Last updated May 2011 by Mick Draper

FoodPlus
Demo of Databases at Uni of Adelaide Library

PubMed

Embase,Web of Knowledge & Google Scholar

You have just won a grant for a zillion dollars from the fishing industry to research the topic

bone development and n3 long-chain pufa

Today we'll look at how to search some important databases to find citations for articles on the topic

I always begin with a logic grid.
A logic grid is useful to sort out the language and logic needed to produce a good search strategy.
You can produce a logic grid on the back of an envelope, but I think that it's useful to use Word or any other program that has a table feature so that you can save your grid to use later if you want to revise your search.

Today's search is simple as far as concepts go. There are two concepts we need to combine to find appropriate sources of info.
A two column grid is needed.

The idea now is to find subject headings, synonyms or alternative terms for both of these concepts.

PubMed
PubMed is a good place to start because it has an excellent search engine and it's free to the universe.
Once you have a PubMed search that works, it's relatively easy to adapt the search to other databases.

I open the PubMed database from the Library home Quick Links.

You can get PubMed from a search engine such as Google but you'll be using a less useful version. This customised version includes links to the Library's online journals.

Most PubMed citations come in 3 formats

[PubMed - as supplied by publisher]

[PubMed - in process]

[PubMed - indexed for MEDLINE]

The citations that are indexed for MEDLINE have subject heading added to the citation.
This makes these citations easier to find, and if you search by the subject headings then you should find fewer irrelevant citations.

You can see these Medical Subject Headings (MeSH) when I search for PMID: 21252652.

MeSH Database
If you can find the subject headings that relate to the concepts you want to search, then you should find most of the citations to articles on that topic.
You can find subject headings by using the MeSH Database.

Type in a single search concept e.g. bone development, and click on Search.

The MeSH database usually provides a definition and tells you when the subject heading was first used.

Scrolling down the screen shows you where this subject heading fits in a hierarchy of subject headings, from broadest to most specific.

If you search Bone Development as a subject heading, then every citation in the PubMed database with this subject heading will be found. Not only that but every citation with one of the more specific subject headings,
Calcification, Physiologic
Maxillofacial Development
Osteogenesis
will also be found.

This explosion of subject terms is one of the things that makes PubMed a good search engine.

It will be useful to tell PubMed that you want to search the term bone development as a subject heading.
Do this by adding [mh] to the end of the term in the logic grid to begin with.

However, the most recent article citations in PubMed don't yet have subject heading added. To find these important recent citations you'll need to search in areas other than the subject headings.
While you can search all fields of a record, it's often better to focus your searches on subject headings, titles, abstracts, and similar fields. This reduces the dross.

I'll demonstrate a search of the PubMed FAQ to show [tiab] and [tw]

I add bone development[tw] to the logic grid.

I return to the MeSH Database to look at the Entry Terms associated with bone development.

You don't need to know what entry terms are, just that they can suggest other terms that authors might use in titles, abstracts, and keywords.

Add bone growth[tw] to the logic grid.

Now I'll scroll down the MeSH screen and look at the more specific terms listed under Bone Development.
We know these more specific terms will be searched as subject headings, but what about adding them to the logic grid (and later to the search) as text words?

I'll click on Calcification, Physiologic.

While it's very unlikely that anyone would use an inverted term such as this in a title, abstract or even as a keyword it is worth looking at the Entry Terms.

I think it would be worth including bone mineralization in the search as a text word.
There is also a spelling variation bone mineralisation.

You could add both of these to the logic grid, or you can include both in a single search term by using truncation.

bone minerali*[tw] will find both spelling variations.

Truncating even further to bone mineral*[tw] would include terms such as bone mineral, and bone minerals.

Now I'll click on the browser back button to return to the list of more specific subject headings.
You may not be particularly interested in maxillofacial development, but perhaps osteogenesis looks interesting.

It might be worth adding osteogenesis[tw] and bone formation[tw] to the logic grid.

Are there other terms that you think might be useful, such as osteoblasts?

Osteoblasts turns out to be a MeSH.

Are there other terms that might be used by authors?

What about bone maturation or ossification?

The second concept n3 long-chain pufa is a bit trickier.
Searching for this in the MeSH database finds nothing.

I could try another search term in the MeSH database, but what I usually do is to search my preferred term in the PubMed database but limit the search to article titles.

Next I check to see that some of the citations include those with MeSH, [PubMed - indexed for MEDLINE]

To view the MeSH, change the display format from Summary to Abstract.
Click on the Display Settings link.
Click in the radio button to the left of Abstract, not Abstract (text)
Click on Apply.

I click on the link to MeSH at the bottom of a citation.

I usually check several citations to make sure there is a consistent MeSH.
It looks like the appropriate MeSH is Fatty Acids, Omega-3.

Look at this term in the MeSH Database.

A MeSH search for Fatty Acids, Omega-3 will also find the subjects alpha-Linolenic Acid, Docosahexaenoic Acids, and Eicosapentaenoic Acid.
Perhaps I don't want to search all of these though.
alpha-Linolenic Acid is found only in plants.

