust search for experts on surgical hemostasis. We are now contacting these physicians and making good progress.

5. Who should do it You The client
Consider as a value added service in any and all work you do?
Or you could request a budget for it upfront -- it can be very time consuming
The client
But will you get the information you need?

6. National Library of Medicine
The NLM Gateway
Simultaneous multiple retrieval system for “one-stop searching”
PubMed
Enormous database of citations and abstracts
MEDLINEPlus
Physician and patient oriented information
ClinicalTrials.gov
A great resource to check on existing clinical trials
Health Services Research Projects in Progress -HSRProj
Provides research information before results are published
Ok, so lets start with The National Library of Medicine. As this slide shows, included within the national Library of Medicine, which itself is part of the National Institute of Health, are numerous resources:
The NLM Gateway, allows simultaneous searching through a portal for many other databases, not just pubmed (hand out sheet)
PubMed, which has a very large and constantly growing database with over 13 million citations from close to 4500 journals spanning from 1966
MedlinePlus, more general and consumer oriented but still a useful, non-biased source. It does not allow ads
ClinicalTrials.gov, where you can check on existing clinical trials
And
HSRProj, which provides information on research that has not even been published yet
We will go into greater details for each of these later

7. The NLM Gateway Simultaneous “one-stop searching”
Journal citations from 1951 to present
Books, Serials, AVs
Consumer health
Meeting abstracts
Other collections
HSRProj
OMIM
HSDB
As mentioned, the NLM Gateway is a portal where you can search through multiple NLM sources. According to their website, the target audience for the Gateway is the Internet user who is new to NLM's online resources and does not know what information is available there or how best to search for it.
This audience may include physicians and other health care providers, researchers, librarians, students, and increasingly, patients, their families, and the public. Other users may find the Gateway useful for an overall search of NLM's information resources. Some searchers may locate what they need immediately, while others will utilize the Gateway as an adjunct tool to other NLM search services such as PubMed® and MedlinePlus®.
NOTE: The Meeting Abstracts Collection is found only in the Gateway
OMIM = Online Mendelian Inheritance in man – a catalog of human genes
HSDB = Hazardous Substances Data Bank

8. Gateway – Synercid Search Results
These are the results for a gateway search on Synercid

9. Gateway – Thrombin-JMI Search Results
Search results with Thrombin-JMI – significantly fewer matches. Also when we viewed the other collections they were not really related to Thrombin-JMI, though I guess they could be for other searches.

10. PubMed Where we search for research from medical journals
13 million citations/abstracts
4,500 journals
From 1966
Covers
Medicine
Nursing
Dentistry
Veterinary medicine
Healtchcare systems
Preclinical sciences
Ok, so what is PubMed? Pubmed is where we usually search for clinical papers. It includes over 13 million citations and covers a broad range of health disciplines.
Technically, PubMed was developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM) and is available on the Entrez retrieval system. New articles are added every day.

11. More About PubMed Links to other databases
OLDMEDLINE ( )
International biomedical journals
1,760,000 citations
Not all journals are strictly scientific or medical
We recently found a Newsweek article in PubMed
Links (LinkOut) to the full-text of articles at participating publishers' web sites
The variety of articles you can find in PubMed is really pretty amazing.
PubMed provides access to bibliographic information from OLDMEDLINE, as well as the National Library of Medicine's online data of approximately 1,760,000 citations to articles from international biomedical journals covering the fields of medicine, preclinical sciences and allied health sciences from 1950 through 1965.
Furthermore, PubMed provides access to the out-of-scope citations (e.g., articles on plate tectonics or astrophysics) from certain MEDLINE journals, primarily general science and chemistry journals, for which the life sciences articles are indexed for MEDLINE.
In addition to all this, PubMed provides access to some additional life science journals that submit full text to PubMEdCentral and receive a qualitative review by the NLM.
You can even find articles from national media, such as Newsweek, political journals, etc.
Finally, PubMed has a feature called LinkOut that provides access to a wide variety of relevant web-accessible online resources, including full-text articles at journal web sites and other related web resources.

12. What Can You Do in PubMed?
Search for articles (usually abstracts)
By keyword
By author
By Journal, etc
Combine searches
Link to related articles
Link to outside sources
To purchase the full article
Look at related books (including pages in the books)
Clinical queries
You can search for articles, really abstracts, by entering keywords, author names, journal titles or by using other more precise features that we will show you examples of. To use PubMed, simply enter your search topics - one or more terms - and click Go.
Retrieved citations are displayed and their associated abstracts can be selected for viewing. A unique feature of PubMed is the ability to instantly find related articles for any citation.
Additional search modes offer the ability to perform more complex searches by specifying data fields, such as age groups, gender, or human or animal studies.
PubMEd allows you to link to outside sources where you can purchase an article if you can’t find the full text for free. You can also link to books and view pages dealing with related topics
A special clinical queries page provides customized searches for studies based on etiology, diagnosis, prognosis, or treatment of a particular disease. Systematic reviews of a topic can also be searched here. Search results can be viewed or downloaded in various formats, including a format suitable for bibliographic management software.

13. The PubMed Homepage http://www.ncbi.nlm.nih.gov/entrez/query.fcgi
This is the first screen that pops up when you go to
((go to pubmed online))
Home Page
PubMed's home page displays:
The page header -- a black bar that provides access to other Entrez databases
A query box where you enter your search terms
A features bar with access to additional search features
A sidebar with links to PubMed's Help, other PubMed Services and related resources It is a fairly easy website to use. For quick, simple searches, you just start typing in keywords or author names etc into the query box. To search by journals, you can go to the journals database or simply use a search field tag [ta]. You can combine then using Boolean, eg, AND or OR. So to find an author in a particular journal just type out the information in the search bar

14. PubMed – Search Overview
Search by keyword
E.g., thrombin, but you get 31,365 results
Use a more specific keyword
Like “Thrombin-JMI”, but now you only get 2 hits
Additional tools
Limits
Search Field Tags
meSH
It usually comes down to a process of narrowing down your searches.
((Read slide))
There are other ways to narrow down searches, but these are what we have found to be most useful for us.
If we have time, we will get into meSH, for very specific searching

15. PubMed – Additional Tools
Limits
Age, groups, gender, type of study, etc
Search Field tags
Qualify terms, used in brackets [ta]
Boolean Statements
And, OR, NOT
meSH
The “vocabulary” of PubMed
Stands for Medical Subjects Headings
Used for indexing biomedical literature
What are Limits
Limit searches to specific fields, age groups, gender, type of study, Entrez or publication date, a specific language, types of articles, or subsets.
Search Field Tags
Terms may be qualified using PubMed's search field tags. [See your PubMed handout.]
Each search term should be followed (qualified) with the appropriate search field tag that indicates which field will be searched. The search field tag must follow the term -- you cannot prequalify them. The tags are enclosed in square brackets.
MeSH
MeSH is the acronym for "Medical Subject Headings." MeSH is the authority list of the vocabulary terms used for subject analysis of biomedical literature at NLM. MeSH vocabulary is used for indexing journal articles for Index Medicus, and MEDLINE and is also used for cataloging books and audiovisuals.
The MeSH controlled vocabulary is a distinctive feature of MEDLINE. It imposes uniformity and consistency to the indexing of biomedical literature. MeSH terms are arranged in a hierarchical categorized manner called MeSH Tree Structures and are updated annually.

16. PubMed -- Limits
Limits allow you to set commonly used parameters for your query, which may result in more relevant retrieval.
All Fields (Field Selection)
Search terms may be limited to a specific search field, e.g., the Text Word field.
The "All Fields" is the default setting.
To select another field, click on the All Fields pull-down menu and make another selection.
Abstracts
Click in the box labeled "only items with abstracts" to retrieve only citations that have abstracts.
Note that citations to articles published before 1975 do not include abstracts.
Publication Types
Retrieval may be limited based on the type of material the article represents.
The Publication Types pull-down menu contains a list of frequently searched publications types.

17. PubMed -- Search Field Tags
Search Field Tags also qualify terms
Letters in brackets
Nature [ta]
Watson JD [au]
1953 [dp]
“Fever of unknown origin” or [ti]
Link to PubMed. Also helps qualify and narrow down terms. We will use Nature and Watson as an example of narrowing down broad searches.
Audience participation

18. Boolean Statements Example: citations on DNA authored by Crick in 1993
Dna [mh] AND crick [au] AND 1993[dp]
Effect of heat or humidity on surgical hemostasis
(heat OR humidity) AND surgical hemostasis

19. PubMed -- The meSH Tree meSH organizes terms in a hierarchal manner
The MeSH Hierarchy
This example displays part of the hierarchy that includes the term, Face. Notice the narrower terms indented under the broader terms.
When PubMed searches a MeSH term, it will automatically include narrower terms in the search, if applicable. This is also called "automatic explosion."

20. PubMed -- meSH Tutorial
Time permitting

21. Real world meSH example
Thrombin-JMI use in bony ingrowth (cementless implants) in hip arthroscopy
On a noncemented hip, can Thrombin JMI be injected into the medullary canal of the femur and will it affect the bony ingrowth?
Can Thrombin JMI be put in the acetabulum and will it affect the bony ingrowth?
("Thrombin"[MeSH] OR "thrombin JMI"[Substance Name]) AND ("Bone Development"[MeSH] OR "Bone Remodeling"[MeSH] OR "Growth Plate"[MeSH])

22. MEDLINEPlus Information on over 650 diseases and conditions
Medical encyclopedia and dictionary
Information on prescription and nonprescription drugs
Links to ClinicalTrials.gov
Links to news
Sponsored by the NIH – no ads
MedlinePlus also comes from the National Library of Medicine. It is meant for health professionals and consumers.
MedlinePlus has information from the NIH and other sources on over 650 diseases and conditions. There are also lists of hospitals and physicians, a medical encyclopedia and a medical dictionary, health information in Spanish, extensive information on prescription and nonprescription drugs, health information from the media, and links to thousands of clinical trials. MedlinePlus is updated daily and can be bookmarked at the URL: There is no advertising on this site, nor does MedlinePlus endorse any company or product.