I can tell PubMed to search Fatty Acids, Omega-3 but not to include the more specific subject headings by using

Fatty Acids, Omega-3[mh:noexp]

Put this in the logic grid along with the entry terms omega 3 fatty acid*[tw], n 3 pufa[tw], n 3 fatty acid*[tw], n 3 polyunsaturated fatty acid*[tw]

Did you notice that as well as putting in n 3 pufa I included n3 pufa as well as similar variations in the other terms?
You need to think of all the terms that authors might use in their titles, abstracts and keywords to describe the concepts in their articles.

Although I might not want to use alpha-Linolenic Acid in my search, I might want to include the other more specific terms docosahexaenoic acids and eicosapentaenoic acid.

I can look at these terms in the MeSH database.

From the Entry Terms I can see that although there are quite a lot of terms most of the useful ones will be covered by the two spelling variations docosahexaenoic acid and docosahexenoic acid.
There is also the term Docosahexaenoate. Using truncation I can combine all of these as docosahex*[tw].

I have to be careful about truncation because this can often produce irrelevant citations, but in this instance I think it's safe to add this term to the logic grid.

If I scroll down the MeSH database screen I can see an even more specific term Neuroprostanes.

After looking at the definition I decided not to include this term in the logic grid, but we can add it in if you think it would be of interest.

I went back to look at eicosapentaenoic acid.

From the Entry Terms I decided to to add timnodonic acid[tw] and eicosapenta*[tw] to the logic grid.

There are other terms that we could use including abbreviations such as dha and lc pufa, but this is enough for today.

Logic Rules
Now the logic grid becomes very useful for formulating the search to go into PubMed.
All the terms that are in the same column are joined using OR logic.
All the terms joined by OR logic are enclosed in round brackets.

I'll demonstrate the reason for the brackets

(bone development[mh] OR bone development[tw] OR bone growth[tw] OR bone minerali*[tw] OR osteogenes*[tw] OR bone formation[tw] OR osteoblasts[mh] OR osteoblast*[tw] OR osteocyte*[tw] OR bone maturation[tw])

(n 3 long chain pufa[tw] OR fatty acids, omega-3[mh:noexp] OR omega 3 fatty acid*[tw] OR n 3 pufa[tw] OR n3 pufa[tw] OR n 3 fatty acid*[tw] OR n3 fatty acid*[tw] OR n 3 polyunsaturated fatty acid*[tw] OR n3 polyunsaturated fatty acid*[tw] OR docosahex*[tw] OR eicosapenta*[tw] OR timnodonic acid*[tw])

Then I use AND logic between the terms from the different columns.

(bone development[mh] OR bone development[tw] OR bone growth[tw] OR bone mineral*[tw] OR osteogenes*[tw] OR bone formation[tw] OR osteoblasts[mh] OR osteoblast*[tw] OR osteocyte*[tw] OR bone maturation[tw]) AND (n 3 long chain pufa[tw] OR fatty acids, omega-3[mh:noexp] OR omega 3 fatty acid*[tw] OR n 3 pufa[tw] OR n3 pufa[tw] OR n 3 fatty acid*[tw] OR n3 fatty acid*[tw] OR n 3 polyunsaturated fatty acid*[tw] OR n3 polyunsaturated fatty acid*[tw] OR docosahex*[tw] OR eicosapenta*[tw] OR timnodonic acid*[tw])

Now is the moment. I paste the search into the PubMed database, while you hold your collective breath in anticipation.

How does this search compare with the 'naive search'

bone development AND n3 long-chain pufa

Clinical Queries
PubMed has some software that tries to limit searches to clinical citations.
This is often worth using as long as you're not expecting to find everything on a topic.
I click on Advanced Search.

I scroll down the screen and click on Clinical Queries.

I enter my search and click on the Search button.

Now I'll get results for three separately limited searches, two of which I can manipulate.

Study types
I've designed some PubMed searches for different sorts of study types such as cross sectional studies and cohort studies, as well as including links to expert searches for randomised controlled trials and systematic reviews.
You can click on any of the study types and then AND in your subject search to find citations on your topic with the appropriate study type.

Study Type link

Using the Abstract display will allow me to find those citations that have links to the online full text articles.
There are two sorts of these articles, those that are free, and those that are covered by The Uni of Adelaide Library's subscriptions.

Access to online full text is through the Uni of Adelaide Online icons.

If an article doesn't have a Uni of Adelaide Online icon it doesn't mean I don't have access to the article.
Older articles may be in print.
In rare cases the icons aren't generated even though we have access to the article online.

Hover your cursor over the abbreviated title of the journal and the full title of the journal appears.

I'll show you that this happens by looking at PMID 20962915

I search for that title in the Library Catalogue or Summon;
Then I can find my way to the appropriate volume number, issue and page number to get the article.

If the Library really doesn't have the article, postgrads and staff can make up to 50 interlibrary requests for articles each calendar year without cost.

Now you can select citations to add to EndNote or other bibliographic management software.