23. The MEDLINEPlus Homepage
Here is the homepage.

24. ClinicalTrials.gov
Information about federally funded and private human clinical trials
Includes the trial’s
Purpose
Locations
Participant requirements
Phone number
ClinicalTrials.gov provides regularly updated information about federally and privately supported clinical research in human volunteers. ClinicalTrials.gov gives you information about a trial's purpose, who may participate, locations, and phone numbers for more details.
• It currently contains approximately 12,400 clinical trials sponsored primarily by NIH, other Federal agencies, and the pharmaceutical industry.
Studies listed in the database are conducted in all 50 States and in over 100 countries. ClinicalTrials.gov receives over 3 million page views per month and hosts approximately 17,000 visitors daily.

25. ClinicalTrials.gov Homepage
Here is the homepage

26. HSRProj Provides research-in-progress before results are available
From ongoing grants and contracts from government or academic studies
Retrieve:
Name of sponsoring agency
Principal investigator
Dates of projects, etc.
What is the purpose of HSRProj?
HSRProj provides information about research-in-progress before results are available in a published format.
Organizations that fund health services research or principal investigators that are conducting health services research are invited to submit a description of their current projects to be included in HSRProj.
The database only accepts research project in the field of health services research and the end date must fall within 6 months prior to the date the project will appear on the HSRProj database.

27. HSRProj Homepage
Here is the homepage

28. Google Images Alerts Groups
Google also has some neat features you may not know about.

29. Images From Google? Yes, you really can find images in Google
A great way to find difficult technical images, like the coagulation cascade, a ribosome, etc.

30. Google Alerts Currently in Beta tests Enter keywords
Get updates on the keyword (s)
Enter a keyword and whenever news or web info on the keywords hits the internet, you get an message
This is FREE

31. Google Groups
A “forum” dedicated to a specific topic and usually open to the general public
Sometimes moderated and open only to members chosen by the moderator

32. Google Health News
Contains over 4,500 news sources updated continuously.
Shows how long ago the story came out or was updated

33. FDA Webpage – Tons of Info.
Contains MedWatch
product safety alerts
Alerts be sent to your address as they happen
Find
Warning Letters
Approved drugs and patent information
Using the Electronic Orange Book database
Devices
Guidance documents
This is also an enormous source for information. Lets look at the site map
MEDWATCH
Medical product safety alerts, recalls, withdrawals, and important labeling changes that may affect the health of all Americans are quickly disseminated to the medical community and the general public via this web site and the MedWatch E-list. Select Safety Information to see reports, safety notifications, and labeling changes posted to the website since 1996.
MedWatch allows healthcare professionals and consumers to report serious problems that they suspect are associated with the drugs and medical devices they prescribe, dispense, or use. Reporting can be done on line, by phone, or by submitting the MedWatch 3500 form by mail or fax.

34. FDA Promotional Guidance
Guidance documents represent the Agency's current thinking on a particular subject. Of course, we are interested in advertising and promotional guidance.
Documents are in PDF format and cover a broad range of topics, you may even be able to find guidance on your exact topic. The documents can be broad, like how to present efficacy data, to very specific, like guidance on analgesics, antacids, acceptance of foreign clinical studies, etc.
As you can imagine, It is a very robust website.

35. National Guidelines Clearinghouse
A comprehensive database of evidence-based clinical practice guidelines and related documents
Sponsored by the Agency for Healthcare Research and Quality (AHRQ)
Updated weekly
The National Guidelines Clearinghouse is a great source to check on existing clinical guidelines. It is sponsored by the Agency for Healthcare Research and Quality and is updated weekly.
It is a comprehensive database of evidence-based clinical practice guidelines and related documents. NGC is an initiative of the Agency for Healthcare Research and Quality (AHRQ), U.S. Department of Health and Human Services. NGC was originally created by AHRQ in partnership with the American Medical Association and the American Association of Health Plans (now America's Health Insurance Plans [AHIP]).

36. National Guidelines Clearinghouse

37. Obtaining Articles for Clients
Free
Check online – sometimes PubMed has links to free articles
Freemedicaljournals.com
Pay
Through Emory
$12 normal; $24 rush
Fax versions
Can be generated into PDF
External sources (e.g., publisher web sites)
Prices vary ($20-30)
PDF versions (usually)