You can view similar citations by clicking on the Related citations links.

You can limit your search by date, language, and other options but you should be warned that most of the Limits are MeSH and if you use them you will lose your in process and as supplied by publisher citations.

MyNCBI allows me to save searches and create email alerts.
New users of MyNCBI have to register and wait for their registration to take effect before saving.

Details of how to do this are available here Saving Searches and Creating E mail Alerts.

Embase.com
The Library has only just gained access to Embase.
Embase covers more European journals than PubMed and it purports to search part of PubMed at the same time as searching Embase, but it's better to search both databases and remove any duplicates later.

One of the things Embase does better than PubMed is providing more synonyms for subject headings.

Here's a search for the subject heading Bone Development.

I've converted the PubMed search aboveto Embase format

Searching for subject headings
'bone development'/exp
'omega 3 fatty acid'/exp

Searching for terms in titles and abstracts
'bone growth':ti,ab

('bone development'/exp OR 'bone development':ti,ab OR 'bone growth':ti,ab OR 'bone mineral':ti,ab OR 'bone minerals':ti,ab OR 'bone minerali?ation':ab,ti OR osteogenes*:ti,ab OR 'bone formation':ti,ab OR osteoblast*:ti,ab OR osteocyte*:ti,ab OR 'bone maturation':ti,ab OR 'skeletal development':ab,ti OR 'skeleton development':ab,ti OR skeletogenesis:ab,ti) AND ('n 3 long chain pufa':ab,ti OR 'omega 3 fatty acid'/exp OR 'n 3 pufa':ab,ti OR 'n3 pufa':ab,ti OR 'n 3 fatty acid':ab,ti OR 'n 3 fatty acids':ab,ti OR 'n3 fatty acid':ab,ti OR 'n3 fatty acids':ab,ti OR 'n 3 polyunsaturated fatty acid':ab,ti OR 'n 3 polyunsaturated fatty acids':ab,ti OR 'n3 polyunsaturated fatty acid':ab,ti OR 'n3 polyunsaturated fatty acids':ab,ti OR docosahex*:ab,ti OR 'eicosapentaenoic acid':ab,ti OR 'eicosapentaenoic acids':ab,ti OR 'timnodonic acid':ab,ti OR 'timnodonic acids':ab,ti)

To search Embase I click on Search

.

Then I click on Advanced.
I click on the button Map to preferred terminology.
The tick mark should disappear.

I enter my search.
then, click on the Search button.

I'm thinking that in future I'll start my searches in Embase because it has more synonyms for subject headings.
I could add these new terms to my PubMed search.

Web of Knowledge
There are several databases that are part of Web of Knowledge that might be useful.
Web of Science includes conference paper publications that might not turn up in PubMed and Embase.

("bone development" OR "bone growth" OR "bone mineral*" OR osteogenes* OR "bone formation" OR osteoblasts OR osteoblast* OR osteocyte* OR "bone maturation" OR "skeletal development" OR "skeleton development" OR skeletogenesis) AND ("n 3 long chain pufa" OR "omega 3 fatty acid*" OR "n 3 pufa" OR "n3 pufa" OR "n 3 fatty acid*" OR "n3 fatty acid*" OR "n 3 polyunsaturated fatty acid*" OR "n3 polyunsaturated fatty acid*" OR docosahex* OR "eicosapentaenoic acid*" OR "timnodonic acid")

Google Scholar
Scholar is a good search engine but it has serious limitations with big searches.
Here is what I'd call a comprehensive search in Google Scholar style

("bone development" OR "bone growth" OR "bone mineral" OR "bone minerals" OR "bone mineralisation" OR "bone mineralization" OR osteogenesis OR "bone formation" OR osteoblasts OR osteoblast OR osteocytes OR osteocyte OR "bone maturation" OR "skeletal development" OR "skeleton development" OR skeletogenesis) ("n 3 long chain pufa" OR "omega 3 fatty acid" OR OR "omega 3 fatty acids" OR "n 3 pufa" OR "n3 pufa" OR "n 3 fatty acid" OR "n 3 fatty acids" OR "n3 fatty acid" OR "n3 fatty acids" OR "n 3 polyunsaturated fatty acid" OR "n 3 polyunsaturated fatty acids" OR "n3 polyunsaturated fatty acid" OR "n3 polyunsaturated fatty acids" OR docosahexaenoic OR "eicosapentaenoic acid" OR OR "eicosapentaenoic acids"OR "timnodonic acid")

but it won't fit in the search box.

Instead if you want to use Google Scholar you'll have to abbreviate the search, or do several searches leaving out terms.

("bone development" OR "bone growth" OR "bone mineral" OR "bone minerals" OR "bone mineralisation" OR "bone mineralization") "omega 3 fatty acid"

then

(osteogenesis OR "bone formation" OR osteoblasts OR osteoblast OR osteocytes OR osteocyte OR "bone maturation" OR "skeletal development" OR "skeleton development" OR skeletogenesis) "omega 3 fatty acid"

You can continue to search like this until you've covered all your terms or gone mad.